Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold872
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: 251851
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
File 2 of 2
Found at i:151821 original size:27 final size:24
Alignment explanation
Indices: 151779--151849 Score: 88
Period size: 27 Copynumber: 2.8 Consensus size: 24
151769 ATAAAATATA
151779 TATTAAAATTATATTTATGTTAAAT
1 TATT-AAATTATATTTATGTTAAAT
*
151804 AATAATTAAATTATATTTATATTAAAT
1 --T-ATTAAATTATATTTATGTTAAAT
*
151831 TATTAAAATATATTTATGT
1 TATTAAATTATATTTATGT
151850 AAAAAATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
24 16 0.40
25 1 0.03
27 20 0.50
28 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (24 bp):
TATTAAATTATATTTATGTTAAAT
Found at i:154830 original size:21 final size:21
Alignment explanation
Indices: 154804--154859 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
154794 AGATATAAAG
154804 AAAATAAATAAAA-TTAATTTA
1 AAAATAAATAAAAGTTAA-TTA
**
154825 AAAATATCTAAAAAGTTAATTA
1 AAAATAAAT-AAAAGTTAATTA
*
154847 AAACTAAATAAAA
1 AAAATAAATAAAA
154860 ACCATTAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 11 0.39
22 13 0.46
23 4 0.14
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAATAAATAAAAGTTAATTA
Found at i:157170 original size:25 final size:24
Alignment explanation
Indices: 157124--157186 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 24
157114 AATTATAAAC
*
157124 AAAACAAAAGCTTTAAACTTTTTT
1 AAAAAAAAAGCTTTAAACTTTTTT
* **
157148 AAAAATAAAAGCTTTTATTTTTTTT
1 AAAAA-AAAAGCTTTAAACTTTTTT
* *
157173 TAAAAAAAACCTTT
1 AAAAAAAAAGCTTT
157187 CAAAAACCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 12 0.38
25 20 0.62
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (24 bp):
AAAAAAAAAGCTTTAAACTTTTTT
Found at i:157839 original size:22 final size:25
Alignment explanation
Indices: 157790--157850 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 25
157780 AATTATAAAC
*
157790 AAAACAAAAGCTTTAAACTTTTTCT
1 AAAAAAAAAGCTTTAAACTTTTTCT
* *
157815 AAAATAAAAGCTTT-TA-TTTTT-T
1 AAAAAAAAAGCTTTAAACTTTTTCT
*
157837 AAAAAAAAACCTTT
1 AAAAAAAAAGCTTT
157851 CAAAAACTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 13 0.41
23 5 0.16
24 1 0.03
25 13 0.41
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (25 bp):
AAAAAAAAAGCTTTAAACTTTTTCT
Found at i:158163 original size:661 final size:663
Alignment explanation
Indices: 156956--158284 Score: 2277
Period size: 667 Copynumber: 2.0 Consensus size: 663
156946 ATGGTTGAAG
*
156956 ATCATCAAGCTCATAACTCTTCAACCAAAGAAAACAAAGAGAATATTTATACAAATATATTATCC
1 ATCATCAAGCTCATAACTCTTCAACCAAAGAAAACAAAAAGAATATTTATACAAATATATTATCC
*
157021 ACAACAGACTTTAGCCATGACAAATAAATATGCAAATATAAAAGGTATGCAAATGCATAAACTAG
66 ACAACAGACGTTAGCCATGACAAATAAATATGCAAATATAAAAGGTATGCAAATGCATAAACTAG
157086 TATAATAATAGTTTAGAATAAGGCTTGCAATTATAAACAAAACAAAAGCTTTAAACTTTTTTAAA
131 TATAATAATAGTTTAGAATAAGGCTTGCAATTATAAACAAAACAAAAGCTTTAAACTTTTTTAAA
*
157151 AATAAAAGCTTTTATTTTTTTTTAAAAAAAACCTTTCAAAAACCTTTAGAAAAATGAAAAAATGA
196 AATAAAAGCTTTTA-TTTTTTTAAAAAAAAACCTTTCAAAAACCTTTAGAAAAATGAAAAAATGA
157216 AGGATAATTACAATGTAAAACAAAGGCAAAGGAGAAGAAAAAAAAACTACCTTTAAGCTAGAAAC
260 AGGATAATTACAATGTAAAACAAAGGCAAAGGAGAAGAAAAAAAAACTACCTTTAAGCTAGAAAC
* *
157281 TAAAAAATCTTACTCTTTATTCTTTGTTTTCTGTATTTTTTTTTTTGGTTTTTTTTTGTGAAAGG
325 TAAAAAATCTCACTCTTTATTCTTTGTTTTCTGTATTTTTTTTTTTGGTTTTTTTTTGTGAAAAG
* *
157346 TTTTTGAGAAAATAGGCAATTTTTTTATGAACTTTTTTTTTCTTTTTTTTTTCAACTAAATATGC
390 TTTTTGAGAAAATAGGCAATTTTTTTATGAACTTTTTTTCTCTTTTTTTTTTCAACTAAATAAGC
* *
157411 AATATGTGTAAGTAAAAAAGAAGAAAAAGTTTAAACGTCTCCTTAGCTAACCAAGAAAAGTGCCC
455 AATATGTGTAAGTAAAAAAGAAGAAAAAGTTTAAACGTCTCCTTAGCTAACCAAAAAAAGTGCCA
* *
157476 TCTCCTCCTTTTTTTCTTAATTTTTTGACCTCTCTCTTTTGGCACTATGTATACTTTGTCTTTTT
520 TCTCCTCCTTCTTTTCTTAATTTTTTG--C-CTCTCTTTTGGCACTATGTATACTTTGTCTTTTC
* *
157541 TTCAATGTCATTGGCCAAATTCCTATTAATTTAGATCCAAATAAGAATTCTATTAGCCAAGCTTA
582 TCCAATGTCATTGACCAAATTCCTATTAATTTAGATCCAAATAAGAATTCTATTAGCCAAGCTTA
157606 GTACCACTTTCTTATTA
647 GTACCACTTTCTTATTA
*
157623 ATCATCAAGCTTATAACTCTTCAACCAAAGAAAACAAAAAGAATATTTATACAAATATATTATCC
1 ATCATCAAGCTCATAACTCTTCAACCAAAGAAAACAAAAAGAATATTTATACAAATATATTATCC
157688 ACAACAGACGTTAGCCATGACAAATAAATATGCAAATATAAAAGGTATGCAAATGCATAAACTAG
66 ACAACAGACGTTAGCCATGACAAATAAATATGCAAATATAAAAGGTATGCAAATGCATAAACTAG
157753 TATAATAATAGTTTAGAAT-AGGCTTGCAATTATAAACAAAACAAAAGCTTTAAACTTTTTCT-A
131 TATAATAATAGTTTAGAATAAGGCTTGCAATTATAAACAAAACAAAAGCTTTAAACTTTTT-TAA
157816 AAATAAAAGCTTTTA-TTTTTTAAAAAAAAACCTTTCAAAAA-CTTCTA-AAAAATG-AAAAATG
195 AAATAAAAGCTTTTATTTTTTTAAAAAAAAACCTTTCAAAAACCTT-TAGAAAAATGAAAAAATG
*
157877 AAGGATAATTACAATGTAAAACAAAGGCAAAGGAGAAGAAAAAAAAACTA-CTTTAGGCTAGAAA
259 AAGGATAATTACAATGTAAAACAAAGGCAAAGGAGAAGAAAAAAAAACTACCTTTAAGCTAGAAA
*
157941 CTAAAAAATCTCACTCTTTATTTTTTGTTTTCTGTATTTTTCTTTTTTTGGTTTTTTTTTGTGAA
324 CTAAAAAATCTCACTCTTTATTCTTTGTTTTCTGTA-TTTT-TTTTTTTGGTTTTTTTTTGTGAA
*
158006 AAGTTTTTGAGAGAATAGGCAA-TTTTTTATGAACTTTTTTTCTC-TTTTTTTTTCAACTAAATA
387 AAGTTTTTGAGAAAATAGGCAATTTTTTTATGAACTTTTTTTCTCTTTTTTTTTTCAACTAAATA
* *
158069 AGCAATATGTGTGAA-TAAAAAAGAAGAAAAAGTTTAAATGTCTCCTTAGCTAGCCAAAAAAAGT
452 AGCAATATGTGT-AAGTAAAAAAGAAGAAAAAGTTTAAACGTCTCCTTAGCTAACCAAAAAAAGT
158133 GCCATCTTCC-CC-TCTTTTCTTAATTTTTTTGCCTCTCTTTTGGCACTATGTATACTTTGTCTT
516 GCCATC-TCCTCCTTCTTTTCTTAA-TTTTTTGCCTCTCTTTTGGCACTATGTATACTTTGTCTT
*
158196 TTCTCCAATGTCATTGACCAAATTCCTATTAATTTAGGTCCAAATAAGAATTCTATTAGCCAAGC
579 TTCTCCAATGTCATTGACCAAATTCCTATTAATTTAGATCCAAATAAGAATTCTATTAGCCAAGC
* *
158261 TTAGTATCACTTTTTTATTA
644 TTAGTACCACTTTCTTATTA
158281 ATCA
1 ATCA
158285 CAAAATTATA
Statistics
Matches: 633, Mismatches: 22, Indels: 23
0.93 0.03 0.03
Matches are distributed among these distances:
658 114 0.18
659 1 0.00
660 10 0.02
661 137 0.22
662 87 0.14
663 53 0.08
664 27 0.04
666 57 0.09
667 147 0.23
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (663 bp):
ATCATCAAGCTCATAACTCTTCAACCAAAGAAAACAAAAAGAATATTTATACAAATATATTATCC
ACAACAGACGTTAGCCATGACAAATAAATATGCAAATATAAAAGGTATGCAAATGCATAAACTAG
TATAATAATAGTTTAGAATAAGGCTTGCAATTATAAACAAAACAAAAGCTTTAAACTTTTTTAAA
AATAAAAGCTTTTATTTTTTTAAAAAAAAACCTTTCAAAAACCTTTAGAAAAATGAAAAAATGAA
GGATAATTACAATGTAAAACAAAGGCAAAGGAGAAGAAAAAAAAACTACCTTTAAGCTAGAAACT
AAAAAATCTCACTCTTTATTCTTTGTTTTCTGTATTTTTTTTTTTGGTTTTTTTTTGTGAAAAGT
TTTTGAGAAAATAGGCAATTTTTTTATGAACTTTTTTTCTCTTTTTTTTTTCAACTAAATAAGCA
ATATGTGTAAGTAAAAAAGAAGAAAAAGTTTAAACGTCTCCTTAGCTAACCAAAAAAAGTGCCAT
CTCCTCCTTCTTTTCTTAATTTTTTGCCTCTCTTTTGGCACTATGTATACTTTGTCTTTTCTCCA
ATGTCATTGACCAAATTCCTATTAATTTAGATCCAAATAAGAATTCTATTAGCCAAGCTTAGTAC
CACTTTCTTATTA
Found at i:160498 original size:3 final size:3
Alignment explanation
Indices: 160490--160530 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
160480 ATGCTCAATA
160490 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
160531 AATAATAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:160535 original size:3 final size:3
Alignment explanation
Indices: 160529--160553 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
160519 GATGATGATG
160529 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
160554 GCTGAAAATT
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:161829 original size:2 final size:2
Alignment explanation
Indices: 161822--161854 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
161812 TAAAGACTTA
161822 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 A
161855 ACACTACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:161943 original size:14 final size:14
Alignment explanation
Indices: 161924--161960 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
161914 ATTACATGTG
161924 TGTATGCATATATA
1 TGTATGCATATATA
*
161938 TGTATGCATATATG
1 TGTATGCATATATA
*
161952 TTTATGCAT
1 TGTATGCAT
161961 GGATCTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (14 bp):
TGTATGCATATATA
Found at i:163882 original size:4 final size:4
Alignment explanation
Indices: 163873--163898 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
163863 GATGTTCAGG
163873 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
163899 TTTGCATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:164282 original size:21 final size:22
Alignment explanation
Indices: 164244--164286 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
164234 TTATCAACTT
*
164244 ATTTATTTATTTAATAAATTTA
1 ATTTAATTATTTAATAAATTTA
*
164266 ATTTAATT-TTTATTAAATTTA
1 ATTTAATTATTTAATAAATTTA
164287 TAAAATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTAATTATTTAATAAATTTA
Found at i:164636 original size:2 final size:2
Alignment explanation
Indices: 164625--164664 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
164615 AAGAAAGATG
* *
164625 TA TA -A TA TA TA TA CA TA TG TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
164665 CCAAATGAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:165827 original size:3 final size:3
Alignment explanation
Indices: 165819--165862 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
165809 CCTACCTTCT
165819 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
165863 TACATAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:166389 original size:35 final size:35
Alignment explanation
Indices: 166340--166413 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
166330 CTTTTCCATT
*
166340 ATAATGAGAAAGATAAATTAAA-CAAATGCCATGCC
1 ATAATGAGAAAGATAAATTAAAGCAAA-GCCATGCA
* * *
166375 ATAATTAGACAGATAAATTAAAGGAAAGCCATGCA
1 ATAATGAGAAAGATAAATTAAAGCAAAGCCATGCA
166410 ATAA
1 ATAA
166414 CCGGTTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 31 0.91
36 3 0.09
ACGTcount: A:0.53, C:0.12, G:0.15, T:0.20
Consensus pattern (35 bp):
ATAATGAGAAAGATAAATTAAAGCAAAGCCATGCA
Found at i:167041 original size:22 final size:22
Alignment explanation
Indices: 167008--167055 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
166998 AGATTTCTAT
* *
167008 TTTTAAAAAATATATA-TTTAA
1 TTTTAAAAAATAAATAGGTTAA
*
167029 TTTTAAAGCAATAAATAGGTTAA
1 TTTTAAA-AAATAAATAGGTTAA
167052 TTTT
1 TTTT
167056 TGAACTTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 7 0.32
22 7 0.32
23 8 0.36
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (22 bp):
TTTTAAAAAATAAATAGGTTAA
Found at i:167712 original size:120 final size:115
Alignment explanation
Indices: 167560--167787 Score: 314
Period size: 120 Copynumber: 1.9 Consensus size: 115
167550 ACATAAGTAA
* * *
167560 TTCAGTAATCACATGCAATGCATAAAGTAAAGAA-CCTCAAAACAAAAATGGTTTCAAATTAATT
1 TTCAGCAATCACATACAAAGCATAAAGTAAAGAATCCT-AAAACAAAAATGGTTTCAAATTAA--
* * *
167624 TTTTTTAAAAAATTATCTATTATCATGTTAATGAACTCAAAACTTTGCATAGGAAT
63 -ATTTT--AAAATTATCCATTATCATGTTAACGAACTCAAAACTTTGCATAGGAAT
* *
167680 TTCAGCAATCACATACAAAGTATAAAGTAAAGAATCCTAAAATAAAAATGGTTTCAAATTAAATT
1 TTCAGCAATCACATACAAAGCATAAAGTAAAGAATCCTAAAACAAAAATGGTTTCAAATTAAATT
*
167745 TTACAATTATCCATTATCATGTTAACGAACTCAAAACTTTGCA
66 TTAAAATTATCCATTATCATGTTAACGAACTCAAAACTTTGCA
167788 AGTTCTCATT
Statistics
Matches: 98, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
115 38 0.39
117 4 0.04
120 53 0.54
121 3 0.03
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.32
Consensus pattern (115 bp):
TTCAGCAATCACATACAAAGCATAAAGTAAAGAATCCTAAAACAAAAATGGTTTCAAATTAAATT
TTAAAATTATCCATTATCATGTTAACGAACTCAAAACTTTGCATAGGAAT
Found at i:170220 original size:19 final size:18
Alignment explanation
Indices: 170187--170227 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
170177 AAATATTTGG
170187 TTATTTAGTTTTATTTAT
1 TTATTTAGTTTTATTTAT
*
170205 TTATTTATTGTTTATTTAT
1 TTATTTAGT-TTTATTTAT
170224 TTAT
1 TTAT
170228 GATTTCATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (18 bp):
TTATTTAGTTTTATTTAT
Found at i:170237 original size:23 final size:23
Alignment explanation
Indices: 170196--170246 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
170186 GTTATTTAGT
* *
170196 TTTATTTATTTATTTATTGTTTA
1 TTTATTTATTGATTTATTGATTA
*
170219 TTTATTTA-TGATTTCATTGATTC
1 TTTATTTATTGATTT-ATTGATTA
170242 TTTAT
1 TTTAT
170247 CTGATTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.69
Consensus pattern (23 bp):
TTTATTTATTGATTTATTGATTA
Found at i:171956 original size:23 final size:23
Alignment explanation
Indices: 171930--171975 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
171920 AAGTATTATT
* *
171930 TTATGTATTTTAAAAATATTTAA
1 TTATATATTTTAAAAATAATTAA
*
171953 TTATATATTTTATAAATAATTAA
1 TTATATATTTTAAAAATAATTAA
171976 AATTATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATATATTTTAAAAATAATTAA
Found at i:171979 original size:25 final size:23
Alignment explanation
Indices: 171930--171981 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
171920 AAGTATTATT
* *
171930 TTATGTATTTTAAAAATATTTAA
1 TTATATATTTTAAAAATATTAAA
*
171953 TTATATATTTTATAAATAATTAAAA
1 TTATATATTTTAAAAAT-ATT-AAA
171978 TTAT
1 TTAT
171982 TAAATGTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 15 0.62
24 3 0.12
25 6 0.25
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATATATTTTAAAAATATTAAA
Found at i:172242 original size:17 final size:17
Alignment explanation
Indices: 172210--172255 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
172200 ATATTTAACG
172210 AAAAACTTTTAATAAAAT
1 AAAAA-TTTTAATAAAAT
* *
172228 TAAAATTTTATTAAAAT
1 AAAAATTTTAATAAAAT
172245 AAAAATGTTTA
1 AAAAAT-TTTA
172256 CTATTACAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
AAAAATTTTAATAAAAT
Found at i:173631 original size:2 final size:2
Alignment explanation
Indices: 173626--173651 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
173616 ATGTGTGTGA
173626 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
173652 GAATTCGATT
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:175592 original size:3 final size:3
Alignment explanation
Indices: 175584--175616 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
175574 TATCTGGTAC
*
175584 TTA TTA TTA TTA -TA TTA TTA ATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
175617 GTTTAAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:175693 original size:16 final size:16
Alignment explanation
Indices: 175660--175701 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
175650 AACCGGCATA
*
175660 TTATTAAATTTTACTT
1 TTATTATATTTTACTT
175676 TTATTATATTTTGA-TT
1 TTATTATATTTT-ACTT
175692 TT-TTATATTT
1 TTATTATATTT
175702 ATATCTTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 15 0.62
17 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (16 bp):
TTATTATATTTTACTT
Found at i:177542 original size:20 final size:19
Alignment explanation
Indices: 177519--177566 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
177509 TGTATTTTTA
177519 TTTATATTTTATCT-TAATTT
1 TTTATATTTT-T-TGTAATTT
*
177539 TTTATGTTTTTTGTAATTT
1 TTTATATTTTTTGTAATTT
177558 TGTTATATT
1 T-TTATATT
177567 ACTGTTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.04
19 8 0.33
20 15 0.62
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.71
Consensus pattern (19 bp):
TTTATATTTTTTGTAATTT
Found at i:177903 original size:19 final size:20
Alignment explanation
Indices: 177875--177916 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
177865 AATTAAGATG
177875 TATTTAATTATTATAT-ATT
1 TATTTAATTATTATATAATT
* *
177894 TATTTTATTATTTTATAATT
1 TATTTAATTATTATATAATT
177914 TAT
1 TAT
177917 ATTTGAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTAATTATTATATAATT
Found at i:178266 original size:3 final size:3
Alignment explanation
Indices: 178248--178287 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
178238 TGAATTTTTA
178248 TAT TA- TAT TA- 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
178288 ATAAATAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:178461 original size:15 final size:16
Alignment explanation
Indices: 178432--178469 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
178422 AAATTAAATG
*
178432 ATTATATATTAAGTTT
1 ATTATTTATTAAGTTT
178448 ATTATTTATT-AGTTT
1 ATTATTTATTAAGTTT
*
178463 ATGATTT
1 ATTATTT
178470 TATATTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (16 bp):
ATTATTTATTAAGTTT
Found at i:181018 original size:22 final size:23
Alignment explanation
Indices: 180972--181027 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
180962 TGGACATGTT
180972 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
180995 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
181017 AAAAATGCATG
1 AAAAATGCATG
181028 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:181987 original size:20 final size:20
Alignment explanation
Indices: 181940--182014 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
181930 AAAAGGACAT
* ** *
181940 AATGTATCTATACATTGTAG
1 AATGTATCGATACATTCAAA
* *
181960 AATATATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* * *
181980 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCAAA
182000 AATGTATCGATACAT
1 AATGTATCGATACAT
182015 CAAGGTAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:182008 original size:40 final size:39
Alignment explanation
Indices: 181937--182014 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
181927 GGTAAAAGGA
* * *
181937 CATAATGTATCTATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
181976 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
182015 CAAGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:183043 original size:86 final size:84
Alignment explanation
Indices: 182625--183732 Score: 1420
Period size: 86 Copynumber: 12.9 Consensus size: 84
182615 CACTGACACA
** * *
182625 TGTGGGCTTTGAAAAGAGTGTTACTGACTTGCGTGGGCTTT-AAAAAGGTGCCACTAACTTGCGT
1 TGTGGGCTTTG-AAAGAGTGCCACTGACTT--GTGGGCTTTGAAAGA-GTGCCACTGACTT--GT
182689 GGGCTTTGAAAGGATGCCACTGACT
60 GGGCTTTGAAAGGATGCCACTGACT
* *
182714 CGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG-GTGCCACTGACTCGTGGGCTT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTT
* *
182778 TGAAAAGG-TACCACTAACT
66 TG-AAAGGATGCCACTGACT
* * *
182797 CGTGGGC-TTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTT
*
182861 TGAAAAGG-TGCCACTAACT
66 TG-AAAGGATGCCACTGACT
* * * *
182880 TGCGTGGGCTTTGAAAGGAGTGCCATTGACTTGTGTGGGCTTTGAAAGGGTGCCACTAACTCGTG
1 T--GTGGGCTTTGAAA-GAGTGCCACTGAC-T-TGTGGGCTTTGAAAGAGTGCCACTGACTTGTG
182945 GGCTTTGAAAGGATGCCACTGACT
61 GGCTTTGAAAGGATGCCACTGACT
* * * * * *
182969 TGTGGACTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAAATACCACTGACTTGCGTGAGC
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTT--GTGGGC
*
183034 TTTAAAAGGAGTGCCACTGACTT
64 TTTGAAAGGA-TGCCACTGAC-T
* *
183057 GTGTGGGCTTTAAAATG-GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGAATTGTGGGC
1 -TGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC
* *
183121 TTCGCAATGG-TGCCACTGACT
64 TTTG-AAAGGATGCCACTGACT
* * * * *
183142 TGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGCTT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTT
*
183207 TGAAAGGGTGCCACTGACT
66 TGAAAGGATGCCACTGACT
* *
183226 TGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTAACTTGTGGGC
1 TGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGC
183291 TTTGAAAGGAGTGCCACTGACT
64 TTTGAAAGGA-TGCCACTGACT
* * * *
183313 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAATTTGTAGGCT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCT
*
183378 TTGAAAAGAGTGCCACTGACT
65 TTGAAAGGA-TGCCACTGACT
*
183399 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCT
*
183464 TTGAAAGGGTGCCACTGACT
65 TTGAAAGGATGCCACTGACT
*
183484 TGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGC
183549 TTTGAAAGGAGTGCCACTGACT
64 TTTGAAAGGA-TGCCACTGACT
* * * * *
183571 TGTGGGCTTTGAAAGGGTGCCACTAACTTGAGGGCTTTGAAAGGATTGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCT
*
183636 TTGAAAGGGTGCCACTGACT
65 TTGAAAGGATGCCACTGACT
* *
183656 TGTGGGCTTTGAAAAGAGTGCCACCGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCT
183721 TTGAAAGTGATG
65 TTGAAAG-GATG
183733 AACATTCTAG
Statistics
Matches: 908, Mismatches: 82, Indels: 61
0.86 0.08 0.06
Matches are distributed among these distances:
82 34 0.04
83 70 0.08
84 106 0.12
85 144 0.16
86 306 0.34
87 114 0.13
88 27 0.03
89 106 0.12
90 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (84 bp):
TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTT
TGAAAGGATGCCACTGACT
Found at i:183251 original size:29 final size:29
Alignment explanation
Indices: 182579--183726 Score: 1382
Period size: 28 Copynumber: 39.9 Consensus size: 29
182569 AAAGAAAAAT
*
182579 GTGCCACT-AGCTTGTGTAGGCTTTGAAAAAA
1 GTGCCACTGA-CTTGTG--GGCTTTGAAAAGA
*
182610 GTTGCCACTGACACATGTGGGCTTTGAAAAGA
1 G-TGCCACTG--ACTTGTGGGCTTTGAAAAGA
** *
182642 GTGTTACTGACTTGCGTGGGCTTTAAAAAG-
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
* *
182672 GTGCCACTAACTTGCGTGGGCTTTGAAAGGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
*
182703 -TGCCACTGACTCGTGGGCTTTG-AAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
182730 GTGCCACTGACTTGTGGGCTTTG-AAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
182757 GTGCCACTGACTCGTGGGCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
182785 GTACCACTAACTCGTGGGC-TTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
182812 GTGCCACTGACTTGTGGGCTTTG-AAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
182840 GTGCCACTGACTCGTGGGCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
182868 GTGCCACTAACTTGCGTGGGCTTTGAAAGGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
* *
182899 GTGCCATTGACTTGTGTGGGCTTTG-AAAGG
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAAGA
* * *
182929 GTGCCACTAACTCGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
182958 -TGCCACTGACTTGTGGACTTTG-AAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
182985 GTGCCACTGACTCGTGGGCTTTGAAAA-A
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
183013 ATACCACTGACTTGCGTGAGCTTT-AAAAGGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAA-GA
183044 GTGCCACTGACTTGTGTGGGCTTT-AAAATG-
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAA-GA
183074 GTGCCACTGACTTGTGGGCTTTG-AAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
183102 GTGCCACTGAATTGTGGGCTTCGCAATG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
183130 GTGCCACTGACTTGTGGGCTTCG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
183158 GTGCCACTGACTTGTGGGCTCTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
183186 GTGCCACTAACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
183214 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
183243 GTGCCACTGATTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
183272 GTGCCACTAACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
183301 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
183329 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
183358 GTGCCACTAATTTGTAGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
183387 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
183416 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
183444 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
183472 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
183501 GTGCCACTGATTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
183530 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
183559 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
183587 GTGCCACTAACTTGAGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
183616 TTGCCACTAACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
183644 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
183673 GTGCCACCGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
183701 GTGCCACTGACTTGTGGGCTTTGAAA
1 GTGCCACTGACTTGTGGGCTTTGAAA
183727 GTGATGAACA
Statistics
Matches: 984, Mismatches: 97, Indels: 74
0.85 0.08 0.06
Matches are distributed among these distances:
26 4 0.00
27 53 0.05
28 440 0.45
29 314 0.32
30 80 0.08
31 63 0.06
32 22 0.02
33 2 0.00
34 5 0.01
35 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (29 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:183699 original size:229 final size:228
Alignment explanation
Indices: 182579--183726 Score: 1474
Period size: 229 Copynumber: 5.0 Consensus size: 228
182569 AAAGAAAAAT
* * ** *
182579 GTGCCACTAGCTTGTGTAGGCTTTGAAAAAAGTTGCCACTGACACATGTGGGCTTTGAAAAGAGT
1 GTGCCACT-GATT-TGTGGGCTTTGAAAGGAG-TGCCACTG--ACTTGTGGGCTTTGAAAAGAGT
** * *
182644 GTTACTGACTTGCGTGGGCTTTAAAAAGGTGCCACTAACTTGCGTGGGCTTTGAAAGGA-TGCCA
61 GCCACTGACTT--GTGGGCTTTGAAAGGGTGCCACTAACTT--GTGGGCTTTGAAAGGAGTGCCA
* * *
182708 CTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG-GTGCCACTGACTCGT
122 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGT
* * * * *
182772 GGGCTTTGAAAAGGTACCACTAACTCGTGGGC-TTG-AAAGG
187 GGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
182812 GTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTCGTGGGCTTTGAAAAG-GTGCCAC
1 GTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCAC
* * * *
182875 TAACTTGCGTGGGCTTTGAAAGGAGTGCCATTGACTTGTGTGGGCTTTGAAAGG-GTGCCACTAA
66 TGACTT--GTGGGCTTTGAAAGG-GTGCCACTAAC-T-TGTGGGCTTTGAAAGGAGTGCCACTGA
* * * *
182939 CTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAGAGTGCCACTGACTCGTGGGC
126 CTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC
*** * *
183004 TTTGAAAAAATACCACTGACTTGCGTGAGCTTT-AAAAGGA
191 TTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAA-GA
* *
183044 GTGCCACTGACTTGTGTGGGCTTTAAAATG-GTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCC
1 GTGCCACTGA-TT-TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCC
* * * * * *
183107 ACTGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTCGAAAGG-GTGCCACTGACTT
64 ACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTT
* * *
183171 GTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT
129 GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTT
* * *
183236 GAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGA
194 G-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
183272 GTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCAC
1 GTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCAC
* * * *
183336 TGACTTGTGGGCTTTGAAAAGAGTGCCACTAATTTGTAGGCTTTGAAAAGAGTGCCACTGACTTG
66 TGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTG
*
183401 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT
130 TGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTT
183466 GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
194 GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
*
183501 GTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCAC
1 GTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCAC
* * *
183566 TGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGAGGGCTTTGAAAGGATTGCCACTAACTTGT
66 TGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGT
*
183631 GGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACCGACTTGTGGGCTTTG
131 GGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTG
183696 AAAGGGTGCCACTGACTTGTGGGCTTTGAAA
195 AAAGGGTGCCACTGACTTGTGGGCTTTGAAA
183727 GTGATGAACA
Statistics
Matches: 813, Mismatches: 80, Indels: 48
0.86 0.09 0.05
Matches are distributed among these distances:
226 39 0.05
227 140 0.17
228 105 0.13
229 318 0.39
230 98 0.12
231 28 0.03
232 25 0.03
233 13 0.02
234 46 0.06
235 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (228 bp):
GTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCAC
TGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGT
GGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGA
AAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:184995 original size:10 final size:10
Alignment explanation
Indices: 184948--184996 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
184938 GACCCTTCTA
*
184948 TTTTTTGCTAT
1 TTTTTTGGT-T
**
184959 TTTTTTCTTT
1 TTTTTTGGTT
*
184969 TTTTTTTGTT
1 TTTTTTGGTT
184979 TTTTTTGGTT
1 TTTTTTGGTT
184989 TTTTTTGG
1 TTTTTTGG
184997 GTGTAAAGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
10 26 0.79
11 7 0.21
ACGTcount: A:0.02, C:0.04, G:0.12, T:0.82
Consensus pattern (10 bp):
TTTTTTGGTT
Found at i:197800 original size:22 final size:22
Alignment explanation
Indices: 197772--197826 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
197762 TGGACATGTT
197772 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
197794 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
197816 AAAAATGCATG
1 AAAAATGCATG
197827 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:198768 original size:20 final size:19
Alignment explanation
Indices: 198739--198810 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
198729 AAAAGGACAT
198739 AATGTATCGATATATTGTA
1 AATGTATCGATATATTGTA
* * *
198758 GAATATATCGATACATTCATA
1 -AATGTATCGATATATT-GTA
* *
198779 CATGTATCGATATATTGAAA
1 AATGTATCGATATATTG-TA
198799 AATGTATCGATA
1 AATGTATCGATA
198811 CATCAAGGTA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 39 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (19 bp):
AATGTATCGATATATTGTA
Found at i:198795 original size:40 final size:39
Alignment explanation
Indices: 198736--198813 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
198726 GGTAAAAGGA
* *
198736 CATAATGTATCGATATATTGTAGAATATATCGATACATT
1 CATAATGTATCGATATATTGAAAAATATATCGATACATT
*
198775 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATATATTGAAAAATATATCGATACAT
198814 CAAGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATATATTGAAAAATATATCGATACATT
Found at i:201274 original size:18 final size:19
Alignment explanation
Indices: 201239--201274 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
201229 TAATTGAATA
*
201239 ATTTAATCTATTTTGTATT
1 ATTTAATCTATATTGTATT
201258 ATTTAAT-TATATTGTAT
1 ATTTAATCTATATTGTAT
201275 AACTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (19 bp):
ATTTAATCTATATTGTATT
Found at i:206114 original size:11 final size:11
Alignment explanation
Indices: 206098--206133 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
206088 TATTTTCAAA
206098 TTAAATTATAT
1 TTAAATTATAT
206109 TTAAATTATAT
1 TTAAATTATAT
206120 ATTAAATTAT-T
1 -TTAAATTATAT
206131 TTA
1 TTA
206134 TTTTTCTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 3 0.12
11 12 0.50
12 9 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTAAATTATAT
Found at i:206122 original size:13 final size:12
Alignment explanation
Indices: 206097--206129 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
206087 TTATTTTCAA
206097 ATTAAATTATAT
1 ATTAAATTATAT
206109 -TTAAATTATAT
1 ATTAAATTATAT
206120 ATTAAATTAT
1 ATTAAATTAT
206130 TTTATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTAAATTATAT
Found at i:207188 original size:23 final size:23
Alignment explanation
Indices: 207161--207243 Score: 114
Period size: 23 Copynumber: 3.5 Consensus size: 23
207151 TTTGGGGTGG
207161 ATAAATAAATTT-TTAATTTTTTT
1 ATAAATAAATTTATTAA-TTTTTT
207184 ATAAATAAAAGTTTATTAATTTTTT
1 ATAAAT-AAA-TTTATTAATTTTTT
*
207209 ATAAATAATTTTATTAATTTTTT
1 ATAAATAAATTTATTAATTTTTT
*
207232 ATAAATTAATTT
1 ATAAATAAATTT
207244 TTTTATAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
23 30 0.56
24 5 0.09
25 15 0.28
26 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (23 bp):
ATAAATAAATTTATTAATTTTTT
Found at i:207233 original size:11 final size:11
Alignment explanation
Indices: 207195--207238 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
207185 TAAATAAAAG
*
207195 TTTATTAATTT
1 TTTATAAATTT
*
207206 TTTATAAATAAT
1 TTTATAAAT-TT
*
207218 TTTATTAATTT
1 TTTATAAATTT
207229 TTTATAAATT
1 TTTATAAATT
207239 AATTTTTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTATAAATTT
Found at i:207256 original size:15 final size:16
Alignment explanation
Indices: 207221--207253 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
207211 AAATAATTTT
207221 ATTAA-TTTTTTATAA
1 ATTAATTTTTTTATAA
207236 ATTAATTTTTTTATAA
1 ATTAATTTTTTTATAA
207252 AT
1 AT
207254 AATAGTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTAATTTTTTTATAA
Found at i:207394 original size:19 final size:20
Alignment explanation
Indices: 207366--207412 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
207356 AATTAAGATA
*
207366 TATTTAATTATTATAT-ATT
1 TATTTTATTATTATATAATT
*
207385 TATTTTATTATTTTATAATT
1 TATTTTATTATTATATAATT
207405 TATATTTA
1 TAT-TTTA
207413 GATTTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.58
20 6 0.25
21 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTTTATTATTATATAATT
Found at i:207405 original size:20 final size:20
Alignment explanation
Indices: 207366--207465 Score: 68
Period size: 20 Copynumber: 5.1 Consensus size: 20
207356 AATTAAGATA
* *
207366 TATTTAATTATTATAT-ATT
1 TATTTTATTATTTTATAATT
207385 TATTTTATTATTTTATAATT
1 TATTTTATTATTTTATAATT
*
207405 TATATTTA-GATTTTATAA--
1 TAT-TTTATTATTTTATAATT
* * *
207423 TAATTT-TTATTTTGGTATTT
1 TATTTTATTATTTT-ATAATT
207443 GTATATTTATTATTTT-TAATT
1 -TAT-TTTATTATTTTATAATT
207464 TA
1 TA
207466 AATAATTAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
17 8 0.13
18 4 0.06
19 14 0.22
20 17 0.27
21 10 0.16
22 3 0.05
23 7 0.11
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (20 bp):
TATTTTATTATTTTATAATT
Found at i:207969 original size:2 final size:2
Alignment explanation
Indices: 207962--208004 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
207952 AGGCTAATTT
207962 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
208004 T
1 T
208005 TGGATCGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:210643 original size:15 final size:15
Alignment explanation
Indices: 210623--210662 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
210613 ATACAATTCG
*
210623 AATAAACTAAATAAA
1 AATAAAATAAATAAA
210638 AATAAAATAAATAAA
1 AATAAAATAAATAAA
210653 TAA-AAAATAA
1 -AATAAAATAA
210663 TTTTAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 21 0.91
16 2 0.09
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (15 bp):
AATAAAATAAATAAA
Found at i:211184 original size:15 final size:16
Alignment explanation
Indices: 211164--211193 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
211154 TTTATTATTT
211164 ATAAAAAT-AATTTTA
1 ATAAAAATAAATTTTA
211179 ATAAAAATAAATTTT
1 ATAAAAATAAATTTT
211194 TTTATCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAAAAATAAATTTTA
Found at i:211236 original size:16 final size:16
Alignment explanation
Indices: 211215--211245 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
211205 AATTTAATTT
211215 TTATTAATTTATTAAA
1 TTATTAATTTATTAAA
*
211231 TTATTAATTTTTTAA
1 TTATTAATTTATTAA
211246 TAAATATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTAATTTATTAAA
Found at i:217739 original size:14 final size:14
Alignment explanation
Indices: 217722--217770 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
217712 TCCATCATTG
*
217722 ATTTTTTTAATTTT
1 ATTTTATTAATTTT
*
217736 ATTTTATTAAATTT
1 ATTTTATTAATTTT
* *
217750 ATTATATTATTTTT
1 ATTTTATTAATTTT
217764 ATTTTAT
1 ATTTTAT
217771 ATTTAAATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTTATTAATTTT
Found at i:218266 original size:20 final size:20
Alignment explanation
Indices: 218228--218266 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
218218 TTTAGACCAC
* *
218228 AATGTATCAATATATAAGTG
1 AATGTATCAATAAACAAGTG
218248 AATGTATCAATAAACAAGT
1 AATGTATCAATAAACAAGT
218267 AAGTGTGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.31
Consensus pattern (20 bp):
AATGTATCAATAAACAAGTG
Found at i:219506 original size:79 final size:80
Alignment explanation
Indices: 219300--219525 Score: 248
Period size: 79 Copynumber: 2.9 Consensus size: 80
219290 TGGAGATAAC
* * * *
219300 AACGGGGCTAGAGTATCCTCGATTATGAAAAATTGGTATTC--TAGAAATAAAATCGGGGTTGGA
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAA-TCG-ATTCTTTAGAAATAAAATCGGGGTTGGA
*
219363 GTAT-TCCCTCGGAAAT
64 GTATCTCCCTCGAAAAT
* * * * *
219379 AACAGGGTTGGAGTATCCCTGATTAT-AGAAAATCGGTAT-TTTAAAAATAAAATCGGGGTCGGA
1 AACGGGGTTGGAGTATCCCCGATTATGA-AAAATCGAT-TCTTTAGAAATAAAATCGGGGTTGGA
219442 GTATCT-CCTCGAAAAT
64 GTATCTCCCTCGAAAAT
* ***
219458 AACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATTCTTTAGAAATAATGCCGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATTCTTTAGAAATAAAATCGGGGTTGGAGT
219523 ATC
66 ATC
219526 CCCGATTGTG
Statistics
Matches: 121, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
77 1 0.01
78 5 0.04
79 113 0.93
80 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (80 bp):
AACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATTCTTTAGAAATAAAATCGGGGTTGGAGT
ATCTCCCTCGAAAAT
Found at i:219527 original size:51 final size:51
Alignment explanation
Indices: 219460--219630 Score: 256
Period size: 51 Copynumber: 3.4 Consensus size: 51
219450 TCGAAAATAA
*
219460 CGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATTCTTTAGAAATAATGC
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATTCTTTAGAAATAATGT
219511 CGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATTCTTTAGAAATAATGT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATTCTTTAGAAATAATGT
* * * *
219562 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT-TTT-GAAAATAAAGT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATCGAT-TCTTTAG-AAATAATGT
*
219613 CGGGGTTAGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
219631 TCAGAAATAA
Statistics
Matches: 112, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
50 1 0.01
51 110 0.98
52 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATTCTTTAGAAATAATGT
Found at i:219627 original size:181 final size:182
Alignment explanation
Indices: 219383--219710 Score: 475
Period size: 181 Copynumber: 1.8 Consensus size: 182
219373 GGAAATAACA
* ** * *
219383 GGGTTGGAGTATCCCTGATTATAGAAAATCGGTATTTTAAAAATAAAATCGGGGTCGGAGTATCT
1 GGGTTGGAGTATCCCCGATTATAGAAAATCAATATTTTAAAAATAAAATCGGGGTCAGAGTATCC
* * * * *
219448 CCTC-GAAAATAACGGGGTTGGAGTATCCCCGATTGTG-AAAAATCGAT-TCTTTAGAAATAATG
66 CCTCAG-AAATAACGGGGTTGAAATATCCCCGATTGTGAAAAAATCAATAT-TTCAGAAATAAAG
219510 CCGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATTCTTTAGAAATAATGTCG
129 CCGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATTCTTTAGAAATAATGTCG
* * *
219564 GGGTTGGAGTATCCCCGATTAT-GAGAAATCAATATTTTGAAAATAAAGTCGGGGTTAGAGTATC
1 GGGTTGGAGTATCCCCGATTATAGA-AAATCAATATTTTAAAAATAAAATCGGGGTCAGAGTATC
*
219628 CCCTCAGAAATAACGGGGTTGAAATATCCCCGATTGTGAAAAAATCAATATTTCAGATATAAAGC
65 CCCTCAGAAATAACGGGGTTGAAATATCCCCGATTGTGAAAAAATCAATATTTCAGAAATAAAGC
219693 CGGGGTTGGAGTATCCCC
130 CGGGGTTGGAGTATCCCC
219711 TCGAAAATAA
Statistics
Matches: 129, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
180 2 0.02
181 87 0.67
182 39 0.30
183 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28
Consensus pattern (182 bp):
GGGTTGGAGTATCCCCGATTATAGAAAATCAATATTTTAAAAATAAAATCGGGGTCAGAGTATCC
CCTCAGAAATAACGGGGTTGAAATATCCCCGATTGTGAAAAAATCAATATTTCAGAAATAAAGCC
GGGGTTGGAGTATCCCCGATTGTGAAAAATCGATTCTTTAGAAATAATGTCG
Found at i:219697 original size:80 final size:79
Alignment explanation
Indices: 219562--219723 Score: 211
Period size: 80 Copynumber: 2.0 Consensus size: 79
219552 GAAATAATGT
* * * * *
219562 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGAAAATAAAGTCGGGGTTAGAGTAT
1 CGGGGTTGAAATATCCCCGATTATGAAAAATCAATATTTAGAAAATAAAGCCGGGGTTAGAGTAT
219627 CCCCTC-AGAAATAA
66 CCCCTCGA-AAATAA
* * *
219641 CGGGGTTGAAATATCCCCGATTGTGAAAAAATCAATATTTCAG-ATATAAAGCCGGGGTTGGAGT
1 CGGGGTTGAAATATCCCCGATTATG-AAAAATCAATATTT-AGAAAATAAAGCCGGGGTTAGAGT
219705 ATCCCCTCGAAAATAA
64 ATCCCCTCGAAAATAA
219721 CGG
1 CGG
219724 AGTTAGAGTA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
79 22 0.31
80 48 0.67
81 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (79 bp):
CGGGGTTGAAATATCCCCGATTATGAAAAATCAATATTTAGAAAATAAAGCCGGGGTTAGAGTAT
CCCCTCGAAAATAA
Found at i:219795 original size:105 final size:108
Alignment explanation
Indices: 219617--219814 Score: 244
Period size: 105 Copynumber: 1.9 Consensus size: 108
219607 TAAAGTCGGG
* * *
219617 GTTAGAGTATCCCCTCAGAAATAACGGGGTTGAAATATCCCCGATTGTGAAAAAATCAATATTTC
1 GTTAGAGTATCCCATCAGAAATAACGGGGTTGAAATATCCCCAATTATGAAAAAATCAATATTTC
* * *
219682 AGATATAAAGCCGGGGTTGGAGTATCCCCTCGAAAATAACGGA
66 AGAAATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGA
* ***
219725 GTTAGAGTATCCCGAT-A-AAATAACGGGGTTG-AGTATCCCCAATTATG-AAAAATTGGTATTT
1 GTTAGAGTATCCC-ATCAGAAATAACGGGGTTGAAATATCCCCAATTATGAAAAAATCAATA-TT
*
219786 TC-GAAATAAAATCGGAGTTGGAGTATCCC
64 TCAGAAATAAAACCGGAGTTGGAGTATCCC
219815 TAATTGCGAA
Statistics
Matches: 77, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
105 31 0.40
106 17 0.22
107 14 0.18
108 14 0.18
109 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (108 bp):
GTTAGAGTATCCCATCAGAAATAACGGGGTTGAAATATCCCCAATTATGAAAAAATCAATATTTC
AGAAATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGA
Found at i:219826 original size:51 final size:51
Alignment explanation
Indices: 219755--219918 Score: 150
Period size: 51 Copynumber: 3.2 Consensus size: 51
219745 TAACGGGGTT
* * * * *
219755 GAGTATCCCCAATTATGAAAAATTGGTATTTTCGAAATAAAATCGGAGTTG
1 GAGTATCCCCAATTACGAAAAATCGATACTTTAGAAATAAAATCGGAGTTG
* * * *
219806 GAGTATCCCTAATTGCGAAAAATCGATGCTTTAGAAATAAAATTGGAGTTG
1 GAGTATCCCCAATTACGAAAAATCGATACTTTAGAAATAAAATCGGAGTTG
** * * ** * *
219857 GAGTATCCCCGTTTAAGAAAAATTGATGTTTTGGAAATAATAATCGG-GATTA
1 GAGTATCCCCAATTACGAAAAATCGATACTTTAGAAATAA-AATCGGAG-TTG
219909 GAGTATCCCC
1 GAGTATCCCC
219919 GAGATGAAAA
Statistics
Matches: 92, Mismatches: 19, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
51 75 0.82
52 17 0.18
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCAATTACGAAAAATCGATACTTTAGAAATAAAATCGGAGTTG
Found at i:222292 original size:13 final size:13
Alignment explanation
Indices: 222274--222303 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
222264 GTAAATCCAG
*
222274 AATGTATCGATAT
1 AATGTATCGATAC
222287 AATGTATCGATAC
1 AATGTATCGATAC
222300 AATG
1 AATG
222304 AACAATGTAC
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:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:228469 original size:30 final size:29
Alignment explanation
Indices: 228413--228469 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
228403 ATTTATATTA
* * *
228413 TATAAAAATAAATATATATTATATTATAG
1 TATAAAAATAAAAATATATAAAATTATAG
*
228442 TATAAATATTAAAAATATATAAAATTAT
1 TATAAA-AATAAAAATATATAAAATTAT
228470 TTATATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 6 0.26
30 17 0.74
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
TATAAAAATAAAAATATATAAAATTATAG
Found at i:229766 original size:17 final size:17
Alignment explanation
Indices: 229744--229782 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
229734 CAATAATACG
*
229744 TAATTATTTTAAAATAA
1 TAATTAATTTAAAATAA
**
229761 TAATTAATTTAATTTAA
1 TAATTAATTTAAAATAA
229778 TAATT
1 TAATT
229783 TTAAAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATTAATTTAAAATAA
Found at i:230615 original size:2 final size:2
Alignment explanation
Indices: 230608--230652 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
230598 CTTCGATGGC
230608 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
230650 TA T
1 TA T
230653 TAATTTTAAA
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:231613 original size:11 final size:11
Alignment explanation
Indices: 231565--231623 Score: 57
Period size: 11 Copynumber: 5.1 Consensus size: 11
231555 TGATACGAGT
*
231565 AAATATTATAA
1 AAATAATATAA
231576 AAATAAT-TAAA
1 AAATAATAT-AA
*
231587 ATAAGTCATGATAA
1 A-AA-TAAT-ATAA
231601 AAATAATATAA
1 AAATAATATAA
231612 AAATAATATAA
1 AAATAATATAA
231623 A
1 A
231624 TAAACGAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
10 1 0.03
11 25 0.62
12 5 0.12
13 5 0.12
14 3 0.08
15 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (11 bp):
AAATAATATAA
Found at i:231658 original size:16 final size:16
Alignment explanation
Indices: 231637--231692 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 16
231627 ACGAATATAT
231637 TAAATTTTATATAAAA
1 TAAATTTTATATAAAA
231653 TAAATTATTAATGTATAAAA
1 TAAATT-TT-A--TATAAAA
231673 T-AA-TTTATATAAAA
1 TAAATTTTATATAAAA
231687 TAAATT
1 TAAATT
231693 ATACAAGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
14 8 0.24
15 2 0.06
16 8 0.24
17 4 0.12
18 2 0.06
19 2 0.06
20 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
TAAATTTTATATAAAA
Found at i:232269 original size:19 final size:20
Alignment explanation
Indices: 232245--232283 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
232235 TGAAAGGAAT
232245 ATTAAA-ATAATAAAAATTA
1 ATTAAATATAATAAAAATTA
*
232264 ATTAAATATATTAAAAATTA
1 ATTAAATATAATAAAAATTA
232284 TGATATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTAAATATAATAAAAATTA
Found at i:232723 original size:5 final size:5
Alignment explanation
Indices: 232699--232757 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
232689 ATAATTAAAA
* * * *
232699 AATAA AATAA AATAT AATAT AATAT -ATA- AAAAT AATAT ATACAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT A-ATAT AATAT
232748 AAATAT AATA
1 -AATAT AATA
232758 ATATTTTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
4 5 0.11
5 31 0.69
6 9 0.20
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (5 bp):
AATAT
Found at i:232730 original size:20 final size:20
Alignment explanation
Indices: 232707--232757 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
232697 AAAATAAAAT
232707 AAAATATAATATA-ATATATA
1 AAAATATAATATACATA-ATA
232727 AAAATA-ATATATACATAATA
1 AAAATATA-ATATACATAATA
*
232747 TAAATATAATA
1 AAAATATAATA
232758 ATATTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 1 0.04
20 22 0.81
21 4 0.15
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATATAATATACATAATA
Found at i:232750 original size:41 final size:40
Alignment explanation
Indices: 232680--232757 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
232670 TCATTCACAT
232680 TATATAAAAATAATTAAAAAATAAAATAAAATATAATATAA
1 TATATAAAAATAATTAAAAAATAAAAT-AAATATAATATAA
* * *
232721 TATATAAAAATAA-TATATACATAATATAAATATAATA
1 TATATAAAAATAATTA-AAAAATAAAATAAATATAATA
232758 ATATTTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 12 0.36
41 21 0.64
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (40 bp):
TATATAAAAATAATTAAAAAATAAAATAAATATAATATAA
Found at i:232757 original size:25 final size:23
Alignment explanation
Indices: 232700--232761 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
232690 TAATTAAAAA
*
232700 ATAAAATAA-AATATAATATAAT
1 ATAAAATAATAATATAACATAAT
232722 ATATAAA-AATAATATATACATAAT
1 ATA-AAATAATAATATA-ACATAAT
232746 ATAAATATAATAATAT
1 ATAAA-ATAATAATAT
232762 TTTAAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
22 5 0.15
23 11 0.32
24 10 0.29
25 8 0.24
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
ATAAAATAATAATATAACATAAT
Found at i:232782 original size:24 final size:25
Alignment explanation
Indices: 232743--232799 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
232733 ATATATACAT
232743 AATA-TAAATATAATAATATT-TTAA
1 AATATTAAATATAATAA-ATTATTAA
232767 AAT-TTAAATA-ATATAAATTATTAA
1 AATATTAAATATA-ATAAATTATTAA
*
232791 TATATTAAA
1 AATATTAAA
232800 ATTTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 19 0.68
25 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AATATTAAATATAATAAATTATTAA
Found at i:232799 original size:32 final size:33
Alignment explanation
Indices: 232741--232803 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
232731 TAATATATAC
*
232741 ATAATATAAATATAATAATATTTTAAAATTTAA
1 ATAATATAAATATAATAATATATTAAAATTTAA
*
232774 ATAATATAAAT-TATTAATATATTAAAATTT
1 ATAATATAAATATAATAATATATTAAAATTT
232804 TTAAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
ATAATATAAATATAATAATATATTAAAATTTAA
Found at i:232847 original size:20 final size:21
Alignment explanation
Indices: 232807--232848 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
232797 AAAATTTTTA
* *
232807 AAAATTTATAATATTTTAAAT
1 AAAATTTATAATATATAAAAT
232828 AAAA-TTATAATATATAAAAT
1 AAAATTTATAATATATAAAAT
232848 A
1 A
232849 TTTAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATTTATAATATATAAAAT
Found at i:232855 original size:28 final size:29
Alignment explanation
Indices: 232816--232873 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
232806 AAAAATTTAT
232816 AATATTTTAAATAAAAT-TATAATATATAA
1 AATATTTTAAATAAAATATA-AATATATAA
*
232845 AATA-TTTAAATATAATATAAATATATAA
1 AATATTTTAAATAAAATATAAATATATAA
232873 A
1 A
232874 TTTAGACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
AATATTTTAAATAAAATATAAATATATAA
Found at i:232858 original size:17 final size:17
Alignment explanation
Indices: 232768--232874 Score: 57
Period size: 17 Copynumber: 6.5 Consensus size: 17
232758 ATATTTTAAA
*
232768 ATTTAAATAATATAAATT
1 ATTTAAAT-ATATAAAAT
232786 A-TT-AATATATTAAAAT
1 ATTTAAATATA-TAAAAT
* * * *
232802 TTTTAAAAATTTATAAT
1 ATTTAAATATATAAAAT
*
232819 ATTT---TAAATAAAAT
1 ATTTAAATATATAAAAT
*
232833 -TAT-AATATATAAAAT
1 ATTTAAATATATAAAAT
232848 ATTTAAATATAATATAAAT
1 ATTTAAATAT-ATA-AAAT
*
232867 ATATAAAT
1 ATTTAAAT
232875 TTAGACTTAT
Statistics
Matches: 66, Mismatches: 14, Indels: 17
0.68 0.14 0.18
Matches are distributed among these distances:
13 2 0.03
14 6 0.09
15 12 0.18
16 10 0.15
17 17 0.26
18 8 0.12
19 11 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAAATATATAAAAT
Found at i:232868 original size:19 final size:17
Alignment explanation
Indices: 232826--232874 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 17
232816 AATATTTTAA
232826 ATAAAAT-TAT-AATAT
1 ATAAAATATATAAATAT
*
232841 ATAAAATATTTAAATAT
1 ATAAAATATATAAATAT
232858 AATATAAATATATAAAT
1 -ATA-AAATATATAAAT
232875 TTAGACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 7 0.25
16 2 0.07
17 5 0.18
18 3 0.11
19 11 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAAATATATAAATAT
Found at i:232976 original size:7 final size:7
Alignment explanation
Indices: 232958--232988 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
232948 AATATATATT
232958 ATTTATAA
1 ATTTA-AA
232966 ATTTAAA
1 ATTTAAA
232973 ATTTAAA
1 ATTTAAA
232980 ATTTAAA
1 ATTTAAA
232987 AT
1 AT
232989 ATATAATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.78
8 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
ATTTAAA
Found at i:232983 original size:14 final size:15
Alignment explanation
Indices: 232958--232994 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
232948 AATATATATT
232958 ATTTATAAATTTAAA
1 ATTTATAAATTTAAA
232973 ATTTA-AAATTTAAA
1 ATTTATAAATTTAAA
*
232987 ATATATAA
1 ATTTATAA
232995 TCATACTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTTATAAATTTAAA
Found at i:233412 original size:22 final size:22
Alignment explanation
Indices: 233391--233458 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 22
233381 ACGTTTAATA
*
233391 ATTA-ATAATTATATTTAAAAT
1 ATTATATAATTATATATAAAAT
*
233412 ATTATATATTTATATAT-AAAT
1 ATTATATAATTATATATAAAAT
*
233433 -TT-TATTA-TAT-TATAAAAAT
1 ATTATATAATTATATAT-AAAAT
233452 ATTATAT
1 ATTATAT
233459 TTTAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
17 3 0.08
18 3 0.08
19 7 0.18
20 4 0.11
21 11 0.29
22 10 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTATATAATTATATATAAAAT
Found at i:233432 original size:21 final size:20
Alignment explanation
Indices: 233408--233493 Score: 78
Period size: 19 Copynumber: 4.5 Consensus size: 20
233398 ATTATATTTA
233408 AAATATTATATATTTATATAT
1 AAATATTATATATTTATA-AT
*
233429 AAATTTTAT-TATATTATAA-
1 AAATATTATATAT-TTATAAT
233448 AAATATTATAT-TTTA-AAT
1 AAATATTATATATTTATAAT
233466 AAAT-TT-TATATTATATAAT
1 AAATATTATATATT-TATAAT
*
233485 -TATATTATA
1 AAATATTATA
233494 CGGTACGCTA
Statistics
Matches: 54, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
16 3 0.06
17 6 0.11
18 11 0.20
19 14 0.26
20 7 0.13
21 13 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAATATTATATATTTATAAT
Found at i:233440 original size:16 final size:16
Alignment explanation
Indices: 233421--233493 Score: 51
Period size: 16 Copynumber: 4.3 Consensus size: 16
233411 TATTATATAT
233421 TTATATATAAATTTTA
1 TTATATATAAATTTTA
233437 TTATATTATAAAAATATTATA
1 TTATA-TAT--AAAT-TT-TA
* *
233458 TTTTAAATAAATTTTA
1 TTATATATAAATTTTA
*
233474 -TAT-TATATAATTATA
1 TTATATATA-AATTTTA
233489 TTATA
1 TTATA
233494 CGGTACGCTA
Statistics
Matches: 44, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
14 3 0.07
15 8 0.18
16 10 0.23
17 5 0.11
18 4 0.09
19 4 0.09
20 4 0.09
21 6 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATATATAAATTTTA
Found at i:233440 original size:38 final size:37
Alignment explanation
Indices: 233398--233474 Score: 113
Period size: 40 Copynumber: 2.1 Consensus size: 37
233388 ATAATTAATA
233398 ATTATATT-T-AAAATATTATATATTTATATATAAATTTT
1 ATTATATTATAAAAATATTATAT-TTTA-A-ATAAATTTT
233436 ATTATATTATAAAAATATTATATTTTAAATAAATTTT
1 ATTATATTATAAAAATATTATATTTTAAATAAATTTT
233473 AT
1 AT
233475 ATTATATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
37 11 0.30
38 9 0.24
39 5 0.14
40 12 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (37 bp):
ATTATATTATAAAAATATTATATTTTAAATAAATTTT
Found at i:234622 original size:19 final size:19
Alignment explanation
Indices: 234576--234612 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
234566 TAATTGAAGG
*
234576 TAATAAATTTTAATTAAAA
1 TAATATATTTTAATTAAAA
*
234595 TAATATATTTTATTTAAA
1 TAATATATTTTAATTAAA
234613 TTTAATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATATATTTTAATTAAAA
Found at i:234645 original size:27 final size:28
Alignment explanation
Indices: 234609--234669 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
234599 ATATTTTATT
*
234609 TAAATTTAATTATTAA-ATATATAAATA
1 TAAATATAATTATTAATATATATAAATA
* * *
234636 TAAATATAATTTTTAATATTTTTAAATA
1 TAAATATAATTATTAATATATATAAATA
*
234664 AAAATA
1 TAAATA
234670 AATAATAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TAAATATAATTATTAATATATATAAATA
Found at i:234862 original size:10 final size:10
Alignment explanation
Indices: 234832--234886 Score: 67
Period size: 10 Copynumber: 5.6 Consensus size: 10
234822 TATTTACATA
*
234832 TTATTTTAAT
1 TTATATTAAT
* *
234842 TTGTATAAAT
1 TTATATTAAT
234852 TTATATTAA-
1 TTATATTAAT
234861 TTATATTAAT
1 TTATATTAAT
234871 TTATATTAAT
1 TTATATTAAT
*
234881 CTATAT
1 TTATAT
234887 CGATTAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
9 9 0.24
10 29 0.76
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (10 bp):
TTATATTAAT
Found at i:234864 original size:29 final size:29
Alignment explanation
Indices: 234831--234886 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
234821 TTATTTACAT
* * *
234831 ATTATTTTAATTTGTATAAATTTATATTA
1 ATTATATTAATTTATATAAATCTATATTA
*
234860 ATTATATTAATTTATATTAATCTATAT
1 ATTATATTAATTTATATAAATCTATAT
234887 CGATTAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (29 bp):
ATTATATTAATTTATATAAATCTATATTA
Found at i:234873 original size:19 final size:20
Alignment explanation
Indices: 234849--234886 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
234839 AATTTGTATA
234849 AATTTATATTAAT-TATATT
1 AATTTATATTAATCTATATT
234868 AATTTATATTAATCTATAT
1 AATTTATATTAATCTATAT
234887 CGATTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTTATATTAATCTATATT
Found at i:234896 original size:20 final size:19
Alignment explanation
Indices: 234849--234897 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
234839 AATTTGTATA
* *
234849 AATTTATATTAATTATATT
1 AATTAATATTAATTATATC
*
234868 AATTTATATTAATCTATATC
1 AATTAATATTAAT-TATATC
*
234888 GATTAATATT
1 AATTAATATT
234898 TATTGTTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (19 bp):
AATTAATATTAATTATATC
Found at i:234958 original size:20 final size:20
Alignment explanation
Indices: 234913--234959 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
234903 TTACAAAATT
234913 TTAATT-TTTATATTTTTTC
1 TTAATTATTTATATTTTTTC
* * *
234932 TTGATTATTTTTATTTTTTG
1 TTAATTATTTATATTTTTTC
234952 TTAATTAT
1 TTAATTAT
234960 ATTTCTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72
Consensus pattern (20 bp):
TTAATTATTTATATTTTTTC
Found at i:235074 original size:15 final size:15
Alignment explanation
Indices: 235036--235075 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
235026 TTAATATTAA
235036 AAAATTTA-AATATT
1 AAAATTTATAATATT
*
235050 AAATATTTATAATTTT
1 AAA-ATTTATAATATT
235066 AAAATTTATA
1 AAAATTTATA
235076 TTTATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 3 0.13
15 12 0.52
16 8 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATTTATAATATT
Found at i:237086 original size:146 final size:142
Alignment explanation
Indices: 236825--237110 Score: 421
Period size: 146 Copynumber: 2.0 Consensus size: 142
236815 GAAAAGTATA
* * *
236825 TGAAGGCTAGCAGTAGAAGTAGAAAAGAGGGTTGTTTAGGTAAATTGAGTTACGAATTCTGTAAA
1 TGAAGGCTAGCAATAAAAGTAGAAAAGAGGGTTGTTGAGGTAAATTGAGTTACGAATTCTGTAAA
* * * *
236890 GTGAAAAGCGTGCTGCCTCTGGGCGCTGGCTGCCACGGGGAGTAGTTGAGGACAGCTAGTCTTTT
66 GTAAAAAACGTGCTGCCGCTGGGCGCCGGCTGCCACGGGGAGTAGTTGAGGACAGCTA-T-TTTT
236955 TTTTTTT-TTTGGG
129 TTTTTTTATTTGGG
*
236968 TGAAGGCTAGCAATAAAAGTAGAAAAGAGGTTTGTTGAGGTAAATTCGAGTTTCACGAATTCTGT
1 TGAAGGCTAGCAATAAAAGTAGAAAAGAGGGTTGTTGAGGTAAATT-GAG-TT-ACGAATTCTGT
* * *
237033 GAAGTAAAAAACGTGCTGCCGCTGGGCGCCGGCTGCCATGGGGGGTAGTTGAGGACAGCTATTTT
63 AAAGTAAAAAACGTGCTGCCGCTGGGCGCCGGCTGCCACGGGGAGTAGTTGAGGACAGCTATTTT
237098 TTTTTTTTATTTG
128 TTTTTTTTATTTG
237111 TGTTCTTTGC
Statistics
Matches: 128, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
143 42 0.33
144 14 0.11
145 7 0.05
146 65 0.51
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.31
Consensus pattern (142 bp):
TGAAGGCTAGCAATAAAAGTAGAAAAGAGGGTTGTTGAGGTAAATTGAGTTACGAATTCTGTAAA
GTAAAAAACGTGCTGCCGCTGGGCGCCGGCTGCCACGGGGAGTAGTTGAGGACAGCTATTTTTTT
TTTTTATTTGGG
Found at i:237649 original size:71 final size:71
Alignment explanation
Indices: 237528--237674 Score: 240
Period size: 71 Copynumber: 2.1 Consensus size: 71
237518 CTCCACAAAA
* * *
237528 ACAAAAAGCAAATAGTTTTCCTTGAACAAAAGAAAAAATATATATTTTGAAGATTAATCTTTATA
1 ACAAAAAGCAAATAGTTTTCCTTGAACAAAAGAAAAAAAAAATATATTGAAGATTAATCTTTATA
237593 CATTCT
66 CATTCT
* *
237599 ACAAAAAGCAAATAGTTTTTCTTGAACCAAAGAAAAAAAAAATATATTGAAGATTAATCTTTATA
1 ACAAAAAGCAAATAGTTTTCCTTGAACAAAAGAAAAAAAAAATATATTGAAGATTAATCTTTATA
*
237664 CGTTCT
66 CATTCT
237670 ACAAA
1 ACAAA
237675 GATTTAGGTT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (71 bp):
ACAAAAAGCAAATAGTTTTCCTTGAACAAAAGAAAAAAAAAATATATTGAAGATTAATCTTTATA
CATTCT
Found at i:238548 original size:20 final size:20
Alignment explanation
Indices: 238511--238549 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
238501 CAAAAAATGG
*
238511 GATTTGAATGTCTGTTTTAA
1 GATTTGAATGTCTCTTTTAA
238531 GATTTCGAATGTC-CTTTTA
1 GATTT-GAATGTCTCTTTTA
238550 GGCAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.49
Consensus pattern (20 bp):
GATTTGAATGTCTCTTTTAA
Found at i:242474 original size:20 final size:20
Alignment explanation
Indices: 242449--242505 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
242439 TTTACCTAGA
*
242449 TGTATCAATACATTTTGCAT
1 TGTATCGATACATTTTGCAT
*
242469 TGTATCGATACATTGCT-CAT
1 TGTATCGATACATT-TTGCAT
242489 TGTATCGATACATTTTG
1 TGTATCGATACATTTTG
242506 GATTTACCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATTTTGCAT
Found at i:244886 original size:51 final size:51
Alignment explanation
Indices: 244803--244929 Score: 141
Period size: 51 Copynumber: 2.5 Consensus size: 51
244793 AAATTTCTAG
* * * *
244803 ATTTTTCAT-CTCGAGGATACTCCAATCTCGATTCCATTTCTAAAACATCA
1 ATTTTTCATAATCGGGGATACTCCAATCTCGATTCCATTTCCAAAACACCA
* * ** *
244853 ATTTTTCTTAATCGGGGATACTCTAA-CTCCGATTTTATTTCCAAAATACCA
1 ATTTTTCATAATCGGGGATACTCCAATCT-CGATTCCATTTCCAAAACACCA
*
244904 ATTTTTCATAATTGGGGATACTCCAA
1 ATTTTTCATAATCGGGGATACTCCAA
244930 CCCCGTTATT
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
50 10 0.16
51 53 0.84
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (51 bp):
ATTTTTCATAATCGGGGATACTCCAATCTCGATTCCATTTCCAAAACACCA
Found at i:244984 original size:28 final size:29
Alignment explanation
Indices: 244917--244990 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 29
244907 TTTCATAATT
244917 GGGGATACTCCAACCCCGTTATTTCATCGA
1 GGGGATACTCCAACCCCGTTATTTCA-CGA
* *
244947 --GGATATTCCAACCTCGTTATTTC-CGA
1 GGGGATACTCCAACCCCGTTATTTCACGA
*
244973 GGGGACACTCCAACCCCG
1 GGGGATACTCCAACCCCG
244991 GCTTTATAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
26 3 0.08
28 34 0.92
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.24
Consensus pattern (29 bp):
GGGGATACTCCAACCCCGTTATTTCACGA
Found at i:245020 original size:107 final size:107
Alignment explanation
Indices: 244895--245144 Score: 311
Period size: 107 Copynumber: 2.3 Consensus size: 107
244885 TTTTATTTCC
* * *
244895 AAAATACCAATTTTTCATAATTGGGGATACTCCAACCCCGTTATTTCATCGAGGATATTCCAACC
1 AAAATACCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATGTCATCGAGAATATTCCAACC
* *
244960 TCGTTATTTCCGAGGGGACACTCCAACCCCGGCTTTATAACT
66 TCGTTATTTCCGAAGGGACACTCCAACCCCGACTTTATAACT
*** * * * **
245002 AAAATATTGATTTTTCATAATCGGGGGTACTCGAACCCCGTTATGTCATCGAGAATATTCTAATT
1 AAAATACCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATGTCATCGAGAATATTCCAACC
** * * **
245067 TCGTTATTTTTGAAGGGATACTCCAACCCCGATTTTATTTCT
66 TCGTTATTTCCGAAGGGACACTCCAACCCCGACTTTATAACT
* *
245109 AAAATACCAATTTTTCACAATCGGCGATACTCCAAC
1 AAAATACCAATTTTTCATAATCGGGGATACTCCAAC
245145 TCCGATTTTA
Statistics
Matches: 117, Mismatches: 26, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
107 117 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (107 bp):
AAAATACCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATGTCATCGAGAATATTCCAACC
TCGTTATTTCCGAAGGGACACTCCAACCCCGACTTTATAACT
Found at i:245150 original size:51 final size:51
Alignment explanation
Indices: 245083--245199 Score: 164
Period size: 51 Copynumber: 2.3 Consensus size: 51
245073 TTTTTGAAGG
* *
245083 GATACTCCAACCCCGATTTTA-TTTCTAAAATACCAATTTTTCACAATCGGC
1 GATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTCTCACAATCGGC
* * *
245134 GATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTCACAATTGGG
1 GATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCTCACAATCGGC
*
245185 GATACTCTAACCCCG
1 GATACTCCAACCCCG
245200 TTATTTTCAC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 54 0.93
52 4 0.07
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.32
Consensus pattern (51 bp):
GATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCTCACAATCGGC
Found at i:245316 original size:130 final size:130
Alignment explanation
Indices: 245082--245329 Score: 318
Period size: 130 Copynumber: 1.9 Consensus size: 130
245072 ATTTTTGAAG
** * *
245082 GGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATCGGCGATACTCCAACTC
1 GGATACTCCAACCCCGACCTTATTTCTAAAATACCAATTTTTCACAATCGGAGATACTCCAACCC
** *
245147 CGATTTTATTTTCAAAACACCAATTTCTCACAATTGGGGATACTCTAACCCCGTTATTTTCACGA
66 CGACCTTATTTTCAAAACACCAATTTCTCACAATCGGGGATACTCTAACCCCGTTATTTTCACGA
* * *
245212 GGATACTTCAACCCCGACCTTATTTCT-AAATCATCGATTTTTCACAATCGGAGATACTCCAACC
1 GGATACTCCAACCCCGACCTTATTTCTAAAAT-ACCAATTTTTCACAATCGGAGATACTCCAACC
* * * * * * * *
245276 CCGGCCTTATTTTTAAAGCATCGATTTTTCATAATCGGGGATACTCTAGCCCCG
65 CCGACCTTATTTTCAAAACACCAATTTCTCACAATCGGGGATACTCTAACCCCG
245330 CGGTTATCTC
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
129 4 0.04
130 95 0.96
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.32
Consensus pattern (130 bp):
GGATACTCCAACCCCGACCTTATTTCTAAAATACCAATTTTTCACAATCGGAGATACTCCAACCC
CGACCTTATTTTCAAAACACCAATTTCTCACAATCGGGGATACTCTAACCCCGTTATTTTCACGA
Found at i:245329 original size:51 final size:51
Alignment explanation
Indices: 245213--245321 Score: 164
Period size: 51 Copynumber: 2.1 Consensus size: 51
245203 TTTTCACGAG
* *
245213 GATACTTCAACCCCGACCTTATTTCTAAATCATCGATTTTTCACAATCGGA
1 GATACTCCAACCCCGACCTTATTTCTAAAGCATCGATTTTTCACAATCGGA
* * * *
245264 GATACTCCAACCCCGGCCTTATTTTTAAAGCATCGATTTTTCATAATCGGG
1 GATACTCCAACCCCGACCTTATTTCTAAAGCATCGATTTTTCACAATCGGA
245315 GATACTC
1 GATACTC
245322 TAGCCCCGCG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.33
Consensus pattern (51 bp):
GATACTCCAACCCCGACCTTATTTCTAAAGCATCGATTTTTCACAATCGGA
Found at i:250042 original size:2 final size:2
Alignment explanation
Indices: 250029--250071 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
250019 TTCAAAAACA
*
250029 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
250071 A
1 A
250072 AAACAATTTT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:251472 original size:27 final size:26
Alignment explanation
Indices: 251440--251530 Score: 105
Period size: 27 Copynumber: 3.5 Consensus size: 26
251430 AAACTACCCA
*
251440 TTGTTTGTCAAAAATTGTGGTTACTT
1 TTGTTTGTCAAAAATGGTGGTTACTT
*
251466 TGTGTTTGTCAAAAATGGTGGTTTCTTT
1 T-TGTTTGTCAAAAATGGTGGTTAC-TT
* * *
251494 TTATTTGTCAAAAATGGTGG-CA-TG
1 TTGTTTGTCAAAAATGGTGGTTACTT
251518 TTGTTTGTCAAAA
1 TTGTTTGTCAAAA
251531 TTTGTGGCTA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
24 13 0.23
26 1 0.02
27 39 0.70
28 3 0.05
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (26 bp):
TTGTTTGTCAAAAATGGTGGTTACTT
Found at i:251610 original size:13 final size:13
Alignment explanation
Indices: 251592--251636 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
251582 AGCTCCCTCC
251592 TCCCTCTCAAGTA
1 TCCCTCTCAAGTA
*
251605 TCCCTCTCAAGCA
1 TCCCTCTCAAGTA
**
251618 T-CCTCTCTTGTA
1 TCCCTCTCAAGTA
251630 TCCCTCT
1 TCCCTCT
251637 TCAATTCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.16, C:0.42, G:0.07, T:0.36
Consensus pattern (13 bp):
TCCCTCTCAAGTA
Done.