Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 8 of 105
Found at i:1274355 original size:110 final size:110
Alignment explanation
Indices: 1274175--1274532 Score: 334
Period size: 109 Copynumber: 3.2 Consensus size: 110
1274165 AGAAACGCTA
* * *
1274175 TATTTGTTCAATAAAAAATAATTATTTTTTAAATAATAAATATCATGTTTCATTGGTCA-AAAC-
1 TATTTGTTCAATAAAAAAT--TTATTTTTTAAATAACAAATATCACGTTTCATTGGTAAGAAACA
* * * *
1274238 CGTAATATTTATGAATACTAAAGCTGCGTTTTTTACATTAGAAATACAG
64 C--AATATTTGTGAATACTAAAGATACGTTTTTCACATTAGAAATACAG
* * * *
1274287 TATTTGTTTAATAAAAAATTTATTTTTTAAATAACAAATACCACATTTCATTGATAAGAAACACA
1 TATTTGTTCAATAAAAAATTTATTTTTTAAATAACAAATATCACGTTTCATTGGTAAGAAACACA
* * *
1274352 ATATTTGTAAATA-TAAAAATTCTGTTTTTCACATTA-AAA-ACGTAG
66 ATATTTGTGAATACTAAAGATAC-GTTTTTCACATTAGAAATAC--AG
* ** * * *
1274397 TATTTATTCAATAAAAAA-TTATTTTTTAAATAACAAATATCACGGCTCATTGGTTAGAAATACG
1 TATTTGTTCAATAAAAAATTTATTTTTTAAATAACAAATATCACGTTTCATTGGTAAGAAACACA
* * * * * *
1274461 GTGTTTGTGAATAC-AAAGATTATGTTTTTGACACTAGAAATATAG
66 ATATTTGTGAATACTAAAGA-TACGTTTTTCACATTAGAAATACAG
* * *
1274506 TACTTGTTTAATAAAAAAATTATTTTT
1 TATTTGTTCAATAAAAAATTTATTTTT
1274533 AGAGTCTAAG
Statistics
Matches: 201, Mismatches: 35, Indels: 22
0.78 0.14 0.09
Matches are distributed among these distances:
108 2 0.01
109 89 0.44
110 86 0.43
111 5 0.02
112 19 0.09
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.40
Consensus pattern (110 bp):
TATTTGTTCAATAAAAAATTTATTTTTTAAATAACAAATATCACGTTTCATTGGTAAGAAACACA
ATATTTGTGAATACTAAAGATACGTTTTTCACATTAGAAATACAG
Found at i:1274456 original size:109 final size:110
Alignment explanation
Indices: 1274163--1274456 Score: 298
Period size: 110 Copynumber: 2.7 Consensus size: 110
1274153 GTTTCTTACG
* *
1274163 TTAG-AAACGCTA-TATTTGTTCAATAAAAAATAATTATTTTTTAAATAATAAATATCATGTTTC
1 TTAGAAAACG-TAGTATTTGTTCAAT--AAAA-AATTATTTTTTAAATAACAAATATCACGTTTC
* * ** *
1274226 ATTGGTCA-AAACCGTAATATTTATGAATACTAAAGCTGCGTTTTTTACA
62 ATTGGTAAGAAACCG-AATATTTATAAATACTAAAAATGCGTTTTTCACA
* * *
1274275 TTAGAAATAC--AGTATTTGTTTAATAAAAAATTTATTTTTTAAATAACAAATACCACATTTCAT
1 TTAGAAA-ACGTAGTATTTGTTCAATAAAAAA-TTATTTTTTAAATAACAAATATCACGTTTCAT
* * *
1274338 TGATAAGAAACAC-AATATTTGTAAATA-TAAAAATTCTGTTTTTCACA
64 TGGTAAGAAAC-CGAATATTTATAAATACTAAAAATGC-GTTTTTCACA
* **
1274385 TTA-AAAACGTAGTATTTATTCAATAAAAAATTATTTTTTAAATAACAAATATCACGGCTCATTG
1 TTAGAAAACGTAGTATTTGTTCAATAAAAAATTATTTTTTAAATAACAAATATCACGTTTCATTG
*
1274449 GTTAGAAA
66 GTAAGAAA
1274457 TACGGTGTTT
Statistics
Matches: 152, Mismatches: 21, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
108 2 0.01
109 47 0.31
110 78 0.51
111 5 0.03
112 16 0.11
113 2 0.01
114 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.39
Consensus pattern (110 bp):
TTAGAAAACGTAGTATTTGTTCAATAAAAAATTATTTTTTAAATAACAAATATCACGTTTCATTG
GTAAGAAACCGAATATTTATAAATACTAAAAATGCGTTTTTCACA
Found at i:1274947 original size:92 final size:92
Alignment explanation
Indices: 1274837--1275021 Score: 300
Period size: 92 Copynumber: 2.0 Consensus size: 92
1274827 AGTATTTTTT
* * *
1274837 ATTTTTTTTGGTGAAATTTTTTTAATACAATAACGGTATTTTGT-ATGAACAAAAAGTTATATTT
1 ATTTTTTTTGGTGAAATTTTTTTAATACAATAACGATATTTT-TCACGAACAAAAAATTATATTT
1274901 AATCAAGGATCATATTTTTATATTTATA
65 AATCAAGGATCATATTTTTATATTTATA
* * *
1274929 ATTTTTTTTTGTGAAATTTTTTTAATACAATGACGATATTTTTCACGAACAAAAAATTGTATTTA
1 ATTTTTTTTGGTGAAATTTTTTTAATACAATAACGATATTTTTCACGAACAAAAAATTATATTTA
1274994 ATCAAGGATCATATTTTTATATTTATA
66 ATCAAGGATCATATTTTTATATTTATA
1275021 A
1 A
1275022 ACCTAGTATT
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
91 1 0.01
92 85 0.99
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (92 bp):
ATTTTTTTTGGTGAAATTTTTTTAATACAATAACGATATTTTTCACGAACAAAAAATTATATTTA
ATCAAGGATCATATTTTTATATTTATA
Found at i:1276046 original size:14 final size:13
Alignment explanation
Indices: 1276027--1276056 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1276017 ACTTATTATT
1276027 TAAACGAATAAATA
1 TAAACGAATAAA-A
1276041 TAAACGAATAAAA
1 TAAACGAATAAAA
1276054 TAA
1 TAA
1276057 TTTTTTTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (13 bp):
TAAACGAATAAAA
Found at i:1283772 original size:36 final size:36
Alignment explanation
Indices: 1283718--1283829 Score: 129
Period size: 36 Copynumber: 3.1 Consensus size: 36
1283708 TAACTATGAA
*
1283718 AATA-CTCTCCTA-TCATCATTTGCCAAAATTACTAT
1 AATACCTCTCCTACT-ATCATTTGCCAAAATTATTAT
** * * *
1283753 AATGTCTTTCTTATTATCATTTGCCAAAATTATTAT
1 AATACCTCTCCTACTATCATTTGCCAAAATTATTAT
* *
1283789 AATACCTCTCCTACTATAATTTGTCAAAATTATTAT
1 AATACCTCTCCTACTATCATTTGCCAAAATTATTAT
1283825 AATAC
1 AATAC
1283830 TTTTATATCA
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
35 3 0.05
36 60 0.94
37 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.42
Consensus pattern (36 bp):
AATACCTCTCCTACTATCATTTGCCAAAATTATTAT
Found at i:1288423 original size:3 final size:3
Alignment explanation
Indices: 1288415--1288451 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1288405 CTATTAAGTC
1288415 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1288452 TACAAGGGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1289890 original size:26 final size:27
Alignment explanation
Indices: 1289835--1289890 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
1289825 TTTCTTGCAT
* *
1289835 CTTTGTCAATTTTTTTTCTTTTCTTTC
1 CTTTGTCAATTTTATTTCTTTTCTTAC
*
1289862 CTTTGTC-CTTTTATTT-TTTTCATTAC
1 CTTTGTCAATTTTATTTCTTTTC-TTAC
1289888 CTT
1 CTT
1289891 AAAATGGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 5 0.20
26 13 0.52
27 7 0.28
ACGTcount: A:0.09, C:0.20, G:0.04, T:0.68
Consensus pattern (27 bp):
CTTTGTCAATTTTATTTCTTTTCTTAC
Found at i:1294787 original size:2 final size:2
Alignment explanation
Indices: 1294780--1294813 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1294770 CCAGACCCCT
1294780 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
1294814 AGAGCTTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1297003 original size:8 final size:7
Alignment explanation
Indices: 1296975--1297001 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1296965 TAAATTCATG
1296975 TTTTTTA
1 TTTTTTA
1296982 TTTTTTA
1 TTTTTTA
1296989 TTTTTTA
1 TTTTTTA
1296996 TTTTTT
1 TTTTTT
1297002 TAAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:1297450 original size:4 final size:4
Alignment explanation
Indices: 1297426--1297486 Score: 65
Period size: 4 Copynumber: 15.8 Consensus size: 4
1297416 TATCAATTAT
* * *
1297426 TTTA TTTCA TTT- TTCA TTTA TTTA -TTA TTTA -TTA TTTG TCTA TTTA
1 TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1297472 TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTT
1297487 GGGTTTATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
3 8 0.17
4 35 0.74
5 4 0.09
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:1298682 original size:24 final size:25
Alignment explanation
Indices: 1298630--1298685 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 25
1298620 AATAAGTATT
1298630 AATTATCCAATGATAGAATTTATAAA
1 AATT-TCCAATGATAGAATTTATAAA
* *
1298656 AATTTCCAATGATA-AATTTCTATA
1 AATTTCCAATGATAGAATTTATAAA
1298680 AATTTC
1 AATTTC
1298686 TTAAGTGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 14 0.50
25 10 0.36
26 4 0.14
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (25 bp):
AATTTCCAATGATAGAATTTATAAA
Found at i:1300803 original size:28 final size:28
Alignment explanation
Indices: 1300760--1300817 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
1300750 CATTTGATTC
* *
1300760 AAAATCACATATTTCAAGATGTAATTTA
1 AAAATCACATACTTCAAGATGTAATCTA
1300788 AAAATCACATACTTCAAGATGTAATCTA
1 AAAATCACATACTTCAAGATGTAATCTA
1300816 AA
1 AA
1300818 GTAGAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (28 bp):
AAAATCACATACTTCAAGATGTAATCTA
Found at i:1302534 original size:24 final size:24
Alignment explanation
Indices: 1302482--1302551 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
1302472 ATTATCATAC
* *
1302482 AAAT-ATGTTATAA-ATCATACCA
1 AAATCATGTAATAATATCATGCCA
*
1302504 AATATCATGTAATAATATCATGCCT
1 AA-ATCATGTAATAATATCATGCCA
1302529 AAATCATGCTAA-AATATTCATGC
1 AAATCATG-TAATAATA-TCATGC
1302552 AAGAATGTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 2 0.05
23 2 0.05
24 18 0.45
25 18 0.45
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (24 bp):
AAATCATGTAATAATATCATGCCA
Found at i:1302584 original size:20 final size:20
Alignment explanation
Indices: 1302559--1302614 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1302549 TGCAAGAATG
* *
1302559 TCATGCAAATATATTAATTA
1 TCATGCAAATATATAAAATA
1302579 TCATGC-AATAATATAAAATA
1 TCATGCAAAT-ATATAAAATA
*
1302599 CCATGCAAATATATAA
1 TCATGCAAATATATAA
1302615 TCATGAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 3 0.10
20 25 0.81
21 3 0.10
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.32
Consensus pattern (20 bp):
TCATGCAAATATATAAAATA
Found at i:1302754 original size:25 final size:24
Alignment explanation
Indices: 1302710--1302757 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
1302700 TATCATTCAA
*
1302710 ATATAATATTAATCATGCAATAAC
1 ATATAATATCAATCATGCAATAAC
1302734 ATATAATATCATATCATGCAATAA
1 ATATAATATCA-ATCATGCAATAA
1302758 TAATCATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.33
Consensus pattern (24 bp):
ATATAATATCAATCATGCAATAAC
Found at i:1302782 original size:30 final size:28
Alignment explanation
Indices: 1302728--1302784 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
1302718 TTAATCATGC
*
1302728 AATAACATATAATATCATATCATGCAAT
1 AATAACATATAATATCATACCATGCAAT
1302756 AATAATCATATAAATAT-ATAACCATGCAA
1 AATAA-CATAT-AATATCAT-ACCATGCAA
1302785 ATAAATATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 5 0.20
29 7 0.28
30 13 0.52
ACGTcount: A:0.53, C:0.14, G:0.04, T:0.30
Consensus pattern (28 bp):
AATAACATATAATATCATACCATGCAAT
Found at i:1302965 original size:73 final size:73
Alignment explanation
Indices: 1302819--1302971 Score: 166
Period size: 73 Copynumber: 2.1 Consensus size: 73
1302809 TCACACAAAT
* * * * * * * *
1302819 AAATAAAT-TAATAATCATGCAAATACATATGCAATTAAATAGATGATCACACAATTAACAATGT
1 AAATAAATAT-ATAACCATGCAAATAAACATACAATTAAATAGATAATAACACAAATAACAATAT
1302883 AAAATATGC
65 AAAATATGC
* * * *
1302892 AATTAAATATATAACCATGCAAATAAACATACAATTAAATATATAATAATACAAATAATAATAT-
1 AAATAAATATATAACCATGCAAATAAACATACAATTAAATAGATAATAACACAAATAACAATATA
1302956 AAATCATGC
66 AAAT-ATGC
1302965 AAATAAA
1 AAATAAA
1302972 CATGCAATTA
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
72 4 0.06
73 60 0.92
74 1 0.02
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.27
Consensus pattern (73 bp):
AAATAAATATATAACCATGCAAATAAACATACAATTAAATAGATAATAACACAAATAACAATATA
AAATATGC
Found at i:1303040 original size:20 final size:20
Alignment explanation
Indices: 1303015--1303139 Score: 112
Period size: 20 Copynumber: 6.3 Consensus size: 20
1303005 TCACACAAAT
*
1303015 AAATAAATTCATAATCATGC
1 AAATAAATTAATAATCATGC
* *
1303035 AAATAAATTAATAATAATGT
1 AAATAAATTAATAATCATGC
* *
1303055 AGATAAATTAATATTCATGC
1 AAATAAATTAATAATCATGC
* * *
1303075 AAACATATTAATAGTCATGC
1 AAATAAATTAATAATCATGC
**
1303095 AAATTTATTAATAA--AT-C
1 AAATAAATTAATAATCATGC
* *
1303112 ACATAAATATACTAATCATGC
1 AAATAAAT-TAATAATCATGC
1303133 AAATAAA
1 AAATAAA
1303140 ATATTAAAAA
Statistics
Matches: 82, Mismatches: 19, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
17 6 0.07
18 7 0.09
20 62 0.76
21 7 0.09
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (20 bp):
AAATAAATTAATAATCATGC
Found at i:1314476 original size:23 final size:24
Alignment explanation
Indices: 1314440--1314485 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1314430 TTTGACAAAT
*
1314440 TAAATCAATCAATA-TATAATTAA
1 TAAATCAATAAATATTATAATTAA
*
1314463 TAAATTAATAAATATTATAATTA
1 TAAATCAATAAATATTATAATTA
1314486 CAATTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAATCAATAAATATTATAATTAA
Found at i:1315323 original size:661 final size:681
Alignment explanation
Indices: 1314340--1315707 Score: 1705
Period size: 661 Copynumber: 2.0 Consensus size: 681
1314330 CAAAAAATTA
* * * *
1314340 AATTGATTATATTTATGTTTTTATTATTGATTTTAAATCACTCTCAATTCAATTCATATTAAAAG
1 AATTGACTATAATTATATTTTTATTATTGACTTTAAATCACTCTCAATTCAATTCATATTAAAAG
1314405 AATTAAAATTTTAAAAATTTCTTAATTTGACAAATTAAATCAATCAATATATAATTAATAAATTA
66 AATTAAAATTTTAAAAATTTCTTAATTTGACAAATTAAATCAATCAATATATAATTAATAAATTA
* * * * * *
1314470 ATAAATATTATAATTACAATTATAAAATAGTTGATTCTTTAATTAATTATTTGACAGATTTATAT
131 ATAAATAGTACAATTACAATTATAAAATAATTGATTCTCTAATCAATTATTTGACACATTTATAT
* *
1314535 TTGATTAAATATAGTATCTATTTGAGTAATTGATGTATTTCATGATGTATCTCATGTGTAAATAT
196 TTGATTAAATATAGTATCCATTT--GTAA-T-ATGTA-TACATGATGTATCTCATGTGTAAATAT
* *
1314600 ATAAAGCAAACATATCAAATTAATTCTCCATAATTAAATTAATAGAATACAATATTTTATTAATT
256 AGAAAGCAAACATATCAAATTAATTCTCCATAATTAAATTAATAGAATAAAATATTTTATTAATT
* * *
1314665 TATATTTGATTGATACATTTATATTTCATTAAATATGATTTTATTTTATTTCA-TTT-G-ATAA-
321 TATATTTGATTGATACATTTATATTTCATTAAATATGATTTCATTTGATTTCAGTTTGGTAAAAT
*
1314726 A-AAT-A-TTAA-TCCATGTTG-AT-TT-A-AT-TT-G-T-TTTCATTTGCAACGTTTTATAATT
386 ACAATCACTTAATTCCAT-TTGAATATTAATATATTGGTTATTTCATTTGCAACATTTTATAATT
** *** * * ***
1314779 TTATTATTTA-ATATTAATGCATGTTGATTTAATTAAAATTTATTTTATTTTATTGTTATTATTA
450 TTAAAATTTAGATATTAATGCACAATGATTTAATGAAAATTTAATTTATTTTATTACCATTATTA
* * * * *
1314843 AATATAATAAATTTAATTTGTTTTATTTTTCTAAATTAATGA-ATCTCTAAATGTTAATTATAGA
515 AATACAATAAATTTAATTTGTTTTATTGTTCTAAATTAA-GAGATCTCTAAATATTAATGACAGA
* * *
1314907 ATAAAATATTTCAATATCAA-TAACTTGCTATTGTTAGA-CTATTATTTACTCACAATGTTTATT
579 ATAAAATATTTCAATATCAATTAACTTGCCATTATTAGATC-ATTATTCACTCACAATGTTTATT
1314970 ATTTC-ATCATTAACTTTCATAATTTAAAATTATCTTATT
643 ATTTCAAT-ATTAACTTTCATAATTTAAAATTATCTTATT
* *
1315009 AATTGACTATAATTATATTTTTATTATTGACTTTATATCACTTTCAATTCAATTCATATTAAAAG
1 AATTGACTATAATTATATTTTTATTATTGACTTTAAATCACTCTCAATTCAATTCATATTAAAAG
* * *
1315074 TATTAAAATTTTAAAAATTTCTTAATTTGATAAATTAAATCAATTAATATATAATTAATTAATAA
66 AATTAAAATTTTAAAAATTTCTTAATTTGACAAATTAAATCAATCAATATATAATTAA-T-A-AA
* * *
1315139 TTTAATAAATAGTGCAATTACAATTATAAAATAATTTATTCTCTAATCAATTATTTGATACATTT
128 -TTAATAAATAGTACAATTACAATTATAAAATAATTGATTCTCTAATCAATTATTTGACACATTT
* *
1315204 ATGTTTGATTAAATATAGTATCCA-TT-T-A-A-GTA-AC-TGATGTATTTCATGTGTAAATATA
192 ATATTTGATTAAATATAGTATCCATTTGTAATATGTATACATGATGTATCTCATGTGTAAATATA
* *
1315262 GAAAGCAAATATATCAAATTAATTCTCCATATTTAAATTAAT-GAAATAAAATATTTTATTAATT
257 GAAAGCAAACATATCAAATTAATTCTCCATAATTAAATTAATAG-AATAAAATATTTTATTAATT
* *
1315326 TATATTTGATTGATAGATTTATATTTCATTAAATATGATTTCATTTGATTTTAGTTTGGTAAAAT
321 TATATTTGATTGATACATTTATATTTCATTAAATATGATTTCATTTGATTTCAGTTTGGTAAAAT
*
1315391 ACTAATGCACGTTTAATTTCATTTGATAAAATATTAATATACTTGGATTTCATTTCATTTCATTT
386 AC-AAT-CAC--TTAATTCCATTTG----AATATTAATATA-TTGG-------TT-ATTTCATTT
* * * *
1315456 GTAACATTTTATAATTTTAAAATTTAGATATTAATGTACAATGATTTGATGAAAATTTAATTTGT
434 GCAACATTTTATAATTTTAAAATTTAGATATTAATGCACAATGATTTAATGAAAATTTAATTTAT
*
1315521 TTTATTACCATTATTAAATACAATATATTTAATTTGTTTTATTGTTCTAAATTAAGAGATCTCTA
499 TTTATTACCATTATTAAATACAATAAATTTAATTTGTTTTATTGTTCTAAATTAAGAGATCTCTA
* * *
1315586 AATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGCCATTATTAGATCATTATTCAC
564 AATATTAATGACAGAATAAAATATTTCAATATCAATTAACTTGCCATTATTAGATCATTATTCAC
* *
1315651 TCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATTATCTTATT
629 TCACAATGTTTATTATTTCAATATTAACTTTCATAATTTAAAATTATCTTATT
1315704 AATT
1 AATT
1315708 AACCTACAAT
Statistics
Matches: 595, Mismatches: 61, Indels: 60
0.83 0.09 0.08
Matches are distributed among these distances:
660 1 0.00
661 130 0.22
662 4 0.01
663 1 0.00
664 6 0.01
665 2 0.00
667 3 0.01
668 1 0.00
669 116 0.19
670 1 0.00
671 1 0.00
672 11 0.02
673 81 0.14
677 2 0.00
678 2 0.00
679 1 0.00
680 2 0.00
682 2 0.00
683 1 0.00
691 1 0.00
693 32 0.05
694 115 0.19
695 76 0.13
696 3 0.01
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (681 bp):
AATTGACTATAATTATATTTTTATTATTGACTTTAAATCACTCTCAATTCAATTCATATTAAAAG
AATTAAAATTTTAAAAATTTCTTAATTTGACAAATTAAATCAATCAATATATAATTAATAAATTA
ATAAATAGTACAATTACAATTATAAAATAATTGATTCTCTAATCAATTATTTGACACATTTATAT
TTGATTAAATATAGTATCCATTTGTAATATGTATACATGATGTATCTCATGTGTAAATATAGAAA
GCAAACATATCAAATTAATTCTCCATAATTAAATTAATAGAATAAAATATTTTATTAATTTATAT
TTGATTGATACATTTATATTTCATTAAATATGATTTCATTTGATTTCAGTTTGGTAAAATACAAT
CACTTAATTCCATTTGAATATTAATATATTGGTTATTTCATTTGCAACATTTTATAATTTTAAAA
TTTAGATATTAATGCACAATGATTTAATGAAAATTTAATTTATTTTATTACCATTATTAAATACA
ATAAATTTAATTTGTTTTATTGTTCTAAATTAAGAGATCTCTAAATATTAATGACAGAATAAAAT
ATTTCAATATCAATTAACTTGCCATTATTAGATCATTATTCACTCACAATGTTTATTATTTCAAT
ATTAACTTTCATAATTTAAAATTATCTTATT
Found at i:1316608 original size:444 final size:444
Alignment explanation
Indices: 1315565--1318577 Score: 5190
Period size: 444 Copynumber: 6.8 Consensus size: 444
1315555 TGTTTTATTG
*
1315565 TTCTAAATTAAGAGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
1 TTCTAGATTAAGAGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
*
1315630 CATTATTAGATCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
66 CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
1315695 TATCTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
131 TATCTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
*
1315760 TTTAACCACTTATCACTAA-TTTAAATC-TTTGATCAACTACTC-ACTCTATTTTAA-TTTCTCT
196 TTTAACCACTTTTCACTAATTTTAAATCTTTTGATC-ACTACTCAACTCTATTTTAATTTTCTCT
* *
1315821 CTAATTTTTCACTTTACATCATCGTTTCTTGGTTTGTGTTACTCAAAG--TTATTTTTTATACTC
260 CTAA-TTTTCACTTTACAT--T-ATTTCTTGGTTTGTGTTACTCAAAGATTTTTTTTTTATACTC
*
1315884 ATATTTTATATTTCTTTAACTATAATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATT
321 ATATTTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATT
* * *
1315949 GATTTAAAAATGATTGAGTATATACAAAGAAATGTTTCACCAGTAGAGTCATTATTATA
386 GATTTAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAGTAGAGTCATTATTATA
*
1316008 TTCTAGATTAAGATATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
1 TTCTAGATTAAGAGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
* *
1316073 CATTATTAAACCATTATTCACTTACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
66 CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
1316138 TATCTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
131 TATCTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
*
1316203 TTTAACCACTTTTCACTAATTTTAAATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTC
196 TTTAACCACTTTTCACTAATTTTAAATCTTTTGATCACTACTCAACTCTATTTTAATTTTCTCTC
* *
1316268 TAATTTTCACTTTACATTGTTTTTTGGTTTGTGTTACTCAAAGATTTTTTTTTATATACTCATAT
261 TAATTTTCACTTTACATTATTTCTTGGTTTGTGTTACTCAAAGATTTTTTTTT-TATACTCATAT
1316333 TTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATT
325 TTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATT
* *
1316398 TAAAAATGATTGAGTATATACGAAGAAATGTTTCACCAGTAGAGTCATTATTATA
390 TAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAGTAGAGTCATTATTATA
1316453 TTCTAGATTAAGA-ATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
1 TTCTAGATTAAGAGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
1316517 CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
66 CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
*
1316582 TATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
131 TATCTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
*
1316647 TTTAACCACTTTTCACTAATTTTAAATCTTTTGATTACTACTCAACTCTATTTTAATTTTCTCTC
196 TTTAACCACTTTTCACTAATTTTAAATCTTTTGATCACTACTCAACTCTATTTTAATTTTCTCTC
* *
1316712 TAATTTTCACTTTACATCATTTCTTGTTTTGTGTTACTCAAAGGTTATTTTTTTTTTATACTCAT
261 TAATTTTCACTTTACATTATTTCTTGGTTTGTGTTACTCAAA-G--ATTTTTTTTTTATACTCAT
1316777 ATTTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGA
323 ATTTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGA
* *
1316842 TTTAAAGATGATTGAGTATATATGAGGAAATGTTTCACCAATAGAGTCATTATTATA
388 TTTAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAGTAGAGTCATTATTATA
** * * *
1316899 TTCTAGATTAAGAGATCTCTAAATATTAATGGTAGAATAAAATATTTCAATATCCATTAACTTGC
1 TTCTAGATTAAGAGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
* * * * *
1316964 CATTGTTAGACAATTATTCGCTCACAATTTTTATTATTTCAATATTAACTTTCATAACTTAAAAT
66 CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
1317029 TATCTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
131 TATCTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
*
1317094 TTTAACCACTTTTCACTAATTTT-AATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTC
196 TTTAACCACTTTTCACTAATTTTAAATCTTTTGATCACTACTCAACTCTATTTTAATTTTCTCTC
* * * *
1317158 TAATTTTCACTTTACATTATTTCTTAGTCTGTG-TACTCAAAGGTTATTTCTTTTTATACTTATA
261 TAATTTTCACTTTACATTATTTCTTGGTTTGTGTTACTCAAAGATT-TTT-TTTTTATACTCATA
*
1317222 TTTTATATTTCTTTAACTATGATATTAGCATTC-TTTTTTTAATATTTGTTTGTTGATGATTGAT
324 TTTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGAT
*
1317286 TTAAAGATGATTGAGTATATACGAGGAAATGTTTAACCAGTAGAGTCATTATTATA
389 TTAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAGTAGAGTCATTATTATA
*
1317342 TTCTAGATTAA-A-ATCTCTAAATATTAATGCTATAATAAAATATTTTAATATCAATTAACTTGC
1 TTCTAGATTAAGAGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
1317405 CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
66 CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
*
1317470 TATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
131 TATCTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
*
1317535 TTTAACCACTTTTCACTAATTTTAAATCTTTTGATTACTACTCAACTCTATTTTAATTTTCTCTC
196 TTTAACCACTTTTCACTAATTTTAAATCTTTTGATCACTACTCAACTCTATTTTAATTTTCTCTC
* * *
1317600 TAATTTTCACTTTACATCATTTCTTAGTTTGTGTTACTCAAAGGTTATTTTTTTTTATACTCATA
261 TAATTTTCACTTTACATTATTTCTTGGTTTGTGTTACTCAAA-GAT-TTTTTTTTTATACTCATA
1317665 TTTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGAT
324 TTTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGAT
*
1317730 TTAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAATAGAGTCATTATTATA
389 TTAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAGTAGAGTCATTATTATA
** * * *
1317786 TTCTAGATTAAGAGATCTCTAAATATTAATGGTAGAATAAAATATTTCAATATCCATTAACTTGC
1 TTCTAGATTAAGAGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
* * * * *
1317851 CATTGTTAGACAATTATT-GCTCACAATTTTTATTATTTCAATATTAACTTTCATAACTTAAAAT
66 CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
1317915 TATCTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
131 TATCTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
*
1317980 TTTAACCACTTTTCACTAATTTTAAATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTC
196 TTTAACCACTTTTCACTAATTTTAAATCTTTTGATCACTACTCAACTCTATTTTAATTTTCTCTC
* *
1318045 TAATTTTCACTTTACATTGTTTCTTGGTCTGTGTTACTCAAAGATTATTTTTTTTATACTCATAT
261 TAATTTTCACTTTACATTATTTCTTGGTTTGTGTTACTCAAAGATT-TTTTTTTTATACTCATAT
1318110 TTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATT
325 TTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATT
*
1318175 TAAAGATGATTGAGTATATACGAGGAAATGTTTAACCAGTAGAGTCATTATTATA
390 TAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAGTAGAGTCATTATTATA
1318230 TTCTAGATTAAGA-ATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
1 TTCTAGATTAAGAGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
1318294 CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
66 CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
*
1318359 TATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
131 TATCTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
*
1318424 TTTAACCACTTTTCACTAATTTTAAATCTTTTGATTACTACTCAACTCTATTTTAATTTTCTCTC
196 TTTAACCACTTTTCACTAATTTTAAATCTTTTGATCACTACTCAACTCTATTTTAATTTTCTCTC
* *
1318489 TAATTTTCACTTTACATCATTTCTTAGTTTGTGTTACTCAAAGGTTATTTTTTTTTTATACTCAT
261 TAATTTTCACTTTACATTATTTCTTGGTTTGTGTTACTCAAA-G--ATTTTTTTTTTATACTCAT
1318554 ATTTTATATTTCTTTAACTATGAT
323 ATTTTATATTTCTTTAACTATGAT
1318578 CCATTAGACA
Statistics
Matches: 2443, Mismatches: 102, Indels: 47
0.94 0.04 0.02
Matches are distributed among these distances:
441 194 0.08
442 97 0.04
443 423 0.17
444 807 0.33
445 394 0.16
446 322 0.13
447 206 0.08
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (444 bp):
TTCTAGATTAAGAGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
TATCTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
TTTAACCACTTTTCACTAATTTTAAATCTTTTGATCACTACTCAACTCTATTTTAATTTTCTCTC
TAATTTTCACTTTACATTATTTCTTGGTTTGTGTTACTCAAAGATTTTTTTTTTATACTCATATT
TTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATTT
AAAGATGATTGAGTATATACGAGGAAATGTTTCACCAGTAGAGTCATTATTATA
Found at i:1317705 original size:888 final size:891
Alignment explanation
Indices: 1315565--1318577 Score: 5502
Period size: 887 Copynumber: 3.4 Consensus size: 891
1315555 TGTTTTATTG
*
1315565 TTCTAAATTAAGAGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
1 TTCTAGATTAAGA-ATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
*
1315630 CATTATTAGATCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
65 CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
*
1315695 TATCTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
130 TATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
* *
1315760 TTTAACCACTTATCACTAA-TTTAAATC-TTTGATCAACTACTC-ACTCTATTTTAA-TTTCTCT
195 TTTAACCACTTTTCACTAATTTTAAATCTTTTGAT-TACTACTCAACTCTATTTTAATTTTCTCT
*
1315821 CTAATTTTTCACTTTACATCATCGTTTCTTGGTTTGTGTTACTCAAA-GTTA----TTTTTTATA
259 CTAA-TTTTCACTTTACATCA---TTTCTTAGTTTGTGTTACTCAAAGGTTATTTTTTTTTTATA
*
1315881 CTCATATTTTATATTTCTTTAACTATAATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATG
320 CTCATATTTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATG
* * * *
1315946 ATTGATTTAAAAATGATTGAGTATATACAAAGAAATGTTTCACCAGTAGAGTCATTATTATATTC
385 ATTGATTTAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAATAGAGTCATTATTATATTC
* ** * * *
1316011 TAGATTAAGATATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGCCAT
450 TAGATTAAGAGATCTCTAAATATTAATGGTAGAATAAAATATTTCAATATCCATTAACTTGCCAT
* * * * * * *
1316076 TATTAAACCATTATTCACTTACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATTAT
515 TGTTAGACAATTATTCGCTCACAATTTTTATTATTTCAATATTAACTTTCATAACTTAAAATTAT
1316141 CTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCTTT
580 CTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCTTT
1316206 AACCACTTTTCACTAATTTTAAATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTCTAA
645 AACCACTTTTCACTAATTTTAAATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTCTAA
* *
1316271 TTTTCACTTTACATTGTTTTTTGGTTTGTGTTACTCAAAGATT-TTTTTTTATATACTCATATTT
710 TTTTCACTTTACATTGTTTCTTGGTCTGTGTTACTCAAAGATTATTTTTTT-TATACTCATATTT
1316335 TATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATTTA
774 TATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATTTA
* * *
1316400 AAAATGATTGAGTATATACGAAGAAATGTTTCACCAGTAGAGTCATTATTATA
839 AAGATGATTGAGTATATACGAGGAAATGTTTAACCAGTAGAGTCATTATTATA
1316453 TTCTAGATTAAGAATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGCC
1 TTCTAGATTAAGAATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGCC
1316518 ATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATT
66 ATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATT
1316583 ATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCT
131 ATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCT
1316648 TTAACCACTTTTCACTAATTTTAAATCTTTTGATTACTACTCAACTCTATTTTAATTTTCTCTCT
196 TTAACCACTTTTCACTAATTTTAAATCTTTTGATTACTACTCAACTCTATTTTAATTTTCTCTCT
1316713 AATTTTCACTTTACATCATTTCTT-GTTTTGTGTTACTCAAAGGTTATTTTTTTTTTATACTCAT
261 AATTTTCACTTTACATCATTTCTTAG-TTTGTGTTACTCAAAGGTTATTTTTTTTTTATACTCAT
1316777 ATTTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGA
325 ATTTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGA
*
1316842 TTTAAAGATGATTGAGTATATATGAGGAAATGTTTCACCAATAGAGTCATTATTATATTCTAGAT
390 TTTAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAATAGAGTCATTATTATATTCTAGAT
1316907 TAAGAGATCTCTAAATATTAATGGTAGAATAAAATATTTCAATATCCATTAACTTGCCATTGTTA
455 TAAGAGATCTCTAAATATTAATGGTAGAATAAAATATTTCAATATCCATTAACTTGCCATTGTTA
1316972 GACAATTATTCGCTCACAATTTTTATTATTTCAATATTAACTTTCATAACTTAAAATTATCTTAT
520 GACAATTATTCGCTCACAATTTTTATTATTTCAATATTAACTTTCATAACTTAAAATTATCTTAT
1317037 TAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCTTTAACCA
585 TAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCTTTAACCA
1317102 CTTTTCACTAATTTT-AATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTCTAATTTTC
650 CTTTTCACTAATTTTAAATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTCTAATTTTC
* * * *
1317166 ACTTTACATTATTTCTTAGTCTGTG-TACTCAAAGGTTATTTCTTTTTATACTTATATTTTATAT
715 ACTTTACATTGTTTCTTGGTCTGTGTTACTCAAAGATTATTT-TTTTTATACTCATATTTTATAT
*
1317230 TTCTTTAACTATGATATTAGCATTC-TTTTTTTAATATTTGTTTGTTGATGATTGATTTAAAGAT
779 TTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATTTAAAGAT
1317294 GATTGAGTATATACGAGGAAATGTTTAACCAGTAGAGTCATTATTATA
844 GATTGAGTATATACGAGGAAATGTTTAACCAGTAGAGTCATTATTATA
*
1317342 TTCTAGATTAA-AATCTCTAAATATTAATGCTATAATAAAATATTTTAATATCAATTAACTTGCC
1 TTCTAGATTAAGAATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGCC
1317406 ATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATT
66 ATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATT
1317471 ATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCT
131 ATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCT
1317536 TTAACCACTTTTCACTAATTTTAAATCTTTTGATTACTACTCAACTCTATTTTAATTTTCTCTCT
196 TTAACCACTTTTCACTAATTTTAAATCTTTTGATTACTACTCAACTCTATTTTAATTTTCTCTCT
1317601 AATTTTCACTTTACATCATTTCTTAGTTTGTGTTACTCAAAGGTTA-TTTTTTTTTATACTCATA
261 AATTTTCACTTTACATCATTTCTTAGTTTGTGTTACTCAAAGGTTATTTTTTTTTTATACTCATA
1317665 TTTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGAT
326 TTTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGAT
1317730 TTAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAATAGAGTCATTATTATATTCTAGATT
391 TTAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAATAGAGTCATTATTATATTCTAGATT
1317795 AAGAGATCTCTAAATATTAATGGTAGAATAAAATATTTCAATATCCATTAACTTGCCATTGTTAG
456 AAGAGATCTCTAAATATTAATGGTAGAATAAAATATTTCAATATCCATTAACTTGCCATTGTTAG
1317860 ACAATTATT-GCTCACAATTTTTATTATTTCAATATTAACTTTCATAACTTAAAATTATCTTATT
521 ACAATTATTCGCTCACAATTTTTATTATTTCAATATTAACTTTCATAACTTAAAATTATCTTATT
1317924 AATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCTTTAACCAC
586 AATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCTTTAACCAC
1317989 TTTTCACTAATTTTAAATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTCTAATTTTCA
651 TTTTCACTAATTTTAAATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTCTAATTTTCA
1318054 CTTTACATTGTTTCTTGGTCTGTGTTACTCAAAGATTATTTTTTTTATACTCATATTTTATATTT
716 CTTTACATTGTTTCTTGGTCTGTGTTACTCAAAGATTATTTTTTTTATACTCATATTTTATATTT
1318119 CTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATTTAAAGATGA
781 CTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATTTAAAGATGA
1318184 TTGAGTATATACGAGGAAATGTTTAACCAGTAGAGTCATTATTATA
846 TTGAGTATATACGAGGAAATGTTTAACCAGTAGAGTCATTATTATA
1318230 TTCTAGATTAAGAATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGCC
1 TTCTAGATTAAGAATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGCC
1318295 ATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATT
66 ATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATT
1318360 ATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCT
131 ATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCT
1318425 TTAACCACTTTTCACTAATTTTAAATCTTTTGATTACTACTCAACTCTATTTTAATTTTCTCTCT
196 TTAACCACTTTTCACTAATTTTAAATCTTTTGATTACTACTCAACTCTATTTTAATTTTCTCTCT
1318490 AATTTTCACTTTACATCATTTCTTAGTTTGTGTTACTCAAAGGTTATTTTTTTTTTATACTCATA
261 AATTTTCACTTTACATCATTTCTTAGTTTGTGTTACTCAAAGGTTATTTTTTTTTTATACTCATA
1318555 TTTTATATTTCTTTAACTATGAT
326 TTTTATATTTCTTTAACTATGAT
1318578 CCATTAGACA
Statistics
Matches: 2065, Mismatches: 42, Indels: 34
0.96 0.02 0.02
Matches are distributed among these distances:
885 1 0.00
886 155 0.08
887 539 0.26
888 431 0.21
889 434 0.21
890 166 0.08
891 339 0.16
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (891 bp):
TTCTAGATTAAGAATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGCC
ATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATT
ATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCT
TTAACCACTTTTCACTAATTTTAAATCTTTTGATTACTACTCAACTCTATTTTAATTTTCTCTCT
AATTTTCACTTTACATCATTTCTTAGTTTGTGTTACTCAAAGGTTATTTTTTTTTTATACTCATA
TTTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGAT
TTAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAATAGAGTCATTATTATATTCTAGATT
AAGAGATCTCTAAATATTAATGGTAGAATAAAATATTTCAATATCCATTAACTTGCCATTGTTAG
ACAATTATTCGCTCACAATTTTTATTATTTCAATATTAACTTTCATAACTTAAAATTATCTTATT
AATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCTTTAACCAC
TTTTCACTAATTTTAAATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTCTAATTTTCA
CTTTACATTGTTTCTTGGTCTGTGTTACTCAAAGATTATTTTTTTTATACTCATATTTTATATTT
CTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATTTAAAGATGA
TTGAGTATATACGAGGAAATGTTTAACCAGTAGAGTCATTATTATA
Found at i:1318774 original size:282 final size:282
Alignment explanation
Indices: 1318298--1318859 Score: 930
Period size: 282 Copynumber: 2.0 Consensus size: 282
1318288 ACTTGCCATT
* * *
1318298 ATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATTATC
1 ATTAGACAATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTCATAATTAAAAATTATC
** *
1318363 TTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCTTTA
66 TTATTAATTAACCTACAACACACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGCATCTTTA
* * *
1318428 ACCACTTTTCACTAATTTTAAATCTTTTGATTACTACTCAACTCTATTTTAATTTTCTCTCTAAT
131 ACCACTTTTCACTAATTTTAAATCTTTTGATCACTAATCAACTCTACTTTAATTTTCTCTCTAAT
* * * *
1318493 TTTCACTTTACATCATTTCTTAGTTTGTGTTACTCAAAGGTTATTTTTTTTTTATACTCATATTT
196 TTTCACTTTACATCATTTCTTAGTCTGTGCTACTCAAAGGTTATTCTCTTTTTATACTCATATTT
1318558 TATATTTCTTTAACTATGATCC
261 TATATTTCTTTAACTATGATCC
*
1318580 ATTAGACAATTATTCGCTCACAATTTTTATTATTTCAATATTAAC-TTCATAACTTAAAAATTAT
1 ATTAGACAATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTCATAA-TTAAAAATTAT
*
1318644 CTT-TTAATTATACCTACAACACACATTTTTTATAAGTAGCTCTAGGTTAAGCATAATGCATCTT
65 CTTATTAATTA-ACCTACAACACACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGCATCTT
*
1318708 TAACCACTTTTCACTAATTTTATATCTTTTGATCACTAATCAACTCTACTTTAATTTTCTCTCTA
129 TAACCACTTTTCACTAATTTTAAATCTTTTGATCACTAATCAACTCTACTTTAATTTTCTCTCTA
* *
1318773 ATTTTCACTTTACATCGTTTCTTAGTCTGTGCTACTCAAAGGTTATTCTCTTTTTATACTTATAT
194 ATTTTCACTTTACATCATTTCTTAGTCTGTGCTACTCAAAGGTTATTCTCTTTTTATACTCATAT
1318838 TTTATATTTCTTTAACTATGAT
259 TTTATATTTCTTTAACTATGAT
1318860 ATTAGCATTT
Statistics
Matches: 260, Mismatches: 18, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
281 13 0.05
282 247 0.95
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.48
Consensus pattern (282 bp):
ATTAGACAATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTCATAATTAAAAATTATC
TTATTAATTAACCTACAACACACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGCATCTTTA
ACCACTTTTCACTAATTTTAAATCTTTTGATCACTAATCAACTCTACTTTAATTTTCTCTCTAAT
TTTCACTTTACATCATTTCTTAGTCTGTGCTACTCAAAGGTTATTCTCTTTTTATACTCATATTT
TATATTTCTTTAACTATGATCC
Found at i:1320096 original size:42 final size:42
Alignment explanation
Indices: 1320044--1320130 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
1320034 TAGCTTATAT
*
1320044 TATCATTTTAAAAAATT-TATATTTATATAAAATTTATTGATA
1 TATCATTTT-AAAAATTCTATATTTATATAAAATCTATTGATA
*
1320086 TATCATTTTAAAAATTCTATATTTATATAAGATCTATTGATA
1 TATCATTTTAAAAATTCTATATTTATATAAAATCTATTGATA
1320128 TAT
1 TAT
1320131 GAATATATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 7 0.17
42 35 0.83
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (42 bp):
TATCATTTTAAAAATTCTATATTTATATAAAATCTATTGATA
Found at i:1320595 original size:13 final size:14
Alignment explanation
Indices: 1320571--1320599 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1320561 TATAAATATA
1320571 TAATTATAATATTT
1 TAATTATAATATTT
1320585 TAATTAT-ATATTT
1 TAATTATAATATTT
1320598 TA
1 TA
1320600 TTCGGATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATAATATTT
Found at i:1322102 original size:13 final size:13
Alignment explanation
Indices: 1322084--1322109 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1322074 CATGCCTGTG
1322084 CATAGTTTATAGA
1 CATAGTTTATAGA
1322097 CATAGTTTATAGA
1 CATAGTTTATAGA
1322110 GAATATGTGA
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:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
CATAGTTTATAGA
Found at i:1323028 original size:32 final size:32
Alignment explanation
Indices: 1322967--1323029 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
1322957 TTTGTGTAAA
* *
1322967 ATATGATATAAATATATAAATTTTAATATTTT
1 ATATGATACAAATATATAAATGTTAATATTTT
*
1322999 ATATGATACGAATATATAAAATGTT-ATATTT
1 ATATGATACAAATATAT-AAATGTTAATATTT
1323030 ATAATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 21 0.78
33 6 0.22
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (32 bp):
ATATGATACAAATATATAAATGTTAATATTTT
Found at i:1329231 original size:21 final size:22
Alignment explanation
Indices: 1329191--1329236 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1329181 CTAAAATTTT
*
1329191 AATTGAAATATAACAAATATTA
1 AATTGAAATATAACAAATATGA
1329213 AATT-AAATATAA-AATATATGA
1 AATTGAAATATAACAA-ATATGA
1329234 AAT
1 AAT
1329237 GGGTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 2 0.09
21 16 0.73
22 4 0.18
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (22 bp):
AATTGAAATATAACAAATATGA
Found at i:1329948 original size:36 final size:36
Alignment explanation
Indices: 1329872--1329963 Score: 98
Period size: 36 Copynumber: 2.6 Consensus size: 36
1329862 ATATAAAAGT
* **
1329872 ATTATAATAATTTTGACAAATTATAATATGAGAGGT
1 ATTATAATAATTTTGACAAATAATAATATGAGAGCC
* *
1329908 ATTATAATAATTTTGGCAAATAATAGTA-GAAGAGCC
1 ATTATAATAATTTTGACAAATAATAATATG-AGAGCC
**
1329944 ATTAT-AGCATTTTGACAAAT
1 ATTATAATAATTTTGACAAAT
1329964 GATGGTAGGA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
35 13 0.28
36 34 0.72
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (36 bp):
ATTATAATAATTTTGACAAATAATAATATGAGAGCC
Found at i:1334276 original size:15 final size:15
Alignment explanation
Indices: 1334256--1334284 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1334246 CTAGTTCTGG
1334256 TTGTTTAGAATGAAA
1 TTGTTTAGAATGAAA
1334271 TTGTTTAGAATGAA
1 TTGTTTAGAATGAA
1334285 GCAATTTGTC
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:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (15 bp):
TTGTTTAGAATGAAA
Found at i:1336905 original size:3 final size:3
Alignment explanation
Indices: 1336897--1336927 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1336887 TAGAATGTAC
1336897 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1336928 TACAATAGAG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1344801 original size:32 final size:31
Alignment explanation
Indices: 1344749--1344828 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 31
1344739 TATGATTTCA
* * *
1344749 TTTGATTTTAATTTGGTAAAATACTAATGCAC
1 TTTGA-TTTCATTTGATAAAATACTAATACAC
* *
1344781 GTTTGATTTCATTTGATAAAATATTAATATAC
1 -TTTGATTTCATTTGATAAAATACTAATACAC
*
1344813 TTGGATTTCATTTGAT
1 TTTGATTTCATTTGAT
1344829 TTCATTTGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 15 0.37
32 21 0.51
33 5 0.12
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.47
Consensus pattern (31 bp):
TTTGATTTCATTTGATAAAATACTAATACAC
Found at i:1346036 original size:444 final size:445
Alignment explanation
Indices: 1344945--1346706 Score: 2845
Period size: 444 Copynumber: 4.0 Consensus size: 445
1344935 TGTTTTATTG
* *
1344945 TTCTAAATTAAAAGATCTCT-AATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
1 TTCTAGATTAAGAGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
* *
1345009 CATTATTAGATCATTATTCACTCACAATTTTTATTATTTCAGTATTAACTTTTATAATTTAAAAT
66 CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
*
1345074 TATCTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
131 TATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
* *
1345139 TTTAACCACTTTTCACTAATTTTAAATCTTTTGATTACTACTCAACTCTATTTTAATTTTCTCTC
196 TTTAACCACTTTTCACTAATTTTAAATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTC
** *
1345204 TAATTTTCACTTTACATTTTTTCTTGGTTTGTGTTACTCAAAGGTTTTTTTTTTTATACTCATAT
261 TAATTTTCACTTTACATCATTTCTTGGTTTGTGTTACTCAAAGGTTATTTTTTTTATACTCATAT
1345269 TTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATA----TTTGTT--TG-TTGA--
326 TTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATT
* *
1345325 T---GATGATTGAGTATATACAAAGAAATGTTTCACCAATAGAGTCATTATTATA
391 TAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAATAGAGTCATTATTATA
*
1345377 TTCTAGATTAAGAGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGT
1 TTCTAGATTAAGAGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
* *
1345442 CATTATTAAACCATTATTCACTCACAATTTTTACTATTTCAATATTAACTTTTATAATTTAAAAT
66 CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
* *
1345507 TATCTTATTAATTAACCTACAATGCACCTTTTGTATAAGTAGCTCTAAGTTAAGCATAATGTATC
131 TATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
1345572 TTTAACCACTTTTCACTAATTTTAAATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTC
196 TTTAACCACTTTTCACTAATTTTAAATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTC
* ** *
1345637 CAATTTTCACTTTACATTGTTTCTTGGTTTGTGTTACTCAAAGATTATTTTTTTTATACTCATAT
261 TAATTTTCACTTTACATCATTTCTTGGTTTGTGTTACTCAAAGGTTATTTTTTTTATACTCATAT
1345702 TTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATT
326 TTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATT
* *
1345767 TAAAGATGATTGAGTATATATGAGGAAATGTTTCACCAGTAGAGTCATTATTATA
391 TAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAATAGAGTCATTATTATA
1345822 TTCTAGATTAAGA-ATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
1 TTCTAGATTAAGAGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
*
1345886 CATTATTAGACCATTATTCACTCGCAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
66 CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
1345951 TATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
131 TATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
* *
1346016 TTTAACCACTTTTCACTAATTTTAAATCTTTTGATTACTACTCAACTCTATTTTAATTTT-TCTC
196 TTTAACCACTTTTCACTAATTTTAAATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTC
* * * *
1346080 TAATTTTCACTTTATATCATTTCTTGGTTTATGTTACTCAAATGTTATTTTTTTTTTACTCATAT
261 TAATTTTCACTTTACATCATTTCTTGGTTTGTGTTACTCAAAGGTTATTTTTTTTATACTCATAT
1346145 TTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATT
326 TTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATT
1346210 TAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAATAGAGTCATTATTATA
391 TAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAATAGAGTCATTATTATA
** *
1346265 TTCTAGATTAAGAGATCTCTAAATATTAATGGTATAATAAAATATTTCAATATCAATTAACTTGC
1 TTCTAGATTAAGAGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
* * * * *
1346330 CATTGTTAGACAATTATTCGCTCACAATTTTTATTATTTCAATATTAACTTTCATAACTTAAAAT
66 CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
* ** * *
1346395 TATTTTATTAATTAACCTACAACACACATTTTTTATAAGTAGCTCTAGGTTAAGCATAATGCATC
131 TATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
* * * *
1346460 TTTAACCACTTTTTACTAATTTTATATCTTTTAATCACTACTCAACTCTACTTCAATTTTCTCTC
196 TTTAACCACTTTTCACTAATTTTAAATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTC
* * * * *
1346525 TAATTTTCACTTTACGTCATTTCTTAGTCTGTGCTACTCAAAGGTTATTCTCTTTTTATACTTAT
261 TAATTTTCACTTTACATCATTTCTTGGTTTGTGTTACTCAAAGGTTATT-T-TTTTTATACTCAT
* * *
1346590 ATTTTATATTTCTTTAACTATGATATTAACATTC-TTTTTTTAATATTTGTTTATTGATGATTGA
324 ATTTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGA
* * * * * *
1346654 TTTAAAGATGATTGGGTATATACAAGAAAATCTTTCACTAGTAGAGTCATTAT
389 TTTAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAATAGAGTCATTAT
1346707 CATAAAAGTT
Statistics
Matches: 1239, Mismatches: 74, Indels: 20
0.93 0.06 0.02
Matches are distributed among these distances:
432 18 0.01
433 336 0.27
437 6 0.00
439 2 0.00
440 4 0.00
442 1 0.00
443 192 0.15
444 454 0.37
445 106 0.09
446 77 0.06
447 43 0.03
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.47
Consensus pattern (445 bp):
TTCTAGATTAAGAGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGC
CATTATTAGACCATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAAT
TATCTTATTAATTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATC
TTTAACCACTTTTCACTAATTTTAAATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTC
TAATTTTCACTTTACATCATTTCTTGGTTTGTGTTACTCAAAGGTTATTTTTTTTATACTCATAT
TTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATT
TAAAGATGATTGAGTATATACGAGGAAATGTTTCACCAATAGAGTCATTATTATA
Found at i:1347852 original size:42 final size:42
Alignment explanation
Indices: 1347800--1347886 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
1347790 TAGCTTATAT
1347800 TATCATTTTAAAAAATTTATATTTATATAAAATTTATTGATA
1 TATCATTTTAAAAAATTTATATTTATATAAAATTTATTGATA
* *
1347842 TATCATTTTAAAAATTTTATATTTATATAAGATTTATTGATA
1 TATCATTTTAAAAAATTTATATTTATATAAAATTTATTGATA
1347884 TAT
1 TAT
1347887 GAATATATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (42 bp):
TATCATTTTAAAAAATTTATATTTATATAAAATTTATTGATA
Found at i:1349885 original size:13 final size:13
Alignment explanation
Indices: 1349867--1349892 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1349857 CATGCCTGTG
1349867 CATAGTTTATAGA
1 CATAGTTTATAGA
1349880 CATAGTTTATAGA
1 CATAGTTTATAGA
1349893 GAATATGTGA
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:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
CATAGTTTATAGA
Found at i:1350812 original size:32 final size:32
Alignment explanation
Indices: 1350751--1350812 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1350741 TTTGTGTAAA
* *
1350751 ATATGATATAAATATATAAATTTTAATATTTT
1 ATATGATACAAATATATAAATGTTAATATTTT
*
1350783 ATATGATACGAATATATAAAATGTT-ATATT
1 ATATGATACAAATATAT-AAATGTTAATATT
1350813 ATAATAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 20 0.77
33 6 0.23
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (32 bp):
ATATGATACAAATATATAAATGTTAATATTTT
Found at i:1351675 original size:12 final size:12
Alignment explanation
Indices: 1351658--1351685 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1351648 CTCTCTCTTA
1351658 CGACCATCCTTC
1 CGACCATCCTTC
1351670 CGACCATCCTTC
1 CGACCATCCTTC
1351682 CGAC
1 CGAC
1351686 GCCGGTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.50, G:0.11, T:0.21
Consensus pattern (12 bp):
CGACCATCCTTC
Found at i:1356862 original size:18 final size:18
Alignment explanation
Indices: 1356839--1356884 Score: 85
Period size: 17 Copynumber: 2.6 Consensus size: 18
1356829 AAAAAATGAG
1356839 TATTTTTTAATATTTTGT
1 TATTTTTTAATATTTTGT
1356857 TA-TTTTTAATATTTTGT
1 TATTTTTTAATATTTTGT
1356874 TATTTTTTAAT
1 TATTTTTTAAT
1356885 TGTTTTGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.63
18 10 0.37
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (18 bp):
TATTTTTTAATATTTTGT
Found at i:1357181 original size:22 final size:23
Alignment explanation
Indices: 1357156--1357199 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1357146 TTAATTTTTT
* *
1357156 AAAATTTTAAT-TGAAATATAAC
1 AAAATTTAAATATAAAATATAAC
1357178 AAAATTTAAATATAAAATATAA
1 AAAATTTAAATATAAAATATAA
1357200 AATATATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
AAAATTTAAATATAAAATATAAC
Found at i:1357893 original size:36 final size:36
Alignment explanation
Indices: 1357853--1357947 Score: 111
Period size: 36 Copynumber: 2.6 Consensus size: 36
1357843 AGATATAAAA
*
1357853 GTATTATAATAATTTTGACAAATTATAATATG-AGAG
1 GTATTATAATAATTTTGACAAATAATAATA-GAAGAG
* *
1357889 GTATTATAATAATTTTGGCAAATAATAGTAGAAGAG
1 GTATTATAATAATTTTGACAAATAATAATAGAAGAG
** **
1357925 CCATTATAGCAATTTTGACAAAT
1 GTATTATAATAATTTTGACAAAT
1357948 GATGGTAGGA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
35 1 0.02
36 49 0.98
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (36 bp):
GTATTATAATAATTTTGACAAATAATAATAGAAGAG
Found at i:1364916 original size:1 final size:1
Alignment explanation
Indices: 1364906--1364942 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
1364896 ATTATTATTA
* *
1364906 TTTTTCTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1364943 ACAATAGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:1364922 original size:11 final size:11
Alignment explanation
Indices: 1364906--1364942 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
1364896 ATTATTATTA
1364906 TTTTTCTTTTT
1 TTTTTCTTTTT
1364917 TTTTTCTTTTT
1 TTTTTCTTTTT
1364928 TTTTT-TTTTT
1 TTTTTCTTTTT
1364938 TTTTT
1 TTTTT
1364943 ACAATAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:1378213 original size:445 final size:444
Alignment explanation
Indices: 1376709--1378464 Score: 2696
Period size: 443 Copynumber: 4.0 Consensus size: 444
1376699 TTAATTAAAA
* *
1376709 AGATCTGCT-AATATATAATGACATAATAAAATATTTTAATAATTCAATTAACTTGCCATTATTA
1 AGATCT-CTAAATAT-TAATGCCATAATAAAATATTTTAAT-A-TCAATTAACTTGTCATTATTA
* * *
1376773 GATCATTTATTCACTCACAATTTTTATTATTGCAGTATTAACTTTTATAATTTAAAATTATCTTA
62 GA-CAATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATTATCTTA
*
1376838 TTTAATTTAACCTTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCTTTA
126 -TTAA-TTAACC-TACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCTTTA
*
1376903 ACCACTTTTCACTAA-TTTAAAT-TTTTGATTACTACTCAACTCTATTTTAATTTTCTCTCTAAT
188 ACCACTTTTCACTAATTTTAAATCTTTTGATCACTACTCAACTCTATTTTAATTTTCTCTCTAAT
*
1376966 TTTCACTTTACAT-TTTTCTTGGTTTGTGTTACTCAAAGGTTTTTTTTTTTTTTCTTATACTCAT
253 TTTCACTTTACATCATTTCTTGGTTTGTGTTACTCAAAGG-----TTTTTTTTT-TTATACTCAT
1377030 ATTTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGA-TGA
312 ATTTTATATTTCTTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGA
* * *
1377094 --T-----TGA---GTATATACGAAGAAATGTTTCACTAGTAGAGTCATTATTATATTTTAGATT
377 TTTAAAGATGATTGGTATATACGAGGAAATGTTTCACCAGTAGAGTCATTATTATATTCTAGATT
1377149 AAG
442 AAG
* *
1377152 AGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGTCATTATTAAACC
1 AGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGTCATTATTAGACA
1377217 ATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATTATCTTATTAAT
66 ATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATTATCTTATTAAT
*
1377282 TAACCTACAATGCACCTTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCTTTAACCACTTT
131 TAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCTTTAACCACTTT
*
1377347 TCACTAATTTTAAATCTTTTAATCACTACTCAACTCTATTTTAATTTTCTCTCTAATTTTCACTT
196 TCACTAATTTTAAATCTTTTGATCACTACTCAACTCTATTTTAATTTTCTCTCTAATTTTCACTT
** * *
1377412 TACATTGTTTCTTGGTTTGTGTTACTCAAA-GATTATTTTTTTATACTCATATTTTATATTTCTT
261 TACATCATTTCTTGGTTTGTGTTACTCAAAGGTTTTTTTTTTTATACTCATATTTTATATTTCTT
1377476 TAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATTTAAAGATGATTG
326 TAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATTTAAAGATGATTG
1377541 AGTATATACGAGGAAATGTTTCACCAGTAGAGTCATTATTATATTCTAGATTAAG
391 -GTATATACGAGGAAATGTTTCACCAGTAGAGTCATTATTATATTCTAGATTAAG
1377596 A-ATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTG-CTATTATTAGAC
1 AGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGTC-ATTATTAGAC
* *
1377659 CATTATTCACTCGCAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATTATCTTATTAA
65 AATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATTATCTTATTAA
1377724 TTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCTTTAACCACTT
130 TTAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCTTTAACCACTT
* *
1377789 TTCACTAATTTTAAATCTTTTGATTACTACTCAACTCTATTTTAATTTTATCTCTAATTTTCACT
195 TTCACTAATTTTAAATCTTTTGATCACTACTCAACTCTATTTTAATTTTCTCTCTAATTTTCACT
* *
1377854 TTATATCATTTCTTGGTTTGTGTTACTCAAAGGTTTTTTTTTTTATACTCATACTTTATATTTCT
260 TTACATCATTTCTTGGTTTGTGTTACTCAAAGGTTTTTTTTTTTATACTCATATTTTATATTTCT
1377919 TTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATTTAAAGATGATT
325 TTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATTTAAAGATGATT
* *
1377984 GAGCATATACGAGGAAATGTTTCACCAATAGAGTCATTATTATATTCTAGATTAAG
390 G-GTATATACGAGGAAATGTTTCACCAGTAGAGTCATTATTATATTCTAGATTAAG
** * *
1378040 AGATCTCTAAATATTAATGGTATAATAAAATATTTCAATATCAATTAACTTGTCATTGTTAGACA
1 AGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGTCATTATTAGACA
* * *
1378105 ATTATTCGCTCACAATTTTTATTATTTCAATATTAACTTTCATAACTTAAAATTATCTTATTAAT
66 ATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATTATCTTATTAAT
** * *
1378170 TAACCTACAACACACATTTTTTATAAGTAGCTCTAGGTTAAGCATAATGCATCTTTAACCACTTT
131 TAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCTTTAACCACTTT
* * *
1378235 TCACTAATTTTATATCTTTTGATCACTACTCAACTCTACTTCAATTTTCTCTCTAATTTTCACTT
196 TCACTAATTTTAAATCTTTTGATCACTACTCAACTCTATTTTAATTTTCTCTCTAATTTTCACTT
* * * * * *
1378300 TACTTCATTTCTTAGTCTGTGCTACTCAAAGGTTATTCTCTTTTTATACTTATATTTTATATTTC
261 TACATCATTTCTTGGTTTGTGTTACTCAAAGGTT-TT-TTTTTTTATACTCATATTTTATATTTC
* *
1378365 TTTAACTATGATATTAGCATTC---TTTTTAATATTTGTTT-AT--TGATTGATTTAAAGATGAT
324 TTTAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATTTAAAGATGAT
* * *
1378424 TGGATATATACAAGGAAATCTTTCACTAGTAGAGTCATTAT
389 TGG-TATATACGAGGAAATGTTTCACCAGTAGAGTCATTAT
1378465 CATAAAAGTT
Statistics
Matches: 1228, Mismatches: 62, Indels: 48
0.92 0.05 0.04
Matches are distributed among these distances:
432 71 0.06
433 10 0.01
435 1 0.00
436 67 0.05
437 13 0.01
438 57 0.05
439 81 0.07
440 25 0.02
441 54 0.04
442 27 0.02
443 289 0.24
444 218 0.18
445 267 0.22
446 3 0.00
447 45 0.04
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.47
Consensus pattern (444 bp):
AGATCTCTAAATATTAATGCCATAATAAAATATTTTAATATCAATTAACTTGTCATTATTAGACA
ATTATTCACTCACAATTTTTATTATTTCAATATTAACTTTTATAATTTAAAATTATCTTATTAAT
TAACCTACAATGCACATTTTGTATAAGTAGCTCTAGGTTAAGCATAATGTATCTTTAACCACTTT
TCACTAATTTTAAATCTTTTGATCACTACTCAACTCTATTTTAATTTTCTCTCTAATTTTCACTT
TACATCATTTCTTGGTTTGTGTTACTCAAAGGTTTTTTTTTTTATACTCATATTTTATATTTCTT
TAACTATGATATTAGCTTTCTTTTTTTTAATATTTGTTTGTTGATGATTGATTTAAAGATGATTG
GTATATACGAGGAAATGTTTCACCAGTAGAGTCATTATTATATTCTAGATTAAG
Found at i:1379612 original size:42 final size:42
Alignment explanation
Indices: 1379560--1379646 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
1379550 TAGCTTATAT
1379560 TATCATTTTAAAAAATTTATATTTATATAAAATTTATTGATA
1 TATCATTTTAAAAAATTTATATTTATATAAAATTTATTGATA
* *
1379602 TATCATTTTAAAAATTTTATATTTATATAAGATTTATTGATA
1 TATCATTTTAAAAAATTTATATTTATATAAAATTTATTGATA
1379644 TAT
1 TAT
1379647 GAATATATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (42 bp):
TATCATTTTAAAAAATTTATATTTATATAAAATTTATTGATA
Found at i:1381634 original size:13 final size:13
Alignment explanation
Indices: 1381616--1381641 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1381606 CATGCCTGTG
1381616 CATAGTTTATAGA
1 CATAGTTTATAGA
1381629 CATAGTTTATAGA
1 CATAGTTTATAGA
1381642 GAATATGTGA
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:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
CATAGTTTATAGA
Found at i:1382394 original size:18 final size:17
Alignment explanation
Indices: 1382358--1382396 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1382348 ATTAGATTTG
*
1382358 ATAATTTAAAATATGAT
1 ATAATTTAAAATATAAT
*
1382375 ATAATATTATAATATAAT
1 ATAAT-TTAAAATATAAT
1382393 ATAA
1 ATAA
1382397 AAAAATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
ATAATTTAAAATATAAT
Found at i:1386562 original size:33 final size:33
Alignment explanation
Indices: 1386520--1386586 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
1386510 AGAAGAAAAA
* * *
1386520 ACAAATAAGGTCATTGCTTATCGAGTATCACTC
1 ACAAATAAGGTCATTGCTAATCAAGTAACACTC
1386553 ACAAATAAGGTCATTGCTAATCAAGTAACACTC
1 ACAAATAAGGTCATTGCTAATCAAGTAACACTC
1386586 A
1 A
1386587 ACCCTGTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (33 bp):
ACAAATAAGGTCATTGCTAATCAAGTAACACTC
Found at i:1390594 original size:2 final size:2
Alignment explanation
Indices: 1390587--1390611 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1390577 AATGTACTTA
1390587 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1390612 TGATAATACA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1400529 original size:34 final size:35
Alignment explanation
Indices: 1400459--1400527 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
1400449 TCATTGACTC
*
1400459 ATCTTTTTTCTGCACTTGAGTTTTATAAAATTTTT
1 ATCTTTTTTCTGCACTTGAGTTATATAAAATTTTT
*
1400494 ATCTTTTTTCTGTACTTGAGTTATATAAAATTTT
1 ATCTTTTTTCTGCACTTGAGTTATATAAAATTTT
1400528 ATATGTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.25, C:0.10, G:0.09, T:0.57
Consensus pattern (35 bp):
ATCTTTTTTCTGCACTTGAGTTATATAAAATTTTT
Found at i:1401961 original size:35 final size:33
Alignment explanation
Indices: 1401920--1402003 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 33
1401910 TATCTCTTTT
* *
1401920 ACTTTTAAACTTTTGGATGATTTATAAATCTAAAA
1 ACTTTTAAAATTTT--ATGATTTACAAATCTAAAA
* *
1401955 ACTTTTAAAAATTTTTTGATTTACAAATCTGAAA
1 ACTTTT-AAAATTTTATGATTTACAAATCTAAAA
1401989 ACTTTTAAAAATTTT
1 ACTTTT-AAAATTTT
1402004 CAAACTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
34 31 0.70
35 6 0.14
36 7 0.16
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.45
Consensus pattern (33 bp):
ACTTTTAAAATTTTATGATTTACAAATCTAAAA
Found at i:1401983 original size:34 final size:34
Alignment explanation
Indices: 1401937--1402003 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
1401927 AACTTTTGGA
*
1401937 TGATTTATAAATCTAAAAACTTTTAAAAATTTTT
1 TGATTTACAAATCTAAAAACTTTTAAAAATTTTT
*
1401971 TGATTTACAAATCTGAAAACTTTTAAAAATTTT
1 TGATTTACAAATCTAAAAACTTTTAAAAATTTT
1402004 CAAACTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (34 bp):
TGATTTACAAATCTAAAAACTTTTAAAAATTTTT
Found at i:1410021 original size:2 final size:2
Alignment explanation
Indices: 1410014--1410038 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1410004 CCATTTTGAT
1410014 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1410039 TATTAATTGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1417007 original size:14 final size:15
Alignment explanation
Indices: 1416988--1417018 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1416978 CGACGAATTT
1416988 AAAAAT-AAAAATAA
1 AAAAATAAAAAATAA
1417002 AAAAATAAAAAATAA
1 AAAAATAAAAAATAA
1417017 AA
1 AA
1417019 TCATTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAATAAAAAATAA
Found at i:1418134 original size:21 final size:21
Alignment explanation
Indices: 1418099--1418144 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1418089 ATAAATATTA
* *
1418099 AAAATAATAATTAAAATAACT
1 AAAATAATAATTAAAAAAAAT
1418120 AAAATAAT-ATATAAAAAAAAT
1 AAAATAATAAT-TAAAAAAAAT
1418141 AAAA
1 AAAA
1418145 ATTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAATAATAATTAAAAAAAAT
Found at i:1421089 original size:25 final size:25
Alignment explanation
Indices: 1421038--1421089 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
1421028 TATAAATATG
** * *
1421038 AAAACTTTTAAAAATTTTTAGATTT
1 AAAACTTTTAAAAATTTCCAAACTT
1421063 AAAACTTTTAAAAATTTCCAAACTT
1 AAAACTTTTAAAAATTTCCAAACTT
1421088 AA
1 AA
1421090 CTATCTGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (25 bp):
AAAACTTTTAAAAATTTCCAAACTT
Found at i:1423928 original size:2 final size:2
Alignment explanation
Indices: 1423921--1423964 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
1423911 AGGCCATTTT
* * * *
1423921 GA GA GA GA AA GA CA GA GA GA CA GA GA AA 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
1423963 GA
1 GA
1423965 TATTAATTGA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.55, C:0.05, G:0.41, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1426324 original size:14 final size:14
Alignment explanation
Indices: 1426305--1426334 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1426295 TCTCATCTAC
1426305 ACGTCTTCAAAACG
1 ACGTCTTCAAAACG
1426319 ACGTCTTCAAAACG
1 ACGTCTTCAAAACG
1426333 AC
1 AC
1426335 ATCATCATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.30, G:0.13, T:0.20
Consensus pattern (14 bp):
ACGTCTTCAAAACG
Found at i:1436122 original size:24 final size:23
Alignment explanation
Indices: 1436074--1436134 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
1436064 TTAATTTTAT
*
1436074 AATAAAATATATAAAAATTAAAAAA
1 AATAAAATA-A-AAAAATCAAAAAA
* *
1436099 AATTAAAGTAAAAAAATCATAAAA
1 AA-TAAAATAAAAAAATCAAAAAA
1436123 AATAAAATAAAA
1 AATAAAATAAAA
1436135 GTAATGCCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 9 0.29
24 13 0.42
25 3 0.10
26 6 0.19
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (23 bp):
AATAAAATAAAAAAATCAAAAAA
Found at i:1444988 original size:28 final size:29
Alignment explanation
Indices: 1444935--1444990 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
1444925 CTAATGATAA
* *
1444935 ATTTTAATTATTAAAATTAAATATTCAAC
1 ATTTTAATTAATAAAAATAAATATTCAAC
1444964 ATTTT-ATTAATAAATAATAAA-ATTCAA
1 ATTTTAATTAATAAA-AATAAATATTCAA
1444991 TTCAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (29 bp):
ATTTTAATTAATAAAAATAAATATTCAAC
Found at i:1461687 original size:31 final size:32
Alignment explanation
Indices: 1461625--1461687 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
1461615 TATATTTGTA
* * **
1461625 TCATGTTTTACATAAAAATCATGTAATATAAT
1 TCATGTCTAACATAAAAATCATAAAATATAAT
1461657 TCATGTCTAACATAAAAAT-ATAAAATATAAT
1 TCATGTCTAACATAAAAATCATAAAATATAAT
1461688 CTTTTGTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 10 0.37
32 17 0.63
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.37
Consensus pattern (32 bp):
TCATGTCTAACATAAAAATCATAAAATATAAT
Found at i:1462598 original size:3 final size:3
Alignment explanation
Indices: 1462585--1462620 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
1462575 TACGAAACTC
*
1462585 TTA TGTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1462621 GAAGGTAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1464922 original size:25 final size:26
Alignment explanation
Indices: 1464881--1464931 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
1464871 TGATTTTTAA
* *
1464881 ATTTTAAATTTAATTTTTTATATATT
1 ATTTTAAATATAATTTTTAATATATT
1464907 ATTTT-AATATAATTTTTAATATATT
1 ATTTTAAATATAATTTTTAATATATT
1464932 TAAATAAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
ATTTTAAATATAATTTTTAATATATT
Found at i:1464923 original size:12 final size:12
Alignment explanation
Indices: 1464880--1464929 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
1464870 TTGATTTTTA
* *
1464880 AATTTTAAATTT
1 AATTTTTAATAT
*
1464892 AATTTTTTATAT
1 AATTTTTAATAT
*
1464904 ATTATTTTAATAT
1 AAT-TTTTAATAT
1464917 AATTTTTAATAT
1 AATTTTTAATAT
1464929 A
1 A
1464930 TTTAAATAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
12 21 0.68
13 10 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
AATTTTTAATAT
Found at i:1464994 original size:10 final size:10
Alignment explanation
Indices: 1464979--1465003 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1464969 GTAATAATTT
1464979 AAAATTAATA
1 AAAATTAATA
1464989 AAAATTAATA
1 AAAATTAATA
1464999 AAAAT
1 AAAAT
1465004 ATATGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAATTAATA
Found at i:1465170 original size:16 final size:17
Alignment explanation
Indices: 1465139--1465171 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1465129 GAACATTATA
1465139 ATTTTAAATTAAATTTTG
1 ATTTTAAA-TAAATTTTG
1465157 ATTTTAAA-AAATTTT
1 ATTTTAAATAAATTTT
1465172 TCTCACCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTTTAAATAAATTTTG
Found at i:1468907 original size:16 final size:16
Alignment explanation
Indices: 1468863--1468915 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1468853 CAATTGAGAG
*
1468863 TTTAAGTAAATAAAAA
1 TTTAATTAAATAAAAA
* *
1468879 TATAA--ATATAAAAA
1 TTTAATTAAATAAAAA
1468893 TTTAATTAAATAAAAA
1 TTTAATTAAATAAAAA
*
1468909 TTAAATT
1 TTTAATT
1468916 TTAAAGGTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 12 0.40
16 18 0.60
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
TTTAATTAAATAAAAA
Found at i:1468927 original size:30 final size:30
Alignment explanation
Indices: 1468861--1468928 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
1468851 TCCAATTGAG
*
1468861 AGTTTAAGTAAATAAAAATATAAATATAAA
1 AGTTTAATTAAATAAAAATATAAATATAAA
* *
1468891 AATTTAATTAAATAAAAAT-TAAATTTTAAA
1 AGTTTAATTAAATAAAAATATAAA-TATAAA
*
1468921 GGTTTAAT
1 AGTTTAAT
1468929 AATTTAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (30 bp):
AGTTTAATTAAATAAAAATATAAATATAAA
Found at i:1468950 original size:16 final size:16
Alignment explanation
Indices: 1468931--1468961 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1468921 GGTTTAATAA
1468931 TTTAAAATAAAAAATT
1 TTTAAAATAAAAAATT
1468947 TTTAAAATAAAAAAT
1 TTTAAAATAAAAAAT
1468962 AAAAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTTAAAATAAAAAATT
Found at i:1469275 original size:3 final size:3
Alignment explanation
Indices: 1469267--1469299 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1469257 TTGACGTTAC
*
1469267 AGA AGA AGA AGA AGA AGA AG- AGA AGA GGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1469300 AAAAAAAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1472586 original size:22 final size:22
Alignment explanation
Indices: 1472538--1472604 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
1472528 AAATAAAAAA
1472538 TTAATTTAAAATTATAATATTTAAT
1 TTAATTT-AAA-T-TAATATTTAAT
* * * *
1472563 TTGATTTGAATTAATTTTTTAT
1 TTAATTTAAATTAATATTTAAT
1472585 TTAATTTAAATTAA-ATTTAA
1 TTAATTTAAATTAATATTTAA
1472605 ATATTAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
21 4 0.12
22 21 0.62
23 1 0.03
24 2 0.06
25 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (22 bp):
TTAATTTAAATTAATATTTAAT
Found at i:1472604 original size:6 final size:6
Alignment explanation
Indices: 1472583--1472641 Score: 50
Period size: 6 Copynumber: 9.5 Consensus size: 6
1472573 TTAATTTTTT
* *
1472583 ATTT-A ATTTAA A-TTAA ATTTAA ATATTAA ATATATAA ATATAT ATATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA AT-T-TAA ATTTAA AT-TTAA
1472633 ATTTAA ATT
1 ATTTAA ATT
1472642 GAATTTCAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
5 9 0.20
6 19 0.42
7 12 0.27
8 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
ATTTAA
Found at i:1472757 original size:20 final size:21
Alignment explanation
Indices: 1472732--1472783 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1472722 AAATAATTAT
*
1472732 TATATATAAA-TTTATTTAAA
1 TATATATAAATTTTATTAAAA
*
1472752 TATATAAAAATTTTATTAAAA
1 TATATATAAATTTTATTAAAA
1472773 TAATATATAAA
1 T-ATATATAAA
1472784 AAATAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 9 0.33
21 10 0.37
22 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATATATAAATTTTATTAAAA
Found at i:1490123 original size:22 final size:21
Alignment explanation
Indices: 1490082--1490125 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
1490072 GTTGACAAAA
*
1490082 AATTAATAATTATTTTTATTT
1 AATTAATAATTATTTATATTT
1490103 AATTAAATAATT-TTTAATATTT
1 AATT-AATAATTATTT-ATATTT
1490125 A
1 A
1490126 TCTCTAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTAATAATTATTTATATTT
Found at i:1490784 original size:3 final size:3
Alignment explanation
Indices: 1490742--1490766 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1490732 CCTTCTCCTA
1490742 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1490767 TTTTAATAAT
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):
AAT
Found at i:1497584 original size:30 final size:30
Alignment explanation
Indices: 1497545--1497601 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1497535 TTATTAATTT
* * *
1497545 ATATATATATTTATATAATGATATTTTTAA
1 ATATATATATTTAAAAAATAATATTTTTAA
*
1497575 ATATTTATATTTAAAAAATAATATTTT
1 ATATATATATTTAAAAAATAATATTTT
1497602 ATATTTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
ATATATATATTTAAAAAATAATATTTTTAA
Found at i:1497604 original size:21 final size:22
Alignment explanation
Indices: 1497574--1497625 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
1497564 GATATTTTTA
1497574 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
*
1497594 AATATTTTATATTTTTAAAAAT
1 AATATTTTATATTTTAAAAAAT
1497616 AATATTTTAT
1 AATATTTTAT
1497626 TAATTTCGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 4 0.14
21 6 0.21
22 19 0.66
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:1499973 original size:33 final size:33
Alignment explanation
Indices: 1499931--1500032 Score: 122
Period size: 32 Copynumber: 3.1 Consensus size: 33
1499921 TTATATGACT
* *
1499931 TTTTC-AAATTTTATTTTTAAAAAATTTATA-AA
1 TTTTCAAAAATTTATTTTCAAAAAA-TTATACAA
1499963 TTTT-AAAAATTTATTTTCAAAAAATTATACAA
1 TTTTCAAAAATTTATTTTCAAAAAATTATACAA
*
1499995 CTTTTCAAAAATTCA-TTTCAAAAAAATTATACAA
1 -TTTTCAAAAATTTATTTTC-AAAAAATTATACAA
1500029 TTTT
1 TTTT
1500033 TCGAAGAATC
Statistics
Matches: 62, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
31 5 0.08
32 23 0.37
33 12 0.19
34 22 0.35
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (33 bp):
TTTTCAAAAATTTATTTTCAAAAAATTATACAA
Found at i:1500034 original size:34 final size:34
Alignment explanation
Indices: 1499943--1500032 Score: 116
Period size: 34 Copynumber: 2.7 Consensus size: 34
1499933 TTCAAATTTT
* * *
1499943 ATTTTTAAAAAATTTATA-AATTTT-AAAAATTT
1 ATTTTCAAAAAAATTATACAATTTTCAAAAATTC
1499975 ATTTTC-AAAAAATTATACAACTTTTCAAAAATTC
1 ATTTTCAAAAAAATTATACAA-TTTTCAAAAATTC
1500009 A-TTTCAAAAAAATTATACAATTTT
1 ATTTTCAAAAAAATTATACAATTTT
1500033 TCGAAGAATC
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
31 10 0.20
32 7 0.14
33 12 0.24
34 22 0.43
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (34 bp):
ATTTTCAAAAAAATTATACAATTTTCAAAAATTC
Found at i:1506103 original size:14 final size:14
Alignment explanation
Indices: 1506080--1506114 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1506070 CTCAAGCAAA
*
1506080 AAATAAAAATGAAT
1 AAATAAAAATAAAT
*
1506094 AAATATAAATAAAT
1 AAATAAAAATAAAT
1506108 AAATAAA
1 AAATAAA
1506115 TAAAGCTTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:1511963 original size:12 final size:12
Alignment explanation
Indices: 1511948--1512009 Score: 58
Period size: 11 Copynumber: 5.2 Consensus size: 12
1511938 TTTAATTTTT
1511948 ATTTTAAATTAA
1 ATTTTAAATTAA
1511960 A-TTTAAATTTAA
1 ATTTTAAA-TTAA
*
1511972 ATTTAAAATTTAA
1 ATTTTAAA-TTAA
*
1511985 AATTT-AATTAA
1 ATTTTAAATTAA
*
1511996 A-TTTAAATCAA
1 ATTTTAAATTAA
1512007 ATT
1 ATT
1512010 CAAACTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
10 3 0.07
11 17 0.40
12 9 0.21
13 13 0.31
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTTTAAATTAA
Found at i:1511965 original size:6 final size:6
Alignment explanation
Indices: 1511925--1512003 Score: 71
Period size: 6 Copynumber: 13.8 Consensus size: 6
1511915 CTTGATTAAA
* * *
1511925 TAAATT TAAA-- T-AATT TAATTT TTATTT TAAA-T TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
1511969 TAAATT TAAAATT TAAAATT T-AA-T TAAATT TAAAT
1 TAAATT T-AAATT T-AAATT TAAATT TAAATT TAAAT
1512004 CAAATTCAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 14
0.77 0.05 0.17
Matches are distributed among these distances:
3 2 0.03
4 3 0.05
5 10 0.16
6 34 0.55
7 13 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:1511982 original size:7 final size:7
Alignment explanation
Indices: 1511958--1511991 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1511948 ATTTTAAATT
1511958 AAATTT-
1 AAATTTA
1511964 AAATTT-
1 AAATTTA
1511970 AAATTTA
1 AAATTTA
1511977 AAATTTA
1 AAATTTA
1511984 AAATTTA
1 AAATTTA
1511991 A
1 A
1511992 TTAAATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTA
Found at i:1512891 original size:20 final size:20
Alignment explanation
Indices: 1512866--1512915 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1512856 TTCGAAATTA
1512866 ATAAAATATTATTTTTAAAT
1 ATAAAATATTATTTTTAAAT
1512886 ATAAAATATTATTTTTAAAT
1 ATAAAATATTATTTTTAAAT
1512906 ATAAATATAT
1 ATAAA-ATAT
1512916 AATTATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAAAATATTATTTTTAAAT
Found at i:1512937 original size:18 final size:18
Alignment explanation
Indices: 1512904--1512938 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1512894 TTATTTTTAA
* *
1512904 ATATAAATATATAATTAT
1 ATATAAATAAAAAATTAT
1512922 ATATAAATAAAAAATTA
1 ATATAAATAAAAAATTA
1512939 AAAAATCAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATATAAATAAAAAATTAT
Found at i:1513081 original size:37 final size:37
Alignment explanation
Indices: 1513025--1513099 Score: 134
Period size: 37 Copynumber: 2.0 Consensus size: 37
1513015 AATTCAAAAG
1513025 AATGAAACCCATAAGACTCGGATTAGACTCACAACCC
1 AATGAAACCCATAAGACTCGGATTAGACTCACAACCC
1513062 AATGAAAACCCATAA-ACTCGGATTAGACTCACAACCC
1 AATG-AAACCCATAAGACTCGGATTAGACTCACAACCC
1513099 A
1 A
1513100 GTTGACACGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 27 0.73
38 10 0.27
ACGTcount: A:0.43, C:0.29, G:0.12, T:0.16
Consensus pattern (37 bp):
AATGAAACCCATAAGACTCGGATTAGACTCACAACCC
Found at i:1521374 original size:7 final size:7
Alignment explanation
Indices: 1521356--1521397 Score: 52
Period size: 6 Copynumber: 6.1 Consensus size: 7
1521346 AATGAGTAGA
1521356 TAAAAAT
1 TAAAAAT
1521363 T-AAAAT
1 TAAAAAT
1521369 TAAAAAT
1 TAAAAAT
1521376 T-AAAAT
1 TAAAAAT
*
1521382 TAATAGAT
1 TAA-AAAT
1521390 TAAAAAT
1 TAAAAAT
1521397 T
1 T
1521398 TTCATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
6 12 0.40
7 12 0.40
8 6 0.20
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (7 bp):
TAAAAAT
Found at i:1521374 original size:14 final size:13
Alignment explanation
Indices: 1521356--1521394 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
1521346 AATGAGTAGA
1521356 TAAAAATTAAAAT
1 TAAAAATTAAAAT
1521369 TAAAAATTAAAAT
1 TAAAAATTAAAAT
*
1521382 TAATAGATTAAAA
1 TAA-AAATTAAAA
1521395 ATTTTCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.67
14 8 0.33
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
TAAAAATTAAAAT
Found at i:1521420 original size:23 final size:21
Alignment explanation
Indices: 1521393--1521465 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 21
1521383 AATAGATTAA
1521393 AAATTTTCATTATATAAAATTTT
1 AAATTTT-ATTA-ATAAAATTTT
*
1521416 AAATTTTTTTTAAT-AAATTTT
1 AAA-TTTTATTAATAAAATTTT
*
1521437 GATATATTTATTAAATAAATATTTT
1 -AAAT-TTTATT-AATAAA-ATTTT
1521462 AAAT
1 AAAT
1521466 AAAAATATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
21 8 0.20
22 9 0.22
23 9 0.22
24 9 0.22
25 5 0.12
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (21 bp):
AAATTTTATTAATAAAATTTT
Found at i:1523477 original size:15 final size:18
Alignment explanation
Indices: 1523443--1523480 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
1523433 TTTATTAAAA
1523443 TTTATTTAATATAAATTT
1 TTTATTTAATATAAATTT
1523461 TTTATTTAA-A-AAATTT
1 TTTATTTAATATAAATTT
1523477 TTTA
1 TTTA
1523481 ATTATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.50
17 1 0.05
18 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTATTTAATATAAATTT
Found at i:1523508 original size:22 final size:21
Alignment explanation
Indices: 1523482--1523527 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
1523472 AATTTTTTAA
1523482 TTATAATTATAATAATTTATTT
1 TTATAATTATAATAA-TTATTT
* *
1523504 TTATAATTATTATTATTATTT
1 TTATAATTATAATAATTATTT
1523525 TTA
1 TTA
1523528 ATTAATTGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATAATTATAATAATTATTT
Found at i:1524784 original size:28 final size:30
Alignment explanation
Indices: 1524753--1524835 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 30
1524743 ATTTAATAAA
* *
1524753 ATTAAAAAAA-TATATTTTAT-ATTTTTAT
1 ATTAAAAAAATTATAATATATAATTTTTAT
1524781 ATTAATAAAAATTATAATATATAATTTTTAT
1 ATTAA-AAAAATTATAATATATAATTTTTAT
* *
1524812 A-TAAAATATAATAAAAATATATAA
1 ATTAAAA-A-AATTATAATATATAA
1524836 ATTATTAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
28 5 0.11
29 7 0.15
30 12 0.26
31 22 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
ATTAAAAAAATTATAATATATAATTTTTAT
Found at i:1524808 original size:31 final size:31
Alignment explanation
Indices: 1524723--1524813 Score: 84
Period size: 30 Copynumber: 3.0 Consensus size: 31
1524713 ATTTAAAATT
* * *
1524723 TTAATAAAAATTCTAA-ATA-AATTTAATAAAA
1 TTAATAAAAATTATAATATATAATTT--TTATA
* *
1524754 TTAA-AAAAA-TATATTTTAT-ATTTTTATA
1 TTAATAAAAATTATAATATATAATTTTTATA
1524782 TTAATAAAAATTATAATATATAATTTTTATA
1 TTAATAAAAATTATAATATATAATTTTTATA
1524813 T
1 T
1524814 AAAATATAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
28 7 0.15
29 8 0.17
30 19 0.40
31 14 0.29
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (31 bp):
TTAATAAAAATTATAATATATAATTTTTATA
Found at i:1543047 original size:20 final size:22
Alignment explanation
Indices: 1543022--1543070 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1543012 TAATATCATA
*
1543022 AATTTTTTA-A-AATTTGAATC
1 AATTTTTTATATAATTCGAATC
1543042 AATTTTTTATATAATTCGAATC
1 AATTTTTTATATAATTCGAATC
*
1543064 AAATTTT
1 AATTTTT
1543071 ACATATTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.36
21 1 0.04
22 15 0.60
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (22 bp):
AATTTTTTATATAATTCGAATC
Found at i:1543057 original size:22 final size:20
Alignment explanation
Indices: 1543022--1543070 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 20
1543012 TAATATCATA
*
1543022 AATTTTTTAAAATTTGAATC
1 AATTTTTTAAAATTCGAATC
1543042 AATTTTTTATATAATTCGAATC
1 AATTTTTTA-A-AATTCGAATC
1543064 AAATTTT
1 -AATTTT
1543071 ACATATTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 9 0.36
21 1 0.04
22 9 0.36
23 6 0.24
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (20 bp):
AATTTTTTAAAATTCGAATC
Found at i:1543076 original size:23 final size:22
Alignment explanation
Indices: 1543032--1543076 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1543022 AATTTTTTAA
* **
1543032 AATTTGAATCAATTTTTTATAT
1 AATTCGAATCAATTTTACATAT
1543054 AATTCGAATCAAATTTTACATAT
1 AATTCGAATC-AATTTTACATAT
1543077 TCATTTATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (22 bp):
AATTCGAATCAATTTTACATAT
Found at i:1546993 original size:70 final size:70
Alignment explanation
Indices: 1546880--1547025 Score: 283
Period size: 70 Copynumber: 2.1 Consensus size: 70
1546870 GCAATGAACC
1546880 TAAAAGAAACAATGCCTTCATTTCATCATCCATCTTAAGCTCCATAGTAGTCATCCGATTAAATA
1 TAAAAGAAACAATGCCTTCATTTCATCATCCATCTTAAGCTCCATAGTAGTCATCCGATTAAATA
1546945 TATCT
66 TATCT
1546950 TAAAAGAAACAATGCCTTCATTTCATCATCCATCTTAAGCTCCATAGTAGTCATCCGATTAAATA
1 TAAAAGAAACAATGCCTTCATTTCATCATCCATCTTAAGCTCCATAGTAGTCATCCGATTAAATA
1547015 TATCT
66 TATCT
1547020 TGAAAA
1 T-AAAA
1547026 TCACTCAAGT
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 71 0.95
71 4 0.05
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (70 bp):
TAAAAGAAACAATGCCTTCATTTCATCATCCATCTTAAGCTCCATAGTAGTCATCCGATTAAATA
TATCT
Found at i:1547898 original size:19 final size:19
Alignment explanation
Indices: 1547866--1547907 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1547856 GTTCAATCAA
1547866 CTCTTACTTCTCTT-TTTT
1 CTCTTACTTCTCTTGTTTT
*
1547884 CTCTCTACTTTTCTTGTTTT
1 CTCT-TACTTCTCTTGTTTT
1547904 -TCTT
1 CTCTT
1547908 CTTTTTCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.24
19 12 0.57
20 4 0.19
ACGTcount: A:0.05, C:0.26, G:0.02, T:0.67
Consensus pattern (19 bp):
CTCTTACTTCTCTTGTTTT
Found at i:1548413 original size:2 final size:2
Alignment explanation
Indices: 1548406--1548434 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1548396 AATGGAGTTT
1548406 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1548435 TGGGCATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1558164 original size:28 final size:28
Alignment explanation
Indices: 1558121--1558174 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1558111 TTTCTTCTTA
*
1558121 AAAACTCTCGACTTTTACATTTAACTGC
1 AAAACTCTCAACTTTTACATTTAACTGC
* **
1558149 AAAACTCTCAATTTTTATGTTTAACT
1 AAAACTCTCAACTTTTACATTTAACT
1558175 ACTTTTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (28 bp):
AAAACTCTCAACTTTTACATTTAACTGC
Found at i:1562602 original size:2 final size:2
Alignment explanation
Indices: 1562595--1562634 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1562585 CTTTAAGTTT
1562595 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
1562635 ATTTCTCACC
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):
TA
Found at i:1565484 original size:13 final size:13
Alignment explanation
Indices: 1565466--1565507 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1565456 TTTTAAAGAG
* *
1565466 TTTATTCAAAATT
1 TTTATTTAAAATA
1565479 TTTATTTTAAAATA
1 TTTA-TTTAAAATA
1565493 TTTATTTAAAA-A
1 TTTATTTAAAATA
1565505 TTT
1 TTT
1565508 GATTGAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 4 0.15
13 11 0.42
14 11 0.42
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTATTTAAAATA
Found at i:1577299 original size:67 final size:67
Alignment explanation
Indices: 1577175--1577335 Score: 173
Period size: 67 Copynumber: 2.4 Consensus size: 67
1577165 TGATCGCTAT
* * * * *
1577175 AACCATTTCTCTGACAGCTGAACAGTTTAGCAAAATGTTCTGCTTTTGCTTGGGCTTGGAG-CAA
1 AACCATTTCTCAGGCAGCTGAACAGTTCAGCAAAATGTGCAGCTTTTGCTTGGGCTTGG-GTCAA
1577239 TAG
65 TAG
* * * ** *
1577242 AGCCATTTCTCAGGCAGTTTAACAGTTCAGCAAAATGTGGCAG-TTTTGCTTTTGCTTGGGTCAC
1 AACCATTTCTCAGGCAGCTGAACAGTTCAGCAAAATGT-GCAGCTTTTGCTTGGGCTTGGGTCAA
*
1577306 TGG
65 TAG
*
1577309 AACCATGTCTCAGGCAGCTGAACAGTT
1 AACCATTTCTCAGGCAGCTGAACAGTT
1577336 AACATGTTGA
Statistics
Matches: 76, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
66 1 0.01
67 73 0.96
68 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (67 bp):
AACCATTTCTCAGGCAGCTGAACAGTTCAGCAAAATGTGCAGCTTTTGCTTGGGCTTGGGTCAAT
AG
Found at i:1577595 original size:2 final size:2
Alignment explanation
Indices: 1577559--1577585 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1577549 TCATATGTAA
1577559 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
1577586 ATTCATATAT
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:1581533 original size:16 final size:16
Alignment explanation
Indices: 1581483--1581535 Score: 67
Period size: 15 Copynumber: 3.4 Consensus size: 16
1581473 AAATTTTTTC
1581483 AAAATTTTAACTTTTTG-
1 AAAATTTT-A-TTTTTGA
1581500 AAAA-TTTATTTTT-A
1 AAAATTTTATTTTTGA
1581514 AAAATTTTATTTTTGA
1 AAAATTTTATTTTTGA
1581530 AAAATT
1 AAAATT
1581536 ATATAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
14 9 0.27
15 10 0.30
16 10 0.30
17 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (16 bp):
AAAATTTTATTTTTGA
Found at i:1581537 original size:14 final size:14
Alignment explanation
Indices: 1581494--1581537 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1581484 AAATTTTAAC
*
1581494 TTTTTGAAAATTTA
1 TTTTTGAAAAATTA
1581508 TTTTT-AAAAATTTTA
1 TTTTTGAAAAA--TTA
1581523 TTTTTGAAAAATTA
1 TTTTTGAAAAATTA
1581537 T
1 T
1581538 ATAATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 4 0.15
14 9 0.35
15 8 0.31
16 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (14 bp):
TTTTTGAAAAATTA
Found at i:1581843 original size:52 final size:52
Alignment explanation
Indices: 1581765--1581882 Score: 236
Period size: 52 Copynumber: 2.3 Consensus size: 52
1581755 CTAAAATAAA
1581765 AATTTAATGCTAAATACTTGTTCATAATCAATACTACTTTACTATATTTTGT
1 AATTTAATGCTAAATACTTGTTCATAATCAATACTACTTTACTATATTTTGT
1581817 AATTTAATGCTAAATACTTGTTCATAATCAATACTACTTTACTATATTTTGT
1 AATTTAATGCTAAATACTTGTTCATAATCAATACTACTTTACTATATTTTGT
1581869 AATTTAATGCTAAA
1 AATTTAATGCTAAA
1581883 GTAGACATAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (52 bp):
AATTTAATGCTAAATACTTGTTCATAATCAATACTACTTTACTATATTTTGT
Found at i:1582959 original size:24 final size:23
Alignment explanation
Indices: 1582927--1582988 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 23
1582917 ATAATGGAGC
1582927 TTTTAATTTTAATATATTTTATTA
1 TTTTAATTTTAATATATTTT-TTA
*
1582951 TTTTAA-TTTAA-A-AATTTTTA
1 TTTTAATTTTAATATATTTTTTA
*
1582971 TTTTATTTTTACATATAT
1 TTTTAATTTTA-ATATAT
1582989 ATCAATTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 8 0.26
21 8 0.26
22 2 0.06
23 6 0.19
24 7 0.23
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTAATTTTAATATATTTTTTA
Found at i:1582969 original size:23 final size:24
Alignment explanation
Indices: 1582927--1582972 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1582917 ATAATGGAGC
* *
1582927 TTTTAATTTTAATATATTTTATTA
1 TTTTAATTTAAAAATATTTTATTA
1582951 TTTTAATTTAAAAAT-TTTTATT
1 TTTTAATTTAAAAATATTTTATT
1582973 TTATTTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTAATTTAAAAATATTTTATTA
Found at i:1586358 original size:18 final size:18
Alignment explanation
Indices: 1586335--1586373 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1586325 ATATATAATT
*
1586335 TATTATG-TATTATATTCA
1 TATTATGTTATCATA-TCA
1586353 TATTATGTTATCATATCA
1 TATTATGTTATCATATCA
1586371 TAT
1 TAT
1586374 CTAAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (18 bp):
TATTATGTTATCATATCA
Found at i:1595367 original size:2 final size:2
Alignment explanation
Indices: 1595360--1595385 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1595350 CCAGTCAAGC
1595360 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
1595386 CATTTACAAA
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:1604400 original size:2 final size:2
Alignment explanation
Indices: 1604393--1604428 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1604383 CTAAGTCCAA
* *
1604393 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1604429 TTGAGGTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1614584 original size:2 final size:2
Alignment explanation
Indices: 1614577--1614610 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1614567 CTTTCTTCTC
1614577 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
1614611 TCAAGGAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1615675 original size:27 final size:27
Alignment explanation
Indices: 1615626--1615679 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1615616 CATTAATAAG
*
1615626 TAATAAAAATTATTTATGATATTAAAT
1 TAATAAAAATTATTTAAGATATTAAAT
*
1615653 TAATAAAAA-TATTTCAAGTTATTAAAT
1 TAATAAAAATTATTT-AAGATATTAAAT
1615680 AAAAAATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (27 bp):
TAATAAAAATTATTTAAGATATTAAAT
Found at i:1620131 original size:217 final size:217
Alignment explanation
Indices: 1619743--1620159 Score: 543
Period size: 217 Copynumber: 1.9 Consensus size: 217
1619733 CACCAATTTA
* **
1619743 AAATTTTATCTGTGATAAATTTTTTCTAATAGATTTAGGTAACATTATTAATTTTTGTCACAAAT
1 AAATTTTATCTGTGATAAATTTTTTCTAATAAATTTAGGTAACATTAACAATTTTTGTCACAAAT
* * * *
1619808 TGAATACTTTAGTTAACTATTAATGACATTGCAATTTCGACAAATCAATGTATGGTGTTATATGA
66 TGAACACTTTAATTAACTATTAATAACATTGCAATTTCGACAAATCAATGTATGGTATTATATGA
* * * *
1619873 CAATAATATAAATGTCACAAAATTTTACTATCAATTTTATTTGGTG-AAATTTTTTTTGTGATGT
131 CAATAACATAAATGTCACAAAATTTTACTATCAAATTTATTTGGTGAAAAATTTTTTTGTGACGT
1619937 TTTTTTATCTTAGGTGATGTTT
196 TTTTTTATCTTAGGTGATGTTT
* * * ** *
1619959 AAATTTTAATCTGTGATGAATTTTTTCTTATAAATTTTAGGTGATGTTAACAATTTTT-TCATAA
1 AAATTTT-ATCTGTGATAAATTTTTTCTAATAAA-TTTAGGTAACATTAACAATTTTTGTCACAA
* **
1620023 A-TGTAACACTTTAATTAACTATTAATAACATTGCAATTTCGTCATGTCAATGTATGGTATTATA
64 ATTG-AACACTTTAATTAACTATTAATAACATTGCAATTTCGACAAATCAATGTATGGTATTATA
** ** ** *
1620087 TGATGATAACATAAATGTCACAATTTTTTGTTGTCAAATTTATTTGGTGAAAAATTTTTTTGTGA
128 TGACAATAACATAAATGTCACAAAATTTTACTATCAAATTTATTTGGTGAAAAATTTTTTTGTGA
1620152 CGTTTTTT
193 CGTTTTTT
1620160 ATTTTTGGTG
Statistics
Matches: 170, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
216 9 0.05
217 122 0.72
218 39 0.23
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (217 bp):
AAATTTTATCTGTGATAAATTTTTTCTAATAAATTTAGGTAACATTAACAATTTTTGTCACAAAT
TGAACACTTTAATTAACTATTAATAACATTGCAATTTCGACAAATCAATGTATGGTATTATATGA
CAATAACATAAATGTCACAAAATTTTACTATCAAATTTATTTGGTGAAAAATTTTTTTGTGACGT
TTTTTTATCTTAGGTGATGTTT
Found at i:1620767 original size:219 final size:218
Alignment explanation
Indices: 1620389--1620805 Score: 521
Period size: 219 Copynumber: 1.9 Consensus size: 218
1620379 TTTTTTGTGA
* * * * * *
1620389 TTTTTTTTATTTTATGTGACGTTATAATTTTGTTATCAATTTAAAATTTTATTTTTGATAAATTT
1 TTTTTTTTATTTTAGGTGACATTATAATTTTGTTACCAATATAAAATTTTATATATGATAAATTT
* * * * * * * *
1620454 TTTTATATATTTTAAGTGACGTTATTAATTTTTGTTATAAATTGAATACTTTAGTTCACTATTAA
66 TTTAATAGACTTTAAGTGACATTATTAATTTTTGTCACAAATTGAATACTTTAATTAACTATTAA
* * * * ** * * *
1620519 TGACATTATAATTTTGTCATGTCAATGTATGGTGTTATATGACGATAACATAAATATTACAAACT
131 TAACAGTATAACTTCGTCACATCAATGTATGATATTATATGACGATAACATAAATATCACAAACT
1620584 TTTGAAAAAAATTTTGTGATTTT
196 TTTGAAAAAAATTTTGTGATTTT
* *
1620607 TTTTTTTTGTTTTAGGTGACATTATAATTTT-TTCACCAATATAAAATTTTATATATGATGAATT
1 TTTTTTTTATTTTAGGTGACATTATAATTTTGTT-ACCAATATAAAATTTTATATATGATAAATT
* * *
1620671 TTTCTAATAGACTTTAAGTGATATTATTAATTTTTGTCACAAATTGAATAGTTTAATTAATTATT
65 TTT-TAATAGACTTTAAGTGACATTATTAATTTTTGTCACAAATTGAATACTTTAATTAACTATT
* * * *
1620736 AATAACAGTATAACTTCGTCACATTAATGTATGATATTATATGATGATAACATAATTGTCACAAA
129 AATAACAGTATAACTTCGTCACATCAATGTATGATATTATATGACGATAACATAAATATCACAAA
1620801 CTTTT
194 CTTTT
1620806 AAATGATGTT
Statistics
Matches: 165, Mismatches: 32, Indels: 3
0.82 0.16 0.01
Matches are distributed among these distances:
217 2 0.01
218 56 0.34
219 107 0.65
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (218 bp):
TTTTTTTTATTTTAGGTGACATTATAATTTTGTTACCAATATAAAATTTTATATATGATAAATTT
TTTAATAGACTTTAAGTGACATTATTAATTTTTGTCACAAATTGAATACTTTAATTAACTATTAA
TAACAGTATAACTTCGTCACATCAATGTATGATATTATATGACGATAACATAAATATCACAAACT
TTTGAAAAAAATTTTGTGATTTT
Found at i:1624533 original size:23 final size:23
Alignment explanation
Indices: 1624503--1624556 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
1624493 ATAAGACTTT
1624503 ATCATTTATTTAGTGATGATTAA
1 ATCATTTATTTAGTGATGATTAA
1624526 ATCATTTATTTAGTGATGATTAA
1 ATCATTTATTTAGTGATGATTAA
1624549 ATCATTTA
1 ATCATTTA
1624557 ATGACATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (23 bp):
ATCATTTATTTAGTGATGATTAA
Found at i:1625094 original size:203 final size:199
Alignment explanation
Indices: 1624657--1625194 Score: 609
Period size: 203 Copynumber: 2.7 Consensus size: 199
1624647 TTATCTTACA
* * *
1624657 ATAATTTTGTCACCAATATTGTGATGATTTATCTTTTGTCATTAATATATTAGATTTTATCATTT
1 ATAATTTTGTCACAAATATTGTGATGATTTATCTTTCGTCACTAATATATTAGATTTTATCATTT
* * * * *
1624722 ATTTTGTAATGGTTATAGCCTTCAATGATGTTTTTCTTTATAAAT-A---ACGAAAATTAACATC
66 ATTTTGTGATGATTATAGCCTTCAATGA-CTTTTTCTTTATAAATAATTGACGAAAACTAACGTC
* * * * * * * *
1624783 ATAAAAAAAGTATAAGGTGACATTTAATTTTATTGTCACATTTGATAATATTTTATAATCATTGG
130 ACAAAAAAAGCATAAGGTGACATTGAATTTTATTGTCACAGTAGACAATATCTTACAATCATTGG
1624848 TGATG
195 TGATG
* * * * * *
1624853 ATAATTATATCACAAATATTGTAATGATTTATCTTTCGTCACAAATATATCATATTTTATCATTT
1 ATAATTTTGTCACAAATATTGTGATGATTTATCTTTCGTCACTAATATATTAGATTTTATCATTT
* * * * * *
1624918 ATTTTATGATGATTATAGCCTTTAATAACATTTTTGTTTATAAATAATTGATGAAAACTAACGTT
66 ATTTTGTGATGATTATAGCCTTCAATGAC-TTTTTCTTTATAAATAATTGACGAAAACTAACGTC
* * *
1624983 ACAAAAATTAATGCATAAGGTGACATTGGATTTTATTGTCATAGTAGACATTATCTTACAATCAT
130 ACAAAAA--AA-GCATAAGGTGACATTGAATTTTATTGTCACAGTAGACAATATCTTACAATCAT
1625048 TGGTGATG
192 TGGTGATG
* * * * * *
1625056 ATAATTTTGTTACTAATATTGTGATAATTTAGCTTTCGTCACTAGTATATTAGGTTTTACTCATT
1 ATAATTTTGTCACAAATATTGTGATGATTTATCTTTCGTCACTAATATATTAGATTTTA-TCATT
* * * *
1625121 T-TTTTGTGATGAATATAGCCTTCAATGACTTTTTTTTTCATAAATAGTTGACGAAAACTAATGT
65 TATTTTGTGATGATTATAGCCTTCAATGACTTTTTCTTT-ATAAATAATTGACGAAAACTAACGT
1625185 CACAAAAAAA
129 CACAAAAAAA
1625195 AAGGGTGACG
Statistics
Matches: 280, Mismatches: 52, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
196 93 0.33
197 1 0.00
200 17 0.06
201 2 0.01
202 10 0.04
203 151 0.54
204 6 0.02
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (199 bp):
ATAATTTTGTCACAAATATTGTGATGATTTATCTTTCGTCACTAATATATTAGATTTTATCATTT
ATTTTGTGATGATTATAGCCTTCAATGACTTTTTCTTTATAAATAATTGACGAAAACTAACGTCA
CAAAAAAAGCATAAGGTGACATTGAATTTTATTGTCACAGTAGACAATATCTTACAATCATTGGT
GATG
Found at i:1627450 original size:21 final size:20
Alignment explanation
Indices: 1627424--1627463 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1627414 AATATTTTAT
*
1627424 TAAAATTGATTAAATAAAAAA
1 TAAAATCGA-TAAATAAAAAA
1627445 TAAAATCGATAAATTAAAA
1 TAAAATCGATAAA-TAAAA
1627464 GTTTGTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAATCGATAAATAAAAAA
Found at i:1627463 original size:20 final size:21
Alignment explanation
Indices: 1627424--1627463 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1627414 AATATTTTAT
*
1627424 TAAAATTGATTAAATAAAAAA
1 TAAAATCGATTAAATAAAAAA
*
1627445 TAAAATCGA-TAAATTAAAA
1 TAAAATCGATTAAATAAAAA
1627464 GTTTGTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (21 bp):
TAAAATCGATTAAATAAAAAA
Found at i:1627564 original size:12 final size:12
Alignment explanation
Indices: 1627522--1627565 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
1627512 ATTATAATAT
1627522 TTTTTATATAAACA
1 TTTTTA-ATAAA-A
1627536 TTTTTAATAAAA
1 TTTTTAATAAAA
* *
1627548 ATTTTGATAAAA
1 TTTTTAATAAAA
1627560 TTTTTA
1 TTTTTA
1627566 TTTTTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 15 0.58
13 5 0.19
14 6 0.23
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (12 bp):
TTTTTAATAAAA
Done.