Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008920.1 Hibiscus syriacus cultivar Beakdansim tig00112224_pilon, 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: 1287743
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:981407 original size:2 final size:2
Alignment explanation
Indices: 981400--981426 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
981390 GTAGCTTAAG
981400 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
981427 ATCAATTGGC
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:983755 original size:2 final size:2
Alignment explanation
Indices: 983748--983815 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
983738 AGTCACCTTA
983748 AT AT AT 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
983790 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
983816 GAATGATTTG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:983968 original size:2 final size:2
Alignment explanation
Indices: 983957--983993 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
983947 AATATTATCT
983957 TA TA -A 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
983994 CTTCATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:984155 original size:2 final size:2
Alignment explanation
Indices: 984148--984180 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
984138 AAAACTTAAG
984148 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
984181 TTATTTATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:985396 original size:21 final size:21
Alignment explanation
Indices: 985371--985412 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
985361 CTTCCTTGTG
985371 GAAAAAGCTTGGATTCGTGGA
1 GAAAAAGCTTGGATTCGTGGA
985392 GAAAAAGCTTGGATTCGTGGA
1 GAAAAAGCTTGGATTCGTGGA
985413 ATATCAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.33, T:0.24
Consensus pattern (21 bp):
GAAAAAGCTTGGATTCGTGGA
Found at i:987072 original size:43 final size:43
Alignment explanation
Indices: 986790--987063 Score: 245
Period size: 43 Copynumber: 6.4 Consensus size: 43
986780 AATTGATAAT
* * * * * *
986790 CCTAAGTTTTTCAATCCCACTTTGTACCTTTATAATTAAGCT-
1 CCTAATTTTTTCAATCTCACTTTTTACCTATATAATTGAGGTC
* * * *
986832 CTTGATTTTTTCAATCTCACTTTTCACCTTTATAATTGAGG-C
1 CCTAATTTTTTCAATCTCACTTTTTACCTATATAATTGAGGTC
* * * * **
986874 CCTAATTTTTTTCGATCTCATTTTTTACTTATATAATTTAGACC
1 CCTAA-TTTTTTCAATCTCACTTTTTACCTATATAATTGAGGTC
* *
986918 CCTAATTTTTTTCAATAC-CATTTTTTA-CTCATATAATTTA-GTCC
1 CCTAA-TTTTTTCAAT-CTCACTTTTTACCT-ATATAATTGAGGT-C
* * *
986962 CCTAATTTTTTAAATCTCACTTTTTACCTTTAAAATTGAGGTC
1 CCTAATTTTTTCAATCTCACTTTTTACCTATATAATTGAGGTC
*
987005 CC-ATATTTTTTTAATCTCACTTTTTACCTATATAATTGAGGTC
1 CCTA-ATTTTTTCAATCTCACTTTTTACCTATATAATTGAGGTC
*
987048 CCTAATCTTTTCAATC
1 CCTAATTTTTTCAATC
987064 ATATTTTTTT
Statistics
Matches: 190, Mismatches: 31, Indels: 21
0.79 0.13 0.09
Matches are distributed among these distances:
42 38 0.20
43 105 0.55
44 46 0.24
45 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.48
Consensus pattern (43 bp):
CCTAATTTTTTCAATCTCACTTTTTACCTATATAATTGAGGTC
Found at i:987072 original size:130 final size:130
Alignment explanation
Indices: 986836--987099 Score: 313
Period size: 130 Copynumber: 2.0 Consensus size: 130
986826 TAAGCTCTTG
* * * *
986836 ATTTTTTCAATCTCACTTTTCACCTTTATAATTGAGGCCCTAATTTTTTTCGATCTCATTTTTTA
1 ATTTTTTAAATCTCACTTTTCACCTTTAAAATTGAGGCCCTAATTTTTTTCAATCTCACTTTTTA
* * *
986901 CTTATATAATTTAGACCCCTAATTTTTTTCAATACCATTTTTTACTCATATAATTT-AGTCCCCT
66 CCTATATAATTGAGACCCCTAATTCTTTTCAATACCATTTTTTACTCATATAATTTAAG-CCCCT
986965 A
130 A
*
986966 ATTTTTTAAATCTCACTTTTTACCTTTAAAATTGAGGTCCC-ATATTTTTTT-AATCTCACTTTT
1 ATTTTTTAAATCTCACTTTTCACCTTTAAAATTGAGG-CCCTA-ATTTTTTTCAATCTCACTTTT
** * * ** *
987029 TACCTATATAATTGAGGTCCCTAA-TCTTTTCAAT-CATATTTTTTTTCTTTTATAGTTTAAGCC
64 TACCTATATAATTGAGACCCCTAATTCTTTTCAATAC-CA-TTTTTTACTCATATAATTTAAGCC
987092 CCTA
127 CCTA
987096 ATTT
1 ATTT
987100 AATCATTTTT
Statistics
Matches: 114, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
128 1 0.01
129 10 0.09
130 90 0.79
131 13 0.11
ACGTcount: A:0.25, C:0.19, G:0.05, T:0.50
Consensus pattern (130 bp):
ATTTTTTAAATCTCACTTTTCACCTTTAAAATTGAGGCCCTAATTTTTTTCAATCTCACTTTTTA
CCTATATAATTGAGACCCCTAATTCTTTTCAATACCATTTTTTACTCATATAATTTAAGCCCCTA
Found at i:991925 original size:19 final size:19
Alignment explanation
Indices: 991901--991974 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
991891 ATGCAAAAAT
991901 GGTATCGATACCATAATAG
1 GGTATCGATACCATAATAG
991920 GGTATC-AGTACCATAGTATAG
1 GGTATCGA-TACCATA--ATAG
* **
991941 TAGTATCGATACCATGGTAAG
1 -GGTATCGATACCATAAT-AG
*
991962 GGTATCAATACCA
1 GGTATCGATACCA
991975 GGCAACATCG
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
18 1 0.02
19 13 0.30
20 12 0.27
21 6 0.14
22 11 0.25
23 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (19 bp):
GGTATCGATACCATAATAG
Found at i:991972 original size:20 final size:21
Alignment explanation
Indices: 991901--991974 Score: 73
Period size: 22 Copynumber: 3.6 Consensus size: 21
991891 ATGCAAAAAT
*
991901 GGTATCGATACCATA--ATAG
1 GGTATCAATACCATAGTATAG
*
991920 GGTATCAGTACCATAGTATAG
1 GGTATCAATACCATAGTATAG
* * *
991941 TAGTATCGATACCATGGTA-AG
1 -GGTATCAATACCATAGTATAG
991962 GGTATCAATACCA
1 GGTATCAATACCA
991975 GGCAACATCG
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
19 13 0.30
20 11 0.25
21 6 0.14
22 14 0.32
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (21 bp):
GGTATCAATACCATAGTATAG
Found at i:992523 original size:20 final size:20
Alignment explanation
Indices: 992452--992715 Score: 132
Period size: 20 Copynumber: 11.7 Consensus size: 20
992442 TATATAAAAT
992452 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * * *
992472 ACCTTAAAGGATGACATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
992498 GCATGAAAGGATGCATTACG
1 GCATGAAAGGATGCATTAAG
*
992518 GCATGAAAGGATGCCATAATCAATAT
1 GCATGAAAGGATG-CAT--T--A-AG
*
992544 GCATGAAAGGATCCATTAAG
1 GCATGAAAGGATGCATTAAG
*
992564 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
992590 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
992610 GCATGAAAGGCTGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
992636 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
992656 GCATGAAAGGATGTCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
* *
992682 GCATGAAAGGATTCATTAAC
1 GCATGAAAGGATGCATTAAG
*
992702 GCATGAAATGATGC
1 GCATGAAAGGATGC
992716 CATAATTTAA
Statistics
Matches: 189, Mismatches: 25, Indels: 60
0.69 0.09 0.22
Matches are distributed among these distances:
20 80 0.42
21 8 0.04
22 12 0.06
23 2 0.01
24 12 0.06
25 8 0.04
26 67 0.35
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:992755 original size:46 final size:46
Alignment explanation
Indices: 992446--992746 Score: 451
Period size: 46 Copynumber: 6.5 Consensus size: 46
992436 TTAGAGTATA
* * * *
992446 TAAAATGCATGAAAGGATGCATTAAGACCTTAAAGGATGACATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
*
992492 TAAAATGCATGAAAGGATGCATTACGGCATGAAAGGATGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* * *
992538 CAATATGCATGAAAGGATCCATTAAGGCATGAAAGGATGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
*
992584 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGCTGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
*
992630 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* * *
992676 TAAAATGCATGAAAGGATTCATTAACGCATGAAATGATGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* *
992722 TTAAATGTAT-AAATGGATGCATTAA
1 TAAAATGCATGAAA-GGATGCATTAA
992747 TACGTGAAAA
Statistics
Matches: 232, Mismatches: 22, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
45 3 0.01
46 229 0.99
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (46 bp):
TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
Found at i:995789 original size:34 final size:36
Alignment explanation
Indices: 995746--995826 Score: 112
Period size: 34 Copynumber: 2.3 Consensus size: 36
995736 CCCCTTAAAA
995746 ATTTTAAATTAGTATATATCTT-ATATTTT-TTTAT
1 ATTTTAAATTAGTATATATCTTAATATTTTCTTTAT
* *
995780 ATTTTAAATTATTATATATCTTAAATATTTTCTTTGT
1 ATTTTAAATTAGTATATATCTT-AATATTTTCTTTAT
*
995817 ATTTTCAATT
1 ATTTTAAATT
995827 GATAATTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
34 21 0.51
36 7 0.17
37 13 0.32
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.60
Consensus pattern (36 bp):
ATTTTAAATTAGTATATATCTTAATATTTTCTTTAT
Found at i:995797 original size:17 final size:17
Alignment explanation
Indices: 995749--995805 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
995739 CTTAAAAATT
*
995749 TTAAATTAGTATATATC
1 TTAAATTATTATATATC
* * * *
995766 TTATATTTTTTTATATT
1 TTAAATTATTATATATC
995783 TTAAATTATTATATATC
1 TTAAATTATTATATATC
995800 TTAAAT
1 TTAAAT
995806 ATTTTCTTTG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (17 bp):
TTAAATTATTATATATC
Found at i:996289 original size:168 final size:174
Alignment explanation
Indices: 996083--996399 Score: 416
Period size: 173 Copynumber: 1.9 Consensus size: 174
996073 TGGATTGTTT
* * *
996083 TATAAAATTGAAAAAAATAGGGCCCCTTAGTTATAAACCTGGA-TGAAAACT-AAAAA-A-ACC-
1 TATAAAATTGAAAAAAATAGGGACCCTTAATTATAAACCTGGAGCGAAAACTCAAAAATAGACCT
** * * * * *
996143 TATAGAATGAAACTATATTATATT-TATTTGAAAAGACTAATTTAATATTACATTAATGAACCAT
66 TATAGAACAAAAATAGACTATATTAT-TTTGAAAA-ACTAATTAAATATTACATTAATAAACCAT
*
996207 AG-AAAATGATTAAATTATGACTCTTATTTATAAAAATAGAAAGTA
129 AGAAAAAAGATTAAATTATGACTCTTATTTATAAAAATAGAAAGTA
* * *
996252 TATAAAATT-AAAAAAATAGGGATCCTTAATTATAAACCTTGAGCGAAAACTCAAAAATAGGCCT
1 TATAAAATTGAAAAAAATAGGGACCCTTAATTATAAACCTGGAGCGAAAACTCAAAAATAGACCT
* *
996316 TATAGAACAAAAATAGACTATATTATTTTGAAAAAGTAATTAAATATTACATTAATAAATCATAG
66 TATAGAACAAAAATAGACTATATTATTTTGAAAAACTAATTAAATATTACATTAATAAACCATAG
996381 AAAAAAGATTAAATTATGA
131 AAAAAAGATTAAATTATGA
996400 TTCCTCAATT
Statistics
Matches: 125, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
168 29 0.23
169 16 0.13
170 5 0.04
171 1 0.01
172 29 0.23
173 44 0.35
174 1 0.01
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.30
Consensus pattern (174 bp):
TATAAAATTGAAAAAAATAGGGACCCTTAATTATAAACCTGGAGCGAAAACTCAAAAATAGACCT
TATAGAACAAAAATAGACTATATTATTTTGAAAAACTAATTAAATATTACATTAATAAACCATAG
AAAAAAGATTAAATTATGACTCTTATTTATAAAAATAGAAAGTA
Found at i:1001809 original size:35 final size:37
Alignment explanation
Indices: 1001758--1001839 Score: 114
Period size: 35 Copynumber: 2.3 Consensus size: 37
1001748 ACATTTAAAA
1001758 ATTTTAAATTAGTATATATCATAGAT-TTTT-TTTAT
1 ATTTTAAATTAGTATATATCATAGATATTTTCTTTAT
* * *
1001793 ATTTTAAATTATTATATATCTTAGATATTTTCTTTTT
1 ATTTTAAATTAGTATATATCATAGATATTTTCTTTAT
*
1001830 ATTTTCAATT
1 ATTTTAAATT
1001840 GATTTTTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 24 0.59
36 4 0.10
37 13 0.32
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (37 bp):
ATTTTAAATTAGTATATATCATAGATATTTTCTTTAT
Found at i:1015308 original size:23 final size:23
Alignment explanation
Indices: 1015267--1015334 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1015257 TCCAGACCCC
*
1015267 GTGGGGGTATCGATT-CCCTTCA
1 GTGGGGGAATCGATTCCCCTTCA
*
1015289 GTGGGGGAATCGGTTCCCCTTCA
1 GTGGGGGAATCGATTCCCCTTCA
**
1015312 AAGGGGGAATCGATTCCCCTTCA
1 GTGGGGGAATCGATTCCCCTTCA
1015335 AGGCGGTATC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 13 0.32
23 27 0.68
ACGTcount: A:0.18, C:0.25, G:0.31, T:0.26
Consensus pattern (23 bp):
GTGGGGGAATCGATTCCCCTTCA
Found at i:1015349 original size:22 final size:23
Alignment explanation
Indices: 1015302--1015350 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
1015292 GGGGAATCGG
* *
1015302 TTCCCCTTCAAAGGGGGAATCGA
1 TTCCCCTTCAAAGGCGGAATCAA
*
1015325 TTCCCCTTC-AAGGCGGTATCAA
1 TTCCCCTTCAAAGGCGGAATCAA
1015347 TTCC
1 TTCC
1015351 TACTGCTCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (23 bp):
TTCCCCTTCAAAGGCGGAATCAA
Found at i:1021133 original size:20 final size:20
Alignment explanation
Indices: 1021108--1021158 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1021098 ACAAGGGAGA
1021108 AATCGGTATCCCCTGGGGGG
1 AATCGGTATCCCCTGGGGGG
*
1021128 AATCGGTACCCCCTGGGGGG
1 AATCGGTATCCCCTGGGGGG
1021148 AATCGGT-TCCC
1 AATCGGTATCCC
1021159 TCCGAGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.16, C:0.29, G:0.35, T:0.20
Consensus pattern (20 bp):
AATCGGTATCCCCTGGGGGG
Found at i:1022426 original size:20 final size:21
Alignment explanation
Indices: 1022387--1022439 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1022377 AAATTTTTGG
*
1022387 GAAACTGTCTTGGA-AAGTTTT
1 GAAACT-TCTTGTAGAAGTTTT
1022408 GAAAC-TCTTGTAGAAGTTTT
1 GAAACTTCTTGTAGAAGTTTT
1022428 GAAACTTCTTGT
1 GAAACTTCTTGT
1022440 CAAAATACTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 6 0.21
20 12 0.41
21 11 0.38
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (21 bp):
GAAACTTCTTGTAGAAGTTTT
Found at i:1023420 original size:26 final size:25
Alignment explanation
Indices: 1023391--1023439 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
1023381 TTTCTTTTCT
1023391 TTTTC-TTTTCAAGTTTTCATTTTTTG
1 TTTTCATTTT-AAGTTTT-ATTTTTTG
1023417 TTTTCATTTTAAGTTTTATTTTT
1 TTTTCATTTTAAGTTTTATTTTT
1023440 AAACATGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.27
26 12 0.55
27 4 0.18
ACGTcount: A:0.14, C:0.08, G:0.06, T:0.71
Consensus pattern (25 bp):
TTTTCATTTTAAGTTTTATTTTTTG
Found at i:1023441 original size:13 final size:14
Alignment explanation
Indices: 1023391--1023441 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 14
1023381 TTTCTTTTCT
*
1023391 TTTTC-TTTTCAAG
1 TTTTCATTTTTAAG
*
1023404 TTTTCATTTTT-TG
1 TTTTCATTTTTAAG
1023417 TTTTCA-TTTTAAG
1 TTTTCATTTTTAAG
1023430 TTTT-ATTTTTAA
1 TTTTCATTTTTAA
1023442 ACATGCTAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 5 0.16
13 23 0.72
14 4 0.12
ACGTcount: A:0.18, C:0.08, G:0.06, T:0.69
Consensus pattern (14 bp):
TTTTCATTTTTAAG
Found at i:1030579 original size:19 final size:20
Alignment explanation
Indices: 1030540--1030595 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
1030530 GAAATCCCTT
*
1030540 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATCTTTAA
1030560 TGAAAATACATGA-CTTTAA
1 TGAAAATACATGATCTTTAA
* *
1030579 TGAAAATGCATGCTCTT
1 TGAAAATACATGATCTT
1030596 GGCCGAATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATCTTTAA
Found at i:1042068 original size:15 final size:15
Alignment explanation
Indices: 1042048--1042080 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1042038 TCTGTCCAAA
1042048 ATAATTCTCTCTTAC
1 ATAATTCTCTCTTAC
1042063 ATAATTCTCTCTTAC
1 ATAATTCTCTCTTAC
1042078 ATA
1 ATA
1042081 CCCTAAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTCTCTCTTAC
Found at i:1044184 original size:64 final size:64
Alignment explanation
Indices: 1044082--1044315 Score: 355
Period size: 64 Copynumber: 3.7 Consensus size: 64
1044072 AAGGGATTAA
* * * * * *
1044082 CCTAGACCCCTAGAATAT-GGAGTCCAATATGGAAGATCATAACATGAATCCATAAGGACTTAC
1 CCTAGACCCCTAGGATCTAGGAGTCCAATATGAAAGATCATAACAAGCATCCGTAAGGACTTAC
1044145 CCTAGACCCCTAGGATCTAGGAGTCCAATAT-ACAAGATCATAACAAGCATCCGTAAGGACTTAC
1 CCTAGACCCCTAGGATCTAGGAGTCCAATATGA-AAGATCATAACAAGCATCCGTAAGGACTTAC
* **
1044209 CCTAGACCCCTAGGATCTAAGAGTCCAATATGAATTATCATAACAAGCATCCGTAAGGACTTAC
1 CCTAGACCCCTAGGATCTAGGAGTCCAATATGAAAGATCATAACAAGCATCCGTAAGGACTTAC
*
1044273 CCTAGACCCCTATGATCTAGGAGTCCAATATGAAAGATCATAA
1 CCTAGACCCCTAGGATCTAGGAGTCCAATATGAAAGATCATAA
1044316 TAGAAAGGAA
Statistics
Matches: 155, Mismatches: 13, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
63 16 0.10
64 138 0.89
65 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (64 bp):
CCTAGACCCCTAGGATCTAGGAGTCCAATATGAAAGATCATAACAAGCATCCGTAAGGACTTAC
Found at i:1046296 original size:12 final size:12
Alignment explanation
Indices: 1046281--1046306 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1046271 TAATAATAAT
1046281 AATAACAACAAC
1 AATAACAACAAC
1046293 AATAACAACAAC
1 AATAACAACAAC
1046305 AA
1 AA
1046307 ATGCTTACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.23, G:0.00, T:0.08
Consensus pattern (12 bp):
AATAACAACAAC
Found at i:1046378 original size:14 final size:14
Alignment explanation
Indices: 1046354--1046396 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1046344 TAAAAAAAAT
**
1046354 ATAATTAATAATATG
1 ATAA-TAATAATAAA
1046369 ATAATAATAATAAA
1 ATAATAATAATAAA
*
1046383 ATAATATTAATAAA
1 ATAATAATAATAAA
1046397 TAAAACTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
ATAATAATAATAAA
Found at i:1046519 original size:23 final size:22
Alignment explanation
Indices: 1046488--1046533 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
1046478 TTAAAAGAAG
1046488 AAGAAAAAAA-GTTAAATTTTAAA
1 AAGAAAAAAATGTT-AA-TTTAAA
*
1046511 AAGATAAAAATGTTAATTTAAA
1 AAGAAAAAAATGTTAATTTAAA
1046533 A
1 A
1046534 CTTTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 11 0.52
24 3 0.14
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (22 bp):
AAGAAAAAAATGTTAATTTAAA
Found at i:1046525 original size:24 final size:21
Alignment explanation
Indices: 1046488--1046533 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 21
1046478 TTAAAAGAAG
1046488 AAGAAAAAAAGTTAAATTTTAAA
1 AAGAAAAAAAGTT-AA-TTTAAA
*
1046511 AAGATAAAAATGTTAATTTAAA
1 AAGA-AAAAAAGTTAATTTAAA
1046533 A
1 A
1046534 CTTTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 6 0.29
24 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (21 bp):
AAGAAAAAAAGTTAATTTAAA
Found at i:1046826 original size:29 final size:29
Alignment explanation
Indices: 1046784--1046850 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
1046774 GTATGTTTTA
1046784 ATACCTAAATTTTTAATTTTTTCAAAATC
1 ATACCTAAATTTTTAATTTTTTCAAAATC
1046813 ATACCTAAATTTTTAATTTTTTCAAAATC
1 ATACCTAAATTTTTAATTTTTTCAAAATC
1046842 ATACCTAAA
1 ATACCTAAA
1046851 GTTCAGTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (29 bp):
ATACCTAAATTTTTAATTTTTTCAAAATC
Found at i:1046861 original size:29 final size:29
Alignment explanation
Indices: 1046784--1046861 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
1046774 GTATGTTTTA
* *
1046784 ATACCTAAATTTTTAATTTTTTCAAAATC
1 ATACCTAAATGTTCAATTTTTTCAAAATC
* *
1046813 ATACCTAAATTTTTAATTTTTTCAAAATC
1 ATACCTAAATGTTCAATTTTTTCAAAATC
*
1046842 ATACCTAAA-GTTCAGTTTTT
1 ATACCTAAATGTTCAATTTTT
1046862 GTTTCATTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 8 0.17
29 38 0.83
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (29 bp):
ATACCTAAATGTTCAATTTTTTCAAAATC
Found at i:1047913 original size:143 final size:143
Alignment explanation
Indices: 1047730--1047994 Score: 386
Period size: 143 Copynumber: 1.9 Consensus size: 143
1047720 AAGAGGTCAT
* * * *
1047730 GGTGAAGCGACCCATGAAATATGAGACCGAATAACCACCATCTATGGTGGTTAACAACGACCAAC
1 GGTGAAACGACCCATGAAATATGAGACCGAACAACCACCATCTATGGTGGTCAACAACAACCAAC
* * *
1047795 GTTTCAGTTTTCTCACTTTTGATATGATTTATAGCATGTTCCAACAAAATGAAGGTCGGATTCAG
66 GTTTCAGTTTTCTCACTTTTGATAGGATTCAGAGCATGTTCCAACAAAATGAAGGTCGGATTCAG
1047860 GCTCAAGGGTCGA
131 GCTCAAGGGTCGA
* * * * *
1047873 GGTGAAACGACCCATGAAATATGAGATCGAACAAGCACCATCTATGGTTGTCGACAATAACCAAC
1 GGTGAAACGACCCATGAAATATGAGACCGAACAACCACCATCTATGGTGGTCAACAACAACCAAC
** * *
1047938 GTTTTGGTTTTCTCACTTTTGATCGGATTCAGAGCATGTTCCAATAAAATGAAGGTC
66 GTTTCAGTTTTCTCACTTTTGATAGGATTCAGAGCATGTTCCAACAAAATGAAGGTC
1047995 AGTTTCAAAC
Statistics
Matches: 106, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
143 106 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (143 bp):
GGTGAAACGACCCATGAAATATGAGACCGAACAACCACCATCTATGGTGGTCAACAACAACCAAC
GTTTCAGTTTTCTCACTTTTGATAGGATTCAGAGCATGTTCCAACAAAATGAAGGTCGGATTCAG
GCTCAAGGGTCGA
Found at i:1050566 original size:16 final size:16
Alignment explanation
Indices: 1050545--1050578 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1050535 TATTGATCTA
1050545 TTATTTTATATAAT-TT
1 TTATTTTAT-TAATATT
1050561 TTATTTTATTAATATT
1 TTATTTTATTAATATT
1050577 TT
1 TT
1050579 CGATATGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTTATTAATATT
Found at i:1054876 original size:20 final size:21
Alignment explanation
Indices: 1054839--1054878 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1054829 CGATGTATTA
1054839 TGTTGGAAATTAAGGTTAGAG
1 TGTTGGAAATTAAGGTTAGAG
* *
1054860 TGTT-GAAATTGATGTTAGA
1 TGTTGGAAATTAAGGTTAGA
1054879 ATATGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.38
Consensus pattern (21 bp):
TGTTGGAAATTAAGGTTAGAG
Found at i:1057774 original size:11 final size:11
Alignment explanation
Indices: 1057758--1057782 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1057748 AATACAAAAA
1057758 GAAGTGCAAGT
1 GAAGTGCAAGT
1057769 GAAGTGCAAGT
1 GAAGTGCAAGT
1057780 GAA
1 GAA
1057783 AGAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:1061079 original size:90 final size:91
Alignment explanation
Indices: 1060925--1061106 Score: 267
Period size: 90 Copynumber: 2.0 Consensus size: 91
1060915 CCTAGAACAC
* *
1060925 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAAGATCATTTAGGTGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAAGATCATTTAGGCGCCAAGATG
*
1060990 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
** * ** * *
1061016 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAAGATCATTTAGGCGCCAAGATG
1061080 AAGAGCTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
1061106 C
1 C
1061107 ATCATTTCCC
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 62 0.77
91 19 0.23
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.28
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAAGATCATTTAGGCGCCAAGATG
AAGAGCTCTCTCCCTATTCGGCCAAG
Found at i:1061981 original size:22 final size:22
Alignment explanation
Indices: 1061939--1061981 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1061929 CTAGTTCTTG
* *
1061939 TATATGATGTTTATCATGAATA
1 TATATGATGTCTATCACGAATA
*
1061961 TATATGATGTCTATTACGAAT
1 TATATGATGTCTATCACGAAT
1061982 GTTTATTCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (22 bp):
TATATGATGTCTATCACGAATA
Found at i:1062257 original size:70 final size:70
Alignment explanation
Indices: 1062139--1062275 Score: 204
Period size: 70 Copynumber: 2.0 Consensus size: 70
1062129 ACATATCTGG
* * **
1062139 TTTAGCACTAGAGTGTATGTAAAATACACTTAGTGTAGGTGGTGGGCACGACCTTATGTGTTATA
1 TTTAGCACTAGAGTGTATATAAAAGACACTTAGTGTAGAAGGTGGGCACGACCTTATGTGTTATA
1062204 TTCGC
66 TTCGC
* *
1062209 TTTAGCACTAGAGTGTATATAAAAGACACTTAGTGT-GCAAGGTTGGCACGTCCTTATGTGTTAT
1 TTTAGCACTAGAGTGTATATAAAAGACACTTAGTGTAG-AAGGTGGGCACGACCTTATGTGTTAT
1062273 ATT
65 ATT
1062276 TGGTTTTAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
69 1 0.02
70 59 0.98
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (70 bp):
TTTAGCACTAGAGTGTATATAAAAGACACTTAGTGTAGAAGGTGGGCACGACCTTATGTGTTATA
TTCGC
Found at i:1065902 original size:29 final size:29
Alignment explanation
Indices: 1065860--1065951 Score: 112
Period size: 31 Copynumber: 3.0 Consensus size: 29
1065850 AAAATTTTCG
1065860 TTAGTGACCAAAATGTAATTTTTAAAAGT
1 TTAGTGACCAAAATGTAATTTTTAAAAGT
* *
1065889 TTAGTGGCCAAAATGTAATGTTTGGAAAAGT
1 TTAGTGACCAAAATGTAAT-TTT-TAAAAGT
* *
1065920 TTAGCGACCAAAAGGGTAATTTTTTAAAAGT
1 TTAGTGACCAAAA-TGTAA-TTTTTAAAAGT
1065951 T
1 T
1065952 AGATTTTTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
29 18 0.34
30 3 0.06
31 24 0.45
32 7 0.13
33 1 0.02
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.35
Consensus pattern (29 bp):
TTAGTGACCAAAATGTAATTTTTAAAAGT
Found at i:1071388 original size:13 final size:14
Alignment explanation
Indices: 1071354--1071388 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1071344 TAAGATTTTC
1071354 TTTGAAAATCAAGT
1 TTTGAAAATCAAGT
1071368 TTTG-AAATCAAG-
1 TTTGAAAATCAAGT
1071380 TTTGAAAAT
1 TTTGAAAAT
1071389 TACTCCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 12 0.60
14 4 0.20
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (14 bp):
TTTGAAAATCAAGT
Found at i:1071641 original size:2 final size:2
Alignment explanation
Indices: 1071634--1071664 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1071624 ACCAAACCTA
1071634 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
1071665 AGCTCAAAAT
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:1105366 original size:13 final size:12
Alignment explanation
Indices: 1105344--1105378 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
1105334 ATACATTGGG
1105344 ATATGAAAGTAA
1 ATATGAAAGTAA
*
1105356 ATATGGAAAGTGA
1 ATAT-GAAAGTAA
1105369 ATATGAAAGT
1 ATATGAAAGT
1105379 TAAGAAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (12 bp):
ATATGAAAGTAA
Found at i:1111224 original size:12 final size:13
Alignment explanation
Indices: 1111209--1111243 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1111199 AATTACATTT
1111209 TTATTTATTTTA-
1 TTATTTATTTTAG
1111221 TTATTTA-TTTAG
1 TTATTTATTTTAG
1111233 TTATTTATTTT
1 TTATTTATTTT
1111244 TCTGAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 14 0.67
13 3 0.14
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TTATTTATTTTAG
Found at i:1114073 original size:21 final size:21
Alignment explanation
Indices: 1114049--1114094 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1114039 TTTATATTTT
1114049 ATTTAAAAATTATTTTC-TAAA
1 ATTTAAAAATTA-TTTCATAAA
*
1114070 ATTTAAATATTATTTCATAAA
1 ATTTAAAAATTATTTCATAAA
1114091 ATTT
1 ATTT
1114095 TAAAGGCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTAAAAATTATTTCATAAA
Found at i:1114140 original size:26 final size:27
Alignment explanation
Indices: 1114091--1114144 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
1114081 ATTTCATAAA
** *
1114091 ATTTTAAAGGCTTTATTATAAATATTT
1 ATTTTAAAGGCTAAATTAAAAATATTT
1114118 ATTTTAAA-GCTAAATTAAAAATATTT
1 ATTTTAAAGGCTAAATTAAAAATATTT
1114144 A
1 A
1114145 ATAATGTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (27 bp):
ATTTTAAAGGCTAAATTAAAAATATTT
Found at i:1115203 original size:30 final size:29
Alignment explanation
Indices: 1115138--1115314 Score: 99
Period size: 30 Copynumber: 5.9 Consensus size: 29
1115128 TTAAATAAAA
* *
1115138 AAAAATAAAAATTAAAGTACCAAAAT-AT
1 AAAAACAAAAATTAAAGTACTAAAATAAT
* *
1115166 CACAAACAAAAACTTAATGTACTAAAATAAT
1 -AAAAACAAAAA-TTAAAGTACTAAAATAAT
* * *
1115197 AAAAACATATAATTAAAGAACTAAAATAGT
1 AAAAACA-AAAATTAAAGTACTAAAATAAT
* * * *
1115227 AAAAATAGAAAATTAAGGAACTAGAATAGGA-
1 AAAAACA-AAAATTAAAGTACTAAAATA--AT
* *
1115258 AAAAAGCAATAATTCAAAGGACTAAAATAAT
1 AAAAA-CAAAAATT-AAAGTACTAAAATAAT
* * *
1115289 -TAAACTAAGAACTTAAAGGACTAAAA
1 AAAAAC-AA-AAATTAAAGTACTAAAA
1115315 CCGAAAACAT
Statistics
Matches: 115, Mismatches: 23, Indels: 19
0.73 0.15 0.12
Matches are distributed among these distances:
29 10 0.09
30 75 0.65
31 18 0.16
32 12 0.10
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.20
Consensus pattern (29 bp):
AAAAACAAAAATTAAAGTACTAAAATAAT
Found at i:1117226 original size:128 final size:128
Alignment explanation
Indices: 1117050--1117907 Score: 818
Period size: 128 Copynumber: 6.7 Consensus size: 128
1117040 CTTTAGGAAA
* * * *
1117050 GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCTAGGTTGACATAGTTCCTACATA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTCCTACATA
* * * * * * *
1117115 TTGAGGAAGTCTAGTCGGGTGATGACACGACTCATACGTGATGAAGA-GTTCTGGCCATCTAAG
66 ATGAGGAAATCTGGTCGGGTGATGACACGATTCATACGCGATGAGGACG-TCAGGCCATCTAAG
* ** * * * *
1117178 GGTGATAACACAGTTCCTACGTGATGAGGATTGATGGTTATATGGGTTGACACAACTCTTACATA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTCCTACATA
* * * * * ** * **
1117243 ATGAAGAGATTTGGTCGGGTGATGACACGGTTCCTACGTTATGAGGATGAAAGGCCATCTAAG
66 ATGAGGAAATCTGGTCGGGTGATGACACGATTCATACGCGATGAGGACGTCAGGCCATCTAAG
* * * *
1117306 GGTGATAACACGCTTCCTACGTGATGTGGACGGCTGGTTATCTGGGTTCATACCA-CTCCTACAT
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACA-CAGCTCCTACAT
* * * * * * * *
1117370 AATGAGGAAATCTGGTCGGATGATGAAACGGTT-TTATGCGAAGAGGACGAT-AAGCCATCCAAG
65 AATGAGGAAATCTGGTCGGGTGATGACACGATTCATACGCGATGAGGACG-TCAGGCCATCTAAG
* *
1117433 GGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTTCTACATA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTCCTACATA
* * * * *
1117498 ATGAGGATATATGGTCGGGTGATGACACGATTCTTACGCGATGAGGATGAT-ATGCCATCTAAG
66 ATGAGGAAATCTGGTCGGGTGATGACACGATTCATACGCGATGAGGACG-TCAGGCCATCTAAG
* * * * * * *
1117561 GGTAATAACACGATTCCTACGAGATGAGGATGGTTGGTTATTTGGGTTGACACAACTCCTACATA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTCCTACATA
* ** * * * * * *
1117626 ATGAGGAAATTTATTCAGGTGATGACACAATTCATAAGCGATGAGGACGGCAAGTCATCTAAG
66 ATGAGGAAATCTGGTCGGGTGATGACACGATTCATACGCGATGAGGACGTCAGGCCATCTAAG
* * * * *
1117689 GGTGATAACACGGTTCCTATGTGATGAGTACGGCTGCTTATATGAGTT-AGCACAGCTCCTACAT
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGA-CACAGCTCCTACAT
* * * * * * * *
1117753 AATGAGGAAATTTGGTCAGGTGATGACACTG-CTCAT-C-TGTTCATGA-GTCTTGGCCATCTAA
65 AATGAGGAAATCTGGTCGGGTGATGACAC-GATTCATACGCGATGAGGACGTC-AGGCCATCTAA
*
1117814 A
128 G
* * * * * *
1117815 GGTGAGAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGAGTTGAGATAGCTCCCACATA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTCCTACATA
* *
1117880 ATGAGGAGATCTGGTCAGGTGATGACAC
66 ATGAGGAAATCTGGTCGGGTGATGACAC
1117908 TGCTCAACTA
Statistics
Matches: 598, Mismatches: 122, Indels: 22
0.81 0.16 0.03
Matches are distributed among these distances:
125 2 0.00
126 95 0.16
127 105 0.18
128 393 0.66
129 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (128 bp):
GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTCCTACATA
ATGAGGAAATCTGGTCGGGTGATGACACGATTCATACGCGATGAGGACGTCAGGCCATCTAAG
Found at i:1117515 original size:255 final size:256
Alignment explanation
Indices: 1117050--1117904 Score: 864
Period size: 255 Copynumber: 3.4 Consensus size: 256
1117040 CTTTAGGAAA
* * * * **
1117050 GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCTAGGTTGACATAGTTCCTACATA
1 GGTGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAACTCCTACATA
* * * * * * * * * * * * **
1117115 TTGAGGAAGTCTAGTCGGGTGATGACACGACTCATACGTGATGAAGA-GTTCTGGCCATCTAAGG
66 ATGAGGAAATCTGGTCAGGTGATGAAACAATTCATAAGCGAAGAGGACG-ACAAGCCATCTAAGG
* ** * *
1117179 GTGATAACACAGTTCCTACGTGATGAGGATTGATGGTTATATGGGTTGACACAAC-TCTTACATA
130 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATATGGGTTGACACAGCTTC-TACATA
* * * *
1117243 ATGAAGAGATTTGGTCGGGTGATGACACGGTTCCTACGTTATGAGGATGAAAGGCCATCTAAG
194 ATGAGGAAATTTGGTCGGGTGATGACACGGTTCATACGTTATGAGGATGATAGGCCATCTAAG
* * * * *
1117306 GGTGATAACACGCTTCCTACGTGATGTGGACGGCTGGTTATCTGGGTTCATACCACTCCTACATA
1 GGTGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAACTCCTACATA
** * * * *
1117371 ATGAGGAAATCTGGTC-GGATGATGAAACGGTT-TTATGCGAAGAGGACGATAAGCCATCCAAGG
66 ATGAGGAAATCTGGTCAGG-TGATGAAACAATTCATAAGCGAAGAGGACGACAAGCCATCTAAGG
* *
1117434 GTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTTCTACATAA
130 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATATGGGTTGACACAGCTTCTACATAA
* * * * ** *
1117499 TGAGGATATATGGTCGGGTGATGACACGATTCTTACGCGATGAGGATGATATGCCATCTAAG
195 TGAGGAAATTTGGTCGGGTGATGACACGGTTCATACGTTATGAGGATGATAGGCCATCTAAG
* * * * *
1117561 GGTAATAACACGATTCCTACGAGATGAGGATGGTTGGTTATTTGGGTTGACACAACTCCTACATA
1 GGTGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAACTCCTACATA
* ** * * * *
1117626 ATGAGGAAATTTATTCAGGTGATGACACAATTCATAAGCGATGAGGACGGCAAGTCATCTAAGGG
66 ATGAGGAAATCTGGTCAGGTGATGAAACAATTCATAAGCGAAGAGGACGACAAGCCATCTAAGGG
* * * * *
1117691 TGATAACACGGTTCCTATGTGATGAGTACGGCTGCTTATATGAGTT-AGCACAGCTCCTACATAA
131 TGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATATGGGTTGA-CACAGCTTCTACATAA
* * * * * *
1117755 TGAGGAAATTTGGTCAGGTGATGACACTGCTCAT-CTGTTCATGA-G-T-CTTGGCCATCTAAA
195 TGAGGAAATTTGGTCGGGTGATGACACGGTTCATAC-GTT-ATGAGGATGATAGGCCATCTAAG
* * * * * * * *
1117815 GGTGAGAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGAGTTGAGATAGCTCCCACATA
1 GGTGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAACTCCTACATA
*
1117880 ATGAGGAGATCTGGTCAGGTGATGA
66 ATGAGGAAATCTGGTCAGGTGATGA
1117905 CACTGCTCAA
Statistics
Matches: 489, Mismatches: 102, Indels: 18
0.80 0.17 0.03
Matches are distributed among these distances:
254 83 0.17
255 210 0.43
256 192 0.39
257 4 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (256 bp):
GGTGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAACTCCTACATA
ATGAGGAAATCTGGTCAGGTGATGAAACAATTCATAAGCGAAGAGGACGACAAGCCATCTAAGGG
TGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATATGGGTTGACACAGCTTCTACATAAT
GAGGAAATTTGGTCGGGTGATGACACGGTTCATACGTTATGAGGATGATAGGCCATCTAAG
Found at i:1117757 original size:383 final size:380
Alignment explanation
Indices: 1117047--1117907 Score: 995
Period size: 383 Copynumber: 2.2 Consensus size: 380
1117037 CATCTTTAGG
*
1117047 AAAGGTGATAAC-TCGGTTCCTACGTGATGAGGACGGCTGGTTATCTAGGTTGACATAG-TTCCT
1 AAAGGTGATAACAT-GGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACATAGCTT-CT
* * * * *
1117110 ACATATTGAGGAAGTCTAGTCGGGTGATGACACGACTCATACGTGATGAAGAGTTCTGGCCATCT
64 ACATAATGAGGAA-TCTGGTCGGGTGATGACACGACTCATACGCGATGAAGAGATATGGCCATCT
* * * *
1117175 AAGGGTGATAACACAGTTCCTACGTGATGAGGATTGATGGTTATATGGGTTGACACAACTCTTAC
128 AAGGGTAATAACACAGTTCCTACGAGATGAGGATGGATGGTTATATGGGTTGACACAACTCCTAC
* * * ** * * ** *
1117240 ATAATGAAGAGATTTGGTCGGGTGATGACACGGTTCCTACGTTATGAGGATGAAAGGCCATCTAA
193 ATAATGAAGAAATTTAGTCAGGTGATGACACAATTCATAAGCGATGAGGAGGAAAGGCCATCTAA
* * * * *
1117305 GGGTGATAACACGCTTCCTACGTGATGTGGACGGCTGGTTATCTGGGTTCATACCACTCCTACAT
258 GGGTGATAACACGCTTCCTACGTGATGAGGACGGCTGCTTATATGAGTTCACACCACTCCTACAT
* *
1117370 AATGAGGAAATCTGGTC-GGATGATGAAAC-GGT-TTTATGCGAAGAGGACGATAAGCCATCC
323 AATGAGGAAATCTGGTCAGG-TGATGAAACTGCTATCTATGC-AAGA-GAC--TAAGCCATCC
* *
1117430 AAGGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTTCTAC
1 AAAGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACATAGCTTCTAC
* * * *
1117495 ATAATGAGGATATATGGTCGGGTGATGACACGATTCTTACGCGATGAGGATGATAT-GCCATCTA
66 ATAATGAGGA-ATCTGGTCGGGTGATGACACGACTCATACGCGATGAAGA-GATATGGCCATCTA
* *
1117559 AGGGTAATAACAC-GATTCCTACGAGATGAGGATGGTTGGTTATTTGGGTTGACACAACTCCTAC
129 AGGGTAATAACACAG-TTCCTACGAGATGAGGATGGATGGTTATATGGGTTGACACAACTCCTAC
* * * *
1117623 ATAATGAGGAAATTTATTCAGGTGATGACACAATTCATAAGCGATGAGGACGGCAA-GTCATCTA
193 ATAATGAAGAAATTTAGTCAGGTGATGACACAATTCATAAGCGATGAGGA-GGAAAGGCCATCTA
* * *
1117687 AGGGTGATAACACGGTTCCTATGTGATGAGTACGGCTGCTTATATGAGTT-AGCA-CAGCTCCTA
257 AGGGTGATAACACGCTTCCTACGTGATGAGGACGGCTGCTTATATGAGTTCA-CACCA-CTCCTA
* * * * * * ** *
1117750 CATAATGAGGAAATTTGGTCAGGTGATGACACTGCTCATCTGTTCATGAGTCTTGGCCATCT
320 CATAATGAGGAAATCTGGTCAGGTGATGAAACTGCT-ATCTATGCAAGAGACTAAGCCATCC
* * * * *
1117812 AAAGGTGAGAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGAGTTGAGATAGCTCCCAC
1 AAAGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACATAGCTTCTAC
*
1117877 ATAATGAGGAGATCTGGTCAGGTGATGACAC
66 ATAATGAGGA-ATCTGGTCGGGTGATGACAC
1117908 TGCTCAACTA
Statistics
Matches: 405, Mismatches: 61, Indels: 25
0.82 0.12 0.05
Matches are distributed among these distances:
382 97 0.24
383 285 0.70
384 16 0.04
385 3 0.01
386 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (380 bp):
AAAGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACATAGCTTCTAC
ATAATGAGGAATCTGGTCGGGTGATGACACGACTCATACGCGATGAAGAGATATGGCCATCTAAG
GGTAATAACACAGTTCCTACGAGATGAGGATGGATGGTTATATGGGTTGACACAACTCCTACATA
ATGAAGAAATTTAGTCAGGTGATGACACAATTCATAAGCGATGAGGAGGAAAGGCCATCTAAGGG
TGATAACACGCTTCCTACGTGATGAGGACGGCTGCTTATATGAGTTCACACCACTCCTACATAAT
GAGGAAATCTGGTCAGGTGATGAAACTGCTATCTATGCAAGAGACTAAGCCATCC
Found at i:1120612 original size:8 final size:8
Alignment explanation
Indices: 1120590--1120629 Score: 73
Period size: 8 Copynumber: 5.1 Consensus size: 8
1120580 AAATAAATGC
1120590 AGATGCAA
1 AGATGCAA
1120598 A-ATGCAA
1 AGATGCAA
1120605 AGATGCAA
1 AGATGCAA
1120613 AGATGCAA
1 AGATGCAA
1120621 AGATGCAA
1 AGATGCAA
1120629 A
1 A
1120630 TGCAGATGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 7 0.23
8 24 0.77
ACGTcount: A:0.53, C:0.12, G:0.23, T:0.12
Consensus pattern (8 bp):
AGATGCAA
Found at i:1120620 original size:16 final size:15
Alignment explanation
Indices: 1120590--1120642 Score: 76
Period size: 16 Copynumber: 3.7 Consensus size: 15
1120580 AAATAAATGC
1120590 AGATGCAAAATGCAA
1 AGATGCAAAATGCAA
1120605 AGATGCAAAGATGCAA
1 AGATGCAAA-ATGCAA
1120621 AGATGC-AAATGC--
1 AGATGCAAAATGCAA
1120633 AGATGCAAAA
1 AGATGCAAAA
1120643 ATGTTGACCC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.17
13 3 0.08
14 4 0.11
15 11 0.31
16 12 0.33
ACGTcount: A:0.51, C:0.13, G:0.23, T:0.13
Consensus pattern (15 bp):
AGATGCAAAATGCAA
Found at i:1122762 original size:30 final size:29
Alignment explanation
Indices: 1122727--1122833 Score: 81
Period size: 30 Copynumber: 3.5 Consensus size: 29
1122717 AACTTAAGGT
1122727 ACTAAAATAATAAAAACATATAATTAAAGA
1 ACTAAAATAATAAAAACA-ATAATTAAAGA
* * * *
1122757 ACTAAAATAGTAAACATAGAA-AAATAAGGA
1 ACTAAAATAATAAA-A-ACAATAATTAAAGA
* * *
1122787 ACTAGAATAGCAAAAAAATCAATAATTCAAAGG
1 ACTAAAATA--ATAAAAA-CAATAATT-AAAGA
1122820 ACTAAAATAATAAA
1 ACTAAAATAATAAA
1122834 CGTAAGAACT
Statistics
Matches: 57, Mismatches: 13, Indels: 13
0.69 0.16 0.16
Matches are distributed among these distances:
30 29 0.51
31 9 0.16
32 8 0.14
33 11 0.19
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.20
Consensus pattern (29 bp):
ACTAAAATAATAAAAACAATAATTAAAGA
Found at i:1129236 original size:948 final size:930
Alignment explanation
Indices: 1127403--1129842 Score: 3081
Period size: 948 Copynumber: 2.7 Consensus size: 930
1127393 ATTTTGTGGT
* * *
1127403 AATATTGGAAAAGGGTAAAATATTTGGTTCATATCTAACTTTGGAAAGATGATAAGGTTATGTGG
1 AATATTGGAAAAGGGTAAAATATTTAGTTCAT-TTTGACTTTGGAAAGATGATAAGGTTATGTGG
* * *
1127468 CTTGGTATTATTGTAAATATCACGCTTT-ATTAATGG-CAAAATGGACATTTCTCGTTAAATGAA
65 CTTGGTATTATTGTAAATATCAAG-TTTCATTAATGGAC-AAAT-GACAATTCTCATTAAATGAA
1127531 TATTTTATTCATTTATGCTTAAATAAAGGTTAAATTAACATGAAATTAAAGGAAAATTTCATGAA
127 TATTTTATTCATTTATGCTTAAATAAAGGTTAAATTAACATGAAATTAAA-GAAAATTTCATGAA
* * * * * ** * * * *
1127596 GTTGAGTAACTTTCAACCATCATTGTCGCGAGCCTCCTCATAAGGTAGGAAAACTTCTCTTTT-A
191 GTTGGGTAATTTTCAGCCACCAATGTCAAGA-CCTCCTCTTAAGGTAAGAAAAATTTTCTTTTCA
* *
1127660 TATTTTTGATCGATTTTCTTTGGATTTTGGATCAT-TCCATGAAATAGAAAATTGTTCTATTCGA
255 -ATTTTTGATCGATTTCCTTTGGATTTTGGATCATGT-CGTGAAATAGAAAATTGTTCTATTCGA
* * *
1127724 AAAACGCTATCATTTCGTACCATTATTGCTTGCTAATTTGGTTTGTATTGAAAGATCCCAAATTT
318 AAAACGCTATCATTTGGTACCATTATTGCTTGTTAATTTGGTTTGTGTTGAAAGATCCCAAATTT
* * * * *
1127789 TAGGGTTTGTGTTCACATTAGGGTTTATAGAAATGATGAAGGATTTTGATGTTTTTAAGGTTGTA
383 TAAGGTTTGTGTTCACATTAGGGTTTATGGAATTGAT-AAAGA-TTTGATGTTTTTGAGGTTGTA
*
1127854 GAATCATATACAAGCATGATTGATTATTAAAATCACTTGTACATGGCTACATAAGAACATGTTGA
446 GAATCATATACAAGCATGATTGATAATTAAAATCACTTGTACATGGCTACATAAGAACATGTTGA
*
1127919 ATTCGGCCAAACCCTAGCTTTAGGGGAAAGAAGTGTTTTGATGAAATTTGATTAGGGCTTTGAAT
511 ATTCGGCCAAACCCTAGCTTTAGGGGAAAGAAGTGTTTTGATGAAATTTGATTAGGGCTTTGATT
* * *
1127984 CTAGAGGTGTTAAAATGTTGAATCGAGGTTGATTTCATGTTTGAACCTAGTGAAACTCTTAAACC
576 CTAGAGGTCTTGAAATGTTGAATCGAGGTTGATTTCATGTTCGAACCTAGTGAAACTCTTAAACC
*
1128049 CTAAATTACATACCATTCAACCTTGAGGAAATAGGTTGGGAAAAATTCTGGAAAAATTACCATGT
641 CTAAATTACATACCATTCAACCTTGAGGAAATAGGTTGGGAAAAATTCTGGAAAAATTACCATGG
* * * * *
1128114 CTTAGAAATTATATTTGGAAGGTTCTACAAGCCTTATAAATTTTTTTGGGACATTTTGTAATTTT
706 CTTAGAAATGATATTTGGAAGGTACTACAAGCCTTAGAAAATATTTTGGGACATTTTGTAATTTT
* *
1128179 TCAAAATTTGAGGGACCTATTTGAAAATTTTGAAAAAGTTATAGGTTGAATGAATAATTACTCAA
771 TCAAAAGTTGAGGGACCTATTTCAAAATTTTGAAAAAGTTATAGGTTGAATGAATAATTACTCAA
1128244 TAATTGATATACATTGCTAGAAATTACTATTTAAGGACTGAAATTGAAGTTAGAATGTGAAAGTT
836 TAATTGATATACATTGCTAGAAATTACTATTTAAGGACTGAAATTGAAGTTAGAATGTGAAAGTT
*
1128309 AGCCATTTTGGAAATTTGGCAAAATTTAAGTATAAAACAGC
901 AGCCATTCTGGAAATTTGGC-AAA-TT---T-T---A-A-C
*
1128350 AAATATTGGAAAAGGGTAAAATATTTAGTTCATCTTTGACTTTGGAAAGATGATAAGGTTACGTG
1 -AATATTGGAAAAGGGTAAAATATTTAGTTCAT-TTTGACTTTGGAAAGATGATAAGGTTATGTG
*
1128415 GCTTGTTATTATTGTAAATATCAAGTTTCATTAATGGACAAATGTACAATTCTCATTAAATGAAT
64 GCTTGGTATTATTGTAAATATCAAGTTTCATTAATGGACAAATG-ACAATTCTCATTAAATGAAT
*
1128480 ATTTTATTCATTTATGCTTAAATAAAGGTTAAATTAACATGAAATTAAATGAAAATTTAATGAAG
128 ATTTTATTCATTTATGCTTAAATAAAGGTTAAATTAACATGAAATTAAA-GAAAATTTCATGAAG
* ** *
1128545 TTGGGTAATTTTTAGCCACCAATGTCTTGACCTCCTCTTAAGGTAAGAAAATTTTTCTTTTCAAT
192 TTGGGTAATTTTCAGCCACCAATGTCAAGACCTCCTCTTAAGGTAAGAAAAATTTTCTTTTCAAT
* *
1128610 TTTTGATCGATTTCCTTTGGATTTTGGATCATGTCGTGAAATAAAAAAATTGTTTTATTCGAAAA
257 TTTTGATCGATTTCCTTTGGATTTTGGATCATGTCGTGAAAT-AGAAAATTGTTCTATTCGAAAA
*
1128675 ACGCTATCAATTGGTACCATTATTGCTTGTTAATTTGGTTTGTGTTGAAAGATCCCAAATTTTAA
321 ACGCTATCATTTGGTACCATTATTGCTTGTTAATTTGGTTTGTGTTGAAAGATCCCAAATTTTAA
* ** *
1128740 GGTTTGTGTTCATATTAGGGTTTATGGAATTGATAAAGAATTATGATGTTTTTGAGACTGTAAAA
386 GGTTTGTGTTCACATTAGGGTTTATGGAATTGATAAAG-ATT-TGATGTTTTTGAGGTTGTAGAA
* * * *
1128805 TCATATACAAGTATGATTGATGATTAAAATCACTTATACATGGCTATATAAGAACATGTTGAATT
449 TCATATACAAGCATGATTGATAATTAAAATCACTTGTACATGGCTACATAAGAACATGTTGAATT
* * * *
1128870 TGGCTAAACCATAGCTTTAGGGGAAAGAAGTGTTTTGATGAAATTTGATTAGGGATTTGATTCTA
514 CGGCCAAACCCTAGCTTTAGGGGAAAGAAGTGTTTTGATGAAATTTGATTAGGGCTTTGATTCTA
* * *
1128935 GATGTCTTGAAATGTTGAATCGAGATTGATTTCATGTTCGATCCTAGTGGAAA-TCTTAAACCCT
579 GAGGTCTTGAAATGTTGAATCGAGGTTGATTTCATGTTCGAACCTAGT-GAAACTCTTAAACCCT
* * * * * * *
1128999 ATATTACATCCCATTCGACCTTGAGGAAATAGGTTTTGGAAGAATTGTGGAAAAATTCCCATGGC
643 AAATTACATACCATTCAACCTTGAGGAAATAGG-TTGGGAAAAATTCTGGAAAAATTACCATGGC
**
1129064 TTAGAAATGATATTTGGAAGGTACTACAAGCCTTAGAAAATATTTTGGGTTATTTTGTAATTTTT
707 TTAGAAATGATATTTGGAAGGTACTACAAGCCTTAGAAAATATTTTGGGACATTTTGTAATTTTT
* *
1129129 CAAAAGTTGAGGGACCTA-TTCAATAATTTTG-AAAAGTTATAGGTTGAAT-ATGTAATTACTTA
772 CAAAAGTTGAGGGACCTATTTCAA-AATTTTGAAAAAGTTATAGGTTGAATGA-ATAATTACTCA
* * * * * *
1129191 ATAATTGTTGTACATTTCTATAAATTATTGTTTAAAGG-CTGAAATTGAAGTTAGAATGTGAAAG
835 ATAATTGATATACATTGCTAGAAATTACTATTT-AAGGACTGAAATTGAAGTTAGAATGTGAAAG
1129255 TTAGCCATTCTGGAAATTTGGCAAATTTTAAC
899 TTAGCCATTCTGGAAATTTGGCAAATTTTAAC
* * *
1129287 --TA--CG-AAATGG---CA-A---A--T-A-TTTG----T--AAAGATGATAAGGTTATGTGGC
1 AATATTGGAAAAGGGTAAAATATTTAGTTCATTTTGACTTTGGAAAGATGATAAGGTTATGTGGC
* *
1129330 TTGGTATTATTGTAAATATCAAGTTTCATTAATGGAAAAATG--GA----CATT---T--ATA--
66 TTGGTATTATTGTAAATATCAAGTTTCATTAATGGACAAATGACAATTCTCATTAAATGAATATT
*
1129382 --A-T-A--TATGCTTAAATAAAGGTTAAATTAACATGAAATTAAAGGAAATTTCATGAAGTTGG
131 TTATTCATTTATGCTTAAATAAAGGTTAAATTAACATGAAATTAAAGAAAATTTCATGAAGTTGG
* * **
1129441 GTAATTTTCAGCCACCAGTGTCGAAAACCTCCTCTTAAGGTAAGAAAAATTTTCTTTTCTCTTTT
196 GTAATTTTCAGCCACCAATGTC-AAGACCTCCTCTTAAGGTAAGAAAAATTTTCTTTTCAATTTT
* * *
1129506 CTTATCGATTTCCTTTGGATTTTGGATCATGTCGTGAAATAGAAAAGTGTTCTATTCGAAAAATG
260 -TGATCGATTTCCTTTGGATTTTGGATCATGTCGTGAAATAGAAAATTGTTCTATTCGAAAAACG
1129571 CTATCATTTGGTACCATTATTGCTT-TCTAATTTGGTTTGTGTTGAAAGATCCCAAATTTT-AGG
324 CTATCATTTGGTACCATTATTGCTTGT-TAATTTGGTTTGTGTTGAAAGATCCCAAATTTTAAGG
* * * *
1129634 ATTTTTGTTCACATTAAGGTTTATGGAATTGATTAAG----GA---TTCTGAGGTTGTAGAATCA
388 -TTTGTGTTCACATTAGGGTTTATGGAATTGATAAAGATTTGATGTTTTTGAGGTTGTAGAATCA
* * * *
1129692 TATAAAAGCATGATTGA-AATT----T---TTGTACATGGCTACATTAGCACATGTTGAATTCGA
452 TATACAAGCATGATTGATAATTAAAATCACTTGTACATGGCTACATAAGAACATGTTGAATTCGG
* * *
1129749 CCAAACCCTAGATTTAGGGGGAAAGAAGTGTTTGGATGAAATTTTATTAGGGCTTTGATTCTAGA
517 CCAAACCCTAGCTTTA-GGGGAAAGAAGTGTTTTGATGAAATTTGATTAGGGCTTTGATTCTAGA
* *
1129814 GGTCTTG-AACGTTGAATTGAGGTTGATTT
581 GGTCTTGAAATGTTGAATCGAGGTTGATTT
1129843 TGAAAGGAAA
Statistics
Matches: 1343, Mismatches: 131, Indels: 108
0.85 0.08 0.07
Matches are distributed among these distances:
876 61 0.05
877 51 0.04
879 1 0.00
883 3 0.00
884 30 0.02
887 2 0.00
892 41 0.03
893 183 0.14
894 38 0.03
895 1 0.00
896 1 0.00
897 1 0.00
901 3 0.00
903 1 0.00
906 4 0.00
910 1 0.00
913 61 0.05
915 1 0.00
919 4 0.00
921 1 0.00
922 1 0.00
924 1 0.00
927 1 0.00
928 1 0.00
931 5 0.00
932 1 0.00
934 2 0.00
937 1 0.00
938 1 0.00
939 1 0.00
942 1 0.00
943 1 0.00
946 2 0.00
947 80 0.06
948 638 0.48
949 117 0.09
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.37
Consensus pattern (930 bp):
AATATTGGAAAAGGGTAAAATATTTAGTTCATTTTGACTTTGGAAAGATGATAAGGTTATGTGGC
TTGGTATTATTGTAAATATCAAGTTTCATTAATGGACAAATGACAATTCTCATTAAATGAATATT
TTATTCATTTATGCTTAAATAAAGGTTAAATTAACATGAAATTAAAGAAAATTTCATGAAGTTGG
GTAATTTTCAGCCACCAATGTCAAGACCTCCTCTTAAGGTAAGAAAAATTTTCTTTTCAATTTTT
GATCGATTTCCTTTGGATTTTGGATCATGTCGTGAAATAGAAAATTGTTCTATTCGAAAAACGCT
ATCATTTGGTACCATTATTGCTTGTTAATTTGGTTTGTGTTGAAAGATCCCAAATTTTAAGGTTT
GTGTTCACATTAGGGTTTATGGAATTGATAAAGATTTGATGTTTTTGAGGTTGTAGAATCATATA
CAAGCATGATTGATAATTAAAATCACTTGTACATGGCTACATAAGAACATGTTGAATTCGGCCAA
ACCCTAGCTTTAGGGGAAAGAAGTGTTTTGATGAAATTTGATTAGGGCTTTGATTCTAGAGGTCT
TGAAATGTTGAATCGAGGTTGATTTCATGTTCGAACCTAGTGAAACTCTTAAACCCTAAATTACA
TACCATTCAACCTTGAGGAAATAGGTTGGGAAAAATTCTGGAAAAATTACCATGGCTTAGAAATG
ATATTTGGAAGGTACTACAAGCCTTAGAAAATATTTTGGGACATTTTGTAATTTTTCAAAAGTTG
AGGGACCTATTTCAAAATTTTGAAAAAGTTATAGGTTGAATGAATAATTACTCAATAATTGATAT
ACATTGCTAGAAATTACTATTTAAGGACTGAAATTGAAGTTAGAATGTGAAAGTTAGCCATTCTG
GAAATTTGGCAAATTTTAAC
Found at i:1134567 original size:84 final size:84
Alignment explanation
Indices: 1134424--1134590 Score: 262
Period size: 84 Copynumber: 2.0 Consensus size: 84
1134414 TGCACTTAGC
* *
1134424 CGAAAGACTTCTGTAGATTTACGAGTTTTGGATGCATGTTTATCGTTAAAGAAAGATGGTTCCAT
1 CGAAAGACTTCTGTAGATTTACGAGTTTTGGATGCACGTTTATCATTAAAGAAAGATGGTTCCAT
1134489 GATTGTTGAGATAAAGTTT
66 GATTGTTGAGATAAAGTTT
* * * * *
1134508 CGAAAGACTTTTGTAGATTTTCGTGTTTTGGATGCACGTTTATCATTAAAGAAATATGGTTCCTT
1 CGAAAGACTTCTGTAGATTTACGAGTTTTGGATGCACGTTTATCATTAAAGAAAGATGGTTCCAT
*
1134573 GATTGTTGAGCTAAAGTT
66 GATTGTTGAGATAAAGTT
1134591 AAAGCCGATG
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (84 bp):
CGAAAGACTTCTGTAGATTTACGAGTTTTGGATGCACGTTTATCATTAAAGAAAGATGGTTCCAT
GATTGTTGAGATAAAGTTT
Found at i:1140210 original size:46 final size:46
Alignment explanation
Indices: 1140143--1140236 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
1140133 AATGCTCACA
* *
1140143 AGGCTCGTCAGTAATATCTAACAGAGAATTAATGGTTTTGCACACT
1 AGGCTCATCAATAATATCTAACAGAGAATTAATGGTTTTGCACACT
* *
1140189 AGGCTCATCAATAATATCTAACAGAGCATTAATGGTTTTGCCCACT
1 AGGCTCATCAATAATATCTAACAGAGAATTAATGGTTTTGCACACT
1140235 AG
1 AG
1140237 TGGACCATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (46 bp):
AGGCTCATCAATAATATCTAACAGAGAATTAATGGTTTTGCACACT
Found at i:1141027 original size:30 final size:29
Alignment explanation
Indices: 1140993--1141066 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
1140983 AAAATTACCC
* * * *
1140993 TTTTGGTCATTAAATTTTTCAAACTTTATA
1 TTTTGGTCACTAAA-CTTTCAAAATTTACA
*
1141023 TTTTGGCCACTAAACTTTCAAAATTTACA
1 TTTTGGTCACTAAACTTTCAAAATTTACA
*
1141052 TTTTGGTTACTAAAC
1 TTTTGGTCACTAAAC
1141067 AAAATTTTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 25 0.68
30 12 0.32
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (29 bp):
TTTTGGTCACTAAACTTTCAAAATTTACA
Found at i:1146716 original size:22 final size:20
Alignment explanation
Indices: 1146691--1146733 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
1146681 AAAATATTGG
*
1146691 TTTGAAATGGAATTGATTGAAA
1 TTTGAAATGCAA-TGATT-AAA
*
1146713 TTTGATATGCAATGATTAAA
1 TTTGAAATGCAATGATTAAA
1146733 T
1 T
1146734 GGATAGTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 5 0.26
22 10 0.53
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (20 bp):
TTTGAAATGCAATGATTAAA
Found at i:1153802 original size:14 final size:14
Alignment explanation
Indices: 1153783--1153810 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1153773 AAGTTTAAAA
1153783 ATTTATTAATAAGT
1 ATTTATTAATAAGT
1153797 ATTTATTAATAAGT
1 ATTTATTAATAAGT
1153811 TACTCCCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATTTATTAATAAGT
Found at i:1158763 original size:14 final size:14
Alignment explanation
Indices: 1158744--1158770 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1158734 TTCCTTGTAT
1158744 GTGAATCATCTTGC
1 GTGAATCATCTTGC
1158758 GTGAATCATCTTG
1 GTGAATCATCTTG
1158771 TTGTAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (14 bp):
GTGAATCATCTTGC
Found at i:1160798 original size:50 final size:50
Alignment explanation
Indices: 1160734--1160852 Score: 154
Period size: 48 Copynumber: 2.4 Consensus size: 50
1160724 GAATACGATG
*
1160734 AGTGACACCTTTTATGCCAAAAATGA-ACCGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCAAAAAT-ACACCGTTATGCATTTAACTTTCATT
** *
1160784 AGTGGCACCTTTTATG--TGAAATACACCGTTATGCATTTAACTTTCGTT
1 AGTGGCACCTTTTATGCCAAAAATACACCGTTATGCATTTAACTTTCATT
* *
1160832 TGTGGTACCTTTTATGCCAAA
1 AGTGGCACCTTTTATGCCAAA
1160853 GTACACCTCT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
47 1 0.02
48 41 0.71
50 16 0.28
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (50 bp):
AGTGGCACCTTTTATGCCAAAAATACACCGTTATGCATTTAACTTTCATT
Found at i:1165562 original size:21 final size:21
Alignment explanation
Indices: 1165532--1165572 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1165522 GTGTAGAACC
*
1165532 AGGGTTAACTAAATCAAACAT
1 AGGGTCAACTAAATCAAACAT
1165553 AGGGTCAACTAAATCAAACA
1 AGGGTCAACTAAATCAAACA
1165573 CAGGTTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.20
Consensus pattern (21 bp):
AGGGTCAACTAAATCAAACAT
Found at i:1167643 original size:49 final size:48
Alignment explanation
Indices: 1167566--1167664 Score: 153
Period size: 49 Copynumber: 2.0 Consensus size: 48
1167556 ATGTTGTCGA
* *
1167566 AAATGCACCGTTATGCATTTCACCTTCATTAGTGGCACCTTTTATGCCG
1 AAATACACCGTTATGCATTTAACCTTCATTAGTGGCA-CTTTTATGCCG
* *
1167615 AAATACACCGTTATGCATTTAACTTTCATTTGTGGCACTTTTATGCCG
1 AAATACACCGTTATGCATTTAACCTTCATTAGTGGCACTTTTATGCCG
1167663 AA
1 AA
1167665 GTGCACCTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 13 0.28
49 33 0.72
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.36
Consensus pattern (48 bp):
AAATACACCGTTATGCATTTAACCTTCATTAGTGGCACTTTTATGCCG
Found at i:1168320 original size:21 final size:21
Alignment explanation
Indices: 1168293--1168348 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1168283 TCGATACCCA
1168293 CATCAGTATCGATACTAATTG
1 CATCAGTATCGATACTAATTG
*
1168314 TATCAGTATCGATACTAATTG
1 CATCAGTATCGATACTAATTG
1168335 CATCAGTATCGATA
1 CATCAGTATCGATA
1168349 TTGTTCTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (21 bp):
CATCAGTATCGATACTAATTG
Found at i:1171187 original size:40 final size:40
Alignment explanation
Indices: 1171143--1171223 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
1171133 TTGAAAAGTT
1171143 TTATAATAAGGCATCATGTCATGTATATTAAAATATGGTG
1 TTATAATAAGGCATCATGTCATGTATATTAAAATATGGTG
1171183 TTATAATAAGGCATCATGTCATGTATATTAAAATATGGTG
1 TTATAATAAGGCATCATGTCATGTATATTAAAATATGGTG
1171223 T
1 T
1171224 ACTCTTTCTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.38
Consensus pattern (40 bp):
TTATAATAAGGCATCATGTCATGTATATTAAAATATGGTG
Found at i:1172155 original size:17 final size:17
Alignment explanation
Indices: 1172130--1172163 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1172120 TTTTTATTAT
*
1172130 TATATAATATAAAATAA
1 TATAAAATATAAAATAA
1172147 TATAAAATATAAAATAA
1 TATAAAATATAAAATAA
1172164 AAACAAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TATAAAATATAAAATAA
Found at i:1172797 original size:22 final size:22
Alignment explanation
Indices: 1172769--1172811 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1172759 TATAAATATG
1172769 TTTTTTTAATTCTTAATTTAAA
1 TTTTTTTAATTCTTAATTTAAA
*
1172791 TTTTTTTAATTCTTATTTTAA
1 TTTTTTTAATTCTTAATTTAA
1172812 TGTTTGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTTTTAATTCTTAATTTAAA
Found at i:1172811 original size:12 final size:12
Alignment explanation
Indices: 1172772--1172812 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1172762 AAATATGTTT
1172772 TTTTAATTCTTA
1 TTTTAATTCTTA
* *
1172784 ATTTAAAT-TT-
1 TTTTAATTCTTA
1172794 TTTTAATTCTTA
1 TTTTAATTCTTA
1172806 TTTTAAT
1 TTTTAAT
1172813 GTTTGAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 6 0.26
11 4 0.17
12 13 0.57
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTAATTCTTA
Found at i:1180662 original size:22 final size:23
Alignment explanation
Indices: 1180624--1180670 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
1180614 AATCTTATAT
1180624 TAAATTATATTACAAA-TCATCAA
1 TAAATTATATTACAAATTCAT-AA
1180647 TAAA-TATATTGA-AAATTCATAA
1 TAAATTATATT-ACAAATTCATAA
1180669 TA
1 TA
1180671 TTTACAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (23 bp):
TAAATTATATTACAAATTCATAA
Found at i:1185506 original size:16 final size:16
Alignment explanation
Indices: 1185483--1185528 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
1185473 ATCAAGTTTG
1185483 ACCCAAACCGAAAGCA
1 ACCCAAACCGAAAGCA
* *
1185499 ACCTAAACTGAAAGCA
1 ACCCAAACCGAAAGCA
*
1185515 ACCCGAACCGAAAG
1 ACCCAAACCGAAAG
1185529 TAATTCGAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.48, C:0.33, G:0.15, T:0.04
Consensus pattern (16 bp):
ACCCAAACCGAAAGCA
Found at i:1185555 original size:17 final size:17
Alignment explanation
Indices: 1185518--1185558 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1185508 GAAAGCAACC
* *
1185518 CGAACCG-AAAGTAATT
1 CGAACCGAAAAATAACT
1185534 CGAACCGAAAAATAACT
1 CGAACCGAAAAATAACT
1185551 CGAACCGA
1 CGAACCGA
1185559 TAGCAACCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.46, C:0.24, G:0.17, T:0.12
Consensus pattern (17 bp):
CGAACCGAAAAATAACT
Found at i:1185576 original size:33 final size:33
Alignment explanation
Indices: 1185539--1185603 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
1185529 TAATTCGAAC
* *
1185539 CGAAAAATAACTCGAACCGATAGCAACCCAAAT
1 CGAAAAATAAATCGAACCAATAGCAACCCAAAT
1185572 CGAAAAATAAATCGAACCAATAGCAACCCAAA
1 CGAAAAATAAATCGAACCAATAGCAACCCAAA
1185604 CCAAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.52, C:0.26, G:0.11, T:0.11
Consensus pattern (33 bp):
CGAAAAATAAATCGAACCAATAGCAACCCAAAT
Found at i:1185676 original size:15 final size:16
Alignment explanation
Indices: 1185653--1185685 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
1185643 ATCTGAACCG
1185653 AAGCAATCCGAACCTA
1 AAGCAATCCGAACCTA
1185669 AAGC-ATCCGAACCTA
1 AAGCAATCCGAACCTA
1185684 AA
1 AA
1185686 ATCTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.45, C:0.30, G:0.12, T:0.12
Consensus pattern (16 bp):
AAGCAATCCGAACCTA
Found at i:1190322 original size:20 final size:20
Alignment explanation
Indices: 1190256--1190331 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1190246 AACAATGAAG
* *
1190256 GGATGGATCCCTTTTCAAAA
1 GGATCGATCCTTTTTCAAAA
** *
1190276 GGATAAATCCTTTTACAAAA
1 GGATCGATCCTTTTTCAAAA
*
1190296 GGGATCGATCCTTTTTCAAAT
1 -GGATCGATCCTTTTTCAAAA
*
1190317 GGATCGATCATTTTT
1 GGATCGATCCTTTTT
1190332 ATGTAAATTG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
20 30 0.65
21 16 0.35
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (20 bp):
GGATCGATCCTTTTTCAAAA
Found at i:1191490 original size:47 final size:47
Alignment explanation
Indices: 1191416--1191532 Score: 141
Period size: 47 Copynumber: 2.5 Consensus size: 47
1191406 GTACTCTTTT
* *
1191416 ATATCCAAAGGT-CACATTAAGATCAAATTG-CTAATCAATCT-ACCTTC
1 ATATCCAAAGGTCCA-ATTAAGAACAAATTGAC-AATCAAT-TGAACTTC
* *
1191463 ATATCCAAAAGTCCAATTAAGAACAAATTGACAATCAATTGAAGTTC
1 ATATCCAAAGGTCCAATTAAGAACAAATTGACAATCAATTGAACTTC
*
1191510 ATATCCAAAGGTCCCATTAAGAA
1 ATATCCAAAGGTCCAATTAAGAA
1191533 AAAAAAATTC
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
46 1 0.02
47 57 0.93
48 3 0.05
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (47 bp):
ATATCCAAAGGTCCAATTAAGAACAAATTGACAATCAATTGAACTTC
Found at i:1233026 original size:24 final size:24
Alignment explanation
Indices: 1232984--1233038 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
1232974 CATATATTTC
*
1232984 CAGGAGTACACAAATGTACTAACA
1 CAGGAGTACACAAAGGTACTAACA
* * *
1233008 CAGGAGTACCCAGAGGTACTAATA
1 CAGGAGTACACAAAGGTACTAACA
*
1233032 TAGGAGT
1 CAGGAGT
1233039 GCATGGATGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (24 bp):
CAGGAGTACACAAAGGTACTAACA
Found at i:1233052 original size:24 final size:24
Alignment explanation
Indices: 1233025--1233151 Score: 78
Period size: 24 Copynumber: 5.3 Consensus size: 24
1233015 ACCCAGAGGT
**
1233025 ACTAATATAGGAGTGCATGGATGC
1 ACTAATATAGGAGTGCATAAATGC
* * * *
1233049 ACTATTATAAGAGTGTATAAATGT
1 ACTAATATAGGAGTGCATAAATGC
* * *
1233073 ACTAATACAGGAGTGCATAAAAGA
1 ACTAATATAGGAGTGCATAAATGC
* ** *
1233097 ACTAAT-TCAGAAGTGCACGAATTC
1 ACTAATAT-AGGAGTGCATAAATGC
* * *
1233121 ACTAATA-ATGAGTGCAAAAAAGGC
1 ACTAATATAGGAGTGC-ATAAATGC
1233145 ACTAATA
1 ACTAATA
1233152 CTAGAGTACA
Statistics
Matches: 75, Mismatches: 25, Indels: 6
0.71 0.24 0.06
Matches are distributed among these distances:
23 6 0.08
24 69 0.92
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (24 bp):
ACTAATATAGGAGTGCATAAATGC
Found at i:1244113 original size:41 final size:41
Alignment explanation
Indices: 1244001--1244208 Score: 145
Period size: 41 Copynumber: 5.1 Consensus size: 41
1243991 CCTTGATTTA
* * * * * *
1244001 AATTGATTTGGATTGTGAATTAATACATGTTACCATTATCT
1 AATTGAATTGAATTATGAATTAATGCATGTTACCATGATCG
** * *
1244042 AATTGAATT-TTTCTATGAATAAATGAATGTTACCATGATCG
1 AATTGAATTGAAT-TATGAATTAATGCATGTTACCATGATCG
* ** *
1244083 AATTGAATTGAATTATGAATTATTGCATGTTGTCGTGATCG
1 AATTGAATTGAATTATGAATTAATGCATGTTACCATGATCG
* ** *
1244124 AA-TCAAGTTGAA-TAGTGAATTCCTGCATGCTT-CCATGATTG
1 AATTGAA-TTGAATTA-TGAATTAATGCATG-TTACCATGATCG
* * * * *
1244165 AATTGAATCGAATTGTGAATTATTGCATGCTACGATGATCG
1 AATTGAATTGAATTATGAATTAATGCATGTTACCATGATCG
1244206 AAT
1 AAT
1244209 CAAGTTGAAT
Statistics
Matches: 128, Mismatches: 31, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
40 7 0.05
41 114 0.89
42 7 0.05
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (41 bp):
AATTGAATTGAATTATGAATTAATGCATGTTACCATGATCG
Found at i:1244143 original size:82 final size:82
Alignment explanation
Indices: 1244057--1244265 Score: 229
Period size: 82 Copynumber: 2.6 Consensus size: 82
1244047 AATTTTTCTA
* * *
1244057 TGAATAAATGAATG-TTACCATGATCGAATTGAATTGAATTATGAATTATTGCATGTTGTCG-TG
1 TGAATAAATGAATGCTT-CCATGATCGAATTGAATCGAATTATGAATTATTGCATGCT-ACGATG
1244120 ATCGAATCAAGTTGAATAG
64 ATCGAATCAAGTTGAATAG
*** * * *
1244139 TGAATTCCTGCATGCTTCCATGATTGAATTGAATCGAATTGTGAATTATTGCATGCTACGATGAT
1 TGAATAAATGAATGCTTCCATGATCGAATTGAATCGAATTATGAATTATTGCATGCTACGATGAT
1244204 CGAATCAAGTTGAAT-G
66 CGAATCAAGTTGAATAG
* *
1244220 -G--TGAAT---TGCTTCCATGATCGAATTGAATCGAATTGTGAACTTATTG
1 TGAATAAATGAATGCTTCCATGATCGAATTGAATCGAATTATGAA-TTATTG
1244266 TGTTTCCATG
Statistics
Matches: 111, Mismatches: 13, Indels: 12
0.82 0.10 0.09
Matches are distributed among these distances:
75 32 0.29
76 6 0.05
78 2 0.02
80 1 0.01
81 3 0.03
82 65 0.59
83 2 0.02
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (82 bp):
TGAATAAATGAATGCTTCCATGATCGAATTGAATCGAATTATGAATTATTGCATGCTACGATGAT
CGAATCAAGTTGAATAG
Found at i:1244224 original size:41 final size:41
Alignment explanation
Indices: 1244076--1244226 Score: 146
Period size: 41 Copynumber: 3.7 Consensus size: 41
1244066 GAATGTTACC
* * *
1244076 ATGATCGAATTGAATTGAATTATGAATTATTGCATGTTGTCG
1 ATGATCGAATTCAATTGAATTGTGAATTATTGCATGCT-TCG
* ** *
1244118 -TGATCGAA-TCAAGTTGAATAGTGAATTCCTGCATGCTTCC
1 ATGATCGAATTCAA-TTGAATTGTGAATTATTGCATGCTTCG
* * * *
1244158 ATGATTGAATTGAATCGAATTGTGAATTATTGCATGCTACG
1 ATGATCGAATTCAATTGAATTGTGAATTATTGCATGCTTCG
*
1244199 ATGATCGAA-TCAAGTTGAATGGTGAATT
1 ATGATCGAATTCAA-TTGAATTGTGAATT
1244227 GCTTCCATGA
Statistics
Matches: 86, Mismatches: 19, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
40 8 0.09
41 75 0.87
42 3 0.03
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (41 bp):
ATGATCGAATTCAATTGAATTGTGAATTATTGCATGCTTCG
Found at i:1251142 original size:24 final size:24
Alignment explanation
Indices: 1251110--1251170 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
1251100 TTAATTGAGT
1251110 GTTAAATTAATTGAATTACATAGG
1 GTTAAATTAATTGAATTACATAGG
*
1251134 GTTAAATTAATTGAATTACATATG
1 GTTAAATTAATTGAATTACATAGG
* *
1251158 ATTAATTTAATTG
1 GTTAAATTAATTG
1251171 CCTAAGTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.43
Consensus pattern (24 bp):
GTTAAATTAATTGAATTACATAGG
Found at i:1252960 original size:82 final size:82
Alignment explanation
Indices: 1252856--1253078 Score: 266
Period size: 82 Copynumber: 2.7 Consensus size: 82
1252846 GAATTGGTTT
* * * * * ** *
1252856 GTGAATAAATGCATGTTACCATGATCGAATTGAATTAAATTATGAATTATTGCATGTTGCCCTAA
1 GTGAATTATTGCATGCTGCCATGATTGAATTGAATCGAATTGTGAATTATTGCATGTTGCCCTAA
*
1252921 TCGAATCAAGTTGAATG
66 TCGAAACAAGTTGAATG
* * * * * * *
1252938 GTTAATTCTTGCATGCTGCCATGATTGAATTGAATCGAATTGTGAATTGTTGCATGCTACCGTGA
1 GTGAATTATTGCATGCTGCCATGATTGAATTGAATCGAATTGTGAATTATTGCATGTTGCCCTAA
1253003 TCGAAACAAGTTGAATG
66 TCGAAACAAGTTGAATG
* * * *
1253020 GTGAATTATTACATGCTGCCACGATTGAATTGAATCGAATTGTGAATTAGTACATGTTG
1 GTGAATTATTGCATGCTGCCATGATTGAATTGAATCGAATTGTGAATTATTGCATGTTG
1253079 TCAAGATCGA
Statistics
Matches: 116, Mismatches: 25, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
82 116 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (82 bp):
GTGAATTATTGCATGCTGCCATGATTGAATTGAATCGAATTGTGAATTATTGCATGTTGCCCTAA
TCGAAACAAGTTGAATG
Found at i:1252991 original size:41 final size:41
Alignment explanation
Indices: 1252801--1253068 Score: 189
Period size: 41 Copynumber: 6.5 Consensus size: 41
1252791 CCTTGACTTA
* * * * * * * *
1252801 AATTTAATTGGATTGTGAATTAATACATGTTACCATGGTCT
1 AATTGAATTGAATTGTGAATTATTGCATGCTGCCATGATCG
** * * * *
1252842 AATTGAATTGGTTTGTGAATAAATGCATGTTACCATGATCG
1 AATTGAATTGAATTGTGAATTATTGCATGCTGCCATGATCG
* * * * *
1252883 AATTGAATTAAATTATGAATTATTGCATGTTGCCCTAATCG
1 AATTGAATTGAATTGTGAATTATTGCATGCTGCCATGATCG
* * * * *
1252924 AA-TCAAGTTGAATGGTTAATTCTTGCATGCTGCCATGATTG
1 AATTGAA-TTGAATTGTGAATTATTGCATGCTGCCATGATCG
* * * *
1252965 AATTGAATCGAATTGTGAATTGTTGCATGCTACCGTGATCG
1 AATTGAATTGAATTGTGAATTATTGCATGCTGCCATGATCG
** * * * *
1253006 AA-ACAAGTTGAATGGTGAATTATTACATGCTGCCACGATTG
1 AATTGAA-TTGAATTGTGAATTATTGCATGCTGCCATGATCG
*
1253047 AATTGAATCGAATTGTGAATTA
1 AATTGAATTGAATTGTGAATTA
1253069 GTACATGTTG
Statistics
Matches: 176, Mismatches: 47, Indels: 8
0.76 0.20 0.03
Matches are distributed among these distances:
40 5 0.03
41 166 0.94
42 5 0.03
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (41 bp):
AATTGAATTGAATTGTGAATTATTGCATGCTGCCATGATCG
Found at i:1259853 original size:20 final size:20
Alignment explanation
Indices: 1259776--1259846 Score: 142
Period size: 20 Copynumber: 3.5 Consensus size: 20
1259766 ATCCTATTCC
1259776 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
1259796 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
1259816 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
1259836 CTGGTAATCTT
1 CTGGTAATCTT
1259847 ACATTCCGTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCCCA
Found at i:1261344 original size:16 final size:18
Alignment explanation
Indices: 1261323--1261366 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
1261313 ATTTAAAATT
1261323 TTATAAAAAA-AAT-TAA
1 TTATAAAAAAGAATATAA
1261339 TTATAAATAAAGAATATAA
1 TTATAAA-AAAGAATATAA
*
1261358 TTTTAAAAA
1 TTATAAAAA
1261367 TAGATAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.29
17 3 0.12
18 5 0.21
19 9 0.38
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
TTATAAAAAAGAATATAA
Found at i:1261364 original size:19 final size:17
Alignment explanation
Indices: 1261319--1261366 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
1261309 AAATATTTAA
1261319 AATTTTATAAAAAAAATT
1 AATTTTA-AAAAAAAATT
* *
1261337 AATTATAAATAAAGAATAT
1 AATTTTAAA-AAAAAAT-T
1261356 AATTTTAAAAA
1 AATTTTAAAAA
1261367 TAGATAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 2 0.08
18 14 0.56
19 9 0.36
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AATTTTAAAAAAAAATT
Found at i:1261472 original size:15 final size:16
Alignment explanation
Indices: 1261443--1261476 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
1261433 TTTTACATGG
1261443 AAAAATAAAATATAAA
1 AAAAATAAAATATAAA
1261459 AAAAATAATAATAATAAA
1 AAAAATAA-AAT-ATAAA
1261477 TGTAGTTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATAAAATATAAA
Found at i:1261846 original size:13 final size:13
Alignment explanation
Indices: 1261830--1261857 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1261820 TTTAATTGCG
1261830 AAAATTAAAATTT
1 AAAATTAAAATTT
1261843 AAAATTAAAATTT
1 AAAATTAAAATTT
1261856 AA
1 AA
1261858 GCATTCCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:1261935 original size:6 final size:6
Alignment explanation
Indices: 1261926--1261960 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
1261916 AATTAAGGTT
1261926 AAATAA AAATAA AAATAAAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAAT--AA AAATAA AAATAA AAA
1261961 AGTACTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 21 0.78
8 6 0.22
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAATAA
Found at i:1261949 original size:14 final size:14
Alignment explanation
Indices: 1261930--1261975 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
1261920 AAGGTTAAAT
1261930 AAAAATAAAAATAA
1 AAAAATAAAAATAA
1261944 AAAAATAAAAATAA
1 AAAAATAAAAATAA
*
1261958 AAAAGTACTAAAATAA
1 AAAAATA--AAAATAA
1261974 AA
1 AA
1261976 CCTATTGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 20 0.69
16 9 0.31
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.15
Consensus pattern (14 bp):
AAAAATAAAAATAA
Found at i:1263174 original size:20 final size:19
Alignment explanation
Indices: 1263140--1263179 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1263130 ATATAATATA
*
1263140 ATATAATACTATAAATAAT
1 ATATAATAATATAAATAAT
1263159 ATATAATATATATAAATAAT
1 ATATAATA-ATATAAATAAT
1263179 A
1 A
1263180 CGTATGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATAATAATATAAATAAT
Found at i:1263470 original size:3 final size:3
Alignment explanation
Indices: 1263462--1263505 Score: 61
Period size: 3 Copynumber: 13.7 Consensus size: 3
1263452 TCTAGATTTC
1263462 TCT TCT TCT TCTT TCT TCT TCTT TCT TCT TCTT TCT TCT TCT TC
1 TCT TCT TCT TC-T TCT TCT TC-T TCT TCT TC-T TCT TCT TCT TC
1263506 CCCGTGAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 29 0.76
4 9 0.24
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1263478 original size:13 final size:13
Alignment explanation
Indices: 1263458--1263505 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
1263448 AGTTTCTAGA
1263458 TTTC-TCTTCTTC
1 TTTCTTCTTCTTC
1263470 -TTCTTTCTTCTTC
1 TTTC-TTCTTCTTC
1263483 TTTCTTCTTCTT-
1 TTTCTTCTTCTTC
1263495 TCTTCTTCTTC
1 T-TTCTTCTTC
1263506 CCCGTGAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 3 0.09
12 1 0.03
13 25 0.78
14 3 0.09
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCTTCTTCTTC
Found at i:1263479 original size:10 final size:10
Alignment explanation
Indices: 1263459--1263504 Score: 83
Period size: 10 Copynumber: 4.5 Consensus size: 10
1263449 GTTTCTAGAT
1263459 TTCTCTTCTTC
1 TTCT-TTCTTC
1263470 TTCTTTCTTC
1 TTCTTTCTTC
1263480 TTCTTTCTTC
1 TTCTTTCTTC
1263490 TTCTTTCTTC
1 TTCTTTCTTC
1263500 TTCTT
1 TTCTT
1263505 CCCCGTGAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 31 0.89
11 4 0.11
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TTCTTTCTTC
Found at i:1264566 original size:31 final size:30
Alignment explanation
Indices: 1264528--1264587 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 30
1264518 TTATATAAGC
1264528 TATGTGATAAAGTGATGGAACATGATATGTT
1 TATGTGATAAAGTGATGGAA-ATGATATGTT
*
1264559 TATGTGATAAAGTGATGGAAATTATATGT
1 TATGTGATAAAGTGATGGAAATGATATGT
1264588 CTATACAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 8 0.29
31 20 0.71
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
TATGTGATAAAGTGATGGAAATGATATGTT
Found at i:1264845 original size:23 final size:23
Alignment explanation
Indices: 1264819--1264869 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1264809 TAGCACTACA
*
1264819 GTGCAATTCTACGCGGCAGTTCG
1 GTGCAATTCTACGCGGCACTTCG
* *
1264842 GTGCAATTCTACGTGGTACTTCG
1 GTGCAATTCTACGCGGCACTTCG
1264865 GTGCA
1 GTGCA
1264870 TTTATATGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (23 bp):
GTGCAATTCTACGCGGCACTTCG
Found at i:1265590 original size:22 final size:22
Alignment explanation
Indices: 1265542--1265602 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
1265532 CAATAGCTAT
* *
1265542 ATATACTATATGTTTTCAAAACT
1 ATATA-TATATATTTTCAAAACC
1265565 ATATA-ATATATTTTCAAAAACC
1 ATATATATATATTTTC-AAAACC
1265587 ATATATTATATATTTT
1 ATATA-TATATATTTT
1265603 TTTGAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 9 0.27
22 10 0.30
23 5 0.15
24 9 0.27
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.46
Consensus pattern (22 bp):
ATATATATATATTTTCAAAACC
Found at i:1272430 original size:15 final size:15
Alignment explanation
Indices: 1272410--1272443 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1272400 GGTAGGTTAG
*
1272410 ATTTTTGGGAGTATC
1 ATTTTTGGGACTATC
1272425 ATTTTTGGGACTATC
1 ATTTTTGGGACTATC
1272440 ATTT
1 ATTT
1272444 CCCCATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.50
Consensus pattern (15 bp):
ATTTTTGGGACTATC
Found at i:1275180 original size:22 final size:22
Alignment explanation
Indices: 1275152--1275200 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1275142 AGAATTTTCA
1275152 GCTTCTAGCTTTCTCAGTCTTT
1 GCTTCTAGCTTTCTCAGTCTTT
1275174 GCTTCTAGCTTTCTCAGTCTTT
1 GCTTCTAGCTTTCTCAGTCTTT
1275196 GCTTC
1 GCTTC
1275201 AATTCCTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.08, C:0.29, G:0.14, T:0.49
Consensus pattern (22 bp):
GCTTCTAGCTTTCTCAGTCTTT
Found at i:1279780 original size:81 final size:81
Alignment explanation
Indices: 1279510--1279911 Score: 535
Period size: 81 Copynumber: 5.0 Consensus size: 81
1279500 AAATTTTTTA
* **
1279510 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACATAAATATGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
1279575 AGGTTAGATACCTTTG
66 AGGTTAAATACCTTTG
* * *
1279591 AGTAAAAGATTAATGGCCTAGATGTGCATTTGATAGAAAGATGTCAATTATG-CAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
1279655 AGGTTAGATACCTTTG
66 AGGTTAAATACCTTTG
* * *
1279671 AGTAAAAGATTAATGGCCTAGTTGTGCATTTGGA-AAAAATGTGTCAATTATGCCAGTTAGATGA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTT-GACAGAAAGGTGTCAATTATGCCAGTTAGATGA
*
1279735 AAGGTTAAATACCTTTC
65 AAGGTTAAATACCTTTG
* * *
1279752 AGTAAAAGATTAAAT-GTCTAGCTATGCATTTGACAGAAAGGTGTCAACTATGCCAGTTAGATGA
1 AGTAAAAGATT-AATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGA
1279816 AAGGTTAAATACCTTTG
65 AAGGTTAAATACCTTTG
** * ** *
1279833 AGTAAAAGATTAAAT-GTATAGTTGTGCATTTGGTAGAAAGGTG-CCATTCATGCCAGTTAGATG
1 AGTAAAAGATT-AATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATT-ATGCCAGTTAGATG
*
1279896 AAAGGTTAAATGCCTT
64 AAAGGTTAAATACCTT
1279912 CACGTGAATG
Statistics
Matches: 291, Mismatches: 25, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
80 78 0.27
81 210 0.72
82 3 0.01
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (81 bp):
AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:1279782 original size:161 final size:162
Alignment explanation
Indices: 1279510--1279911 Score: 562
Period size: 161 Copynumber: 2.5 Consensus size: 162
1279500 AAATTTTTTA
* * *
1279510 AGTAAAAGATTAATGGCCTAGCTGTGCATTT-GACATAAATATGTCAATTATGCCAGTTAGATGA
1 AGTAAAAGATTAATGGCCTAGTTGTGCATTTGGA-AAAAATGTGTCAATTATGCCAGTTAGATGA
* * * * *
1279574 AAGGTTAGATACCTTTGAGTAAAAGATTAATGGCCTAGATGTGCATTTGATAGAAAGATGTCAAT
65 AAGGTTAAATACCTTTCAGTAAAAGATTAATGGCCTAGATATGCATTTGACAGAAAGATGTCAAC
*
1279639 TATG-CAGTTAGATGAAAGGTTAGATACCTTTG
130 TATGCCAGTTAGATGAAAGGTTAAATACCTTTG
1279671 AGTAAAAGATTAATGGCCTAGTTGTGCATTTGGAAAAAATGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGTTGTGCATTTGGAAAAAATGTGTCAATTATGCCAGTTAGATGAA
* * *
1279736 AGGTTAAATACCTTTCAGTAAAAGATTAAAT-GTCTAGCTATGCATTTGACAGAAAGGTGTCAAC
66 AGGTTAAATACCTTTCAGTAAAAGATT-AATGGCCTAGATATGCATTTGACAGAAAGATGTCAAC
1279800 TATGCCAGTTAGATGAAAGGTTAAATACCTTTG
130 TATGCCAGTTAGATGAAAGGTTAAATACCTTTG
** * * * *
1279833 AGTAAAAGATTAAAT-GTATAGTTGTGCATTTGGTAGAAAGGTG-CCATTCATGCCAGTTAGATG
1 AGTAAAAGATT-AATGGCCTAGTTGTGCATTTGGAAAAAATGTGTCAATT-ATGCCAGTTAGATG
*
1279896 AAAGGTTAAATGCCTT
64 AAAGGTTAAATACCTT
1279912 CACGTGAATG
Statistics
Matches: 217, Mismatches: 19, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
161 119 0.55
162 95 0.44
163 3 0.01
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (162 bp):
AGTAAAAGATTAATGGCCTAGTTGTGCATTTGGAAAAAATGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTCAGTAAAAGATTAATGGCCTAGATATGCATTTGACAGAAAGATGTCAACT
ATGCCAGTTAGATGAAAGGTTAAATACCTTTG
Found at i:1279990 original size:45 final size:45
Alignment explanation
Indices: 1279925--1280194 Score: 371
Period size: 45 Copynumber: 6.0 Consensus size: 45
1279915 GTGAATGACT
* * * * * *
1279925 AAATGCTTAGCGGTGCATTAAAGACATGAAAGGATTCTATATATG
1 AAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATG
* * * *
1279970 AAATGCATAGA-GGTTCATTAAAGGCATGAAAGGGTGTCATAAATT
1 AAATGCATA-ACGGTGCATTAAAGGCATGAAAGGATGCCATAAATG
*
1280015 AAATGCATAACTGTGCATTAAAGGCATGAAAGGATGCCATAAATG
1 AAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATG
* * *
1280060 AAATGCATAACGGTGTATTAAAAGCATGAATGGATGCCATAAATG
1 AAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATG
*
1280105 AAATGCATAACGGTTCATTAAAGGCATGAAAGGATGCCATAAATG
1 AAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATG
* *
1280150 AAATGCATAACAGTGCATTAAAGGCATGAAATGATGCCATAAATG
1 AAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATG
1280195 GAAACAATGA
Statistics
Matches: 197, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
44 1 0.01
45 196 0.99
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.24
Consensus pattern (45 bp):
AAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATG
Found at i:1280239 original size:135 final size:133
Alignment explanation
Indices: 1279967--1280224 Score: 324
Period size: 135 Copynumber: 1.9 Consensus size: 133
1279957 GATTCTATAT
* * * *
1279967 ATGAAATGCATAGAGGTTCATTAAAGGCATGAAAGGGTGTCATAAATTAAATGCATAACTGTGCA
1 ATGAAATGCATAGAGGTTCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACAGTGCA
* * ** * *
1280032 TTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGTATTAAAAGCATGAATGGATGC
66 TTAAAGGCATGAAAGGATGCCATAAATGAAATGAATAA--GTGTACTAAAAAAATAAATGAATGC
*
1280097 CATAA
129 CAAAA
1280102 ATGAAATGCATA-ACGGTTCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACAGTGC
1 ATGAAATGCATAGA-GGTTCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACAGTGC
*
1280166 ATTAAAGGCATGAAATGATGCCATAAATGGAAACAATGAATAA-T-TACTAAAAAAATAAA
65 ATTAAAGGCATGAAAGGATGCCATAAAT-G--A-AATGAATAAGTGTACTAAAAAAATAAA
1280225 ATAATGGGAA
Statistics
Matches: 108, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
134 1 0.01
135 96 0.89
136 2 0.02
138 1 0.01
139 8 0.07
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (133 bp):
ATGAAATGCATAGAGGTTCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACAGTGCA
TTAAAGGCATGAAAGGATGCCATAAATGAAATGAATAAGTGTACTAAAAAAATAAATGAATGCCA
AAA
Found at i:1285574 original size:45 final size:45
Alignment explanation
Indices: 1285510--1285777 Score: 353
Period size: 45 Copynumber: 6.0 Consensus size: 45
1285500 TCATTGTTTC
* *
1285510 CATTTATGGCATCATTTCATGCCTTTAATGCACTGTTATGCATTT
1 CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTT
*
1285555 CATTTATGGCATCCTTTCATGCC-TTAATGAACCGTTATGCATTT
1 CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTT
* * *
1285599 CATTTATGGCATCCATTCATGCTTTTAATACACCGTTATGCATTT
1 CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTT
*
1285644 CATTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGCATTT
1 CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTT
* * * *
1285689 -AATTATGACACCCTTTCATGCCTTTAATGAACC-TCTATGCATTT
1 CATTTATGGCATCCTTTCATGCCTTTAATGCACCGT-TATGCATTT
* * * * * *
1285733 CATATATAGAATCCTTTCATGTCTTTAATGCACCGCTAAGCATTT
1 CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTT
1285778 AGTCATCACG
Statistics
Matches: 193, Mismatches: 26, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
43 1 0.01
44 77 0.40
45 115 0.60
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (45 bp):
CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTT
Found at i:1285611 original size:89 final size:89
Alignment explanation
Indices: 1285510--1285777 Score: 326
Period size: 89 Copynumber: 3.0 Consensus size: 89
1285500 TCATTGTTTC
1285510 CATTTATGGCATCATTTCATGCCTTTAATGCACTGTTATGCATTTCATTTATGGCATCCTTTCAT
1 CATTTATGGCATCATTTCATGCCTTTAATGCACTGTTATGCATTTCATTTATGGCATCCTTTCAT
*
1285575 GCCTTAATGAACCGTTATGCATTT
66 GCCTTAATGCACCGTTATGCATTT
* * *
1285599 CATTTATGGCATCCA-TTCATGCTTTTAATACACCGTTATGCATTTCATTTATGGCATCCTTTCA
1 CATTTATGGCAT-CATTTCATGCCTTTAATGCACTGTTATGCATTTCATTTATGGCATCCTTTCA
*
1285663 TGCCTTTAATGCACAGTTATGCATTT
65 TGCC-TTAATGCACCGTTATGCATTT
* * * * * * * * *
1285689 -AATTATGACACCCTTTCATGCCTTTAATGAACCT-CTATGCATTTCATATATAGAATCCTTTCA
1 CATTTATGGCATCATTTCATGCCTTTAATGCA-CTGTTATGCATTTCATTTATGGCATCCTTTCA
* * *
1285752 TGTCTTTAATGCACCGCTAAGCATTT
65 TG-CCTTAATGCACCGTTATGCATTT
1285778 AGTCATCACG
Statistics
Matches: 153, Mismatches: 21, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
88 1 0.01
89 129 0.84
90 23 0.15
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (89 bp):
CATTTATGGCATCATTTCATGCCTTTAATGCACTGTTATGCATTTCATTTATGGCATCCTTTCAT
GCCTTAATGCACCGTTATGCATTT
Found at i:1285716 original size:134 final size:134
Alignment explanation
Indices: 1285510--1285777 Score: 380
Period size: 134 Copynumber: 2.0 Consensus size: 134
1285500 TCATTGTTTC
* * * *
1285510 CATTTATGGCATCATTTCATGCCTTTAATGCACTGTTATGCATTTCATTTATGGCATCCTTTCAT
1 CATTTATGGCATCATTTCATGCCTTTAATGCACAGTTATGCATTTCAATTATGACACCCTTTCAT
* * * * *
1285575 GCCTTAATGAACCGT-TATGCATTTCATTTATGGCATCCATTCATG-CTTTTAATACACCGTTAT
66 GCCTTAATGAACC-TCTATGCATTTCATATATAGAATCCATTCATGTC-TTTAATACACCGCTAA
1285638 GCATTT
129 GCATTT
*
1285644 CATTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGCATTT-AATTATGACACCCTTTCAT
1 CATTTATGGCATCATTTCATGCCTTTAATGCACAGTTATGCATTTCAATTATGACACCCTTTCAT
* *
1285708 GCCTTTAATGAACCTCTATGCATTTCATATATAGAATCCTTTCATGTCTTTAATGCACCGCTAAG
66 GCC-TTAATGAACCTCTATGCATTTCATATATAGAATCCATTCATGTCTTTAATACACCGCTAAG
1285773 CATTT
130 CATTT
1285778 AGTCATCACG
Statistics
Matches: 119, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
133 20 0.17
134 98 0.82
135 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (134 bp):
CATTTATGGCATCATTTCATGCCTTTAATGCACAGTTATGCATTTCAATTATGACACCCTTTCAT
GCCTTAATGAACCTCTATGCATTTCATATATAGAATCCATTCATGTCTTTAATACACCGCTAAGC
ATTT
Found at i:1285887 original size:80 final size:80
Alignment explanation
Indices: 1285790--1286187 Score: 477
Period size: 80 Copynumber: 5.0 Consensus size: 80
1285780 TCATCACGTG
* * * *
1285790 AAGGCATTTAACCTTTCATCTAACTGGCATGAA-TGGCACCTTTCTACCAATGCACAACTA-TAC
1 AAGGTATTTAACCTTTCATCTAACTGGCAT-AATTGACACCTTTCTACAAATGCACAACTAGGAC
1285853 ATTTAATCTTTTACTCA
65 A-TTAATCTTTTACTCA
* * * *
1285870 AAGGTATTTAACCTTTCATCTAACTGGCATAGTTGACACCTTTCTGTCAAATGC-TAGCTA-GAC
1 AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCT-ACAAATGCACAACTAGGAC
*
1285933 ATTTAATCTTTTACTGA
65 A-TTAATCTTTTACTCA
* * * *
1285950 AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTTTTCCAAATGCACAACTAGGCC
1 AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACAC-CTTTCTACAAATGCACAACTAGGAC
1286015 ATTAATCTTTTACTCA
65 ATTAATCTTTTACTCA
* * * *
1286031 AAGGTATCTAACCTTTCATCTAACT-GCATAATTGACATCTTTCTATCAAATGCACATCTAGGCC
1 AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTA-CAAATGCACAACTAGGAC
1286095 ATTAATCTTTTACTC-
65 ATTAATCTTTTACTCA
* ** * * *
1286110 AAGGTATCTAACCTTTCATCTAACTGGCATAATTGACATATTATGT-CAAATGCACAGCTAGGCC
1 AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTT-TCTACAAATGCACAACTAGGAC
1286174 ATTAATCTTTTACT
65 ATTAATCTTTTACT
1286188 TAAAAAATTT
Statistics
Matches: 284, Mismatches: 26, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
79 61 0.21
80 166 0.58
81 54 0.19
82 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (80 bp):
AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTACAAATGCACAACTAGGACA
TTAATCTTTTACTCA
Done.