Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 5 of 24
Found at i:952517 original size:22 final size:22
Alignment explanation
Indices: 952486--952535 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
952476 AATAAGTTAT
*
952486 TTATTCATATAATATTTATTTTA
1 TTATTTATATAATA-TTATTTTA
*
952509 -TATTTATATTATATTATTTTA
1 TTATTTATATAATATTATTTTA
952530 TTATTT
1 TTATTT
952536 CATAGCTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATTTATATAATATTATTTTA
Found at i:961985 original size:13 final size:13
Alignment explanation
Indices: 961967--961992 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
961957 CTTATAAATG
961967 TTGATTCAAGTTT
1 TTGATTCAAGTTT
961980 TTGATTCAAGTTT
1 TTGATTCAAGTTT
961993 GATTTAGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
TTGATTCAAGTTT
Found at i:962263 original size:2 final size:2
Alignment explanation
Indices: 962256--962302 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
962246 GAAAAGTGTT
962256 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
962298 TA TA T
1 TA TA T
962303 CATGATGCAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:963452 original size:2 final size:2
Alignment explanation
Indices: 963445--963476 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
963435 AAAGATCCTT
963445 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
963477 ATGCAATCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:970982 original size:50 final size:50
Alignment explanation
Indices: 970917--971118 Score: 352
Period size: 50 Copynumber: 4.0 Consensus size: 50
970907 CCACTATAAG
* *
970917 ATGGGTCTTACTTACATGCTAGCATTTCATCATCTCTTCTAAGATAAAAGT
1 ATGGGCCTT-CTTACATGCTAGCATTTCATCATCTCTTCTAAGATAAAACT
970968 ATGGGCCTTCTTACATGCTAGCATTTCATCATCTCTTCTAAGATAAAACT
1 ATGGGCCTTCTTACATGCTAGCATTTCATCATCTCTTCTAAGATAAAACT
971018 ATGGGCCTTCTTACATGCTAGCATTTCATCATCTCTTCTAAGATAAAACT
1 ATGGGCCTTCTTACATGCTAGCATTTCATCATCTCTTCTAAGATAAAACT
*
971068 ATGGGCCTTCTTACATGTTAGCATTTCATCATCT-TCTCTAAGATAAAACT
1 ATGGGCCTTCTTACATGCTAGCATTTCATCATCTCT-TCTAAGATAAAACT
971118 A
1 A
971119 AGTGTCAATG
Statistics
Matches: 147, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
49 1 0.01
50 138 0.94
51 8 0.05
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (50 bp):
ATGGGCCTTCTTACATGCTAGCATTTCATCATCTCTTCTAAGATAAAACT
Found at i:978702 original size:2 final size:2
Alignment explanation
Indices: 978697--978732 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
978687 ATATAAGTAC
978697 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
978733 GAAAATGGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:979961 original size:2 final size:2
Alignment explanation
Indices: 979954--979990 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
979944 ATAATGAAAA
*
979954 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
979991 GAGAAACTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:981840 original size:14 final size:15
Alignment explanation
Indices: 981821--981849 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
981811 TAACATTTAA
981821 TAAATTT-AAAATTT
1 TAAATTTCAAAATTT
981835 TAAATTTCAAAATTT
1 TAAATTTCAAAATTT
981850 ATACCATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAATTTCAAAATTT
Found at i:985588 original size:12 final size:12
Alignment explanation
Indices: 985573--985599 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
985563 AATTTATTTA
985573 TAAAATTAAATT
1 TAAAATTAAATT
985585 TAAAATTAAATT
1 TAAAATTAAATT
985597 TAA
1 TAA
985600 TTTATTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATTAAATT
Found at i:987344 original size:22 final size:21
Alignment explanation
Indices: 987297--987348 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
987287 TCTTCCATCG
*
987297 ATTTTAATTAATTAATTATTA
1 ATTTTAATTAATTAAATATTA
987318 ATTTTATATTATATTAAATA-TA
1 ATTTTA-ATTA-ATTAAATATTA
*
987340 TTTTTAATT
1 ATTTTAATT
987349 TTCAATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 9 0.33
22 11 0.41
23 7 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTAATTAATTAAATATTA
Found at i:989680 original size:2 final size:2
Alignment explanation
Indices: 989667--989709 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
989657 GGATAGAGTG
*
989667 GA GA GA GC GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
989709 G
1 G
989710 TTAAGGCTTG
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:0.47, C:0.02, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:992788 original size:20 final size:20
Alignment explanation
Indices: 992765--992821 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
992755 ATTAATATTT
*
992765 ATAATTAATTTTAAATAAAA
1 ATAATTTATTTTAAATAAAA
* *
992785 ATAATTTATCTTAAATTAAA
1 ATAATTTATTTTAAATAAAA
992805 A-AATTTATATTTAAATA
1 ATAATTTAT-TTTAAATA
992822 TAATATAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 7 0.23
20 24 0.77
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAATTTATTTTAAATAAAA
Found at i:995117 original size:2 final size:2
Alignment explanation
Indices: 995110--995159 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
995100 AAATGCTTGG
995110 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
995152 AT AT AT AT
1 AT AT AT AT
995160 CCCAAAAGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:996168 original size:14 final size:14
Alignment explanation
Indices: 996129--996171 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
996119 AAAGTAATTA
996129 AGTTTTTATATTATT
1 AGTTTTTATATT-TT
** *
996144 AAATTTAATATTTT
1 AGTTTTTATATTTT
996158 AGTTTTTATATTTT
1 AGTTTTTATATTTT
996172 TAAAATTATA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (14 bp):
AGTTTTTATATTTT
Found at i:1006964 original size:2 final size:2
Alignment explanation
Indices: 1006957--1006983 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1006947 ATAGAAACTT
1006957 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1006984 GCAAAACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1007252 original size:25 final size:26
Alignment explanation
Indices: 1007210--1007265 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
1007200 TATTTTTAAA
1007210 ATTTATAAATATTATATT-TATATCAT
1 ATTTATAAATATTATATTATA-ATCAT
* * *
1007236 ATTTAT-ATTATTTTATTATAATTAT
1 ATTTATAAATATTATATTATAATCAT
1007261 ATTTA
1 ATTTA
1007266 ATGTATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
ATTTATAAATATTATATTATAATCAT
Found at i:1009624 original size:2 final size:2
Alignment explanation
Indices: 1009617--1009647 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1009607 TTCTTTTCTT
1009617 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 T
1009648 CTTTTACAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1013806 original size:2 final size:2
Alignment explanation
Indices: 1013801--1013828 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1013791 ATACACATAC
1013801 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
1013829 TAGTCAATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1016007 original size:19 final size:19
Alignment explanation
Indices: 1015983--1016040 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
1015973 TTGCATTGTA
1015983 AATAAATAATATTAAATAT
1 AATAAATAATATTAAATAT
*
1016002 AATAAATAA-A--AAGTA-
1 AATAAATAATATTAAATAT
*
1016017 AAGTACATAATATTAAATAT
1 AA-TAAATAATATTAAATAT
1016037 AATA
1 AATA
1016041 GTTTGTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
15 2 0.06
16 10 0.32
17 1 0.03
18 1 0.03
19 15 0.48
20 2 0.06
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (19 bp):
AATAAATAATATTAAATAT
Found at i:1022196 original size:20 final size:20
Alignment explanation
Indices: 1022171--1022220 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1022161 TTTTTTTTAC
* *
1022171 TTGAAGCAGTTTTGTAATTG
1 TTGAAGCAGTTCTGTAATTA
1022191 TTGAAGCAGTTCTGTAATTA
1 TTGAAGCAGTTCTGTAATTA
1022211 TTGAAGCAGT
1 TTGAAGCAGT
1022221 ACAATATATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (20 bp):
TTGAAGCAGTTCTGTAATTA
Found at i:1025222 original size:2 final size:2
Alignment explanation
Indices: 1025215--1025246 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1025205 AATAATAAGA
1025215 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
1025247 CCCTTAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1026728 original size:19 final size:20
Alignment explanation
Indices: 1026701--1026741 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1026691 AGTAAGATAA
1026701 TTTATATATT-TATATTATAT
1 TTTATATATTATA-ATTATAT
1026721 TTTA-ATATTATAATTATAT
1 TTTATATATTATAATTATAT
1026740 TT
1 TT
1026742 AAAATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTATATATTATAATTATAT
Found at i:1026773 original size:20 final size:20
Alignment explanation
Indices: 1026750--1026811 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
1026740 TTAAAATAAT
1026750 ATATATTTATATAAATTTTA
1 ATATATTTATATAAATTTTA
1026770 ATATA-TTA-AT-AA--TT-
1 ATATATTTATATAAATTTTA
1026784 -TAT-TTTATATAAATTTTA
1 ATATATTTATATAAATTTTA
1026802 ATATATTTAT
1 ATATATTTAT
1026812 TTATGATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
13 6 0.18
14 2 0.06
15 4 0.12
17 4 0.12
18 2 0.06
19 6 0.18
20 10 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATATTTATATAAATTTTA
Found at i:1026790 original size:21 final size:24
Alignment explanation
Indices: 1026764--1026813 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1026754 ATTTATATAA
1026764 ATTTTA-AT-ATATTAATA-ATTT
1 ATTTTATATAATATTAATATATTT
*
1026785 ATTTTATATAAATTTTAATATATTT
1 ATTTTATAT-AATATTAATATATTT
1026810 ATTT
1 ATTT
1026814 ATGATATACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 6 0.25
22 2 0.08
24 8 0.33
25 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTTTATATAATATTAATATATTT
Found at i:1026793 original size:32 final size:33
Alignment explanation
Indices: 1026744--1026808 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
1026734 TTATATTTAA
1026744 AATAATATATATTTATATAAATTTTAATATATT
1 AATAATATATATTTATATAAATTTTAATATATT
*
1026777 AATAATTTAT-TTTATATAAATTTTAATATATT
1 AATAATATATATTTATATAAATTTTAATATATT
1026809 TATTTATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 22 0.71
33 9 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
AATAATATATATTTATATAAATTTTAATATATT
Found at i:1026814 original size:24 final size:25
Alignment explanation
Indices: 1026775--1026848 Score: 71
Period size: 27 Copynumber: 2.9 Consensus size: 25
1026765 TTTTAATATA
1026775 TTAATA-ATTTATTT-TATATAAATT
1 TTAATATATTTATTTATATAT-AATT
*
1026799 TTAATATATTTATTTATGATATACTT
1 TTAATATATTTATTTAT-ATATAATT
* *
1026825 TTATTATTTTTTATATTATATATA
1 TTAATA-TATTTAT-TTATATATA
1026849 TATATAGATG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 6 0.14
25 8 0.19
26 9 0.21
27 15 0.36
28 4 0.10
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (25 bp):
TTAATATATTTATTTATATATAATT
Found at i:1034366 original size:18 final size:18
Alignment explanation
Indices: 1034343--1034410 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 18
1034333 AAAAATTAAA
1034343 ATATAATATAAATAAAAT
1 ATATAATATAAATAAAAT
*
1034361 ATATAATAGAAATTATTAATAT
1 ATATAATATAAA-TA--AA-AT
* * *
1034383 ATTAAAATTTATATAAAAT
1 A-TATAATATAAATAAAAT
1034402 ATATAATAT
1 ATATAATAT
1034411 TTAAAATAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
18 17 0.45
19 5 0.13
20 2 0.05
21 2 0.05
22 5 0.13
23 7 0.18
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (18 bp):
ATATAATATAAATAAAAT
Found at i:1034424 original size:27 final size:28
Alignment explanation
Indices: 1034343--1034436 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 28
1034333 AAAAATTAAA
* *
1034343 ATATAATATAAATAAAATATATAATAGAAAT
1 ATATAATAT-ATTAAAATA-ATTATA-AAAT
*
1034374 -TATTAATATATTAAAAT-TTATATAAAAT
1 ATA-TAATATATTAAAATAAT-TATAAAAT
*
1034402 ATATAATAT-TTAAAATAATTATAATAT
1 ATATAATATATTAAAATAATTATAAAAT
*
1034429 ATAAAATA
1 ATATAATA
1034437 ATACAATCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
27 21 0.40
28 12 0.23
29 5 0.09
30 9 0.17
31 6 0.11
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (28 bp):
ATATAATATATTAAAATAATTATAAAAT
Found at i:1034426 original size:18 final size:18
Alignment explanation
Indices: 1034392--1034438 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
1034382 TATTAAAATT
1034392 TATATAAAAT-A-TATAA
1 TATATAAAATAATTATAA
*
1034408 TATTTAAAATAATTATAA
1 TATATAAAATAATTATAA
1034426 TATATAAAATAAT
1 TATATAAAATAAT
1034439 ACAATCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 9 0.33
17 1 0.04
18 17 0.63
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TATATAAAATAATTATAA
Found at i:1035075 original size:19 final size:19
Alignment explanation
Indices: 1035034--1035081 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
1035024 AAAAACTTAT
*
1035034 TTTATAATTTAAATTAATT
1 TTTATAATTTAAATTAATA
*
1035053 TTTATTATTTAAA-TAATAA
1 TTTATAATTTAAATTAAT-A
1035072 TTTA-AATTTA
1 TTTATAATTTA
1035082 CTCAAGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTATAATTTAAATTAATA
Found at i:1040384 original size:6 final size:6
Alignment explanation
Indices: 1040373--1040409 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
1040363 TAATCTAATA
* *
1040373 AAATTT AAATTT AAATTT AAATCT AAATTT AATTTT A
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT A
1040410 TATGAATCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:1044449 original size:2 final size:2
Alignment explanation
Indices: 1044442--1044468 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1044432 TATTAATTAT
1044442 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1044469 TATATATACC
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1045547 original size:2 final size:2
Alignment explanation
Indices: 1045540--1045568 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1045530 TGGGAAAGAC
1045540 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 A
1045569 ATCCACATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1047226 original size:26 final size:24
Alignment explanation
Indices: 1047179--1047226 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
1047169 TATTATATGA
* *
1047179 ATTAAAAATAAATAACACAAATTC
1 ATTAAAAATAAATAAAAAAAATTC
1047203 ATTAAAAATCTAAATAAAAAAAAT
1 ATTAAAAA--TAAATAAAAAAAAT
1047227 GTTTTCAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
26 12 0.60
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (24 bp):
ATTAAAAATAAATAAAAAAAATTC
Found at i:1047760 original size:16 final size:16
Alignment explanation
Indices: 1047728--1047789 Score: 62
Period size: 14 Copynumber: 4.0 Consensus size: 16
1047718 CATGTTTAAA
1047728 ATATTTTTATATA--T
1 ATATTTTTATATATTT
1047742 ATATTTTTATATATTT
1 ATATTTTTATATATTT
1047758 ATATTATATTAT-T-TTT
1 ATATT-T-TTATATATTT
1047774 ATA-TTTTATTATATTT
1 ATATTTTTA-TATATTT
1047790 TAATTTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.07
14 15 0.37
15 2 0.05
16 15 0.37
17 2 0.05
18 4 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATATTTTTATATATTT
Found at i:1047791 original size:10 final size:10
Alignment explanation
Indices: 1047741--1047805 Score: 62
Period size: 10 Copynumber: 6.3 Consensus size: 10
1047731 TTTTTATATA
1047741 TATATTTT-T
1 TATATTTTAT
1047750 ATATATTTATAT
1 -TATATTT-TAT
*
1047762 TATATTATTTT
1 TATATT-TTAT
1047773 TATATTTTAT
1 TATATTTTAT
1047783 TATATTTTAAT
1 TATATTTT-AT
*
1047794 T-TTTTTTAT
1 TATATTTTAT
1047803 TAT
1 TAT
1047806 GTCAGACCCA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
9 3 0.06
10 24 0.51
11 18 0.38
12 2 0.04
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TATATTTTAT
Found at i:1047795 original size:16 final size:17
Alignment explanation
Indices: 1047739--1047796 Score: 68
Period size: 16 Copynumber: 3.5 Consensus size: 17
1047729 TATTTTTATA
1047739 TATATATTT-TTATATATT
1 TATAT-TTTATTATAT-TT
*
1047757 TATATTATATTAT-TTT
1 TATATTTTATTATATTT
1047773 TATATTTTATTATATTT
1 TATATTTTATTATATTT
1047790 TA-ATTTT
1 TATATTTT
1047797 TTTTATTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
16 19 0.53
17 8 0.22
18 9 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATATTTTATTATATTT
Found at i:1050563 original size:54 final size:50
Alignment explanation
Indices: 1050482--1050583 Score: 125
Period size: 54 Copynumber: 2.0 Consensus size: 50
1050472 ATTATAACCA
* *
1050482 TAACTAACAAAGTAGTAGTAGGAACATCTTTTAGGCTTTTCATTTTGCCACCT
1 TAACTAACAAAGTAGTAGGAGGAACATC--GTAGGCTTTT-ATTTTGCCACCT
*
1050535 TAACTAACCAAA-TGAGTAGGAGGAACATCGTAGGCTTTTATTTTTCCAC
1 TAACTAA-CAAAGT-AGTAGGAGGAACATCGTAGGCTTTTATTTTGCCAC
1050584 ACAAAGCTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
51 9 0.20
52 9 0.20
53 8 0.18
54 18 0.41
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (50 bp):
TAACTAACAAAGTAGTAGGAGGAACATCGTAGGCTTTTATTTTGCCACCT
Found at i:1050667 original size:8 final size:8
Alignment explanation
Indices: 1050650--1050678 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1050640 TTGCTTATAA
1050650 ATTT-AAT
1 ATTTAAAT
1050657 ATTTAAAT
1 ATTTAAAT
1050665 ATTTAAAT
1 ATTTAAAT
1050673 ATTTAA
1 ATTTAA
1050679 TTCAAAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 4 0.19
8 17 0.81
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
ATTTAAAT
Found at i:1052381 original size:49 final size:48
Alignment explanation
Indices: 1052327--1052433 Score: 139
Period size: 49 Copynumber: 2.2 Consensus size: 48
1052317 ATACAATATG
*
1052327 TTAAGAATTTCATATAT-AACTAT-TGAATTCAAACCCATACAACATCAAT
1 TTAAGAATTTCATAT-TGAACTATCT-AATTCAAA-ACATACAACATCAAT
*
1052376 TTAAGACTTTCATATTGAACTATCTAATTCAAAACATACAACATCAAT
1 TTAAGAATTTCATATTGAACTATCTAATTCAAAACATACAACATCAAT
*
1052424 TT-TGAATTTC
1 TTAAGAATTTC
1052434 TCACACCTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
47 6 0.12
48 17 0.33
49 28 0.54
50 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.36
Consensus pattern (48 bp):
TTAAGAATTTCATATTGAACTATCTAATTCAAAACATACAACATCAAT
Found at i:1056715 original size:28 final size:29
Alignment explanation
Indices: 1056666--1056741 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 29
1056656 CTTTTATATT
*
1056666 CAAATAAATT-TTTAATATTTTATTTGTAA
1 CAAAT-AATTCTTTAATATTTTAATTGTAA
* *
1056695 CAAATAATTCTTT-ATCTTTTAATTGTAT
1 CAAATAATTCTTTAATATTTTAATTGTAA
1056723 CTAAATAAGTTC-TTAATAT
1 C-AAATAA-TTCTTTAATAT
1056742 AAATTAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 17 0.44
29 16 0.41
30 6 0.15
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (29 bp):
CAAATAATTCTTTAATATTTTAATTGTAA
Found at i:1057708 original size:16 final size:18
Alignment explanation
Indices: 1057657--1057720 Score: 69
Period size: 17 Copynumber: 3.6 Consensus size: 18
1057647 AATAAATTTA
1057657 AAAAAAT-AAAATTAATT
1 AAAAAATAAAAATTAATT
** *
1057674 ATCAAAT-TAAATTAATT
1 AAAAAATAAAAATTAATT
1057691 AATAAAAATAAAAATTAATT
1 -A-AAAAATAAAAATTAATT
1057711 AAAAAATAAA
1 AAAAAATAAA
1057721 TTATTTATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 14 0.37
18 10 0.26
19 5 0.13
20 9 0.24
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAAATAAAAATTAATT
Found at i:1057715 original size:17 final size:17
Alignment explanation
Indices: 1057658--1057720 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 17
1057648 ATAAATTTAA
1057658 AAAAAT-AAAATTAATT
1 AAAAATAAAAATTAATT
*
1057674 ATCAAATTAAATTAATTAA-T
1 A--AAAATAAA--AATTAATT
1057694 AAAAATAAAAATTAATT
1 AAAAATAAAAATTAATT
1057711 AAAAAATAAA
1 -AAAAATAAA
1057721 TTATTTATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
16 7 0.18
17 1 0.03
18 20 0.53
19 2 0.05
20 2 0.05
21 6 0.16
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAATAAAAATTAATT
Found at i:1057721 original size:36 final size:35
Alignment explanation
Indices: 1057654--1057723 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 35
1057644 TTGAATAAAT
* *
1057654 TTAAAAAAATAAAATTAATTATCAAATTAAATTAA
1 TTAAAAAAATAAAATTAATTATAAAAATAAATTAA
1057689 TTAATAAAAATAAAAATTAATTA-AAAAATAAATTA
1 TTAA-AAAAAT-AAAATTAATTATAAAAATAAATTA
1057724 TTTATATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 4 0.13
36 16 0.52
37 11 0.35
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (35 bp):
TTAAAAAAATAAAATTAATTATAAAAATAAATTAA
Found at i:1057874 original size:5 final size:5
Alignment explanation
Indices: 1057851--1057929 Score: 51
Period size: 5 Copynumber: 16.2 Consensus size: 5
1057841 CTGTTAGTTG
* * *
1057851 AATT- AATTAA AAATA AATTA AATT- AA-TA AATTA ATTTAA AATTA AATAA
1 AATTA AATT-A AATTA AATTA AATTA AATTA AATTA AATT-A AATTA AATTA
* *
1057900 TAATT- AATTA AATTT AATT- GATTA AATTA A
1 -AATTA AATTA AATTA AATTA AATTA AATTA A
1057930 TTGAAATTGA
Statistics
Matches: 58, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
3 1 0.02
4 15 0.26
5 32 0.55
6 10 0.17
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (5 bp):
AATTA
Found at i:1057923 original size:14 final size:13
Alignment explanation
Indices: 1057900--1057933 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1057890 AATTAAATAA
*
1057900 TAATTAATTAAATT
1 TAATTGATTAAA-T
1057914 TAATTGATTAAAT
1 TAATTGATTAAAT
1057927 TAATTGA
1 TAATTGA
1057934 AATTGATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (13 bp):
TAATTGATTAAAT
Found at i:1068822 original size:22 final size:22
Alignment explanation
Indices: 1068779--1068822 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1068769 ATTGATAAAA
* *
1068779 AATTAATTTAATTAATTTATAT
1 AATTAATTTAATTAAATAATAT
1068801 AATT-ATTTATATTAAATAATAT
1 AATTAATTTA-ATTAAATAATAT
1068823 TTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTAATTTAATTAAATAATAT
Found at i:1072097 original size:18 final size:18
Alignment explanation
Indices: 1072062--1072100 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1072052 TTTATATCCA
* **
1072062 ATATTTATATATTTATAT
1 ATATTTAAATATAAATAT
1072080 ATATTTAAATATAAATAT
1 ATATTTAAATATAAATAT
1072098 ATA
1 ATA
1072101 ATTTTTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTTAAATATAAATAT
Found at i:1077861 original size:21 final size:23
Alignment explanation
Indices: 1077832--1077876 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
1077822 ATTTTCAATA
* *
1077832 ATAATATTT-TTTCATT-TAAAT
1 ATAAAATTTATTTAATTATAAAT
1077853 ATAAAATTTATTTAATTATAAAT
1 ATAAAATTTATTTAATTATAAAT
1077876 A
1 A
1077877 ACTAAATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 6 0.30
23 6 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
ATAAAATTTATTTAATTATAAAT
Found at i:1078375 original size:39 final size:39
Alignment explanation
Indices: 1078332--1078425 Score: 90
Period size: 38 Copynumber: 2.4 Consensus size: 39
1078322 ATTATAAGTT
1078332 TATTTATTATTTATTTAAT-AATTAAATT-TTAATTTTTTA
1 TATTTATTATTTATTTAATAAATT-AATTATT-ATTTTTTA
* * *
1078371 TATTTA-AATTTATGT-ATAAATTTATTAATTATTTTTTA
1 TATTTATTATTTATTTAATAAATTAATT-ATTATTTTTTA
1078409 TATTT-TTAATTTATTTA
1 TATTTATT-ATTTATTTA
1078426 TAGCTTTTAG
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
37 5 0.11
38 24 0.55
39 15 0.34
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (39 bp):
TATTTATTATTTATTTAATAAATTAATTATTATTTTTTA
Found at i:1078722 original size:3 final size:3
Alignment explanation
Indices: 1078714--1078738 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1078704 TTTTTATCAT
1078714 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1078739 ATTAATTAAA
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:1079062 original size:2 final size:2
Alignment explanation
Indices: 1079055--1079084 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1079045 CAATTTTTCC
1079055 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
1079085 TAATTTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1079694 original size:15 final size:15
Alignment explanation
Indices: 1079653--1079701 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 15
1079643 AATGAAGAAA
1079653 TATTTTAATA-TTAT
1 TATTTTAATATTTAT
* * *
1079667 TACTATAAAATTTAT
1 TATTTTAATATTTAT
1079682 TATTTTAATATTT-T
1 TATTTTAATATTTAT
1079696 TATTTT
1 TATTTT
1079702 TTAAAATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 14 0.50
15 14 0.50
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTTTAATATTTAT
Found at i:1079773 original size:19 final size:20
Alignment explanation
Indices: 1079738--1079775 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1079728 TAATTATAAT
1079738 TAAAATTATTTAAATGTCAA
1 TAAAATTATTTAAATGTCAA
*
1079758 TAAAATT-TTTATATGTCA
1 TAAAATTATTTAAATGTCA
1079776 TTTAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
TAAAATTATTTAAATGTCAA
Found at i:1079917 original size:25 final size:25
Alignment explanation
Indices: 1079889--1079936 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1079879 AAAATTTAAA
1079889 AAAATATATTA-ATAATATAAAAATT
1 AAAAT-TATTATATAATATAAAAATT
*
1079914 AAAATTTTTATATAATATAAAAA
1 AAAATTATTATATAATATAAAAA
1079937 CTCCTAAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
AAAATTATTATATAATATAAAAATT
Found at i:1082203 original size:13 final size:13
Alignment explanation
Indices: 1082185--1082209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1082175 TATTTATATT
1082185 TAAATATAAAATA
1 TAAATATAAAATA
1082198 TAAATATAAAAT
1 TAAATATAAAAT
1082210 TAATATTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAATATAAAATA
Found at i:1082800 original size:17 final size:17
Alignment explanation
Indices: 1082780--1082854 Score: 62
Period size: 17 Copynumber: 4.2 Consensus size: 17
1082770 TATTTATAAA
* *
1082780 AAATAATAATTTTAATT
1 AAATAATAAATTAAATT
*
1082797 AAATTATAAATTAAATT
1 AAATAATAAATTAAATT
1082814 AAATTAATATAATTAATATT
1 AAA-TAATA-AATTAA-ATT
* *
1082834 -AATATTATATTTAAATT
1 AAATAATA-AATTAAATT
1082851 AAAT
1 AAAT
1082855 CTAAACGTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
17 20 0.42
18 17 0.35
19 8 0.17
20 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATAATAAATTAAATT
Found at i:1082836 original size:15 final size:14
Alignment explanation
Indices: 1082810--1082852 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 14
1082800 TTATAAATTA
1082810 AATTAAATTAATAT
1 AATTAAATTAATAT
1082824 AATTAATATTAATATT
1 AATTAA-ATTAATA-T
1082840 ATATTTAAATTAA
1 A-A-TTAAATTAA
1082853 ATCTAAACGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.24
15 7 0.28
16 2 0.08
17 6 0.24
18 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATTAAATTAATAT
Found at i:1083258 original size:15 final size:15
Alignment explanation
Indices: 1083238--1083266 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1083228 ATTACACATA
1083238 TATTTTATTTTAATT
1 TATTTTATTTTAATT
1083253 TATTTTATTTTAAT
1 TATTTTATTTTAAT
1083267 AATAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TATTTTATTTTAATT
Found at i:1083360 original size:20 final size:17
Alignment explanation
Indices: 1083321--1083355 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1083311 ATTTATATAT
1083321 TTTTATAATTAAAATAA
1 TTTTATAATTAAAATAA
1083338 TTTTATTAATT-AAATAA
1 TTTTA-TAATTAAAATAA
1083355 T
1 T
1083356 AATTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTATAATTAAAATAA
Found at i:1088294 original size:12 final size:12
Alignment explanation
Indices: 1088277--1088301 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1088267 TTTAAATGCT
1088277 AAAAAAAAGAAA
1 AAAAAAAAGAAA
1088289 AAAAAAAAGAAA
1 AAAAAAAAGAAA
1088301 A
1 A
1088302 GGAATTCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:1094895 original size:2 final size:2
Alignment explanation
Indices: 1094890--1094914 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1094880 GAAAAAAAAA
1094890 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1094915 AAGAATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1095293 original size:19 final size:19
Alignment explanation
Indices: 1095269--1095306 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1095259 TACATCAACC
*
1095269 AATTTT-TTTATTATAATTT
1 AATTTTATTT-TTAAAATTT
1095288 AATTTTATTTTTAAAATTT
1 AATTTTATTTTTAAAATTT
1095307 TAAATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
AATTTTATTTTTAAAATTT
Found at i:1095375 original size:35 final size:34
Alignment explanation
Indices: 1095275--1095377 Score: 84
Period size: 35 Copynumber: 2.9 Consensus size: 34
1095265 AACCAATTTT
* * * *
1095275 TTTATTATAATTTAATTTTATTTTTAAAATTTTAAA
1 TTTATAATAA-TTATTTTTA-TATTAATATTTTAAA
**
1095311 TTTA-AATAAAATTATTTTTA-AAAATATATTTTACAA
1 TTTATAAT--AATTATTTTTATATTA-ATATTTTA-AA
1095347 TTTATAATAATTATTTTTATATTAATATTTT
1 TTTATAATAATTATTTTTATATTAATATTTT
1095378 TATATTTTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
34 1 0.02
35 27 0.51
36 20 0.38
37 5 0.09
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (34 bp):
TTTATAATAATTATTTTTATATTAATATTTTAAA
Found at i:1095377 original size:14 final size:15
Alignment explanation
Indices: 1095347--1095383 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
1095337 TATTTTACAA
*
1095347 TTTATAATAATTATT
1 TTTATATTAATTATT
1095362 TTTATATTAA-TATT
1 TTTATATTAATTATT
1095376 TTTATATT
1 TTTATATT
1095384 TTTATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTATATTAATTATT
Found at i:1095427 original size:23 final size:22
Alignment explanation
Indices: 1095399--1095451 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
1095389 AATTAAACTT
**
1095399 AAATAAAATATTTTTAATTATTA
1 AAATAAAAT-TTAATAATTATTA
*
1095422 AAATAATAATTTAATATTTATTA
1 AAATAA-AATTTAATAATTATTA
1095445 AAATAAA
1 AAATAAA
1095452 TCAACTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 22 0.85
24 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATAAAATTTAATAATTATTA
Found at i:1095469 original size:24 final size:24
Alignment explanation
Indices: 1095416--1095473 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
1095406 ATATTTTTAA
*
1095416 TTATTAAAAT-AATAATTTAATAT
1 TTATTAAAATAAATAACTTAATAT
1095439 TTATTAAAATAAATCAACTTAA-AT
1 TTATTAAAATAAAT-AACTTAATAT
*
1095463 TTTTTAAAATA
1 TTATTAAAATA
1095474 TTATTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 10 0.32
24 15 0.48
25 6 0.19
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (24 bp):
TTATTAAAATAAATAACTTAATAT
Found at i:1096516 original size:28 final size:27
Alignment explanation
Indices: 1096484--1096541 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
1096474 CTAATTAATT
* *
1096484 TAATTTATTATTTATTTAATAAAAA-ATA
1 TAATTTA-AATTTAATT-ATAAAAATATA
1096512 TAATTTAAATTTAATTATAAAAATATA
1 TAATTTAAATTTAATTATAAAAATATA
1096539 TAA
1 TAA
1096542 AAATAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 7 0.26
27 13 0.48
28 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TAATTTAAATTTAATTATAAAAATATA
Found at i:1097107 original size:16 final size:16
Alignment explanation
Indices: 1097082--1097128 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
1097072 GATTTAATTA
*
1097082 TAAA-TTAAATTGAAT
1 TAAATTTAAATTAAAT
*
1097097 TGAATTTAAATTAAAT
1 TAAATTTAAATTAAAT
*
1097113 TAAATTTAAATAAAAT
1 TAAATTTAAATTAAAT
1097129 ATTAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 3 0.11
16 24 0.89
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (16 bp):
TAAATTTAAATTAAAT
Found at i:1097108 original size:21 final size:22
Alignment explanation
Indices: 1097077--1097118 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1097067 TGTTAGATTT
*
1097077 AATTATAAATTAAATTGAATTG
1 AATTATAAATTAAATTAAATTG
1097099 AATT-TAAATTAAATTAAATT
1 AATTATAAATTAAATTAAATT
1097119 TAAATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
AATTATAAATTAAATTAAATTG
Found at i:1097121 original size:11 final size:11
Alignment explanation
Indices: 1097073--1097160 Score: 56
Period size: 11 Copynumber: 8.1 Consensus size: 11
1097063 ATTATGTTAG
1097073 ATTT-AATTATA
1 ATTTAAATTA-A
* *
1097084 AATTAAATTGA
1 ATTTAAATTAA
* *
1097095 ATTGAATTTAA
1 ATTTAAATTAA
1097106 A-TTAAATTAA
1 ATTTAAATTAA
*
1097116 ATTTAAATAAA
1 ATTTAAATTAA
1097127 ATATT-AATTAA
1 AT-TTAAATTAA
* * *
1097138 TTTTATATTTA
1 ATTTAAATTAA
*
1097149 ATTTAATTTAA
1 ATTTAAATTAA
1097160 A
1 A
1097161 ATATCAATAA
Statistics
Matches: 56, Mismatches: 17, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
10 10 0.18
11 40 0.71
12 6 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (11 bp):
ATTTAAATTAA
Found at i:1097128 original size:21 final size:21
Alignment explanation
Indices: 1097073--1097160 Score: 68
Period size: 22 Copynumber: 4.0 Consensus size: 21
1097063 ATTATGTTAG
*
1097073 ATTTAATTATAAATTAAATTGA
1 ATTTAATTA-AAATTAAATTAA
* *
1097095 ATTGAATTTAAATTAAATTAA
1 ATTTAATTAAAATTAAATTAA
* *
1097116 ATTTAAATAAAATATTAATTAA
1 ATTTAATTAAAAT-TAAATTAA
* * * *
1097138 TTTTATATTTAATTTAATTTAA
1 ATTTA-ATTAAAATTAAATTAA
1097160 A
1 A
1097161 ATATCAATAA
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
21 21 0.42
22 24 0.48
23 5 0.10
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATTTAATTAAAATTAAATTAA
Found at i:1097264 original size:17 final size:17
Alignment explanation
Indices: 1097228--1097266 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1097218 TATAAAATAT
*
1097228 TTTTTAGAAAAAATTGA
1 TTTTTAGAAAAAATTAA
1097245 TTTTTA-AAAAAATTAAA
1 TTTTTAGAAAAAATT-AA
1097262 TTTTT
1 TTTTT
1097267 TTAATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (17 bp):
TTTTTAGAAAAAATTAA
Found at i:1098446 original size:19 final size:20
Alignment explanation
Indices: 1098424--1098471 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1098414 TTTATTATAT
1098424 TATTAAAATAT-TATTTTTA
1 TATTAAAATATATATTTTTA
*
1098443 TATTAATATTATATATTTTTA
1 TATTAA-AATATATATTTTTA
1098464 TAATTAAA
1 T-ATTAAA
1098472 TTTATTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 6 0.24
20 4 0.16
21 10 0.40
22 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTAAAATATATATTTTTA
Found at i:1098446 original size:22 final size:22
Alignment explanation
Indices: 1098409--1098500 Score: 73
Period size: 23 Copynumber: 4.1 Consensus size: 22
1098399 AAACTTTTTT
1098409 TATTATTTATTATATTATTAAAA
1 TATTATTT-TTATATTATTAAAA
* **
1098432 TATTATTTTTATATTAATATTA
1 TATTATTTTTATATTATTAAAA
*
1098454 TA-TATTTTTATA--ATTAAATT
1 TATTATTTTTATATTATTAAA-A
*
1098474 TATTTAATTTTTTTATTATTAATAA
1 TA-TT-ATTTTTATATTATTAA-AA
1098499 TA
1 TA
1098501 ATTCATATCG
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
19 3 0.06
20 2 0.04
21 10 0.19
22 14 0.26
23 16 0.30
25 7 0.13
26 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTATTTTTATATTATTAAAA
Found at i:1098477 original size:25 final size:22
Alignment explanation
Indices: 1098435--1098495 Score: 54
Period size: 25 Copynumber: 2.6 Consensus size: 22
1098425 ATTAAAATAT
1098435 TATTTTTATATT-AATA-TTATA
1 TATTTTTATATTAAATATTTA-A
1098456 TATTTTTATAATTAAATTTATTTAA
1 TATTTTTAT-ATTAAA--TATTTAA
*
1098481 TTTTTTTATTATTAA
1 TATTTTTA-TATTAA
1098496 TAATAATTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 9 0.27
22 3 0.09
23 2 0.06
25 15 0.45
26 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTTATATTAAATATTTAA
Found at i:1101858 original size:14 final size:13
Alignment explanation
Indices: 1101825--1101974 Score: 126
Period size: 13 Copynumber: 11.4 Consensus size: 13
1101815 ATTATTGTCA
1101825 AAGTACCTGTGCC
1 AAGTACCTGTGCC
*
1101838 AAGTACCTGTACC
1 AAGTACCTGTGCC
1101851 AGAGTACCTGTGCC
1 A-AGTACCTGTGCC
*
1101865 AAGTACCTGTGCT
1 AAGTACCTGTGCC
*
1101878 AAGTACCTATGCC
1 AAGTACCTGTGCC
*
1101891 AAAGTACCT-TGTC
1 -AAGTACCTGTGCC
*
1101904 AAGTACTTGTGCC
1 AAGTACCTGTGCC
* * * *
1101917 -TGTGCCAAGTACCCC
1 AAGTACC-TGT--GCC
1101932 AAGTACCTGTGCC
1 AAGTACCTGTGCC
* *
1101945 AAATACCTATGCC
1 AAGTACCTGTGCC
*
1101958 AAGTATCT-TGCC
1 AAGTACCTGTGCC
1101970 AAGTA
1 AAGTA
1101975 ACCATTCAAA
Statistics
Matches: 109, Mismatches: 21, Indels: 15
0.75 0.14 0.10
Matches are distributed among these distances:
12 19 0.17
13 62 0.57
14 20 0.18
15 4 0.04
16 4 0.04
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (13 bp):
AAGTACCTGTGCC
Found at i:1101882 original size:40 final size:39
Alignment explanation
Indices: 1101825--1101962 Score: 125
Period size: 40 Copynumber: 3.5 Consensus size: 39
1101815 ATTATTGTCA
* *
1101825 AAGTACCTGTGCCAAGTACCTGTACCAGAGTACCTGTGCC
1 AAGTACCTGTGCCAAGTACCTATACCAAAGTACCT-TGCC
* * *
1101865 AAGTACCTGTGCTAAGTACCTATGCCAAAGTACCTTGTC
1 AAGTACCTGTGCCAAGTACCTATACCAAAGTACCTTGCC
* * * * *
1101904 AAGTACTTGTGCC-TGTGCCAAGTACCCCAAGTACCTGTGCC
1 AAGTACCTGTGCCAAGTACCTA-TA-CCAAAGTACCT-TGCC
* *
1101945 AAATACCTATGCCAAGTA
1 AAGTACCTGTGCCAAGTA
1101963 TCTTGCCAAG
Statistics
Matches: 76, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
38 5 0.07
39 15 0.20
40 41 0.54
41 13 0.17
42 2 0.03
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (39 bp):
AAGTACCTGTGCCAAGTACCTATACCAAAGTACCTTGCC
Found at i:1104225 original size:13 final size:13
Alignment explanation
Indices: 1104154--1104240 Score: 68
Period size: 13 Copynumber: 6.6 Consensus size: 13
1104144 ATTATTGCCA
*
1104154 AAGTACCTGTACT
1 AAGTACCTGTGCT
**
1104167 AAAGTACCT-TATT
1 -AAGTACCTGTGCT
*
1104180 AAGTACATGTGCT
1 AAGTACCTGTGCT
* * *
1104193 AAGCAACTGTGTCA
1 AAGTACCTGTG-CT
1104207 AAGTACCTGTGCT
1 AAGTACCTGTGCT
* *
1104220 AAGTACTTATGCT
1 AAGTACCTGTGCT
1104233 AAGTACCT
1 AAGTACCT
1104241 ATGTCAAATA
Statistics
Matches: 57, Mismatches: 14, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
12 7 0.12
13 32 0.56
14 18 0.32
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (13 bp):
AAGTACCTGTGCT
Found at i:1104275 original size:27 final size:26
Alignment explanation
Indices: 1104205--1104278 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
1104195 GCAACTGTGT
* * * *
1104205 CAAAGTACCTGTGCTAAGTACTTATG
1 CAAAGTACCTGTGCCAAATACATATA
* * *
1104231 CTAAGTACCTATGTCAAATACATATAA
1 CAAAGTACCTGTGCCAAATACATAT-A
1104258 CAAAGTACCTGTGCCAAATAC
1 CAAAGTACCTGTGCCAAATAC
1104279 CTGTATCGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
26 19 0.51
27 18 0.49
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.27
Consensus pattern (26 bp):
CAAAGTACCTGTGCCAAATACATATA
Found at i:1106187 original size:34 final size:34
Alignment explanation
Indices: 1106113--1106191 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 34
1106103 ATTAATATTT
* * *
1106113 TTATGATATAAA-TATATAAATGTTTAAATTTGA
1 TTATAATATAAATTATATAAATATTTAAATATGA
1106146 -TATAATATAAATTAT-TAATATATTTAAATATGA
1 TTATAATATAAATTATATAA-ATATTTAAATATGA
1106179 TTATAATATAAAT
1 TTATAATATAAAT
1106192 AAATAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
32 13 0.32
33 15 0.38
34 12 0.30
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (34 bp):
TTATAATATAAATTATATAAATATTTAAATATGA
Found at i:1106194 original size:21 final size:22
Alignment explanation
Indices: 1106156--1106196 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1106146 TATAATATAA
**
1106156 ATTATTAATATATTTAAATATG
1 ATTATTAATATAAATAAATATG
1106178 ATTA-TAATATAAATAAATA
1 ATTATTAATATAAATAAATA
1106197 AAAATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTATTAATATAAATAAATATG
Found at i:1107087 original size:22 final size:21
Alignment explanation
Indices: 1107065--1107110 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 21
1107055 ATTTTTAATT
1107065 ATTGATAAAAATAAATATTATTA
1 ATTGA-AAAAAT-AATATTATTA
*
1107088 ATTTAAAAAATAATATT-TTA
1 ATTGAAAAAATAATATTATTA
1107108 ATT
1 ATT
1107111 TTTATAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 6 0.27
22 6 0.27
23 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTGAAAAAATAATATTATTA
Found at i:1107114 original size:22 final size:24
Alignment explanation
Indices: 1107052--1107118 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 24
1107042 TATTTTAAGG
*
1107052 TAAAT-TTTTAATTATTGATAAAAA
1 TAAATATTTTAATT-TTTATAAAAA
1107076 TAAATATTATTAA--TTTA-AAAAA
1 TAAATATT-TTAATTTTTATAAAAA
1107098 T-AATATTTTAATTTTTATAAA
1 TAAATATTTTAATTTTTATAAA
1107119 TGTGATTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
20 4 0.11
21 6 0.16
22 10 0.27
23 6 0.16
24 5 0.14
25 2 0.05
26 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (24 bp):
TAAATATTTTAATTTTTATAAAAA
Found at i:1107119 original size:21 final size:22
Alignment explanation
Indices: 1107071--1107111 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
1107061 AATTATTGAT
1107071 AAAAATAAATATTATTAATTTA
1 AAAAATAAATATTATTAATTTA
1107093 AAAAAT-AATATT-TTAATTT
1 AAAAATAAATATTATTAATTT
1107112 TTATAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 6 0.32
22 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAAATAAATATTATTAATTTA
Found at i:1107962 original size:2 final size:2
Alignment explanation
Indices: 1107955--1107980 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1107945 ATTGTCTAAT
1107955 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
1107981 GGATTGATTC
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):
TA
Found at i:1108529 original size:5 final size:5
Alignment explanation
Indices: 1108516--1108546 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1108506 TTCTGAAAAT
*
1108516 TTTTG TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1108547 AAAAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1108860 original size:16 final size:15
Alignment explanation
Indices: 1108835--1108865 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1108825 TTTATAAATT
1108835 TATAAATAAATTAAA
1 TATAAATAAATTAAA
1108850 TATAAATTAAATTAAA
1 TATAAA-TAAATTAAA
1108866 CAAATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TATAAATAAATTAAA
Found at i:1109316 original size:4 final size:4
Alignment explanation
Indices: 1109307--1109332 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1109297 GCTGTAACCC
1109307 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
1109333 GAAAAAGATT
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:1109752 original size:20 final size:21
Alignment explanation
Indices: 1109710--1109753 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1109700 TTCCTTTTTT
* * *
1109710 TTTCCTTTTGATTTGCTCTGC
1 TTTCCTTTGGATATGCTCCGC
1109731 TTTCCTTTGGATATG-TCCGC
1 TTTCCTTTGGATATGCTCCGC
1109751 TTT
1 TTT
1109754 TATAGCGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.07, C:0.23, G:0.16, T:0.55
Consensus pattern (21 bp):
TTTCCTTTGGATATGCTCCGC
Found at i:1112163 original size:17 final size:16
Alignment explanation
Indices: 1112125--1112163 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
1112115 AGTATTTTTA
*
1112125 ATTTATTATAATAATT
1 ATTTATTAAAATAATT
1112141 ATTTTATTACAAATAATT
1 A-TTTATTA-AAATAATT
1112159 ATTTA
1 ATTTA
1112164 ATTTATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 11 0.55
18 8 0.40
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTATTAAAATAATT
Found at i:1112336 original size:17 final size:17
Alignment explanation
Indices: 1112306--1112382 Score: 52
Period size: 17 Copynumber: 4.5 Consensus size: 17
1112296 TACTATCTCA
**
1112306 TATAATTAAATTATTAT
1 TATAATTATTTTATTAT
*
1112323 TATAATTATTTTATTTT
1 TATAATTATTTTATTAT
*
1112340 TAT-TTTATTTTA-TAT
1 TATAATTATTTTATTAT
*
1112355 TCACATAATAATTATT-TTAT
1 T---ATAATTATT-TTATTAT
1112375 TATAATTA
1 TATAATTA
1112383 AATATATTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
15 3 0.07
16 8 0.17
17 23 0.50
18 2 0.04
19 4 0.09
20 6 0.13
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
TATAATTATTTTATTAT
Found at i:1114817 original size:2 final size:2
Alignment explanation
Indices: 1114810--1114846 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1114800 CAACCATTGC
*
1114810 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1114847 AGATTATGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1118941 original size:37 final size:38
Alignment explanation
Indices: 1118891--1118977 Score: 158
Period size: 38 Copynumber: 2.3 Consensus size: 38
1118881 ATTGTGTACA
*
1118891 CTATTTTGCTTTTAGA-TAGAATTCCCATGACAAGATG
1 CTATTTTGCTTTTAGATTAGAATTCCCATAACAAGATG
1118928 CTATTTTGCTTTTAGATTAGAATTCCCATAACAAGATG
1 CTATTTTGCTTTTAGATTAGAATTCCCATAACAAGATG
1118966 CTATTTTGCTTT
1 CTATTTTGCTTT
1118978 CAATGTTTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 16 0.33
38 32 0.67
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (38 bp):
CTATTTTGCTTTTAGATTAGAATTCCCATAACAAGATG
Found at i:1125319 original size:5 final size:5
Alignment explanation
Indices: 1125309--1125445 Score: 53
Period size: 5 Copynumber: 28.2 Consensus size: 5
1125299 CTGATACTTA
* *
1125309 TATAT TATATT GTATAT TATAAT TATAT T-TAA AATAAT ATATAT T-TA-
1 TATAT TATA-T -TATAT TAT-AT TATAT TATAT TAT-AT -TATAT TATAT
* * * * *
1125356 TATAT TATA- -ATAT TA-AT AAT-T TATAT TATA- TAAAT TTTAA AATA-
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
* *
1125400 TATAT TAATAT TATAT TATAT TTTAAT TATTT TAT-T TA-AT TATAT T
1 TATAT T-ATAT TATAT TATAT TAT-AT TATAT TATAT TATAT TATAT T
1125446 TATGTAATTT
Statistics
Matches: 98, Mismatches: 16, Indels: 36
0.65 0.11 0.24
Matches are distributed among these distances:
3 4 0.04
4 24 0.24
5 45 0.46
6 19 0.19
7 6 0.06
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:1125348 original size:23 final size:20
Alignment explanation
Indices: 1125322--1125426 Score: 74
Period size: 22 Copynumber: 5.1 Consensus size: 20
1125312 ATTATATTGT
*
1125322 ATATTATAATTATATTTAAA
1 ATATTATAATTATATTTATA
*
1125342 ATAATATATATTTATATATTATA
1 AT-AT-TATAATTATAT-TTATA
1125365 ATATTAATAATTTATATTATATA
1 ATATT-ATAA-TTATATT-TATA
* * *
1125388 A-ATTTTAA-AATATATATTA
1 ATATTATAATTATATTTA-TA
1125407 ATATTAT-ATTATATTT-TA
1 ATATTATAATTATATTTATA
1125425 AT
1 AT
1125427 TATTTTATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
18 6 0.09
19 8 0.12
20 11 0.16
21 6 0.09
22 19 0.28
23 17 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTATAATTATATTTATA
Found at i:1125364 original size:29 final size:28
Alignment explanation
Indices: 1125321--1125422 Score: 90
Period size: 29 Copynumber: 3.7 Consensus size: 28
1125311 TATTATATTG
1125321 TATATTATA-ATTATATTTAAAATAATA
1 TATATTATATATTATATTTAAAATAATA
*
1125348 TATATTTATATATTATAATATT--AATAATT
1 TATA-TTATATATTAT-AT-TTAAAATAATA
*
1125377 TATATTATATA-AAT-TTTAAAAT-ATA
1 TATATTATATATTATATTTAAAATAATA
*
1125402 TATTAATATTATATTATATTT
1 TA-TATTA-TATATTATATTT
1125423 TAATTATTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
24 2 0.03
25 5 0.08
26 7 0.12
27 10 0.17
28 14 0.23
29 18 0.30
30 2 0.03
31 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TATATTATATATTATATTTAAAATAATA
Found at i:1125365 original size:20 final size:20
Alignment explanation
Indices: 1125321--1125368 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 20
1125311 TATTATATTG
1125321 TATATTATAAT-TATATTTA
1 TATATTATAATATATATTTA
1125340 -A-A--ATAATATATATTTA
1 TATATTATAATATATATTTA
1125356 TATATTATAATAT
1 TATATTATAATAT
1125369 TAATAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
15 5 0.21
16 8 0.33
17 2 0.08
18 2 0.08
20 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATATTATAATATATATTTA
Found at i:1125386 original size:18 final size:18
Alignment explanation
Indices: 1125365--1125421 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 18
1125355 ATATATTATA
1125365 ATATTAATAATTTATATT
1 ATATTAATAATTTATATT
* *
1125383 ATA-TAA-ATTTTAAAATAT
1 ATATTAATAATTT-ATAT-T
1125401 ATATTAAT-A-TTATATT
1 ATATTAATAATTTATATT
1125417 ATATT
1 ATATT
1125422 TTAATTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
16 10 0.32
17 9 0.29
18 9 0.29
19 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTAATAATTTATATT
Found at i:1125425 original size:18 final size:18
Alignment explanation
Indices: 1125309--1125426 Score: 65
Period size: 18 Copynumber: 6.9 Consensus size: 18
1125299 CTGATACTTA
*
1125309 TATATTATATTGT-ATAT
1 TATATTATATTTTAATAT
*
1125326 TATAATTATA-TTTAAAAT
1 TAT-ATTATATTTTAATAT
*
1125344 AATA-TATA-TTTATATAT
1 TATATTATATTTTA-ATAT
*
1125361 TATA--ATATTAATAAT-T
1 TATATTATATT-TTAATAT
* *
1125377 TATATTATA--TAAATTT
1 TATATTATATTTTAATAT
* * *
1125393 TAAAATATATATTAATAT
1 TATATTATATTTTAATAT
1125411 TATATTATATTTTAAT
1 TATATTATATTTTAAT
1125427 TATTTTATTT
Statistics
Matches: 76, Mismatches: 15, Indels: 19
0.69 0.14 0.17
Matches are distributed among these distances:
15 3 0.04
16 24 0.32
17 15 0.20
18 34 0.45
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (18 bp):
TATATTATATTTTAATAT
Found at i:1125453 original size:14 final size:14
Alignment explanation
Indices: 1125409--1125461 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
1125399 ATATATTAAT
1125409 ATTATATTATATTTTA
1 ATTATATT-TA-TTTA
1125425 ATTAT-TTTATTTA
1 ATTATATTTATTTA
*
1125438 ATTATATTTATGTA
1 ATTATATTTATTTA
*
1125452 ATTTTATTTA
1 ATTATATTTA
1125462 ATATTATTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 9 0.26
14 18 0.53
15 2 0.06
16 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
ATTATATTTATTTA
Found at i:1126374 original size:3 final size:3
Alignment explanation
Indices: 1126359--1126405 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
1126349 AATGACCCAC
* *
1126359 CTT CTT -TT TTT CTT CTT CTT CTT CTT CTT CTT CTT CTT TTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1126406 TTCACTTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
CTT
Found at i:1134342 original size:3 final size:3
Alignment explanation
Indices: 1134334--1134364 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1134324 TTTATCCATC
1134334 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1134365 AGTTCAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1135599 original size:18 final size:17
Alignment explanation
Indices: 1135540--1135600 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 17
1135530 TTATAAATGA
1135540 ATTAATAAAATATAATAT
1 ATTAATAAAATATAA-AT
1135558 ATT--TAAAATAGTAAAT
1 ATTAATAAAATA-TAAAT
1135574 ATTAAATAAAATATAAAT
1 ATT-AATAAAATATAAAT
1135592 ATGTAATAA
1 AT-TAATAA
1135601 TTTTTTAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
16 12 0.32
17 3 0.08
18 15 0.39
19 8 0.21
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
ATTAATAAAATATAAAT
Found at i:1139825 original size:2 final size:2
Alignment explanation
Indices: 1139820--1139846 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1139810 TAAAGTTTAC
1139820 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
1139847 ATTATAATAG
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:1142956 original size:2 final size:2
Alignment explanation
Indices: 1142949--1142988 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1142939 CTTCTTTGTA
1142949 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
1142989 TCAACAAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1143934 original size:18 final size:18
Alignment explanation
Indices: 1143913--1143995 Score: 76
Period size: 18 Copynumber: 4.6 Consensus size: 18
1143903 ATCATCGTCA
* *
1143913 TCATTCTCATTCTCATCC
1 TCATCCTCATCCTCATCC
*
1143931 TCATCCTCATCCTCTTCC
1 TCATCCTCATCCTCATCC
* * *
1143949 TCCTCATCATCCTCGTCC
1 TCATCCTCATCCTCATCC
** * *
1143967 TCATCAACATCATCATCT
1 TCATCCTCATCCTCATCC
1143985 TCATCCTCATC
1 TCATCCTCATC
1143996 TTCTGTGTCT
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.18, C:0.43, G:0.01, T:0.37
Consensus pattern (18 bp):
TCATCCTCATCCTCATCC
Found at i:1143954 original size:15 final size:15
Alignment explanation
Indices: 1143925--1143972 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1143915 ATTCTCATTC
*
1143925 TCATCCTCATCCTCA
1 TCATCCTCCTCCTCA
* *
1143940 TCCTCTTCCTCCTCA
1 TCATCCTCCTCCTCA
*
1143955 TCATCCTCGTCCTCA
1 TCATCCTCCTCCTCA
1143970 TCA
1 TCA
1143973 ACATCATCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.15, C:0.48, G:0.02, T:0.35
Consensus pattern (15 bp):
TCATCCTCCTCCTCA
Found at i:1143998 original size:12 final size:12
Alignment explanation
Indices: 1143913--1143995 Score: 76
Period size: 12 Copynumber: 6.9 Consensus size: 12
1143903 ATCATCGTCA
* *
1143913 TCATTCTCATTC
1 TCATCCTCATCC
1143925 TCATCCTCATCC
1 TCATCCTCATCC
*
1143937 TCATCCTCTTCC
1 TCATCCTCATCC
* *
1143949 TCCTCATCATCC
1 TCATCCTCATCC
* *
1143961 TCGTCCTCATCA
1 TCATCCTCATCC
* * *
1143973 ACATCATCATCT
1 TCATCCTCATCC
1143985 TCATCCTCATC
1 TCATCCTCATC
1143996 TTCTGTGTCT
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 56 1.00
ACGTcount: A:0.18, C:0.43, G:0.01, T:0.37
Consensus pattern (12 bp):
TCATCCTCATCC
Found at i:1145867 original size:23 final size:25
Alignment explanation
Indices: 1145823--1145875 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 25
1145813 ACAAAATATC
1145823 AAAAACTAAAACAGAGAAAAACAAA
1 AAAAACTAAAACAGAGAAAAACAAA
*
1145848 GAAAAC-AAAACA-AGAAAAACAAA
1 AAAAACTAAAACAGAGAAAAACAAA
1145871 AAAAA
1 AAAAA
1145876 AATTCCAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 15 0.58
24 6 0.23
25 5 0.19
ACGTcount: A:0.79, C:0.11, G:0.08, T:0.02
Consensus pattern (25 bp):
AAAAACTAAAACAGAGAAAAACAAA
Found at i:1146407 original size:28 final size:29
Alignment explanation
Indices: 1146369--1146443 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 29
1146359 TTTTAATATC
* *
1146369 ATAATATATTTAAATTATTTAATATTTAT
1 ATAATATATTTAAATTATATAAAATTTAT
*
1146398 ATAATA-ATTTATATTATATAAAATTTA-
1 ATAATATATTTAAATTATATAAAATTTAT
* *
1146425 AT-ATGTATTTATATTATAT
1 ATAATATATTTAAATTATAT
1146444 TTTAATTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 2 0.05
27 15 0.37
28 18 0.44
29 6 0.15
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (29 bp):
ATAATATATTTAAATTATATAAAATTTAT
Found at i:1146483 original size:25 final size:25
Alignment explanation
Indices: 1146390--1146486 Score: 83
Period size: 25 Copynumber: 3.9 Consensus size: 25
1146380 AAATTATTTA
1146390 ATATTTATATAA-TA-ATTTATATT
1 ATATTTATATAATTATATTTATATT
** * *
1146413 ATATAAAATTTAATATGTATTTATATT
1 ATAT-TTATATAAT-TATATTTATATT
* * *
1146440 ATATTT-TAATTATTTTATTTATATC
1 ATATTTAT-ATAATTATATTTATATT
1146465 ATATTTATATAATTATATTTAT
1 ATATTTATATAATTATATTTAT
1146487 TGATTATTGA
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
23 4 0.07
24 5 0.09
25 29 0.52
26 5 0.09
27 13 0.23
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (25 bp):
ATATTTATATAATTATATTTATATT
Found at i:1146772 original size:21 final size:20
Alignment explanation
Indices: 1146743--1146805 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 20
1146733 TTATATTTTT
*
1146743 ATATTAATTATATAAATATAA
1 ATATAAATTAT-TAAATATAA
1146764 ATATAAATTATTAAATAT--
1 ATATAAATTATTAAATATAA
* *
1146782 GT-TAAGTT-TTAAATATAA
1 ATATAAATTATTAAATATAA
1146800 ATATAA
1 ATATAA
1146806 TATATATATC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 8 0.23
17 5 0.14
18 2 0.06
19 3 0.09
20 7 0.20
21 10 0.29
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (20 bp):
ATATAAATTATTAAATATAA
Found at i:1147680 original size:19 final size:19
Alignment explanation
Indices: 1147656--1147700 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1147646 GGTTGTCAAG
**
1147656 GTACTGTTTATGTATACGA
1 GTACTGTTTACATATACGA
1147675 GTACTGTTTACATATACGA
1 GTACTGTTTACATATACGA
*
1147694 TTACTGT
1 GTACTGT
1147701 GCATGTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (19 bp):
GTACTGTTTACATATACGA
Found at i:1151806 original size:50 final size:50
Alignment explanation
Indices: 1151744--1152002 Score: 365
Period size: 50 Copynumber: 5.2 Consensus size: 50
1151734 CAAGTGGGAG
* * * * *
1151744 AATTGTTGACTATTTTTCACCAACTTTTGACAATCGAGATAGGTGGCCGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGT
* *
1151794 AATTATTGACTATTCTTCACCAACCTTTGACAATAAAGAGAGGTGACCGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGT
* * * *
1151844 AATTGTTGACTATTTTTCACCAACTTTTGACAATAGGGAGAGGTGGCCGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGT
* * * *
1151894 AATTGTTGATTATTCTTCACCAACCTTTGACAATCGAGAGAAGTAACCGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGT
* *
1151944 AATTGCTGACTATTCTTCATCAACCTTTGACAATAGAGAGAGGTGACCGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGT
1151994 AATTGTTGA
1 AATTGTTGA
1152003 TTTTAAGCAA
Statistics
Matches: 181, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 181 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (50 bp):
AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGT
Found at i:1153880 original size:16 final size:16
Alignment explanation
Indices: 1153833--1153883 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1153823 TTATATTTTT
*
1153833 TATATTAATTTTATAAG
1 TATATTAATTTT-TAAA
* *
1153850 TACA-T-ATTATTAAA
1 TATATTAATTTTTAAA
1153864 TATATTAATTTTTAAA
1 TATATTAATTTTTAAA
1153880 TATA
1 TATA
1153884 AATATAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 6 0.22
15 5 0.19
16 13 0.48
17 3 0.11
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
TATATTAATTTTTAAA
Found at i:1154310 original size:22 final size:22
Alignment explanation
Indices: 1154285--1154357 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 22
1154275 ACTCAAGTAG
1154285 TAAAATTATATAAAACTTAAAT
1 TAAAATTATATAAAACTTAAAT
* * *
1154307 TAAATTTATAATAAAAATAAAAT
1 TAAAATTAT-ATAAAACTTAAAT
* * * *
1154330 TAAAAATATTTAAATCATTTAAT
1 TAAAATTATATAAAAC-TTAAAT
1154353 TAAAA
1 TAAAA
1154358 AATCGCTCAC
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
22 12 0.31
23 27 0.69
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAATTATATAAAACTTAAAT
Found at i:1159247 original size:47 final size:47
Alignment explanation
Indices: 1159176--1159269 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
1159166 TGAGATGGGG
* *
1159176 TGGATATGTAAATAAGGGACAAGATAGGGGCTTATATTTGGCAGAGA
1 TGGATATGTAAATAAGGGAAAAGATAGGGGCTTATATTAGGCAGAGA
* *
1159223 TGGATATGTAAATAAGGGAAAAGATAGGGGTTTATATTAGGTAGAGA
1 TGGATATGTAAATAAGGGAAAAGATAGGGGCTTATATTAGGCAGAGA
1159270 CAATAGAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.38, C:0.03, G:0.32, T:0.27
Consensus pattern (47 bp):
TGGATATGTAAATAAGGGAAAAGATAGGGGCTTATATTAGGCAGAGA
Found at i:1162157 original size:33 final size:33
Alignment explanation
Indices: 1162117--1162184 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1162107 TAAATCAAAT
1162117 TAAAATAATTTATTTAATTT-AATTT-ATTTGAAA
1 TAAAATAATTT-TTT-ATTTAAATTTAATTTGAAA
*
1162150 TAAAATAATTTTTTATTTAAATTTAATTTTAAA
1 TAAAATAATTTTTTATTTAAATTTAATTTGAAA
1162183 TA
1 TA
1162185 TTAATATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 4 0.12
32 8 0.25
33 20 0.62
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (33 bp):
TAAAATAATTTTTTATTTAAATTTAATTTGAAA
Found at i:1162475 original size:21 final size:21
Alignment explanation
Indices: 1162451--1162533 Score: 60
Period size: 21 Copynumber: 3.8 Consensus size: 21
1162441 TAAAAATATA
1162451 TTTTATTTTTAATATTTTATT
1 TTTTATTTTTAATATTTTATT
* *
1162472 TTTTGTATTTAAATATTTTA-T
1 TTTTAT-TTTTAATATTTTATT
* *
1162493 ATTTATGTTTAGATATGTATTATT
1 TTTTATTTTTA-ATAT-T-TTATT
* *
1162517 TATTATTTATTATTATT
1 TTTTATTT-TTAATATT
1162534 AAACGTTGAA
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
20 3 0.07
21 14 0.30
22 13 0.28
23 4 0.09
24 9 0.20
25 3 0.07
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTTATTTTTAATATTTTATT
Done.