Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 68 of 105
Found at i:12105212 original size:38 final size:38
Alignment explanation
Indices: 12105135--12105213 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 38
12105125 CTAAAAATAA
** * **
12105135 TTTTTTTACTTTTTTATCATTTTTTAATTTCTGAGATT
1 TTTTTTTACTTTTTTAAAACTTTTTAATTTCAAAGATT
*
12105173 TTTTTTTA-TTTTTTAAAACTTTTTAATTTTCAAATATT
1 TTTTTTTACTTTTTTAAAACTTTTTAA-TTTCAAAGATT
12105211 TTT
1 TTT
12105214 CTGAAAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 15 0.44
38 19 0.56
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.68
Consensus pattern (38 bp):
TTTTTTTACTTTTTTAAAACTTTTTAATTTCAAAGATT
Found at i:12105213 original size:37 final size:39
Alignment explanation
Indices: 12105129--12105213 Score: 95
Period size: 37 Copynumber: 2.3 Consensus size: 39
12105119 AAAAACCTAA
* ** * *
12105129 AAATAATTTTTTTACTTTTTTATCATTTTTTAATTTCTG
1 AAATATTTTTTTTACTTTTTTAAAACTTTTTAATTTCTC
*
12105168 AGAT-TTTTTTTTA-TTTTTTAAAACTTTTTAATTT-TC
1 AAATATTTTTTTTACTTTTTTAAAACTTTTTAATTTCTC
12105204 AAATATTTTT
1 AAATATTTTT
12105214 CTGAAAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
36 4 0.11
37 23 0.61
38 8 0.21
39 3 0.08
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (39 bp):
AAATATTTTTTTTACTTTTTTAAAACTTTTTAATTTCTC
Found at i:12106558 original size:3 final size:3
Alignment explanation
Indices: 12106550--12106579 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12106540 TTATCAAACA
12106550 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12106580 GGACACTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12113315 original size:22 final size:22
Alignment explanation
Indices: 12113287--12113330 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12113277 ATTTTTTGTC
* *
12113287 CTTAATTTTAGGGAAACAAATA
1 CTTAATTCTAGAGAAACAAATA
*
12113309 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGAAACAAATA
12113331 TAAATATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGAAACAAATA
Found at i:12119155 original size:2 final size:2
Alignment explanation
Indices: 12119148--12119181 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12119138 TTCTTTCTGT
12119148 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
12119182 AGAGAGAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:12122707 original size:62 final size:62
Alignment explanation
Indices: 12122641--12122997 Score: 208
Period size: 62 Copynumber: 5.7 Consensus size: 62
12122631 ATTTAAGCCG
** *
12122641 TTTTTCAACCAAAAACACCTTAAATAATTCTTAATATTTTTAAAAAAAAATTATTTAAGGTA
1 TTTTTCAATAAAAAAAACCTTAAATAATTCTTAATATTTTTAAAAAAAAATTATTTAAGGTA
* * ** * * * *** ***
12122703 TTTTTTATTAAAAAATGCATTAAATAATTATTCATATCTTTT-AAAAGGGATTATTTAAGACG
1 TTTTTCAATAAAAAAAACCTTAAATAATTCTTAATAT-TTTTAAAAAAAAATTATTTAAGGTA
* * *** *
12122765 TTTTT-AATTGAAAAAAGCCTTAAATAATTACCTTCAA-A-AAATAAAAAAAGATTATTTAAGGT
1 TTTTTCAA-TAAAAAAAACCTTAAATAATT--CTT-AATATTTTTAAAAAAAAATTATTTAAGGT
12122827 -
62 A
* * * * * * *
12122827 GTTTTCAAATAAAAAAACTCCTTAAATAATCCTTAAT-TTTTT-TAAGAGAATTATTTAAAGTA
1 TTTTTC-AATAAAAAAA-ACCTTAAATAATTCTTAATATTTTTAAAAAAAAATTATTTAAGGTA
** * * * * * *
12122889 TTTTTTGATAAAAAAAATCTTAAATAATCCTCTCATATTTTTTAAAAATAATTATTTAAGGCA
1 TTTTTCAATAAAAAAAACCTTAAATAATTCT-TAATATTTTTAAAAAAAAATTATTTAAGGTA
* *
12122952 TTTTTCAATTAAAAAAATCTTAAATAATTGTCTT-ATACTTTTTAAA
1 TTTTTCAATAAAAAAAACCTTAAATAA-T-TCTTAATA-TTTTTAAA
12122998 GAGGATTATT
Statistics
Matches: 221, Mismatches: 56, Indels: 34
0.71 0.18 0.11
Matches are distributed among these distances:
60 13 0.06
61 29 0.13
62 83 0.38
63 68 0.31
64 25 0.11
65 3 0.01
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (62 bp):
TTTTTCAATAAAAAAAACCTTAAATAATTCTTAATATTTTTAAAAAAAAATTATTTAAGGTA
Found at i:12122945 original size:63 final size:62
Alignment explanation
Indices: 12122835--12123043 Score: 206
Period size: 63 Copynumber: 3.4 Consensus size: 62
12122825 GTGTTTTCAA
* * *
12122835 ATAAAAAAACTCCTTAAATAATCCT-TA-ATTTTTTTAAGAGAATTATTTAAAGTATTTTTTG
1 ATAAAAAAAAT-CTTAAATAATCCTCTATATTTTTTAAAGAGAATTATTTAAAGAATTTTTTG
* * * * **
12122896 ATAAAAAAAATCTTAAATAATCCTCTCATATTTTTTAAAAATAATTATTTAAGGCATTTTTCA
1 ATAAAAAAAATCTTAAATAATCCTCT-ATATTTTTTAAAGAGAATTATTTAAAGAATTTTTTG
* ** * * * *
12122959 ATTAAAAAAATCTTAAATAATTGTCTTATACTTTTTAAAGAGGATTATTAAAAGAATATTTTG
1 ATAAAAAAAATCTTAAATAATCCTC-TATATTTTTTAAAGAGAATTATTTAAAGAATTTTTTG
* * *
12123022 TTAAAAAATACCTTAAATAATC
1 ATAAAAAAAATCTTAAATAATC
12123044 TCTTTAAAAA
Statistics
Matches: 118, Mismatches: 26, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
60 13 0.11
61 11 0.09
62 1 0.01
63 92 0.78
64 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (62 bp):
ATAAAAAAAATCTTAAATAATCCTCTATATTTTTTAAAGAGAATTATTTAAAGAATTTTTTG
Found at i:12123037 original size:126 final size:125
Alignment explanation
Indices: 12122806--12123043 Score: 295
Period size: 126 Copynumber: 1.9 Consensus size: 125
12122796 CTTCAAAAAA
* *
12122806 TAAAAAAAGATTATTTAAGGTGTTTTCAAATAAAAAAACTCCTTAAATAATCCTTAATTTTTTTA
1 TAAAAAAAGATTATTTAAGGTGTTTTCAAATAAAAAAACTCCTTAAATAATCCTTAACTTTTTAA
* * * *
12122871 AGAGAATTATTTAAAGTATTTTTTGATAAAAAAAATCTTAAATAATCCTCTCATATTTTT
66 AGAGAATTATTAAAAGAATATTTTGATAAAAAAAACCTTAAATAATCCTCTCATATTTTT
* * *
12122931 TAAAAATA-ATTATTTAAGGCAT-TTTTCAATTAAAAAAA-T-CTTAAATAATTGTCTTATACTT
1 TAAAAAAAGATTATTTAAGG--TGTTTTCAAATAAAAAAACTCCTTAAATAA-T-CCTTA-ACTT
* * *
12122992 TTTAAAGAGGATTATTAAAAGAATATTTTGTTAAAAAATACCTTAAATAATC
61 TTTAAAGAGAATTATTAAAAGAATATTTTGATAAAAAAAACCTTAAATAATC
12123044 TCTTTAAAAA
Statistics
Matches: 96, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
123 9 0.09
124 13 0.14
125 26 0.27
126 48 0.50
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.41
Consensus pattern (125 bp):
TAAAAAAAGATTATTTAAGGTGTTTTCAAATAAAAAAACTCCTTAAATAATCCTTAACTTTTTAA
AGAGAATTATTAAAAGAATATTTTGATAAAAAAAACCTTAAATAATCCTCTCATATTTTT
Found at i:12123820 original size:26 final size:24
Alignment explanation
Indices: 12123763--12123823 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 24
12123753 TAATTTCTTA
12123763 TTTAATATTTTAAATATAAATATT
1 TTTAATATTTTAAATATAAATATT
* *
12123787 TTAAAATATTATTAGATATAAATATAT
1 TT-TAATATT-TTAAATATAAATAT-T
12123814 TTTAATATTT
1 TTTAATATTT
12123824 AATAATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 2 0.06
25 7 0.23
26 19 0.61
27 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTAATATTTTAAATATAAATATT
Found at i:12124012 original size:25 final size:23
Alignment explanation
Indices: 12123994--12124084 Score: 71
Period size: 26 Copynumber: 3.8 Consensus size: 23
12123984 TATTTTCGAT
12123994 ATAA-ATAAATATTAATATTTTA
1 ATAATATAAATATTAATATTTTA
*
12124016 ATAATATAAATATTTTTTATATTTTA
1 ATAATATAAATA---TTAATATTTTA
*
12124042 TAGTAACAATAAATATTAATATTTT-
1 -A-TAA-TATAAATATTAATATTTTA
*
12124067 -TAATATTATATATTAATA
1 ATAATA-TAAATATTAATA
12124085 GAAATAATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
21 1 0.02
22 18 0.32
23 7 0.12
26 19 0.34
27 1 0.02
28 3 0.05
29 7 0.12
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (23 bp):
ATAATATAAATATTAATATTTTA
Found at i:12124063 original size:26 final size:23
Alignment explanation
Indices: 12123982--12124071 Score: 72
Period size: 26 Copynumber: 3.5 Consensus size: 23
12123972 TTTAATAATA
*
12123982 AATATTTTCGATATAAATAAATATT
1 AATATTTT-AATA-AAATAAATATT
*
12124007 AATATTTTAATAATATAAATATTTTT
1 AATATTTTAATAAAATAAATA---TT
*
12124033 TATATTTTATAGTAACAATAAATATT
1 AATATTTTA-A-TAA-AATAAATATT
12124059 AATATTTTTAATA
1 AATA-TTTTAATA
12124072 TTATATATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
23 8 0.15
24 3 0.06
25 10 0.19
26 16 0.30
27 6 0.11
28 3 0.06
29 7 0.13
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
AATATTTTAATAAAATAAATATT
Found at i:12124208 original size:25 final size:25
Alignment explanation
Indices: 12124177--12124309 Score: 69
Period size: 25 Copynumber: 5.2 Consensus size: 25
12124167 TTAAGTATTT
12124177 AATATTATATAATATTTTAATAATA
1 AATATTATATAATATTTTAATAATA
* * *
12124202 AATATTATTACTAAAATATTACTAATTTA
1 AATATTA-TA-TAATATTTTAATAA--TA
* * *
12124231 AA-A-TCT-TAATACTTTCAATAATT
1 AATATTATATAATA-TTTTAATAATA
* *
12124254 AATATT-TTTAAATATTATAATAATA
1 AATATTATAT-AATATTTTAATAATA
* * *
12124279 AATA-AATTTCAATATTTTGATAATA
1 AATATTATAT-AATATTTTAATAATA
12124304 AATATT
1 AATATT
12124310 TTAGTGTTTT
Statistics
Matches: 80, Mismatches: 17, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
23 3 0.04
24 6 0.08
25 47 0.59
26 7 0.09
27 12 0.15
28 1 0.01
29 4 0.05
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.46
Consensus pattern (25 bp):
AATATTATATAATATTTTAATAATA
Found at i:12125115 original size:20 final size:20
Alignment explanation
Indices: 12125087--12125131 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
12125077 AATTATAATA
* *
12125087 AAATATTTAATATGATACTT
1 AAATTTTTAATATAATACTT
*
12125107 AAATTTTTAATATAATATTT
1 AAATTTTTAATATAATACTT
12125127 AAATT
1 AAATT
12125132 ATAAATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
AAATTTTTAATATAATACTT
Found at i:12125294 original size:28 final size:28
Alignment explanation
Indices: 12125235--12125293 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
12125225 AATTAATAAA
* * **
12125235 TTTATAATTTAAGTGTCATATTAAAATT
1 TTTAAAATTTAAATGTCATACCAAAATT
12125263 TTTAAAATTTAAATGTCATACCAAATATT
1 TTTAAAATTTAAATGTCATACCAAA-ATT
12125292 TT
1 TT
12125294 ATTAGAATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 21 0.81
29 5 0.19
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (28 bp):
TTTAAAATTTAAATGTCATACCAAAATT
Found at i:12141712 original size:22 final size:22
Alignment explanation
Indices: 12141670--12141713 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12141660 ATTTTTTGTT
*
12141670 CTTAATTCTAGGAATATAAATA
1 CTTAATTCTAGGAATACAAATA
12141692 CTTAATTCTA-GATATACAAATA
1 CTTAATTCTAGGA-ATACAAATA
12141714 TAAATACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (22 bp):
CTTAATTCTAGGAATACAAATA
Found at i:12145474 original size:25 final size:25
Alignment explanation
Indices: 12145435--12145522 Score: 90
Period size: 25 Copynumber: 3.5 Consensus size: 25
12145425 TATAATGGCT
* * *
12145435 ATGAAGGCCTTAACAGGGTTTGACA
1 ATGAAGGTCTAAACAGGGTTCGACA
*
12145460 ATGAAGGTCTAAACAGGGTTCGGCA
1 ATGAAGGTCTAAACAGGGTTCGACA
* *
12145485 ATGAAGGTCTAAATAGAAG-TC-AGCA
1 ATGAAGGTCTAAACAG-GGTTCGA-CA
12145510 ATGAAGGTCTAAA
1 ATGAAGGTCTAAA
12145523 TAGAAGTCAG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
25 53 0.98
26 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.22
Consensus pattern (25 bp):
ATGAAGGTCTAAACAGGGTTCGACA
Found at i:12145523 original size:25 final size:25
Alignment explanation
Indices: 12145458--12145546 Score: 128
Period size: 25 Copynumber: 3.6 Consensus size: 25
12145448 CAGGGTTTGA
* * *
12145458 CAATGAAGGTCTAAACAG-GGTTCGG
1 CAATGAAGGTCTAAATAGAAG-TCAG
12145483 CAATGAAGGTCTAAATAGAAGTCAG
1 CAATGAAGGTCTAAATAGAAGTCAG
12145508 CAATGAAGGTCTAAATAGAAGTCAG
1 CAATGAAGGTCTAAATAGAAGTCAG
12145533 CAATGAAGG-CTAAA
1 CAATGAAGGTCTAAA
12145547 AGTTTTGTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
24 5 0.08
25 54 0.90
26 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.26, T:0.19
Consensus pattern (25 bp):
CAATGAAGGTCTAAATAGAAGTCAG
Found at i:12150206 original size:7 final size:7
Alignment explanation
Indices: 12150190--12150229 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
12150180 AATAATATTA
*
12150190 TAAAAAT
1 TAAAATT
12150197 TAAAATT
1 TAAAATT
12150204 TAAAATT
1 TAAAATT
12150211 TAAAATT
1 TAAAATT
12150218 TAAAATT
1 TAAAATT
12150225 TAAAA
1 TAAAA
12150230 ATTGATGAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
TAAAATT
Found at i:12150220 original size:21 final size:21
Alignment explanation
Indices: 12150174--12150229 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
12150164 TTAAAAATCT
*
12150174 AATTAAAA--TAATATTATAAA
1 AATTAAAATTTAAAATT-TAAA
12150194 AATTAAAATTTAAAATTTAAA
1 AATTAAAATTTAAAATTTAAA
*
12150215 ATTTAAAATTTAAAA
1 AATTAAAATTTAAAA
12150230 ATTGATGAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 8 0.25
21 18 0.56
22 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTAAAATTTAAAATTTAAA
Found at i:12150935 original size:15 final size:15
Alignment explanation
Indices: 12150915--12150944 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12150905 ATAAAAAAGG
12150915 TATAAAAAATATAAA
1 TATAAAAAATATAAA
*
12150930 TATAAAAACTATAAA
1 TATAAAAAATATAAA
12150945 AACAAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
TATAAAAAATATAAA
Found at i:12155951 original size:19 final size:20
Alignment explanation
Indices: 12155927--12155968 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
12155917 TTATTACACA
12155927 TATATGAAATAAT-AAATTT
1 TATATGAAATAATAAAATTT
*
12155946 TATATGTAATAATAAAATTT
1 TATATGAAATAATAAAATTT
12155966 TAT
1 TAT
12155969 TATAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TATATGAAATAATAAAATTT
Found at i:12155974 original size:19 final size:18
Alignment explanation
Indices: 12155934--12155989 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
12155924 ACATATATGA
*
12155934 AATAATAAATTTTATATGT
1 AATAATAAATTTTAT-TAT
12155953 AATAATAAAATTTTATTAT
1 AATAAT-AAATTTTATTAT
*
12155972 AAT-ATAAATTTTTTTAT
1 AATAATAAATTTTATTAT
12155989 A
1 A
12155990 TTTTTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 12 0.35
18 2 0.06
19 11 0.32
20 9 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AATAATAAATTTTATTAT
Found at i:12163971 original size:24 final size:24
Alignment explanation
Indices: 12163944--12163995 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
12163934 TTAAGTCATC
*
12163944 TTTACTTT-AGTTAAGAGTTCATTT
1 TTTACTTTAAGTT-AGAGATCATTT
*
12163968 TTTAGTTTCAAGTTAGAGATCATTT
1 TTTACTTT-AAGTTAGAGATCATTT
12163993 TTT
1 TTT
12163996 TATATTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 13 0.54
26 4 0.17
ACGTcount: A:0.25, C:0.08, G:0.13, T:0.54
Consensus pattern (24 bp):
TTTACTTTAAGTTAGAGATCATTT
Found at i:12164003 original size:27 final size:26
Alignment explanation
Indices: 12163952--12164004 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
12163942 TCTTTACTTT
* *
12163952 AGTTAAGAGTTCATTTTTTAGTTTCA
1 AGTTAAGAGATCATTTTTTAATTTCA
12163978 AGTT-AGAGATCATTTTTTTATATTTCA
1 AGTTAAGAGATCA-TTTTTTA-ATTTCA
12164005 TGTTTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 7 0.30
26 11 0.48
27 5 0.22
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.51
Consensus pattern (26 bp):
AGTTAAGAGATCATTTTTTAATTTCA
Found at i:12166947 original size:23 final size:24
Alignment explanation
Indices: 12166913--12166963 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
12166903 TGTCCCTTAT
* * *
12166913 TTAATATAAATATGGATAATATAA
1 TTAATATAAATAAGAATAAAATAA
12166937 TTAAT-TAAATAAGAATAAAATAA
1 TTAATATAAATAAGAATAAAATAA
12166960 TTAA
1 TTAA
12166964 ATATTTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (24 bp):
TTAATATAAATAAGAATAAAATAA
Found at i:12167038 original size:17 final size:18
Alignment explanation
Indices: 12167013--12167046 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
12167003 TAATATTGTC
12167013 TTTTATTTAATAACAAAA
1 TTTTATTTAATAACAAAA
12167031 TTTT-TTTAATAACAAA
1 TTTTATTTAATAACAAA
12167047 TATTATGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTTATTTAATAACAAAA
Found at i:12167043 original size:68 final size:69
Alignment explanation
Indices: 12166967--12167098 Score: 185
Period size: 69 Copynumber: 1.9 Consensus size: 69
12166957 TAATTAAATA
* * * * ** *
12166967 TTTAATAACAAATATTCTGAT-AGATAAAGAAATAATTAATATTGTCTTTTATTTAATAACAAAA
1 TTTAATAACAAATATTATGATAAAATAAAGAAATAATTAACAATGTCACTTATTTAAAAACAAAA
12167031 TTTT
66 TTTT
*
12167035 TTTAATAACAAATATTATGATAAAATTAAGAAATAATTAACAATGTCACTTATTTAAAAACAAA
1 TTTAATAACAAATATTATGATAAAATAAAGAAATAATTAACAATGTCACTTATTTAAAAACAAA
12167099 TAAGCATAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
68 20 0.36
69 35 0.64
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (69 bp):
TTTAATAACAAATATTATGATAAAATAAAGAAATAATTAACAATGTCACTTATTTAAAAACAAAA
TTTT
Found at i:12168314 original size:21 final size:21
Alignment explanation
Indices: 12168290--12168335 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
12168280 CTCAATGCTC
* *
12168290 TTCATGAACAAATGCAATCTT
1 TTCAGGAACAAAGGCAATCTT
* *
12168311 TTCAGGGACAGAGGCAATCTT
1 TTCAGGAACAAAGGCAATCTT
12168332 TTCA
1 TTCA
12168336 AGAGCAATGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (21 bp):
TTCAGGAACAAAGGCAATCTT
Found at i:12168422 original size:12 final size:12
Alignment explanation
Indices: 12168405--12168434 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
12168395 AGCGGATGAG
12168405 CCTTGAAGATAA
1 CCTTGAAGATAA
12168417 CCTTGAAGATAA
1 CCTTGAAGATAA
*
12168429 GCTTGA
1 CCTTGA
12168435 GGCTAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (12 bp):
CCTTGAAGATAA
Found at i:12171006 original size:2 final size:2
Alignment explanation
Indices: 12170999--12171026 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12170989 ATGGATTTTA
12170999 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
12171027 GTAGAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12171733 original size:21 final size:21
Alignment explanation
Indices: 12171707--12171750 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
12171697 ACTAACCATA
12171707 AAGCCTTAAAACACTTGTTAG
1 AAGCCTTAAAACACTTGTTAG
12171728 AAGCCTTAAAACACTTGTTAG
1 AAGCCTTAAAACACTTGTTAG
12171749 AA
1 AA
12171751 CAAAAGCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (21 bp):
AAGCCTTAAAACACTTGTTAG
Found at i:12182402 original size:27 final size:28
Alignment explanation
Indices: 12182371--12182427 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
12182361 ATATTGATTT
12182371 ATGATTTACGAAATG-TTTGACATAATG
1 ATGATTTACGAAATGTTTTGACATAATG
** *
12182398 ATGATTTTGGAAATGTTTTGACATTATG
1 ATGATTTACGAAATGTTTTGACATAATG
12182426 AT
1 AT
12182428 TTTATTAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.42
Consensus pattern (28 bp):
ATGATTTACGAAATGTTTTGACATAATG
Found at i:12187351 original size:16 final size:16
Alignment explanation
Indices: 12187326--12187358 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12187316 CAATAAATGA
12187326 ATGATAATGATGATTT
1 ATGATAATGATGATTT
*
12187342 ATGATGATGATGATTT
1 ATGATAATGATGATTT
12187358 A
1 A
12187359 CAATGATTTT
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:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (16 bp):
ATGATAATGATGATTT
Found at i:12187364 original size:16 final size:16
Alignment explanation
Indices: 12187332--12187365 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12187322 ATGAATGATA
**
12187332 ATGATGATTTATGATG
1 ATGATGATTTACAATG
12187348 ATGATGATTTACAATG
1 ATGATGATTTACAATG
12187364 AT
1 AT
12187366 TTTTAATGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.41
Consensus pattern (16 bp):
ATGATGATTTACAATG
Found at i:12187494 original size:27 final size:28
Alignment explanation
Indices: 12187462--12187518 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
12187452 ATATTAATTT
12187462 ATGATTTACGAAAT-GTTTGACATAATG
1 ATGATTTACGAAATAGTTTGACATAATG
** * *
12187489 ATGATTTTGGAAATATTTTGACATTATG
1 ATGATTTACGAAATAGTTTGACATAATG
12187517 AT
1 AT
12187519 TTGACGAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (28 bp):
ATGATTTACGAAATAGTTTGACATAATG
Found at i:12189109 original size:19 final size:19
Alignment explanation
Indices: 12189056--12189112 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
12189046 CTTGAAAAGC
*
12189056 TTAAATTAAACTTGCAAAAAT
1 TTAAATTAAA-TTG-AAAAAA
* *
12189077 TTAAAGTAACTTGAAAAAA
1 TTAAATTAAATTGAAAAAA
*
12189096 TTGAATTAAATTGAAAA
1 TTAAATTAAATTGAAAA
12189113 CTTAAGGAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 19 0.63
20 3 0.10
21 8 0.27
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.32
Consensus pattern (19 bp):
TTAAATTAAATTGAAAAAA
Found at i:12191252 original size:45 final size:45
Alignment explanation
Indices: 12191188--12191278 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
12191178 TCCACAGGAC
*
12191188 CAAGATCACACCAGACCATCGTGTAACACTTAGTGACTCCCACGA
1 CAAGATCACACCAGACCATCATGTAACACTTAGTGACTCCCACGA
12191233 CAAGATCACACCAGACCATCATGTAACACTTAGTGACTCCCACGA
1 CAAGATCACACCAGACCATCATGTAACACTTAGTGACTCCCACGA
12191278 C
1 C
12191279 TGCGGACTGG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.18
Consensus pattern (45 bp):
CAAGATCACACCAGACCATCATGTAACACTTAGTGACTCCCACGA
Found at i:12193932 original size:23 final size:21
Alignment explanation
Indices: 12193888--12193936 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
12193878 TCAAGCCAGG
* * *
12193888 ATTTTTTATTGAAGATAGTTAA
1 ATTTTTTATTGAAAAAAATT-A
12193910 ATTTTTTATTTGAAAAAAATTA
1 ATTTTTTA-TTGAAAAAAATTA
12193932 ATTTT
1 ATTTT
12193937 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (21 bp):
ATTTTTTATTGAAAAAAATTA
Found at i:12194248 original size:62 final size:63
Alignment explanation
Indices: 12194171--12194334 Score: 217
Period size: 63 Copynumber: 2.6 Consensus size: 63
12194161 ATAAATTGAT
*
12194171 TTATT-CAAAGTA-TTTTTATTTTAAAATATCTTAAATAATATTTA-AAAATTTTTATGAAAAAA
1 TTATTACAAA-TATTTTTTA-TTAAAAATATCTTAAATAATATTTATAAAATTTTTATGAAAAAA
* * **
12194233 TTATTACAAATATTTTTTGTTAAAAATATCTTAAATAATTTTTATTTAATTTTTATGAAAAAA
1 TTATTACAAATATTTTTTATTAAAAATATCTTAAATAATATTTATAAAATTTTTATGAAAAAA
* * *
12194296 TTATTAAAAATATTTTTTATCAAAAATATTTTAAATAAT
1 TTATTACAAATATTTTTTATTAAAAATATCTTAAATAAT
12194335 CTCGACCAAT
Statistics
Matches: 90, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
62 30 0.33
63 60 0.67
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (63 bp):
TTATTACAAATATTTTTTATTAAAAATATCTTAAATAATATTTATAAAATTTTTATGAAAAAA
Found at i:12194281 original size:26 final size:24
Alignment explanation
Indices: 12194201--12194281 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 24
12194191 TTAAAATATC
12194201 TTAAATAATATTTAAAAATTTTTAT
1 TTAAA-AATATTTAAAAATTTTTAT
**
12194226 GAAAAAAT-TATTACAAATATTTTT-T
1 TTAAAAATAT-TTA-AAA-ATTTTTAT
12194251 GTTAAAAATATCTTAAATAATTTTTAT
1 -TTAAAAATAT-TTAAA-AATTTTTAT
12194278 TTAA
1 TTAA
12194282 TTTTTATGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
23 1 0.02
24 6 0.14
25 7 0.16
26 24 0.55
27 6 0.14
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
TTAAAAATATTTAAAAATTTTTAT
Found at i:12194320 original size:16 final size:16
Alignment explanation
Indices: 12194296--12194327 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12194286 TATGAAAAAA
*
12194296 TTATTAAAAATATTTT
1 TTATCAAAAATATTTT
12194312 TTATCAAAAATATTTT
1 TTATCAAAAATATTTT
12194328 AAATAATCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATCAAAAATATTTT
Found at i:12194349 original size:63 final size:63
Alignment explanation
Indices: 12194217--12194348 Score: 176
Period size: 63 Copynumber: 2.1 Consensus size: 63
12194207 AATATTTAAA
* * * * ** **
12194217 AATTTTTATGAAAAAATTATTACAAATATTTTTTGTTAAAAATATCTTAAATAATTTTTATTT
1 AATTTTTATGAAAAAATTATTAAAAATATTTTTTATCAAAAATATCTTAAATAATCTCGATCC
*
12194280 AATTTTTATGAAAAAATTATTAAAAATATTTTTTATCAAAAATATTTTAAATAATCTCGA-CC
1 AATTTTTATGAAAAAATTATTAAAAATATTTTTTATCAAAAATATCTTAAATAATCTCGATCC
12194342 AATTTTT
1 AATTTTT
12194349 TGCAGTGGCC
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
62 7 0.12
63 53 0.88
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (63 bp):
AATTTTTATGAAAAAATTATTAAAAATATTTTTTATCAAAAATATCTTAAATAATCTCGATCC
Found at i:12194863 original size:17 final size:17
Alignment explanation
Indices: 12194831--12194865 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12194821 CTTTTGCTGA
*
12194831 TTTTAGTTTCATTTTTT
1 TTTTAGTTTCAGTTTTT
*
12194848 TTTTAGTTTTAGTTTTT
1 TTTTAGTTTCAGTTTTT
12194865 T
1 T
12194866 AATTTATACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.11, C:0.03, G:0.09, T:0.77
Consensus pattern (17 bp):
TTTTAGTTTCAGTTTTT
Found at i:12195581 original size:18 final size:18
Alignment explanation
Indices: 12195558--12195596 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12195548 TTTCAAAAAC
* *
12195558 AAATCTTAAATTTTTTAA
1 AAATCTCAAATATTTTAA
12195576 AAATCTCAAATATTTTAA
1 AAATCTCAAATATTTTAA
12195594 AAA
1 AAA
12195597 ACTAGAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATCTCAAATATTTTAA
Found at i:12195735 original size:17 final size:16
Alignment explanation
Indices: 12195713--12195793 Score: 72
Period size: 17 Copynumber: 4.8 Consensus size: 16
12195703 AAAGTTTTTG
12195713 AAATTTTCAAAAAATAA
1 AAATTTT-AAAAAATAA
12195730 AAATTTTAATAAAATAA
1 AAATTTTAA-AAAATAA
* * *
12195747 AATTTTCTTAAAATTCACA
1 AAATTT-TAAAAAAT-A-A
*
12195766 AAAATTTAAAAAATAA
1 AAATTTTAAAAAATAA
*
12195782 AAATATTAAAAA
1 AAATTTTAAAAA
12195794 TCTAAATTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
16 13 0.25
17 24 0.47
18 9 0.18
19 5 0.10
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTTTAAAAAATAA
Found at i:12196060 original size:22 final size:22
Alignment explanation
Indices: 12196012--12196070 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 22
12196002 ATAATTTTTT
* * **
12196012 AAAATTTTAAGAATTTTTCTAA
1 AAAATTTTTAGATTTTTTAAAA
*
12196034 TAAATTTTTAGATTTTTTAAAA
1 AAAATTTTTAGATTTTTTAAAA
12196056 AAAA--TTTAGATTTTT
1 AAAATTTTTAGATTTTT
12196071 ATTTTCAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 11 0.35
22 20 0.65
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (22 bp):
AAAATTTTTAGATTTTTTAAAA
Found at i:12196227 original size:19 final size:18
Alignment explanation
Indices: 12196185--12196245 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
12196175 TTAAAAAATG
*
12196185 TAAAATTTTTATAATTTCT
1 TAAAATTTTCATAATTT-T
* *
12196204 AAAAATATTTCATATTTTT
1 TAAAAT-TTTCATAATTTT
*
12196223 TAAAATTTTTATAATTTT
1 TAAAATTTTCATAATTTT
12196241 TAAAA
1 TAAAA
12196246 ACCTTTTTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
18 15 0.43
19 11 0.31
20 9 0.26
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TAAAATTTTCATAATTTT
Found at i:12196246 original size:19 final size:19
Alignment explanation
Indices: 12196186--12196246 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
12196176 TAAAAAATGT
*
12196186 AAAATTTTTATAATTTCTA
1 AAAATTTTTATAATTTTTA
* *
12196205 AAAATATTTCAT-ATTTTTT
1 AAAAT-TTTTATAATTTTTA
12196224 AAAATTTTTATAATTTTTA
1 AAAATTTTTATAATTTTTA
12196243 AAAA
1 AAAA
12196247 CCTTTTTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 5 0.14
19 25 0.71
20 5 0.14
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (19 bp):
AAAATTTTTATAATTTTTA
Found at i:12197309 original size:21 final size:23
Alignment explanation
Indices: 12197270--12197316 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
12197260 TTTTTGAACA
*
12197270 TTTAAAACTCTTTTTTTTAT-AT
1 TTTAAAACTCATTTTTTTATAAT
12197292 TTTAAAACT-ATTTTTTTATAAT
1 TTTAAAACTCATTTTTTTATAAT
12197314 TTT
1 TTT
12197317 TTTTACATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTAAAACTCATTTTTTTATAAT
Found at i:12203045 original size:30 final size:32
Alignment explanation
Indices: 12202992--12203052 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
12202982 AAAATATAAA
*
12202992 ATATAATTTTTTTATTTTATTAAACC-TATTT
1 ATATAATTTTTTTATATTATTAAACCGTATTT
12203023 ATATATATTTTTTTA-ATT-TTAAACCGTATT
1 ATATA-ATTTTTTTATATTATTAAACCGTATT
12203053 ATCTTCATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 7 0.26
31 11 0.41
32 9 0.33
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.59
Consensus pattern (32 bp):
ATATAATTTTTTTATATTATTAAACCGTATTT
Found at i:12203457 original size:14 final size:14
Alignment explanation
Indices: 12203434--12203473 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
12203424 TAAACAATTT
*
12203434 TTAATAATAAGTAA
1 TTAATTATAAGTAA
12203448 TTAATTATAATGTAA
1 TTAATTATAA-GTAA
12203463 -TAATTATAAGT
1 TTAATTATAAGT
12203474 GATATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 2 0.08
14 18 0.75
15 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (14 bp):
TTAATTATAAGTAA
Found at i:12204821 original size:2 final size:2
Alignment explanation
Indices: 12204720--12204802 Score: 82
Period size: 2 Copynumber: 42.5 Consensus size: 2
12204710 AATTATTGAC
* * *
12204720 AT AT AT AT AT AT AT AT AT -T AA AG AT AT AT AT AT -T AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * *
12204761 AT AT AT AA AT AT AT AT AT AT AT AT AT A- AA AT CT 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
12204802 A
1 A
12204803 AAATGCTGAA
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
1 3 0.04
2 63 0.94
3 1 0.01
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:12206030 original size:35 final size:35
Alignment explanation
Indices: 12205984--12206055 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
12205974 AAAGGCGCCT
12205984 CACAAGGCGGAGGTGATGTGAACCCTTTTATACCC
1 CACAAGGCGGAGGTGATGTGAACCCTTTTATACCC
*
12206019 CACAAGGCGGAGGTGATGTGAACCCTTTTATATCC
1 CACAAGGCGGAGGTGATGTGAACCCTTTTATACCC
12206054 CA
1 CA
12206056 GGGACCCTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (35 bp):
CACAAGGCGGAGGTGATGTGAACCCTTTTATACCC
Found at i:12217096 original size:20 final size:20
Alignment explanation
Indices: 12217071--12217109 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12217061 ATGATAAAAT
12217071 TCAAAGTAAA-ATCAGATTTA
1 TCAAAG-AAATATCAGATTTA
*
12217091 TCAAAGAAATATTAGATTT
1 TCAAAGAAATATCAGATTT
12217110 CTGTAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (20 bp):
TCAAAGAAATATCAGATTTA
Found at i:12219420 original size:31 final size:31
Alignment explanation
Indices: 12219385--12219453 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
12219375 TTCAATTGGT
* *
12219385 GTAAATTTACTATTATGCTTTTAATTTTGAA
1 GTAAATTTACTATTATACCTTTAATTTTGAA
*
12219416 GTAAATTTATTATTATACCTTTAATTTTGAA
1 GTAAATTTACTATTATACCTTTAATTTTGAA
12219447 G-AAATTT
1 GTAAATTT
12219454 TGGTTAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 6 0.17
31 29 0.83
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.51
Consensus pattern (31 bp):
GTAAATTTACTATTATACCTTTAATTTTGAA
Found at i:12220591 original size:3 final size:3
Alignment explanation
Indices: 12220577--12220606 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
12220567 TTAAGTATAT
*
12220577 TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12220607 ATATTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:12220618 original size:16 final size:16
Alignment explanation
Indices: 12220584--12220646 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
12220574 TATTAATACT
12220584 AATA-ATAATAA-TAA
1 AATATATAATAATTAA
*
12220598 TAATA-ATAAATATTTAA
1 -AATATAT-AATAATTAA
12220615 AATATATAATAATTAA
1 AATATATAATAATTAA
* *
12220631 AAAAT-TAAAAATTAA
1 AATATATAATAATTAA
12220646 A
1 A
12220647 TTAAATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 16 0.39
16 20 0.49
17 5 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATATATAATAATTAA
Found at i:12220649 original size:12 final size:12
Alignment explanation
Indices: 12220632--12220665 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12220622 AATAATTAAA
12220632 AAATTAAAAATT
1 AAATTAAAAATT
**
12220644 AAATTAAATTTT
1 AAATTAAAAATT
12220656 AAATTAAAAA
1 AAATTAAAAA
12220666 AAAAAAGAAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAATTAAAAATT
Found at i:12220787 original size:23 final size:23
Alignment explanation
Indices: 12220721--12220777 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
12220711 TGCCGCTGCC
*
12220721 GCCCCCTGTCAGTCT-CTAGACCA
1 GCCCCCTGTCAGCCTCCT-GACCA
12220744 GCCCCCTGTCAGCCTCCTGACCA
1 GCCCCCTGTCAGCCTCCTGACCA
12220767 GCCCCCTGTCA
1 GCCCCCTGTCA
12220778 CCCCTTTGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 30 0.94
24 2 0.06
ACGTcount: A:0.14, C:0.49, G:0.18, T:0.19
Consensus pattern (23 bp):
GCCCCCTGTCAGCCTCCTGACCA
Found at i:12221572 original size:16 final size:16
Alignment explanation
Indices: 12221538--12221572 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12221528 CCCGCTTCAG
*
12221538 CCAACCTTGAATCGAT
1 CCAACCTTGAACCGAT
*
12221554 CCAACCTTGAACCGGT
1 CCAACCTTGAACCGAT
12221570 CCA
1 CCA
12221573 GAAGAACCGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.37, G:0.14, T:0.20
Consensus pattern (16 bp):
CCAACCTTGAACCGAT
Found at i:12222219 original size:33 final size:32
Alignment explanation
Indices: 12222184--12222319 Score: 92
Period size: 32 Copynumber: 4.3 Consensus size: 32
12222174 AAACCCTCTA
*
12222184 AAAATCCAAAATCCCTTAAATCCAAAAC-CCAT
1 AAAATCCAAAATCCCTCAAATCCAAAACTCC-T
* *
12222216 AAAATCCGAAA-CTCCTCAAATCCAAAACTCCCC
1 AAAATCCAAAATC-CCTCAAATCCAAAACT-CCT
* *
12222249 AAAATCCAAAAT-CCACAAA-CCTTTAAACT-CT
1 AAAATCCAAAATCCCTCAAATCC--AAAACTCCT
*
12222280 TAAATCC-AAA-CCC-CAAAATCCAAAA-TCTCT
1 AAAATCCAAAATCCCTC-AAATCCAAAACTC-CT
12222310 AAAATCCAAA
1 AAAATCCAAA
12222320 CCCTTAAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
28 1 0.01
29 4 0.05
30 16 0.20
31 14 0.17
32 30 0.37
33 15 0.18
34 2 0.02
ACGTcount: A:0.49, C:0.32, G:0.01, T:0.18
Consensus pattern (32 bp):
AAAATCCAAAATCCCTCAAATCCAAAACTCCT
Found at i:12222315 original size:16 final size:15
Alignment explanation
Indices: 12222184--12222377 Score: 83
Period size: 16 Copynumber: 12.2 Consensus size: 15
12222174 AAACCCTCTA
12222184 AAAATCCAAAATCCCT
1 AAAATCCAAAA-CCCT
*
12222200 TAAATCCAAAACCCAT
1 AAAATCCAAAACCC-T
*
12222216 AAAATCCGAAACTCCT
1 AAAATCCAAAAC-CCT
* *
12222232 CAAATCCAAAACTCCCC
1 AAAATCCAAAA--CCCT
*
12222249 AAAATCCAAAATCC-
1 AAAATCCAAAACCCT
* *
12222263 ACAAA-CCTTTAAACTCT
1 A-AAATCC--AAAACCCT
* *
12222280 TAAATCC-AAACCCC
1 AAAATCCAAAACCCT
*
12222294 AAAATCCAAAATCTCT
1 AAAATCCAAAA-CCCT
12222310 AAAATCC-AAACCCTTAAATT
1 AAAATCCAAAACCC------T
* *
12222330 AAAACCCCAAACCCT
1 AAAATCCAAAACCCT
* *
12222345 AAAATCTCCAAACTCT
1 AAAATC-CAAAACCCT
12222361 AAAAT-CAAAACCCT
1 AAAATCCAAAACCCT
12222375 AAA
1 AAA
12222378 CCTTTCATAT
Statistics
Matches: 136, Mismatches: 23, Indels: 40
0.68 0.12 0.20
Matches are distributed among these distances:
14 26 0.19
15 20 0.15
16 60 0.44
17 16 0.12
18 1 0.01
20 7 0.05
21 6 0.04
ACGTcount: A:0.48, C:0.32, G:0.01, T:0.19
Consensus pattern (15 bp):
AAAATCCAAAACCCT
Found at i:12227673 original size:16 final size:16
Alignment explanation
Indices: 12227654--12227702 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
12227644 AAGATGCGGC
12227654 ATAAAAAAAAAACAAA
1 ATAAAAAAAAAACAAA
* *
12227670 ATAAAACAAAAATAAA
1 ATAAAAAAAAAACAAA
*
12227686 AAAAAAGAAAAAACAAA
1 ATAAAA-AAAAAACAAA
12227703 CAAAATGGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 19 0.70
17 8 0.30
ACGTcount: A:0.86, C:0.06, G:0.02, T:0.06
Consensus pattern (16 bp):
ATAAAAAAAAAACAAA
Found at i:12227675 original size:11 final size:11
Alignment explanation
Indices: 12227656--12227707 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
12227646 GATGCGGCAT
12227656 AAAAAAAAAAC
1 AAAAAAAAAAC
*
12227667 -AAAATAAAAC
1 AAAAAAAAAAC
12227677 AAAAATAAAAA-
1 AAAAA-AAAAAC
12227688 AAAAGAAAAAAC
1 AAAA-AAAAAAC
12227700 AAACAAAA
1 AAA-AAAA
12227708 TGGACATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
10 9 0.26
11 13 0.38
12 11 0.32
13 1 0.03
ACGTcount: A:0.87, C:0.08, G:0.02, T:0.04
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:12227684 original size:27 final size:27
Alignment explanation
Indices: 12227657--12227707 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
12227647 ATGCGGCATA
* *
12227657 AAAAAAAAACAAAATA-AAACAAAAAT
1 AAAAAAAAAGAAAAAACAAACAAAAAT
12227683 AAAAAAAAAGAAAAAACAAACAAAA
1 AAAAAAAAAGAAAAAACAAACAAAA
12227708 TGGACATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.86, C:0.08, G:0.02, T:0.04
Consensus pattern (27 bp):
AAAAAAAAAGAAAAAACAAACAAAAAT
Found at i:12227697 original size:10 final size:10
Alignment explanation
Indices: 12227656--12227698 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
12227646 GATGCGGCAT
12227656 AAAAAA-AAA
1 AAAAAATAAA
*
12227665 ACAAAATAAA
1 AAAAAATAAA
12227675 ACAAAAATAAA
1 A-AAAAATAAA
*
12227686 AAAAAAGAAA
1 AAAAAATAAA
12227696 AAA
1 AAA
12227699 CAAACAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 5 0.17
10 15 0.52
11 9 0.31
ACGTcount: A:0.88, C:0.05, G:0.02, T:0.05
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:12227707 original size:10 final size:9
Alignment explanation
Indices: 12227658--12227707 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
12227648 TGCGGCATAA
12227658 AAAAAAAAC
1 AAAAAAAAC
12227667 AAAATAAAAC
1 AAAA-AAAAC
12227677 AAAAATAAA-
1 AAAAA-AAAC
12227686 AAAAAAGAA-
1 AAAAAA-AAC
*
12227695 AAAACAAAC
1 AAAAAAAAC
12227704 AAAA
1 AAAA
12227708 TGGACATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
8 3 0.08
9 21 0.58
10 12 0.33
ACGTcount: A:0.86, C:0.08, G:0.02, T:0.04
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:12229966 original size:21 final size:23
Alignment explanation
Indices: 12229911--12229966 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 23
12229901 TATCCTAGTC
12229911 AATTCTATAAGACCTCCGGACAT
1 AATTCTATAAGACCTCCGGACAT
* *
12229934 GATT-TTTAAGACCTCC-GA-AT
1 AATTCTATAAGACCTCCGGACAT
*
12229954 AATTCTGTAAGAC
1 AATTCTATAAGAC
12229967 TTTCGAGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 5 0.18
21 9 0.32
22 11 0.39
23 3 0.11
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (23 bp):
AATTCTATAAGACCTCCGGACAT
Found at i:12230165 original size:23 final size:23
Alignment explanation
Indices: 12230133--12230176 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
12230123 TGAATAATTT
* *
12230133 TGTAAGACCTCTAGGCATGATTC
1 TGTAAAACCTCCAGGCATGATTC
12230156 TGTAAAACCTCCAGGCATGAT
1 TGTAAAACCTCCAGGCATGAT
12230177 GTCTAAGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (23 bp):
TGTAAAACCTCCAGGCATGATTC
Found at i:12230271 original size:175 final size:175
Alignment explanation
Indices: 12229802--12230398 Score: 737
Period size: 175 Copynumber: 3.5 Consensus size: 175
12229792 TAAGACATTC
* * * * *
12229802 AGGCATTATTCTGTAAGACCTCTGGGCATGATGTCTAAGACCTCTGGGT-TCAA-TTTG--T---
1 AGGCATGATTTTGTAAGACCTCCGGGCATGATGTCTAAGACCTCCGAGTAT-AATTTTGATTCGC
* * * *
12229860 GATGTTGTCTCTATCGATTCTTTATTTTTGACTTGCGATGTTATCCTAGTCAATTCTATAAGACC
65 GATATTATCTCGATCGATTCTTTATTTTTGACTTGCGGTGTTATCCTAGTCAATTCTATAAGACC
* * *
12229925 TCCGGACATGATTTTTAAGACCTCCGAATAATTCTGTAAGA-CTTT
130 TCCGGACATGATTTCTAAGACCTCTGAATAATTCTGTAAGACCTCT
* * * * * * *
12229970 CGAGTATGATTTTGTAAGACCTTCGGGTAT-ATGTCTAAGACCTCCGGGTATAATTTCGATTGGC
1 AG-GCATGATTTTGTAAGACCTCCGGGCATGATGTCTAAGACCTCCGAGTATAATTTTGATTCGC
*
12230034 GATATTGTCTCGATCGATTCTTTATTTTTGACTTGCGGTGTTATCCTAGTCAATTCTATAAGACC
65 GATATTATCTCGATCGATTCTTTATTTTTGACTTGCGGTGTTATCCTAGTCAATTCTATAAGACC
* * *
12230099 TTCGGGCATGATTTCTAAGACCTCTGAATAATTTTGTAAGACCTCT
130 TCCGGACATGATTTCTAAGACCTCTGAATAATTCTGTAAGACCTCT
* * * * *
12230145 AGGCATGATTCTGTAAAACCTCCAGGCATGATGTCTAAGACCTCCGTGCATAATTTTGATTCGCG
1 AGGCATGATTTTGTAAGACCTCCGGGCATGATGTCTAAGACCTCCGAGTATAATTTTGATTCGCG
* * * * * *
12230210 ATATTATCCCGATCGATTCTTTATTTCTGACTTACGGTGTTATCCCAATCAATTTTATAAGACCT
66 ATATTATCTCGATCGATTCTTTATTTTTGACTTGCGGTGTTATCCTAGTCAATTCTATAAGACCT
* * * *
12230275 CCGGACATGATTTCTAAAACCT-TCAGACAATTCTGTAAGACCTCC
131 CCGGACATGATTTCTAAGACCTCTGA-ATAATTCTGTAAGACCTCT
* *
12230320 GGGCATGATTTTGTAAGACCTCCGGGCATGATGTCTAAGACCTCCGAGTATAATTTTGATTCACG
1 AGGCATGATTTTGTAAGACCTCCGGGCATGATGTCTAAGACCTCCGAGTATAATTTTGATTCGCG
12230385 ATATTATCTCGATC
66 ATATTATCTCGATC
12230399 ATTTCATTCT
Statistics
Matches: 367, Mismatches: 51, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
168 21 0.06
169 25 0.07
171 1 0.00
174 121 0.33
175 199 0.54
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (175 bp):
AGGCATGATTTTGTAAGACCTCCGGGCATGATGTCTAAGACCTCCGAGTATAATTTTGATTCGCG
ATATTATCTCGATCGATTCTTTATTTTTGACTTGCGGTGTTATCCTAGTCAATTCTATAAGACCT
CCGGACATGATTTCTAAGACCTCTGAATAATTCTGTAAGACCTCT
Found at i:12230334 original size:23 final size:23
Alignment explanation
Indices: 12230261--12230365 Score: 92
Period size: 22 Copynumber: 4.7 Consensus size: 23
12230251 ATCCCAATCA
*
12230261 ATTTTATAAGACCTCCGGACATG
1 ATTTTCTAAGACCTCCGGACATG
* * *
12230284 A-TTTCTAAAACCTTCAGACA--
1 ATTTTCTAAGACCTCCGGACATG
* * *
12230304 ATTCTGTAAGACCTCCGGGCATG
1 ATTTTCTAAGACCTCCGGACATG
* *
12230327 ATTTTGTAAGACCTCCGGGCATG
1 ATTTTCTAAGACCTCCGGACATG
*
12230350 A-TGTCTAAGACCTCCG
1 ATTTTCTAAGACCTCCG
12230366 AGTATAATTT
Statistics
Matches: 66, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.02
21 13 0.20
22 28 0.42
23 24 0.36
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (23 bp):
ATTTTCTAAGACCTCCGGACATG
Found at i:12230512 original size:73 final size:73
Alignment explanation
Indices: 12230417--12231243 Score: 802
Period size: 73 Copynumber: 11.5 Consensus size: 73
12230407 CTTTGGCTTA
* * *
12230417 CGGTTCAGTCCCAATCATCTTTAATCTTTGACTCGTAGTTTAATCTCGATCATTTCATTAATTCT
1 CGGTTCAGTCTCAGTCATCTTTAATCTTTGACTCGTAGTTTAATCCCGATCATTTCATTAATTCT
12230482 TCGACTTG
66 TCGACTTG
* * * *
12230490 CGATTCAGTCTCAGTCATCTTTAATCTCTGACTCGTGGTTTAATCTCGATCA-TT--TT-ATTC-
1 CGGTTCAGTCTCAGTCATCTTTAATCTTTGACTCGTAGTTTAATCCCGATCATTTCATTAATTCT
* *
12230550 TCTGACCTA
66 TC-GACTTG
* *
12230559 CGGTTCAGTCTCAATCATTTTTAATCTTTGACTCGT-GTTTAATCCCGATCATTTC----ATTCT
1 CGGTTCAGTCTCAGTCATCTTTAATCTTTGACTCGTAGTTTAATCCCGATCATTTCATTAATTCT
* *
12230619 TTGGCTTG
66 TCGACTTG
* * * * *
12230627 TGGTTCAGTTTCAGTCATCTTTAATCCTTGACTCGT-GATTTAATCCCGATCATTTTATTAATTT
1 CGGTTCAGTCTCAGTCATCTTTAATCTTTGACTCGTAG-TTTAATCCCGATCATTTCATTAATTC
*
12230691 TTTGACTTG
65 TTCGACTTG
* * * * * *
12230700 CAGTTCAGTCCCAGTCATCTTTAATCTCTGATTCAT-GATTTAATCCCGATCATTTCATT--CTC
1 CGGTTCAGTCTCAGTCATCTTTAATCTTTGACTCGTAG-TTTAATCCCGATCATTTCATTAATTC
* *
12230762 -T-AACTTA
65 TTCGACTTG
* *
12230769 CGGTTCAGTCCCAATCATCTTTAATCTTTGACT--TATGATTTAATCCCGATCATTTCATTAATT
1 CGGTTCAGTCTCAGTCATCTTTAATCTTTGACTCGTA-G-TTTAATCCCGATCATTTCATTAATT
* **
12230832 TTTTAACTTG
64 CTTCGACTTG
* * * * * *
12230842 TGATTTAGTCCCAGTCATCTTTAATCTTTGGCTCGT-GATTTAATCTCGATCATTTCATTAATTC
1 CGGTTCAGTCTCAGTCATCTTTAATCTTTGACTCGTAG-TTTAATCCCGATCATTTCATTAATTC
12230906 TTCGACTTG
65 TTCGACTTG
* * * * *
12230915 CGGTTAAGTCTCAGTCATCTTTAATATTTGGCTCGCAGTTTAATCCTGATCATTTCATTAATTCT
1 CGGTTCAGTCTCAGTCATCTTTAATCTTTGACTCGTAGTTTAATCCCGATCATTTCATTAATTCT
*
12230980 TCGACTTA
66 TCGACTTG
* *
12230988 CGGTTCAGTTTCAGTCATCTTTAATCTTTGACT--TACGATTTAATCCCAATCATTTCATTAATT
1 CGGTTCAGTCTCAGTCATCTTTAATCTTTGACTCGTA-G-TTTAATCCCGATCATTTCATTAATT
* *
12231051 TTCTCGACTTA
64 CT-TCGACTTG
* *
12231062 CAGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTAGTTTAATCCCGATCATTTCATTAATT-T
1 CGGTTCAGTCTCAGTCATCTTTAATCTTTGACTCGTAGTTTAATCCCGATCATTTCATTAATTCT
*
12231126 TCTTACTTG
66 TC-GACTTG
** * * ** *
12231135 CAATTCAGT-TCCAATTATCTTTAATCTTTGACTCGCGGTTTAATCTCGATCATTTCATTAATTC
1 CGGTTCAGTCT-CAGTCATCTTTAATCTTTGACTCGTAGTTTAATCCCGATCATTTCATTAATT-
* * *
12231199 CCTCGATTTA
64 CTTCGACTTG
* *
12231209 TGGTTCAGTC-CTAGTCATCTTTAATCCTTGACTCG
1 CGGTTCAGTCTC-AGTCATCTTTAATCTTTGACTCG
12231244 CAGTGTCGTC
Statistics
Matches: 632, Mismatches: 93, Indels: 57
0.81 0.12 0.07
Matches are distributed among these distances:
67 1 0.00
68 55 0.09
69 116 0.18
70 3 0.00
71 3 0.00
72 6 0.01
73 350 0.55
74 92 0.15
75 4 0.01
76 2 0.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (73 bp):
CGGTTCAGTCTCAGTCATCTTTAATCTTTGACTCGTAGTTTAATCCCGATCATTTCATTAATTCT
TCGACTTG
Found at i:12230576 original size:34 final size:33
Alignment explanation
Indices: 12230493--12230593 Score: 96
Period size: 34 Copynumber: 2.9 Consensus size: 33
12230483 CGACTTGCGA
*
12230493 TTCAGTCTCAGTCATCTTTAATCTCTGACTCGTGG
1 TTCAGTCTCAATCAT-TTTAATCTCTGACTCG-GG
* * * *
12230528 TTTAATCTCGATCATTTTATTCTCTGACCTAC-GG
1 TTCAGTCTCAATCATTTTAATCTCTGA-CT-CGGG
*
12230562 TTCAGTCTCAATCATTTTTAATCTTTGACTCG
1 TTCAGTCTCAATCA-TTTTAATCTCTGACTCG
12230594 TGTTTAATCC
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
33 1 0.02
34 26 0.50
35 24 0.46
36 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.44
Consensus pattern (33 bp):
TTCAGTCTCAATCATTTTAATCTCTGACTCGGG
Found at i:12230762 original size:210 final size:210
Alignment explanation
Indices: 12230394--12231193 Score: 865
Period size: 210 Copynumber: 3.7 Consensus size: 210
12230384 GATATTATCT
* *
12230394 CGATCATTTCATTCTTTGGCTTACGGTTCAGTCCCAATCATCTTTAATCTTTGACTCGTAGTTTA
1 CGATCATTTCATTCTTTGACTTACGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTAGTTTA
* *
12230459 ATCTCGATCATTTCATTAATTCTTCGACTTGC-GATTCAGTCTCAGTCATCTTTAATCTCTGACT
66 ATCCCGATCATTTCATTAATTCTTCGACTTGCAG-TTCAGTCCCAGTCATCTTTAATCTCTGACT
* * * * *
12230523 CGTGGTTTAATCTCGATCATTTTATTCTCTGACCTACGGTTCAGTCTCAATCATTTTTAATCTTT
130 CGTGATTTAATCCCGATCATTTCATTCTCTGACTTACGGTTCAGTCTCAATCATCTTTAATCTTT
12230588 GACTCGTGTTTAATCC
195 GACTCGTGTTTAATCC
* ** ** *
12230604 CGATCATTTCATTCTTTGGCTTGTGGTTCAGTTTCAGTCATCTTTAATCCTTGACTCGT-GATTT
1 CGATCATTTCATTCTTTGACTTACGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTAG-TTT
* * * *
12230668 AATCCCGATCATTTTATTAATTTTTTGACTTGCAGTTCAGTCCCAGTCATCTTTAATCTCTGATT
65 AATCCCGATCATTTCATTAATTCTTCGACTTGCAGTTCAGTCCCAGTCATCTTTAATCTCTGACT
* * *
12230733 CATGATTTAATCCCGATCATTTCATTCTCTAACTTACGGTTCAGTCCCAATCATCTTTAATCTTT
130 CGTGATTTAATCCCGATCATTTCATTCTCTGACTTACGGTTCAGTCTCAATCATCTTTAATCTTT
**
12230798 GACTTATGATTTAATCC
195 GACTCGTG-TTTAATCC
* * ** * * *
12230815 CGATCATTTCATTAATTTTTTAACTTGTGATTTAGTCCCAGTCATCTTTAATCTTTGGCTCGT-G
1 CGATCATTTC----ATTCTTTGACTTACGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTAG
* * * * * *
12230879 ATTTAATCTCGATCATTTCATTAATTCTTCGACTTGCGGTTAAGTCTCAGTCATCTTTAATATTT
62 -TTTAATCCCGATCATTTCATTAATTCTTCGACTTGCAGTTCAGTCCCAGTCATCTTTAATCTCT
* * * * * *
12230944 GGCTCG-CAGTTTAATCCTGATCATTTCATTAATTCTTCGACTTACGGTTCAGTTTCAGTCATCT
126 GACTCGTGA-TTTAATCCCGATCATTTCATT--CTC-T-GACTTACGGTTCAGTCTCAATCATCT
*
12231008 TTAATCTTTGACTTACG-ATTTAATCC
186 TTAATCTTTGAC-T-CGTGTTTAATCC
* * *
12231034 CAATCATTTCATTAATTTTCTCGACTTACAGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTA
1 CGATCATTTCA-T--TCTT-T-GACTTACGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTA
* * * * * *
12231099 GTTTAATCCCGATCATTTCATTAATT-TTCTTACTTGCAATTCAGTTCCAATTATCTTTAATCTT
61 GTTTAATCCCGATCATTTCATTAATTCTTC-GACTTGCAGTTCAGTCCCAGTCATCTTTAATCTC
* * *
12231163 TGACTCGCGGTTTAATCTCGATCATTTCATT
125 TGACTCGTGATTTAATCCCGATCATTTCATT
12231194 AATTCCCTCG
Statistics
Matches: 492, Mismatches: 76, Indels: 34
0.82 0.13 0.06
Matches are distributed among these distances:
209 1 0.00
210 176 0.36
211 19 0.04
214 1 0.00
215 121 0.25
216 1 0.00
217 2 0.00
218 5 0.01
219 55 0.11
220 110 0.22
221 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (210 bp):
CGATCATTTCATTCTTTGACTTACGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTAGTTTA
ATCCCGATCATTTCATTAATTCTTCGACTTGCAGTTCAGTCCCAGTCATCTTTAATCTCTGACTC
GTGATTTAATCCCGATCATTTCATTCTCTGACTTACGGTTCAGTCTCAATCATCTTTAATCTTTG
ACTCGTGTTTAATCC
Found at i:12230846 original size:38 final size:38
Alignment explanation
Indices: 12230789--12230907 Score: 113
Period size: 38 Copynumber: 3.2 Consensus size: 38
12230779 CCAATCATCT
* *
12230789 TTAA-TCTTTGACTTATGATTTAATCCCGATCATTTCA
1 TTAATTCTTTAACTTGTGATTTAATCCCGATCATTTCA
* * *
12230826 TTAATTTTTTAACTTGTGATTTAGTCCC-AGTCA--TCT
1 TTAATTCTTTAACTTGTGATTTAATCCCGA-TCATTTCA
** * *
12230862 TTAA-TCTTTGGCTCGTGATTTAATCTCGATCATTTCA
1 TTAATTCTTTAACTTGTGATTTAATCCCGATCATTTCA
12230899 TTAATTCTT
1 TTAATTCTT
12230908 CGACTTGCGG
Statistics
Matches: 64, Mismatches: 12, Indels: 11
0.74 0.14 0.13
Matches are distributed among these distances:
35 20 0.31
36 7 0.11
37 11 0.17
38 26 0.41
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.49
Consensus pattern (38 bp):
TTAATTCTTTAACTTGTGATTTAATCCCGATCATTTCA
Found at i:12231060 original size:39 final size:39
Alignment explanation
Indices: 12230951--12231133 Score: 111
Period size: 35 Copynumber: 4.9 Consensus size: 39
12230941 TTTGGCTCGC
**
12230951 AGTTTAATCCTGATCATTTCATTAATTCTTC-GACTTACG
1 AGTTTAATCCCAATCATTTCATTAATT-TTCTGACTTACG
* * ** * * *
12230990 -GTTCAGTTTCAGTCA--TCTTTAATCTT-TGACTTACG
1 AGTTTAATCCCAATCATTTCATTAATTTTCTGACTTACG
12231025 A-TTTAATCCCAATCATTTCATTAATTTTCTCGACTTAC-
1 AGTTTAATCCCAATCATTTCATTAATTTTCT-GACTTACG
* * * * *
12231063 AGTTCAGTCCCAGTCA--TCTTTAATCTT-TGAC-T-CG
1 AGTTTAATCCCAATCATTTCATTAATTTTCTGACTTACG
* *
12231097 TAGTTTAATCCCGATCATTTCATTAATTTTCTTACTT
1 -AGTTTAATCCCAATCATTTCATTAATTTTCTGACTT
12231134 GCAATTCAGT
Statistics
Matches: 103, Mismatches: 28, Indels: 26
0.66 0.18 0.17
Matches are distributed among these distances:
33 1 0.01
34 1 0.01
35 34 0.33
36 8 0.08
37 27 0.26
38 13 0.13
39 19 0.18
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (39 bp):
AGTTTAATCCCAATCATTTCATTAATTTTCTGACTTACG
Found at i:12231260 original size:147 final size:146
Alignment explanation
Indices: 12230417--12231243 Score: 825
Period size: 142 Copynumber: 5.7 Consensus size: 146
12230407 CTTTGGCTTA
*
12230417 CGGTTCAGTCCCAATCATCTTTAATCTTTGACTCGT-AGTTTAATCTCGATCATTTCATTAATTC
1 CGGTTCAGTCCCAATCATCTTTAATCTTTGACTCGTGA-TTTAATCCCGATCATTTCATTAATTC
* * * * *
12230481 TTCGACTTGCGATTCAGTCTCAGTCATCTTTAAT-CTCTGACTCGTGGTTTAATCTCGATCA-TT
65 CTCGACTTACGGTTCAGTCTCAGTCATCTTTAATCCT-TGACTCGTAGTTTAATCCCGATCATTT
* * * *
12230544 --TT-ATTCTCTGACCTA
129 CATTAATTTTCTTACTTG
* * *
12230559 CGGTTCAGTCTCAATCATTTTTAATCTTTGACTCGTG-TTTAATCCCGATCATTTCATT-CTT--
1 CGGTTCAGTCCCAATCATCTTTAATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTCC
* ** * *
12230620 T-GGCTTGTGGTTCAGTTTCAGTCATCTTTAATCCTTGACTCGT-GATTTAATCCCGATCATTTT
66 TCGACTTACGGTTCAGTCTCAGTCATCTTTAATCCTTGACTCGTAG-TTTAATCCCGATCATTTC
12230683 ATTAATTTT-TTGACTTG
130 ATTAATTTTCTT-ACTTG
* * * * * *
12230700 CAGTTCAGTCCCAGTCATCTTTAATCTCTGATTCATGATTTAATCCCGATCATTTCATT--CT-C
1 CGGTTCAGTCCCAATCATCTTTAATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTCC
* * * *
12230762 T-AACTTACGGTTCAGTCCCAATCATCTTTAATCTTTGACT--TATGATTTAATCCCGATCATTT
66 TCGACTTACGGTTCAGTCTCAGTCATCTTTAATCCTTGACTCGTA-G-TTTAATCCCGATCATTT
12230824 CATTAATTTT-TTAACTTG
129 CATTAATTTTCTT-ACTTG
* * * * * * *
12230842 TGATTTAGTCCCAGTCATCTTTAATCTTTGGCTCGTGATTTAATCTCGATCATTTCATTAATTCT
1 CGGTTCAGTCCCAATCATCTTTAATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTCC
* * ** * * *
12230907 TCGACTTGCGGTTAAGTCTCAGTCATCTTTAATATTTGGCTCGCAGTTTAATCCTGATCATTTCA
66 TCGACTTACGGTTCAGTCTCAGTCATCTTTAATCCTTGACTCGTAGTTTAATCCCGATCATTTCA
* *
12230972 TTAATTCTTC-GACTTA
131 TTAATT-TTCTTACTTG
** * *** * *
12230988 CGGTTCAGTTTCAGTCATCTTTAATCTTTGACTTACGATTTAATCCCAATCATTTCATTAATTTT
1 CGGTTCAGTCCCAATCATCTTTAATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAA-TTC
* * *
12231053 CTCGACTTACAGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTAGTTTAATCCCGATCATTTC
65 CTCGACTTACGGTTCAGTCTCAGTCATCTTTAATCCTTGACTCGTAGTTTAATCCCGATCATTTC
12231118 ATTAATTTTCTTACTTG
130 ATTAATTTTCTTACTTG
** * * * * *
12231135 CAATTCAGTTCCAATTATCTTTAATCTTTGACTCGCGGTTTAATCTCGATCATTTCATTAATTCC
1 CGGTTCAGTCCCAATCATCTTTAATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATT-C
* *
12231200 CTCGATTTATGGTTCAGTC-CTAGTCATCTTTAATCCTTGACTCG
65 CTCGACTTACGGTTCAGTCTC-AGTCATCTTTAATCCTTGACTCG
12231244 CAGTGTCGTC
Statistics
Matches: 570, Mismatches: 91, Indels: 43
0.81 0.13 0.06
Matches are distributed among these distances:
136 1 0.00
137 48 0.08
138 5 0.01
140 6 0.01
141 58 0.10
142 172 0.30
144 1 0.00
145 1 0.00
146 116 0.20
147 161 0.28
148 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (146 bp):
CGGTTCAGTCCCAATCATCTTTAATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTCC
TCGACTTACGGTTCAGTCTCAGTCATCTTTAATCCTTGACTCGTAGTTTAATCCCGATCATTTCA
TTAATTTTCTTACTTG
Found at i:12231506 original size:12 final size:12
Alignment explanation
Indices: 12231489--12231522 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12231479 CATTTTAAGT
*
12231489 ATATTAATACTA
1 ATATTAATAATA
12231501 ATATTAATAATA
1 ATATTAATAATA
*
12231513 ATAATAATAA
1 ATATTAATAA
12231523 ATATTTAAAA
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:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATTAATAATA
Found at i:12231534 original size:16 final size:16
Alignment explanation
Indices: 12231500--12231563 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
12231490 TATTAATACT
12231500 AATAT-TAATAA-TAA
1 AATATATAATAATTAA
*
12231514 TAATA-ATAAATATTTAA
1 -AATATAT-AATAATTAA
12231531 AATATATAATAATTAA
1 AATATATAATAATTAA
*
12231547 AAAAT-TAA-AATTAA
1 AATATATAATAATTAA
12231561 AAT
1 AAT
12231564 TAAAATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
14 8 0.20
15 8 0.20
16 20 0.49
17 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATATATAATAATTAA
Found at i:12231558 original size:6 final size:6
Alignment explanation
Indices: 12231547--12231587 Score: 73
Period size: 6 Copynumber: 6.7 Consensus size: 6
12231537 TAATAATTAA
12231547 AAAATT AAAATT AAAATT AAAATT AAAATT AAAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT -AAAATT AAAA
12231588 AAAAGAAGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 28 0.82
7 6 0.18
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:12233086 original size:16 final size:15
Alignment explanation
Indices: 12233067--12233120 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 15
12233057 AAAATCTCTT
12233067 AAATCCAAACCCCCTA
1 AAATCCAAA-CCCCTA
*
12233083 AAATTCGAAACCCCTA
1 AAA-TCCAAACCCCTA
12233099 AAATCCAAAACCCCTCA
1 AAATCC-AAACCCCT-A
12233116 AAATC
1 AAATC
12233121 TAAAATCCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
15 2 0.06
16 20 0.61
17 11 0.33
ACGTcount: A:0.46, C:0.37, G:0.02, T:0.15
Consensus pattern (15 bp):
AAATCCAAACCCCTA
Found at i:12233103 original size:32 final size:33
Alignment explanation
Indices: 12233040--12233119 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 33
12233030 TTAAGTTTTT
* * * *
12233040 AAACCCCATAAAAATTCAAAATCTCTTAAATCC
1 AAACCCCCTAAAAATTCAAAACCCCTAAAATCC
*
12233073 AAACCCCCT-AAAATTCGAAACCCCTAAAATCC
1 AAACCCCCTAAAAATTCAAAACCCCTAAAATCC
* *
12233105 AAAACCCCTCAAAAT
1 AAACCCCCTAAAAAT
12233120 CTAAAATCCA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
32 27 0.68
33 13 0.32
ACGTcount: A:0.47, C:0.33, G:0.01, T:0.19
Consensus pattern (33 bp):
AAACCCCCTAAAAATTCAAAACCCCTAAAATCC
Found at i:12234530 original size:12 final size:12
Alignment explanation
Indices: 12234513--12234537 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12234503 AATTTATTGA
12234513 TATTTATTTTTG
1 TATTTATTTTTG
12234525 TATTTATTTTTG
1 TATTTATTTTTG
12234537 T
1 T
12234538 CAATTAATCG
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TATTTATTTTTG
Found at i:12237447 original size:158 final size:156
Alignment explanation
Indices: 12237155--12237440 Score: 382
Period size: 156 Copynumber: 1.8 Consensus size: 156
12237145 CATTAAATTC
*
12237155 TAAATTTTAAATTTAAAATGCATAATTAATTTTAAACACATGTAAAATTTTTTTTAATTATCCAC
1 TAAATTTTAAATTTAAAATGCATAATTAATTTTAAACACATGTAAAA--TCTTTTAATTATCCAC
* * * * *
12237220 ATGTAAAAAATGTAAACTATCTCCATTTGATTATTTTCTTCTTTTTTTTAGAGGCTTTAGTTTTA
64 ATGTAAAAAATATAAACTATCTACATTAGATTATTTTCTTCATTTTGTTAGAGGCTTTAGTTTTA
12237285 TATATTTACAGAATATTTATTTTACCAT
129 TATATTTACAGAATATTTATTTTACCAT
* *
12237313 TAAATTTTTAAATTT-AAATGCATAATTAATTTTAAACACATGTAAAA-CTTTTAGATTGTTCAC
1 TAAA-TTTTAAATTTAAAATGCATAATTAATTTTAAACACATGTAAAATCTTTTA-ATTATCCAC
* * * * *
12237376 ATGTCAAAAATATAGATTATCTACATTAGATTATTTTC-T-ATTTTGTTAGTGGCTTTGGCTTTT
64 ATGTAAAAAATATAAACTATCTACATTAGATTATTTTCTTCATTTTGTTAGAGGCTTTAG-TTTT
12237439 AT
128 AT
12237441 TTTATATAAT
Statistics
Matches: 112, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
154 15 0.13
155 12 0.11
156 39 0.35
158 36 0.32
159 10 0.09
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (156 bp):
TAAATTTTAAATTTAAAATGCATAATTAATTTTAAACACATGTAAAATCTTTTAATTATCCACAT
GTAAAAAATATAAACTATCTACATTAGATTATTTTCTTCATTTTGTTAGAGGCTTTAGTTTTATA
TATTTACAGAATATTTATTTTACCAT
Found at i:12239474 original size:45 final size:45
Alignment explanation
Indices: 12239423--12239511 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
12239413 ACTATTATTA
12239423 AATTAAATATTGCCATAATCATTAATAAATAAATTTAAAAATTTT
1 AATTAAATATTGCCATAATCATTAATAAATAAATTTAAAAATTTT
12239468 AATTAAATATTGCCATAATCATTAATAAATAAATTTAAAAATTT
1 AATTAAATATTGCCATAATCATTAATAAATAAATTTAAAAATTT
12239512 AAAAAATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (45 bp):
AATTAAATATTGCCATAATCATTAATAAATAAATTTAAAAATTTT
Found at i:12239492 original size:23 final size:22
Alignment explanation
Indices: 12239426--12239498 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
12239416 ATTATTAAAT
12239426 TAAATATTGCCATAATCATTAA
1 TAAATATTGCCATAATCATTAA
** * *
12239448 TAAATAAATT-TAAAAAT-TTTAA
1 TAAAT--ATTGCCATAATCATTAA
12239470 TTAAATATTGCCATAATCATTAA
1 -TAAATATTGCCATAATCATTAA
12239493 TAAATA
1 TAAATA
12239499 AATTTAAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
21 3 0.08
22 19 0.50
23 13 0.34
24 3 0.08
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (22 bp):
TAAATATTGCCATAATCATTAA
Found at i:12239518 original size:9 final size:9
Alignment explanation
Indices: 12239493--12239545 Score: 63
Period size: 9 Copynumber: 5.9 Consensus size: 9
12239483 TAATCATTAA
12239493 TAAATAAATT
1 TAAA-AAATT
12239503 T-AAAAATT
1 TAAAAAATT
12239511 TAAAAAATT
1 TAAAAAATT
*
12239520 TTAAAAATT
1 TAAAAAATT
* *
12239529 GAAAAAAAT
1 TAAAAAATT
12239538 TAAAAAAT
1 TAAAAAAT
12239546 AAGTCGAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
8 6 0.17
9 29 0.81
10 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (9 bp):
TAAAAAATT
Found at i:12242995 original size:20 final size:19
Alignment explanation
Indices: 12242958--12242996 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12242948 TATGCTCAAT
* *
12242958 TTTTTTCCTTTCATTATTC
1 TTTTTTCCTTTAACTATTC
12242977 TTTTTTCCTTTGAACTATTC
1 TTTTTTCCTTT-AACTATTC
12242997 CAATGTGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.13, C:0.21, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTTTCCTTTAACTATTC
Found at i:12249311 original size:3 final size:3
Alignment explanation
Indices: 12249303--12249332 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12249293 AAAAATTAAA
12249303 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
12249333 TTGATTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12252135 original size:19 final size:19
Alignment explanation
Indices: 12252111--12252173 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
12252101 TTTGAGTCAC
12252111 TTATTTCCTACTTCAGTTA
1 TTATTTCCTACTTCAGTTA
* *
12252130 TTATTTCC-A-TGTTA-TTC
1 TTATTTCCTACT-TCAGTTA
*
12252147 TTATTTCCTCCTTCAGTTA
1 TTATTTCCTACTTCAGTTA
12252166 TTATTTCC
1 TTATTTCC
12252174 ATGTTATTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
17 11 0.31
18 5 0.14
19 19 0.54
ACGTcount: A:0.17, C:0.22, G:0.05, T:0.56
Consensus pattern (19 bp):
TTATTTCCTACTTCAGTTA
Found at i:12252151 original size:36 final size:36
Alignment explanation
Indices: 12252110--12252181 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
12252100 ATTTGAGTCA
12252110 CTTATTTCCTACTTCAGTTATTATTTCCATGTTATT
1 CTTATTTCCTACTTCAGTTATTATTTCCATGTTATT
*
12252146 CTTATTTCCTCCTTCAGTTATTATTTCCATGTTATT
1 CTTATTTCCTACTTCAGTTATTATTTCCATGTTATT
12252182 GTAAAATGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.56
Consensus pattern (36 bp):
CTTATTTCCTACTTCAGTTATTATTTCCATGTTATT
Found at i:12256407 original size:24 final size:23
Alignment explanation
Indices: 12256380--12256428 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
12256370 TGATAACAAT
*
12256380 ATTACAAAAAAGAAAAAACTTAAA
1 ATTAC-AAAAAGAAAAAACCTAAA
* *
12256404 ATTACAACAATAAAAAACCTAAA
1 ATTACAAAAAGAAAAAACCTAAA
12256427 AT
1 AT
12256429 CGAGTCCCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.67, C:0.12, G:0.02, T:0.18
Consensus pattern (23 bp):
ATTACAAAAAGAAAAAACCTAAA
Found at i:12266039 original size:34 final size:34
Alignment explanation
Indices: 12266001--12266065 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
12265991 CTGTTAGATG
*
12266001 AAATCTTTCGTACACAATTTATGGC-TGAATCACA
1 AAATCTTTCATACACAATTTAT-GCTTGAATCACA
12266035 AAATCTTTCATACACAATTTATGCTTGAATC
1 AAATCTTTCATACACAATTTATGCTTGAATC
12266066 TGGATCTTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 2 0.07
34 27 0.93
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.35
Consensus pattern (34 bp):
AAATCTTTCATACACAATTTATGCTTGAATCACA
Found at i:12268118 original size:16 final size:17
Alignment explanation
Indices: 12268099--12268130 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12268089 TGATGTTTGA
12268099 TAATT-ATTTTAAATTT
1 TAATTAATTTTAAATTT
12268115 TAATTAATTTTAAATT
1 TAATTAATTTTAAATT
12268131 AAATTGATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATTAATTTTAAATTT
Found at i:12277292 original size:2 final size:2
Alignment explanation
Indices: 12277285--12277321 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
12277275 CCTTTAAATC
12277285 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12277322 TTACTATTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12279459 original size:144 final size:140
Alignment explanation
Indices: 12279244--12279717 Score: 348
Period size: 144 Copynumber: 3.3 Consensus size: 140
12279234 AAAACTTTAT
** * * * *
12279244 ATCATGTTTTGATATTATTTCATGATTTTTAATG-CATAAAGAACCCTAATTGCACCTTGA-AAG
1 ATCATGTTTTGATATTATTTCATGATTTTTAATGTGTTAAA-AATCATGA-T-CACCTTTATAAG
*
12279307 AGTAGAAATTATCAAAATACCTTTTATGGGTATTTTCATAATTTGACATTTTCAAGTTAATTTTT
63 AGTTGAAATTATCAAAAT-CC-TTTATGGGTATTTTCATAATTTGACATTTTCAAGTTAATTTTT
* *
12279372 TACAAAAAAATGCAAG
126 AACGAAAAAATGC-AG
12279388 ATCATGTTTTGATATTATTTCATGATTTTTAATGTGTTAAAAATCATGATCACACTTTATAAG-G
1 ATCATGTTTTGATATTATTTCATGATTTTTAATGTGTTAAAAATCATGATCAC-CTTTATAAGAG
* * * * * *
12279452 ATTGAAATTATCAAAATGC-TCATCGGAGATATTTTCGTAATTTGACCTTTTTAAGGTTGATTTT
65 -TTGAAATTATCAAAATCCTTTAT-GG-G-TATTTTCATAATTTGACATTTTCAA-GTTAATTTT
* * ** *
12279516 TCATGAAAACTTTCAG
125 TAACGAAAAAATGCAG
* * * * * * * * * * * *
12279532 ATCATATTTTAATATTATTTTATAATTTTTGATATATTAAAAATCTTGATTACCCCTTCTGAGAG
1 ATCATGTTTTGATATTATTTCATGATTTTTAATGTGTTAAAAATCATGATCA-CCTTTATAAGAG
* * * *
12279597 TTGAAATTATCAAAATGCCCTTTA-GAAGTATTTTCATAATTTGATATTTTCGAGATTAGTTTTT
65 TTGAAATTATCAAAAT--CCTTTATG-GGTATTTTCATAATTTGACATTTTCAAG-TTAATTTTT
** *
12279661 AACGAAAAGCTGTAG
126 AACGAAAAAATGCAG
* * * * *
12279676 ATCATAG-ATAGATATTATTTTATGAATTTTGATGTGTTAAAA
1 ATCAT-GTTTTGATATTATTTCATGATTTTTAATGTGTTAAAA
12279718 TCACAATAAT
Statistics
Matches: 259, Mismatches: 55, Indels: 32
0.75 0.16 0.09
Matches are distributed among these distances:
141 3 0.01
142 5 0.02
143 9 0.03
144 215 0.83
145 24 0.09
146 1 0.00
147 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (140 bp):
ATCATGTTTTGATATTATTTCATGATTTTTAATGTGTTAAAAATCATGATCACCTTTATAAGAGT
TGAAATTATCAAAATCCTTTATGGGTATTTTCATAATTTGACATTTTCAAGTTAATTTTTAACGA
AAAAATGCAG
Found at i:12281382 original size:26 final size:27
Alignment explanation
Indices: 12281344--12281395 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
12281334 TAAATCAAAG
*
12281344 TTAAACCCTAAACCAACCC-TAAACCT
1 TTAAACCCCAAACCAACCCTTAAACCT
12281370 TTAAACCCCAAACCAACCCTTAAACC
1 TTAAACCCCAAACCAACCCTTAAACC
12281396 ATAAACTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.17
Consensus pattern (27 bp):
TTAAACCCCAAACCAACCCTTAAACCT
Found at i:12281400 original size:26 final size:26
Alignment explanation
Indices: 12281345--12281401 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
12281335 AAATCAAAGT
* *
12281345 TAAACCCTAAACCAACCCTAAACCTT
1 TAAACCCCAAACCAACCCTAAACCTA
12281371 TAAACCCCAAACCAACCCTTAAACC-A
1 TAAACCCCAAACCAACCC-TAAACCTA
12281397 TAAAC
1 TAAAC
12281402 TAATCCAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 22 0.79
27 6 0.21
ACGTcount: A:0.46, C:0.39, G:0.00, T:0.16
Consensus pattern (26 bp):
TAAACCCCAAACCAACCCTAAACCTA
Found at i:12281414 original size:24 final size:24
Alignment explanation
Indices: 12281384--12281499 Score: 64
Period size: 25 Copynumber: 4.8 Consensus size: 24
12281374 ACCCCAAACC
*
12281384 AACCCTTAAACCATAAACTAATCCA
1 AACCTTTAAACC-TAAACTAATCCA
*
12281409 AACCTTTAAACCT----TAA-CTA
1 AACCTTTAAACCTAAACTAATCCA
*
12281428 AACCTTTAGATCCTAAACTAATCCTTA
1 AACCTTTA-AACCTAAACTAATCC--A
* * * *
12281455 AACC-CTAAACCAACAATTAATCTA
1 AACCTTTAAACCTA-AACTAATCCA
*
12281479 AACCTTTAAACCCTAACCTAA
1 AACCTTTAAA-CCTAAACTAA
12281500 ACCCTTAGAT
Statistics
Matches: 67, Mismatches: 13, Indels: 22
0.66 0.13 0.22
Matches are distributed among these distances:
19 10 0.15
20 7 0.10
24 9 0.13
25 24 0.36
26 12 0.18
27 5 0.07
ACGTcount: A:0.44, C:0.29, G:0.01, T:0.26
Consensus pattern (24 bp):
AACCTTTAAACCTAAACTAATCCA
Found at i:12281429 original size:63 final size:64
Alignment explanation
Indices: 12281361--12281535 Score: 174
Period size: 63 Copynumber: 2.6 Consensus size: 64
12281351 CTAAACCAAC
* * *
12281361 CCTAAACCTTTAAACCCCAAACCAACCCTTAAACCATAAAC-TAATCCAAACCTTTAAACCTTAA
1 CCTAAACCTTTAGATCCCAAACCAACCCTTAAACCA-AAACATAATCCAAACCTTTAAACCCTAA
* * * *
12281425 -CTAAACCTTTAGATCCTAAACTAATCCTTAAACCCTAAACCAACAATTAATCTAAACCTTTAAA
1 CCTAAACCTTTAGATCCCAAACCAACCCTTAAA-CC--AA--AAC-A-TAATCCAAACCTTTAAA
12281489 CCCTAA
59 CCCTAA
* *
12281495 CCTAAACCCTTAGATCTCAAACCAACCCTTAAAACCAAAAC
1 CCTAAACCTTTAGATCCCAAACCAACCCTT-AAACCAAAAC
12281536 CAACATAAAC
Statistics
Matches: 89, Mismatches: 12, Indels: 17
0.75 0.10 0.14
Matches are distributed among these distances:
63 27 0.30
64 2 0.02
65 1 0.01
66 1 0.01
67 6 0.07
69 2 0.02
70 21 0.24
71 26 0.29
72 3 0.03
ACGTcount: A:0.43, C:0.33, G:0.01, T:0.23
Consensus pattern (64 bp):
CCTAAACCTTTAGATCCCAAACCAACCCTTAAACCAAAACATAATCCAAACCTTTAAACCCTAA
Found at i:12281448 original size:20 final size:19
Alignment explanation
Indices: 12281408--12281464 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
12281398 AAACTAATCC
*
12281408 AAACCTTTAAACCTTAACT
1 AAACCTTTAAACCTAAACT
*
12281427 AAACCTTTAGATCCTAAACT
1 AAACCTTTA-AACCTAAACT
*
12281447 AATCC-TTAAACCCTAAAC
1 AAACCTTTAAA-CCTAAAC
12281465 CAACAATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.03
19 19 0.59
20 12 0.38
ACGTcount: A:0.42, C:0.28, G:0.02, T:0.28
Consensus pattern (19 bp):
AAACCTTTAAACCTAAACT
Found at i:12281464 original size:70 final size:71
Alignment explanation
Indices: 12281384--12281540 Score: 194
Period size: 71 Copynumber: 2.2 Consensus size: 71
12281374 ACCCCAAACC
* *
12281384 AACCCTTAAACCATA-AACTAATCCAAACCTTTAAACCTTAA-CTAAACCTTTAGATC-CTAAAC
1 AACCC-TAAACCA-ACAACTAATCCAAACCTTTAAACCCTAACCTAAACCCTTAGATCTC-AAAC
* *
12281446 TAATCCTTA
63 CAACCCTTA
* *
12281455 AACCCTAAACCAACAATTAATCTAAACCTTTAAACCCTAACCTAAACCCTTAGATCTCAAACCAA
1 AACCCTAAACCAACAACTAATCCAAACCTTTAAACCCTAACCTAAACCCTTAGATCTCAAACCAA
12281520 CCCTTA
66 CCCTTA
* *
12281526 AAACCAAAACCAACA
1 AACCCTAAACCAACA
12281541 TAAACCCTAA
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
69 1 0.01
70 30 0.40
71 43 0.57
72 1 0.01
ACGTcount: A:0.45, C:0.31, G:0.01, T:0.23
Consensus pattern (71 bp):
AACCCTAAACCAACAACTAATCCAAACCTTTAAACCCTAACCTAAACCCTTAGATCTCAAACCAA
CCCTTA
Found at i:12281904 original size:18 final size:18
Alignment explanation
Indices: 12281881--12281930 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
12281871 AACCCTAACC
12281881 CCAAACCCTTAAACCCAA
1 CCAAACCCTTAAACCCAA
12281899 CCAAACCCTTAAACCCAA
1 CCAAACCCTTAAACCCAA
12281917 CCAAACCC-TAAACC
1 CCAAACCCTTAAACC
12281931 TTAAACCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 6 0.19
18 26 0.81
ACGTcount: A:0.44, C:0.46, G:0.00, T:0.10
Consensus pattern (18 bp):
CCAAACCCTTAAACCCAA
Found at i:12285643 original size:125 final size:125
Alignment explanation
Indices: 12285495--12285745 Score: 484
Period size: 125 Copynumber: 2.0 Consensus size: 125
12285485 TTTTATGTTT
*
12285495 TTATATTGACATGAATTATGACACTTAATTTTTGTATAAAATATAGTATGAATACATAAATTTTA
1 TTATATTGACATGAATTATGACACTTAATTTTTGTATAAAATACAGTATGAATACATAAATTTTA
12285560 ATATTTTACACAACATAAATACATAAATCATCAAGTTTGTATACCAGTAGAATAAGCCCA
66 ATATTTTACACAACATAAATACATAAATCATCAAGTTTGTATACCAGTAGAATAAGCCCA
12285620 TTATATTGACATGAATTATGACACTTAATTTTTGTATAAAATACAGTATGAATACATAAATTTTA
1 TTATATTGACATGAATTATGACACTTAATTTTTGTATAAAATACAGTATGAATACATAAATTTTA
*
12285685 ATATTTTACACAACATAAATACATAAATCATCAAGTTTGTATACCAGTCGAATAAGCCCA
66 ATATTTTACACAACATAAATACATAAATCATCAAGTTTGTATACCAGTAGAATAAGCCCA
12285745 T
1 T
12285746 AACTAGTCTT
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 124 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.36
Consensus pattern (125 bp):
TTATATTGACATGAATTATGACACTTAATTTTTGTATAAAATACAGTATGAATACATAAATTTTA
ATATTTTACACAACATAAATACATAAATCATCAAGTTTGTATACCAGTAGAATAAGCCCA
Found at i:12286294 original size:20 final size:20
Alignment explanation
Indices: 12286266--12286304 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12286256 AAGTTAAAAA
*
12286266 AAAATGAAAGTCTGAAAATG
1 AAAAGGAAAGTCTGAAAATG
*
12286286 AAAAGGAAAGTTTGAAAAT
1 AAAAGGAAAGTCTGAAAAT
12286305 CTTGGATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (20 bp):
AAAAGGAAAGTCTGAAAATG
Found at i:12287285 original size:26 final size:26
Alignment explanation
Indices: 12287234--12287287 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
12287224 TTTGGTTTAG
* * *
12287234 GCCCATATTTGAGTTGGTTAGTCCAA
1 GCCCAGATTTGAGTTGATCAGTCCAA
12287260 GCCCAGATTTGAGTTGATCA-TGCCAA
1 GCCCAGATTTGAGTTGATCAGT-CCAA
12287286 GC
1 GC
12287288 TTTCATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (26 bp):
GCCCAGATTTGAGTTGATCAGTCCAA
Found at i:12287456 original size:20 final size:20
Alignment explanation
Indices: 12287428--12287472 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
12287418 TTTACATGTA
12287428 TTTTTAAAT-TC-ATAATTTT
1 TTTTTAAATATCTA-AATTTT
12287447 TTTTTGAAATATCTAAATTTT
1 TTTTT-AAATATCTAAATTTT
12287468 TTTTT
1 TTTTT
12287473 TATAAAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.22
20 4 0.17
21 13 0.57
22 1 0.04
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTTAAATATCTAAATTTT
Found at i:12287482 original size:22 final size:21
Alignment explanation
Indices: 12287441--12287482 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12287431 TTAAATTCAT
*
12287441 AATTTTTTTTTGAAATATCTA
1 AATTTTTTTTTGAAAAATCTA
*
12287462 AATTTTTTTTTTATAAAATCT
1 AATTTTTTTTTGA-AAAATCT
12287483 TACAAAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (21 bp):
AATTTTTTTTTGAAAAATCTA
Found at i:12288894 original size:34 final size:34
Alignment explanation
Indices: 12288825--12288900 Score: 102
Period size: 34 Copynumber: 2.2 Consensus size: 34
12288815 ATTATCGGAC
* *
12288825 ATGCATATCTAGTAATGTATAATGAATTTCGGAT
1 ATGCATATCTAGTAATGAATAATGAATTTCAGAT
12288859 ATGCATATCTAGTAATGCAAT-ATG-ATTTCTAGAT
1 ATGCATATCTAGTAATG-AATAATGAATTTC-AGAT
12288893 ATGCATAT
1 ATGCATAT
12288901 TTGATAACAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
33 5 0.13
34 31 0.82
35 2 0.05
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (34 bp):
ATGCATATCTAGTAATGAATAATGAATTTCAGAT
Found at i:12289178 original size:20 final size:20
Alignment explanation
Indices: 12289155--12289198 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
12289145 GATTTAATAA
*
12289155 TTGTTTCAAAAATTTATGGT
1 TTGTTTCAAAAATTTAGGGT
*
12289175 TTGTTTCAAAGATTTAGGGT
1 TTGTTTCAAAAATTTAGGGT
12289195 TTGT
1 TTGT
12289199 AATATTAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (20 bp):
TTGTTTCAAAAATTTAGGGT
Found at i:12291446 original size:121 final size:121
Alignment explanation
Indices: 12291309--12291552 Score: 452
Period size: 121 Copynumber: 2.0 Consensus size: 121
12291299 AATTCTAAAA
* *
12291309 AATTGACAAGCATTTACTCATCAGTAATCATTACTCCAATTCAATTCATAATCCAATCTCTAAAT
1 AATTGACAAGCATTTACACATCAGTAATCACTACTCCAATTCAATTCATAATCCAATCTCTAAAT
*
12291374 TTGATATATATTAGTTTTCTTTTTCATTCAATCTTGTGAGATATCTATCTCCCAAC
66 TTGATATATATTAGTTTTCTCTTTCATTCAATCTTGTGAGATATCTATCTCCCAAC
12291430 AATTGACAAGCATTTACACATCAGTAATCACTACTCCAATTCAATTCATAATCCAATCTCTAAAT
1 AATTGACAAGCATTTACACATCAGTAATCACTACTCCAATTCAATTCATAATCCAATCTCTAAAT
*
12291495 TTGATATATATTAGTTTTCTCTTTCATTCAATCTTGTGAGATATCTATCTCCTAAC
66 TTGATATATATTAGTTTTCTCTTTCATTCAATCTTGTGAGATATCTATCTCCCAAC
12291551 AA
1 AA
12291553 AAAAAAAATT
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 119 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (121 bp):
AATTGACAAGCATTTACACATCAGTAATCACTACTCCAATTCAATTCATAATCCAATCTCTAAAT
TTGATATATATTAGTTTTCTCTTTCATTCAATCTTGTGAGATATCTATCTCCCAAC
Found at i:12294997 original size:19 final size:19
Alignment explanation
Indices: 12294955--12294997 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
12294945 GACTAATAAA
*
12294955 AAAAAGGCAGACAATCAAG
1 AAAAAGGCAAACAATCAAG
*
12294974 GAAAAGGCAAACAATCAAG
1 AAAAAGGCAAACAATCAAG
12294993 AAAAA
1 AAAAA
12294998 TGTTATCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.63, C:0.14, G:0.19, T:0.05
Consensus pattern (19 bp):
AAAAAGGCAAACAATCAAG
Found at i:12296144 original size:30 final size:28
Alignment explanation
Indices: 12296110--12296190 Score: 108
Period size: 28 Copynumber: 2.8 Consensus size: 28
12296100 TAACTATTTG
12296110 CAAATCTTTAAAATAAAAAAAAAGTTGTAA
1 CAAATCTTTAAAAT-AAAAAAAA-TTGTAA
* *
12296140 CAAATCTTAAAAATAAAACAAATTGTAA
1 CAAATCTTTAAAATAAAAAAAATTGTAA
* *
12296168 CAAATCTTTAAAATCATAAAAAT
1 CAAATCTTTAAAATAAAAAAAAT
12296191 GTGAACTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 25 0.56
29 7 0.16
30 13 0.29
ACGTcount: A:0.59, C:0.10, G:0.04, T:0.27
Consensus pattern (28 bp):
CAAATCTTTAAAATAAAAAAAATTGTAA
Found at i:12296166 original size:28 final size:30
Alignment explanation
Indices: 12296110--12296181 Score: 112
Period size: 28 Copynumber: 2.5 Consensus size: 30
12296100 TAACTATTTG
12296110 CAAATCTTTAAAATAAAAAAAAAGTTGTAA
1 CAAATCTTTAAAATAAAAAAAAAGTTGTAA
* *
12296140 CAAATCTTAAAAAT-AAAACAAA-TTGTAA
1 CAAATCTTTAAAATAAAAAAAAAGTTGTAA
12296168 CAAATCTTTAAAAT
1 CAAATCTTTAAAAT
12296182 CATAAAAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
28 19 0.49
29 7 0.18
30 13 0.33
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.28
Consensus pattern (30 bp):
CAAATCTTTAAAATAAAAAAAAAGTTGTAA
Found at i:12296545 original size:13 final size:13
Alignment explanation
Indices: 12296511--12296549 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
12296501 CTCTGGTAAT
12296511 TAAAAAATTAAAAA
1 TAAAAAA-TAAAAA
*
12296525 -AAATAATAAAAA
1 TAAAAAATAAAAA
12296537 TAAAAAATAAAAA
1 TAAAAAATAAAAA
12296550 AAAGTGTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:12296552 original size:9 final size:9
Alignment explanation
Indices: 12296512--12296552 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
12296502 TCTGGTAATT
*
12296512 AAAAAATTA
1 AAAAAAATA
12296521 AAAAAAATA
1 AAAAAAATA
*
12296530 ATAAAAAT-
1 AAAAAAATA
12296538 -AAAAAATA
1 AAAAAAATA
12296546 AAAAAAA
1 AAAAAAA
12296553 GTGTTTGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
7 6 0.22
9 21 0.78
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAAAATA
Found at i:12296552 original size:16 final size:16
Alignment explanation
Indices: 12296522--12296552 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12296512 AAAAAATTAA
*
12296522 AAAAAATAATAAAAAT
1 AAAAAATAAAAAAAAT
12296538 AAAAAATAAAAAAAA
1 AAAAAATAAAAAAAA
12296553 GTGTTTGAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAAATAAAAAAAAT
Found at i:12297386 original size:21 final size:21
Alignment explanation
Indices: 12297337--12297409 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
12297327 AGCCGTTTCG
*
12297337 ATTTTTTTTTGTTTATTTTCTTT
1 ATTTTTTTTTG-GTATTTT-TTT
**
12297360 GGTTTTTTTTGGTATTTTTTT
1 ATTTTTTTTTGGTATTTTTTT
* *
12297381 ATTTTTTATTT-GTGTTTGTTT
1 ATTTTTT-TTTGGTATTTTTTT
12297402 ATTTTTTT
1 ATTTTTTT
12297410 AAAAGTATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
20 1 0.02
21 23 0.55
22 9 0.21
23 9 0.21
ACGTcount: A:0.08, C:0.01, G:0.11, T:0.79
Consensus pattern (21 bp):
ATTTTTTTTTGGTATTTTTTT
Found at i:12297535 original size:16 final size:16
Alignment explanation
Indices: 12297514--12297545 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12297504 AAGTATCAAT
*
12297514 TTTTTTTAAAAATAAA
1 TTTTTTAAAAAATAAA
12297530 TTTTTTAAAAAATAAA
1 TTTTTTAAAAAATAAA
12297546 AAAAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTTTTAAAAAATAAA
Found at i:12297572 original size:64 final size:67
Alignment explanation
Indices: 12297477--12297608 Score: 198
Period size: 64 Copynumber: 2.0 Consensus size: 67
12297467 AATTTTCAAG
* * *
12297477 AAAAAAATATTTTTAAGAAAAAGTTAAAAGTATCAATTTTTTTTAAAAAT-AAATTTTTTAAAAA
1 AAAAAAATATTTTTAAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAAATTTCTAAAAA
12297541 AT
66 AT
* *
12297543 AAAAAAA-ATTTTT-AGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTCTAAAAA
1 AAAAAAATATTTTTAAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAAATTTCTAAAAA
12297606 AT
66 AT
12297608 A
1 A
12297609 TTTTGAGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
64 32 0.53
65 21 0.35
66 7 0.12
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (67 bp):
AAAAAAATATTTTTAAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAAATTTCTAAAAA
AT
Done.