Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold82
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: 2626005
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.31
Warning! 196346 characters in sequence are not A, C, G, or T
File 2 of 17
Found at i:115137 original size:25 final size:26
Alignment explanation
Indices: 115092--115148 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
115082 ATAAAATATA
* *
115092 AAATTTATTTATTTATATTTTAAATT
1 AAATTAATTTATTTACATTTTAAATT
*
115118 AAATTAATTT-TTTACATTTTAACTT
1 AAATTAATTTATTTACATTTTAAATT
115143 -AATTAA
1 AAATTAA
115149 CATTCAATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 6 0.21
25 13 0.46
26 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (26 bp):
AAATTAATTTATTTACATTTTAAATT
Found at i:120170 original size:2 final size:2
Alignment explanation
Indices: 120159--120221 Score: 71
Period size: 2 Copynumber: 33.5 Consensus size: 2
120149 TCCCTCTCTC
* *
120159 AT AT AC AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
120199 AT A- AT AT AT AT A- AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
120222 GAAACTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
1 4 0.08
2 47 0.92
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:120198 original size:22 final size:22
Alignment explanation
Indices: 120159--120221 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 22
120149 TCCCTCTCTC
*
120159 ATATACATATATATATATATATAT
1 ATATA-ATATAAATATATA-ATAT
120183 AATATAATATAAATATATAATAT
1 -ATATAATATAAATATATAATAT
120206 ATATAATATAAATATA
1 ATATAATATAAATATA
120222 GAAACTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
22 16 0.43
23 4 0.11
24 12 0.32
25 5 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATAATATAAATATATAATAT
Found at i:122931 original size:2 final size:2
Alignment explanation
Indices: 122924--122966 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
122914 TTTTGTTTAA
*
122924 AC AC AC AC AC AC AC AC AC CC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
122966 A
1 A
122967 TATATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:123687 original size:14 final size:14
Alignment explanation
Indices: 123670--123697 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
123660 TTTAATTATA
123670 AAATATATAAATAT
1 AAATATATAAATAT
123684 AAATATATAAATAT
1 AAATATATAAATAT
123698 TTTTTAATAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATATATAAATAT
Found at i:125912 original size:2 final size:2
Alignment explanation
Indices: 125905--125943 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
125895 ATAAACCAAG
125905 AT AT AT AT AT 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 AT AT AT AT AT A
125944 AGAACAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:126000 original size:2 final size:2
Alignment explanation
Indices: 125993--126021 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
125983 TTATAATAGT
125993 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 T
126022 TTGCTTTCGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:126279 original size:2 final size:2
Alignment explanation
Indices: 126272--126316 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
126262 TGCTTTCTTT
126272 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
126314 TA T
1 TA T
126317 TTTTCTCCAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:127560 original size:2 final size:2
Alignment explanation
Indices: 127555--127581 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
127545 TGTGTGTATG
127555 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
127582 CTTTTTCTAC
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:127785 original size:30 final size:30
Alignment explanation
Indices: 127753--127864 Score: 102
Period size: 30 Copynumber: 3.7 Consensus size: 30
127743 GATTTATATT
*
127753 AAAGATTTATTTAGATATAATTTAAAAGTT-
1 AAAG-TTTATTTAGATATAAATTAAAAGTTA
* *
127783 AAAGTATTATTT-GAATATAAATTATATGTTA
1 AAAGT-TTATTTAG-ATATAAATTAAAAGTTA
* * *
127814 AAAGCTTAATTAAATATAAATTAAACAGTTA
1 AAAGTTTATTTAGATATAAATTAAA-AGTTA
* *
127845 AAATTTTATTTAGATGTAAA
1 AAAGTTTATTTAGATATAAA
127865 AAAGTATAGC
Statistics
Matches: 64, Mismatches: 13, Indels: 9
0.74 0.15 0.10
Matches are distributed among these distances:
29 2 0.03
30 39 0.61
31 23 0.36
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (30 bp):
AAAGTTTATTTAGATATAAATTAAAAGTTA
Found at i:128722 original size:3 final size:3
Alignment explanation
Indices: 128714--128741 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
128704 TAATCAATTC
128714 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
128742 CCAGAAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:133138 original size:2 final size:2
Alignment explanation
Indices: 133133--133162 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
133123 AGCTTGTGTC
*
133133 AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
133163 GTTCATGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:133199 original size:2 final size:2
Alignment explanation
Indices: 133192--133228 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
133182 TTTTCCTTTC
133192 AT AT AT AT 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 AT AT AT AT A
133229 AACATGGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:137159 original size:22 final size:22
Alignment explanation
Indices: 137131--137172 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
137121 TGTTGATGTA
137131 ACAACGAAGATCGATGCATCAG
1 ACAACGAAGATCGATGCATCAG
*
137153 ACAACGAAGATCGGTGCATC
1 ACAACGAAGATCGATGCATC
137173 GAACAAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.14
Consensus pattern (22 bp):
ACAACGAAGATCGATGCATCAG
Found at i:137178 original size:22 final size:21
Alignment explanation
Indices: 137130--137178 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 21
137120 ATGTTGATGT
137130 AACAACGAAGATCGATGCATC
1 AACAACGAAGATCGATGCATC
*
137151 AGACAACGAAGATCGGTGCATC
1 A-ACAACGAAGATCGATGCATC
137173 GAACAA
1 -AACAA
137179 GGTTCTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (21 bp):
AACAACGAAGATCGATGCATC
Found at i:138030 original size:19 final size:20
Alignment explanation
Indices: 137995--138032 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
137985 TAGTGACTTA
137995 CTTTTTTTTCTTGTTTTCAG
1 CTTTTTTTTCTTGTTTTCAG
138015 CTTTTTGTTT-TT-TTTTCA
1 CTTTTT-TTTCTTGTTTTCA
138033 CTACACTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 8 0.47
21 3 0.18
ACGTcount: A:0.05, C:0.13, G:0.08, T:0.74
Consensus pattern (20 bp):
CTTTTTTTTCTTGTTTTCAG
Found at i:144977 original size:287 final size:287
Alignment explanation
Indices: 144461--145018 Score: 1089
Period size: 287 Copynumber: 1.9 Consensus size: 287
144451 GTTATATAAT
144461 ATACTGCTATTACTAGCTTTGTTTTTTTCATTGCTGGTTAACCTAGAATGATATTATACGTGGAC
1 ATACTGCTATTACTAGCTTTGTTTTTTTCATTGCTGGTTAACCTAGAATGATATTATACGTGGAC
144526 GGTTGGTCGATTACCAAAAAGTCTACCATAAAGGTAACATTACGCTTGTCATCGTCAAAAGTTAC
66 GGTTGGTCGATTACCAAAAAGTCTACCATAAAGGTAACATTACGCTTGTCATCGTCAAAAGTTAC
* * *
144591 TGGCAGCGTTACAGTACGTTTAACAGGTATCGACTGATTGACGAAGCCATAAATGGGTAATGATG
131 TAGCAACGTTACAGTACCTTTAACAGGTATCGACTGATTGACGAAGCCATAAATGGGTAATGATG
144656 GGTTCAAGTCATCAACTTGGTATCCCATTTTTTTGAAAGCTTCCTATTGTAGAATGTCAATAGCA
196 GGTTCAAGTCATCAACTTGGTATCCCATTTTTTTGAAAGCTTCCTATTGTAGAATGTCAATAGCA
144721 ACACCATTATCCCATTGTAGAATGTCA
261 ACACCATTATCCCATTGTAGAATGTCA
144748 ATACTGCTATTACTAGCTTTGTTTTTTTCATTGCTGGTTAACCTAGAATGATATTATACGTGGAC
1 ATACTGCTATTACTAGCTTTGTTTTTTTCATTGCTGGTTAACCTAGAATGATATTATACGTGGAC
144813 GGTTGGTCGATTACCAAAAAGTCTACCATAAAGGTAACATTACGCTTGTCATCGTCAAAAGTTAC
66 GGTTGGTCGATTACCAAAAAGTCTACCATAAAGGTAACATTACGCTTGTCATCGTCAAAAGTTAC
144878 TAGCAACGTTACAGTACCTTTAACAGGTATCGACTGATTGACGAAGCCATAAATGGGTAATGATG
131 TAGCAACGTTACAGTACCTTTAACAGGTATCGACTGATTGACGAAGCCATAAATGGGTAATGATG
144943 GGTTCAAGTCATCAACTTGGTATCCCATTTTTTTGAAAGCTTCCTATTGTAGAATGTCAATAGCA
196 GGTTCAAGTCATCAACTTGGTATCCCATTTTTTTGAAAGCTTCCTATTGTAGAATGTCAATAGCA
145008 ACACCATTATC
261 ACACCATTATC
145019 AATTAAAATT
Statistics
Matches: 268, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
287 268 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (287 bp):
ATACTGCTATTACTAGCTTTGTTTTTTTCATTGCTGGTTAACCTAGAATGATATTATACGTGGAC
GGTTGGTCGATTACCAAAAAGTCTACCATAAAGGTAACATTACGCTTGTCATCGTCAAAAGTTAC
TAGCAACGTTACAGTACCTTTAACAGGTATCGACTGATTGACGAAGCCATAAATGGGTAATGATG
GGTTCAAGTCATCAACTTGGTATCCCATTTTTTTGAAAGCTTCCTATTGTAGAATGTCAATAGCA
ACACCATTATCCCATTGTAGAATGTCA
Found at i:147872 original size:20 final size:19
Alignment explanation
Indices: 147838--147900 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
147828 ATAATATGAT
147838 TATAAATATATTAATAATTTA
1 TATAAA-AT-TTAATAATTTA
*
147859 TATAAAATTATAATATTTTA
1 TATAAAATT-TAATAATTTA
* * *
147879 AATATAATTTAA-AAATTA
1 TATAAAATTTAATAATTTA
147897 TATA
1 TATA
147901 TTAATTTTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 7 0.20
19 4 0.11
20 18 0.51
21 6 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATAAAATTTAATAATTTA
Found at i:147901 original size:40 final size:39
Alignment explanation
Indices: 147825--147901 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 39
147815 CCAAAACATT
*
147825 ATTATAATATGATTATAAATATATTAATAATTTATATAAA
1 ATTATAATAT-ATTATAAATATATTAAAAATTTATATAAA
147865 ATTATAATAT-TT-TAAATATAATTTAAAAATTATATAT
1 ATTATAATATATTATAAATAT-A-TTAAAAATT-TATAT
147902 TAATTTTCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
37 7 0.21
38 3 0.09
39 8 0.24
40 15 0.45
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (39 bp):
ATTATAATATATTATAAATATATTAAAAATTTATATAAA
Found at i:149918 original size:19 final size:18
Alignment explanation
Indices: 149882--149917 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
149872 TTATTTTAAG
149882 GTTTTTTTTAATGCTTTT
1 GTTTTTTTTAATGCTTTT
149900 GTTTTTTGTTAATG-TTTT
1 GTTTTTT-TTAATGCTTTT
149918 TCCTTAGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.11, C:0.03, G:0.14, T:0.72
Consensus pattern (18 bp):
GTTTTTTTTAATGCTTTT
Found at i:153192 original size:19 final size:20
Alignment explanation
Indices: 153168--153226 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
153158 TAAATATATT
153168 ATATTAT-TTATATTTAAAA
1 ATATTATATTATATTTAAAA
153187 ATATTATATT-TA-TTAAATA
1 ATATTATATTATATTTAAA-A
* *
153206 TATTTTATAATATATTTAAAA
1 -ATATTATATTATATTTAAAA
153227 TTTTTATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 5 0.15
19 10 0.30
20 10 0.30
21 3 0.09
22 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTATATTATATTTAAAA
Found at i:153209 original size:9 final size:9
Alignment explanation
Indices: 153134--153209 Score: 58
Period size: 9 Copynumber: 9.2 Consensus size: 9
153124 ATATAATTTT
153134 TTAAATATA
1 TTAAATATA
153143 TTAAA-AT-
1 TTAAATATA
153150 TTAAA-ATA
1 TTAAATATA
153158 -TAAATATA
1 TTAAATATA
*
153166 TTATAT-TA
1 TTAAATATA
*
153174 TT-TATAT-
1 TTAAATATA
*
153181 TTAAAAATA
1 TTAAATATA
* *
153190 TTATATTTA
1 TTAAATATA
153199 TTAAATATA
1 TTAAATATA
153208 TT
1 TT
153210 TTATAATATA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
7 16 0.30
8 13 0.25
9 24 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TTAAATATA
Found at i:153924 original size:18 final size:20
Alignment explanation
Indices: 153884--153927 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
153874 AAATTTTTAT
*
153884 TATTTTAAATATATATTTAA
1 TATTTTAAATATATATATAA
153904 TATTTTAAAT-TAT-TATAA
1 TATTTTAAATATATATATAA
153922 TATTTT
1 TATTTT
153928 TTTAATAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.43
19 3 0.13
20 10 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTTAAATATATATATAA
Found at i:155604 original size:21 final size:21
Alignment explanation
Indices: 155567--155606 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
155557 ACTTCTTCAA
*
155567 TTAATCTTTTAAATTAATTTT
1 TTAATCTTTAAAATTAATTTT
155588 TTAAT-TTTAAAATTTAATT
1 TTAATCTTTAAAA-TTAATT
155607 AAAACTCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAATCTTTAAAATTAATTTT
Found at i:156418 original size:2 final size:2
Alignment explanation
Indices: 156405--156440 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
156395 TGTCTTTGGA
*
156405 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
156441 TTGAACTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:156705 original size:5 final size:5
Alignment explanation
Indices: 156689--156757 Score: 63
Period size: 5 Copynumber: 13.8 Consensus size: 5
156679 CATTTTAAAA
*
156689 ATAAT AATAAT ATAAT ATAAT AT-AT -TAAT ATAAT ATTAAT GTAAAT
1 ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT AT-AAT
* *
156735 ATATT ATAAT AT-AT ATAGT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAA
156758 AATATTAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
3 1 0.02
4 8 0.15
5 30 0.58
6 13 0.25
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:156710 original size:16 final size:16
Alignment explanation
Indices: 156689--156751 Score: 55
Period size: 16 Copynumber: 4.2 Consensus size: 16
156679 CATTTTAAAA
156689 ATAATAATAATATAAT
1 ATAATAATAATATAAT
156705 ATAAT-AT-AT-TAAT
1 ATAATAATAATATAAT
* *
156718 ATAATATTAATGTAA-
1 ATAATAATAATATAAT
*
156733 ATATATTATAATAT-AT
1 ATA-ATAATAATATAAT
156749 ATA
1 ATA
156752 GTATAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
13 9 0.24
14 3 0.08
15 8 0.21
16 18 0.47
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
ATAATAATAATATAAT
Found at i:158264 original size:9 final size:9
Alignment explanation
Indices: 158252--158314 Score: 53
Period size: 9 Copynumber: 7.2 Consensus size: 9
158242 GTAATTAAAA
158252 TAATATATT
1 TAATATATT
*
158261 TAATATATA
1 TAATATATT
158270 T-ATATCATAT
1 TAATAT-AT-T
158280 T--TATATT
1 TAATATATT
* *
158287 TAAAATTTT
1 TAATATATT
158296 TAATATATT
1 TAATATATT
158305 TAATA-ATT
1 TAATATATT
158313 TA
1 TA
158315 TATTTAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
7 2 0.05
8 11 0.25
9 30 0.68
10 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (9 bp):
TAATATATT
Found at i:158319 original size:32 final size:35
Alignment explanation
Indices: 158259--158322 Score: 98
Period size: 32 Copynumber: 1.9 Consensus size: 35
158249 AAATAATATA
158259 TTTAATATATATATATCATATTTATATTTAAAATT
1 TTTAATATATATATATCATATTTATATTTAAAATT
*
158294 TTTAATATATTTA-AT-A-ATTTATATTTAAA
1 TTTAATATATATATATCATATTTATATTTAAA
158323 TAATTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.46
33 1 0.04
34 2 0.07
35 12 0.43
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (35 bp):
TTTAATATATATATATCATATTTATATTTAAAATT
Found at i:158326 original size:15 final size:15
Alignment explanation
Indices: 158299--158337 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
158289 AAATTTTTAA
158299 TATATTT-AATAATT
1 TATATTTAAATAATT
158313 TATATTTAAATAATT
1 TATATTTAAATAATT
* *
158328 AAAATTTAAA
1 TATATTTAAA
158338 AATAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATTTAAATAATT
Found at i:159149 original size:23 final size:25
Alignment explanation
Indices: 159093--159149 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 25
159083 AAATACTAAA
159093 TTTATATTTTGATATTTATAATTTT
1 TTTATATTTTGATATTTATAATTTT
159118 TTTAT-TTTTGA-A-TTA-AATTTT
1 TTTATATTTTGATATTTATAATTTT
159139 TTTATAATTTT
1 TTTAT-ATTTT
159150 TTTTGTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 11 0.37
22 3 0.10
23 5 0.17
24 6 0.20
25 5 0.17
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (25 bp):
TTTATATTTTGATATTTATAATTTT
Found at i:160107 original size:19 final size:19
Alignment explanation
Indices: 160085--160135 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
160075 AAAATACGAT
160085 AATTATATTAAAAAA-TATA
1 AATTATA-TAAAAAATTATA
160104 AATTATATAAAAAATTATAA
1 AATTATATAAAAAATTAT-A
*
160124 AAATATATAAAA
1 AATTATATAAAA
160136 TTAATTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 7 0.24
19 10 0.34
20 12 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTATATAAAAAATTATA
Found at i:162015 original size:20 final size:21
Alignment explanation
Indices: 161971--162015 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
161961 TAACAAAAAA
161971 TTTTAATTTTTAAAAATAAAT
1 TTTTAATTTTTAAAAATAAAT
* *
161992 TTTTATTTTTTGAAAAT-AAT
1 TTTTAATTTTTAAAAATAAAT
162012 TTTT
1 TTTT
162016 CATGAAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTTAATTTTTAAAAATAAAT
Found at i:162160 original size:26 final size:26
Alignment explanation
Indices: 162126--162175 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
162116 TTAGTTAAAA
* *
162126 ATTACAAATCAATTTAATTATAAATC
1 ATTAAAAATCAATATAATTATAAATC
* *
162152 ATTAAAAATTAATATAATTTTAAA
1 ATTAAAAATCAATATAATTATAAA
162176 AAAATTAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (26 bp):
ATTAAAAATCAATATAATTATAAATC
Found at i:162202 original size:14 final size:15
Alignment explanation
Indices: 162166--162196 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
162156 AAAATTAATA
162166 TAATTTTAAAAAAAT
1 TAATTTTAAAAAAAT
*
162181 TAATTTTAAAATAAT
1 TAATTTTAAAAAAAT
162196 T
1 T
162197 TTTTTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATTTTAAAAAAAT
Found at i:163296 original size:3 final size:3
Alignment explanation
Indices: 163284--163316 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
163274 TCTTCTTTGG
163284 CTT CTT -TT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
163317 ACAAGAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:166537 original size:19 final size:20
Alignment explanation
Indices: 166515--166553 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
166505 TCTCAGAATA
166515 CTAAAATT-ACAAAAATTAT
1 CTAAAATTCACAAAAATTAT
* *
166534 CTAAAGTTCACAAAATTTAT
1 CTAAAATTCACAAAAATTAT
166554 ATCAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (20 bp):
CTAAAATTCACAAAAATTAT
Found at i:169440 original size:11 final size:12
Alignment explanation
Indices: 169424--169452 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
169414 TTAAAATTTG
169424 ATTTTTT-ATTA
1 ATTTTTTAATTA
169435 ATTTTTTAATTA
1 ATTTTTTAATTA
169447 ATTTTT
1 ATTTTT
169453 ATTTTTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTTTTAATTA
Found at i:169812 original size:15 final size:16
Alignment explanation
Indices: 169782--169814 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
169772 ATATTTAAAA
*
169782 TATTTTTAATTAAATT
1 TATTTTTAAATAAATT
169798 TATTTTTAAAT-AATT
1 TATTTTTAAATAAATT
169813 TA
1 TA
169815 AAATTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTTTAAATAAATT
Found at i:171446 original size:2 final size:2
Alignment explanation
Indices: 171439--171468 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
171429 TTGATGATCA
171439 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
171469 TTTATAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:172018 original size:27 final size:28
Alignment explanation
Indices: 171981--172064 Score: 84
Period size: 27 Copynumber: 3.0 Consensus size: 28
171971 ATATTGATTA
*
171981 AATTAATATTATAAATTAAT-TAAAAATT
1 AATTAA-ATTATAAAATAATATAAAAATT
*
172009 AATTTAATTA-AAAATAATATAAAAATT
1 AATTAAATTATAAAATAATATAAAAATT
* *
172036 TATTAAATATATAATAA-AATTTAAAAATT
1 AATTAAAT-TATAA-AATAATATAAAAATT
172065 TATGTAATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
26 7 0.15
27 18 0.38
28 7 0.15
29 13 0.28
30 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
AATTAAATTATAAAATAATATAAAAATT
Found at i:172042 original size:22 final size:21
Alignment explanation
Indices: 172009--172058 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
171999 ATTAAAAATT
172009 AATTTAATTAAAAATA-ATATAAA
1 AATTT-ATTAAAAATATA-AT-AA
*
172032 AATTTATTAAATATATAATAA
1 AATTTATTAAAAATATAATAA
172053 AATTTA
1 AATTTA
172059 AAAATTTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 8 0.32
22 11 0.44
23 6 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTTATTAAAAATATAATAA
Found at i:172429 original size:21 final size:18
Alignment explanation
Indices: 172405--172457 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 18
172395 CAATCAATTT
172405 AAATTATAATTTAAAATTTTA
1 AAATTATAATTTAAAA---TA
*
172426 AAATTATTTATTTAAAATA
1 AAATTA-TAATTTAAAATA
172445 AAATTA-AATTTAA
1 AAATTATAATTTAA
172458 TTAATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 6 0.21
19 8 0.28
21 6 0.21
22 9 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATTATAATTTAAAATA
Found at i:172461 original size:21 final size:19
Alignment explanation
Indices: 172424--172474 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
172414 TTTAAAATTT
*
172424 TAAAATTATTTATTTAAAA
1 TAAAATTATTTAATTAAAA
*
172443 TAAAATTAAATTTAATT-AAT
1 TAAAATT--ATTTAATTAAAA
*
172463 TTAAATTATTTA
1 TAAAATTATTTA
172475 TATTTATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 5 0.19
19 7 0.26
20 8 0.30
21 7 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAAATTATTTAATTAAAA
Found at i:172598 original size:30 final size:31
Alignment explanation
Indices: 172558--172615 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
172548 AAATAAAAAT
* * *
172558 AATTTTAATTATTAAATATTA-ATTTAACTA
1 AATTTAAATTAATAAAAATTATATTTAACTA
172588 AATTTAAATTAATAAAAATTATATTTAA
1 AATTTAAATTAATAAAAATTATATTTAA
172616 AATTTAACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (31 bp):
AATTTAAATTAATAAAAATTATATTTAACTA
Found at i:172985 original size:25 final size:25
Alignment explanation
Indices: 172957--173004 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
172947 TAAAATATTA
*
172957 ATATTTTATTAATTTAATAATAAAT
1 ATATTTTATTAATTAAATAATAAAT
172982 ATATTTTATTAATTAAATAATAA
1 ATATTTTATTAATTAAATAATAA
173005 TTTTAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATATTTTATTAATTAAATAATAAAT
Found at i:173027 original size:17 final size:16
Alignment explanation
Indices: 172966--173028 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 16
172956 AATATTTTAT
172966 TAATTTAA-TAATAAA
1 TAATTTAATTAATAAA
*
172981 TATATTTTATTAATTAAA
1 TA-ATTTAATTAA-TAAA
172999 TAA--TAATTTTAATAAAA
1 TAATTTAA--TTAAT-AAA
173016 TAATTTAATTAAT
1 TAATTTAATTAAT
173029 TTAAATTACA
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
15 4 0.11
16 6 0.16
17 19 0.50
18 6 0.16
19 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTTAATTAATAAA
Found at i:175442 original size:6 final size:6
Alignment explanation
Indices: 175431--175457 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
175421 AAAATATCAT
175431 CAACTC CAACTC CAACTC CAACTC CAA
1 CAACTC CAACTC CAACTC CAACTC CAA
175458 AATATTGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.48, G:0.00, T:0.15
Consensus pattern (6 bp):
CAACTC
Found at i:177645 original size:2 final size:2
Alignment explanation
Indices: 177638--177676 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
177628 TATTTTCTAT
177638 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
177677 ATATATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:177681 original size:2 final size:2
Alignment explanation
Indices: 177676--177707 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
177666 TCTCTCTCTC
177676 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
177708 CGTTGGTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:180749 original size:34 final size:34
Alignment explanation
Indices: 180702--180819 Score: 116
Period size: 34 Copynumber: 3.5 Consensus size: 34
180692 TTGTTTTTTT
180702 TTGGCCTTAATTGCCAGATATTTGGTGAAGTTTC
1 TTGGCCTTAATTGCCAGATATTTGGTGAAGTTTC
* * * * **
180736 TTGGCCTTTATTGCCATCACCATATT-CTG-TTTTTC
1 TTGGCCTTAATTGCCA-GA-TAT-TTGGTGAAGTTTC
*
180771 -TGGCCTTAATTGCCAGATATTTGGTGAAGTTTT
1 TTGGCCTTAATTGCCAGATATTTGGTGAAGTTTC
*
180804 TTGGCCTTTATTGCCA
1 TTGGCCTTAATTGCCA
180820 TCACCATTTT
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
31 2 0.03
32 4 0.06
33 4 0.06
34 43 0.67
35 5 0.08
36 4 0.06
37 2 0.03
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (34 bp):
TTGGCCTTAATTGCCAGATATTTGGTGAAGTTTC
Found at i:180808 original size:68 final size:68
Alignment explanation
Indices: 180697--180833 Score: 247
Period size: 68 Copynumber: 2.0 Consensus size: 68
180687 TTCCTTTGTT
*
180697 TTTTTTTGGCCTTAATTGCCAGATATTTGGTGAAGTTTCTTGGCCTTTATTGCCATCACCATATT
1 TTTTTCTGGCCTTAATTGCCAGATATTTGGTGAAGTTTCTTGGCCTTTATTGCCATCACCATATT
180762 CTG
66 CTG
* *
180765 TTTTTCTGGCCTTAATTGCCAGATATTTGGTGAAGTTTTTTGGCCTTTATTGCCATCACCATTTT
1 TTTTTCTGGCCTTAATTGCCAGATATTTGGTGAAGTTTCTTGGCCTTTATTGCCATCACCATATT
180830 CTG
66 CTG
180833 T
1 T
180834 CCTTAGAGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.17, C:0.19, G:0.18, T:0.47
Consensus pattern (68 bp):
TTTTTCTGGCCTTAATTGCCAGATATTTGGTGAAGTTTCTTGGCCTTTATTGCCATCACCATATT
CTG
Found at i:185372 original size:24 final size:25
Alignment explanation
Indices: 185345--185395 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
185335 GTGCAGCTAG
185345 GTGCTGT-GAGTTGTGTACAACTAT
1 GTGCTGTAGAGTTGTGTACAACTAT
*
185369 GTGCTGTAAGGAGTTGTGTACAGCTAT
1 GTGCTGT-A-GAGTTGTGTACAACTAT
185396 ATGTGCAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
27 16 0.70
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.35
Consensus pattern (25 bp):
GTGCTGTAGAGTTGTGTACAACTAT
Found at i:185409 original size:63 final size:63
Alignment explanation
Indices: 185310--185434 Score: 232
Period size: 63 Copynumber: 2.0 Consensus size: 63
185300 TGAGGGGGAG
185310 TGTAAGGAATTGTGTACAGCTATATGTGCAGCTAGGTGCTGTGAGTTGTGTACAACTATGTGC
1 TGTAAGGAATTGTGTACAGCTATATGTGCAGCTAGGTGCTGTGAGTTGTGTACAACTATGTGC
* *
185373 TGTAAGGAGTTGTGTACAGCTATATGTGCAGCTAGGTGCTGTGAGTTGTGTACAGCTATGTG
1 TGTAAGGAATTGTGTACAGCTATATGTGCAGCTAGGTGCTGTGAGTTGTGTACAACTATGTG
185435 TACAACTAAG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.34
Consensus pattern (63 bp):
TGTAAGGAATTGTGTACAGCTATATGTGCAGCTAGGTGCTGTGAGTTGTGTACAACTATGTGC
Found at i:185421 original size:36 final size:36
Alignment explanation
Indices: 185358--185476 Score: 148
Period size: 36 Copynumber: 3.2 Consensus size: 36
185348 CTGTGAGTTG
*
185358 TGTACAACTATGTGCTGTAAGGAGTTGTGTACAGCTATA
1 TGTACAACTAAGTGCTGT---GAGTTGTGTACAGCTATA
* * * *
185397 TGTGCAGCTAGGTGCTGTGAGTTGTGTACAGCTATG
1 TGTACAACTAAGTGCTGTGAGTTGTGTACAGCTATA
* *
185433 TGTACAACTAAGTGCTGTAAGTTGTGTACAGCTATG
1 TGTACAACTAAGTGCTGTGAGTTGTGTACAGCTATA
185469 TGTACAAC
1 TGTACAAC
185477 CAGGTTATAG
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
36 57 0.79
39 15 0.21
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (36 bp):
TGTACAACTAAGTGCTGTGAGTTGTGTACAGCTATA
Found at i:185436 original size:12 final size:12
Alignment explanation
Indices: 185419--185474 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
185409 TGCTGTGAGT
185419 TGTGTACAGCTA
1 TGTGTACAGCTA
*
185431 TGTGTACAACTAA
1 TGTGTACAGCT-A
185444 GTGCTGTA-AG-T-
1 -TG-TGTACAGCTA
185455 TGTGTACAGCTA
1 TGTGTACAGCTA
185467 TGTGTACA
1 TGTGTACA
185475 ACCAGGTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
9 4 0.11
10 4 0.11
11 1 0.03
12 18 0.50
13 2 0.06
14 3 0.08
15 4 0.11
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (12 bp):
TGTGTACAGCTA
Found at i:186776 original size:18 final size:18
Alignment explanation
Indices: 186753--186791 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
186743 TAGTATTCTA
186753 GTAGGAATAAGAAG-TCTT
1 GTAGGAAT-AGAAGATCTT
*
186771 GTAGGACTAGAAGATCTT
1 GTAGGAATAGAAGATCTT
186789 GTA
1 GTA
186792 TTTAAGCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (18 bp):
GTAGGAATAGAAGATCTT
Found at i:189489 original size:3 final size:3
Alignment explanation
Indices: 189481--189506 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
189471 ATCTGTAAAT
189481 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
189507 TTGTAAGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:189733 original size:28 final size:30
Alignment explanation
Indices: 189677--189741 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
189667 AATTAAATTT
189677 TTTATTATTTTATTTAAAATAATATTTAAA
1 TTTATTATTTTATTTAAAATAATATTTAAA
189707 TATTATT-TTTTACTTTAAAA-AA-A-TTAAA
1 T-TTATTATTTTA-TTTAAAATAATATTTAAA
189735 TTTATTA
1 TTTATTA
189742 AAAATTTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
27 5 0.16
28 6 0.19
29 1 0.03
30 8 0.25
31 12 0.38
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (30 bp):
TTTATTATTTTATTTAAAATAATATTTAAA
Found at i:190113 original size:29 final size:30
Alignment explanation
Indices: 190055--190113 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
190045 AAAATAATTT
* * *
190055 TTTAATTAAAATAATATATTTTTATTTAAA
1 TTTAATTAAAATAATATATATTAATATAAA
*
190085 TTTAATTATAA-AATATATATTAATATAAA
1 TTTAATTAAAATAATATATATTAATATAAA
190114 AATAAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TTTAATTAAAATAATATATATTAATATAAA
Found at i:193377 original size:19 final size:19
Alignment explanation
Indices: 193355--193392 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
193345 AATTAAATTA
*
193355 TTTA-TAAATTTTAAATTTT
1 TTTATTAAAATTT-AATTTT
193374 TTTATTAAAATTTAATTTT
1 TTTATTAAAATTTAATTTT
193393 AGTCAGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTATTAAAATTTAATTTT
Found at i:194078 original size:21 final size:21
Alignment explanation
Indices: 194044--194107 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
194034 ATATGATATT
* *
194044 TTATTAATTAAATTTAAATTA
1 TTATTTATTTAATTTAAATTA
194065 TTATTTATTTAA-TTAAATAATA
1 TTATTTATTTAATTTAAAT--TA
*
194087 TT-TTTATTTAATTTTAATTA
1 TTATTTATTTAATTTAAATTA
194107 T
1 T
194108 AAAATATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 9 0.24
21 19 0.51
22 9 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTATTTAATTTAAATTA
Found at i:194113 original size:27 final size:25
Alignment explanation
Indices: 194043--194114 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 25
194033 GATATGATAT
*
194043 TTTA-TTAATTAAATTTAA-ATTATTA
1 TTTATTTAATTAAA--TAATATTTTTA
194068 TTTATTTAATTAAATAATATTTTTA
1 TTTATTTAATTAAATAATATTTTTA
194093 TTTAATTTTAATTATAA-AATAT
1 TTT-A-TTTAATTA-AATAATAT
194115 ATAAATATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
24 3 0.07
25 13 0.32
26 10 0.24
27 13 0.32
28 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTATTTAATTAAATAATATTTTTA
Found at i:194980 original size:13 final size:11
Alignment explanation
Indices: 194957--195038 Score: 62
Period size: 11 Copynumber: 7.5 Consensus size: 11
194947 TTGATTATTT
*
194957 TAAAAATGATA
1 TAAATATGATA
194968 TAATTATATGATA
1 TAA--ATATGATA
194981 TAAATATGATA
1 TAAATATGATA
* *
194992 TAAAAATAAT-
1 TAAATATGATA
*
195002 TAAA-ATAATA
1 TAAATATGATA
*
195012 TAAATATAATA
1 TAAATATGATA
*
195023 TGAATAT-ATA
1 TAAATATGATA
*
195033 AAAATA
1 TAAATA
195039 ATAAAATTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
9 5 0.08
10 15 0.25
11 31 0.51
13 10 0.16
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (11 bp):
TAAATATGATA
Found at i:194989 original size:11 final size:11
Alignment explanation
Indices: 194973--195146 Score: 79
Period size: 11 Copynumber: 16.2 Consensus size: 11
194963 TGATATAATT
*
194973 ATATGATATAA
1 ATATAATATAA
*
194984 ATATGATATAA
1 ATATAATATAA
*
194995 AAATAAT-TAA
1 ATATAATATAA
195005 A-ATAATATAA
1 ATATAATATAA
*
195015 ATATAATATGA
1 ATATAATATAA
195026 ATAT-ATA-AA
1 ATATAATATAA
195035 A-ATAATA-AA
1 ATATAATATAA
* *
195044 AT-TTATAT-T
1 ATATAATATAA
*
195053 ATATGAATTATTA
1 ATAT-AA-TATAA
*
195066 ATAT-GTCA-AA
1 ATATAAT-ATAA
*
195076 AT-TTATATAAA
1 ATATAATAT-AA
195087 TATATAATATCTCAA
1 -ATATAATA--T-AA
195102 ATATAAT-TATA
1 ATATAATATA-A
195113 ATAT-ATA-AA
1 ATATAATATAA
195122 ATTATAATATAA
1 A-TATAATATAA
195134 ATATAATATAA
1 ATATAATATAA
195145 AT
1 AT
195147 CGTGTCAAAT
Statistics
Matches: 128, Mismatches: 13, Indels: 44
0.69 0.07 0.24
Matches are distributed among these distances:
8 2 0.02
9 23 0.18
10 24 0.19
11 53 0.41
12 8 0.06
13 8 0.06
14 7 0.05
15 3 0.02
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.39
Consensus pattern (11 bp):
ATATAATATAA
Found at i:195044 original size:9 final size:9
Alignment explanation
Indices: 194991--195044 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
194981 TAAATATGAT
194991 ATAAAAATA
1 ATAAAAATA
*
195000 ATTAAAATA
1 ATAAAAATA
195009 ATATAAATATA
1 ATA-AAA-ATA
**
195020 ATATGAATA
1 ATAAAAATA
195029 TATAAAAATA
1 -ATAAAAATA
195039 ATAAAA
1 ATAAAA
195045 TTTATATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 19 0.53
10 11 0.31
11 6 0.17
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
ATAAAAATA
Found at i:195081 original size:27 final size:27
Alignment explanation
Indices: 195051--195102 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
195041 AAAATTTATA
* *
195051 TTATATGAAT-TATTAATATGTCAAAAT
1 TTATATAAATATA-TAATATCTCAAAAT
195078 TTATATAAATATATAATATCTCAAA
1 TTATATAAATATATAATATCTCAAA
195103 TATAATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (27 bp):
TTATATAAATATATAATATCTCAAAAT
Found at i:195120 original size:13 final size:13
Alignment explanation
Indices: 195102--195143 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 13
195092 AATATCTCAA
195102 ATATAATTATAAT
1 ATATAATTATAAT
195115 ATATAAAATTATAAT
1 ATAT--AATTATAAT
195130 ATA-AA-TATAAT
1 ATATAATTATAAT
195141 ATA
1 ATA
195144 AATCGTGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 9 0.33
12 2 0.07
13 4 0.15
15 12 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAATTATAAT
Found at i:195123 original size:20 final size:20
Alignment explanation
Indices: 194989--195139 Score: 73
Period size: 20 Copynumber: 7.3 Consensus size: 20
194979 TATAAATATG
*
194989 ATATAAAA-ATAATTAAAAT
1 ATATAAAATATAATTATAAT
195008 A-ATATAAATATAA-TATGAAT
1 ATATA-AAATATAATTAT-AAT
*
195028 ATATAAAA-ATAA-TAAAAT
1 ATATAAAATATAATTATAAT
* **
195046 TTATATTATATGAATTATTAAT
1 ATATAAAATAT-AATTA-TAAT
*
195068 ATGTCAAAATTTATATAAATATATAAT
1 ATAT--AAA---ATAT-AAT-TATAAT
* *
195095 ATCTCAAATATAATTATAAT
1 ATATAAAATATAATTATAAT
195115 ATATAAAATTATAA-TATAA-
1 ATATAAAA-TATAATTATAAT
195134 ATATAA
1 ATATAA
195140 TATAAATCGT
Statistics
Matches: 102, Mismatches: 15, Indels: 30
0.69 0.10 0.20
Matches are distributed among these distances:
18 11 0.11
19 20 0.20
20 30 0.29
21 13 0.13
22 9 0.09
24 1 0.01
25 2 0.02
27 14 0.14
28 2 0.02
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
ATATAAAATATAATTATAAT
Found at i:197810 original size:19 final size:19
Alignment explanation
Indices: 197768--197826 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 19
197758 TTGAATCGAA
*
197768 AATTAAAAATTTATTATATATT
1 AATTAAAAATTTA--A-ATTTT
197790 AAGTTAAAAA-TTAAATTTT
1 AA-TTAAAAATTTAAATTTT
197809 AATTAAAAATTTAAATTT
1 AATTAAAAATTTAAATTT
197827 ATTATTTGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 7 0.21
19 14 0.41
20 1 0.03
22 5 0.15
23 7 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
AATTAAAAATTTAAATTTT
Found at i:197827 original size:18 final size:18
Alignment explanation
Indices: 197768--197827 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 18
197758 TTGAATCGAA
197768 AATTAAAAATTTATTATATATT
1 AATTAAAAATTTA--A-AT-TT
197790 AAGTTAAAAA-TTAAATTTT
1 AA-TTAAAAATTTAAA-TTT
197809 AATTAAAAATTTAAATTT
1 AATTAAAAATTTAAATTT
197827 A
1 A
197828 TTATTTGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
18 11 0.31
19 10 0.29
20 2 0.06
22 5 0.14
23 7 0.20
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
AATTAAAAATTTAAATTT
Found at i:197892 original size:21 final size:23
Alignment explanation
Indices: 197868--197909 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
197858 ATTAATATTT
197868 ATATATTT-AAT-TTAAATAAAA
1 ATATATTTAAATATTAAATAAAA
*
197889 ATATTTTTAAATATTAAATAA
1 ATATATTTAAATATTAAATAA
197910 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 3 0.17
23 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATATTTAAATATTAAATAAAA
Found at i:197921 original size:41 final size:42
Alignment explanation
Indices: 197840--197923 Score: 104
Period size: 41 Copynumber: 2.0 Consensus size: 42
197830 ATTTGTAAAT
*
197840 AATAAAAATTATTTTTATATTAATATTTATATATTTAATTTA
1 AATAAAAATTATTTTTATATTAATATTAATATATTTAATTTA
197882 AATAAAAA-TATTTTTAAATATTAA-A-TAATA-ATTTAAATTTA
1 AATAAAAATTATTTTT--ATATTAATATTAATATATTT-AATTTA
197923 A
1 A
197924 CCAATTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
40 4 0.11
41 18 0.47
42 9 0.24
43 7 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (42 bp):
AATAAAAATTATTTTTATATTAATATTAATATATTTAATTTA
Found at i:198525 original size:20 final size:19
Alignment explanation
Indices: 198492--198543 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
198482 ATATTTAATT
* *
198492 TAAAATTATTTAATAATAAA
1 TAAAATAATCTAAT-ATAAA
* *
198512 TAAAATAATCTAATTTTAA
1 TAAAATAATCTAATATAAA
*
198531 TATAATAATCTAA
1 TAAAATAATCTAA
198544 ACAATTCAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAATAATCTAATATAAA
Found at i:200200 original size:3 final size:3
Alignment explanation
Indices: 200192--200222 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
200182 TTTAAGTATA
*
200192 TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
200223 TATGTTCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:200273 original size:10 final size:10
Alignment explanation
Indices: 200251--200290 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
200241 AAATATAGAT
200251 TTTAAATTTTA
1 TTTAAA-TTTA
200262 TTTAAATTTA
1 TTTAAATTTA
*
200272 TTTATATTT-
1 TTTAAATTTA
200281 TTTAAATTTA
1 TTTAAATTTA
200291 ATCTTTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 8 0.31
10 12 0.46
11 6 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTAAATTTA
Found at i:202068 original size:16 final size:15
Alignment explanation
Indices: 202041--202070 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
202031 TTTAAATTTT
202041 ATTTAAAATTATTAA
1 ATTTAAAATTATTAA
202056 ATTTAATAATTATTA
1 ATTTAA-AATTATTA
202071 TTAAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTAAAATTATTAA
Found at i:202533 original size:5 final size:5
Alignment explanation
Indices: 202523--202548 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
202513 ATTATTTTAA
202523 AATTT AATTT AATTT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT A
202549 TTCAATTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:202901 original size:27 final size:28
Alignment explanation
Indices: 202871--202936 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
202861 CGTTTGGTGG
202871 ATATTTTTAATTTATTAA-TT-TTTTTAA
1 ATATTTTTAATTTA-TAATTTATTTTTAA
*
202898 ATATTTATATATTTATAATTTATTTTTAA
1 ATATTTTTA-ATTTATAATTTATTTTTAA
202927 A-ATTTTTAAT
1 ATATTTTTAAT
202937 AAAATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 13 0.38
28 13 0.38
29 8 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
ATATTTTTAATTTATAATTTATTTTTAA
Found at i:203019 original size:15 final size:15
Alignment explanation
Indices: 202999--203038 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
202989 TATATATAAA
202999 TATAAATTTTAAAAT
1 TATAAATTTTAAAAT
*
203014 TATAAATATTTAATAT
1 TATAAAT-TTTAAAAT
203030 TA-AAATTTT
1 TATAAATTTT
203039 TTAAATATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 3 0.13
15 11 0.48
16 9 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATAAATTTTAAAAT
Found at i:203855 original size:20 final size:18
Alignment explanation
Indices: 203788--203863 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 18
203778 TAAATAAAAA
203788 AAATTTAATTATTATATTT
1 AAATTTAATTATTATA-TT
203807 AAATTTTAATTATTTATGATT
1 AAA-TTTAATTA-TTAT-ATT
*
203828 ATGA-TTAATTATATAGTATT
1 A-AATTTAATTAT-TA-TATT
*
203848 AAATTTAATTGTTATA
1 AAATTTAATTATTATA
203864 CATATTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
18 2 0.04
19 7 0.15
20 28 0.60
21 8 0.17
22 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
AAATTTAATTATTATATT
Found at i:205203 original size:21 final size:20
Alignment explanation
Indices: 205160--205205 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
205150 ATCGTTAATT
* *
205160 TTAATTTTCCTCAATAATAA
1 TTAATTTTACTCAACAATAA
*
205180 TTAATTTTACTACAACATTAA
1 TTAATTTTACT-CAACAATAA
205201 TTAAT
1 TTAAT
205206 CTCACCATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAATTTTACTCAACAATAA
Found at i:205675 original size:2 final size:2
Alignment explanation
Indices: 205668--205696 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
205658 TTCGGAATCA
205668 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
205697 GGCATTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:207147 original size:16 final size:15
Alignment explanation
Indices: 207126--207155 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
207116 CTCTTAAGTA
207126 ATCCGAACTCGAAATG
1 ATCCGAACTC-AAATG
207142 ATCCGAACTCAAAT
1 ATCCGAACTCAAAT
207156 TAATTTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (15 bp):
ATCCGAACTCAAATG
Found at i:207294 original size:16 final size:16
Alignment explanation
Indices: 207274--207348 Score: 55
Period size: 16 Copynumber: 4.7 Consensus size: 16
207264 TGATTGACCT
207274 AAATCTGAAATGACTC
1 AAATCTGAAATGACTC
* *
207290 GAATCT-AGAATGACTT
1 AAATCTGA-AATGACTC
* * *
207306 AAATTTGAAATGATTTA
1 AAATCTGAAATGA-CTC
207323 AAAT-TGAAATGACTC
1 AAATCTGAAATGACTC
* *
207338 GAATATGAAAT
1 AAATCTGAAAT
207349 AATATAAACC
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
15 5 0.11
16 35 0.76
17 6 0.13
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (16 bp):
AAATCTGAAATGACTC
Found at i:208436 original size:2 final size:2
Alignment explanation
Indices: 208425--208468 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
208415 GTTTGGTTTT
* *
208425 TA TA TA -A TA TA TA TA TA TA TA TA TA TA CA TA CA 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
208466 TA T
1 TA T
208469 TATGGCATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:212937 original size:27 final size:27
Alignment explanation
Indices: 212901--212960 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
212891 AAAAATTATT
* *
212901 TTTTATATTTGTTAAAAATGATAATTA
1 TTTTGTATTTATTAAAAATGATAATTA
* *
212928 TTTTGTATTTATTAAAAATGGTAATTT
1 TTTTGTATTTATTAAAAATGATAATTA
212955 TTTTGT
1 TTTTGT
212961 CAAAAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (27 bp):
TTTTGTATTTATTAAAAATGATAATTA
Found at i:213081 original size:13 final size:12
Alignment explanation
Indices: 213059--213083 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
213049 TTCTTTCTCA
213059 TGTATTTTTTTT
1 TGTATTTTTTTT
213071 TGTATTTTTTTT
1 TGTATTTTTTTT
213083 T
1 T
213084 AATTTATTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (12 bp):
TGTATTTTTTTT
Found at i:213775 original size:6 final size:6
Alignment explanation
Indices: 213764--213795 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
213754 TATTTTTTCC
*
213764 AAACCA AAACCA AAACCA AAACCA AAATCA AA
1 AAACCA AAACCA AAACCA AAACCA AAACCA AA
213796 GTTATGATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.69, C:0.28, G:0.00, T:0.03
Consensus pattern (6 bp):
AAACCA
Found at i:215723 original size:16 final size:16
Alignment explanation
Indices: 215687--215724 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
215677 ATTTGATCAC
* *
215687 TTTAATATTTTAAATT
1 TTTATTATTTTAAATA
215703 TTTATTATTTTAAATA
1 TTTATTATTTTAAATA
215719 TTTATT
1 TTTATT
215725 TCAAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATTATTTTAAATA
Found at i:218674 original size:15 final size:14
Alignment explanation
Indices: 218654--218706 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
218644 ATTTATATGT
218654 AAATATAAATTTTAA
1 AAATATAAATTTT-A
218669 AAATATAAATATTTA
1 AAATATAAAT-TTTA
* * *
218684 ATATTTAAAATTTA
1 AAATATAAATTTTA
218698 AAATATAAA
1 AAATATAAA
218707 CTTATTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
14 11 0.34
15 18 0.56
16 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATATAAATTTTA
Found at i:218680 original size:29 final size:29
Alignment explanation
Indices: 218648--218706 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
218638 ATATATATTT
*
218648 ATATGTAA-ATATAAATTTTAAAAATATAA
1 ATATGTAATATATAAAATTT-AAAATATAA
* *
218677 ATATTTAATATTTAAAATTTAAAATATAA
1 ATATGTAATATATAAAATTTAAAATATAA
218706 A
1 A
218707 CTTATTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (29 bp):
ATATGTAATATATAAAATTTAAAATATAA
Found at i:219862 original size:29 final size:29
Alignment explanation
Indices: 219827--219924 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
219817 AAATATAATC
219827 TAATATAAATATATATTTTAAAATTTTTA
1 TAATATAAATATATATTTTAAAATTTTTA
* * * *
219856 TAATATAAATTATTTTTTATTAAAAATTATA
1 TAATATAAA-TATATATT-TTAAAATTTTTA
**
219887 TAAATATAAA-ATATATTTTAAATATAATTA
1 T-AATATAAATATATATTTTAAA-ATTTTTA
219917 TAATATAA
1 TAATATAA
219925 TAAAATATAT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
29 21 0.38
30 15 0.27
31 11 0.20
32 8 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TAATATAAATATATATTTTAAAATTTTTA
Found at i:219870 original size:18 final size:17
Alignment explanation
Indices: 219849--219917 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 17
219839 ATATTTTAAA
219849 ATTTTTATAATATAAATT
1 ATTTTTA-AATATAAATT
* * *
219867 ATTTTTTATTAAAAATT
1 ATTTTTAAATATAAATT
* *
219884 A--TATAAATATAAAAT
1 ATTTTTAAATATAAATT
219899 ATATTTTAAATAT-AATT
1 AT-TTTTAAATATAAATT
219916 AT
1 AT
219918 AATATAATAA
Statistics
Matches: 38, Mismatches: 10, Indels: 7
0.69 0.18 0.13
Matches are distributed among these distances:
15 10 0.26
17 14 0.37
18 14 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTTAAATATAAATT
Found at i:219916 original size:32 final size:31
Alignment explanation
Indices: 219828--219934 Score: 98
Period size: 32 Copynumber: 3.5 Consensus size: 31
219818 AATATAATCT
*
219828 AATATAAATATATATTTTAAAAT--TTTTAT-
1 AATATAAA-ATATATTTTAAAATAATTATATA
* *
219857 AATATAAATTATTTTTTATTAAA-AATTATATA
1 AATATAAAATATATTTTA--AAATAATTATATA
219889 AATATAAAATATATTTTAAATATAATTATA-A
1 AATATAAAATATATTTTAAA-ATAATTATATA
*
219920 TATAATAAAATATAT
1 AAT-ATAAAATATAT
219935 AACTATGAGT
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
28 8 0.12
29 8 0.12
30 5 0.08
31 9 0.14
32 34 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
AATATAAAATATATTTTAAAATAATTATATA
Found at i:220375 original size:30 final size:27
Alignment explanation
Indices: 220335--220399 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 27
220325 AAATTTTAAC
220335 TTTAATAATTTT-TAATATGATATAAATATGT
1 TTTAA-AATTTTATAA-AT-ATAT-AATAT-T
220366 TTTAAAATTTTGATAAATATATAATATT
1 TTTAAAATTTT-ATAAATATATAATATT
220394 TTTAAA
1 TTTAAA
220400 TATAATTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
28 7 0.22
29 5 0.16
30 10 0.31
31 7 0.22
32 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.51
Consensus pattern (27 bp):
TTTAAAATTTTATAAATATATAATATT
Found at i:229826 original size:26 final size:25
Alignment explanation
Indices: 229789--229847 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
229779 ATTAATTATT
229789 ATATAATATTA-TTAAATATTAAAA
1 ATATAATATTATTTAAATATTAAAA
*
229813 ATATAATAAGTTATTTAAAT-TTTAAA
1 ATATAAT-A-TTATTTAAATATTAAAA
*
229839 ATTTAATAT
1 ATATAATAT
229848 ATATATGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 8 0.27
25 2 0.07
26 14 0.47
27 6 0.20
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
ATATAATATTATTTAAATATTAAAA
Found at i:230978 original size:18 final size:17
Alignment explanation
Indices: 230946--230979 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
230936 TATAATAAAT
*
230946 TATAATTTATTACCTTA
1 TATAATTAATTACCTTA
230963 TATAATTAACTTACCTT
1 TATAATTAA-TTACCTT
230980 TAACTATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (17 bp):
TATAATTAATTACCTTA
Found at i:231962 original size:2 final size:2
Alignment explanation
Indices: 231955--231992 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
231945 AAATTGCTTC
* *
231955 AT AT AT AT AT AT AT AT AT AT AC AT GT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
231993 GCGAATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:232990 original size:35 final size:33
Alignment explanation
Indices: 232934--233002 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 33
232924 TTTAAATTTA
*
232934 TTTTATTTAAATTATTATTTAATAATAAAAAATAT
1 TTTTATTTAAATTAATATTTAA-AAT-AAAAATAT
*
232969 TTTTATTTAAATTTAAT-TTTAAAATATAAATAT
1 TTTTATTTAAA-TTAATATTTAAAATAAAAATAT
233002 T
1 T
233003 ATATTAATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 8 0.26
34 3 0.10
35 16 0.52
36 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TTTTATTTAAATTAATATTTAAAATAAAAATAT
Found at i:233394 original size:23 final size:23
Alignment explanation
Indices: 233341--233407 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
233331 AAAATATTTT
233341 TATTTAAAT-TTAATATAAA-AA
1 TATTTAAATATTAATATAAATAA
*
233362 TATATAAATATTAATATAAATAA
1 TATTTAAATATTAATATAAATAA
*
233385 TATTTTAATA-TAATTATAAATAA
1 TATTTAAATATTAA-TATAAATAA
233408 AAAATAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
21 8 0.20
22 13 0.32
23 19 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATTTAAATATTAATATAAATAA
Found at i:233395 original size:29 final size:30
Alignment explanation
Indices: 233363--233422 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
233353 ATATAAAAAT
* * *
233363 ATATAAATATTAAT-ATAAATAATATTTTA
1 ATATAAATATAAATAAAAAATAAAATTTTA
*
233392 ATATAATTATAAATAAAAAATAAAATTTTA
1 ATATAAATATAAATAAAAAATAAAATTTTA
233422 A
1 A
233423 ATTAATCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
ATATAAATATAAATAAAAAATAAAATTTTA
Found at i:234843 original size:33 final size:36
Alignment explanation
Indices: 234761--234843 Score: 100
Period size: 35 Copynumber: 2.3 Consensus size: 36
234751 GTAATTTTAA
* *
234761 ATTTTTTATTAAAATTTAAATTAAATTATTTAAAAT
1 ATTTTTTATTATAATTTAAATTAAATTATATAAAAT
*
234797 ATATATTTTATTATAA-TTAAATT-TA-TATATAAAAT
1 AT-T-TTTTATTATAATTTAAATTAAATTATATAAAAT
234832 ATTTTTTATTAT
1 ATTTTTTATTAT
234844 TCAAATAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 9 0.21
34 1 0.02
35 11 0.26
36 3 0.07
37 8 0.19
38 10 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (36 bp):
ATTTTTTATTATAATTTAAATTAAATTATATAAAAT
Found at i:236562 original size:2 final size:2
Alignment explanation
Indices: 236555--236580 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
236545 TAAGAGTTCA
236555 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
236581 TACAAATGCA
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:239139 original size:10 final size:10
Alignment explanation
Indices: 239124--239158 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
239114 TTTATCAAGC
239124 AAAAAAAAGA
1 AAAAAAAAGA
*
239134 AAAAAAAAAA
1 AAAAAAAAGA
239144 AAAAAGAAAGA
1 AAAAA-AAAGA
239155 AAAA
1 AAAA
239159 GGAAATTGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:239146 original size:17 final size:18
Alignment explanation
Indices: 239124--239158 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
239114 TTTATCAAGC
239124 AAAAAAAAGAAA-AAAAA
1 AAAAAAAAGAAAGAAAAA
239141 AAAAAAAAGAAAGAAAAA
1 AAAAAAAAGAAAGAAAAA
239159 GGAAATTGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAGAAAAA
Found at i:239159 original size:10 final size:9
Alignment explanation
Indices: 239124--239159 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
239114 TTTATCAAGC
239124 AAAAAAAAG
1 AAAAAAAAG
239133 AAAAAAAA-
1 AAAAAAAAG
239141 AAAAAAAAG
1 AAAAAAAAG
239150 AAAGAAAAAG
1 AAA-AAAAAG
239160 GAAATTGCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.32
9 11 0.44
10 6 0.24
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:240483 original size:11 final size:10
Alignment explanation
Indices: 240460--240494 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
240450 GAGATAAATA
240460 AAAAGAAATAG
1 AAAAGAAA-AG
240471 AAAAGGAAAAG
1 AAAA-GAAAAG
240482 AAAAGAAAAG
1 AAAAGAAAAG
240492 AAA
1 AAA
240495 GGGTTCTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.39
11 10 0.43
12 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (10 bp):
AAAAGAAAAG
Found at i:240486 original size:5 final size:5
Alignment explanation
Indices: 240460--240494 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
240450 GAGATAAATA
240460 AAAAG AAATAG AAAAGG AAAAG AAAAG AAAAG AAA
1 AAAAG AAA-AG AAAA-G AAAAG AAAAG AAAAG AAA
240495 GGGTTCTCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 18 0.64
6 10 0.36
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:242634 original size:17 final size:17
Alignment explanation
Indices: 242608--242651 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
242598 CAAAAGTTAA
*
242608 AATAATAATTAATAATT
1 AATAAAAATTAATAATT
*
242625 AATAAAAATTTAATATTT
1 AATAAAAA-TTAATAATT
*
242643 GATAAAAAT
1 AATAAAAAT
242652 ATCAAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
AATAAAAATTAATAATT
Found at i:242639 original size:18 final size:18
Alignment explanation
Indices: 242616--242651 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
242606 AAAATAATAA
242616 TTAATAATTAATAAAAAT
1 TTAATAATTAATAAAAAT
* *
242634 TTAATATTTGATAAAAAT
1 TTAATAATTAATAAAAAT
242652 ATCAAATTAT
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:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TTAATAATTAATAAAAAT
Found at i:243677 original size:41 final size:39
Alignment explanation
Indices: 243595--243680 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 39
243585 TTTATTTAAA
*
243595 TAAATATATAAATATTAATAAAAATATTTTAATATTTTT
1 TAAATATATAAATATTAATAAAAATAATTTAATATTTTT
* *
243634 TAAATATTTAAATAAATTAAT-AAATTAATTTAA-ATTTAATT
1 TAAATATATAAAT--ATTAATAAAAATAATTTAATATTT--TT
243675 TAAATA
1 TAAATA
243681 AAAAATTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
39 16 0.40
40 10 0.25
41 14 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (39 bp):
TAAATATATAAATATTAATAAAAATAATTTAATATTTTT
Found at i:244072 original size:13 final size:14
Alignment explanation
Indices: 244052--244088 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
244042 CACATGATCA
244052 CTAATTTTTTTTTT
1 CTAATTTTTTTTTT
*
244066 C-AA-TTTTTGTTT
1 CTAATTTTTTTTTT
244078 CTAATTTTTTT
1 CTAATTTTTTT
244089 AAATAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
12 9 0.47
13 4 0.21
14 6 0.32
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (14 bp):
CTAATTTTTTTTTT
Found at i:244325 original size:21 final size:22
Alignment explanation
Indices: 244285--244331 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
244275 AAATATGAAC
**
244285 ATAAAAAATATTTTTTTAAAAT
1 ATAAAAAATATTTTAATAAAAT
*
244307 ATAAAAAA-ATTTTAATAAATT
1 ATAAAAAATATTTTAATAAAAT
244328 ATAA
1 ATAA
244332 TATTCTCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAAAAAATATTTTAATAAAAT
Found at i:245130 original size:18 final size:20
Alignment explanation
Indices: 245093--245131 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
245083 TATTTAAATA
*
245093 TTTAATAAATATAAATATTT
1 TTTAATAAATATAAAAATTT
245113 TTTAA-AAA-ATAAAAATTT
1 TTTAATAAATATAAAAATTT
245131 T
1 T
245132 AAAGTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 3 0.17
20 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTAATAAATATAAAAATTT
Found at i:246477 original size:18 final size:20
Alignment explanation
Indices: 246454--246493 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
246444 TGGATCAATG
246454 TAGGACAT-GTGT-TTTATT
1 TAGGACATAGTGTATTTATT
*
246472 TAGGACATAGTTTATTTATT
1 TAGGACATAGTGTATTTATT
246492 TA
1 TA
246494 TTGTTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 3 0.16
20 8 0.42
ACGTcount: A:0.28, C:0.05, G:0.17, T:0.50
Consensus pattern (20 bp):
TAGGACATAGTGTATTTATT
Found at i:246521 original size:16 final size:18
Alignment explanation
Indices: 246495--246532 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
246485 ATTTATTTAT
246495 TGTTTTGTTT-ATGAGTA
1 TGTTTTGTTTAATGAGTA
*
246512 TGTTTT-TTTAATGATTA
1 TGTTTTGTTTAATGAGTA
246529 TGTT
1 TGTT
246533 GTCAGTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.63
Consensus pattern (18 bp):
TGTTTTGTTTAATGAGTA
Found at i:249908 original size:10 final size:10
Alignment explanation
Indices: 249895--249921 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
249885 AATTATTTAA
249895 TTAAAAAAAT
1 TTAAAAAAAT
249905 TTAAAAAAAT
1 TTAAAAAAAT
249915 TTAAAAA
1 TTAAAAA
249922 TTATATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TTAAAAAAAT
Found at i:249935 original size:20 final size:19
Alignment explanation
Indices: 249899--249944 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
249889 ATTTAATTAA
249899 AAAAATT-TAAAAAAATTT
1 AAAAATTATAAAAAAATTT
*
249917 AAAAATTATATAAATAATTT
1 AAAAATTATA-AAAAAATTT
*
249937 TAAAATTA
1 AAAAATTA
249945 AGTAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.29
19 2 0.08
20 15 0.62
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTATAAAAAAATTT
Found at i:250992 original size:16 final size:16
Alignment explanation
Indices: 250952--251011 Score: 84
Period size: 16 Copynumber: 3.7 Consensus size: 16
250942 TAAAAAAATT
250952 AATAATTTAAATTTAAA
1 AATAATTTAAATTT-AA
*
250969 AATTATTTAAATTTAA
1 AATAATTTAAATTTAA
*
250985 AATAATTTAAAATTAA
1 AATAATTTAAATTTAA
*
251001 AATAACTTAAA
1 AATAATTTAAA
251012 CTTACATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
16 26 0.67
17 13 0.33
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAATTTAAATTTAA
Done.