Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 13 of 117
Found at i:1358114 original size:49 final size:49
Alignment explanation
Indices: 1358038--1358131 Score: 179
Period size: 49 Copynumber: 1.9 Consensus size: 49
1358028 TTATGCATCA
*
1358038 GCTATAATTTTATATATTGATATTGAAAATTTAAAAATTTAAAAACAAT
1 GCTATAATTTTATATATTGATAATGAAAATTTAAAAATTTAAAAACAAT
1358087 GCTATAATTTTATATATTGATAATGAAAATTTAAAAATTTAAAAA
1 GCTATAATTTTATATATTGATAATGAAAATTTAAAAATTTAAAAA
1358132 TGAGATAAGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.40
Consensus pattern (49 bp):
GCTATAATTTTATATATTGATAATGAAAATTTAAAAATTTAAAAACAAT
Found at i:1358190 original size:20 final size:22
Alignment explanation
Indices: 1358153--1358192 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1358143 AGTTGGCACG
1358153 AATTTATTTAATTTTAATAATT
1 AATTTATTTAATTTTAATAATT
1358175 AATTT-TTTAA-TTTAATAA
1 AATTTATTTAATTTTAATAA
1358193 ATATATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTTATTTAATTTTAATAATT
Found at i:1358201 original size:20 final size:21
Alignment explanation
Indices: 1358153--1358201 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
1358143 AGTTGGCACG
*
1358153 AATTTATTTAATTTTAATAATT
1 AATTT-TTTAATTTTAATAAAT
1358175 AATTTTTTAA-TTTAATAAAT
1 AATTTTTTAATTTTAATAAAT
1358195 ATATTTT
1 A-ATTTT
1358202 AGTGGAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 10 0.40
21 10 0.40
22 5 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AATTTTTTAATTTTAATAAAT
Found at i:1358503 original size:2 final size:2
Alignment explanation
Indices: 1358498--1358532 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1358488 TATATATATA
1358498 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1358533 ATGTATGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1360349 original size:20 final size:20
Alignment explanation
Indices: 1360311--1360365 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
1360301 ACTTAAATTA
* *
1360311 AATAAT-ATGATAAATAAAT
1 AATAATAATTATAAAAAAAT
* *
1360330 AATATTACTTATAAAAAAAT
1 AATAATAATTATAAAAAAAT
*
1360350 AGTAATAATTATAAAA
1 AATAATAATTATAAAA
1360366 TAAAGATAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
AATAATAATTATAAAAAAAT
Found at i:1360375 original size:20 final size:20
Alignment explanation
Indices: 1360338--1360375 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1360328 ATAATATTAC
*
1360338 TTATAAAAAAATAGTAATAA
1 TTATAAAAAAAGAGTAATAA
1360358 TTATAAAATAAAGA-TAAT
1 TTATAAAA-AAAGAGTAAT
1360376 TATTTCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
TTATAAAAAAAGAGTAATAA
Found at i:1362296 original size:19 final size:19
Alignment explanation
Indices: 1362274--1362310 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1362264 TTTATATATA
*
1362274 ATAGTTTAGTATGAAAAAT
1 ATAGTTTAATATGAAAAAT
*
1362293 ATAGTTTAATATTAAAAA
1 ATAGTTTAATATGAAAAA
1362311 GATTATGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
ATAGTTTAATATGAAAAAT
Found at i:1362677 original size:49 final size:49
Alignment explanation
Indices: 1362606--1362704 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
1362596 GAAGACTTCA
*
1362606 TAAGTCTTTTAGGAAAGTTTTCACGTTATTCATGATTTACGTGAAAGAC
1 TAAGTCTTTTAGGAAAGTTTTCACGTAATTCATGATTTACGTGAAAGAC
1362655 TAAGTCTTTTAGG-AAGTCTTTCACGTAATTCATGATTTACGTGAAAGAC
1 TAAGTCTTTTAGGAAAGT-TTTCACGTAATTCATGATTTACGTGAAAGAC
1362704 T
1 T
1362705 TCATAAGTCT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 4 0.08
49 44 0.92
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (49 bp):
TAAGTCTTTTAGGAAAGTTTTCACGTAATTCATGATTTACGTGAAAGAC
Found at i:1362957 original size:11 final size:11
Alignment explanation
Indices: 1362943--1362967 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1362933 TATTTAAAAA
1362943 ATTATTAAATT
1 ATTATTAAATT
1362954 ATTATTAAATT
1 ATTATTAAATT
1362965 ATT
1 ATT
1362968 TTATGTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTATTAAATT
Found at i:1363720 original size:11 final size:11
Alignment explanation
Indices: 1363704--1363731 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1363694 TTAGTCTTTG
1363704 TGGAAACTAAC
1 TGGAAACTAAC
1363715 TGGAAACTAAC
1 TGGAAACTAAC
1363726 TGGAAA
1 TGGAAA
1363732 GCGGCTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.18
Consensus pattern (11 bp):
TGGAAACTAAC
Found at i:1363844 original size:4 final size:4
Alignment explanation
Indices: 1363835--1363900 Score: 75
Period size: 4 Copynumber: 17.0 Consensus size: 4
1363825 TATTTTATAT
* * *
1363835 TTTA TTTA TTTA TTTA -TTA TTTA TCTA TCTA CTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1363882 TTT- TTTA GTTTA TTT- TTTA
1 TTTA TTTA -TTTA TTTA TTTA
1363901 GGTTGATTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
3 9 0.17
4 41 0.76
5 4 0.07
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:1363897 original size:11 final size:11
Alignment explanation
Indices: 1363821--1363900 Score: 63
Period size: 12 Copynumber: 6.9 Consensus size: 11
1363811 TCAAGTCCAA
1363821 TTATTATTTTAT
1 TTATT-TTTTAT
*
1363833 ATT-TTATTTAT
1 -TTATTTTTTAT
*
1363844 TTATTTATTAT
1 TTATTTTTTAT
* * *
1363855 TTATCTATCTAC
1 TTAT-TTTTTAT
1363867 TTATTTATTTAT
1 TTATTT-TTTAT
1363879 TTATTTTTTAGT
1 TTATTTTTTA-T
1363891 TTATTTTTTA
1 TTATTTTTTA
1363901 GGTTGATTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
10 2 0.04
11 20 0.38
12 29 0.55
13 2 0.04
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (11 bp):
TTATTTTTTAT
Found at i:1365536 original size:63 final size:63
Alignment explanation
Indices: 1365469--1365669 Score: 187
Period size: 63 Copynumber: 3.2 Consensus size: 63
1365459 CTTCCGATGC
** *
1365469 AAAATGCAATCAATATTCTACTACTCAATTTTTAAGATGGTTAGTGAATGTGTTTATTCTAGA
1 AAAATGCCTTCAATATTCTACTACTCAATTTTTAAGATGGTTAGTGAAGGTGTTTATTCTAGA
* ** * * ** *
1365532 AAAATGCCTTCACTAATTCT--TTTTTAATTTATGT-ACATAATTATTGAAGGTGTTT-TT-TGA
1 AAAATGCCTTCAAT-ATTCTACTACTCAATTT-T-TAAGATGGTTAGTGAAGGTGTTTATTCT-A
1365592 GA
62 GA
* * * *
1365594 ACAAACGCCTTCAATATTCTACTACTCAAATTTTAAGATGGTTAGTGAAGGCGTTTATTCTAAA
1 A-AAATGCCTTCAATATTCTACTACTCAATTTTTAAGATGGTTAGTGAAGGTGTTTATTCTAGA
1365658 AAAATGCCTTCA
1 AAAATGCCTTCA
1365670 CTAATTCTTT
Statistics
Matches: 104, Mismatches: 24, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
61 1 0.01
62 19 0.18
63 66 0.63
64 17 0.16
65 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (63 bp):
AAAATGCCTTCAATATTCTACTACTCAATTTTTAAGATGGTTAGTGAAGGTGTTTATTCTAGA
Found at i:1365636 original size:126 final size:125
Alignment explanation
Indices: 1365478--1365724 Score: 422
Period size: 126 Copynumber: 2.0 Consensus size: 125
1365468 CAAAATGCAA
* * * *
1365478 TCAATATTCTACTACTCAATTTTTAAGATGGTTAGTGAATGTGTTTATTCTAGAAAAATGCCTTC
1 TCAATATTCTACTACTCAAATTTTAAGATGGTTAGTGAAGGCGTTTATTCTAAAAAAATGCCTTC
* *
1365543 ACTAATTCTTTTTTAATTTATGTACATAATTATTGAAGGTGTTTTTTGAGAACAAACGCCT
66 ACTAATTC-TTTTTAATTTACGTACATAATTATTGAAGGTATTTTTTGAGAACAAACGCCT
1365604 TCAATATTCTACTACTCAAATTTTAAGATGGTTAGTGAAGGCGTTTATTCTAAAAAAATGCCTTC
1 TCAATATTCTACTACTCAAATTTTAAGATGGTTAGTGAAGGCGTTTATTCTAAAAAAATGCCTTC
*
1365669 ACTAATTCTTTTTAATTTACGTAGATAATTATTGAAGGTATTTTTTGAGAACAAAC
66 ACTAATTCTTTTTAATTTACGTACATAATTATTGAAGGTATTTTTTGAGAACAAAC
1365725 ACTTTTGATA
Statistics
Matches: 114, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
125 45 0.39
126 69 0.61
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (125 bp):
TCAATATTCTACTACTCAAATTTTAAGATGGTTAGTGAAGGCGTTTATTCTAAAAAAATGCCTTC
ACTAATTCTTTTTAATTTACGTACATAATTATTGAAGGTATTTTTTGAGAACAAACGCCT
Found at i:1365797 original size:186 final size:188
Alignment explanation
Indices: 1365596--1365983 Score: 541
Period size: 187 Copynumber: 2.1 Consensus size: 188
1365586 TTTTGAGAAC
* * * *
1365596 AAACGCCTTCAATATTCTACTACTCAAATTTTAAGATGGTTAGTGAAGGCGTTTATTCTA-AAAA
1 AAACGCCTTCAATATTCCACTACTCAAATTTAAAAATGGTTAGTGAAGACGTTTATTCTAGAAAA
* * **
1365660 AATGCCTTCACTAATTCTTTTTAATTTACGTAGATAATTATTGAAGGTATTTTTTGAGAACAAAC
66 AATGCCTTCACTAATTCTATTTAATTTACGTACATAATTATTGAAGACATTTTTTGAGAACAAAC
* * * *
1365725 ACTTTTGATAA-TTTCTTTTTAAAATTTTTAGG-ATTATTAAAGGCATTTTCCAGTGA-A
131 ACCTTTAATAATTTTCTTTTAAAAATTTGT-GGTATTATTAAAGGCATTTTCCAGT-ATA
*
1365782 AAACGCCTTCAATATTCCACTACTCAAATTTAAAAATGGTTAGTGAAGATGTTTATTCTAGAAAA
1 AAACGCCTTCAATATTCCACTACTCAAATTTAAAAATGGTTAGTGAAGACGTTTATTCTAGAAAA
* * *
1365847 AATGCCTTCACTAATTCTATTTAATTTACGTACATAATTATTGATGACGTTTTTTGAGAACAAAT
66 AATGCCTTCACTAATTCTATTTAATTTACGTACATAATTATTGAAGACATTTTTTGAGAACAAAC
* * **
1365912 GCCTTTAATAATTTTCTTTTAAAAATTTGTGGTATTATTAAAGGTATTTTTTAGTATA
131 ACCTTTAATAATTTTCTTTTAAAAATTTGTGGTATTATTAAAGGCATTTTCCAGTATA
*
1365970 AAACACCTTCAATA
1 AAACGCCTTCAATA
1365984 ATGTTTAAGG
Statistics
Matches: 177, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
186 55 0.31
187 73 0.41
188 49 0.28
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (188 bp):
AAACGCCTTCAATATTCCACTACTCAAATTTAAAAATGGTTAGTGAAGACGTTTATTCTAGAAAA
AATGCCTTCACTAATTCTATTTAATTTACGTACATAATTATTGAAGACATTTTTTGAGAACAAAC
ACCTTTAATAATTTTCTTTTAAAAATTTGTGGTATTATTAAAGGCATTTTCCAGTATA
Found at i:1366779 original size:12 final size:12
Alignment explanation
Indices: 1366762--1366805 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
1366752 TGGTATCGTA
1366762 TGCTGAATGGTT
1 TGCTGAATGGTT
* *
1366774 TGCTGAATCGTA
1 TGCTGAATGGTT
1366786 TGCTGAATGGTT
1 TGCTGAATGGTT
1366798 TGCTGAAT
1 TGCTGAAT
1366806 CGTATTTCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.20, C:0.11, G:0.30, T:0.39
Consensus pattern (12 bp):
TGCTGAATGGTT
Found at i:1366786 original size:29 final size:28
Alignment explanation
Indices: 1366743--1366810 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 28
1366733 GTGATATTGT
*
1366743 TTTGCTTAATGGTATCGTATGCTGAATGG
1 TTTGCTGAAT-GTATCGTATGCTGAATGG
1366772 TTTGCTG-A---ATCGTATGCTGAATGG
1 TTTGCTGAATGTATCGTATGCTGAATGG
1366796 TTTGCTGAATCGTAT
1 TTTGCTGAAT-GTAT
1366811 TTCTAAATGG
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
24 23 0.70
25 1 0.03
28 1 0.03
29 8 0.24
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.41
Consensus pattern (28 bp):
TTTGCTGAATGTATCGTATGCTGAATGG
Found at i:1366788 original size:24 final size:24
Alignment explanation
Indices: 1366756--1366810 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
1366746 GCTTAATGGT
1366756 ATCGTATGCTGAATGGTTTGCTGA
1 ATCGTATGCTGAATGGTTTGCTGA
1366780 ATCGTATGCTGAATGGTTTGCTGA
1 ATCGTATGCTGAATGGTTTGCTGA
1366804 ATCGTAT
1 ATCGTAT
1366811 TTCTAAATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (24 bp):
ATCGTATGCTGAATGGTTTGCTGA
Found at i:1369093 original size:12 final size:12
Alignment explanation
Indices: 1369076--1369100 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1369066 TTATTTAAAG
1369076 AAAAATCAAAAT
1 AAAAATCAAAAT
1369088 AAAAATCAAAAT
1 AAAAATCAAAAT
1369100 A
1 A
1369101 GAAAGGAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAATCAAAAT
Found at i:1369343 original size:120 final size:120
Alignment explanation
Indices: 1369134--1369650 Score: 746
Period size: 120 Copynumber: 4.3 Consensus size: 120
1369124 TTTTGTGTAG
* * * *
1369134 GGAAAATTGATACTTTCAACTTTTTCCC-GAAA-ATGTTTTTTAGAAA-TTT-ATTTTTAAGGAA
1 GGAAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTTTTGAAACTTTGATTTTCAAGGAA
1369195 AATTGATACTTTCAACTTTTCCTCAAAAATCC-CTTTTTTGAAAATTTATTTTTAA
65 AATTGATACTTTCAACTTTTCCTCAAAAATCCTCTTTTTTGAAAATTTATTTTTAA
*
1369250 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAAACTTTGATTTCCAAGGAA
1 GGAAAATTGATACTTTCAACTTTTCC-CAAAAATATTTTTTTTTGAAACTTTGATTTTCAAGGAA
* * *
1369315 AATTGATACTTTCAACTTTTTCTTAAAAA-CCTTTTTTTTGAAAATTTATTTTTAA
65 AATTGATACTTTCAACTTTTCCTCAAAAATCCTCTTTTTTGAAAATTTATTTTTAA
* * *
1369370 GAAAAATTGATACTTGCAACTTTTCCTCAAAAATATTTTTTTTTGAAACTTTGATTTTCAAGGGA
1 GGAAAATTGATACTTTCAACTTTTCC-CAAAAATATTTTTTTTTGAAACTTTGATTTTCAAGGAA
* **
1369435 AATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTTTAAATTTATTTTTAA
65 AATTGATACTTTCAACTTTTCCTCAAAAATCCTCTTTTTTGAAAATTTATTTTTAA
* *
1369491 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTGGAAATTTTGATTTTCAAGGAA
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTTTTGAAACTTTGATTTTCAAGGAA
** *
1369555 AATTGATACTTTCAACTTTTCCTCAAAAATCCT-TTTTTT-TTAACTTATTTTTAA
65 AATTGATACTTTCAACTTTTCCTCAAAAATCCTCTTTTTTGAAAATTTATTTTTAA
*
1369609 GGAAAATTGATACTTTCAACTTCTCCCTAAAAATATTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTT
1369651 GAAAATTTTG
Statistics
Matches: 368, Mismatches: 24, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
115 6 0.02
116 21 0.06
117 3 0.01
118 59 0.16
119 17 0.05
120 207 0.56
121 55 0.15
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (120 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTTTGAAACTTTGATTTTCAAGGAAA
ATTGATACTTTCAACTTTTCCTCAAAAATCCTCTTTTTTGAAAATTTATTTTTAA
Found at i:1369354 original size:60 final size:60
Alignment explanation
Indices: 1369134--1369654 Score: 647
Period size: 60 Copynumber: 8.8 Consensus size: 60
1369124 TTTTGTGTAG
* * *
1369134 GGAAAATTGATACTTTCAACTTTTTCC-CGAAAAT--GTTTTTTAGAAA-TTTATTTTTAA
1 GGAAAATTGATACTTTCAAC-TTTTCCTCAAAAATCCTTTTTTTTGAAACTTTATTTTTAA
* *
1369191 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCC-CTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTGAAACTTTATTTTTAA
** **
1369250 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAAACTTTGATTTCCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTGAAACTTT-ATTTTTAA
* * *
1369311 GGAAAATTGATACTTTCAACTTTTTCTTAAAAA-CCTTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTGAAACTTTATTTTTAA
* * ** *
1369370 GAAAAATTGATACTTGCAACTTTTCCTCAAAAATATTTTTTTTTGAAACTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTGAAACTTT-ATTTTTAA
* *
1369431 GGGAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTTTAAA-TTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCC-TTTTTTTTGAAACTTTATTTTTAA
* * * *
1369491 GGAAAATTGATACTTTCAACTTTTCC-CTAAAAAT-ATTTTTTTGGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAATCCTTTTTTTTGAAACTTT-ATTTTTAA
*
1369551 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTT-TAAC-TTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTGAAACTTTATTTTTAA
* *
1369609 GGAAAATTGATACTTTCAACTTCTCC-CTAAAAAT--ATTTTTTTGAAA
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAATCCTTTTTTTTGAAA
1369655 ATTTTGATTT
Statistics
Matches: 404, Mismatches: 44, Indels: 32
0.84 0.09 0.07
Matches are distributed among these distances:
56 13 0.03
57 29 0.07
58 57 0.14
59 86 0.21
60 122 0.30
61 86 0.21
62 11 0.03
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (60 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTGAAACTTTATTTTTAA
Found at i:1369797 original size:15 final size:16
Alignment explanation
Indices: 1369777--1369811 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1369767 CTAATCTAAT
*
1369777 AAATAAAT-AAAAAAC
1 AAATAAATGAAAAAAA
1369792 AAATAAATGAAAAAAA
1 AAATAAATGAAAAAAA
1369808 AAAT
1 AAAT
1369812 TCAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (16 bp):
AAATAAATGAAAAAAA
Found at i:1370373 original size:26 final size:26
Alignment explanation
Indices: 1370340--1370389 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1370330 GGAAATTTCC
1370340 CAAAAATTTCCAGAAAAATT-TTTCGT
1 CAAAAATTTCCA-AAAAATTATTTCGT
*
1370366 CAAAAATTTCTAAAAAATTATTTC
1 CAAAAATTTCCAAAAAATTATTTC
1370390 TGATCCCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (26 bp):
CAAAAATTTCCAAAAAATTATTTCGT
Found at i:1370962 original size:16 final size:16
Alignment explanation
Indices: 1370862--1370962 Score: 58
Period size: 16 Copynumber: 6.6 Consensus size: 16
1370852 AAAAAATAAT
1370862 ATAATAATAATAAAT-
1 ATAATAATAATAAATA
1370877 AT-ATAACTATATAAATA
1 ATAATAA-TA-ATAAATA
1370894 A-AATACAT-ATAAAT-
1 ATAATA-ATAATAAATA
* *
1370908 CTAAT-CTAA-AAA-A
1 ATAATAATAATAAATA
* *
1370921 ATATATATTAATACATA
1 ATA-ATAATAATAAATA
1370938 ATAATAATAATAAATA
1 ATAATAATAATAAATA
1370954 CATAA-AATA
1 -ATAATAATA
1370963 CAAAAGAGGA
Statistics
Matches: 66, Mismatches: 7, Indels: 25
0.67 0.07 0.26
Matches are distributed among these distances:
13 6 0.09
14 7 0.11
15 16 0.24
16 23 0.35
17 13 0.20
18 1 0.02
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAATAATAATAAATA
Found at i:1371157 original size:1 final size:1
Alignment explanation
Indices: 1371146--1371209 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
1371136 AACATTGTCA
* * * * * * * *
1371146 TTTTTTGTTTTTTGTATTTTTATTTTTTTTTGTGTTTTTTTTTGTTTTTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1371210 ACCAAAGCTC
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.03, C:0.00, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:1371176 original size:20 final size:18
Alignment explanation
Indices: 1371146--1371209 Score: 83
Period size: 18 Copynumber: 3.4 Consensus size: 18
1371136 AACATTGTCA
*
1371146 TTTTTTGTTTTTTGTATTT
1 TTTTTTTTTTTTTGT-TTT
*
1371165 TTATTTTTTTTTGTGTTTT
1 TT-TTTTTTTTTTTGTTTT
*
1371184 TTTTTGTTTTTTTGTTTT
1 TTTTTTTTTTTTTGTTTT
1371202 TTTTTTTT
1 TTTTTTTT
1371210 ACCAAAGCTC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
18 21 0.54
19 7 0.18
20 11 0.28
ACGTcount: A:0.03, C:0.00, G:0.09, T:0.88
Consensus pattern (18 bp):
TTTTTTTTTTTTTGTTTT
Found at i:1371305 original size:42 final size:41
Alignment explanation
Indices: 1371216--1371973 Score: 1174
Period size: 42 Copynumber: 18.1 Consensus size: 41
1371206 TTTTACCAAA
* * *
1371216 GCTCCTCTAAAAAGAGGCTCAACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1371257 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATT
* * *
1371299 GCTCCTCTAAACAGTGGCACCTCGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
1371340 GCTCCTCTAAACAGGGGCACCACGACTTTGAAAAATTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATT
*
1371382 GCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
*
1371424 GCTCCTCTAAGCAGAGGCACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
*
1371466 GCTCCTCTAAATAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
1371507 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATT
*
1371549 GCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
*
1371591 GCTCCTCTAAATAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
1371632 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATT
*
1371674 GCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
*
1371716 GCTCCTCTAAGCAGAGGCACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
* *
1371758 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATT
*
1371800 GCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
*
1371842 GCTCCTCTAAGCAGAGGCACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
*
1371884 GCTCCTCTAAACAGAGGCACCACGAATTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
*
1371926 GCTCCTCTAAATAGAGGCACCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
1371968 GCTCCT
1 GCTCCT
1371974 TGACAATCAT
Statistics
Matches: 661, Mismatches: 43, Indels: 25
0.91 0.06 0.03
Matches are distributed among these distances:
41 157 0.24
42 491 0.74
43 13 0.02
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:1371443 original size:125 final size:125
Alignment explanation
Indices: 1371216--1371973 Score: 1257
Period size: 125 Copynumber: 6.0 Consensus size: 125
1371206 TTTTACCAAA
* * *
1371216 GCTCCTCTAAAAAGAGGCTCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
* *
1371281 ACTTTGAAAAAGTAAATTGCTCCTCTAAACAGTGGCACCTCGACTTT-GGAAAGTAAATT
66 ACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATT
* *
1371340 GCTCCTCTAAACAGGGGCACCACGACTTTGAAAAATTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
** * * *
1371405 GACTTTGGGAAAGTAAATTGCTCCTCTAAGCAGAGGCACCACGACTTTTGAAAAGTAAATT
65 GACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATT
*
1371466 GCTCCTCTAAATAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
*
1371531 ACTTTGAAAAATTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATT
66 ACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATT
* *
1371591 GCTCCTCTAAATAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
*
1371656 ACTTTGAAAAATTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATT
66 ACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATT
*
1371716 GCTCCTCTAAGCAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
* *
1371781 AACTTTGAAAAATTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATT
65 GACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATT
*
1371842 GCTCCTCTAAGCAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
* * * *
1371907 GAATTTGAGAAAGTAAATTGCTCCTCTAAATAGAGGCACCACGACTTTGAGAAAGTAAATT
65 GACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATT
1371968 GCTCCT
1 GCTCCT
1371974 TGACAATCAT
Statistics
Matches: 602, Mismatches: 29, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
124 26 0.04
125 312 0.52
126 264 0.44
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (125 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATT
Found at i:1373235 original size:10 final size:10
Alignment explanation
Indices: 1373222--1373267 Score: 76
Period size: 10 Copynumber: 4.7 Consensus size: 10
1373212 CATTTTCTCA
1373222 TTTTTTCCTT
1 TTTTTTCCTT
1373232 TTTTTT-CTT
1 TTTTTTCCTT
1373241 TTTTTTCCTT
1 TTTTTTCCTT
*
1373251 TTTTTTCTTT
1 TTTTTTCCTT
1373261 TTTTTTC
1 TTTTTTC
1373268 ATCATCTTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
9 9 0.26
10 25 0.74
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTCCTT
Found at i:1373244 original size:19 final size:19
Alignment explanation
Indices: 1373222--1373265 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
1373212 CATTTTCTCA
1373222 TTTTTTCCTTTTTTTTCTT
1 TTTTTTCCTTTTTTTTCTT
1373241 TTTTTTCCTTTTTTTTCTT
1 TTTTTTCCTTTTTTTTCTT
1373260 TTTTTT
1 TTTTTT
1373266 TCATCATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTTTTCCTTTTTTTTCTT
Found at i:1373265 original size:9 final size:9
Alignment explanation
Indices: 1373222--1373265 Score: 70
Period size: 9 Copynumber: 4.8 Consensus size: 9
1373212 CATTTTCTCA
*
1373222 TTTTTTCCT
1 TTTTTTTCT
1373231 TTTTTTTCT
1 TTTTTTTCT
1373240 TTTTTTTCCT
1 TTTTTTT-CT
1373250 TTTTTTTCT
1 TTTTTTTCT
1373259 TTTTTTT
1 TTTTTTT
1373266 TCATCATCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
9 24 0.73
10 9 0.27
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:1377119 original size:12 final size:12
Alignment explanation
Indices: 1377102--1377126 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1377092 TTATTTAAAG
1377102 AAAAATCAAAAT
1 AAAAATCAAAAT
1377114 AAAAATCAAAAT
1 AAAAATCAAAAT
1377126 A
1 A
1377127 GAAAGGAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAATCAAAAT
Found at i:1377285 original size:59 final size:58
Alignment explanation
Indices: 1377161--1377756 Score: 492
Period size: 58 Copynumber: 10.0 Consensus size: 58
1377151 TTTTGTGTAG
* * * *
1377161 GGAAAATTGATACTTTCAACTTTTTCTCGAAAATGTTTTTTAG-AAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAA
*
1377218 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCCTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-CTTTTTTTGAAAATTTATTTTTAA
* * *
1377277 GGAAAATTGATACTTTCAAACTTTTCCTCAAAAATATTTTTTTTGAAACGTTTGA-TTTCAA
1 GGAAAATTGATACTTTC-AACTTTTCCTCAAAAAT-CTTTTTTTGAAA-ATTT-ATTTTTAA
*
1377338 GGAAAATTGATACTTCTTC-ACTTTTCCTCAAAAATTTTTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATAC-T-TTCAACTTTTCCTCAAAAA--TCTTTTTTTGAAAATTTATTTTTAA
* * *
1377399 GG-AAATTGATACTTTACACACTTTTCCCTCAAATTATAT-TTTTTTTGCAACTTTGA-TTTCAA
1 GGAAAATTGATACTTT-CA-ACTTTT-CCTCAAA--A-ATCTTTTTTTGAAAATTT-ATTTTTAA
* * **
1377461 GGGAAATTGATACTTTTCAACTTTCCCTCAAAAATTCCTCTTTTTTTTTTAAATTTATTTTTAA
1 GGAAAATTGATAC-TTTCAACTTTTCCTCAAAAA----TC-TTTTTTTGAAAATTTATTTTTAA
** *
1377525 GGAAAATTGATACTTTTCCACAACTTTTTCCTC--AAATCTTTTTTT--TTATTT-TATTTAA
1 GGAAAATTGATAC-TTT---CAAC-TTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAA
* * * *
1377583 GG--AATTGATAACTTTC-ACTTTTCCT-AAAATAACTTTTTTGGGAAATTTTGATTTTCAA
1 GGAAAATTGAT-ACTTTCAACTTTTCCTCAAAA-ATCTTTTTT-TGAAAATTT-ATTTTTAA
* **
1377641 -GCAAATTGATACTTTCAACTTTTCCTC--AAATCCTTTTTTTTTTAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-C-TTTTTTTGAAAATTTATTTTTAA
*
1377698 GGAAAATTGATACTTTCAACTTTTCC-CTAAAAATATTTTTTTGAAAATTTTGATTTTTA
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAATCTTTTTTTGAAAA-TTT-ATTTTTA
1377757 TTTAAAGAAA
Statistics
Matches: 445, Mismatches: 42, Indels: 101
0.76 0.07 0.17
Matches are distributed among these distances:
51 7 0.02
52 4 0.01
53 9 0.02
56 13 0.03
57 44 0.10
58 70 0.16
59 63 0.14
60 49 0.11
61 66 0.15
62 49 0.11
63 19 0.04
64 37 0.08
65 1 0.00
66 3 0.01
67 4 0.01
68 7 0.02
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.48
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAA
Found at i:1377350 original size:61 final size:58
Alignment explanation
Indices: 1377161--1377743 Score: 502
Period size: 61 Copynumber: 9.8 Consensus size: 58
1377151 TTTTGTGTAG
* * * *
1377161 GGAAAATTGATACTTTCAACTTTTTCTCGAAAAT-GTTTTTTAGAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAATTTATTTTTAA
***
1377218 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCCTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTG-AAATTTATTTTTAA
*
1377277 GGAAAATTGATACTTTCAAACTTTTCCTCAAAAATATTTTTTTTGAAACGTTTGA-TTTCAA
1 GGAAAATTGATACTTTC-AACTTTTCCTCAAAAATATTTTTTTTGAAA--TTT-ATTTTTAA
*
1377338 GGAAAATTGATACTTCTTC-ACTTTTCCTCAAAAATTTTTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATAC-T-TTCAACTTTTCCTCAAAAA-TATTTTTTTTG-AAATTTATTTTTAA
* * *
1377399 GG-AAATTGATACTTTACACACTTTTCCCTCAAATTATATTTTTTTTGCAACTTTGA-TTTCAA
1 GGAAAATTGATACTTT-CA-ACTTTT-CCTCAAA-AATATTTTTTTTG-AAATTT-ATTTTTAA
* * * *
1377461 GGGAAATTGATACTTTTCAACTTTCCCTCAAAAATTCCTCTTTTTTTTTTAAATTTATTTTTAA
1 GGAAAATTGATAC-TTTCAACTTTTCCTCAAAAA----T-ATTTTTTTTGAAATTTATTTTTAA
* * *
1377525 GGAAAATTGATACTTTTCCACAACTTTTTCCTC--AAATCTTTTTTTT--TATTT-TATTTAA
1 GGAAAATTGATAC-TTT---CAAC-TTTTCCTCAAAAATATTTTTTTTGAAATTTATTTTTAA
** *
1377583 GG--AATTGATAACTTTC-ACTTTTCCT--AAAATAACTTTTTTGGGAAATTTTGATTTTCAA
1 GGAAAATTGAT-ACTTTCAACTTTTCCTCAAAAAT-A-TTTTTTTTGAAA-TTT-ATTTTTAA
* ** *
1377641 -GCAAATTGATACTTTCAACTTTTCCTCAAATCCT-TTTTTTTTTAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAA-AATATTTTTTTTGAAATTTATTTTTAA
1377698 GGAAAATTGATACTTTCAACTTTTCC-CTAAAAATA-TTTTTTTGAAA
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTTGAAA
1377744 ATTTTGATTT
Statistics
Matches: 436, Mismatches: 43, Indels: 94
0.76 0.08 0.16
Matches are distributed among these distances:
51 11 0.03
52 2 0.00
53 7 0.02
55 1 0.00
56 13 0.03
57 54 0.12
58 57 0.13
59 65 0.15
60 36 0.08
61 69 0.16
62 48 0.11
63 21 0.05
64 30 0.07
65 8 0.02
66 3 0.01
67 4 0.01
68 7 0.02
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAATTTATTTTTAA
Found at i:1377791 original size:14 final size:15
Alignment explanation
Indices: 1377759--1377805 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
1377749 GATTTTTATT
1377759 TAAAGAAAATAGAATAA
1 TAAAGAAAATA-AA-AA
1377776 TAAA-AAAATAAAAA
1 TAAAGAAAATAAAAA
*
1377790 TAAATAAAGATAAAAA
1 TAAAGAAA-ATAAAAA
1377806 AATAAAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.21
15 5 0.18
16 13 0.46
17 4 0.14
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (15 bp):
TAAAGAAAATAAAAA
Found at i:1377797 original size:18 final size:18
Alignment explanation
Indices: 1377759--1377811 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
1377749 GATTTTTATT
* *
1377759 TAAAGAAAATAGAAT-AA
1 TAAAGAAAAAAAAATAAA
1377776 TAAA-AAAATAAAAATAAA
1 TAAAGAAAA-AAAAATAAA
*
1377794 TAAAGATAAAAAAATAAA
1 TAAAGAAAAAAAAATAAA
1377812 GGAAAGTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 4 0.13
17 8 0.27
18 15 0.50
19 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (18 bp):
TAAAGAAAAAAAAATAAA
Found at i:1377810 original size:35 final size:36
Alignment explanation
Indices: 1377759--1377850 Score: 93
Period size: 35 Copynumber: 2.6 Consensus size: 36
1377749 GATTTTTATT
*
1377759 TAAAGA-AAATAGAATAATAAAAAAATAAAA-ATAAA
1 TAAAGATAAAAAGAATAATAAAAAAATAAAACA-AAA
** *
1377794 TAAAGATAAAAA-AATAA-AGGAAAGTAAAACCAAAA
1 TAAAGATAAAAAGAATAATAAAAAAATAAAA-CAAAA
*
1377829 TAAAGATAAAAAGAATATTAAA
1 TAAAGATAAAAAGAATAATAAA
1377851 TAAACCTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
34 9 0.20
35 26 0.58
36 9 0.20
37 1 0.02
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (36 bp):
TAAAGATAAAAAGAATAATAAAAAAATAAAACAAAA
Found at i:1377821 original size:18 final size:18
Alignment explanation
Indices: 1377785--1377845 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
1377775 ATAAAAAAAT
*
1377785 AAAAATAAATAAAGATAA
1 AAAAATAAAGAAAGATAA
1377803 AAAAATAAAGGAAAG-TAA
1 AAAAATAAA-GAAAGATAA
** *
1377821 AACCA-AAATAAAGATAA
1 AAAAATAAAGAAAGATAA
1377838 AAAGAATA
1 AAA-AATA
1377846 TTAAATAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
16 4 0.12
17 8 0.24
18 16 0.48
19 5 0.15
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (18 bp):
AAAAATAAAGAAAGATAA
Found at i:1378440 original size:26 final size:25
Alignment explanation
Indices: 1378402--1378457 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
1378392 GAATCTGGAA
1378402 ATTTCCCAAAAATTTCCAGAAAAATT
1 ATTTCCCAAAAATTTCCA-AAAAATT
*
1378428 -TTTCGCCAAAAATTTCTAAAAAATT
1 ATTTC-CCAAAAATTTCCAAAAAATT
1378453 ATTTC
1 ATTTC
1378458 TGATCCCTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.36
Consensus pattern (25 bp):
ATTTCCCAAAAATTTCCAAAAAATT
Found at i:1378963 original size:20 final size:19
Alignment explanation
Indices: 1378916--1379026 Score: 61
Period size: 20 Copynumber: 5.7 Consensus size: 19
1378906 TTACAAAACA
*
1378916 AATAAAAAAATAATATAAT
1 AATAAATAAATAATATAAT
1378935 AAT-AATAAAT-ATATAACT
1 AATAAATAAATAATATAA-T
1378953 ATATAAATAAAATACATATAA-
1 A-ATAAAT-AAATA-ATATAAT
* *
1378974 ATCTAATCTAAA-AATAT-AT
1 A-ATAA-ATAAATAATATAAT
* *
1378993 ATATTAATACATAATAATAAT
1 A-ATAAATAAATAAT-ATAAT
*
1379014 AATAAATACATAA
1 AATAAATAAATAA
1379027 AATACAAAAG
Statistics
Matches: 73, Mismatches: 8, Indels: 21
0.72 0.08 0.21
Matches are distributed among these distances:
17 6 0.08
18 12 0.16
19 16 0.22
20 17 0.23
21 15 0.21
22 1 0.01
23 6 0.08
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAAATAAATAATATAAT
Found at i:1379030 original size:16 final size:16
Alignment explanation
Indices: 1378930--1379030 Score: 58
Period size: 16 Copynumber: 6.6 Consensus size: 16
1378920 AAAAAATAAT
1378930 ATAATAATAATAAAT-
1 ATAATAATAATAAATA
1378945 AT-ATAACTATATAAATA
1 ATAATAA-TA-ATAAATA
1378962 A-AATACAT-ATAAAT-
1 ATAATA-ATAATAAATA
* *
1378976 CTAAT-CTAA-AAAT-
1 ATAATAATAATAAATA
* *
1378989 ATATATATTAATACATA
1 ATA-ATAATAATAAATA
1379006 ATAATAATAATAAATA
1 ATAATAATAATAAATA
1379022 CATAA-AATA
1 -ATAATAATA
1379031 CAAAAGGGGA
Statistics
Matches: 67, Mismatches: 7, Indels: 23
0.69 0.07 0.24
Matches are distributed among these distances:
13 7 0.10
14 7 0.10
15 16 0.24
16 24 0.36
17 12 0.18
18 1 0.01
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAATAATAATAAATA
Found at i:1379752 original size:20 final size:21
Alignment explanation
Indices: 1379727--1379777 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1379717 ATTATATATC
1379727 TTTTATTTCTTCA-TAAGTAA
1 TTTTATTTCTTCATTAAGTAA
* *
1379747 TTTTATTTATGCATTAAGTAA
1 TTTTATTTCTTCATTAAGTAA
1379768 TTTT-TTTCTT
1 TTTTATTTCTT
1379778 TTTAATTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.61
Consensus pattern (21 bp):
TTTTATTTCTTCATTAAGTAA
Found at i:1380790 original size:62 final size:63
Alignment explanation
Indices: 1380634--1380794 Score: 177
Period size: 64 Copynumber: 2.6 Consensus size: 63
1380624 TAACAAAATG
* * *
1380634 TTATTGAAGGCATTTTTAACCAAAACTGCCTTCAATAATCCCACCTAAAAATATATTGTGTAGA
1 TTATTGAAGGCATTTTTGACAAAAACTGCCTTCAAGAATCCCA-CTAAAAATATATTGTGTAGA
* * * ***
1380698 ATATTAAAGGCATTTTAGGACAAAAA-TGCCTTCAAGAAT-CCA-TTTCAA-ATATTGTGTATGG
1 TTATTGAAGGCATTTT-TGACAAAAACTGCCTTCAAGAATCCCACTAAAAATATATTGTGTA--G
1380759 A
63 A
1380760 TTATTGAAGGCATTTTTGACAAAAACTGCCTTCAA
1 TTATTGAAGGCATTTTTGACAAAAACTGCCTTCAA
1380795 TAATTTCTGT
Statistics
Matches: 81, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
60 10 0.12
61 11 0.14
62 25 0.31
63 3 0.04
64 26 0.32
65 6 0.07
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (63 bp):
TTATTGAAGGCATTTTTGACAAAAACTGCCTTCAAGAATCCCACTAAAAATATATTGTGTAGA
Found at i:1380884 original size:126 final size:126
Alignment explanation
Indices: 1380634--1380889 Score: 277
Period size: 126 Copynumber: 2.0 Consensus size: 126
1380624 TAACAAAATG
*
1380634 TTATTGAAGGCATTTTTAACCAAAACTGCCTTCAATAATCCCACCTAAAAATATATTGTGTAGAA
1 TTATTGAAGGCATTTTTAACAAAAACTGCCTTCAATAATCCCACCTAAAAATATATTGTGTAGAA
* * * * *
1380699 TATTAAAGGCATTTTAGGACAAAAATGCCTTCAAGAATCCATTTCAAATATTGTGTATGGA
66 TATTAAAGGCATTTCAGCACAAAAATGCCTTCAAAAATCCATTCCAAATATTGTCTATGGA
* ** *** * *
1380760 TTATTGAAGGCATTTTTGACAAAAACTGCCTTCAATAATTTCTGTTAAAAGTTTATTGAT-TAGA
1 TTATTGAAGGCATTTTTAACAAAAACTGCCTTCAATAATCCCACCTAAAAATATATTG-TGTAGA
* * * * *
1380824 TTATTGAAGGCACTTTCA-CCCAAAAATGCCTTCAAAAAT-CACTTCCATAT-TTTTCCTATGGA
65 ATATTAAAGGCA-TTTCAGCACAAAAATGCCTTCAAAAATCCA-TTCCAAATATTGT-CTATGGA
1380886 TTAT
1 TTAT
1380890 CAAGGGCATA
Statistics
Matches: 107, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
125 5 0.05
126 97 0.91
127 5 0.05
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (126 bp):
TTATTGAAGGCATTTTTAACAAAAACTGCCTTCAATAATCCCACCTAAAAATATATTGTGTAGAA
TATTAAAGGCATTTCAGCACAAAAATGCCTTCAAAAATCCATTCCAAATATTGTCTATGGA
Found at i:1384047 original size:17 final size:17
Alignment explanation
Indices: 1384025--1384074 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
1384015 AACGAGCTTT
1384025 CTTTTTTATTTTTTTTG
1 CTTTTTTATTTTTTTTG
*
1384042 CTTTTTTATTTTTCTTG
1 CTTTTTTATTTTTTTTG
1384059 CTTTTTT-TTTTCTTTT
1 CTTTTTTATTTT-TTTT
1384075 TAGTGAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.13
17 26 0.87
ACGTcount: A:0.04, C:0.10, G:0.04, T:0.82
Consensus pattern (17 bp):
CTTTTTTATTTTTTTTG
Found at i:1384360 original size:2 final size:2
Alignment explanation
Indices: 1384353--1384377 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1384343 TAAAATAGAT
1384353 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 T
1384378 TCACAGCATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1386105 original size:9 final size:9
Alignment explanation
Indices: 1386097--1386147 Score: 59
Period size: 9 Copynumber: 5.4 Consensus size: 9
1386087 CTTATGTTTC
*
1386097 TTTCATTTC
1 TTTCATTTT
1386106 TTTCATTTTTTT
1 TTTCA--TT-TT
1386118 TTTCATTTT
1 TTTCATTTT
1386127 TTTCA-TTT
1 TTTCATTTT
1386135 TTTCATTTT
1 TTTCATTTT
1386144 TTTC
1 TTTC
1386148 GAACTTCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
8 8 0.22
9 19 0.51
10 2 0.05
11 2 0.05
12 6 0.16
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTCATTTT
Found at i:1386121 original size:21 final size:21
Alignment explanation
Indices: 1386097--1386137 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1386087 CTTATGTTTC
1386097 TTTCATTTCTTTCATTTTTTT
1 TTTCATTTCTTTCATTTTTTT
*
1386118 TTTCATTTTTTTCATTTTTT
1 TTTCATTTCTTTCATTTTTT
1386138 CATTTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTCATTTCTTTCATTTTTTT
Found at i:1386128 original size:8 final size:8
Alignment explanation
Indices: 1386115--1386145 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1386105 CTTTCATTTT
1386115 TTTTTTCA
1 TTTTTTCA
1386123 TTTTTTTCA
1 -TTTTTTCA
1386132 TTTTTTCA
1 TTTTTTCA
1386140 TTTTTT
1 TTTTTT
1386146 TCGAACTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTCA
Found at i:1386137 original size:17 final size:17
Alignment explanation
Indices: 1386115--1386147 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1386105 CTTTCATTTT
1386115 TTTTTTCATTTTTTTCA
1 TTTTTTCATTTTTTTCA
1386132 TTTTTTCATTTTTTTC
1 TTTTTTCATTTTTTTC
1386148 GAACTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTCATTTTTTTCA
Found at i:1386202 original size:3 final size:3
Alignment explanation
Indices: 1386196--1386264 Score: 97
Period size: 3 Copynumber: 23.3 Consensus size: 3
1386186 CTTCTTTTTA
* *
1386196 ATT ATT ATT ATT A-T ATA ATT -TT GTTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT
1386240 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1386265 ATCTTTAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.07
3 54 0.90
4 2 0.03
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1387274 original size:16 final size:16
Alignment explanation
Indices: 1387253--1387307 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
1387243 TTTTTAGAAA
1387253 AAAAAATAAATATAAT
1 AAAAAATAAATATAAT
1387269 AAAAAATGAAACTA-AA-
1 AAAAAAT-AAA-TATAAT
*
1387285 ATAAAATAAATAT-AT
1 AAAAAATAAATATAAT
1387300 AAAAAATA
1 AAAAAATA
1387308 TAAATAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 3 0.09
15 10 0.30
16 13 0.39
17 5 0.15
18 2 0.06
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (16 bp):
AAAAAATAAATATAAT
Found at i:1387274 original size:17 final size:17
Alignment explanation
Indices: 1387252--1387313 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 17
1387242 ATTTTTAGAA
1387252 AAAAAAATAAATATAAT
1 AAAAAAATAAATATAAT
*
1387269 -AAAAAATGAAA-CTAA-
1 AAAAAAAT-AAATATAAT
*
1387284 AATAAAATAAATAT-AT
1 AAAAAAATAAATATAAT
1387300 AAAAAATATAAATA
1 AAAAAA-ATAAATA
1387314 AAAATTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
15 4 0.11
16 22 0.61
17 10 0.28
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (17 bp):
AAAAAAATAAATATAAT
Found at i:1387311 original size:27 final size:30
Alignment explanation
Indices: 1387250--1387307 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
1387240 TAATTTTTAG
*
1387250 AAAAAAAAATAAATATAATAAAAAATGAAACT
1 AAAATAAAATAAATATAATAAAAAAT--AACT
1387282 AAAATAAAATAAATAT-ATAAAAAATA
1 AAAATAAAATAAATATAATAAAAAATA
1387308 TAAATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 1 0.04
31 9 0.36
32 15 0.60
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.21
Consensus pattern (30 bp):
AAAATAAAATAAATATAATAAAAAATAACT
Found at i:1387316 original size:11 final size:11
Alignment explanation
Indices: 1387256--1387316 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
1387246 TTAGAAAAAA
1387256 AAAT-AAATAT
1 AAATAAAATAT
*
1387266 -AATAAAAAAT
1 AAATAAAATAT
1387276 GAAACTAAAATA-
1 -AAA-TAAAATAT
1387288 AAAT-AAATAT
1 AAATAAAATAT
1387298 ATAA-AAAATAT
1 A-AATAAAATAT
1387309 AAATAAAA
1 AAATAAAA
1387317 ATTTAATAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 15
0.71 0.03 0.26
Matches are distributed among these distances:
9 8 0.20
10 9 0.22
11 16 0.39
12 2 0.05
13 6 0.15
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (11 bp):
AAATAAAATAT
Found at i:1387316 original size:31 final size:32
Alignment explanation
Indices: 1387250--1387317 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
1387240 TAATTTTTAG
*
1387250 AAAAAAAAATAAATATAATAAAAAATGAAACT
1 AAAAAAAAATAAATATAATAAAAAATGAAAAT
*
1387282 AAAATAAAATAAATAT-ATAAAAAAT-ATAAAT
1 AAAAAAAAATAAATATAATAAAAAATGA-AAAT
1387313 AAAAA
1 AAAAA
1387318 TTTAATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 16 0.50
32 15 0.47
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (32 bp):
AAAAAAAAATAAATATAATAAAAAATGAAAAT
Found at i:1391516 original size:33 final size:33
Alignment explanation
Indices: 1391474--1391538 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1391464 CATATCTTTA
* *
1391474 ATTTAAAGTTTGTTGCCTTTGGTTAAATGAGCC
1 ATTTAAAGTTCGTTGCCTTTGGTCAAATGAGCC
*
1391507 ATTTAAAGTTCGTTGCCTTTGGTCAGATGAGC
1 ATTTAAAGTTCGTTGCCTTTGGTCAAATGAGC
1391539 TTTTCAACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (33 bp):
ATTTAAAGTTCGTTGCCTTTGGTCAAATGAGCC
Found at i:1391681 original size:39 final size:39
Alignment explanation
Indices: 1391473--1391951 Score: 373
Period size: 39 Copynumber: 12.3 Consensus size: 39
1391463 TCATATCTTT
*
1391473 AATTTAAAGTTTGTTGCCTTTGGTTAAATGAGC------
1 AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTA
* * * * * *
1391506 CATTTAAAGTTCGTTGCCTTTGGTCAGATGAGCTTTTCA
1 AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTA
* *
1391545 ACATTTAAAGTTTGTTGCATTTGGTTAAAGGAGCTTTTTTG
1 A-ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGC-TTTTTA
** * *
1391586 AATTTAAAGTTCATTGCCTCTGGTCAAAGGAGCTTTTTA
1 AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTA
* * *
1391625 ACATTTAAAATTTGTTGCCTTTAGTTAAAGGAGCTTTTTG
1 A-ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTA
* * * *
1391665 AATTTAAAGTTTGTTGCCTCTGGTCAGAGGAGCCTTTTA
1 AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTA
* * * *
1391704 ATATTTAAAGTTTGTTGCCTTTGGTCAGAGGAGCCTTTTG
1 A-ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTA
* * * * *
1391744 GATTTAAAGTTCGTTGCCTCTAGTCATAAA--AGCCTTTTA
1 AATTTAAAGTTTGTTGCCTTTGGT--TAAAGGAGCTTTTTA
** * ** *
1391783 ATATTTAAAGTTTGCCGTCTTTAATTAAAGGAGCTTTTTG
1 A-ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTA
* ** * * *
1391823 GATTTAAAGTTCATTGCCTTT-GTTGAGAGGAGCCTTTTG
1 AATTTAAAGTTTGTTGCCTTTGGTT-AAAGGAGCTTTTTA
* *
1391862 AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAACTCTTTA
1 AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTA
* ** * * * *
1391901 GATTTAAAGTTCATTGCCTCTGATGAGAGGAGCTTTTTA
1 AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTA
1391940 AATTTAAAGTTT
1 AATTTAAAGTTT
1391952 TATAGCCTCT
Statistics
Matches: 351, Mismatches: 78, Indels: 28
0.77 0.17 0.06
Matches are distributed among these distances:
33 29 0.08
38 6 0.02
39 160 0.46
40 149 0.42
41 7 0.02
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (39 bp):
AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTA
Found at i:1391703 original size:79 final size:78
Alignment explanation
Indices: 1391473--1391951 Score: 515
Period size: 79 Copynumber: 6.2 Consensus size: 78
1391463 TCATATCTTT
* * * *
1391473 AATTTAAAGTTTGTTGCCTTTGGTTAAATGAGC------CATTTAAAGTTCGTTGCCTTTGGTCA
1 AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGAATTTAAAGTTCATTGCCTCTGGTCA
*
1391532 GATGAG-CTTTTCA
66 GAGGAGCCTTTT-A
*
1391545 ACATTTAAAGTTTGTTGCATTTGGTTAAAGGAGCTTTTTTGAATTTAAAGTTCATTGCCTCTGGT
1 A-ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGC-TTTTTGAATTTAAAGTTCATTGCCTCTGGT
* *
1391610 CAAAGGAGCTTTTTA
64 CAGAGGAGCCTTTTA
* * **
1391625 ACATTTAAAATTTGTTGCCTTTAGTTAAAGGAGCTTTTTGAATTTAAAGTTTGTTGCCTCTGGTC
1 A-ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGAATTTAAAGTTCATTGCCTCTGGTC
1391690 AGAGGAGCCTTTTA
65 AGAGGAGCCTTTTA
* * * * * *
1391704 ATATTTAAAGTTTGTTGCCTTTGGTCAGAGGAGCCTTTTGGATTTAAAGTTCGTTGCCTCTAGTC
1 A-ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGAATTTAAAGTTCATTGCCTCTGGTC
* **
1391769 ATAAAAGCCTTTTA
65 AGAGGAGCCTTTTA
** * ** * * * *
1391783 ATATTTAAAGTTTGCCGTCTTTAATTAAAGGAGCTTTTTGGATTTAAAGTTCATTGCCTTTGTTG
1 A-ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGAATTTAAAGTTCATTGCCTCTGGTC
*
1391848 AGAGGAGCCTTTTG
65 AGAGGAGCCTTTTA
* * * *
1391862 AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAACTCTTT-AGATTTAAAGTTCATTGCCTCTGATG
1 AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGA-ATTTAAAGTTCATTGCCTCTGGTC
*
1391926 AGAGGAGCTTTTTA
65 AGAGGAGCCTTTTA
1391940 AATTTAAAGTTT
1 AATTTAAAGTTT
1391952 TATAGCCTCT
Statistics
Matches: 341, Mismatches: 56, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
72 1 0.00
73 30 0.09
78 76 0.22
79 171 0.50
80 59 0.17
81 4 0.01
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (78 bp):
AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGAATTTAAAGTTCATTGCCTCTGGTCA
GAGGAGCCTTTTA
Found at i:1391983 original size:40 final size:39
Alignment explanation
Indices: 1391902--1391984 Score: 94
Period size: 40 Copynumber: 2.1 Consensus size: 39
1391892 AACTCTTTAG
* * * *
1391902 ATTTAAAGTTCATTGCCTCTGATGAGAGGAGCTTTTTAA
1 ATTTAAAGTTCATAGCCTCTGATGAGAGAAGCCTTTCAA
* * *
1391941 ATTTAAAGTTTTATAGCCTCTGTTTAGAGAAGCCTTTCAA
1 ATTTAAAG-TTCATAGCCTCTGATGAGAGAAGCCTTTCAA
1391981 ATTT
1 ATTT
1391985 TCTCTCTAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
39 8 0.22
40 28 0.78
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (39 bp):
ATTTAAAGTTCATAGCCTCTGATGAGAGAAGCCTTTCAA
Found at i:1393201 original size:5 final size:4
Alignment explanation
Indices: 1393184--1393250 Score: 50
Period size: 4 Copynumber: 16.0 Consensus size: 4
1393174 AAAAAAAAAC
*
1393184 AAAT AAAT AAAT AGAAT AAA- AAAT GAAATT GAAAT AAAAT AAAT ATAT
1 AAAT AAAT AAAT A-AAT AAAT AAAT -AAA-T -AAAT -AAAT AAAT AAAT
1393232 AAA- AATAT AAAT AAA- AAAT
1 AAAT AA-AT AAAT AAAT AAAT
1393251 TTAATAATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
3 8 0.15
4 26 0.49
5 14 0.26
6 5 0.09
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1397222 original size:52 final size:53
Alignment explanation
Indices: 1397137--1397292 Score: 219
Period size: 52 Copynumber: 3.0 Consensus size: 53
1397127 ATAACCATAA
* * * *
1397137 AAACTTGCCCATTAAGAAT-CTCTCTCCTCTTAGAATTCTTCTCCTGTAAGTC
1 AAACTTGCCTATTAAGAATCCTCTTTCCTTTTAGAATTCTTCTCCTGCAAGTC
*
1397189 AAACTTGCCTATTAAGAATCCT-TTTCCTTTTAGAATTCTTCTCTTGCAAGTC
1 AAACTTGCCTATTAAGAATCCTCTTTCCTTTTAGAATTCTTCTCCTGCAAGTC
* **
1397241 AAACTTACCTATTAAGAATCCTCTTT-CTTTTAGAATTCTTCTTTTGCAAGTC
1 AAACTTGCCTATTAAGAATCCTCTTTCCTTTTAGAATTCTTCTCCTGCAAGTC
1397293 TTCTTGTCCA
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
52 90 0.95
53 5 0.05
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (53 bp):
AAACTTGCCTATTAAGAATCCTCTTTCCTTTTAGAATTCTTCTCCTGCAAGTC
Found at i:1397333 original size:11 final size:11
Alignment explanation
Indices: 1397317--1397346 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1397307 GCAATATCTG
1397317 ACAAATCTCAA
1 ACAAATCTCAA
1397328 ACAAATCTCAA
1 ACAAATCTCAA
1397339 ACAAATCT
1 ACAAATCT
1397347 TTTATAGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:1397493 original size:17 final size:18
Alignment explanation
Indices: 1397473--1397506 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1397463 GAAGATTAGC
1397473 AGAAAAAGAATT-TTAAA
1 AGAAAAAGAATTCTTAAA
*
1397490 AGAAAAATAATTCTTAA
1 AGAAAAAGAATTCTTAA
1397507 TAGGTAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.26
Consensus pattern (18 bp):
AGAAAAAGAATTCTTAAA
Found at i:1397528 original size:52 final size:52
Alignment explanation
Indices: 1397466--1397569 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 52
1397456 TGAACAAGAA
1397466 GATTAGCAGAAAAAGAATTTTAA-AAGAAAAATAATTCTTAATAGGTAAGTTT
1 GATTAGCAGAAAAAGAATTTTAAGAAGAAAAA-AATTCTTAATAGGTAAGTTT
* * * *
1397518 GATTTGCAGAAAAAGAATTTTAAGAGGAAAAAATTTTTTAATAGGTAAGTTT
1 GATTAGCAGAAAAAGAATTTTAAGAAGAAAAAAATTCTTAATAGGTAAGTTT
1397570 TTATGATTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
52 40 0.85
53 7 0.15
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (52 bp):
GATTAGCAGAAAAAGAATTTTAAGAAGAAAAAAATTCTTAATAGGTAAGTTT
Found at i:1400187 original size:42 final size:42
Alignment explanation
Indices: 1400140--1400223 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
1400130 TTAGCCTCTT
*
1400140 GGTTTTATTCACTAACTATAAAGTCAAGTGACGGGATTGGTA
1 GGTTTTATTCACTAACTATAAAGCCAAGTGACGGGATTGGTA
1400182 GGTTTTATTCACTAACTATAAAGCCAAGTGACGGGATTGGTA
1 GGTTTTATTCACTAACTATAAAGCCAAGTGACGGGATTGGTA
1400224 AGAAATAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (42 bp):
GGTTTTATTCACTAACTATAAAGCCAAGTGACGGGATTGGTA
Found at i:1400591 original size:42 final size:43
Alignment explanation
Indices: 1400518--1400604 Score: 158
Period size: 42 Copynumber: 2.0 Consensus size: 43
1400508 GTATTAGGAA
*
1400518 TTGTATAAGATAGTTTTTTAAAACTATTTATTGACTTATTAAT
1 TTGTATAAGATAATTTTTTAAAACTATTTATTGACTTATTAAT
1400561 TTGTATAAGATAATTTTTT-AAACTATTTATTGACTTATTAAT
1 TTGTATAAGATAATTTTTTAAAACTATTTATTGACTTATTAAT
1400603 TT
1 TT
1400605 TTTTTATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 25 0.58
43 18 0.42
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (43 bp):
TTGTATAAGATAATTTTTTAAAACTATTTATTGACTTATTAAT
Found at i:1408702 original size:6 final size:6
Alignment explanation
Indices: 1408656--1408701 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
1408646 TGTCAATATC
* *
1408656 GATGTT GATGTT GATGTT GATGTT GATGTT GATGTC GATGAT GATG
1 GATGTT GATGTT GATGTT GATGTT GATGTT GATGTT GATGTT GATG
1408702 ACAAACATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.20, C:0.02, G:0.35, T:0.43
Consensus pattern (6 bp):
GATGTT
Found at i:1409638 original size:11 final size:11
Alignment explanation
Indices: 1409622--1409653 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1409612 AAATCCCATA
1409622 AGAGATTTGTT
1 AGAGATTTGTT
1409633 AGAGATTTGTT
1 AGAGATTTGTT
*
1409644 TGAGATTTGT
1 AGAGATTTGT
1409654 CAGATATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (11 bp):
AGAGATTTGTT
Found at i:1409758 original size:52 final size:53
Alignment explanation
Indices: 1409678--1409834 Score: 230
Period size: 52 Copynumber: 3.0 Consensus size: 53
1409668 TGGACAAGAA
*
1409678 GACTTGCAAAAGAAGAATTCTAAGAGAAAGA-GGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGGATTCTTAATAGGTAAGTTT
*
1409730 GACTTGCAAGAGAAGAATTCTAAAAGAAA-AGGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGGATTCTTAATAGGTAAGTTT
* * * * *
1409782 GACTTACAGGAGAAGAATTCTAAGAG-GAGAGGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGGATTCTTAATAGGTAAGTTT
1409834 G
1 G
1409835 TATGGTTATA
Statistics
Matches: 95, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 93 0.98
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.26
Consensus pattern (53 bp):
GACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGGATTCTTAATAGGTAAGTTT
Found at i:1410393 original size:25 final size:25
Alignment explanation
Indices: 1410365--1410419 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
1410355 AAGTGGTATC
*
1410365 AGAGCTGA-AGGTTCGAAACGTGGGA
1 AGAGCTGACA-GTTCGAAACATGGGA
* * *
1410390 AGAGTTGACAGTTCGAGATATGGGA
1 AGAGCTGACAGTTCGAAACATGGGA
1410415 AGAGC
1 AGAGC
1410420 CATGGTTTGA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.33, C:0.11, G:0.38, T:0.18
Consensus pattern (25 bp):
AGAGCTGACAGTTCGAAACATGGGA
Found at i:1410474 original size:18 final size:19
Alignment explanation
Indices: 1410451--1410487 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1410441 AAGCAAGTTC
1410451 AGAAGAGCTCG-ATTCGAG
1 AGAAGAGCTCGAATTCGAG
*
1410469 AGAAGAGTTCGAATTCGAG
1 AGAAGAGCTCGAATTCGAG
1410488 TTTTGAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.35, C:0.14, G:0.32, T:0.19
Consensus pattern (19 bp):
AGAAGAGCTCGAATTCGAG
Found at i:1410674 original size:11 final size:11
Alignment explanation
Indices: 1410658--1410689 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1410648 AAATCCCATA
1410658 AGAGATTTGTT
1 AGAGATTTGTT
1410669 AGAGATTTGTT
1 AGAGATTTGTT
*
1410680 TGAGATTTGT
1 AGAGATTTGT
1410690 CAGATATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (11 bp):
AGAGATTTGTT
Found at i:1410794 original size:52 final size:53
Alignment explanation
Indices: 1410714--1410869 Score: 219
Period size: 52 Copynumber: 3.0 Consensus size: 53
1410704 TGGACAAGAA
*
1410714 AACTTGCAAAAGAAGAATTCTAAGAGAAAGA-GGATTCTTAATAGGTAAGTTT
1 AACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGGATTCTTAATAGGTAAGTTT
*
1410766 AACTTGCAAGAGAAGAATTCTAAAAGAAA-AGGGATTCTTAATAGGTAAGTTT
1 AACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGGATTCTTAATAGGTAAGTTT
* * * * * *
1410818 GACTTACAGGAGAAGAATTCTAAGAG-GAGAGGGATTCTTAATGGGCAAGTTT
1 AACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGGATTCTTAATAGGTAAGTTT
1410870 GTATGGTTAT
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 91 0.98
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.26
Consensus pattern (53 bp):
AACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGGATTCTTAATAGGTAAGTTT
Found at i:1411429 original size:25 final size:25
Alignment explanation
Indices: 1411401--1411455 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
1411391 AAGTGGTATC
*
1411401 AGAGCTGA-AGGTTCGAAACGTGGGA
1 AGAGCTGACA-GTTCGAAACATGGGA
* * *
1411426 AGAGTTGACAGTTCGAGATATGGGA
1 AGAGCTGACAGTTCGAAACATGGGA
1411451 AGAGC
1 AGAGC
1411456 CATGGTTTGA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.33, C:0.11, G:0.38, T:0.18
Consensus pattern (25 bp):
AGAGCTGACAGTTCGAAACATGGGA
Found at i:1411710 original size:11 final size:11
Alignment explanation
Indices: 1411694--1411725 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1411684 AAATCCCATA
1411694 AGAGATTTGTT
1 AGAGATTTGTT
1411705 AGAGATTTGTT
1 AGAGATTTGTT
*
1411716 TGAGATTTGT
1 AGAGATTTGT
1411726 CAGATATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (11 bp):
AGAGATTTGTT
Found at i:1411830 original size:52 final size:53
Alignment explanation
Indices: 1411751--1411905 Score: 217
Period size: 52 Copynumber: 3.0 Consensus size: 53
1411741 GGACAAGAAG
*
1411751 ACTTGCAAAAGAAGAATTCTAAGAGAAAGA-GGATTCTTAATAGGTAAGTTTA
1 ACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGGATTCTTAATAGGTAAGTTTA
* *
1411803 ACTTGCAAGAGAAGAATTCTAAAAGAAA-AGGGATTCTTAATAGGTAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGGATTCTTAATAGGTAAGTTTA
* * * * *
1411855 ACTTACAGGAGAAGAATTCTAAGAG-GAGAGGGATTCTTAATGGGCAAGTTT
1 ACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGGATTCTTAATAGGTAAGTTT
1411906 GTATGGTTAT
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 90 0.98
ACGTcount: A:0.41, C:0.08, G:0.25, T:0.26
Consensus pattern (53 bp):
ACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGGATTCTTAATAGGTAAGTTTA
Found at i:1414027 original size:144 final size:144
Alignment explanation
Indices: 1413798--1414532 Score: 1175
Period size: 144 Copynumber: 5.2 Consensus size: 144
1413788 TTCGACATGC
* * * *
1413798 TTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCCAAGTCAGTGAGAGAT
1 TTCCTATGAAAGCAGGGATTGAACCAGAGAAATTATTATAACTCAACTCAAAGTCAGTGAGAGAT
* *
1413863 TTAAGCATCCCTATCTCTTGAGGTATCGATCCAGAAAACATGTTTTGATGAAGGTAGAGAGTGGA
66 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGAGTGGA
1413928 TAGGCTGGTCAAGT
131 TAGGCTGGTCAAGT
* * *
1413942 TTCCTATGGAAGCAGGGATTGAACTAGAGAAATTATTATAACTCAACTCCAAGTCAGTGAGAGAT
1 TTCCTATGAAAGCAGGGATTGAACCAGAGAAATTATTATAACTCAACTCAAAGTCAGTGAGAGAT
*
1414007 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTCGATGAAGGTAGAGAGTGGA
66 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGAGTGGA
*
1414072 TAGACTGGTCAAGT
131 TAGGCTGGTCAAGT
1414086 TTCCTATGAAAGCAGGGATTGAACCAGAGAAATTATTATAACTCAACTCAAAGTCAGTGAGAGAT
1 TTCCTATGAAAGCAGGGATTGAACCAGAGAAATTATTATAACTCAACTCAAAGTCAGTGAGAGAT
**
1414151 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGACCAAGGTAGAGAGTGGA
66 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGAGTGGA
1414216 TAGGCTGGTCAAGT
131 TAGGCTGGTCAAGT
1414230 TTCCTATGAAAGCAGGGATTGAACCAGAG----------AACTCAACTCAAAGTCAGTGAGAGAT
1 TTCCTATGAAAGCAGGGATTGAACCAGAGAAATTATTATAACTCAACTCAAAGTCAGTGAGAGAT
**
1414285 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGACCAAGGTAGAGAGTGGA
66 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGAGTGGA
*
1414350 TAGGCCGGTCAAGT
131 TAGGCTGGTCAAGT
* * *
1414364 TTCCTATGAAAGCAGGGATTGAACCAGAGAAATTATTATAACTCAACGCAAAGTCGGCGAGAGAT
1 TTCCTATGAAAGCAGGGATTGAACCAGAGAAATTATTATAACTCAACTCAAAGTCAGTGAGAGAT
* *
1414429 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTCGATGAAGGTGGAGAGTGGA
66 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGAGTGGA
**
1414494 TATACTGGTCAAGT
131 TAGGCTGGTCAAGT
* *
1414508 TTCCTAGGGAAGCAGGGATTGAACC
1 TTCCTATGAAAGCAGGGATTGAACC
1414533 GCATAGATAG
Statistics
Matches: 554, Mismatches: 27, Indels: 20
0.92 0.04 0.03
Matches are distributed among these distances:
134 133 0.24
144 421 0.76
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.25
Consensus pattern (144 bp):
TTCCTATGAAAGCAGGGATTGAACCAGAGAAATTATTATAACTCAACTCAAAGTCAGTGAGAGAT
TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGAGTGGA
TAGGCTGGTCAAGT
Found at i:1414365 original size:134 final size:135
Alignment explanation
Indices: 1414125--1414532 Score: 620
Period size: 134 Copynumber: 3.0 Consensus size: 135
1414115 AAATTATTAT
1414125 AACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAAC
1 AACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAAC
1414190 ATATTTTGACCAAGGTAGAGAGTGGATAGGCTGGTCAAGTTTCCTATGAAAGCAGGGATTGAACC
66 ATATTTTGACCAAGGTAGAGAGTGGATAGGCTGGTCAAGTTTCCTATGAAAGCAGGGATTGAACC
1414255 AGAG-
131 AGAGA
1414259 AACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAAC
1 AACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAAC
*
1414324 ATATTTTGACCAAGGTAGAGAGTGGATAGGCCGGTCAAGTTTCCTATGAAAGCAGGGATTGAACC
66 ATATTTTGACCAAGGTAGAGAGTGGATAGGCTGGTCAAGTTTCCTATGAAAGCAGGGATTGAACC
1414389 AGAGAAATTATTA
131 AGAG--------A
* * *
1414402 TAACTCAACGCAAAGTCGGCGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAA
1 -AACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAA
* ** * ** * *
1414467 CATATTTCGATGAAGGTGGAGAGTGGATATACTGGTCAAGTTTCCTAGGGAAGCAGGGATTGAAC
65 CATATTTTGACCAAGGTAGAGAGTGGATAGGCTGGTCAAGTTTCCTATGAAAGCAGGGATTGAAC
1414532 C
130 C
1414533 GCATAGATAG
Statistics
Matches: 251, Mismatches: 13, Indels: 10
0.92 0.05 0.04
Matches are distributed among these distances:
134 133 0.53
144 118 0.47
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (135 bp):
AACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAAC
ATATTTTGACCAAGGTAGAGAGTGGATAGGCTGGTCAAGTTTCCTATGAAAGCAGGGATTGAACC
AGAGA
Found at i:1414410 original size:278 final size:279
Alignment explanation
Indices: 1413798--1414532 Score: 1166
Period size: 278 Copynumber: 2.6 Consensus size: 279
1413788 TTCGACATGC
* * * *
1413798 TTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCCAAGTCAGTGAGAGAT
1 TTCCTATGAAAGCAGGGATTGAACCAGAGAAATTATTATAACTCAACTCAAAGTCAGTGAGAGAT
* *
1413863 TTAAGCATCCCTATCTCTTGAGGTATCGATCCAGAAAACATGTTTTGATGAAGGTAGAGAGTGGA
66 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGAGTGGA
* *
1413928 TAGGCTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACTAGAGAAATTATTATAACTCAACTCCA
131 TAGGCTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACCAGAG--------A-AACTCAACTCAA
**
1413993 AGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTCGATGA
187 AGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTCGACCA
*
1414058 AGGTAGAGAGTGGATAGACTGGTCAAGT
252 AGGTAGAGAGTGGATAGACCGGTCAAGT
1414086 TTCCTATGAAAGCAGGGATTGAACCAGAGAAATTATTATAACTCAACTCAAAGTCAGTGAGAGAT
1 TTCCTATGAAAGCAGGGATTGAACCAGAGAAATTATTATAACTCAACTCAAAGTCAGTGAGAGAT
**
1414151 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGACCAAGGTAGAGAGTGGA
66 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGAGTGGA
*
1414216 TAGGCTGGTCAAGTTTCCTATGAAAGCAGGGATTGAACCAGAG-AACTCAACTCAAAGTCAGTGA
131 TAGGCTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACCAGAGAAACTCAACTCAAAGTCAGTGA
*
1414280 GAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGACCAAGGTAGAGA
196 GAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTCGACCAAGGTAGAGA
*
1414345 GTGGATAGGCCGGTCAAGT
261 GTGGATAGACCGGTCAAGT
* * *
1414364 TTCCTATGAAAGCAGGGATTGAACCAGAGAAATTATTATAACTCAACGCAAAGTCGGCGAGAGAT
1 TTCCTATGAAAGCAGGGATTGAACCAGAGAAATTATTATAACTCAACTCAAAGTCAGTGAGAGAT
* *
1414429 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTCGATGAAGGTGGAGAGTGGA
66 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGAGTGGA
** *
1414494 TATACTGGTCAAGTTTCCTAGGGAAGCAGGGATTGAACC
131 TAGGCTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACC
1414533 GCATAGATAG
Statistics
Matches: 420, Mismatches: 27, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
278 257 0.61
288 163 0.39
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.25
Consensus pattern (279 bp):
TTCCTATGAAAGCAGGGATTGAACCAGAGAAATTATTATAACTCAACTCAAAGTCAGTGAGAGAT
TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGAGTGGA
TAGGCTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACCAGAGAAACTCAACTCAAAGTCAGTGA
GAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTCGACCAAGGTAGAGA
GTGGATAGACCGGTCAAGT
Found at i:1417586 original size:39 final size:38
Alignment explanation
Indices: 1417543--1417628 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 38
1417533 ATACATGAGG
* *
1417543 TAATTAATTCATATAGTAAGATAATATTCAATTAGTTTA
1 TAATTAATTCATACAATAAGATAATATTCAATTA-TTTA
*
1417582 TAATTAATTCATACAATGAGATAATATTCAATTATTTA
1 TAATTAATTCATACAATAAGATAATATTCAATTATTTA
1417620 TAATTAATT
1 TAATTAATT
1417629 AAAAAAACGA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 13 0.30
39 31 0.70
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (38 bp):
TAATTAATTCATACAATAAGATAATATTCAATTATTTA
Found at i:1417647 original size:39 final size:39
Alignment explanation
Indices: 1417565--1417647 Score: 96
Period size: 38 Copynumber: 2.1 Consensus size: 39
1417555 ATAGTAAGAT
* * * * *
1417565 AATATTCAATTAGTTTATAATTAATTCATACAATGAGAT
1 AATATTCAATTAGTTTATAATTAATTAAAAAAACGAGAG
*
1417604 AATATTCAATTA-TTTATAATTAATTAAAAAAACGATAGG
1 AATATTCAATTAGTTTATAATTAATTAAAAAAACGAGA-G
1417643 AATAT
1 AATAT
1417648 ATTTATTTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
38 20 0.54
39 17 0.46
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (39 bp):
AATATTCAATTAGTTTATAATTAATTAAAAAAACGAGAG
Found at i:1417945 original size:13 final size:13
Alignment explanation
Indices: 1417922--1417955 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1417912 TATTAATATA
1417922 TTAAA-TAAAAAT
1 TTAAATTAAAAAT
*
1417934 TTATATTAAAAAT
1 TTAAATTAAAAAT
1417947 TTAAATTAA
1 TTAAATTAA
1417956 TGAATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAATTAAAAAT
Found at i:1418179 original size:14 final size:14
Alignment explanation
Indices: 1418160--1418186 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1418150 TTTATAAATT
1418160 ATATGAATTGTATA
1 ATATGAATTGTATA
1418174 ATATGAATTGTAT
1 ATATGAATTGTAT
1418187 GACTTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (14 bp):
ATATGAATTGTATA
Found at i:1419970 original size:137 final size:132
Alignment explanation
Indices: 1419758--1420003 Score: 357
Period size: 137 Copynumber: 1.8 Consensus size: 132
1419748 GAAACTAATG
* * ** *
1419758 AATTAAAAATTATATAATATAACTTTTTTAAATTTAAAAAAATTAAAAAATTGGCATGTATTTTG
1 AATTAAAAATGATATAATATAAATTTTTTAAATTTAAAAAAATTAAAAAATTAACATGTATTTTA
*
1419823 TAATAATATATTTATAAAATTTAATAAAACTTTAAAAACTCTATCTTCATAAAATAACAAATTAA
66 TAATAATATATTTATAAAAATTAATAAAACTTTAAAAACTCTATCTTCATAAAATAACAAATTAA
1419888 CA
131 CA
* *
1419890 AATTAAAAGTGATCTAATATAAATTTTTTAAATTTTATAAACAAAATTAAAAAAATTAACATGTA
1 AATTAAAAATGATATAATATAAATTTTTTAAA--TT-TAAA-AAAATT-AAAAAATTAACATGTA
**
1419955 TTTTATAATAATATATTTATAAAAATTAATAAATTTTTAAAAACTCTAT
61 TTTTATAATAATATATTTATAAAAATTAATAAAACTTTAAAAACTCTAT
1420004 GGTCAATATA
Statistics
Matches: 99, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
132 28 0.28
134 2 0.02
135 4 0.04
136 6 0.06
137 59 0.60
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.40
Consensus pattern (132 bp):
AATTAAAAATGATATAATATAAATTTTTTAAATTTAAAAAAATTAAAAAATTAACATGTATTTTA
TAATAATATATTTATAAAAATTAATAAAACTTTAAAAACTCTATCTTCATAAAATAACAAATTAA
CA
Found at i:1419990 original size:18 final size:18
Alignment explanation
Indices: 1419963--1419997 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1419953 TATTTTATAA
*
1419963 TAATATATTTATAAAAAT
1 TAATAAATTTATAAAAAT
*
1419981 TAATAAATTTTTAAAAA
1 TAATAAATTTATAAAAA
1419998 CTCTATGGTC
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAATTTATAAAAAT
Found at i:1425488 original size:17 final size:18
Alignment explanation
Indices: 1425458--1425493 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1425448 TATTTAAGAC
1425458 TATTAAATTAATATTTAA
1 TATTAAATTAATATTTAA
*
1425476 TATT-AATTCATATTTAA
1 TATTAAATTAATATTTAA
1425493 T
1 T
1425494 TTTTTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTAAATTAATATTTAA
Found at i:1427822 original size:58 final size:56
Alignment explanation
Indices: 1427732--1428071 Score: 477
Period size: 58 Copynumber: 5.9 Consensus size: 56
1427722 GTTCTTGTGT
*
1427732 AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTATTTTCA
1 AGGAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTGAAA-TTTTATTTTTA
*
1427790 AGGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTGAAATTTTATTTTTA
1 AGGAAAATTGATACTTTCAACTTTTCC-CAAAAA-TATTTTTTGAAATTTTATTTTTA
* * *
1427848 AGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAACTTTGATTTTCA
1 AGGAAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTT-GAAATTTTATTTTTA
* * *
1427906 AGGAAAATTG-TACTTTTAACTTTTCCTCAAAAATCCTTTTTTGAAAATTTATTTTTA
1 AGGAAAATTGATACTTTCAACTTTTCC-CAAAAAT-ATTTTTTGAAATTTTATTTTTA
* * *
1427963 AGGAAAATTGATACTTTCAACTTTTCCCCAAAACATTTTTTGAAAATTTATTTTTA
1 AGGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGAAATTTTATTTTTA
*
1428019 AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTG-ATTTTTATTT
1 AGGAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTGAAATTTTATTT
1428072 AAAGAAAATA
Statistics
Matches: 254, Mismatches: 20, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
56 60 0.24
57 66 0.26
58 111 0.44
59 17 0.07
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.45
Consensus pattern (56 bp):
AGGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGAAATTTTATTTTTA
Found at i:1427971 original size:115 final size:115
Alignment explanation
Indices: 1427732--1428062 Score: 508
Period size: 115 Copynumber: 2.9 Consensus size: 115
1427722 GTTCTTGTGT
*
1427732 AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTATTTTCAAGGAAAA
1 AGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAC-TTTATTTTCAAGGAAAA
* *
1427797 TTGATACTTTCAACTTTTCCTCAAAAA-CTTTTTTTTGAAATTTTATTTTTA
65 TTGATACTTTCAACTTTTCCTCAAAAATC-ATTTTTTGAAAATTTATTTTTA
*
1427848 AGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAACTTTGATTTTCAAGGAAAA
1 AGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAACTTT-ATTTTCAAGGAAAA
* *
1427913 TTG-TACTTTTAACTTTTCCTCAAAAATCCTTTTTTGAAAATTTATTTTTA
65 TTGATACTTTCAACTTTTCCTCAAAAATCATTTTTTGAAAATTTATTTTTA
* * * *
1427963 AGGAAAATTGATACTTTCAAC-TTTTCCCCAAAACATTTTTTGAAAATTTATTTTTAAGGAAAAT
1 AGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAACTTTATTTTCAAGGAAAAT
*
1428027 TGATACTTTCAACTTTTCCCCAAAAAT-ATTTTTTGA
66 TGATACTTTCAACTTTTCCTCAAAAATCATTTTTTGA
1428063 TTTTTATTTA
Statistics
Matches: 199, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
113 24 0.12
114 46 0.23
115 66 0.33
116 63 0.32
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (115 bp):
AGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAACTTTATTTTCAAGGAAAAT
TGATACTTTCAACTTTTCCTCAAAAATCATTTTTTGAAAATTTATTTTTA
Found at i:1428100 original size:22 final size:22
Alignment explanation
Indices: 1428075--1428116 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1428065 TTTATTTAAA
1428075 GAAAATAGAACAAA-ATAAAAGT
1 GAAAATA-AACAAAGATAAAAGT
*
1428097 GAAAATAAATAAAGATAAAA
1 GAAAATAAACAAAGATAAAA
1428117 AAATAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.02, G:0.12, T:0.14
Consensus pattern (22 bp):
GAAAATAAACAAAGATAAAAGT
Found at i:1428121 original size:18 final size:17
Alignment explanation
Indices: 1428098--1428213 Score: 56
Period size: 18 Copynumber: 6.5 Consensus size: 17
1428088 AATAAAAGTG
1428098 AAAATAAATAAAGATAAA
1 AAAATAAATAAA-ATAAA
*
1428116 AAAATAAAGAAAAGTAAA
1 AAAATAAATAAAA-TAAA
*
1428134 ACAA-AAATAAAAATAAGA
1 AAAATAAAT-AAAATAA-A
*
1428152 TAAAGATAAA-AATATTAAA
1 -AAA-ATAAATAA-AATAAA
* * **
1428171 TAAATCTAATCTAATAAA
1 AAAAT-AAATAAAATAAA
* *
1428189 TAAATAAATAAAACAAA
1 AAAATAAATAAAATAAA
*
1428206 TAAATAAA
1 AAAATAAA
1428214 AAATTCTGAA
Statistics
Matches: 75, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
17 25 0.33
18 37 0.49
19 5 0.07
20 5 0.07
21 3 0.04
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.20
Consensus pattern (17 bp):
AAAATAAATAAAATAAA
Found at i:1428160 original size:17 final size:16
Alignment explanation
Indices: 1428098--1428165 Score: 63
Period size: 17 Copynumber: 4.4 Consensus size: 16
1428088 AATAAAAGTG
1428098 AAAATAAATAAAGAT-
1 AAAATAAATAAAGATA
1428113 AAAA-AAATAAAG--A
1 AAAATAAATAAAGATA
* * *
1428126 AAAGTAAAACAAAAATA
1 AAAAT-AAATAAAGATA
1428143 AAAATAAGATAAAGATA
1 AAAATAA-ATAAAGATA
1428160 AAAATA
1 AAAATA
1428166 TTAAATAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
13 3 0.07
14 8 0.20
15 10 0.24
16 2 0.05
17 18 0.44
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.15
Consensus pattern (16 bp):
AAAATAAATAAAGATA
Found at i:1428208 original size:13 final size:13
Alignment explanation
Indices: 1428190--1428214 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1428180 TCTAATAAAT
1428190 AAATAAATAAAAC
1 AAATAAATAAAAC
1428203 AAATAAATAAAA
1 AAATAAATAAAA
1428215 AATTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATAAATAAAAC
Found at i:1428607 original size:20 final size:20
Alignment explanation
Indices: 1428565--1428607 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1428555 CGTCGGATTC
* *
1428565 TGGAAAATATCGTCGAAATT
1 TGGAAAATATCATCGAAAGT
* *
1428585 TGGAAAATTTCATCGGAAGT
1 TGGAAAATATCATCGAAAGT
1428605 TGG
1 TGG
1428608 CCGGAAGATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (20 bp):
TGGAAAATATCATCGAAAGT
Found at i:1429200 original size:4 final size:4
Alignment explanation
Indices: 1429177--1429262 Score: 61
Period size: 4 Copynumber: 20.8 Consensus size: 4
1429167 AAATATTACA
* * *
1429177 AAAT -AAT AAAT ATAAT -AAT AAAT ATAT AACT ATAT AAAT AAAAT ACATAT
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT A-A-AT
*
1429227 AAAT ATTAAC AAA- AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT A--AAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1429263 GATATATATA
Statistics
Matches: 66, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
3 9 0.14
4 42 0.64
5 9 0.14
6 6 0.09
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:1429252 original size:31 final size:29
Alignment explanation
Indices: 1429149--1429260 Score: 90
Period size: 29 Copynumber: 3.8 Consensus size: 29
1429139 AATATAAAGT
*
1429149 AAAATAAGATAAATCCAA-AAATATT-ACAA
1 AAAATAA-ATAAAT-AAATAAATATTAACAA
1429178 AATAATAAATATAAT-AATAAATATATAAC--
1 AA-AATAAATA-AATAAATAAATAT-TAACAA
* *
1429207 TATATAAATAAAATACATATAAATATTAACAA
1 AAAATAAAT-AAATA-A-ATAAATATTAACAA
1429239 AAAATAAATAAATAAATAAATA
1 AAAATAAATAAATAAATAAATA
1429261 AAGATATATA
Statistics
Matches: 68, Mismatches: 4, Indels: 22
0.72 0.04 0.23
Matches are distributed among these distances:
28 11 0.16
29 20 0.29
30 15 0.22
31 15 0.22
32 7 0.10
ACGTcount: A:0.67, C:0.05, G:0.01, T:0.27
Consensus pattern (29 bp):
AAAATAAATAAATAAATAAATATTAACAA
Found at i:1429288 original size:3 final size:3
Alignment explanation
Indices: 1429274--1429358 Score: 63
Period size: 3 Copynumber: 28.7 Consensus size: 3
1429264 ATATATATAT
1429274 TAA TACA TAA TAA TAA TAA TAA TAA -AA TAA TAAA TAA TAA -AA TACA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA-A
* * * *
1429320 TAA -AA TACA AAA GAA -AA -AA AAA TAA TAA TAA AAA TAA TA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1429359 CCAGATAGAA
Statistics
Matches: 69, Mismatches: 5, Indels: 16
0.77 0.06 0.18
Matches are distributed among these distances:
2 10 0.14
3 48 0.70
4 11 0.16
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.24
Consensus pattern (3 bp):
TAA
Found at i:1429357 original size:12 final size:12
Alignment explanation
Indices: 1429178--1429358 Score: 70
Period size: 12 Copynumber: 14.3 Consensus size: 12
1429168 AATATTACAA
*
1429178 AATAATAAATAT
1 AATAATAAAAAT
1429190 AATAATAAATATAT
1 AATAATAAA-A-AT
1429204 AACTATATAAATAA-
1 AA-TA-ATAAA-AAT
*
1429218 AATACATATAAAT
1 AATA-ATAAAAAT
* *
1429231 ATTAACAAAAAAT
1 AATAA-TAAAAAT
1429244 AAATAAATAAATAAAT
1 -AAT-AAT-AA-AAAT
* *
1429260 AA-AGATATATAT
1 AATA-ATAAAAAT
* *
1429272 ATTAATACATAAT
1 AATAATA-AAAAT
*
1429285 AATAATAATAAT
1 AATAATAAAAAT
1429297 AA-AATAATAAAT
1 AATAATAA-AAAT
*
1429309 AATAA-AATACAT
1 AATAATAA-AAAT
*
1429321 AA-AATACAAAAG
1 AATAATA-AAAAT
1429333 AA-AA-AAAAAT
1 AATAATAAAAAT
1429343 AATAATAAAAAT
1 AATAATAAAAAT
1429355 AATA
1 AATA
1429359 CCAGATAGAA
Statistics
Matches: 130, Mismatches: 20, Indels: 38
0.69 0.11 0.20
Matches are distributed among these distances:
10 6 0.05
11 10 0.08
12 56 0.43
13 28 0.22
14 10 0.08
15 9 0.07
16 11 0.08
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (12 bp):
AATAATAAAAAT
Found at i:1429533 original size:1 final size:1
Alignment explanation
Indices: 1429522--1429591 Score: 68
Period size: 1 Copynumber: 70.0 Consensus size: 1
1429512 AACATTGTCA
* * * * * * * *
1429522 TTTTTTGTTTTTTTATTTTTTGTTCTTTTGTGTTTTTTTTTTTGTTTTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1429587 TTTTT
1 TTTTT
1429592 ACCAAAACTC
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.01, C:0.01, G:0.09, T:0.89
Consensus pattern (1 bp):
T
Found at i:1429535 original size:8 final size:8
Alignment explanation
Indices: 1429522--1429591 Score: 78
Period size: 7 Copynumber: 9.4 Consensus size: 8
1429512 AACATTGTCA
1429522 TTTTTTGT
1 TTTTTTGT
*
1429530 TTTTTT-A
1 TTTTTTGT
1429537 TTTTTTGT
1 TTTTTTGT
*
1429545 TCTTTTG-
1 TTTTTTGT
*
1429552 TGTTTT-T
1 TTTTTTGT
1429559 TTTTTTGT
1 TTTTTTGT
1429567 TTTTTTGT
1 TTTTTTGT
1429575 TTTTTT-T
1 TTTTTTGT
1429582 TTTTTT-T
1 TTTTTTGT
1429589 TTT
1 TTT
1429592 ACCAAAACTC
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
7 27 0.50
8 27 0.50
ACGTcount: A:0.01, C:0.01, G:0.09, T:0.89
Consensus pattern (8 bp):
TTTTTTGT
Found at i:1429562 original size:20 final size:19
Alignment explanation
Indices: 1429532--1429590 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 19
1429522 TTTTTTGTTT
1429532 TTTTATTTTTTGTTCTTTTGTG
1 TTTT-TTTTTTGTT-TTTT-TG
1429554 TTTTTTTTTTTGTTTTTTTG
1 -TTTTTTTTTTGTTTTTTTG
1429574 TTTTTTTTTT-TTTTTTT
1 TTTTTTTTTTGTTTTTTT
1429591 TACCAAAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.19
19 10 0.28
20 2 0.06
21 4 0.11
22 9 0.25
23 4 0.11
ACGTcount: A:0.02, C:0.02, G:0.08, T:0.88
Consensus pattern (19 bp):
TTTTTTTTTTGTTTTTTTG
Found at i:1429591 original size:22 final size:22
Alignment explanation
Indices: 1429522--1429591 Score: 106
Period size: 22 Copynumber: 3.2 Consensus size: 22
1429512 AACATTGTCA
1429522 TTTTTTGTTTTTTTATTTTTTGT
1 TTTTTTGTTTTTTT-TTTTTTGT
* *
1429545 TCTTTTGTGTTTTTTTTTTTGT
1 TTTTTTGTTTTTTTTTTTTTGT
1429567 TTTTTTGTTTTTTTTTTTTT-T
1 TTTTTTGTTTTTTTTTTTTTGT
1429588 TTTT
1 TTTT
1429592 ACCAAAACTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.12
22 26 0.60
23 12 0.28
ACGTcount: A:0.01, C:0.01, G:0.09, T:0.89
Consensus pattern (22 bp):
TTTTTTGTTTTTTTTTTTTTGT
Found at i:1429691 original size:41 final size:41
Alignment explanation
Indices: 1429599--1429987 Score: 540
Period size: 41 Copynumber: 9.4 Consensus size: 41
1429589 TTTACCAAAA
* * *
1429599 CTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTT-TGAAA-ATAAATTG
1429642 CTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATTG
1429683 CTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATTG
*
1429724 CTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTTG-AAAATAAATTG
*
1429766 CTCCTCTAAACAGAGGCA--ACGAAAC-TTTGAAAGTAAATTG
1 CTCCTCTAAACAGAGGCACCACG--ACTTTTGAAAATAAATTG
* *
1429806 CTCCTCTAAACAGAGGTACCACAAC-TTTGAAAAGTAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTTGAAAA-TAAATTG
1429847 CTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTTGAAAA-TAAATTG
* * *
1429888 CTCTTCTAAACAGAGGCA--ACGGAACTTTGGAAAGTAAATTG
1 CTCCTCTAAACAGAGGCACCAC-G-ACTTTTGAAAATAAATTG
*
1429929 CTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTTG-AAAATAAATTG
1429971 CTCCTCTAAACAGAGGC
1 CTCCTCTAAACAGAGGC
1429988 GCTCCTCTAA
Statistics
Matches: 318, Mismatches: 16, Indels: 25
0.89 0.04 0.07
Matches are distributed among these distances:
39 2 0.01
40 40 0.13
41 177 0.56
42 71 0.22
43 28 0.09
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (41 bp):
CTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATTG
Found at i:1429953 original size:205 final size:213
Alignment explanation
Indices: 1429599--1430153 Score: 756
Period size: 205 Copynumber: 2.6 Consensus size: 213
1429589 TTTACCAAAA
* *
1429599 CTCCTCTAAACAGAGGCT-CAACGACTTTGAGAAACATAAATTGCTCCTCTAAACAGAGGCACCA
1 CTCCTCTAAACAGAGG-TACCACGACTTTGA-AAA-GTAAATTGCTCCTCTAAACAGAGGCACCA
* *
1429663 CGACTTTTGAAAA-TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATTGCTC
63 CGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-CACGACTTTGGAAAGTAAATTGCTC
1429727 CTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGA-G-G-C-AAC-G
126 CTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCGCCAAACAG
*
1429787 -A-A-ACTTTG-AAAGTAAATTG
191 CACACACTTTGAAAAATAAATTG
*
1429806 CTCCTCTAAACAGAGGTACCACAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
1 CTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
*
1429871 CTTTGAAAAGTAAATTGCTCTTCTAAACAGAGGCA-ACGGAACTTTGGAAAGTAAATTGCTCCTC
66 CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACAC-G-ACTTTGGAAAGTAAATTGCTCCTC
1429935 TAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCGCTCCTCTAAAC
129 TAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCG---C-C-AAAC
1430000 AGAGGCACCACGACTTTGAAAAAATAAATTG
189 --A-GCA-CAC-ACTTTG-AAAAATAAATTG
* *
1430031 CTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
1 CTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
*
1430096 CTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAGAAGTAAATT
66 CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-CACGACTTTGGA-AAGTAAATT
1430154 AGTCCTTGAC
Statistics
Matches: 309, Mismatches: 12, Indels: 35
0.87 0.03 0.10
Matches are distributed among these distances:
203 2 0.01
204 9 0.03
205 128 0.41
206 5 0.02
207 27 0.09
212 1 0.00
214 3 0.01
218 1 0.00
219 1 0.00
221 1 0.00
223 6 0.02
225 113 0.37
226 10 0.03
227 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (213 bp):
CTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACACGACTTTGGAAAGTAAATTGCTCCTCTA
AACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCGCCAAACAGCACAC
ACTTTGAAAAATAAATTG
Found at i:1429993 original size:18 final size:18
Alignment explanation
Indices: 1429970--1430005 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1429960 AAAATAAATT
1429970 GCTCCTCTAAACAGAGGC
1 GCTCCTCTAAACAGAGGC
1429988 GCTCCTCTAAACAGAGGC
1 GCTCCTCTAAACAGAGGC
1430006 ACCACGACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.17
Consensus pattern (18 bp):
GCTCCTCTAAACAGAGGC
Found at i:1430023 original size:60 final size:60
Alignment explanation
Indices: 1429928--1430047 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
1429918 AAAGTAAATT
*
1429928 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGC
1429988 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGC
1430048 ACCACGACTT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20
Consensus pattern (60 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGC
Found at i:1430081 original size:41 final size:41
Alignment explanation
Indices: 1429988--1430153 Score: 296
Period size: 41 Copynumber: 4.0 Consensus size: 41
1429978 AAACAGAGGC
* *
1429988 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAAGTAAATT
1430030 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1430071 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1430112 GCTCCTCTAAACAGAGGCACCACGACTTTGGAGAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGA-AAGTAAATT
1430154 AGTCCTTGAC
Statistics
Matches: 121, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
41 82 0.68
42 39 0.32
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.22
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
Found at i:1430103 original size:143 final size:141
Alignment explanation
Indices: 1429846--1430129 Score: 491
Period size: 143 Copynumber: 2.0 Consensus size: 141
1429836 AAAGTAAATT
* *
1429846 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCTTCTAAACAGAGGCAACGGA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGA
1429911 ACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCT
66 ACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAATAAATTGCTCCT
1429976 CTAAACAGAGGC
130 CTAAACAGAGGC
1429988 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAATAAATTGCTCCTCTAAACAGAGGCA--AC
*
1430053 -G-ACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTC
63 GGAACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATTGCTC
1430116 CTCTAAACAGAGGC
128 CTCTAAACAGAGGC
1430130 ACCACGACTT
Statistics
Matches: 136, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
142 57 0.42
143 76 0.56
144 1 0.01
145 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (141 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGA
ACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATTGCTCCTC
TAAACAGAGGC
Found at i:1430113 original size:184 final size:183
Alignment explanation
Indices: 1429805--1430153 Score: 594
Period size: 184 Copynumber: 1.9 Consensus size: 183
1429795 AAAGTAAATT
* *
1429805 GCTCCTCTAAACAGAGGTACCACAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACG
*
1429870 ACTTTGAAAAGTAAATTGCTCTTCTAAACAGAGGCAACGGAACTTTGGAAAGTAAATTGCTCCTC
66 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGGAAAGTAAATTGCTCCTC
1429935 TAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGC
131 TAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGC
*
1429988 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACAACTTTG-AAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
*
1430053 GACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC-G-ACTTTGGAAAGTAAATTGCTC
65 GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACGGAACTTTGGAAAGTAAATTGCTC
* *
1430116 CTCTAAACAGAGGCACCACGACTTTGGAGAAGTAAATT
128 CTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
1430154 AGTCCTTGAC
Statistics
Matches: 156, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
183 28 0.18
184 125 0.80
185 1 0.01
186 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (183 bp):
GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGGAAAGTAAATTGCTCCTC
TAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGC
Found at i:1431409 original size:8 final size:7
Alignment explanation
Indices: 1431390--1431448 Score: 57
Period size: 8 Copynumber: 8.1 Consensus size: 7
1431380 AATTTGAATC
1431390 TCTTTTT
1 TCTTTTT
*
1431397 ACATTTTT
1 TC-TTTTT
1431405 TCATTTTT
1 TC-TTTTT
*
1431413 TCTTCTT
1 TCTTTTT
*
1431420 TCTTTCT
1 TCTTTTT
1431427 T-TTTTT
1 TCTTTTT
1431433 TCTTTTTT
1 TC-TTTTT
1431441 TCTTTTT
1 TCTTTTT
1431448 T
1 T
1431449 TTCATCATCT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
6 5 0.12
7 17 0.40
8 21 0.49
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (7 bp):
TCTTTTT
Found at i:1431433 original size:20 final size:19
Alignment explanation
Indices: 1431408--1431470 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 19
1431398 CATTTTTTCA
1431408 TTTTTTCTTCTTTCTTTCTT
1 TTTTTTC-TCTTTCTTTCTT
1431428 TTTTTTCT-TTT-TTTCTT
1 TTTTTTCTCTTTCTTTCTT
1431445 TTTTTTCATCATCTTCTTT-TT
1 TTTTTTC-TC-T-TTCTTTCTT
1431466 TTTTT
1 TTTTT
1431471 GCTCATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
17 13 0.34
18 4 0.11
19 1 0.03
20 8 0.21
21 9 0.24
22 3 0.08
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTCTCTTTCTTTCTT
Found at i:1431448 original size:17 final size:17
Alignment explanation
Indices: 1431400--1431451 Score: 77
Period size: 17 Copynumber: 2.9 Consensus size: 17
1431390 TCTTTTTACA
1431400 TTTTTTCATTTTTTCTTCT
1 TTTTTTC-TTTTTT-TTCT
*
1431419 TTCTTTCTTTTTTTTCT
1 TTTTTTCTTTTTTTTCT
1431436 TTTTTTCTTTTTTTTC
1 TTTTTTCTTTTTTTTC
1431452 ATCATCTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 19 0.61
18 6 0.19
19 6 0.19
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTCTTTTTTTTCT
Found at i:1431450 original size:9 final size:9
Alignment explanation
Indices: 1431400--1431451 Score: 63
Period size: 9 Copynumber: 5.8 Consensus size: 9
1431390 TCTTTTTACA
1431400 TTTTTTCATT
1 TTTTTTC-TT
1431410 TTTTCTTC-T
1 TTTT-TTCTT
*
1431419 TTCTTTCTT
1 TTTTTTCTT
1431428 TTTTTTC-T
1 TTTTTTCTT
1431436 TTTTTTCTT
1 TTTTTTCTT
1431445 TTTTTTC
1 TTTTTTC
1431452 ATCATCTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
8 11 0.30
9 19 0.51
10 4 0.11
11 3 0.08
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:1431476 original size:23 final size:23
Alignment explanation
Indices: 1431433--1431476 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1431423 TTCTTTTTTT
**
1431433 TCTTTTTTTCTTTTTTTTCATCA
1 TCTTTTTTTCTTTTTGCTCATCA
1431456 TCTTCTTTTT-TTTTTGCTCAT
1 TCTT-TTTTTCTTTTTGCTCAT
1431477 TTTTCATCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (23 bp):
TCTTTTTTTCTTTTTGCTCATCA
Found at i:1431825 original size:10 final size:11
Alignment explanation
Indices: 1431810--1431838 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1431800 ATATGTGGCA
1431810 TTTATTTTA-T
1 TTTATTTTATT
1431820 TTTATTTTATT
1 TTTATTTTATT
1431831 TTTATTTT
1 TTTATTTT
1431839 TGAGACCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:1435476 original size:55 final size:54
Alignment explanation
Indices: 1435364--1435543 Score: 299
Period size: 54 Copynumber: 3.3 Consensus size: 54
1435354 TTTCTTGTGT
1435364 AGGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGAAATTTATTTTA
1 AGGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGAAATTTATTTTA
*
1435418 AGGAAAATTGATACTTTCAACTTTTCCTAAAAA-ATTTTTTTGAAATTTATTTTTA
1 AGGAAAATTGATACTTTCAACTTTTCCCAAAAATA-TTTTTTGAAATTTA-TTTTA
*
1435473 AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAATTTGATTTCA
1 AGGAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTGAAATTT-ATTTTA
1435529 AGGAAAATTGATACT
1 AGGAAAATTGATACT
1435544 NNNNNNNNNN
Statistics
Matches: 118, Mismatches: 3, Indels: 8
0.91 0.02 0.06
Matches are distributed among these distances:
53 1 0.01
54 46 0.39
55 30 0.25
56 39 0.33
57 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (54 bp):
AGGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGAAATTTATTTTA
Found at i:1435532 original size:56 final size:55
Alignment explanation
Indices: 1435364--1435543 Score: 301
Period size: 55 Copynumber: 3.3 Consensus size: 55
1435354 TTTCTTGTGT
1435364 AGGAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTGAAATTTATTTTA
1 AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAATTTATTTTA
**
1435418 AGGAAAATTGATACTTTCAACTTTTCCTAAAAAAT-TTTTTTGAAATTTATTTTTA
1 AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAATTTA-TTTTA
*
1435473 AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAATTTGATTTCA
1 AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAATTT-ATTTTA
1435529 AGGAAAATTGATACT
1 AGGAAAATTGATACT
1435544 NNNNNNNNNN
Statistics
Matches: 117, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
54 39 0.33
55 45 0.38
56 32 0.27
57 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (55 bp):
AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAATTTATTTTA
Found at i:1439458 original size:161 final size:161
Alignment explanation
Indices: 1439093--1439552 Score: 745
Period size: 161 Copynumber: 2.9 Consensus size: 161
1439083 TTAGTTGTTG
*
1439093 AAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGA
1 AAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGGA
*
1439158 GTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATT-ATT----TAAAGAA
66 GTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGTAAAAAA
* *
1439218 AAATCAAGATCAACCAATTAATTAATTATCA
131 AAATCAAAATCAACCAAGTAATTAATTATCA
* *
1439249 AAAATTATTCTCAATTGACTCTAATACTTTTAGCAAAAAATTGAGAAAATTCTCTCACCTCAGGA
1 AAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGGA
1439314 GTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGTAAAAAA
66 GTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGTAAAAAA
* *
1439379 AAATCAAAATCAGCCAAGTAATTAATTATCG
131 AAATCAAAATCAACCAAGTAATTAATTATCA
*
1439410 GAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGGA
1 AAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGGA
* *
1439475 GTATGCAAGAAAAACTACTGTTTTTACTTGTAGAGGCTCCGTCGTCGGATTAATTAAAG-AAAAA
66 GTATGCAAGAAAAACTACTG-TTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGTAAAAA
*
1439539 AGAAA-AAAAATCAA
130 A-AAATCAAAATCAA
1439553 GATCAAAATC
Statistics
Matches: 282, Mismatches: 15, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
156 112 0.40
157 3 0.01
161 128 0.45
162 39 0.14
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (161 bp):
AAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGGA
GTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGTAAAAAA
AAATCAAAATCAACCAAGTAATTAATTATCA
Found at i:1439589 original size:14 final size:14
Alignment explanation
Indices: 1439572--1439610 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
1439562 CAAAGTCAAA
1439572 AAAAAAAAAAATTC
1 AAAAAAAAAAATTC
1439586 AAAAAAAAAAATTC
1 AAAAAAAAAAATTC
1439600 AAAAAAAAAAA
1 AAAAAAAAAAA
1439611 CCTGGAGCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAAAAAAAAATTC
Found at i:1439649 original size:15 final size:16
Alignment explanation
Indices: 1439629--1439672 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
1439619 GGCTCGGATC
1439629 GCGGCTCGGCTTGG-T
1 GCGGCTCGGCTTGGCT
*
1439644 GCGGCTCGGCTCGGCT
1 GCGGCTCGGCTTGGCT
1439660 -CGGCTCGGCTTGG
1 GCGGCTCGGCTTGG
1439673 AGGGGCTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 25 0.96
16 1 0.04
ACGTcount: A:0.00, C:0.32, G:0.45, T:0.23
Consensus pattern (16 bp):
GCGGCTCGGCTTGGCT
Done.