Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 2 of 45
Found at i:179695 original size:29 final size:29
Alignment explanation
Indices: 179638--179692 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
179628 AAAGATTTAT
*
179638 TTAATATTTAAAAATTTTAAATAAAAATA
1 TTAATATTTAAAAATATTAAATAAAAATA
179667 TTAAT-TTTAAAAA-ATTAAATTAAAAA
1 TTAATATTTAAAAATATTAAA-TAAAAA
179693 ATAAAATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.21
28 14 0.58
29 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
TTAATATTTAAAAATATTAAATAAAAATA
Found at i:179697 original size:12 final size:13
Alignment explanation
Indices: 179654--179700 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
179644 TTTAAAAATT
179654 TTAAA-TAAAAATA
1 TTAAATTAAAAA-A
*
179667 TTAATTTTAAAAAA
1 TTAA-ATTAAAAAA
179681 TTAAATTAAAAAA
1 TTAAATTAAAAAA
*
179694 TAAAATT
1 TTAAATT
179701 CATTCAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 18 0.62
14 5 0.17
15 6 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAATTAAAAAA
Found at i:179700 original size:18 final size:18
Alignment explanation
Indices: 179677--179714 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
179667 TTAATTTTAA
179677 AAAATTAAATT-AAAAAAT
1 AAAATT-AATTCAAAAAAT
*
179695 AAAATTCATTCAAAAAAT
1 AAAATTAATTCAAAAAAT
179713 AA
1 AA
179715 CTAAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATTAATTCAAAAAAT
Found at i:181151 original size:5 final size:5
Alignment explanation
Indices: 181141--181171 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
181131 AGCGCAGCTT
181141 GAAAA GAAAA GAAAA GAAAA GAAAA -AAAA GA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GA
181172 TAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:181161 original size:15 final size:14
Alignment explanation
Indices: 181141--181181 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
181131 AGCGCAGCTT
181141 GAAAAGAAAAGAAAA
1 GAAAAGAAAA-AAAA
181156 GAAAAGAAAAAAAA
1 GAAAAGAAAAAAAA
181170 GATAAA-AAAAAA
1 GA-AAAGAAAAAA
181182 TGACTCCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (14 bp):
GAAAAGAAAAAAAA
Found at i:181176 original size:10 final size:9
Alignment explanation
Indices: 181141--181179 Score: 51
Period size: 10 Copynumber: 4.0 Consensus size: 9
181131 AGCGCAGCTT
181141 GAAAAGAAAA
1 GAAAA-AAAA
181151 GAAAAGAAAA
1 GAAAA-AAAA
181161 GAAAAAAAA
1 GAAAAAAAA
181170 GATAAAAAAA
1 GA-AAAAAAA
181180 AATGACTCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 6 0.21
10 22 0.79
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:181385 original size:22 final size:23
Alignment explanation
Indices: 181343--181385 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
181333 AGAGAGCAAG
*
181343 AAAGAGAAGAAAAAGCGAAAGAA
1 AAAGAGAAGAAAAAACGAAAGAA
181366 AAAGA-AAGAAAACAAC-AAAG
1 AAAGAGAAGAAAA-AACGAAAG
181386 TAGGTGAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.72, C:0.07, G:0.21, T:0.00
Consensus pattern (23 bp):
AAAGAGAAGAAAAAACGAAAGAA
Found at i:183638 original size:15 final size:15
Alignment explanation
Indices: 183618--183648 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
183608 CATTTTCATA
183618 GTTTCCTATTTACTT
1 GTTTCCTATTTACTT
183633 GTTTCCTATTTACTT
1 GTTTCCTATTTACTT
183648 G
1 G
183649 GAAAAGTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.19, G:0.10, T:0.58
Consensus pattern (15 bp):
GTTTCCTATTTACTT
Found at i:190510 original size:2 final size:2
Alignment explanation
Indices: 190503--190540 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
190493 TTGGAAATGA
190503 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
190541 ATAGTAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:192581 original size:22 final size:22
Alignment explanation
Indices: 192555--192608 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
192545 TGATATTTTA
*
192555 TAATTAAAAAATTATTTAAAT-T
1 TAATTAAAAAA-TATATAAATAT
**
192577 TAATTTTAAAATATATAAATAT
1 TAATTAAAAAATATATAAATAT
192599 TAATATAAAA
1 TAAT-TAAAA
192609 TTTTTTTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 8 0.32
22 14 0.56
23 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATTAAAAAATATATAAATAT
Found at i:195352 original size:15 final size:15
Alignment explanation
Indices: 195332--195366 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
195322 CGTCATTCTG
*
195332 TCGCTGCTTCTCCTC
1 TCGCTGCTCCTCCTC
*
195347 TCGCTGCTCCTCCTT
1 TCGCTGCTCCTCCTC
195362 TCGCT
1 TCGCT
195367 TGATTTTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.46, G:0.14, T:0.40
Consensus pattern (15 bp):
TCGCTGCTCCTCCTC
Found at i:196620 original size:2 final size:2
Alignment explanation
Indices: 196613--196648 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
196603 GCATCCATAC
196613 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
196649 TGATACTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:197358 original size:19 final size:19
Alignment explanation
Indices: 197320--197359 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
197310 TCATCTTGTG
*
197320 AAAATACAAAAAATTAAAT
1 AAAATACAAAAAATAAAAT
197339 AAAAT-CAAAAAATAAGAAT
1 AAAATACAAAAAATAA-AAT
197358 AA
1 AA
197360 TTATTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.75, C:0.05, G:0.03, T:0.17
Consensus pattern (19 bp):
AAAATACAAAAAATAAAAT
Found at i:199153 original size:21 final size:23
Alignment explanation
Indices: 199129--199176 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
199119 ATAAATATTG
199129 TTAATATTAAT-TA-TATATTTT
1 TTAATATTAATATATTATATTTT
**
199150 TTAATATTTTTATATTATATTTT
1 TTAATATTAATATATTATATTTT
199173 TTAA
1 TTAA
199177 AATATATATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 2 0.09
23 12 0.52
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTAATATTAATATATTATATTTT
Found at i:200669 original size:30 final size:30
Alignment explanation
Indices: 200635--200694 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
200625 GAAAGTCCAC
200635 ACCACAAGTTCAGCAGACAAAGAAGTGCAG
1 ACCACAAGTTCAGCAGACAAAGAAGTGCAG
* *
200665 ACCACAAGTTCTGCAGACAAGGAAGTGCAG
1 ACCACAAGTTCAGCAGACAAAGAAGTGCAG
200695 GCGTAGACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (30 bp):
ACCACAAGTTCAGCAGACAAAGAAGTGCAG
Found at i:200783 original size:30 final size:30
Alignment explanation
Indices: 200717--200785 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
200707 AGCTCAGCAA
* *
200717 ACAAGGAAGTGCAGACCACGAGTTCCTCAG
1 ACAAGGAAGTACAGACCACGAGTTCCACAG
* * *
200747 ATAAGGAAGTACA-AGCCACGAGTTTCACCG
1 ACAAGGAAGTACAGA-CCACGAGTTCCACAG
200777 ACAAGGAAG
1 ACAAGGAAG
200786 CGCAGGCTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.13
Consensus pattern (30 bp):
ACAAGGAAGTACAGACCACGAGTTCCACAG
Found at i:200827 original size:36 final size:36
Alignment explanation
Indices: 200779--200858 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
200769 TTTCACCGAC
* * * * *
200779 AAGGAAGCGCAGGCTCAGGCCATGACG-TCTTCAGAT
1 AAGGAAGTGCAGGCGCAGACCATGA-GTTCTGCAGAA
200815 AAGGAAGTGCAGGCGCAGACCATGAGTTCTGCAGAA
1 AAGGAAGTGCAGGCGCAGACCATGAGTTCTGCAGAA
200851 AAGGAAGT
1 AAGGAAGT
200859 ACTACAAACC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
35 1 0.03
36 37 0.97
ACGTcount: A:0.33, C:0.20, G:0.33, T:0.15
Consensus pattern (36 bp):
AAGGAAGTGCAGGCGCAGACCATGAGTTCTGCAGAA
Found at i:200927 original size:104 final size:105
Alignment explanation
Indices: 200776--200970 Score: 275
Period size: 104 Copynumber: 1.9 Consensus size: 105
200766 GAGTTTCACC
* * * * * *
200776 GACAAGGAAGCGCAGGCTCAGGCCATGACGTCTTCAGATAAGGAAGTGCAGGCGCAGACCATGAG
1 GACAAGGAAGCACAGGCACAGGCCACGACGTCTGCAGACAAAGAAGTGCAGGCGCAGACCATGAG
**
200841 TTCTGCAGAAAAGGAAGTAC-TACAAACCACAACTTCCCT
66 TTCCACAGAAAAGGAAGTACATACAAACCACAACTTCCCT
* *
200880 GACAAGGAAGCATAGGCACAGGCCACGACTTCTGCAGACAAAGAAGTGCAGGCGCAGACCATGAG
1 GACAAGGAAGCACAGGCACAGGCCACGACGTCTGCAGACAAAGAAGTGCAGGCGCAGACCATGAG
* *
200945 TTCCACGGACAAGGAAGTACATACAA
66 TTCCACAGAAAAGGAAGTACATACAA
200971 GTAGTTTCGC
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
104 73 0.94
105 5 0.06
ACGTcount: A:0.35, C:0.25, G:0.27, T:0.13
Consensus pattern (105 bp):
GACAAGGAAGCACAGGCACAGGCCACGACGTCTGCAGACAAAGAAGTGCAGGCGCAGACCATGAG
TTCCACAGAAAAGGAAGTACATACAAACCACAACTTCCCT
Found at i:201907 original size:2 final size:2
Alignment explanation
Indices: 201900--201948 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
201890 TTCAATACAA
201900 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
201942 AG AG AG A
1 AG AG AG A
201949 TCATCTTTGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:210714 original size:6 final size:6
Alignment explanation
Indices: 210703--210738 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
210693 TTTTACACAT
210703 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
210739 CTTATTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:210856 original size:2 final size:2
Alignment explanation
Indices: 210849--210877 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
210839 AGAGGACACA
210849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
210878 ACAATTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:211305 original size:13 final size:13
Alignment explanation
Indices: 211287--211317 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
211277 GATTTTTTTT
211287 TTTCTGGGATTCC
1 TTTCTGGGATTCC
211300 TTTCTGGGATTCC
1 TTTCTGGGATTCC
211313 TTTCT
1 TTTCT
211318 ATTTCCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.23, G:0.19, T:0.52
Consensus pattern (13 bp):
TTTCTGGGATTCC
Found at i:211813 original size:2 final size:2
Alignment explanation
Indices: 211806--211835 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
211796 AAATATGCAC
211806 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
211836 CCCTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:215198 original size:21 final size:20
Alignment explanation
Indices: 215174--215247 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
215164 CTTGATGCAA
*
215174 CCACTGCTCCAACTGATTCTT
1 CCACTGCTCCAATTGA-TCTT
*
215195 CCACGGCTCCAATTGACTCTT
1 CCACTGCTCCAATTGA-TCTT
* *
215216 CAACTGCTCTAATTGATCGTT
1 CCACTGCTCCAATTGATC-TT
*
215237 CCACTGTTCCA
1 CCACTGCTCCA
215248 TCCCCGCCAT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
20 2 0.05
21 41 0.95
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.32
Consensus pattern (20 bp):
CCACTGCTCCAATTGATCTT
Found at i:219626 original size:12 final size:12
Alignment explanation
Indices: 219609--219670 Score: 61
Period size: 12 Copynumber: 4.9 Consensus size: 12
219599 TAAGCATGAA
219609 TTTTAAATTAAT
1 TTTTAAATTAAT
219621 TTTTAAATTAAT
1 TTTTAAATTAAT
* * *
219633 ATGTAAATCAAT
1 TTTTAAATTAAT
*
219645 CTCTTTAAATAAAT
1 -T-TTTAAATTAAT
219659 TTTTAATATTAA
1 TTTTAA-ATTAA
219671 AATTAAAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
12 26 0.65
13 5 0.12
14 9 0.22
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (12 bp):
TTTTAAATTAAT
Found at i:220796 original size:23 final size:21
Alignment explanation
Indices: 220768--220848 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 21
220758 CTCTCCTTAC
220768 TTTCTTCTTCTTTTTTTTTTTT
1 TTTCTT-TTCTTTTTTTTTTTT
*
220790 TTGTCTTTCTCTTTTCTTTTTTT
1 TT-TCTTT-TCTTTTTTTTTTTT
*
220813 TTCCTTTTTCCTTTTTTTTTCTTT
1 TTTC-TTTT-CTTTTTTTTT-TTT
220837 CTTTCTCTTTCT
1 -TTTCT-TTTCT
220849 CTTGTTCCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
22 5 0.10
23 31 0.65
24 6 0.12
25 6 0.12
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.79
Consensus pattern (21 bp):
TTTCTTTTCTTTTTTTTTTTT
Found at i:220832 original size:28 final size:28
Alignment explanation
Indices: 220770--220836 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
220760 CTCCTTACTT
*
220770 TCTTCTTCTTTTTTTTTTTTTTGTCTTTC
1 TCTT-TTCTTTTTTTTTTTTTTGCCTTTC
220799 TCTTTTCTTTTTTTTTCCTTTTT-CCTTT-
1 TCTTTTCTTTTTTTTT--TTTTTGCCTTTC
*
220827 TTTTTTCTTT
1 TCTTTTCTTT
220837 CTTTCTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 21 0.62
29 8 0.24
30 5 0.15
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (28 bp):
TCTTTTCTTTTTTTTTTTTTTGCCTTTC
Found at i:220836 original size:17 final size:16
Alignment explanation
Indices: 220767--220836 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 16
220757 TCTCTCCTTA
*
220767 CTTTCTTCTTCTTTTTT
1 CTTT-TTCTTTTTTTTT
* *
220784 -TTTTT-TTTGTCTTT
1 CTTTTTCTTTTTTTTT
220798 CTCTTTTCTTTTTTTTT
1 CT-TTTTCTTTTTTTTT
220815 CCTTTTTCCTTTTTTTTT
1 -CTTTTT-CTTTTTTTTT
220833 CTTT
1 CTTT
220837 CTTTCTCTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
14 6 0.14
15 3 0.07
16 7 0.16
17 15 0.35
18 12 0.28
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (16 bp):
CTTTTTCTTTTTTTTT
Found at i:220847 original size:10 final size:10
Alignment explanation
Indices: 220767--220848 Score: 59
Period size: 10 Copynumber: 8.6 Consensus size: 10
220757 TCTCTCCTTA
*
220767 CTTTCTTCTT
1 CTTTCTTTTT
220777 CTTT-TTTTT
1 CTTTCTTTTT
*
220786 -TTT-TTTGT
1 CTTTCTTTTT
220794 CTTTCTCTTTT
1 CTTTCT-TTTT
220805 C-TT-TTTTT
1 CTTTCTTTTT
*
220813 -TTCCTTTTT
1 CTTTCTTTTT
*
220822 CCTTTTTTTTT
1 -CTTTCTTTTT
*
220833 CTTTCTTTCT
1 CTTTCTTTTT
220843 CTTTCT
1 CTTTCT
220849 CTTGTTCCTA
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
8 12 0.21
9 13 0.23
10 21 0.37
11 11 0.19
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.78
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:221066 original size:19 final size:19
Alignment explanation
Indices: 221033--221092 Score: 65
Period size: 17 Copynumber: 3.4 Consensus size: 19
221023 ATATTACTTT
221033 AAATAT-ATA-AAAAATAA
1 AAATATAATATAAAAATAA
221050 AAATATAATATAAAAAT--
1 AAATATAATATAAAAATAA
* * *
221067 AAATATGACATAAATATAA
1 AAATATAATATAAAAATAA
221086 AAATATA
1 AAATATA
221093 TATGTATATG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 20 0.57
18 3 0.09
19 12 0.34
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
AAATATAATATAAAAATAA
Found at i:221090 original size:101 final size:99
Alignment explanation
Indices: 220979--221162 Score: 230
Period size: 101 Copynumber: 1.8 Consensus size: 99
220969 GTGAAAAAAT
* *
220979 ATATATAAATAAATAAT-TA-ATATATAAA-AATTCATATAAATTTTATATTACTTTAAATATAT
1 ATATAAAAATAAAT-ATGTATATATATAAATAATT-ATATAAA-TTTATAATACTTTAAATATAT
221041 AAAAAATAAAAATATAATATAAAAATAAATATGACATAA
63 AAAAAAT-AAAATA-AATATAAAAATAAATATGACATAA
* * * * *
221080 ATATAAAAATATATATGTATATGTATAAATTATTATATAAATTTATAATATTTTAAATATTTAAA
1 ATATAAAAATAAATATGTATATATATAAATAATTATATAAATTTATAATACTTTAAATATATAAA
*
221145 AAATAATATAAATATAAA
66 AAATAAAATAAATATAAA
221163 TATACACATG
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
99 8 0.11
100 7 0.10
101 39 0.54
102 15 0.21
103 3 0.04
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (99 bp):
ATATAAAAATAAATATGTATATATATAAATAATTATATAAATTTATAATACTTTAAATATATAAA
AAATAAAATAAATATAAAAATAAATATGACATAA
Found at i:226249 original size:2 final size:2
Alignment explanation
Indices: 226242--226282 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
226232 ACACTCCATC
* *
226242 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
226283 TAAATGTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:239331 original size:2 final size:2
Alignment explanation
Indices: 239324--239358 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
239314 AAGGGCTGTT
239324 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
239359 TTTGGAAAGC
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:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:243193 original size:17 final size:17
Alignment explanation
Indices: 243163--243196 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
243153 TTAAAATCAG
243163 TTTATATTTGTATCAAA
1 TTTATATTTGTATCAAA
243180 TTTACTATTT-TATCAAA
1 TTTA-TATTTGTATCAAA
243197 AATGTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTATATTTGTATCAAA
Found at i:246315 original size:10 final size:10
Alignment explanation
Indices: 246271--246314 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
246261 AAGAAAATAC
246271 ATATGTATAT
1 ATATGTATAT
246281 ATATGTGA-AT
1 ATATGT-ATAT
246291 ATATGTATAT
1 ATATGTATAT
*
246301 ATATATATAT
1 ATATGTATAT
246311 ATAT
1 ATAT
246315 AAAATAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 1 0.03
10 29 0.94
11 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (10 bp):
ATATGTATAT
Found at i:249782 original size:2 final size:2
Alignment explanation
Indices: 249775--249811 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
249765 AGAAAGAATA
249775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
249812 GCATGTGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:255301 original size:2 final size:2
Alignment explanation
Indices: 255294--255329 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
255284 GTAATCCATG
255294 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
255330 ACAAACATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:263433 original size:29 final size:29
Alignment explanation
Indices: 263397--263463 Score: 104
Period size: 28 Copynumber: 2.4 Consensus size: 29
263387 ATCTATATGT
263397 AAATTAAAAATTAAAAATTTATTTAAA-A
1 AAATTAAAAATTAAAAATTTATTTAAATA
263425 ACAATT-AAAATTAAAAATTTATTTAAATA
1 A-AATTAAAAATTAAAAATTTATTTAAATA
263454 AAA-TAAAAAT
1 AAATTAAAAAT
263464 ATATAGACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
27 1 0.03
28 29 0.81
29 6 0.17
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (29 bp):
AAATTAAAAATTAAAAATTTATTTAAATA
Found at i:269905 original size:3 final size:3
Alignment explanation
Indices: 269899--269939 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
269889 ACTACAAAAA
*
269899 AAG AAG AAG AAG AAG AAG AAG AAG AAG AGG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
269940 AAACATGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:271129 original size:2 final size:2
Alignment explanation
Indices: 271122--271158 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
271112 TGGGTGCGTC
271122 TG TG TG TG TAG -G TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG T-G TG TG TG TG TG TG TG TG TG TG TG TG TG T
271159 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.94
3 1 0.03
ACGTcount: A:0.03, C:0.00, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:278843 original size:2 final size:2
Alignment explanation
Indices: 278836--278865 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
278826 CGTGAATGTG
278836 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
278866 GGGAGAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:281337 original size:2 final size:2
Alignment explanation
Indices: 281330--281360 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
281320 CGATAATGCT
281330 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
281361 TTCTGTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:283019 original size:12 final size:12
Alignment explanation
Indices: 283002--283027 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
282992 AGAGATTGGG
283002 GAAAGAGAGAGA
1 GAAAGAGAGAGA
283014 GAAAGAGAGAGA
1 GAAAGAGAGAGA
283026 GA
1 GA
283028 GAGAAGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (12 bp):
GAAAGAGAGAGA
Found at i:283558 original size:17 final size:17
Alignment explanation
Indices: 283524--283559 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
283514 GGTGGCAACT
* *
283524 AAGAAAAGAACAAGAAA
1 AAGAAAAGAAAAAAAAA
283541 AAGAAAAGAAAAAAAAA
1 AAGAAAAGAAAAAAAAA
283558 AA
1 AA
283560 AGAGGATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAAAAAAAAA
Found at i:290916 original size:5 final size:5
Alignment explanation
Indices: 290883--290915 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
290873 ATTAATTACA
*
290883 AGGAG AGGAG AGGAG AGGAG AGGAG AGGTG AGG
1 AGGAG AGGAG AGGAG AGGAG AGGAG AGGAG AGG
290916 TATCAAAGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.61, T:0.03
Consensus pattern (5 bp):
AGGAG
Found at i:292917 original size:3 final size:3
Alignment explanation
Indices: 292909--292943 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
292899 TCCTAATTAC
292909 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
292944 ATAGAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:294546 original size:27 final size:27
Alignment explanation
Indices: 294495--294544 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
294485 TTATTAGAGT
294495 ATTAAAATTAAATATTATAATTATAAC
1 ATTAAAATTAAATATTATAATTATAAC
*
294522 ATTAAAATTAATTA-TA-AATTATA
1 ATTAAAATTAAATATTATAATTATA
294545 TATTTCGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
26 2 0.09
27 13 0.59
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
ATTAAAATTAAATATTATAATTATAAC
Found at i:296706 original size:2 final size:2
Alignment explanation
Indices: 296701--296728 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
296691 AAAGGAAAAT
296701 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
296729 ATGTAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:296739 original size:2 final size:2
Alignment explanation
Indices: 296734--296764 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
296724 CTCTCATGTA
296734 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
296765 AAGAACATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:309528 original size:3 final size:3
Alignment explanation
Indices: 309520--309546 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
309510 TTAGTGTTGA
309520 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
309547 AATCTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:312066 original size:2 final size:2
Alignment explanation
Indices: 312055--312089 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
312045 TAATGTTCTA
312055 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
312090 TAATATTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:317507 original size:2 final size:2
Alignment explanation
Indices: 317502--317550 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
317492 CCCCCCCTTC
317502 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
317544 CT CT CT C
1 CT CT CT C
317551 CCATCTTCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:317994 original size:16 final size:16
Alignment explanation
Indices: 317956--317998 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
317946 TATAAAAAAT
*
317956 AAAAATATA-TAATCA
1 AAAAATATATTAAACA
317971 AAATAATATATTAAACA
1 AAA-AATATATTAAACA
*
317988 TAAAATATATT
1 AAAAATATATT
317999 TTAAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.12
16 14 0.58
17 7 0.29
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAATATATTAAACA
Found at i:319514 original size:12 final size:12
Alignment explanation
Indices: 319481--319514 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
319471 CAATTATGGT
*
319481 ACCAAAACCAAA
1 ACCAAAACCTAA
319493 ACCAAAACCTAA
1 ACCAAAACCTAA
*
319505 ACCTAAACCT
1 ACCAAAACCT
319515 GGCCTCATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.35, G:0.00, T:0.09
Consensus pattern (12 bp):
ACCAAAACCTAA
Found at i:319565 original size:6 final size:6
Alignment explanation
Indices: 319554--319611 Score: 80
Period size: 6 Copynumber: 9.0 Consensus size: 6
319544 AGCTTCCTGA
319554 TTCTAC TTCTAC ATTTCTAC TTCTAC TTCTAC ATTTCTAC TTCTAC TTCTAC
1 TTCTAC TTCTAC --TTCTAC TTCTAC TTCTAC --TTCTAC TTCTAC TTCTAC
319606 TTCTAC
1 TTCTAC
319612 ACATACAAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
6 36 0.75
8 12 0.25
ACGTcount: A:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (6 bp):
TTCTAC
Found at i:319579 original size:20 final size:20
Alignment explanation
Indices: 319554--319605 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
319544 AGCTTCCTGA
319554 TTCTACTTCTACATTTCTAC
1 TTCTACTTCTACATTTCTAC
319574 TTCTACTTCTACATTTCTAC
1 TTCTACTTCTACATTTCTAC
319594 TTCTACTTCTAC
1 TTCTACTTCTAC
319606 TTCTACACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (20 bp):
TTCTACTTCTACATTTCTAC
Found at i:319968 original size:2 final size:2
Alignment explanation
Indices: 319961--319993 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
319951 GCCCAATTTC
319961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
319994 GCTTTGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:327944 original size:18 final size:18
Alignment explanation
Indices: 327923--327959 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
327913 TGTTTATTTT
327923 AAATAAAATAAAATATAA
1 AAATAAAATAAAATATAA
**
327941 AAATAATTTAAAATATAA
1 AAATAAAATAAAATATAA
327959 A
1 A
327960 CTCTGAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATAAAATAAAATATAA
Found at i:328206 original size:6 final size:6
Alignment explanation
Indices: 328195--328262 Score: 70
Period size: 6 Copynumber: 11.5 Consensus size: 6
328185 AATAATTGAT
* *
328195 TATAGA TATAG- -ATAGA -ATAGAA TATAGA TATACA TATAGA CATAGA
1 TATAGA TATAGA TATAGA TATAG-A TATAGA TATAGA TATAGA TATAGA
*
328241 TATAGA TATAAA TTATAGA TAT
1 TATAGA TATAGA -TATAGA TAT
328263 GGTTGAATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
4 4 0.08
5 4 0.08
6 35 0.67
7 9 0.17
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.32
Consensus pattern (6 bp):
TATAGA
Found at i:328371 original size:22 final size:21
Alignment explanation
Indices: 328329--328371 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
328319 AATTAATGCA
***
328329 TTCTTTTAATATAATGTAAAT
1 TTCTTTTAATATAAAAAAAAT
328350 TTCTTTTATATATAAAAAAAAT
1 TTCTTTTA-ATATAAAAAAAAT
328372 ATAATTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (21 bp):
TTCTTTTAATATAAAAAAAAT
Found at i:333912 original size:2 final size:2
Alignment explanation
Indices: 333905--333941 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
333895 CATAATTGAC
333905 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
333942 CACTTTAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:340935 original size:4 final size:4
Alignment explanation
Indices: 340926--340959 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
340916 GTCTTGTCTT
340926 AAGA AAGA AAGA AAGA AAGA AAGA GAA-A AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA -AAGA AAGA AA
340960 ATGAGGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 2 0.07
4 24 0.86
5 2 0.07
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:347687 original size:52 final size:52
Alignment explanation
Indices: 347609--347809 Score: 305
Period size: 52 Copynumber: 3.9 Consensus size: 52
347599 CGAAATATGA
*
347609 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
* * *
347661 AAATTTGCCTGCATGTATTGATACATTTTATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
* *
347713 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
* **
347765 AAATTTACCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGTAT-AGTGTATCGATACA
347810 ATGTATCGAT
Statistics
Matches: 136, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
51 2 0.01
52 134 0.99
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
Found at i:347816 original size:13 final size:13
Alignment explanation
Indices: 347798--347822 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
347788 CAAAGATCAG
347798 TGTATCGATACAA
1 TGTATCGATACAA
347811 TGTATCGATACA
1 TGTATCGATACA
347823 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:347900 original size:33 final size:33
Alignment explanation
Indices: 347863--347929 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
347853 AGTAGCTTAA
347863 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
347896 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
347929 A
1 A
347930 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:347903 original size:13 final size:13
Alignment explanation
Indices: 347885--347909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
347875 CAAAAAAATA
347885 TGTATCGATACAT
1 TGTATCGATACAT
347898 TGTATCGATACA
1 TGTATCGATACA
347910 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:351754 original size:3 final size:3
Alignment explanation
Indices: 351746--351779 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
351736 TCAATAAATG
351746 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
351780 GATCAATCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:352066 original size:2 final size:2
Alignment explanation
Indices: 352059--352084 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
352049 TGATAATATA
352059 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
352085 GTGTAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:355481 original size:2 final size:2
Alignment explanation
Indices: 355474--355529 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
355464 ATTTGATGAT
355474 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
355516 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
355530 AAAATGCATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:360742 original size:20 final size:21
Alignment explanation
Indices: 360713--360754 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
360703 CCCTCACGAC
*
360713 TAAGG-AAAAAGTCTGGGGTT
1 TAAGGAAAAAAGTCTAGGGTT
*
360733 TAAGGGAAAAAGTCTAGGGTT
1 TAAGGAAAAAAGTCTAGGGTT
360754 T
1 T
360755 CCACAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.36, C:0.05, G:0.33, T:0.26
Consensus pattern (21 bp):
TAAGGAAAAAAGTCTAGGGTT
Found at i:364130 original size:21 final size:21
Alignment explanation
Indices: 364104--364145 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
364094 AGGAGGAAAG
364104 TTCAAGAAGAAGAAAATTCAA
1 TTCAAGAAGAAGAAAATTCAA
364125 TTCAAGAAGAAGAAAATTCAA
1 TTCAAGAAGAAGAAAATTCAA
364146 CAGTAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.19
Consensus pattern (21 bp):
TTCAAGAAGAAGAAAATTCAA
Found at i:366247 original size:9 final size:9
Alignment explanation
Indices: 366233--366266 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
366223 CACATCTATC
366233 TCTTCACTT
1 TCTTCACTT
*
366242 TCTTCAACCT
1 TCTTC-ACTT
366252 TCTTCACTT
1 TCTTCACTT
366261 TCTTCA
1 TCTTCA
366267 ACCTTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (9 bp):
TCTTCACTT
Found at i:366256 original size:10 final size:10
Alignment explanation
Indices: 366241--366274 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
366231 TCTCTTCACT
366241 TTCTTCAACC
1 TTCTTCAACC
*
366251 TTCTTC-ACT
1 TTCTTCAACC
366260 TTCTTCAACC
1 TTCTTCAACC
366270 TTCTT
1 TTCTT
366275 TTTTATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (10 bp):
TTCTTCAACC
Found at i:366257 original size:19 final size:19
Alignment explanation
Indices: 366233--366274 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
366223 CACATCTATC
366233 TCTTCACTTTCTTCAACCT
1 TCTTCACTTTCTTCAACCT
366252 TCTTCACTTTCTTCAACCT
1 TCTTCACTTTCTTCAACCT
366271 TCTT
1 TCTT
366275 TTTTATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.14, C:0.36, G:0.00, T:0.50
Consensus pattern (19 bp):
TCTTCACTTTCTTCAACCT
Found at i:378574 original size:22 final size:24
Alignment explanation
Indices: 378549--378592 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
378539 TTCCTCGAGA
378549 ATATA-TC-ATTAAATATATATAC
1 ATATATTCTATTAAATATATATAC
*
378571 ATATATTCTTTTAAATATATAT
1 ATATATTCTATTAAATATATAT
378593 CATTAATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 2 0.11
24 12 0.63
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATATTCTATTAAATATATATAC
Found at i:380305 original size:2 final size:2
Alignment explanation
Indices: 380300--380330 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
380290 TATACATAAC
380300 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
380331 CTCATCCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:382457 original size:2 final size:2
Alignment explanation
Indices: 382445--382487 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
382435 AGAGCAAAGA
382445 AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
382486 AG
1 AG
382488 GGGGGGGGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:385306 original size:166 final size:166
Alignment explanation
Indices: 384987--385472 Score: 789
Period size: 166 Copynumber: 2.9 Consensus size: 166
384977 GAAACAATAT
* * * *
384987 CTTAAGCTACAAATAATTCTTGCTTCAAAATTTTGTCTAAAGATTTGACGTCAGGAAGAGGCTTT
1 CTTAAGTTACAAATAATTCTTGCTTCATAATTTTGTCTAAAGATTTGACTTCAGGAAAAGGCTTT
* *
385052 CAAAGAAAAGACTACAAAGATATGACAACTTGACAAACAAAATAAATATTATGCACTGGCTTGAG
66 CAAAGAAAAGACTACAAGGATATGAC-ACTTGACAAACAAAATAAATATTATGCACTTGCTTGAG
*
385117 CACTTTTTCCGTTATTA-TTTCGTCATCGTTTATTTG
130 CACTTTCTCCGTTATTATTTTCGTCATCGTTTATTTG
* *
385153 CTTAAGTTACAAATAATTTTTGCTTCATAATTTTGTCTAAAGATTTGACTTCAGGAAAAGGCTTC
1 CTTAAGTTACAAATAATTCTTGCTTCATAATTTTGTCTAAAGATTTGACTTCAGGAAAAGGCTTT
* * *
385218 CAAAGAGAAGACTACAAGGGTATGACACTTGACAAACAAAGTAAATATTATGCACTTGCTTGAGC
66 CAAAGAAAAGACTACAAGGATATGACACTTGACAAACAAAATAAATATTATGCACTTGCTTGAGC
385283 ACTTTCTCCGTTATTATTTTCGTCATCGTTTATTTG
131 ACTTTCTCCGTTATTATTTTCGTCATCGTTTATTTG
*
385319 CTTAAGTTACAAATAATTCTTGCCTCATAATTTTGTCTAAAGA--TGACTTCAGGAAAAGGCTTT
1 CTTAAGTTACAAATAATTCTTGCTTCATAATTTTGTCTAAAGATTTGACTTCAGGAAAAGGCTTT
* * *
385382 CGAAGAAAAGACTACAAGGATATGACACTTGGCACACAAAATAAATATTATGCACTTGCTTGAGC
66 CAAAGAAAAGACTACAAGGATATGACACTTGACAAACAAAATAAATATTATGCACTTGCTTGAGC
*
385447 ACTTTCTCTGTTATTATTTTCGTCAT
131 ACTTTCTCCGTTATTATTTTCGTCAT
385473 TCTTGCCTCA
Statistics
Matches: 297, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
164 103 0.35
165 52 0.18
166 142 0.48
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (166 bp):
CTTAAGTTACAAATAATTCTTGCTTCATAATTTTGTCTAAAGATTTGACTTCAGGAAAAGGCTTT
CAAAGAAAAGACTACAAGGATATGACACTTGACAAACAAAATAAATATTATGCACTTGCTTGAGC
ACTTTCTCCGTTATTATTTTCGTCATCGTTTATTTG
Found at i:396471 original size:2 final size:2
Alignment explanation
Indices: 396464--396521 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
396454 GGACATAATG
396464 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
396506 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
396522 CAAATTGATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:398650 original size:2 final size:2
Alignment explanation
Indices: 398643--398674 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
398633 TTAGATAAGC
398643 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
398675 CCCCACATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:408788 original size:3 final size:3
Alignment explanation
Indices: 408780--408819 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
408770 TAAAGTTTGA
*
408780 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
408820 GATCTCTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:409323 original size:3 final size:3
Alignment explanation
Indices: 409317--409342 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
409307 AAAAAACAAG
409317 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
409343 AGTAGTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:414897 original size:22 final size:21
Alignment explanation
Indices: 414862--414905 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
414852 TTAATTCCAA
*
414862 TAATGATTTGTGATATTTTGCTT
1 TAATGATTAGTGAT-TTTT-CTT
414885 TAATG-TTAGTGATTTTTCTT
1 TAATGATTAGTGATTTTTCTT
414905 T
1 T
414906 TTCCTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 4 0.20
22 7 0.35
23 5 0.25
ACGTcount: A:0.20, C:0.05, G:0.16, T:0.59
Consensus pattern (21 bp):
TAATGATTAGTGATTTTTCTT
Found at i:415041 original size:13 final size:13
Alignment explanation
Indices: 415025--415049 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
415015 TATTATATAT
415025 TAAAATATAATTA
1 TAAAATATAATTA
415038 TAAAATATAATT
1 TAAAATATAATT
415050 TTTTAAATAT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAAATATAATTA
Found at i:415733 original size:2 final size:2
Alignment explanation
Indices: 415726--415750 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
415716 TATTATTTTC
415726 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
415751 AATCATCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:416189 original size:54 final size:54
Alignment explanation
Indices: 416122--416238 Score: 141
Period size: 54 Copynumber: 2.2 Consensus size: 54
416112 ATGTTTTATC
* *
416122 ATTAAATTTATTTAAATATT-AAATTATTT-ATTTAATTCAA-TAGATTTTATATAA
1 ATTAAATTAATTTAAA-ATTAAAATT-TTTAATTTAATTCAATTAGA-TTAATATAA
* * *
416176 ATTAAATTAATTTAAAATTAAAATTTTTAATTTAGTTCAATTTGATTAATCTAA
1 ATTAAATTAATTTAAAATTAAAATTTTTAATTTAATTCAATTAGATTAATATAA
416230 ATTAAATTA
1 ATTAAATTA
416239 TAAAAAAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
53 6 0.11
54 46 0.84
55 3 0.05
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (54 bp):
ATTAAATTAATTTAAAATTAAAATTTTTAATTTAATTCAATTAGATTAATATAA
Found at i:417589 original size:2 final size:2
Alignment explanation
Indices: 417582--417612 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
417572 TTTTGATCAC
*
417582 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
417613 GTGGCCGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:418799 original size:20 final size:19
Alignment explanation
Indices: 418767--418804 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
418757 AAATTAAATT
418767 AAATTAAATTTATATTAAAA
1 AAATTAAATTTAT-TTAAAA
418787 AAATTATAA-TTATTTAAA
1 AAATTA-AATTTATTTAAA
418805 TTTAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 10 0.59
21 2 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTAAATTTATTTAAAA
Found at i:418831 original size:35 final size:35
Alignment explanation
Indices: 418765--418846 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 35
418755 ATAAATTAAA
*
418765 TTAAATTAAATTTATATTAAAAAAATTATAATTAT
1 TTAAATTAAATTTATATTAAAAAAATAATAATTAT
* * *
418800 TTAAATTTAATTTA-ATTCAAAATATAAATAATTTAT
1 TTAAATTAAATTTATATTAAAAAAAT-AATAA-TTAT
418836 ATTCAAATTAA
1 -TT-AAATTAA
418847 GCTAAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
34 9 0.24
35 17 0.45
36 4 0.11
37 2 0.05
38 6 0.16
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (35 bp):
TTAAATTAAATTTATATTAAAAAAATAATAATTAT
Found at i:420423 original size:3 final size:3
Alignment explanation
Indices: 420415--420456 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
420405 GGCATGGGTT
*
420415 ATG ATG ATG ATG ATG ACG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
420457 TTTTGTAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.31
Consensus pattern (3 bp):
ATG
Found at i:420622 original size:19 final size:20
Alignment explanation
Indices: 420581--420629 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
420571 AAATAGTTTA
* *
420581 ATTTAATTTAAATTATTATTT
1 ATTTAATATAAA-TATTAATT
420602 ATTTAATATAAA-ATTAATT
1 ATTTAATATAAATATTAATT
*
420621 ATTAAATAT
1 ATTTAATAT
420630 TTTAACATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 14 0.56
21 11 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTAATATAAATATTAATT
Found at i:420630 original size:26 final size:26
Alignment explanation
Indices: 420569--420631 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
420559 ATTTTGTAAT
* *
420569 TTAAATAGTTTAATTTAATTTAAATTA
1 TTAAATA-TTTAATTAAAATTAAATTA
**
420596 TTATTTATTTAATATAAAATT-AATTA
1 TTAAATATTTAAT-TAAAATTAAATTA
420622 TTAAATATTT
1 TTAAATATTT
420632 TAACATATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
TTAAATATTTAATTAAAATTAAATTA
Found at i:421226 original size:13 final size:13
Alignment explanation
Indices: 421210--421257 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
421200 TAATTTTTTA
*
421210 TATTAGAAAAATT
1 TATTATAAAAATT
*
421223 TATTATTAAATATT
1 TATTA-TAAAAATT
421237 TAAATTATAAAAATT
1 T--ATTATAAAAATT
421252 TATTAT
1 TATTAT
421258 TAGTCGTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 10 0.34
14 7 0.24
15 8 0.28
16 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
TATTATAAAAATT
Found at i:421229 original size:29 final size:29
Alignment explanation
Indices: 421197--421259 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
421187 AAAATCATAA
* * *
421197 TATTAATTTTTTATATTAGAAAAATTTAT
1 TATTAAATATTTAAATTAGAAAAATTTAT
*
421226 TATTAAATATTTAAATTATAAAAATTTAT
1 TATTAAATATTTAAATTAGAAAAATTTAT
421255 TATTA
1 TATTA
421260 GTCGTATGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
TATTAAATATTTAAATTAGAAAAATTTAT
Found at i:421701 original size:7 final size:7
Alignment explanation
Indices: 421689--421721 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
421679 AATTCATCCG
421689 CCCACCA
1 CCCACCA
421696 CCCACCA
1 CCCACCA
421703 CCCACCA
1 CCCACCA
*
421710 CCCACCG
1 CCCACCA
421717 CCCAC
1 CCCAC
421722 TCTATATAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.24, C:0.73, G:0.03, T:0.00
Consensus pattern (7 bp):
CCCACCA
Found at i:422754 original size:21 final size:22
Alignment explanation
Indices: 422728--422787 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
422718 TGATTTTGAA
*
422728 TAAAAATTTAATAT-ATTCATT
1 TAAAAATTTAATATAATTAATT
*
422749 TAAAAA-TAATATATAATTAATT
1 TAAAAATTTA-ATATAATTAATT
*
422771 TAAAATATTTAACATAA
1 TAAAA-ATTTAATATAA
422788 AAAAGAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 2 0.06
21 10 0.32
22 11 0.35
23 6 0.19
24 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAAATTTAATATAATTAATT
Found at i:429282 original size:57 final size:57
Alignment explanation
Indices: 429220--429405 Score: 151
Period size: 57 Copynumber: 3.2 Consensus size: 57
429210 GATATGGTAG
* *
429220 TGGAGGTGGCGAAGGAGGTGGAGCTGGTGGCGGTGGGTATGGAGGAGCTAGTGGATA
1 TGGAGGTGGCGAAGGAGGTGGAGCTGGTGGTGGTGGGAATGGAGGAGCTAGTGGATA
* ** * * * * * * **
429277 TGGAGGTGGTGGGGGCA-ATGGTGGTGGTGGTGGTAGTGCA-GGTGGAGCTTCTGGATATGGGA
1 TGGAGGTGGCGAAGG-AGGTGGAGCTGGTGGTGGT-GGGAATGGAGGAGCTAGTGG--AT---A
* *
429339 GTGGAGGTGGCGAAGGAGGTGGAGCTGGTGGTGGTGGGAATGGAGGAGCTGGTGGACA
1 -TGGAGGTGGCGAAGGAGGTGGAGCTGGTGGTGGTGGGAATGGAGGAGCTAGTGGATA
429397 TGGAGGTGG
1 TGGAGGTGG
429406 TGGGGGCAAT
Statistics
Matches: 95, Mismatches: 24, Indels: 20
0.68 0.17 0.14
Matches are distributed among these distances:
57 45 0.47
58 5 0.05
59 2 0.02
61 1 0.01
62 5 0.05
63 37 0.39
ACGTcount: A:0.17, C:0.06, G:0.55, T:0.21
Consensus pattern (57 bp):
TGGAGGTGGCGAAGGAGGTGGAGCTGGTGGTGGTGGGAATGGAGGAGCTAGTGGATA
Found at i:429417 original size:18 final size:17
Alignment explanation
Indices: 429365--429417 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
429355 AGGTGGAGCT
429365 GGTGGTGGTGGGAATGGA
1 GGTGGTGG-GGGAATGGA
* * *
429383 GGAGCTGGTGGACATGGA
1 GGTGGTGGGGGA-ATGGA
429401 GGTGGTGGGGGCAATGG
1 GGTGGTGGGGG-AATGG
429418 TAGCGGCGGA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 3 0.11
18 23 0.85
19 1 0.04
ACGTcount: A:0.17, C:0.06, G:0.58, T:0.19
Consensus pattern (17 bp):
GGTGGTGGGGGAATGGA
Found at i:429581 original size:237 final size:237
Alignment explanation
Indices: 429175--430069 Score: 1454
Period size: 237 Copynumber: 3.8 Consensus size: 237
429165 GTGGTGGTGG
* * * * * * *
429175 TGGTGGTGGTGGAGGCATTGCGGGTGGAGCTTCTGGATATGGTAGTGGAGGTGGCGAAGGAGGTG
1 TGGTGGCGGCGGAGGTAGTGCGGGTGGGGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
** * *
429240 GAGCTGGTGGCGGTGGGTATGGAGGAGCTAGTGGATATGGAGGTGGTGGGGGCAATGGTGGTGGT
66 GAGCTGGT---GGTGGGTATGGAGGAGCCGGTGGACATGGAGGTGGTGGGGGCAATGGTGGCGGT
* *
429305 GGTGGTAGTGCAGGTGGAGCTTCTGGATATGGGAGTGGAGGTGGCGAAGGAGGTGGAGCTGGTGG
128 GGAGGTAGTGCAGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGCGAAGGAGGTGGAGCTGGTGG
*
429370 TGGTGGGAATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
193 TGGTGGGTATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
* *
429415 TGGTAGCGGCGGAGGTAGTGCAGGTGGGGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
1 TGGTGGCGGCGGAGGTAGTGCGGGTGGGGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
* * *
429480 GAGCTGGTGGTGGCTATGGAGGAGCCGGTGGACATGGTGGTGGGGGGGGCAATGGTGGCGGTGGA
66 GAGCTGGTGGTGGGTATGGAGGAGCCGGTGGACATGGAGGTGGTGGGGGCAATGGTGGCGGTGGA
* *
429545 GGTAGTGCCGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTGGAGC---TGGTGG
131 GGTAGTGCAGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGCGAAGGAGGTGGAGCTGGTGGTGG
* *
429607 TGGGTATGGAGGAGCTGGGGGACATGGAGGTGGTGGTGGCAA
196 TGGGTATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
*
429649 TGGTGGTGGCGGAGGTAGTGCGGGTGGGGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
1 TGGTGGCGGCGGAGGTAGTGCGGGTGGGGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
* *
429714 GAGCTGGTGGTGGGTATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAATGGTGGCGGCGGA
66 GAGCTGGTGGTGGGTATGGAGGAGCCGGTGGACATGGAGGTGGTGGGGGCAATGGTGGCGGTGGA
* * *
429779 GGTAGTGCGGGTGGGGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGTGG
131 GGTAGTGCAGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGCGAAGGAGGTGGAGCTGGTGGTGG
429844 TGGGTATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
196 TGGGTATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
429886 TGGTGGCGGCGGAGGTAGTGCGGGTGGGGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
1 TGGTGGCGGCGGAGGTAGTGCGGGTGGGGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
429951 GAGCTGGTGGTGGGTATGGAGGAGCCGGTGGACATGGAGGTGGTGGGGGCAATGGTGGCGGTGGA
66 GAGCTGGTGGTGGGTATGGAGGAGCCGGTGGACATGGAGGTGGTGGGGGCAATGGTGGCGGTGGA
* * *
430016 GGTAGTGCTGGTGGAGCTTCCGGATATGGAAGTGGGGGTGGCGAAGGAGGTGGA
131 GGTAGTGCAGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGCGAAGGAGGTGGA
430070 AGTGGAAATG
Statistics
Matches: 609, Mismatches: 43, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
234 221 0.36
237 324 0.53
240 64 0.11
ACGTcount: A:0.17, C:0.08, G:0.55, T:0.21
Consensus pattern (237 bp):
TGGTGGCGGCGGAGGTAGTGCGGGTGGGGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
GAGCTGGTGGTGGGTATGGAGGAGCCGGTGGACATGGAGGTGGTGGGGGCAATGGTGGCGGTGGA
GGTAGTGCAGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGCGAAGGAGGTGGAGCTGGTGGTGG
TGGGTATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
Found at i:430082 original size:120 final size:117
Alignment explanation
Indices: 429175--430069 Score: 1385
Period size: 117 Copynumber: 7.6 Consensus size: 117
429165 GTGGTGGTGG
* * * * * *
429175 TGGTGGTGGTGGAGGCATTGCGGGTGGAGCTTCTGGATATGGTAGTGGAGGTGGCGAAGGAGGTG
1 TGGTGGCGGCGGAGGTAGTGCGGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
* *
429240 GAGCTGGTGGCGGTGGGTATGGAGGAGCTAGTGGATATGGAGGTGGTGGGGGCAA
66 GAGCTGGT---GGTGGGTATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
* * * * * *
429295 TGGTGGTGGTGGTGGTAGTGCAGGTGGAGCTTCTGGATATGGGAGTGGAGGTGGCGAAGGAGGTG
1 TGGTGGCGGCGGAGGTAGTGCGGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
*
429360 GAGCTGGTGGTGGTGGGAATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
66 GAGC---TGGTGGTGGGTATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
* * *
429415 TGGTAGCGGCGGAGGTAGTGCAGGTGGGGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
1 TGGTGGCGGCGGAGGTAGTGCGGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
* * * *
429480 GAGCTGGTGGTGGCTATGGAGGAGCCGGTGGACATGGTGGTGGGGGGGGCAA
66 GAGCTGGTGGTGGGTATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
* *
429532 TGGTGGCGGTGGAGGTAGTGCCGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
1 TGGTGGCGGCGGAGGTAGTGCGGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
* *
429597 GAGCTGGTGGTGGGTATGGAGGAGCTGGGGGACATGGAGGTGGTGGTGGCAA
66 GAGCTGGTGGTGGGTATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
* *
429649 TGGTGGTGGCGGAGGTAGTGCGGGTGGGGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
1 TGGTGGCGGCGGAGGTAGTGCGGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
429714 GAGCTGGTGGTGGGTATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
66 GAGCTGGTGGTGGGTATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
*
429766 TGGTGGCGGCGGAGGTAGTGCGGGTGGGGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
1 TGGTGGCGGCGGAGGTAGTGCGGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
429831 GAGCTGGTGGTGGTGGGTATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
66 GAGC---TGGTGGTGGGTATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
*
429886 TGGTGGCGGCGGAGGTAGTGCGGGTGGGGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
1 TGGTGGCGGCGGAGGTAGTGCGGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
*
429951 GAGCTGGTGGTGGGTATGGAGGAGCCGGTGGACATGGAGGTGGTGGGGGCAA
66 GAGCTGGTGGTGGGTATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
* * * * *
430003 TGGTGGCGGTGGAGGTAGTGCTGGTGGAGCTTCCGGATATGGAAGTGGGGGTGGCGAAGGAGGTG
1 TGGTGGCGGCGGAGGTAGTGCGGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
430068 GA
66 GA
430070 AGTGGAAATG
Statistics
Matches: 725, Mismatches: 44, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
117 437 0.60
120 284 0.39
123 4 0.01
ACGTcount: A:0.17, C:0.08, G:0.55, T:0.21
Consensus pattern (117 bp):
TGGTGGCGGCGGAGGTAGTGCGGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTG
GAGCTGGTGGTGGGTATGGAGGAGCTGGTGGACATGGAGGTGGTGGGGGCAA
Found at i:430133 original size:24 final size:24
Alignment explanation
Indices: 430100--430155 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
430090 TGGATATGCA
*
430100 GGTGGAGGTGGTGGAGGAAATGGT
1 GGTGGAGGTGGAGGAGGAAATGGT
* *
430124 GGTGGTGGTGGAGGAGGATATGGT
1 GGTGGAGGTGGAGGAGGAAATGGT
*
430148 GTTGGAGG
1 GGTGGAGG
430156 GGCACATGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.59, T:0.23
Consensus pattern (24 bp):
GGTGGAGGTGGAGGAGGAAATGGT
Found at i:433381 original size:2 final size:2
Alignment explanation
Indices: 433374--433421 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
433364 CTTTTCCATA
** *
433374 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GC AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
433416 AT AT AT
1 AT AT AT
433422 GTATGCATGC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:433426 original size:18 final size:18
Alignment explanation
Indices: 433374--433429 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
433364 CTTTTCCATA
* **
433374 ATATATATATATATATAT
1 ATATACATATATATATGC
*
433392 ATATATATATATATATGC
1 ATATACATATATATATGC
*
433410 ATATACATATATGTATGC
1 ATATACATATATATATGC
433428 AT
1 AT
433430 GCATAGCTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
ATATACATATATATATGC
Found at i:434342 original size:18 final size:18
Alignment explanation
Indices: 434302--434343 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
434292 AAATTAAATT
*
434302 CATTTTAAAAAAGATAAA
1 CATTTAAAAAAAGATAAA
**
434320 C-TTTAAAAAAATTTAAA
1 CATTTAAAAAAAGATAAA
434337 CATTTAA
1 CATTTAA
434344 TTCAATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (18 bp):
CATTTAAAAAAAGATAAA
Found at i:438866 original size:21 final size:22
Alignment explanation
Indices: 438837--438879 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
438827 GATCATCTGT
*
438837 CGTTAGGGTTTT-ATTAGAAGA
1 CGTTAGGGTTTTCATTAAAAGA
*
438858 CGTTTGGGTTTTCATTAAAAGA
1 CGTTAGGGTTTTCATTAAAAGA
438880 TATTAGAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.28, C:0.07, G:0.26, T:0.40
Consensus pattern (22 bp):
CGTTAGGGTTTTCATTAAAAGA
Found at i:439156 original size:2 final size:2
Alignment explanation
Indices: 439149--439182 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
439139 TCTGGCTTTT
*
439149 GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
439183 CGTTTCATCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:440155 original size:16 final size:16
Alignment explanation
Indices: 440134--440166 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
440124 TAAAGTAACT
440134 TCTTTTTCTTTTTTTG
1 TCTTTTTCTTTTTTTG
*
440150 TCTTTTTTTTTTTTTG
1 TCTTTTTCTTTTTTTG
440166 T
1 T
440167 AAATGTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (16 bp):
TCTTTTTCTTTTTTTG
Found at i:442995 original size:3 final size:3
Alignment explanation
Indices: 442987--443011 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
442977 AAGTGAAATT
442987 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
443012 AATAATAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:445240 original size:7 final size:7
Alignment explanation
Indices: 445228--445258 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
445218 CTATATGGAA
445228 GCACTGT
1 GCACTGT
445235 GCACTGT
1 GCACTGT
445242 GCACTGT
1 GCACTGT
445249 GCACTGT
1 GCACTGT
445256 GCA
1 GCA
445259 TAGTTTCCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GCACTGT
Found at i:446903 original size:3 final size:3
Alignment explanation
Indices: 446895--446928 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
446885 TAAATTATAG
* *
446895 TAA TAA TAA TAA TAA TCA TAA TAA TGA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
446929 GATACAGAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:446929 original size:9 final size:9
Alignment explanation
Indices: 446895--446932 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
446885 TAAATTATAG
*
446895 TAATAATAA
1 TAATAATGA
*
446904 TAATAATCA
1 TAATAATGA
446913 TAATAATGA
1 TAATAATGA
446922 TAATAATGA
1 TAATAATGA
446931 TA
1 TA
446933 CAGAGTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (9 bp):
TAATAATGA
Found at i:447510 original size:17 final size:18
Alignment explanation
Indices: 447476--447543 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 18
447466 AACGTACATA
*
447476 AAAATTAATATGACATATT
1 AAAATTTATAT-ACATATT
447495 AAAATTTATATA-ATA-T
1 AAAATTTATATACATATT
* *
447511 -AAATTTTTA-ACATGTT
1 AAAATTTATATACATATT
* *
447527 AAGATTTATATAAATAT
1 AAAATTTATATACATAT
447544 ATAATACTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
14 1 0.03
15 10 0.26
16 2 0.05
17 10 0.26
18 5 0.13
19 10 0.26
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (18 bp):
AAAATTTATATACATATT
Found at i:448705 original size:19 final size:18
Alignment explanation
Indices: 448681--448728 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
448671 GATTTTAATA
448681 TAAATAAAATAAAAATTAT
1 TAAATAAAATAAAAATT-T
*
448700 TAAAT-AAATTAAAATTT
1 TAAATAAAATAAAAATTT
448717 TAAATATAAATA
1 TAAATA-AAATA
448729 TAATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 6 0.24
18 10 0.40
19 9 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAATAAAATAAAAATTT
Found at i:448815 original size:18 final size:20
Alignment explanation
Indices: 448782--448828 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 20
448772 AATATATTTA
448782 TTATTATATCATTATTATCT
1 TTATTATATCATTATTATCT
*
448802 TTATTATA-CA-TATTATTT
1 TTATTATATCATTATTATCT
448820 TTATTATAT
1 TTATTATAT
448829 TTTTATTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 15 0.60
19 2 0.08
20 8 0.32
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTATATCATTATTATCT
Found at i:449528 original size:13 final size:14
Alignment explanation
Indices: 449513--449546 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
449503 AAAAATCATA
449513 AAAATTTTT-T-AT
1 AAAATTTTTCTGAT
449525 AAAATTTTTCTGAT
1 AAAATTTTTCTGAT
449539 AAAATTTT
1 AAAATTTT
449547 GATATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.45
13 1 0.05
14 10 0.50
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (14 bp):
AAAATTTTTCTGAT
Found at i:451629 original size:14 final size:14
Alignment explanation
Indices: 451610--451637 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
451600 TGGTTGACCC
451610 TTATCTCTTTCATT
1 TTATCTCTTTCATT
451624 TTATCTCTTTCATT
1 TTATCTCTTTCATT
451638 CTGTACTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATCTCTTTCATT
Found at i:452630 original size:4 final size:4
Alignment explanation
Indices: 452621--452646 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
452611 GACAAATAGC
452621 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
452647 AGCACGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:453852 original size:16 final size:18
Alignment explanation
Indices: 453833--453875 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
453823 AATATGATAC
453833 AAATATGA-T-ATATAAT
1 AAATATGAGTGATATAAT
*
453849 AAATATGAAGTGATATAGT
1 AAATATG-AGTGATATAAT
453868 AAATATGA
1 AAATATGA
453876 CATTATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 7 0.30
17 1 0.04
18 2 0.09
19 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (18 bp):
AAATATGAGTGATATAAT
Found at i:454390 original size:28 final size:26
Alignment explanation
Indices: 454359--454410 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
454349 CTATCCCAGC
454359 TTTTAAAAAAATTTAAATAAAATAATTA
1 TTTTAAAAAAATTT-AA-AAAATAATTA
* *
454387 TTTTTATAAAATTTAAAAAATAAT
1 TTTTAAAAAAATTTAAAAAATAAT
454411 ATAATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 2 0.09
28 12 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
TTTTAAAAAAATTTAAAAAATAATTA
Found at i:455239 original size:3 final size:3
Alignment explanation
Indices: 455231--455256 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
455221 TGAGTTATTG
455231 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
455257 CTCAATGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Done.