Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 19 of 117
Found at i:2093158 original size:8 final size:8
Alignment explanation
Indices: 2093140--2093181 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
2093130 CAATTTAATC
2093140 AAATGATAT
1 AAAT-ATAT
2093149 AAATATAT
1 AAATATAT
2093157 AAATATAT
1 AAATATAT
*
2093165 ATATATAT
1 AAATATAT
*
2093173 ATATATAT
1 AAATATAT
2093181 A
1 A
2093182 TCCATATCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
8 28 0.88
9 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (8 bp):
AAATATAT
Found at i:2093164 original size:2 final size:2
Alignment explanation
Indices: 2093145--2093182 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2093135 TAATCAAATG
* *
2093145 AT AT AA AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2093183 CCATATCCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2095168 original size:18 final size:19
Alignment explanation
Indices: 2095145--2095181 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2095135 TAACATTTAC
2095145 AAAAAT-AATAAATTATTT
1 AAAAATCAATAAATTATTT
*
2095163 AAAAATCAGTAAATTATTT
1 AAAAATCAATAAATTATTT
2095182 TTATGACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AAAAATCAATAAATTATTT
Found at i:2095210 original size:18 final size:19
Alignment explanation
Indices: 2095178--2095213 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2095168 TCAGTAAATT
2095178 ATTTTTATGACAAATAATA
1 ATTTTTATGACAAATAATA
*
2095197 ATTTTT-TGATAAATAAT
1 ATTTTTATGACAAATAAT
2095214 TAAAAACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (19 bp):
ATTTTTATGACAAATAATA
Found at i:2096295 original size:3 final size:3
Alignment explanation
Indices: 2096287--2096328 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2096277 TCTCTATCAT
2096287 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2096329 TTATTATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2096333 original size:3 final size:3
Alignment explanation
Indices: 2096327--2096374 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
2096317 ATAATAATAA
2096327 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2096375 CATCAAGTGA
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:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2097009 original size:19 final size:20
Alignment explanation
Indices: 2096981--2097023 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2096971 ATTATTTAAC
2096981 ATTTATAAAATTC-ATAAATA
1 ATTTATAAAA-TCAATAAATA
*
2097001 ATTTA-AAAATCAATAAATT
1 ATTTATAAAATCAATAAATA
2097020 ATTT
1 ATTT
2097024 TTATGTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 14 0.67
20 5 0.24
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTTATAAAATCAATAAATA
Found at i:2098217 original size:2 final size:2
Alignment explanation
Indices: 2098210--2098239 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2098200 AACAATTCTA
2098210 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
2098240 TTATTTATTT
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:2098244 original size:4 final size:4
Alignment explanation
Indices: 2098237--2098270 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
2098227 TATATATATA
2098237 TATT TATT TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TATT TATT TA
2098271 ATATGGTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:2098337 original size:13 final size:13
Alignment explanation
Indices: 2098319--2098348 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2098309 TATCCAATTC
*
2098319 TTTTGGCCTTTCA
1 TTTTGGCCTCTCA
2098332 TTTTGGCCTCTCA
1 TTTTGGCCTCTCA
2098345 TTTT
1 TTTT
2098349 TAATGTGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.23, G:0.13, T:0.57
Consensus pattern (13 bp):
TTTTGGCCTCTCA
Found at i:2098881 original size:122 final size:123
Alignment explanation
Indices: 2098742--2098989 Score: 403
Period size: 122 Copynumber: 2.0 Consensus size: 123
2098732 TGCGCAAGAC
* *
2098742 AAAACACACTATATAAGTGAATCATTATAAAATGAGAATAAAAAATAGAATAATAACTTTGTG-T
1 AAAACACACTATATAAGTGAATCATCAT-AAATGAGAATAAAAAAAAGAATAATAACTTTGTGTT
*
2098806 TTATAATATCTTTTATACG-TATGTGTGTGTAT-GTTTTTTTTTAAAATATTAGGATTGT
65 TTATAATATCTTTTATACGTTATGTGTGTGTATGGTTTTTTTTT-AAATATTACGATTGT
*
2098864 AAAACACACTATATAAGTGAATCATCATAAATGAGAATAAAAAAAAGAATAATAATTTTGTGTTT
1 AAAACACACTATATAAGTGAATCATCATAAATGAGAATAAAAAAAAGAATAATAACTTTGTGTTT
*
2098929 TATAATATCTTTTATATGTTTATGTGTGTGTATGGTTTTTTTTTAAATATTACGATTGT
66 TATAATATCTTTTATACG-TTATGTGTGTGTATGGTTTTTTTTTAAATATTACGATTGT
2098988 AA
1 AA
2098990 TTTTAATATT
Statistics
Matches: 117, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
121 32 0.27
122 46 0.39
124 29 0.25
125 10 0.09
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.42
Consensus pattern (123 bp):
AAAACACACTATATAAGTGAATCATCATAAATGAGAATAAAAAAAAGAATAATAACTTTGTGTTT
TATAATATCTTTTATACGTTATGTGTGTGTATGGTTTTTTTTTAAATATTACGATTGT
Found at i:2099969 original size:18 final size:19
Alignment explanation
Indices: 2099946--2099982 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2099936 TAACATTTAC
2099946 AAAAAT-AATAAATTATTT
1 AAAAATCAATAAATTATTT
*
2099964 AAAAATCAGTAAATTATTT
1 AAAAATCAATAAATTATTT
2099983 TTATGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AAAAATCAATAAATTATTT
Found at i:2100011 original size:18 final size:19
Alignment explanation
Indices: 2099979--2100014 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2099969 TCAGTAAATT
2099979 ATTTTTATGAAAAATAATA
1 ATTTTTATGAAAAATAATA
*
2099998 ATTTTT-TGATAAATAAT
1 ATTTTTATGAAAAATAAT
2100015 TAAAAACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (19 bp):
ATTTTTATGAAAAATAATA
Found at i:2101097 original size:3 final size:3
Alignment explanation
Indices: 2101089--2101113 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2101079 TCTCTATCAT
2101089 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
2101114 CAATGTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2101216 original size:2 final size:2
Alignment explanation
Indices: 2101209--2101239 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2101199 AACAATTCTA
2101209 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 A
2101240 AATTTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2103019 original size:2 final size:2
Alignment explanation
Indices: 2103012--2103037 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2103002 AACAATTCTA
2103012 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
2103038 TTATTATTTA
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:2103785 original size:17 final size:19
Alignment explanation
Indices: 2103752--2103786 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2103742 TTAGTTAATT
2103752 AATTTTTATATAATAATAA
1 AATTTTTATATAATAATAA
2103771 AATTTTTA-A-AATAATA
1 AATTTTTATATAATAATA
2103787 GTTTATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTTTTATATAATAATAA
Found at i:2104288 original size:17 final size:17
Alignment explanation
Indices: 2104263--2104298 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
2104253 TGGATTTTTT
2104263 TATAAAAAAATTG-CAA
1 TATAAAAAAATTGTCAA
2104279 TATAAAAAAATTGTCAA
1 TATAAAAAAATTGTCAA
2104296 TAT
1 TAT
2104299 TGATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (17 bp):
TATAAAAAAATTGTCAA
Found at i:2105345 original size:19 final size:20
Alignment explanation
Indices: 2105323--2105360 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2105313 AAAATTCTAT
*
2105323 AAAATTAATAAA-TATTTTA
1 AAAATCAATAAATTATTTTA
*
2105342 AAAATCAGTAAATTATTTT
1 AAAATCAATAAATTATTTT
2105361 TATGTCAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAATCAATAAATTATTTTA
Found at i:2105557 original size:17 final size:17
Alignment explanation
Indices: 2105515--2105558 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2105505 TTTAGTTAAT
**
2105515 TAATTTTTATATGATAA
1 TAATTTTTATAAAATAA
**
2105532 TAAAATTTATAAAATAA
1 TAATTTTTATAAAATAA
2105549 TAATTTTTAT
1 TAATTTTTAT
2105559 TTCATAATAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TAATTTTTATAAAATAA
Found at i:2105570 original size:22 final size:24
Alignment explanation
Indices: 2105536--2105585 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2105526 TGATAATAAA
*
2105536 ATTT-ATAAAATAA-TA-ATTTTT
1 ATTTCATAAAATAATTATAATTTT
*
2105557 ATTTCATAATATAATTATAATTTT
1 ATTTCATAAAATAATTATAATTTT
2105581 ATTTC
1 ATTTC
2105586 TTTATAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 8 0.33
23 2 0.08
24 10 0.42
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTTCATAAAATAATTATAATTTT
Found at i:2106648 original size:3 final size:3
Alignment explanation
Indices: 2106640--2106670 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2106630 TCTCTATCAT
2106640 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2106671 CAATGTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2106686 original size:3 final size:3
Alignment explanation
Indices: 2106680--2106710 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2106670 ACAATGTATA
2106680 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2106711 AGTGAAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2108467 original size:2 final size:2
Alignment explanation
Indices: 2108460--2108486 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2108450 AAACTCTATC
2108460 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 A
2108487 AACAATGATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2109804 original size:17 final size:17
Alignment explanation
Indices: 2109779--2109814 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
2109769 TGGATTTTTT
2109779 TATAAAAAAATTG-CAA
1 TATAAAAAAATTGTCAA
2109795 TATAAAAAAATTGTCAA
1 TATAAAAAAATTGTCAA
2109812 TAT
1 TAT
2109815 TGATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (17 bp):
TATAAAAAAATTGTCAA
Found at i:2110862 original size:19 final size:20
Alignment explanation
Indices: 2110840--2110877 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2110830 AAAATTCTAT
*
2110840 AAAATTAATAAA-TATTTTA
1 AAAATCAATAAATTATTTTA
*
2110859 AAAATCAGTAAATTATTTT
1 AAAATCAATAAATTATTTT
2110878 TATGTCAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAATCAATAAATTATTTTA
Found at i:2111073 original size:17 final size:17
Alignment explanation
Indices: 2111031--2111074 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2111021 TTTAGTTAAT
**
2111031 TAATTTTTATATGATAA
1 TAATTTTTATAAAATAA
**
2111048 TAAAATTTATAAAATAA
1 TAATTTTTATAAAATAA
2111065 TAATTTTTAT
1 TAATTTTTAT
2111075 TTCATAATAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TAATTTTTATAAAATAA
Found at i:2111086 original size:22 final size:24
Alignment explanation
Indices: 2111052--2111101 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2111042 TGATAATAAA
*
2111052 ATTT-ATAAAATAA-TA-ATTTTT
1 ATTTCATAAAATAATTATAATTTT
*
2111073 ATTTCATAATATAATTATAATTTT
1 ATTTCATAAAATAATTATAATTTT
2111097 ATTTC
1 ATTTC
2111102 TTTATAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 8 0.33
23 2 0.08
24 10 0.42
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTTCATAAAATAATTATAATTTT
Found at i:2112162 original size:3 final size:3
Alignment explanation
Indices: 2112154--2112190 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2112144 TCTCTGTCAT
*
2112154 ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2112191 CAATGTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2114061 original size:2 final size:2
Alignment explanation
Indices: 2114054--2114081 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2114044 AACAATTCTA
2114054 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
2114082 TTATTTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2115321 original size:17 final size:17
Alignment explanation
Indices: 2115297--2115331 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
2115287 GGATTTTTTA
2115297 ATAAAAAAATTG-CAAT
1 ATAAAAAAATTGTCAAT
2115313 ATAAAAAAATTGTCAAT
1 ATAAAAAAATTGTCAAT
2115330 AT
1 AT
2115332 TGATATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (17 bp):
ATAAAAAAATTGTCAAT
Found at i:2116361 original size:19 final size:20
Alignment explanation
Indices: 2116339--2116376 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2116329 AAAATTCTAT
*
2116339 AAAATTAATAAA-TATTTTA
1 AAAATCAATAAATTATTTTA
*
2116358 AAAATCAGTAAATTATTTT
1 AAAATCAATAAATTATTTT
2116377 TATGTCAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAATCAATAAATTATTTTA
Found at i:2116571 original size:17 final size:17
Alignment explanation
Indices: 2116529--2116572 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2116519 TTTAGTCAAT
**
2116529 TAATTTTTATATGATAA
1 TAATTTTTATAAAATAA
**
2116546 TAAAATTTATAAAATAA
1 TAATTTTTATAAAATAA
2116563 TAATTTTTAT
1 TAATTTTTAT
2116573 TTCATAATAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TAATTTTTATAAAATAA
Found at i:2116584 original size:22 final size:24
Alignment explanation
Indices: 2116550--2116599 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2116540 TGATAATAAA
*
2116550 ATTT-ATAAAATAA-TA-ATTTTT
1 ATTTCATAAAATAATTATAATTTT
*
2116571 ATTTCATAATATAATTATAATTTT
1 ATTTCATAAAATAATTATAATTTT
2116595 ATTTC
1 ATTTC
2116600 TTTATAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 8 0.33
23 2 0.08
24 10 0.42
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTTCATAAAATAATTATAATTTT
Found at i:2117244 original size:16 final size:17
Alignment explanation
Indices: 2117223--2117257 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2117213 TGATTTTTTT
*
2117223 TATAAAAA-AGTTGCAA
1 TATAAAAATAATTGCAA
2117239 TATAAAAATAATTGCAA
1 TATAAAAATAATTGCAA
2117256 TA
1 TA
2117258 CTGATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.29
Consensus pattern (17 bp):
TATAAAAATAATTGCAA
Found at i:2117657 original size:3 final size:3
Alignment explanation
Indices: 2117649--2117685 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2117639 TCTCTGTCAT
*
2117649 ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2117686 CAATGTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2118349 original size:19 final size:20
Alignment explanation
Indices: 2118314--2118356 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2118304 ACTATTTAAC
2118314 ATTTATAAAATTCATAAATA
1 ATTTATAAAATTCATAAATA
*
2118334 ATTTA-AAAA-TCAATAAATT
1 ATTTATAAAATTC-ATAAATA
2118353 ATTT
1 ATTT
2118357 TTATGTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 14 0.67
20 5 0.24
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTTATAAAATTCATAAATA
Found at i:2119456 original size:2 final size:2
Alignment explanation
Indices: 2119449--2119473 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2119439 AAACTCTATC
2119449 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 A
2119474 AAACAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2121879 original size:19 final size:20
Alignment explanation
Indices: 2121857--2121894 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2121847 AAAATTCTAT
*
2121857 AAAATTAATAAA-TATTTTA
1 AAAATCAATAAATTATTTTA
*
2121876 AAAATCAGTAAATTATTTT
1 AAAATCAATAAATTATTTT
2121895 TATGTCAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAATCAATAAATTATTTTA
Found at i:2122091 original size:17 final size:17
Alignment explanation
Indices: 2122049--2122092 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2122039 TTTAGTTAAT
**
2122049 TAATTTTTATATGATAA
1 TAATTTTTATAAAATAA
**
2122066 TAAAATTTATAAAATAA
1 TAATTTTTATAAAATAA
2122083 TAATTTTTAT
1 TAATTTTTAT
2122093 TTCATAATAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TAATTTTTATAAAATAA
Found at i:2122104 original size:22 final size:24
Alignment explanation
Indices: 2122070--2122119 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2122060 TGATAATAAA
*
2122070 ATTT-ATAAAATAA-TA-ATTTTT
1 ATTTCATAAAATAATTATAATTTT
*
2122091 ATTTCATAATATAATTATAATTTT
1 ATTTCATAAAATAATTATAATTTT
2122115 ATTTC
1 ATTTC
2122120 TTTATAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 8 0.33
23 2 0.08
24 10 0.42
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTTCATAAAATAATTATAATTTT
Found at i:2122422 original size:13 final size:13
Alignment explanation
Indices: 2122413--2122444 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2122403 TTAAAAATAT
2122413 TAAATT-AAAATC
1 TAAATTGAAAATC
2122425 TAAATTGAAAATC
1 TAAATTGAAAATC
2122438 TAAATTG
1 TAAATTG
2122445 CTAAACTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (13 bp):
TAAATTGAAAATC
Found at i:2123193 original size:3 final size:3
Alignment explanation
Indices: 2123185--2123215 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2123175 TCTCTATCAT
2123185 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2123216 CAATGTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2123227 original size:3 final size:3
Alignment explanation
Indices: 2123221--2123265 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
2123211 AATAACAATG
2123221 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2123266 AGTGAAGATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2128185 original size:5 final size:5
Alignment explanation
Indices: 2128175--2128208 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
2128165 TCAACAAAAA
2128175 TTTAT TTTAT TTTAT TTTAT TTTAT ATTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT TTT
2128209 GTATTTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:2128213 original size:11 final size:11
Alignment explanation
Indices: 2128175--2128214 Score: 57
Period size: 10 Copynumber: 3.8 Consensus size: 11
2128165 TCAACAAAAA
2128175 TTTAT-TTTAT
1 TTTATATTTAT
2128185 TTTAT-TTTAT
1 TTTATATTTAT
2128195 TTTATATTTAT
1 TTTATATTTAT
*
2128206 TTTGTATTT
1 TTTATATTT
2128215 TTTCTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 15 0.54
11 13 0.46
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (11 bp):
TTTATATTTAT
Found at i:2128825 original size:19 final size:19
Alignment explanation
Indices: 2128788--2128825 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2128778 ATCAAAAACT
2128788 AAAATTTCCAAAAGCAAAAA
1 AAAATTTCCAAAAG-AAAAA
*
2128808 AAACTTTCCAAAA-AAAAA
1 AAAATTTCCAAAAGAAAAA
2128826 TCCTCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
20 12 0.71
ACGTcount: A:0.66, C:0.16, G:0.03, T:0.16
Consensus pattern (19 bp):
AAAATTTCCAAAAGAAAAA
Found at i:2130255 original size:157 final size:162
Alignment explanation
Indices: 2129979--2130303 Score: 561
Period size: 157 Copynumber: 2.0 Consensus size: 162
2129969 TGAAATGGAA
*
2129979 AATAAAGCAAGTTAGTATGATGAAAATGAATAAAAAATCATATTCATTATAGAATATACATTTAC
1 AATAAAGCAAGTTAGTATGATGAAAATGAATAAAAAATCATATTCATTATAGAATATACATTCAC
*
2130044 CTAAATCCACTTTCATAACATACATTCACAAATAGATTATGAAAAAGAAGAAT-AAATAGAACAA
66 CTAAATCCACTTTCATAACATACAATCACAAATAGATTATGAAAAAGAAGAATAAAATAGAACAA
2130108 TTTAATTTACTTATATT-AGTTT-ATCAATAC
131 TTTAATTTACTTATATTAAGTTTGATCAATAC
2130138 AATAAAGCAAGTTAGTATGATGAAAATGAAT-AAAAATCATATTCATTA-AGAATATACATTCAC
1 AATAAAGCAAGTTAGTATGATGAAAATGAATAAAAAATCATATTCATTATAGAATATACATTCAC
*** *
2130201 CTAAATCCACTTTCATAACATACAATCATGGATAGATTATGAAAAAGAATAATAAAATAGAACAA
66 CTAAATCCACTTTCATAACATACAATCACAAATAGATTATGAAAAAGAAGAATAAAATAGAACAA
2130266 TTTAATTTACTTATATTAAGTTTGATCAATAC
131 TTTAATTTACTTATATTAAGTTTGATCAATAC
2130298 AATAAA
1 AATAAA
2130304 ATCACAATAT
Statistics
Matches: 157, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
157 62 0.39
158 45 0.29
159 36 0.23
160 14 0.09
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (162 bp):
AATAAAGCAAGTTAGTATGATGAAAATGAATAAAAAATCATATTCATTATAGAATATACATTCAC
CTAAATCCACTTTCATAACATACAATCACAAATAGATTATGAAAAAGAAGAATAAAATAGAACAA
TTTAATTTACTTATATTAAGTTTGATCAATAC
Found at i:2130813 original size:59 final size:58
Alignment explanation
Indices: 2130740--2130858 Score: 143
Period size: 59 Copynumber: 2.0 Consensus size: 58
2130730 AACAAATTTT
* * *
2130740 AACAAATATGTAACCAAAACCTAAACAAATTTCAGCAAACATAA-AACTAATAAAAACTC
1 AACAAATATGTAACCAAAACCCAAACAAATTTCAAC-AA-ATAATAACTAACAAAAACTC
* *
2130799 AACAAAT-TGGTAACCAAAGCCCAAATAAATTTCAACAAATAATTAACTAACAAAAACTC
1 AACAAATAT-GTAACCAAAACCCAAACAAATTTCAACAAATAA-TAACTAACAAAAACTC
2130858 A
1 A
2130859 CTAAAATCCA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
57 4 0.08
58 3 0.06
59 45 0.87
ACGTcount: A:0.56, C:0.20, G:0.04, T:0.19
Consensus pattern (58 bp):
AACAAATATGTAACCAAAACCCAAACAAATTTCAACAAATAATAACTAACAAAAACTC
Found at i:2132621 original size:43 final size:43
Alignment explanation
Indices: 2132512--2132625 Score: 174
Period size: 44 Copynumber: 2.6 Consensus size: 43
2132502 NNNNNGTGCT
2132512 TTTATTTTTCAAAGTTGTTGAGCCTCTACTTAGAGGAGCCTTA
1 TTTATTTTTCAAAGTTGTTGAGCCTCTACTTAGAGGAGCCTTA
* * *
2132555 TTTATTTTTTCAAAGTTGTTGAGCCTTTGCTTAGAGGAGCTTTA
1 TTTA-TTTTTCAAAGTTGTTGAGCCTCTACTTAGAGGAGCCTTA
* *
2132599 TTTATTTTTCAAAATTATTGAGCCTCT
1 TTTATTTTTCAAAGTTGTTGAGCCTCT
2132626 GATCTTAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
43 24 0.38
44 40 0.62
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.46
Consensus pattern (43 bp):
TTTATTTTTCAAAGTTGTTGAGCCTCTACTTAGAGGAGCCTTA
Found at i:2133329 original size:11 final size:11
Alignment explanation
Indices: 2133313--2133364 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
2133303 TCCTGTTTGG
*
2133313 TATTTTTTTAT
1 TATTTTTATAT
2133324 TATTTTT-TAT
1 TATTTTTATAT
2133334 TAATTTATTATATT
1 T-ATTT-TTATA-T
*
2133348 TATTTTCATAT
1 TATTTTTATAT
2133359 TATTTT
1 TATTTT
2133365 GAATGATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 4 0.11
11 18 0.50
12 6 0.17
13 6 0.17
14 2 0.06
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTTTTATAT
Found at i:2138107 original size:12 final size:11
Alignment explanation
Indices: 2138090--2138128 Score: 60
Period size: 12 Copynumber: 3.4 Consensus size: 11
2138080 ATTTTGCTTG
2138090 AAAAAAGAACAA
1 AAAAAAGAA-AA
2138102 AAAAAAGAAAA
1 AAAAAAGAAAA
2138113 AAAAAAGAGAAA
1 AAAAAAGA-AAA
2138125 AAAA
1 AAAA
2138129 TGATATATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:2138116 original size:13 final size:13
Alignment explanation
Indices: 2138090--2138128 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
2138080 ATTTTGCTTG
*
2138090 AAAAAAG-AACAA
1 AAAAAAGAAAAAA
2138102 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
*
2138115 AAAAGAGAAAAAA
1 AAAAAAGAAAAAA
2138128 A
1 A
2138129 TGATATATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:2139195 original size:50 final size:49
Alignment explanation
Indices: 2138973--2139200 Score: 185
Period size: 49 Copynumber: 4.6 Consensus size: 49
2138963 AAGAAAAGAG
* * * * * *
2138973 AATTTTTAAGGTTGTTGAGCTTTTACTTAGATGAACCTTTTTTCAA-ATAA
1 AATTTTTAAAGTTGTTGAGCCTCTACTTAAAAGAA-C-TCTTTCAAGATAA
* * * * * *
2139023 GAATTTTTATAGCTATTGAGCCTCTGCTT-AGAGAAAC-CATTTCAAGATGA
1 -AATTTTTAAAGTTGTTGAGCCTCTACTTAAAAG-AACTC-TTTCAAGATAA
*
2139073 AATTTTTAAAGTTATTGAGCCTCTACTTAAAAGAACTCTTTCAAGATAA
1 AATTTTTAAAGTTGTTGAGCCTCTACTTAAAAGAACTCTTTCAAGATAA
* ** * *
2139122 AATTTTTAAAGTTGTTGACCCTCTGTTTAAAAGAGCAT-TTTTAAGATAA
1 AATTTTTAAAGTTGTTGAGCCTCTACTTAAAAGAAC-TCTTTCAAGATAA
* *
2139171 GAATTTTTAAAATTGTTTAGCCTCTACTTA
1 -AATTTTTAAAGTTGTTGAGCCTCTACTTA
2139201 GAAAAGTTTT
Statistics
Matches: 142, Mismatches: 28, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
49 85 0.60
50 34 0.24
51 23 0.16
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (49 bp):
AATTTTTAAAGTTGTTGAGCCTCTACTTAAAAGAACTCTTTCAAGATAA
Found at i:2139295 original size:50 final size:51
Alignment explanation
Indices: 2139038--2139301 Score: 188
Period size: 49 Copynumber: 5.2 Consensus size: 51
2139028 TTTATAGCTA
** * *
2139038 TTGAGCCTCTGCTTAGAGAAA-CCATTTCAAGATGA-A-ATTTTTAAAGTTA
1 TTGAGCCTCTGCTTAGA-AAAGCTTTTTCAAGATGAGATTTTTTTAAAGTTG
* * * **
2139087 TTGAGCCTCTACTTA-AAAGAACTCTTTCAAGAT-A-AAATTTTTAAAGTTG
1 TTGAGCCTCTGCTTAGAAA-AGCTTTTTCAAGATGAGATTTTTTTAAAGTTG
* * * * *
2139136 TTGACCCTCTGTTTA-AAAGAGCATTTTT-AAGATAAGA-ATTTTTAAAATTG
1 TTGAGCCTCTGCTTAGAAA-AGC-TTTTTCAAGATGAGATTTTTTTAAAGTTG
* * * * *
2139186 TTTAGCCTCTACTTAGAAAAGTTTTTTCCAAGGTGAAGATTTTTTTTTTTAAGTTG
1 TTGAGCCTCTGCTTAGAAAAGCTTTTT-CAAGATG-AGA---TTTTTTTAAAGTTG
* *
2139242 TTGAACCTCTGCTTAGAAAAGCTTTTTCAAGATGAGATTTTTTTTAA-TTG
1 TTGAGCCTCTGCTTAGAAAAGCTTTTTCAAGATGAGATTTTTTTAAAGTTG
2139292 TTGAGCCTCT
1 TTGAGCCTCT
2139302 ACCAAGATGA
Statistics
Matches: 175, Mismatches: 26, Indels: 27
0.77 0.11 0.12
Matches are distributed among these distances:
47 2 0.01
48 4 0.02
49 64 0.37
50 42 0.24
51 18 0.10
52 3 0.02
54 3 0.02
55 6 0.03
56 33 0.19
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (51 bp):
TTGAGCCTCTGCTTAGAAAAGCTTTTTCAAGATGAGATTTTTTTAAAGTTG
Found at i:2139691 original size:28 final size:28
Alignment explanation
Indices: 2139629--2139695 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
2139619 AGGCCTAGAC
*
2139629 CTAATTTTAATTCAACTAGGCTCCAGGA
1 CTAATTTTGATTCAACTAGGCTCCAGGA
* * * *
2139657 CTGATTTTGATTCAACTGGGGCT-GAGGT
1 CTAATTTTGATTCAACT-AGGCTCCAGGA
2139685 CTAATTTTGAT
1 CTAATTTTGAT
2139696 CGGACCTAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 28 0.88
29 4 0.12
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.37
Consensus pattern (28 bp):
CTAATTTTGATTCAACTAGGCTCCAGGA
Found at i:2140705 original size:24 final size:22
Alignment explanation
Indices: 2140661--2140707 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
2140651 GTTGAGATAA
**
2140661 ATTTTATTTATTTATTTATATT
1 ATTTTATTTATTTATGCATATT
2140683 ATTTTATTAATATTTATGCATATT
1 ATTTTATT--TATTTATGCATATT
2140707 A
1 A
2140708 AAATGTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.38
24 13 0.62
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTTATTTATTTATGCATATT
Found at i:2142680 original size:27 final size:27
Alignment explanation
Indices: 2142621--2142682 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
2142611 TTTTTATTAT
* * * *
2142621 ATAAAAAT-ATAAATTATTTAACATTT
1 ATAAAATTAATAAATTATTAAAAATTC
2142647 ATAAAATTAATAAATTATTAAAAATTC
1 ATAAAATTAATAAATTATTAAAAATTC
*
2142674 ATTAAATTA
1 ATAAAATTA
2142683 TTTTTATATC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 7 0.23
27 23 0.77
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (27 bp):
ATAAAATTAATAAATTATTAAAAATTC
Found at i:2143242 original size:12 final size:12
Alignment explanation
Indices: 2143215--2143252 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
2143205 AATTTTTTAT
2143215 TAAAAATATTAAA
1 TAAAAAT-TTAAA
*
2143228 TAAAAATTTAGA
1 TAAAAATTTAAA
2143240 TAAAAATTTAAA
1 TAAAAATTTAAA
2143252 T
1 T
2143253 TGATGAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 16 0.70
13 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (12 bp):
TAAAAATTTAAA
Found at i:2156028 original size:16 final size:17
Alignment explanation
Indices: 2155994--2156029 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2155984 TTAGTTTCAA
2155994 TTATAATTTGAATAATT
1 TTATAATTTGAATAATT
*
2156011 TTATTATTTGAA-AATT
1 TTATAATTTGAATAATT
2156027 TTA
1 TTA
2156030 GGATTATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TTATAATTTGAATAATT
Found at i:2159285 original size:12 final size:12
Alignment explanation
Indices: 2159268--2159292 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2159258 CAAATAAAAT
2159268 GTCACTATAGTA
1 GTCACTATAGTA
2159280 GTCACTATAGTA
1 GTCACTATAGTA
2159292 G
1 G
2159293 AAAAAGATAG
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (12 bp):
GTCACTATAGTA
Found at i:2160678 original size:23 final size:24
Alignment explanation
Indices: 2160648--2160694 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
2160638 CCAAGACTAG
2160648 CAGACAAAAAAT-ACTGTAGCAAA
1 CAGACAAAAAATCACTGTAGCAAA
*
2160671 CAGACAAAACATCACTGTAGCAAA
1 CAGACAAAAAATCACTGTAGCAAA
2160695 AAAAGACAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.53, C:0.21, G:0.13, T:0.13
Consensus pattern (24 bp):
CAGACAAAAAATCACTGTAGCAAA
Found at i:2169233 original size:25 final size:23
Alignment explanation
Indices: 2169205--2169260 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
2169195 AGTTATTAAC
*
2169205 TTTTATATAATAATAAAATAATAAA
1 TTTTAT-TAATAAGAAAATAAT-AA
*
2169230 TTTTAGTTAATAAGATAATAATAA
1 TTTTA-TTAATAAGAAAATAATAA
2169254 TTTTATT
1 TTTTATT
2169261 TATTTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 2 0.07
24 7 0.25
25 18 0.64
26 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
TTTTATTAATAAGAAAATAATAA
Found at i:2171474 original size:22 final size:23
Alignment explanation
Indices: 2171426--2171476 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
2171416 TTGAACTAAG
* * *
2171426 CATATTTTTTGAACTTATTCTAT
1 CATATTTTTTGAACTTAATCAAA
2171449 CATATTTTTTGAAC-TAATCAAA
1 CATATTTTTTGAACTTAATCAAA
2171471 CATATT
1 CATATT
2171477 AATACAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49
Consensus pattern (23 bp):
CATATTTTTTGAACTTAATCAAA
Found at i:2172072 original size:17 final size:17
Alignment explanation
Indices: 2172050--2172098 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
2172040 TTTTTTTTTC
2172050 TTTTTTTATTTAAT-AA
1 TTTTTTTATTTAATAAA
2172066 TTTTTTTAAATTTAATAAA
1 TTTTTTT--ATTTAATAAA
*
2172085 TATTTTTATTTAAT
1 TTTTTTTATTTAAT
2172099 TTTTTTGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.24
17 7 0.24
18 7 0.24
19 8 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTTTATTTAATAAA
Found at i:2173649 original size:17 final size:17
Alignment explanation
Indices: 2173610--2173649 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2173600 AGTTATTAAT
*
2173610 TTTTTATATAATAATAA
1 TTTTTATAAAATAATAA
**
2173627 AATTTATAAAATAATAA
1 TTTTTATAAAATAATAA
2173644 TTTTTA
1 TTTTTA
2173650 ATTCATAATA
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTTATAAAATAATAA
Found at i:2173657 original size:22 final size:22
Alignment explanation
Indices: 2173627--2173669 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2173617 ATAATAATAA
*
2173627 AATTTATAAAATAATAATTTTT
1 AATTCATAAAATAATAATTTTT
*
2173649 AATTCATAATATAATAATTTT
1 AATTCATAAAATAATAATTTT
2173670 ATTTATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTCATAAAATAATAATTTTT
Found at i:2175779 original size:21 final size:20
Alignment explanation
Indices: 2175732--2175780 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
2175722 GTTGACACTA
2175732 ATTTATTTAATTTTAATAATT
1 ATTT-TTTAATTTTAATAATT
*
2175753 ACTTTTTTAA-TTTAATAAAT
1 A-TTTTTTAATTTTAATAATT
*
2175773 ATATTTTA
1 ATTTTTTA
2175781 GTGAAATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 6 0.24
20 10 0.40
21 6 0.24
22 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTTAATTTTAATAATT
Found at i:2176311 original size:20 final size:20
Alignment explanation
Indices: 2176268--2176311 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2176258 TTAAAATTTT
* *
2176268 TAATATTATTCAATCACTTT
1 TAATATTATTCAATCAATTA
2176288 TAATATTATTCAAT-AATATA
1 TAATATTATTCAATCAAT-TA
2176308 TAAT
1 TAAT
2176312 TTTTATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATATTATTCAATCAATTA
Found at i:2181762 original size:24 final size:24
Alignment explanation
Indices: 2181719--2181764 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2181709 TTTGTTATTA
* *
2181719 ATTATTAGAAAGATTCAAATTTTT
1 ATTATTAGAAAGAATAAAATTTTT
*
2181743 ATTATTAGAAATAATAAAATTT
1 ATTATTAGAAAGAATAAAATTT
2181765 GATGTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (24 bp):
ATTATTAGAAAGAATAAAATTTTT
Found at i:2182350 original size:18 final size:18
Alignment explanation
Indices: 2182329--2182363 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2182319 AAATTCAGAA
2182329 AAAAAATTTAAAAATTTT
1 AAAAAATTTAAAAATTTT
*
2182347 AAAAACTTTAAAAATTT
1 AAAAAATTTAAAAATTT
2182364 CAAGTAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAAAATTTAAAAATTTT
Found at i:2182396 original size:18 final size:16
Alignment explanation
Indices: 2182368--2182417 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
2182358 AAATTTCAAG
2182368 TAATTCTAAAAAAATTT
1 TAATT-TAAAAAAATTT
**
2182385 TAATTATGAAAAACTTTT
1 TAATT-T-AAAAAAATTT
2182403 TAATTTAAAAAAATT
1 TAATTTAAAAAAATT
2182418 ATGAAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 7 0.26
17 7 0.26
18 13 0.48
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (16 bp):
TAATTTAAAAAAATTT
Found at i:2182433 original size:22 final size:21
Alignment explanation
Indices: 2182408--2182448 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2182398 CTTTTTAATT
2182408 TAAAAAAATTATGAAAAAATAC
1 TAAAAAAATTAT-AAAAAATAC
*
2182430 TAAAAAATTTATAAAAAAT
1 TAAAAAAATTATAAAAAAT
2182449 TTAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
TAAAAAAATTATAAAAAATAC
Found at i:2182472 original size:18 final size:20
Alignment explanation
Indices: 2182451--2182498 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2182441 TAAAAAATTT
2182451 AAAATTTTTTTAATAT-TCAA
1 AAAATTTTTTTAATATCTC-A
* *
2182471 AAAAATTTTTTAATTTCTC-
1 AAAATTTTTTTAATATCTCA
2182490 AAAATTTTT
1 AAAATTTTT
2182499 AAAAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 8 0.33
20 14 0.58
21 2 0.08
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (20 bp):
AAAATTTTTTTAATATCTCA
Found at i:2182491 original size:21 final size:20
Alignment explanation
Indices: 2182451--2182527 Score: 63
Period size: 18 Copynumber: 4.0 Consensus size: 20
2182441 TAAAAAATTT
*
2182451 AAAATTTTTTTAATATTCAA
1 AAAAATTTTTTAATATTCAA
*
2182471 AAAAATTTTTTAAT-TTC-T
1 AAAAATTTTTTAATATTCAA
* * * *
2182489 CAAAATTTTTAAAAATT-TA
1 AAAAATTTTTTAATATTCAA
*
2182508 AAAAA-TTTTTAAAATTCAA
1 AAAAATTTTTTAATATTCAA
2182527 A
1 A
2182528 CAATTCTAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
18 21 0.47
19 11 0.24
20 13 0.29
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAAATTTTTTAATATTCAA
Found at i:2182511 original size:18 final size:18
Alignment explanation
Indices: 2182432--2182558 Score: 62
Period size: 18 Copynumber: 6.8 Consensus size: 18
2182422 AAAAATACTA
*
2182432 AAAAATTTATAAAAAATTT
1 AAAAATTT-TTAAAAATTT
* * * *
2182451 AAAATTTTTTTAATATTCAA
1 AAAAATTTTTAAAAATT--T
* *
2182471 AAAAATTTTT-TAATTTCT
1 AAAAATTTTTAAAAATT-T
*
2182489 CAAAATTTTTAAAAATTT
1 AAAAATTTTTAAAAATTT
*
2182507 AAAAAATTTTT-AAAATTC
1 -AAAAATTTTTAAAAATTT
*
2182525 AAACAA-TTCTAAAAATTT
1 AAA-AATTTTTAAAAATTT
* *
2182543 AGAAAAATTATAAAAA
1 A-AAAATTTTTAAAAA
2182559 AATTTTCAAA
Statistics
Matches: 81, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
17 6 0.07
18 33 0.41
19 33 0.41
20 9 0.11
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (18 bp):
AAAAATTTTTAAAAATTT
Found at i:2182512 original size:19 final size:19
Alignment explanation
Indices: 2182490--2182590 Score: 82
Period size: 18 Copynumber: 5.3 Consensus size: 19
2182480 TTAATTTCTC
2182490 AAAATTTTTAAAAATTTAA
1 AAAATTTTTAAAAATTTAA
*
2182509 AAAATTTTT-AAAATTCAA
1 AAAATTTTTAAAAATTTAA
* *
2182527 ACAA-TTCTAAAAATTTAGA
1 AAAATTTTTAAAAATTTA-A
** **
2182546 AAAATTATAAAAAAATTTTC
1 AAAATT-TTTAAAAATTTAA
*
2182566 AAAA-TTTTAAAATTTATAA
1 AAAATTTTTAAAAATT-TAA
2182585 AAAATT
1 AAAATT
2182591 AAAAATAAGA
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
17 3 0.05
18 25 0.40
19 19 0.31
20 6 0.10
21 9 0.15
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (19 bp):
AAAATTTTTAAAAATTTAA
Found at i:2182542 original size:56 final size:57
Alignment explanation
Indices: 2182433--2182596 Score: 140
Period size: 56 Copynumber: 2.9 Consensus size: 57
2182423 AAAATACTAA
** * ***
2182433 AAAATTTATAAAAAATTTAAAATTTTTTTAATATTCAAAAAAATTTTTTAATTTCTC
1 AAAATTTATAAAAAATTTAAAAAATTTTTAAAATTCAAAAAAATTTAAAAATTTCTC
* * **
2182490 AAAATTT-TTAAAAATTTAAAAAATTTTTAAAATTC-AAACAATTCTAAAAATTT-AG
1 AAAATTTATAAAAAATTTAAAAAATTTTTAAAATTCAAAAAAATT-TAAAAATTTCTC
* ** *
2182545 AAAAATTATAAAAAAATTTTCAAAA-TTTTAAAATTTATAAAAAA-TTAAAAAT
1 AAAATTTAT-AAAAAATTTAAAAAATTTTTAAAATTCA-AAAAAATTTAAAAAT
2182597 AAGAAATAGT
Statistics
Matches: 86, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
55 13 0.15
56 48 0.56
57 20 0.23
58 5 0.06
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (57 bp):
AAAATTTATAAAAAATTTAAAAAATTTTTAAAATTCAAAAAAATTTAAAAATTTCTC
Found at i:2182587 original size:10 final size:10
Alignment explanation
Indices: 2182490--2182587 Score: 66
Period size: 9 Copynumber: 10.4 Consensus size: 10
2182480 TTAATTTCTC
*
2182490 AAAATTTTTA
1 AAAATTTATA
2182500 AAAATTTA-A
1 AAAATTTATA
*
2182509 AAAATTT-TT
1 AAAATTTATA
*
2182518 AAAATTCA-A
1 AAAATTTATA
* *
2182527 ACAA-TTCTA
1 AAAATTTATA
*
2182536 AAAATTTAGA
1 AAAATTTATA
*
2182546 AAAATTATAAA
1 AAAATT-TATA
*
2182557 AAAATTT-TC
1 AAAATTTATA
2182566 AAAATTT-T-
1 AAAATTTATA
2182574 AAAATTTATA
1 AAAATTTATA
2182584 AAAA
1 AAAA
2182588 ATTAAAAATA
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
8 8 0.12
9 30 0.44
10 21 0.31
11 9 0.13
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (10 bp):
AAAATTTATA
Found at i:2182587 original size:18 final size:18
Alignment explanation
Indices: 2182471--2182587 Score: 60
Period size: 18 Copynumber: 6.3 Consensus size: 18
2182461 TAATATTCAA
** *
2182471 AAAAATTTTTTAATTTCT
1 AAAAATTTTAAAATTTAT
*
2182489 CAAAATTTTTAAAAATTTA-
1 -AAAAATTTT-AAAATTTAT
*
2182508 AAAAATTTTTAAAATTCA-
1 AAAAA-TTTTAAAATTTAT
* * *
2182526 AACAATTCTAAAAATTTAG
1 AAAAATT-TTAAAATTTAT
*
2182545 AAAAATTATAAAAAAATTT-T
1 AAAAATT-T--TAAAATTTAT
*
2182565 CAAAATTTTAAAATTTAT
1 AAAAATTTTAAAATTTAT
2182583 AAAAA
1 AAAAA
2182588 ATTAAAAATA
Statistics
Matches: 76, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
17 9 0.12
18 28 0.37
19 20 0.26
20 11 0.14
21 8 0.11
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (18 bp):
AAAAATTTTAAAATTTAT
Found at i:2182626 original size:9 final size:9
Alignment explanation
Indices: 2182498--2182627 Score: 50
Period size: 9 Copynumber: 14.1 Consensus size: 9
2182488 TCAAAATTTT
2182498 TAAAAATT-
1 TAAAAATTA
*
2182506 TAAAAAATTT
1 T-AAAAATTA
*
2182516 TTAAAATTCA
1 TAAAAATT-A
* *
2182526 -AACAATTC
1 TAAAAATTA
2182534 TAAAAATTTA
1 TAAAAA-TTA
*
2182544 GAAAAATTA
1 TAAAAATTA
*
2182553 TAAAAAAATTT
1 T--AAAAATTA
* *
2182564 TCAAAATTT
1 TAAAAATTA
*
2182573 TAAAATTTA
1 TAAAAATTA
*
2182582 TAAAAAAT-
1 TAAAAATTA
*
2182590 TAAAAATAA
1 TAAAAATTA
* * *
2182599 GAAATAGTTT
1 TAAA-AATTA
*
2182609 TATAAATTA
1 TAAAAATTA
2182618 TAAAAATTA
1 TAAAAATTA
2182627 T
1 T
2182628 TGTATTGTGA
Statistics
Matches: 86, Mismatches: 27, Indels: 17
0.66 0.21 0.13
Matches are distributed among these distances:
8 7 0.08
9 59 0.69
10 12 0.14
11 8 0.09
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.36
Consensus pattern (9 bp):
TAAAAATTA
Found at i:2182912 original size:28 final size:27
Alignment explanation
Indices: 2182794--2182914 Score: 91
Period size: 29 Copynumber: 4.1 Consensus size: 27
2182784 TTTGAAACAT
*
2182794 TTTAAATTTAAAAAATATTAAAAAAAA
1 TTTAAAATTAAAAAATATTAAAAAAAA
* **
2182821 CTTAAAATTTTAATAAAA-ATCCAAAAAAA
1 TTTAAAA--TTAA-AAAATATTAAAAAAAA
*
2182850 TTTAAATTTCAAAAAATATATAAAAATTTGAAA
1 TTTAAAATT-AAAAAATAT-TAAAAA----AAA
*
2182883 TTGTAAAATTAAAAAATATGAAAAAAAA
1 TT-TAAAATTAAAAAATATTAAAAAAAA
2182911 TTTA
1 TTTA
2182915 TCATTCAGAT
Statistics
Matches: 73, Mismatches: 10, Indels: 22
0.70 0.10 0.21
Matches are distributed among these distances:
27 13 0.18
28 9 0.12
29 22 0.30
30 4 0.05
32 5 0.07
33 14 0.19
34 6 0.08
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.32
Consensus pattern (27 bp):
TTTAAAATTAAAAAATATTAAAAAAAA
Found at i:2184774 original size:113 final size:112
Alignment explanation
Indices: 2184574--2184788 Score: 349
Period size: 113 Copynumber: 1.9 Consensus size: 112
2184564 CATAAGTTCG
* *
2184574 AAGATGAAACTTTCATTGCAAAACACACTGGTCCTGGTTTGCTATCAATAGCATGCTGTTTTATA
1 AAGATGAAAATTTCATTGCAAAACACACTGGTCCTGGTTTGCTATCAATAGCATACTGTTTTATA
*
2184639 TATAATATTATGTAGCTGCATTTTTTTCCTTTTCTCTATATTTTTTCA
66 TATAATATTATGTAGCTACA-TTTTTTCCTTTTCTCTATATTTTTTCA
* * * *
2184687 AAGATGAAAATTTCATTGCAAAAGACACTGGTCCTGGTTTGCTATCAATGGTATACTGTTTTCTA
1 AAGATGAAAATTTCATTGCAAAACACACTGGTCCTGGTTTGCTATCAATAGCATACTGTTTTATA
*
2184752 TATAATATTGTGTAGCTACATTTTTTCCTTTTCTCTA
66 TATAATATTATGTAGCTACATTTTTTCCTTTTCTCTA
2184789 AATGATTTTC
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
112 17 0.18
113 77 0.82
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.43
Consensus pattern (112 bp):
AAGATGAAAATTTCATTGCAAAACACACTGGTCCTGGTTTGCTATCAATAGCATACTGTTTTATA
TATAATATTATGTAGCTACATTTTTTCCTTTTCTCTATATTTTTTCA
Found at i:2185796 original size:2 final size:2
Alignment explanation
Indices: 2185789--2185820 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2185779 GTGTCAGGTA
2185789 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2185821 CCCCTTACAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2191542 original size:22 final size:23
Alignment explanation
Indices: 2191517--2191560 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2191507 TTTATTTGTT
2191517 TTTAA-TAAAAAATTTCATGAAC
1 TTTAATTAAAAAATTTCATGAAC
*
2191539 TTTAATTATAAAATTTCATGAA
1 TTTAATTAAAAAATTTCATGAA
2191561 GACTTCCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (23 bp):
TTTAATTAAAAAATTTCATGAAC
Found at i:2194627 original size:8 final size:8
Alignment explanation
Indices: 2194609--2194649 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
2194599 CAATTTAATC
2194609 AAATGATAT
1 AAAT-ATAT
2194618 AAATATAT
1 AAATATAT
2194626 AAATATAT
1 AAATATAT
*
2194634 ATATATAT
1 AAATATAT
*
2194642 ATATATAT
1 AAATATAT
2194650 CCATATCCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
8 27 0.87
9 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (8 bp):
AAATATAT
Found at i:2194633 original size:2 final size:2
Alignment explanation
Indices: 2194614--2194649 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2194604 TAATCAAATG
* *
2194614 AT AT AA AT AT AT AA 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
2194650 CCATATCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2195003 original size:21 final size:20
Alignment explanation
Indices: 2194978--2195029 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
2194968 ATCATATAAA
*
2194978 AATTAAAATTAATTAAAAAT
1 AATTAAAATTAATAAAAAAT
2194998 GAATTAAAAATT-ATAAAAAAT
1 -AATT-AAAATTAATAAAAAAT
*
2195019 AATAAAAATTA
1 AATTAAAATTA
2195030 TCATGCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 6 0.22
20 3 0.11
21 12 0.44
22 6 0.22
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
AATTAAAATTAATAAAAAAT
Found at i:2195792 original size:13 final size:13
Alignment explanation
Indices: 2195758--2195784 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2195748 TTTTTAAAAG
2195758 TGGCTTTTTTTTT
1 TGGCTTTTTTTTT
2195771 TGGCTTTTTTTTT
1 TGGCTTTTTTTTT
2195784 T
1 T
2195785 TGTTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.15, T:0.78
Consensus pattern (13 bp):
TGGCTTTTTTTTT
Found at i:2195792 original size:14 final size:14
Alignment explanation
Indices: 2195758--2195786 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2195748 TTTTTAAAAG
2195758 TGGC-TTTTTTTTT
1 TGGCTTTTTTTTTT
2195771 TGGCTTTTTTTTTT
1 TGGCTTTTTTTTTT
2195785 TG
1 TG
2195787 TTTTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.00, C:0.07, G:0.17, T:0.76
Consensus pattern (14 bp):
TGGCTTTTTTTTTT
Found at i:2198556 original size:84 final size:84
Alignment explanation
Indices: 2198459--2198627 Score: 311
Period size: 84 Copynumber: 2.0 Consensus size: 84
2198449 TGGAGGTAAG
*
2198459 GCCTGATCCAAACATGAAAATGCAAACACTTGAAGAAGCACGATTAGTGCCATGGAATCATCTAG
1 GCCTGATCCAAACAGGAAAATGCAAACACTTGAAGAAGCACGATTAGTGCCATGGAATCATCTAG
2198524 GTAGACTGTTTGAAGTGAA
66 GTAGACTGTTTGAAGTGAA
*
2198543 GCCTGATCCAAACAGGAAAATGGAAACACTTGAAGAAGCACGATTAGTGCCATGGAATCATCTAG
1 GCCTGATCCAAACAGGAAAATGCAAACACTTGAAGAAGCACGATTAGTGCCATGGAATCATCTAG
*
2198608 GTAGGCTGTTTGAAGTGAA
66 GTAGACTGTTTGAAGTGAA
2198627 G
1 G
2198628 TTGCACAATG
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (84 bp):
GCCTGATCCAAACAGGAAAATGCAAACACTTGAAGAAGCACGATTAGTGCCATGGAATCATCTAG
GTAGACTGTTTGAAGTGAA
Found at i:2198939 original size:68 final size:67
Alignment explanation
Indices: 2198830--2198964 Score: 166
Period size: 68 Copynumber: 2.0 Consensus size: 67
2198820 AAAGGGTTGG
* *
2198830 GTAATTGGTTAATTAGTTGGTTTCAATCTAAGAGATTTTGAATTCAAACATTAG-TAAATTTTTT
1 GTAATTGGCTAATTAGTTGGTTTCAATCTAAGAAATTTTGAATTCAAACA-TAGAT-AATTTTTT
2198894 ATAT
64 ATAT
* * * * *
2198898 GTAATTGGCTAATTAGTTTGTTAT-AGTGTAAGAAATTTTGAATTTAAACATCGATAATTTTTTA
1 GTAATTGGCTAATTAGTTGGTT-TCAATCTAAGAAATTTTGAATTCAAACATAGATAATTTTTTA
2198962 TAT
65 TAT
2198965 TATTAAAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
67 14 0.24
68 43 0.74
69 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (67 bp):
GTAATTGGCTAATTAGTTGGTTTCAATCTAAGAAATTTTGAATTCAAACATAGATAATTTTTTAT
AT
Found at i:2203446 original size:32 final size:33
Alignment explanation
Indices: 2203410--2203476 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 33
2203400 AATAAATCGG
*
2203410 CACCGTGAAGTTCA-AAGTG-TGGTTTTGGGGTT
1 CACCGTGAAGTTCATAA-TGATGGTTTTAGGGTT
2203442 CACCGTGAAGTTCATAATGATGGTTTTAGGGTT
1 CACCGTGAAGTTCATAATGATGGTTTTAGGGTT
2203475 CA
1 CA
2203477 AAGTGAGGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 16 0.50
33 16 0.50
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.34
Consensus pattern (33 bp):
CACCGTGAAGTTCATAATGATGGTTTTAGGGTT
Found at i:2207027 original size:33 final size:33
Alignment explanation
Indices: 2206990--2207063 Score: 148
Period size: 33 Copynumber: 2.2 Consensus size: 33
2206980 CTCCTCCTTA
2206990 TCCTCATGCAACAAATCAAGATATCTCTCCTCT
1 TCCTCATGCAACAAATCAAGATATCTCTCCTCT
2207023 TCCTCATGCAACAAATCAAGATATCTCTCCTCT
1 TCCTCATGCAACAAATCAAGATATCTCTCCTCT
2207056 TCCTCATG
1 TCCTCATG
2207064 TGCATTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.28, C:0.34, G:0.07, T:0.31
Consensus pattern (33 bp):
TCCTCATGCAACAAATCAAGATATCTCTCCTCT
Found at i:2208405 original size:25 final size:25
Alignment explanation
Indices: 2208336--2208411 Score: 64
Period size: 25 Copynumber: 2.9 Consensus size: 25
2208326 ATATTATAAA
*
2208336 ATATTTTTTATTTTATTAAATTTATAT
1 ATATTTTTTATTTT-TTAAA-TCATAT
**
2208363 ATAATTTTTTTAAATTTTAAATCATAT
1 AT-A-TTTTTTATTTTTTAAATCATAT
*
2208390 -TATTTTTATATTTTTTATATCA
1 ATATTTTT-TATTTTTTAAATCA
2208412 ATTTGACGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
24 5 0.12
25 12 0.30
26 1 0.03
27 7 0.17
28 6 0.15
29 9 0.22
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (25 bp):
ATATTTTTTATTTTTTAAATCATAT
Found at i:2223213 original size:17 final size:17
Alignment explanation
Indices: 2223193--2223225 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2223183 GAAAACCACA
2223193 CTTACACCAAAAAGAAT
1 CTTACACCAAAAAGAAT
2223210 CTTACACCAAAAAGAA
1 CTTACACCAAAAAGAA
2223226 AAGCAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.24, G:0.06, T:0.15
Consensus pattern (17 bp):
CTTACACCAAAAAGAAT
Found at i:2225078 original size:24 final size:24
Alignment explanation
Indices: 2225046--2225092 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2225036 TAATTGTAAA
*
2225046 AATTTGATTAT-TCTACATTAGTGC
1 AATTTGATTCTCT-TACATTAGTGC
2225070 AATTTGATTCTCTTACATTAGTG
1 AATTTGATTCTCTTACATTAGTG
2225093 TAGCTTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGATTCTCTTACATTAGTGC
Found at i:2228412 original size:22 final size:22
Alignment explanation
Indices: 2228386--2228429 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2228376 TGTACATTTA
*
2228386 TATTTGTATCTCTAAAATTAAG
1 TATTTATATCTCTAAAATTAAG
* *
2228408 TATTTATATCTTTAGAATTAAG
1 TATTTATATCTCTAAAATTAAG
2228430 GACAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (22 bp):
TATTTATATCTCTAAAATTAAG
Found at i:2229024 original size:15 final size:15
Alignment explanation
Indices: 2229004--2229038 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2228994 GATTAATGGG
*
2229004 TTTTGGGTATCAATA
1 TTTTGGGTAACAATA
*
2229019 TTTTGGGTAAGAATA
1 TTTTGGGTAACAATA
2229034 TTTTG
1 TTTTG
2229039 TGTTTCTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.49
Consensus pattern (15 bp):
TTTTGGGTAACAATA
Found at i:2234461 original size:21 final size:20
Alignment explanation
Indices: 2234407--2234462 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
2234397 ATTGACTTGC
*
2234407 CAATTTCTCAACCAGCCCTT
1 CAATTTCTTAACCAGCCCTT
*
2234427 CTAGTTT-TTCAACCAGCCCCTT
1 C-AATTTCTT-AACCAG-CCCTT
2234449 CAATTTCTTAACCA
1 CAATTTCTTAACCA
2234463 TATTTCTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 2 0.07
21 19 0.66
22 8 0.28
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (20 bp):
CAATTTCTTAACCAGCCCTT
Found at i:2236550 original size:25 final size:25
Alignment explanation
Indices: 2236515--2236563 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2236505 GGGATTGTAG
2236515 AAATCTAATTCTCCTACATTAGTGT
1 AAATCTAATTCTCCTACATTAGTGT
* *
2236540 AAATCTGATTCTCCTATATTAGTG
1 AAATCTAATTCTCCTACATTAGTG
2236564 CAGCTTGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (25 bp):
AAATCTAATTCTCCTACATTAGTGT
Found at i:2243832 original size:16 final size:15
Alignment explanation
Indices: 2243811--2243862 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
2243801 AGTAATGGGT
2243811 AAAGGAAAGAAAAAAA
1 AAAGGAAA-AAAAAAA
*
2243827 AAAGGAAAAAATAAA
1 AAAGGAAAAAAAAAA
*
2243842 AAATGAAAAATAAAATA
1 AAAGGAAAAA-AAAA-A
2243859 AAAG
1 AAAG
2243863 TCATCTCCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 15 0.50
16 11 0.37
17 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (15 bp):
AAAGGAAAAAAAAAA
Found at i:2244405 original size:15 final size:15
Alignment explanation
Indices: 2244385--2244414 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2244375 CAACAATTAC
2244385 TTCATGATTAAATAA
1 TTCATGATTAAATAA
2244400 TTCATGATTAAATAA
1 TTCATGATTAAATAA
2244415 AATAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (15 bp):
TTCATGATTAAATAA
Found at i:2244738 original size:14 final size:14
Alignment explanation
Indices: 2244715--2244745 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2244705 TCTTTATACT
*
2244715 ATTTTGATTTAATA
1 ATTTTAATTTAATA
2244729 ATTTTAATTTAATA
1 ATTTTAATTTAATA
2244743 ATT
1 ATT
2244746 AATTTTGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (14 bp):
ATTTTAATTTAATA
Found at i:2250671 original size:12 final size:12
Alignment explanation
Indices: 2250651--2250714 Score: 55
Period size: 12 Copynumber: 5.5 Consensus size: 12
2250641 AATAATATCT
*
2250651 TTAATTTTTATA
1 TTAAATTTTATA
2250663 TTAAA-TTT-TA
1 TTAAATTTTATA
*
2250673 TTAATTTATTGAT-
1 TTAAATT-TT-ATA
2250686 TTAAATTTT-TA
1 TTAAATTTTATA
*
2250697 TTAAAATTTATA
1 TTAAATTTTATA
2250709 TTAAAT
1 TTAAAT
2250715 CATTATTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
10 7 0.17
11 12 0.29
12 15 0.37
13 6 0.15
14 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
TTAAATTTTATA
Found at i:2250700 original size:24 final size:22
Alignment explanation
Indices: 2250651--2250724 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 22
2250641 AATAATATCT
2250651 TTAATTTTTATATTAAATTTTA
1 TTAATTTTTATATTAAATTTTA
2250673 TTAATTTATTGAT-TTAAATTTTTA
1 TTAATTT-TT-ATATTAAA-TTTTA
** *
2250697 TTAAAATTTATATTAAATCATTA
1 TTAATTTTTATATTAAAT-TTTA
2250720 TTAAT
1 TTAAT
2250725 AAAAATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
22 10 0.23
23 21 0.49
24 12 0.28
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (22 bp):
TTAATTTTTATATTAAATTTTA
Found at i:2251960 original size:14 final size:16
Alignment explanation
Indices: 2251941--2251972 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
2251931 GAAAAGCAAT
2251941 AAGAAGC-ATT-CAAG
1 AAGAAGCAATTCCAAG
2251955 AAGAAGCAATTCCAAG
1 AAGAAGCAATTCCAAG
2251971 AA
1 AA
2251973 AGATATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.53, C:0.16, G:0.19, T:0.12
Consensus pattern (16 bp):
AAGAAGCAATTCCAAG
Found at i:2254211 original size:19 final size:18
Alignment explanation
Indices: 2254175--2254214 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
2254165 TATTGTTATT
2254175 TAAAAATAAAAAATAATA
1 TAAAAATAAAAAATAATA
2254193 TAAAAATTAATAAAA-AATA
1 TAAAAA-TAA-AAAATAATA
2254212 TAA
1 TAA
2254215 TTTGACTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 10 0.50
20 4 0.20
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAAAATAAAAAATAATA
Found at i:2255111 original size:18 final size:18
Alignment explanation
Indices: 2255088--2255128 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2255078 TGATTACACG
*
2255088 GATGAAGA-AGAGGATGAC
1 GATGAAGAGAG-GGAGGAC
2255106 GATGAAGAGAGGGAGGAC
1 GATGAAGAGAGGGAGGAC
2255124 GATGA
1 GATGA
2255129 GGAAAATGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.41, C:0.05, G:0.44, T:0.10
Consensus pattern (18 bp):
GATGAAGAGAGGGAGGAC
Found at i:2267720 original size:2 final size:2
Alignment explanation
Indices: 2267713--2267740 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2267703 GCTGCTGAGG
2267713 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
2267741 GATGGATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2269776 original size:11 final size:12
Alignment explanation
Indices: 2269756--2269784 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2269746 ATTTAAAGCG
2269756 AATTTATAGCAA
1 AATTTATAGCAA
2269768 AATTT-TAGCAA
1 AATTTATAGCAA
2269779 AATTTA
1 AATTTA
2269785 ATTATGGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (12 bp):
AATTTATAGCAA
Found at i:2271565 original size:19 final size:19
Alignment explanation
Indices: 2271541--2271580 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2271531 TTGGCATTAT
2271541 AATACTTCCCTATTAATAA
1 AATACTTCCCTATTAATAA
* *
2271560 AATACTTCTCTATTAGTAA
1 AATACTTCCCTATTAATAA
2271579 AA
1 AA
2271581 ACCCGAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (19 bp):
AATACTTCCCTATTAATAA
Found at i:2272195 original size:26 final size:27
Alignment explanation
Indices: 2272166--2272219 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
2272156 TAGTAAGTTT
2272166 TCTATCCAAGATTTGAAAAGGAT-AAA
1 TCTATCCAAGATTTGAAAAGGATGAAA
* *
2272192 TCTATTCAAGCTTTGAAAAGGATGAAA
1 TCTATCCAAGATTTGAAAAGGATGAAA
2272219 T
1 T
2272220 TTGGTGATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.30
Consensus pattern (27 bp):
TCTATCCAAGATTTGAAAAGGATGAAA
Found at i:2273613 original size:15 final size:16
Alignment explanation
Indices: 2273579--2273615 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2273569 TTTTGCATTG
2273579 GAAATTATTAAAATTT
1 GAAATTATTAAAATTT
*
2273595 -AAATT-TTAATATTT
1 GAAATTATTAAAATTT
2273609 GAAATTA
1 GAAATTA
2273616 AAAATTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (16 bp):
GAAATTATTAAAATTT
Found at i:2273613 original size:21 final size:21
Alignment explanation
Indices: 2273589--2273629 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2273579 GAAATTATTA
* * *
2273589 AAATTTAAATTTTAATATTTG
1 AAATTAAAAATTTAACATTTG
2273610 AAATTAAAAATTTAACATTT
1 AAATTAAAAATTTAACATTT
2273630 TACAGCTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
AAATTAAAAATTTAACATTTG
Found at i:2276104 original size:9 final size:9
Alignment explanation
Indices: 2276092--2276125 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
2276082 TATTTTTTCT
2276092 TAAAATATA
1 TAAAATATA
2276101 TAAAATATA
1 TAAAATATA
2276110 TTAATAATATA
1 -TAA-AATATA
2276121 TAAAA
1 TAAAA
2276126 AATTTTTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 11 0.48
10 6 0.26
11 6 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TAAAATATA
Found at i:2276504 original size:18 final size:19
Alignment explanation
Indices: 2276477--2276512 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2276467 TTCATTTTTT
*
2276477 AAAAATTTGTTTCATGTTG
1 AAAAATTTGTTACATGTTG
2276496 AAAAA-TTGTTACATGTT
1 AAAAATTTGTTACATGTT
2276513 CAATATATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (19 bp):
AAAAATTTGTTACATGTTG
Found at i:2276617 original size:11 final size:10
Alignment explanation
Indices: 2276593--2276634 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
2276583 TGCACCTAAA
*
2276593 AATATTTTTT
1 AATATATTTT
2276603 AATATATTATT
1 AATATATT-TT
*
2276614 AATATGTTTT
1 AATATATTTT
2276624 -ATATATTTT
1 AATATATTTT
2276633 AA
1 AA
2276635 GAAAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 8 0.30
10 10 0.37
11 9 0.33
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (10 bp):
AATATATTTT
Found at i:2284684 original size:170 final size:171
Alignment explanation
Indices: 2284351--2284689 Score: 538
Period size: 170 Copynumber: 2.0 Consensus size: 171
2284341 TTCTTCTTTT
*
2284351 TTATTATTATTATTTCAGCCCCTTTAATCAAGCAATAACTAAGAGCCCAAAAAAAAAAAAAAAAC
1 TTATTATTATTATTTCAACCCCTTTAATCAAGCAATAACTAAGAGCCCAAAAAAAAAAAAAAAAC
* *
2284416 AAACTTAAGATGTGCTAAACAAGAACCCTAACGTCCTCATCTCTGTTATGGCAAAGTATTTGTTT
66 AAACTTAAGATGTCCTAAACAAGAACCCTAACGTCCCCA-CTC--TTATGGCAAAGTATTTGTTT
2284481 CCTTCTATCTATGGCGACTTCTCTATTCCATTCTGAAGCTATTA
128 CCTTCTATCTATGGCGACTTCTCTATTCCATTCTGAAGCTATTA
* * *
2284525 TTATTATTATTATTTCAACCCCTTTAATCATGCAATAACTCAGAGCCCAAAAAAGAAAATAAAAA
1 TTATTATTATTATTTCAACCCCTTTAATCAAGCAATAACTAAGAGCCCAAAAAA-AAAAAAAAAA
* *
2284590 CAAACTTAAGATGTCCTAAACAAGAACCCTATCGTCCCCA-TC-TATGGCAAAGTATTTGTTTCT
65 CAAACTTAAGATGTCCTAAACAAGAACCCTAACGTCCCCACTCTTATGGCAAAGTATTTGTTTCC
* *
2284653 TTCTATCTATGGCGACTTGTCTATTCCATTCTTAAGC
130 TTCTATCTATGGCGACTTCTCTATTCCATTCTGAAGC
2284690 CAGAAAGCAT
Statistics
Matches: 154, Mismatches: 10, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
170 55 0.36
173 2 0.01
174 51 0.33
175 46 0.30
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (171 bp):
TTATTATTATTATTTCAACCCCTTTAATCAAGCAATAACTAAGAGCCCAAAAAAAAAAAAAAAAC
AAACTTAAGATGTCCTAAACAAGAACCCTAACGTCCCCACTCTTATGGCAAAGTATTTGTTTCCT
TCTATCTATGGCGACTTCTCTATTCCATTCTGAAGCTATTA
Found at i:2287547 original size:28 final size:27
Alignment explanation
Indices: 2287492--2287543 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2287482 CAGCATTCAA
**
2287492 ATAAAAATTCTAAAATTTTTTTAAATT
1 ATAAAAATTCTAAAATTTTTAAAAATT
2287519 ATAATAAATTC-AAAATTTTTAAAAA
1 ATAA-AAATTCTAAAATTTTTAAAAA
2287544 ATTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (27 bp):
ATAAAAATTCTAAAATTTTTAAAAATT
Done.