Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 175 of 207
Found at i:53993088 original size:21 final size:21
Alignment explanation
Indices: 53993064--53993105 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53993054 CTTTTTGTTC
*
53993064 AATTAATTATCGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
**
53993085 AATTTCTTAACGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
53993106 TACTAACTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AATTAATTAACGAAACTTTAA
Found at i:53995004 original size:6 final size:6
Alignment explanation
Indices: 53994995--53995022 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
53994985 TTTATTTAAA
53994995 TTTTAG TTTTAG TTTTAG TTTTAG TTTT
1 TTTTAG TTTTAG TTTTAG TTTTAG TTTT
53995023 GATTTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (6 bp):
TTTTAG
Found at i:53995004 original size:18 final size:18
Alignment explanation
Indices: 53994983--53995034 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
53994973 TTTTTCTATA
53994983 TTTTTATTTAAATTTTAG
1 TTTTTATTTAAATTTTAG
* *
53995001 -TTTTAGTTTTAGTTTTAG
1 TTTTTA-TTTAAATTTTAG
*
53995019 TTTTGATTTCAAATTT
1 TTTTTATTT-AAATTT
53995035 GATTTTTTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
17 5 0.19
18 13 0.50
19 8 0.31
ACGTcount: A:0.23, C:0.02, G:0.10, T:0.65
Consensus pattern (18 bp):
TTTTTATTTAAATTTTAG
Found at i:53996227 original size:9 final size:9
Alignment explanation
Indices: 53996213--53996347 Score: 51
Period size: 9 Copynumber: 14.4 Consensus size: 9
53996203 TTTTGTTGCA
53996213 TTTTATTAT
1 TTTTATTAT
*
53996222 TTTTATGAT
1 TTTTATTAT
*
53996231 TTTTATAATTT
1 TTTTAT--TAT
*
53996242 TTTTATAAT
1 TTTTATTAT
**
53996251 TTTTACGA-
1 TTTTATTAT
*
53996259 TTTTATAAT
1 TTTTATTAT
* *
53996268 TTTTAATAAA
1 TTTT-ATTAT
*
53996278 TTTTAGATAT
1 TTTTA-TTAT
*
53996288 TTTTATTAAAA
1 TTTTATT--AT
* *
53996299 TTTAATCAT
1 TTTTATTAT
* *
53996308 TTTTATAAC
1 TTTTATTAT
53996317 TTTTATTGAT
1 TTTTATT-AT
53996327 TTTTATT-T
1 TTTTATTAT
53996335 TTTATATT-T
1 TTT-TATTAT
53996344 TTTT
1 TTTT
53996348 GCCACATCTC
Statistics
Matches: 94, Mismatches: 23, Indels: 19
0.69 0.17 0.14
Matches are distributed among these distances:
8 11 0.12
9 48 0.51
10 22 0.23
11 13 0.14
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTATTAT
Found at i:53996246 original size:11 final size:11
Alignment explanation
Indices: 53996230--53996254 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53996220 ATTTTTATGA
53996230 TTTTTATAATT
1 TTTTTATAATT
53996241 TTTTTATAATT
1 TTTTTATAATT
53996252 TTT
1 TTT
53996255 ACGATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:53996246 original size:29 final size:28
Alignment explanation
Indices: 53996213--53996271 Score: 91
Period size: 29 Copynumber: 2.1 Consensus size: 28
53996203 TTTTGTTGCA
* *
53996213 TTTTATTATTTTTATGATTTTTATAATTT
1 TTTTATAATTTTTACGA-TTTTATAATTT
53996242 TTTTATAATTTTTACGATTTTATAATTT
1 TTTTATAATTTTTACGATTTTATAATTT
53996270 TT
1 TT
53996272 AATAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.69
Consensus pattern (28 bp):
TTTTATAATTTTTACGATTTTATAATTT
Found at i:53996261 original size:20 final size:20
Alignment explanation
Indices: 53996221--53996262 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
53996211 CATTTTATTA
* *
53996221 TTTTTATGATTTTTATAATT
1 TTTTTATAATTTTTACAATT
*
53996241 TTTTTATAATTTTTACGATT
1 TTTTTATAATTTTTACAATT
53996261 TT
1 TT
53996263 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTTTATAATTTTTACAATT
Found at i:53996280 original size:19 final size:19
Alignment explanation
Indices: 53996258--53996322 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 19
53996248 AATTTTTACG
53996258 ATTTTATAATTTTTAATAA
1 ATTTTATAATTTTTAATAA
* *
53996277 ATTTTAGATATTTTTATTAAA
1 ATTTTATA-ATTTTTAAT-AA
* *
53996298 ATTTAATCATTTTT-ATAA
1 ATTTTATAATTTTTAATAA
*
53996316 CTTTTAT
1 ATTTTAT
53996323 TGATTTTTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
18 7 0.19
19 8 0.22
20 14 0.39
21 7 0.19
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTTATAATTTTTAATAA
Found at i:53996289 original size:28 final size:30
Alignment explanation
Indices: 53996222--53996290 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 30
53996212 ATTTTATTAT
* * *
53996222 TTTTATGAT-TTTTATAATTTTTTTATAAT
1 TTTTACGATATTTTATAATTTTTTAATAAA
53996251 TTTTACG--ATTTTATAA-TTTTTAATAAA
1 TTTTACGATATTTTATAATTTTTTAATAAA
53996278 TTTTA-GATATTTT
1 TTTTACGATATTTT
53996291 TATTAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 1 0.03
27 14 0.41
28 13 0.38
29 6 0.18
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (30 bp):
TTTTACGATATTTTATAATTTTTTAATAAA
Found at i:53996291 original size:20 final size:20
Alignment explanation
Indices: 53996266--53996331 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
53996256 CGATTTTATA
53996266 ATTTTTAATAAATTTTAGAT-
1 ATTTTTAATAAATTTTA-ATC
* *
53996286 ATTTTTATTAAAATTTAATC
1 ATTTTTAATAAATTTTAATC
* * *
53996306 ATTTTT-ATAACTTTTATTG
1 ATTTTTAATAAATTTTAATC
53996325 ATTTTTA
1 ATTTTTA
53996332 TTTTTTATAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 16 0.43
20 21 0.57
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
ATTTTTAATAAATTTTAATC
Found at i:54013690 original size:131 final size:131
Alignment explanation
Indices: 54013515--54013813 Score: 520
Period size: 131 Copynumber: 2.3 Consensus size: 131
54013505 ATTTACAAAT
* *
54013515 GTAACCAATTGAATTTTCCAATTAA---TCATACAATCATAATCAAATCAGAGTTTGTTCAAATA
1 GTAATCAATTGAATTATCCAATTAATTGTCATACAATCATAATCAAATCAGAGTTTGTTCAAATA
54013577 TAAACCCAAAACTCATGTACTCATTTCTTGAACTATGAACATAATTCCTTAAAAATAATTATGAA
66 TAAACCCAAAACTCATGTACTCATTTCTTGAACTATGAACATAATTCCTTAAAAATAATTATGAA
54013642 C
131 C
*
54013643 GTAATCAATTGAATTATCCAATTAATTGTCATACAATCATAATCAAATCAGAGTTTGTTTAAATA
1 GTAATCAATTGAATTATCCAATTAATTGTCATACAATCATAATCAAATCAGAGTTTGTTCAAATA
*
54013708 TAAACCCAAAACTCATGTACTCATTTCTTGAATTATGAACATAATTCCTTAAAAATAATTATGAA
66 TAAACCCAAAACTCATGTACTCATTTCTTGAACTATGAACATAATTCCTTAAAAATAATTATGAA
54013773 C
131 C
54013774 GTAATCAATTGAATTATCCAATTAATTG---TACAATCATAAT
1 GTAATCAATTGAATTATCCAATTAATTGTCATACAATCATAAT
54013814 TTTACAGTTG
Statistics
Matches: 164, Mismatches: 4, Indels: 6
0.94 0.02 0.03
Matches are distributed among these distances:
128 35 0.21
131 129 0.79
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.34
Consensus pattern (131 bp):
GTAATCAATTGAATTATCCAATTAATTGTCATACAATCATAATCAAATCAGAGTTTGTTCAAATA
TAAACCCAAAACTCATGTACTCATTTCTTGAACTATGAACATAATTCCTTAAAAATAATTATGAA
C
Found at i:54014269 original size:132 final size:131
Alignment explanation
Indices: 54014101--54014343 Score: 335
Period size: 132 Copynumber: 1.8 Consensus size: 131
54014091 ATTGATTGCA
* *
54014101 TTATTCAATTAATCTATAATCATAAAGTTACAATTGAATCGAAAGTTGTT-AAAGTGTAAACCCT
1 TTATCCAATTAATCTATAATCATAAAGTTACAATTGAATCGAAAGTTGTTCAAA-TATAAACCCT
* ** * *
54014165 ACACTCATATCCACATGTCTTGAATTATGAACGTAACCGATTGAATTCTAATTAATTGTACAATC
65 AAACTCATATCCACATGTCTCAAATTATGAACATAACCAATTGAATTCTAATTAATTGTACAATC
54014230 AT
130 AT
* * * *
54014232 TTATCCAATTAATCGTATAATCATGAATTTACAATTGAATCGAAATTTGTTCAAATATGAACCCT
1 TTATCCAATTAATC-TATAATCATAAAGTTACAATTGAATCGAAAGTTGTTCAAATATAAACCCT
** *
54014297 AAACTCATATGTACATGTCTCAAATTTTGAACATAACCAATTGAATT
65 AAACTCATATCCACATGTCTCAAATTATGAACATAACCAATTGAATT
54014344 ATCCAATTAA
Statistics
Matches: 96, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
131 13 0.14
132 80 0.83
133 3 0.03
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (131 bp):
TTATCCAATTAATCTATAATCATAAAGTTACAATTGAATCGAAAGTTGTTCAAATATAAACCCTA
AACTCATATCCACATGTCTCAAATTATGAACATAACCAATTGAATTCTAATTAATTGTACAATCA
T
Found at i:54014724 original size:18 final size:17
Alignment explanation
Indices: 54014676--54014724 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
54014666 TTAATCCTAC
54014676 AATCATAAATTTATATTTG
1 AATCA-AAATTT-TATTTG
54014695 AATCAAAA-TTTATTTG
1 AATCAAAATTTTATTTG
*
54014711 AATATAAAATTTTA
1 AAT-CAAAATTTTA
54014725 AGTGTGTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 9 0.33
17 6 0.22
18 7 0.26
19 5 0.19
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (17 bp):
AATCAAAATTTTATTTG
Found at i:54015058 original size:24 final size:24
Alignment explanation
Indices: 54015015--54015076 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
54015005 CCCTTCAAAG
*
54015015 ATAATGAAATTATAAGTTAATATA
1 ATAATAAAATTATAAGTTAATATA
* * *
54015039 ATGATAAAATTGTAATTTAATATA
1 ATAATAAAATTATAAGTTAATATA
*
54015063 ATAATAAAACTATA
1 ATAATAAAATTATA
54015077 CTTTTAATCC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (24 bp):
ATAATAAAATTATAAGTTAATATA
Found at i:54027930 original size:114 final size:114
Alignment explanation
Indices: 54027728--54027958 Score: 426
Period size: 114 Copynumber: 2.0 Consensus size: 114
54027718 TGCACAATTG
54027728 TGTTTTAAGTGATGTTATTTTGAAAATGTTTCAAAATAGCCAAAATTGGTGCCACAAGGGCGACC
1 TGTTTTAAGTGATGTTATTTTGAAAATGTTTCAAAATAGCCAAAATTGGTGCCACAAGGGCGACC
*
54027793 ATATGGCCGTATGAGATACACAGGCCAGAGGCACGATCGTGTTCTTATT
66 ATACGGCCGTATGAGATACACAGGCCAGAGGCACGATCGTGTTCTTATT
*
54027842 TGTTTTAAGTGATGTTATTTTGAAAATGTTTCAAAATAGCCAAAATTGGTGCCACAAGGGCGGCC
1 TGTTTTAAGTGATGTTATTTTGAAAATGTTTCAAAATAGCCAAAATTGGTGCCACAAGGGCGACC
* *
54027907 ATACGGCCGTATGAGATATACAGGCTAGAGGCACGATCGTGTTCTTATT
66 ATACGGCCGTATGAGATACACAGGCCAGAGGCACGATCGTGTTCTTATT
54027956 TGT
1 TGT
54027959 AAATTTTTTA
Statistics
Matches: 113, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (114 bp):
TGTTTTAAGTGATGTTATTTTGAAAATGTTTCAAAATAGCCAAAATTGGTGCCACAAGGGCGACC
ATACGGCCGTATGAGATACACAGGCCAGAGGCACGATCGTGTTCTTATT
Found at i:54031969 original size:39 final size:41
Alignment explanation
Indices: 54031926--54032009 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
54031916 GCCCGGCCCG
54031926 AATA-TAAT-AAATATATATTTTTT-TATTTTTTAATTTTAA
1 AATATTAATAAAATATATATTTTTTAT-TTTTTTAATTTTAA
** *
54031965 AATATTTTTAAAATATATATTTTTTATTTTTTTATTTTTAA
1 AATATTAATAAAATATATATTTTTTATTTTTTTAATTTTAA
54032006 AATA
1 AATA
54032010 AATTTTTGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
39 4 0.10
40 2 0.05
41 32 0.82
42 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (41 bp):
AATATTAATAAAATATATATTTTTTATTTTTTTAATTTTAA
Found at i:54034676 original size:21 final size:19
Alignment explanation
Indices: 54034632--54034676 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
54034622 ATTTTACATG
*
54034632 CACACATGATTCCACTAAT
1 CACACACGATTCCACTAAT
54034651 CACACACGATTCCACTAAT
1 CACACACGATTCCACTAAT
*
54034670 CAGACAC
1 CACACAC
54034677 CATTAACGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.38, C:0.36, G:0.07, T:0.20
Consensus pattern (19 bp):
CACACACGATTCCACTAAT
Found at i:54041730 original size:3 final size:3
Alignment explanation
Indices: 54041724--54041773 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
54041714 TATTATTATT
54041724 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
54041772 AT
1 AT
54041774 TAAAACTAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:54050721 original size:26 final size:26
Alignment explanation
Indices: 54050685--54050746 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
54050675 ACATGTTTTC
* *
54050685 TCAAATTTTTACT-AGGAGCAAAATTG
1 TCAAAATTTTACTAAAG-GCAAAATTG
* *
54050711 TCAAAATTTTATTAAAGGTAAAATTG
1 TCAAAATTTTACTAAAGGCAAAATTG
54050737 TCAAAATTTT
1 TCAAAATTTT
54050747 GCTGGGGGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 29 0.94
27 2 0.06
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (26 bp):
TCAAAATTTTACTAAAGGCAAAATTG
Found at i:54062660 original size:32 final size:30
Alignment explanation
Indices: 54062600--54062663 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 30
54062590 TAATTGGGTA
*
54062600 CTTAAACTTTCAAAATGTATCAAAAAGACC
1 CTTAAACTTTCAAAAAGTATCAAAAAGACC
*
54062630 CTTAAACTTTTTCAAAAAGTA-CAATTAAGACC
1 CTTAAAC--TTTCAAAAAGTATCAA-AAAGACC
54062662 CT
1 CT
54062664 GCTTTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 7 0.24
31 3 0.10
32 19 0.66
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (30 bp):
CTTAAACTTTCAAAAAGTATCAAAAAGACC
Found at i:54062689 original size:11 final size:11
Alignment explanation
Indices: 54062673--54062697 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54062663 TGCTTTTATT
54062673 AAAAATTATAA
1 AAAAATTATAA
54062684 AAAAATTATAA
1 AAAAATTATAA
54062695 AAA
1 AAA
54062698 TTTAAATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:54062697 original size:20 final size:20
Alignment explanation
Indices: 54062672--54062813 Score: 76
Period size: 20 Copynumber: 6.7 Consensus size: 20
54062662 CTGCTTTTAT
54062672 TAAAAATTATAAAAAAATTA
1 TAAAAATTATAAAAAAATTA
*
54062692 TAAAAATT-TAAATCAATATTA
1 TAAAAATTATAAA--AAAATTA
*
54062713 TTAAATTTTAATTA-AAAAATTCAAATA
1 -TAAA----AATTATAAAAA---AATTA
* *
54062740 TTAAAAATTAGAAAAAAAATA
1 -TAAAAATTATAAAAAAATTA
*
54062761 TAAAAATCATAAAAAAATTA
1 TAAAAATTATAAAAAAATTA
* *
54062781 T-AAAA-TATATAGAAATATA
1 TAAAAATTATAAAAAAAT-TA
*
54062800 AAAAAATTATAAAA
1 TAAAAATTATAAAA
54062814 TTTTATAAAG
Statistics
Matches: 95, Mismatches: 12, Indels: 29
0.70 0.09 0.21
Matches are distributed among these distances:
18 8 0.08
19 10 0.11
20 30 0.32
21 16 0.17
22 4 0.04
23 5 0.05
24 7 0.07
26 7 0.07
27 8 0.08
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.31
Consensus pattern (20 bp):
TAAAAATTATAAAAAAATTA
Found at i:54062812 original size:11 final size:11
Alignment explanation
Indices: 54062742--54062813 Score: 50
Period size: 11 Copynumber: 7.2 Consensus size: 11
54062732 TTCAAATATT
*
54062742 AAAAATTAGAA
1 AAAAATTATAA
*
54062753 AAAAA--ATAT
1 AAAAATTATAA
*
54062762 AAAAATCATAA
1 AAAAATTATAA
54062773 AAAAATTAT--
1 AAAAATTATAA
*
54062782 -AAAA-TATAT
1 AAAAATTATAA
*
54062791 AGAAA-TATAA
1 AAAAATTATAA
54062801 AAAAATTATAA
1 AAAAATTATAA
54062812 AA
1 AA
54062814 TTTTATAAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
7 3 0.06
8 4 0.08
9 7 0.15
10 11 0.23
11 23 0.48
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:54063098 original size:37 final size:37
Alignment explanation
Indices: 54063031--54063109 Score: 115
Period size: 36 Copynumber: 2.1 Consensus size: 37
54063021 GGTCATTAAT
** *
54063031 TTTTTTATGATTTTTATAAAATTTTTTAATTTTT-TA
1 TTTTTTATGATTTTTATAAAAAATTGTAATTTTTATA
54063067 TTTTTTATGATTTTTATAAAAAAATTGTAATTTTTATA
1 TTTTTTATGATTTTTAT-AAAAAATTGTAATTTTTATA
54063105 TTTTT
1 TTTTT
54063110 ATTAAAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 17 0.45
37 14 0.37
38 7 0.18
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (37 bp):
TTTTTTATGATTTTTATAAAAAATTGTAATTTTTATA
Found at i:54063125 original size:28 final size:29
Alignment explanation
Indices: 54063068--54063129 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
54063058 AATTTTTTAT
*
54063068 TTTTTATGATTTTTATAAAAAAATTGTAA
1 TTTTTATGATTTTTATAAAAAAATTATAA
* *
54063097 TTTTTAT-ATTTTTAT-TAAAATTTAATAA
1 TTTTTATGATTTTTATAAAAAAATT-ATAA
54063125 TTTTT
1 TTTTT
54063130 CTAAAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 6 0.21
28 16 0.55
29 7 0.24
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (29 bp):
TTTTTATGATTTTTATAAAAAAATTATAA
Found at i:54067052 original size:59 final size:59
Alignment explanation
Indices: 54066984--54067174 Score: 215
Period size: 59 Copynumber: 3.2 Consensus size: 59
54066974 TTTAGATTAA
54066984 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
1 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
* * ** * * * * * *
54067043 ATTATATATTATGATTTTAGTAAATTCATATAAGAA-TATATTTAATATTAAGAATTTTATTA-A
1 ATTATATATTTTTATTAAATTATATTTA-ATAATAATTAT-TTTAA-ATT-A-TATTTTA-TAGT
*
54067106 ATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGT
1 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
54067165 ATTATATATT
1 ATTATATATT
54067175 ATGATTTTAG
Statistics
Matches: 103, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
58 2 0.02
59 40 0.39
60 12 0.12
61 6 0.06
62 11 0.11
63 30 0.29
64 2 0.02
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (59 bp):
ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
Found at i:54067105 original size:18 final size:18
Alignment explanation
Indices: 54067084--54067129 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
54067074 AAGAATATAT
54067084 TTAATATTA-AGAATTTTA
1 TTAA-ATTATAGAATTTTA
* *
54067102 TTAAATTATATATTTTTA
1 TTAAATTATAGAATTTTA
54067120 TTAAATTATA
1 TTAAATTATA
54067130 TTTAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TTAAATTATAGAATTTTA
Found at i:54067105 original size:122 final size:121
Alignment explanation
Indices: 54066979--54067233 Score: 449
Period size: 122 Copynumber: 2.1 Consensus size: 121
54066969 CAAACTTTAG
*
54066979 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTA
* *
54067044 TTATATATTATGATTTTAGTAAATTCATA-TAAGAATATATTTAATATTAAGAATTTT
66 TTATATATTATGATTTTAGTAAATTAATATTAAG-A-ATATCTAATATTAAGAATTTT
54067101 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTA
*
54067166 TTATATATTATGATTTTAGTAATTTAATATTAAGAATATCTAATATTAAGAATTTT
66 TTATATATTATGATTTTAGTAAATTAATATTAAGAATATCTAATATTAAGAATTTT
54067222 ATTAAATTATAT
1 ATTAAATTATAT
54067234 TTAATAATAA
Statistics
Matches: 128, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
121 32 0.25
122 92 0.72
123 4 0.03
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (121 bp):
ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTA
TTATATATTATGATTTTAGTAAATTAATATTAAGAATATCTAATATTAAGAATTTT
Found at i:54067195 original size:22 final size:21
Alignment explanation
Indices: 54067146--54067197 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
54067136 AATAATTATG
*
54067146 TTAA-ATTATATTTTATAGTA
1 TTAATATTATATTTTATAATA
54067166 TTATATATTATGATTTTAGTAAT-
1 TTA-ATATTAT-ATTTTA-TAATA
54067189 TTAATATTA
1 TTAATATTA
54067198 AGAATATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.11
21 1 0.04
22 11 0.41
23 9 0.33
24 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (21 bp):
TTAATATTATATTTTATAATA
Found at i:54068098 original size:82 final size:83
Alignment explanation
Indices: 54067997--54068159 Score: 211
Period size: 83 Copynumber: 2.0 Consensus size: 83
54067987 CACTTTCGCC
* *
54067997 ACCAAGAAATCGGTTCGGTTTAATTTAAGTAAGT-TCATTGTTTTTGTATCATGTCTAAGAGATA
1 ACCAAGAAATCGGTTCGGTTCAATTCAAGTAAGTATCATTGTTTTTGTATCATGTCTAAGAGATA
* *
54068061 GTTTAATAATGCTTTTCA
66 ATTTAACAATGCTTTTCA
* * * ** * *
54068079 ACCAAGAGATCGGTTCGGTTCAATTCGATTAAGTATGTTTTTTTTTGTATCATGTCTAAGAGTTA
1 ACCAAGAAATCGGTTCGGTTCAATTCAAGTAAGTATCATTGTTTTTGTATCATGTCTAAGAGATA
*
54068144 ATTTAGCAATGCTTTT
66 ATTTAACAATGCTTTT
54068160 TAAAAGTGTT
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
82 29 0.43
83 39 0.57
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (83 bp):
ACCAAGAAATCGGTTCGGTTCAATTCAAGTAAGTATCATTGTTTTTGTATCATGTCTAAGAGATA
ATTTAACAATGCTTTTCA
Found at i:54072101 original size:16 final size:16
Alignment explanation
Indices: 54072063--54072101 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
54072053 AATATATGTT
*
54072063 ATAATAATCAAATGAA
1 ATAATAATAAAATGAA
54072079 A-ATATAATAAAATGAA
1 ATA-ATAATAAAATGAA
54072095 ATAATAA
1 ATAATAA
54072102 AGAAAGTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 1 0.05
16 18 0.90
17 1 0.05
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (16 bp):
ATAATAATAAAATGAA
Found at i:54072154 original size:13 final size:13
Alignment explanation
Indices: 54072136--54072176 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
54072126 CAAAACTAAT
*
54072136 AGAAAAGGAAGAA
1 AGAAAAGAAAGAA
*
54072149 AGAAAAGAAAGGA
1 AGAAAAGAAAGAA
*
54072162 AGACAAGAAAGAA
1 AGAAAAGAAAGAA
54072175 AG
1 AG
54072177 GGGCGCACGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAAGAA
Found at i:54072161 original size:17 final size:17
Alignment explanation
Indices: 54072139--54072177 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
54072129 AACTAATAGA
54072139 AAAGGAAGA-AAGAAAAG
1 AAAGGAAGACAAG-AAAG
54072156 AAAGGAAGACAAGAAAG
1 AAAGGAAGACAAGAAAG
54072173 AAAGG
1 AAAGG
54072178 GGCGCACGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.67, C:0.03, G:0.31, T:0.00
Consensus pattern (17 bp):
AAAGGAAGACAAGAAAG
Found at i:54073297 original size:18 final size:18
Alignment explanation
Indices: 54073274--54073366 Score: 80
Period size: 18 Copynumber: 4.7 Consensus size: 18
54073264 GAAATGACCA
54073274 AGATGAGAAATGAATATG
1 AGATGAGAAATGAATATG
54073292 AGATGAGAAATATTGAAT-TGG
1 AGATGAG-AA-A-TGAATAT-G
54073313 CAAAGATGAGAAATGAATATG
1 ---AGATGAGAAATGAATATG
*
54073334 AGATGAGAAATGTGATATG
1 AGATGAGAAATG-AATATG
*
54073353 AAATGATGAAATGA
1 AGATGA-GAAATGA
54073367 GATGTGAAAC
Statistics
Matches: 62, Mismatches: 3, Indels: 19
0.74 0.04 0.23
Matches are distributed among these distances:
18 19 0.31
19 12 0.19
20 8 0.13
21 12 0.19
22 2 0.03
23 2 0.03
24 7 0.11
ACGTcount: A:0.48, C:0.01, G:0.27, T:0.24
Consensus pattern (18 bp):
AGATGAGAAATGAATATG
Found at i:54073319 original size:42 final size:42
Alignment explanation
Indices: 54073259--54073344 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
54073249 TATGTGATTG
*
54073259 ATATTGAAATGACCAAGATGAGAAATGAATATGAGATGAGAA
1 ATATTGAAATGACAAAGATGAGAAATGAATATGAGATGAGAA
* *
54073301 ATATTGAATTGGCAAAGATGAGAAATGAATATGAGATGAGAA
1 ATATTGAAATGACAAAGATGAGAAATGAATATGAGATGAGAA
54073343 AT
1 AT
54073345 GTGATATGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.49, C:0.03, G:0.24, T:0.23
Consensus pattern (42 bp):
ATATTGAAATGACAAAGATGAGAAATGAATATGAGATGAGAA
Found at i:54077233 original size:37 final size:37
Alignment explanation
Indices: 54077192--54077266 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
54077182 ATCTATTTTC
54077192 ATTTTCTTTCTTCTATCTTTTTCCCTGGTCTGCTGGT
1 ATTTTCTTTCTTCTATCTTTTTCCCTGGTCTGCTGGT
*
54077229 ATTTTTTTTCTTCTATCTTTTTCCCTGGTCTGCTGGT
1 ATTTTCTTTCTTCTATCTTTTTCCCTGGTCTGCTGGT
54077266 A
1 A
54077267 AAGAAGATGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.07, C:0.23, G:0.13, T:0.57
Consensus pattern (37 bp):
ATTTTCTTTCTTCTATCTTTTTCCCTGGTCTGCTGGT
Found at i:54081120 original size:40 final size:40
Alignment explanation
Indices: 54081072--54081164 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 40
54081062 TTTTTTATTC
* * *
54081072 AAACGCCGCTAAAGATTGAGA-ATTAGCGGCGCTAT-TTAGA
1 AAACGCCGCTAAAGATCGA-ACATTAGCGGCACT-TGATAGA
*
54081112 AAACGCCGCTAAAGATCGAACATTAGCGGCACTTGATGGA
1 AAACGCCGCTAAAGATCGAACATTAGCGGCACTTGATAGA
54081152 AAACGCCGCTAAA
1 AAACGCCGCTAAA
54081165 AATAAGAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
39 2 0.04
40 45 0.96
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.18
Consensus pattern (40 bp):
AAACGCCGCTAAAGATCGAACATTAGCGGCACTTGATAGA
Found at i:54081355 original size:41 final size:41
Alignment explanation
Indices: 54081244--54081455 Score: 275
Period size: 41 Copynumber: 5.2 Consensus size: 41
54081234 CTTTCGGGGT
* * *
54081244 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGTTCTGGGA
1 TTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCTGGGA
*
54081285 TTTAGCGGTG-TTTTTAGGAAGCGCCGCTAATGCTCTGGGA
1 TTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCTGGGA
** *
54081325 TTTAGCGGTATTTTTTAGGAAGCGCTGCTAATGCTCTGGGA
1 TTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCTGGGA
* * * *
54081366 TTTAGCGGCGTTTTTTAGGAAGCGCCGCTATTGCTCAGTGC
1 TTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCTGGGA
* * *
54081407 TTTAGCGGCGTTTTTTAGAAAGCGCCACTAATACT-TAGGGA
1 TTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCT-GGGA
54081448 TTTAGCGG
1 TTTAGCGG
54081456 TACTTATGCT
Statistics
Matches: 149, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
40 36 0.24
41 113 0.76
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.33
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCTGGGA
Found at i:54082539 original size:14 final size:14
Alignment explanation
Indices: 54082525--54082603 Score: 90
Period size: 14 Copynumber: 5.6 Consensus size: 14
54082515 GGTTTATGGT
54082525 TTAAGGGTT-GGGG
1 TTAAGGGTTAGGGG
*
54082538 TTTAAGGTTTAGGGG
1 -TTAAGGGTTAGGGG
*
54082553 TTAAGGGTTAGAGG
1 TTAAGGGTTAGGGG
54082567 TT-AGTGGTTAGGGG
1 TTAAG-GGTTAGGGG
*
54082581 TTAGGGGTTAGGGG
1 TTAAGGGTTAGGGG
*
54082595 TTTAGGGTT
1 TTAAGGGTT
54082604 TATGTTTTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
13 2 0.04
14 48 0.87
15 5 0.09
ACGTcount: A:0.18, C:0.00, G:0.47, T:0.35
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:54082541 original size:21 final size:21
Alignment explanation
Indices: 54082515--54082554 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54082505 TATAGATTAT
*
54082515 GGTTTATGGTTTAAGGGTTGG
1 GGTTTAAGGTTTAAGGGTTGG
*
54082536 GGTTTAAGGTTTAGGGGTT
1 GGTTTAAGGTTTAAGGGTT
54082555 AAGGGTTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.42, T:0.42
Consensus pattern (21 bp):
GGTTTAAGGTTTAAGGGTTGG
Found at i:54082569 original size:7 final size:7
Alignment explanation
Indices: 54082546--54082647 Score: 80
Period size: 7 Copynumber: 14.6 Consensus size: 7
54082536 GGTTTAAGGT
54082546 TTAGGGG
1 TTAGGGG
*
54082553 TTAAGGG
1 TTAGGGG
*
54082560 TTAGAGG
1 TTAGGGG
*
54082567 TTAGTGG
1 TTAGGGG
54082574 TTAGGGG
1 TTAGGGG
54082581 TTAGGGG
1 TTAGGGG
54082588 TTAGGGG
1 TTAGGGG
*
54082595 TTTAGGGT
1 -TTAGGGG
* **
54082603 TTATGTT
1 TTAGGGG
* **
54082610 TTATGAT
1 TTAGGGG
54082617 TTAGGGG
1 TTAGGGG
54082624 TTA-GGG
1 TTAGGGG
*
54082630 ATAGGGG
1 TTAGGGG
*
54082637 TTAGGGT
1 TTAGGGG
54082644 TTAG
1 TTAG
54082648 ATTAGTTGGT
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
6 5 0.06
7 67 0.86
8 6 0.08
ACGTcount: A:0.19, C:0.00, G:0.44, T:0.37
Consensus pattern (7 bp):
TTAGGGG
Found at i:54082636 original size:13 final size:13
Alignment explanation
Indices: 54082618--54082642 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54082608 TTTTATGATT
54082618 TAGGGGTTAGGGA
1 TAGGGGTTAGGGA
54082631 TAGGGGTTAGGG
1 TAGGGGTTAGGG
54082643 TTTAGATTAG
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:0.20, C:0.00, G:0.56, T:0.24
Consensus pattern (13 bp):
TAGGGGTTAGGGA
Found at i:54083106 original size:21 final size:21
Alignment explanation
Indices: 54083063--54083106 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
54083053 TTTTATCCAC
* *
54083063 AAATTTTCCCATAAAATCCTA
1 AAATTTCCCCATAAAATCATA
* *
54083084 AAATTTCCCCCTAAAATTATA
1 AAATTTCCCCATAAAATCATA
54083105 AA
1 AA
54083107 CTTAAATTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATTTCCCCATAAAATCATA
Found at i:54086721 original size:15 final size:15
Alignment explanation
Indices: 54086701--54086731 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54086691 GAGTTGAAAG
54086701 TGAAGAAGAAGATGA
1 TGAAGAAGAAGATGA
*
54086716 TGAAGATGAAGATGA
1 TGAAGAAGAAGATGA
54086731 T
1 T
54086732 CCATATCCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.19
Consensus pattern (15 bp):
TGAAGAAGAAGATGA
Found at i:54087038 original size:43 final size:43
Alignment explanation
Indices: 54086972--54087321 Score: 373
Period size: 43 Copynumber: 8.3 Consensus size: 43
54086962 TAATAGTACT
**** *
54086972 TTTAGCGGCGTTTGTAATCAAAGCGTCGCTAAAGGTCTTGAG-C
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTG-GTC
* * * * * * *
54087015 TATAGCGGCATTTGCGGAAAAAGCGCTGCTATAGGTCTGGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
54087058 TTTAGCGACGTTTGTAGGAAAAGCACCGCTAAAGGTC-TGGATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGG-TC
*
54087101 TTTAGCGGCGTTTGTGGGAACAGCGCCGCTAAAGGTC-TGGATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGG-TC
* *
54087144 TTTA---GC------GGGAAAAGCACCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
54087178 TTTAGCGGCGTTTGTGGGAAAATCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
54087221 TTTAGCGGCGTTTTTGGGAAAAGCGTCACTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
54087264 TTTAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTAGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
54087307 TTTAGCGGCGTTTGT
1 TTTAGCGGCGTTTGT
54087322 TTCTAAAAAT
Statistics
Matches: 255, Mismatches: 40, Indels: 24
0.80 0.13 0.08
Matches are distributed among these distances:
34 26 0.10
35 3 0.01
37 2 0.01
40 2 0.01
42 3 0.01
43 219 0.86
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:54087164 original size:34 final size:34
Alignment explanation
Indices: 54087116--54087185 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
54087106 CGGCGTTTGT
* *
54087116 GGGAACAGCGCCGCTAAAGGT-CTGGATCTTTAGC
1 GGGAAAAGCACCGCTAAAGGTCCTGG-TCTTTAGC
54087150 GGGAAAAGCACCGCTAAAGGTCCTGGTCTTTAGC
1 GGGAAAAGCACCGCTAAAGGTCCTGGTCTTTAGC
54087184 GG
1 GG
54087186 CGTTTGTGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 29 0.88
35 4 0.12
ACGTcount: A:0.24, C:0.23, G:0.33, T:0.20
Consensus pattern (34 bp):
GGGAAAAGCACCGCTAAAGGTCCTGGTCTTTAGC
Found at i:54087205 original size:77 final size:77
Alignment explanation
Indices: 54087074--54087314 Score: 281
Period size: 77 Copynumber: 3.0 Consensus size: 77
54087064 GACGTTTGTA
*
54087074 GGAAAAGCACCGCTAAAGGT-CTGGATCTTTAGCGGCGTTTGTGGGAACAGCGCCGCTAAAGGTC
1 GGAAAAGCACCGCTAAAGGTCCTGG-TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC
54087138 TGGATCTTTAGCG
65 TGGATCTTTAGCG
*
54087151 GGAAAAGCACCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAAATCGCCGCTAAAGGTCT
1 GGAAAAGCACCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-
54087216 TGG-TCTTTAGCGGCGTTTTTG
65 TGGATCTTTA---GC------G
** * * *
54087237 GGAAAAGCGTCACTAAAGGTCTTGGTCTTTAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGGTCT
1 GGAAAAGCACCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCT
*
54087302 -TAGTCTTTAGCG
66 GGA-TCTTTAGCG
54087314 G
1 G
54087315 CGTTTGTTTC
Statistics
Matches: 142, Mismatches: 9, Indels: 26
0.80 0.05 0.15
Matches are distributed among these distances:
77 65 0.46
78 7 0.05
80 2 0.01
83 2 0.01
85 1 0.01
86 65 0.46
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.27
Consensus pattern (77 bp):
GGAAAAGCACCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCT
GGATCTTTAGCG
Found at i:54087253 original size:120 final size:120
Alignment explanation
Indices: 54087028--54087270 Score: 330
Period size: 120 Copynumber: 2.0 Consensus size: 120
54087018 AGCGGCATTT
* * *
54087028 GCGGAAAAAGCGCTGCTATAGGTCTGGGTCTTTAGCGACGTTTGTAGGAAAAGCACCGCTAAAGG
1 GCGGAAAAAGCACCGCTAAAGGTCTGGGTCTTTAGCGACGTTTGTAGGAAAAGCACCGCTAAAGG
* *
54087093 TCTGGATCTTTAGCGGCGTTTGTGGGAACAGCGCCGCTAAAGGTC-TGGATCTTTA
66 TCTGGATCTTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCTTGG-TCTTTA
* * * * *
54087148 GCGGGAAAAGCACCGCTAAAGGTCCT-GGTCTTTAGCGGCGTTTGTGGGAAAATCGCCGCTAAAG
1 GCGGAAAAAGCACCGCTAAAGGT-CTGGGTCTTTAGCGACGTTTGTAGGAAAAGCACCGCTAAAG
* *
54087212 GTCTTGG-TCTTTAGCGGCGTTTTTGGGAAAAGCGTCACTAAAGGTCTTGGTCTTTA
65 GTC-TGGATCTTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCTTGGTCTTTA
54087268 GCG
1 GCG
54087271 ACGTTTGTGG
Statistics
Matches: 108, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
120 100 0.93
121 8 0.07
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (120 bp):
GCGGAAAAAGCACCGCTAAAGGTCTGGGTCTTTAGCGACGTTTGTAGGAAAAGCACCGCTAAAGG
TCTGGATCTTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCTTGGTCTTTA
Found at i:54087268 original size:163 final size:163
Alignment explanation
Indices: 54086998--54087314 Score: 424
Period size: 163 Copynumber: 1.9 Consensus size: 163
54086988 ATCAAAGCGT
* * *
54086998 CGCTAAAGGTCTTGAGCTATAGCGGCATTTGCGGAAAAAGCGCTGCTATAGGTCTGGGTCTTTAG
1 CGCTAAAGGTCCTGAGCTATAGCGGCATTTGCGGAAAAAGCGCCGCTAAAGGTCTGGGTCTTTAG
* * *
54087063 CGACGTTTGTAGGAAAAGCACCGCTAAAGGTCTGGATCTTTAGCGGCGTTTGTGGGAACAGCGCC
66 CGACGTTTGTAGGAAAAGCACCACTAAAGGTCTGGATCTTTAGCGACGTTTGTGGGAAAAGCGCC
54087128 GCTAAAGGTCTG-GATCTTTAGCGGGAAAAGCAC
131 GCTAAAGGTCTGAG-TCTTTAGCGGGAAAAGCAC
* * * * * *
54087161 CGCTAAAGGTCCTG-GTCTTTAGCGGCGTTTGTGGGAAAATCGCCGCTAAAGGTCTTGGTCTTTA
1 CGCTAAAGGTCCTGAG-CTATAGCGGCATTTGCGGAAAAAGCGCCGCTAAAGGTCTGGGTCTTTA
* * * **
54087225 GCGGCGTTTTTGGGAAAAGCGTCACTAAAGGTCTTGG-TCTTTAGCGACGTTTGTGGGAAAAGCG
65 GCGACGTTTGTAGGAAAAGCACCACTAAAGGTC-TGGATCTTTAGCGACGTTTGTGGGAAAAGCG
*
54087289 CCGCTAAAGGTCTTAGTCTTTAGCGG
129 CCGCTAAAGGTCTGAGTCTTTAGCGG
54087315 CGTTTGTTTC
Statistics
Matches: 133, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
162 1 0.01
163 128 0.96
164 4 0.03
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.27
Consensus pattern (163 bp):
CGCTAAAGGTCCTGAGCTATAGCGGCATTTGCGGAAAAAGCGCCGCTAAAGGTCTGGGTCTTTAG
CGACGTTTGTAGGAAAAGCACCACTAAAGGTCTGGATCTTTAGCGACGTTTGTGGGAAAAGCGCC
GCTAAAGGTCTGAGTCTTTAGCGGGAAAAGCAC
Found at i:54095612 original size:17 final size:17
Alignment explanation
Indices: 54095590--54095626 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
54095580 TAATCAACAC
54095590 TTAAATAATAATAAAAT
1 TTAAATAATAATAAAAT
54095607 TTAAATAATAATAAAAT
1 TTAAATAATAATAAAAT
54095624 TTA
1 TTA
54095627 TAGTTGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAATAATAATAAAAT
Found at i:54096322 original size:16 final size:17
Alignment explanation
Indices: 54096297--54096329 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
54096287 ACACGTTGAA
54096297 TACAAGTTA-TTCATAT
1 TACAAGTTATTTCATAT
*
54096313 TACAATTTATTTCATAT
1 TACAAGTTATTTCATAT
54096330 GAATATCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (17 bp):
TACAAGTTATTTCATAT
Found at i:54109440 original size:24 final size:24
Alignment explanation
Indices: 54109413--54109458 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
54109403 AACCTAATTC
54109413 TAATCAAA-GTCAAATATATTATGT
1 TAAT-AAATGTCAAATATATTATGT
*
54109437 TAATAAATGTTAAATATATTAT
1 TAATAAATGTCAAATATATTAT
54109459 TCTCATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (24 bp):
TAATAAATGTCAAATATATTATGT
Found at i:54109474 original size:24 final size:24
Alignment explanation
Indices: 54109424--54109475 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
54109414 AATCAAAGTC
**
54109424 AAATATATTATGTTAATAAATGTT
1 AAATATATTATGTTAATAAATACT
*
54109448 AAATATATTAT-TCTCATAAATACT
1 AAATATATTATGT-TAATAAATACT
54109472 AAAT
1 AAAT
54109476 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (24 bp):
AAATATATTATGTTAATAAATACT
Found at i:54110531 original size:20 final size:21
Alignment explanation
Indices: 54110498--54110539 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
54110488 CTTTTTTCTC
54110498 GTGTGATGCACAAGTGTAATGT
1 GTGTGATG-ACAAGTGTAATGT
54110520 GTGTGATG-CAAGTGTAATGT
1 GTGTGATGACAAGTGTAATGT
54110540 ATGTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.60
22 8 0.40
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.33
Consensus pattern (21 bp):
GTGTGATGACAAGTGTAATGT
Found at i:54111779 original size:3 final size:3
Alignment explanation
Indices: 54111771--54111828 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
54111761 TTTAATACTG
* * * *
54111771 TTA TTA TTA TTA TATA ATA TCA CTA ATA TT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54111816 TTTA TTA TTA TTA
1 -TTA TTA TTA TTA
54111829 GTTTTATTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
2 2 0.04
3 38 0.84
4 5 0.11
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:54111822 original size:13 final size:13
Alignment explanation
Indices: 54111804--54111828 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54111794 TAATATTTTA
54111804 TTATTATTATTAT
1 TTATTATTATTAT
54111817 TTATTATTATTA
1 TTATTATTATTA
54111829 GTTTTATTTT
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:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:54111825 original size:19 final size:19
Alignment explanation
Indices: 54111801--54111837 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
54111791 CACTAATATT
54111801 TTATTATTA-TTATTATTTA
1 TTATTATTAGTT-TTATTTA
54111820 TTATTATTAGTTTTATTT
1 TTATTATTAGTTTTATTT
54111838 TCCTTTTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
TTATTATTAGTTTTATTTA
Found at i:54112969 original size:108 final size:108
Alignment explanation
Indices: 54112831--54113245 Score: 717
Period size: 108 Copynumber: 3.9 Consensus size: 108
54112821 AAATAATAAG
*
54112831 TAAGGCAATGTTTTGCGTTT-AGAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
1 TAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
54112895 TTCGTTCGACCAAATAGCCAAATATCCTTATAAAATTTCAAAA
66 TTCGTTCGACCAAATAGCCAAATATCCTTATAAAATTTCAAAA
*
54112938 TAAGACAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
1 TAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
*
54113003 TTCATTCGACCAAATAGCCAAATATCCTTATAAAATTTCAAAA
66 TTCGTTCGACCAAATAGCCAAATATCCTTATAAAATTTCAAAA
** * *
54113046 TAAGGCAATGTTTTGTATTTGGAAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCAATTTT
1 TAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
*
54113111 TTCGTTCGACCAAATAGCCAAAAATCCTTATAAAATTTCAAAA
66 TTCGTTCGACCAAATAGCCAAATATCCTTATAAAATTTCAAAA
* *
54113154 TAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA-TTT
1 TAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
*
54113218 TTCGTTGGACCAAATAGCCAAATATCCT
66 TTCGTTCGACCAAATAGCCAAATATCCT
54113246 CTTGAATCTT
Statistics
Matches: 289, Mismatches: 18, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
107 48 0.17
108 241 0.83
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (108 bp):
TAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
TTCGTTCGACCAAATAGCCAAATATCCTTATAAAATTTCAAAA
Found at i:54114078 original size:36 final size:35
Alignment explanation
Indices: 54114004--54114078 Score: 82
Period size: 36 Copynumber: 2.1 Consensus size: 35
54113994 ATGACTAAAC
*
54114004 AATTCAATAATATAAATAATATAAAATGTGAAATTT
1 AATTCAATAATATAAATAATATAAAA-GTGAAAATT
*
54114040 AATTTAATAATATAAATAGTATATATAAA-T-AAAATT
1 AATTCAATAATATAAATA--ATATA-AAAGTGAAAATT
54114076 AAT
1 AAT
54114079 ACTATTTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
36 25 0.74
37 1 0.03
38 5 0.15
39 3 0.09
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (35 bp):
AATTCAATAATATAAATAATATAAAAGTGAAAATT
Found at i:54114549 original size:9 final size:9
Alignment explanation
Indices: 54114535--54114571 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
54114525 TATAGTTTGA
54114535 TATTCGAAT
1 TATTCGAAT
54114544 TATTCGAAT
1 TATTCGAAT
*
54114553 TATTCGAGT
1 TATTCGAAT
54114562 TATTCGAAT
1 TATTCGAAT
54114571 T
1 T
54114572 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:54119198 original size:10 final size:9
Alignment explanation
Indices: 54119149--54119310 Score: 59
Period size: 9 Copynumber: 17.7 Consensus size: 9
54119139 ACATGTGAAA
54119149 AAAAATTAT
1 AAAAATTAT
*
54119158 AAAAA-AAT
1 AAAAATTAT
*
54119166 AAAAAATCAAT
1 -AAAAAT-TAT
*
54119177 AAAAGTTAT
1 AAAAATTAT
54119186 AAAAATTAT
1 AAAAATTAT
* *
54119195 TAAACTTCAAT
1 AAAAATT--AT
*
54119206 AAAAAATAT
1 AAAAATTAT
54119215 AAAAATATATTT
1 AAAAAT-TA--T
*
54119227 AAAAGTTACT
1 AAAAATTA-T
*
54119237 AAAAATTAG
1 AAAAATTAT
*
54119246 AAATA-TAT
1 AAAAATTAT
*
54119254 -ATAATGTA-
1 AAAAAT-TAT
54119262 AAAAA--AT
1 AAAAATTAT
*
54119269 AAAAATTTT
1 AAAAATTAT
*
54119278 AAAATTTTAT
1 AAAA-ATTAT
*
54119288 AAAAATCAT
1 AAAAATTAT
*
54119297 AAAAAAT-T
1 AAAAATTAT
54119305 AAAAAT
1 AAAAAT
54119311 GCATCAAAAA
Statistics
Matches: 111, Mismatches: 27, Indels: 31
0.66 0.16 0.18
Matches are distributed among these distances:
6 1 0.01
7 7 0.06
8 10 0.09
9 54 0.49
10 22 0.20
11 11 0.10
12 6 0.05
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:54119319 original size:18 final size:17
Alignment explanation
Indices: 54119287--54119320 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
54119277 TAAAATTTTA
54119287 TAAAAATCATAAAAAAT
1 TAAAAATCATAAAAAAT
*
54119304 TAAAAATGCATCAAAAA
1 TAAAAAT-CATAAAAAA
54119321 GACCATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.68, C:0.09, G:0.03, T:0.21
Consensus pattern (17 bp):
TAAAAATCATAAAAAAT
Found at i:54122831 original size:7 final size:7
Alignment explanation
Indices: 54122811--54122865 Score: 67
Period size: 7 Copynumber: 7.7 Consensus size: 7
54122801 TATTTAAAAA
54122811 TATTATT
1 TATTATT
54122818 T-TTATT
1 TATTATT
54122824 TATTATT
1 TATTATT
54122831 TATTATT
1 TATTATT
*
54122838 TAATATT
1 TATTATT
*
54122845 TAATATT
1 TATTATT
54122852 TATATATTT
1 TAT-TA-TT
54122861 TATTA
1 TATTA
54122866 CAATTATACG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
6 6 0.14
7 28 0.65
8 4 0.09
9 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TATTATT
Found at i:54122846 original size:21 final size:20
Alignment explanation
Indices: 54122790--54122864 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
54122780 AACATTGTCC
54122790 ATTTATT-TTTATATTTAA-
1 ATTTATTATTTATATTTAAT
** * *
54122808 AAATATTATTTTTATTTATT
1 ATTTATTATTTATATTTAAT
54122828 ATTTATTATTTAATATTTAAT
1 ATTTATTATTT-ATATTTAAT
54122849 ATTTATATATTT-TATT
1 ATTTAT-TATTTATATT
54122865 ACAATTATAC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
18 5 0.11
19 9 0.20
20 13 0.29
21 13 0.29
22 5 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTATTATTTATATTTAAT
Found at i:54125113 original size:18 final size:18
Alignment explanation
Indices: 54125090--54125140 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
54125080 ACTTCTCGTT
*
54125090 ATTTTTATATATTTTAAA
1 ATTTTTATAAATTTTAAA
54125108 ATTTTTA-AAATTTT-AA
1 ATTTTTATAAATTTTAAA
54125124 ATATTTTATAAATTTTA
1 AT-TTTTATAAATTTTA
54125141 GATTATTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 4 0.14
17 11 0.38
18 14 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTTATAAATTTTAAA
Found at i:54125140 original size:9 final size:9
Alignment explanation
Indices: 54125092--54125140 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
54125082 TTCTCGTTAT
*
54125092 TTTTATATA
1 TTTTATAAA
54125101 TTTTA-AAA
1 TTTTATAAA
54125109 TTTT-TAAAA
1 TTTTAT-AAA
54125118 TTTTA-AATA
1 TTTTATAA-A
54125127 TTTTATAAA
1 TTTTATAAA
54125136 TTTTA
1 TTTTA
54125141 GATTATTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
8 8 0.24
9 24 0.71
10 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTATAAA
Found at i:54125601 original size:22 final size:22
Alignment explanation
Indices: 54125573--54125616 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
54125563 ACACCAGAAC
*
54125573 AGGCCTTTAGCGGCGTTTTTTA
1 AGGCCTTTAGCGGCGCTTTTTA
54125595 AGGCCTTTAGCGGCGCTTTTTA
1 AGGCCTTTAGCGGCGCTTTTTA
54125617 GCGCCACTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.20, G:0.27, T:0.39
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTA
Found at i:54125738 original size:42 final size:42
Alignment explanation
Indices: 54125672--54125813 Score: 180
Period size: 42 Copynumber: 3.4 Consensus size: 42
54125662 AGCGTTTACA
* * *
54125672 AAAATAAACGCCGCTGAAGGTCATGTTCTTTAGCGACGCTTAG
1 AAAA-AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
54125715 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGC-CTTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* * **
54125756 AAAAAAAACGCCGTTAAAGATCATGTTTTTTAGCGGCGCCCAG
1 -AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
*
54125799 -AAAAAACGCCACTAA
1 AAAAAAACGCCGCTAA
54125814 TGTTGGGATT
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
41 18 0.20
42 63 0.72
43 7 0.08
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
Found at i:54126198 original size:21 final size:20
Alignment explanation
Indices: 54126152--54126201 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
54126142 CTTCTTTTGA
* * *
54126152 ACCTCTGCTTCTCTCGCTGT
1 ACCTCTGCATCCCTCGCTGC
54126172 AGCCTCTGCATCCCTCGCTGCC
1 A-CCTCTGCATCCCTCGCTG-C
54126194 ACCTCTGC
1 ACCTCTGC
54126202 TTTAAGTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.08, C:0.46, G:0.16, T:0.30
Consensus pattern (20 bp):
ACCTCTGCATCCCTCGCTGC
Found at i:54131587 original size:18 final size:19
Alignment explanation
Indices: 54131564--54131601 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
54131554 ATTTTCCGTA
54131564 AAATGATTT-CTGGAAAAT
1 AAATGATTTACTGGAAAAT
54131582 AAATGATTTACTGGAAAAT
1 AAATGATTTACTGGAAAAT
54131601 A
1 A
54131602 TTTTCTGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.32
Consensus pattern (19 bp):
AAATGATTTACTGGAAAAT
Found at i:54132285 original size:9 final size:9
Alignment explanation
Indices: 54132271--54132509 Score: 103
Period size: 9 Copynumber: 27.4 Consensus size: 9
54132261 AGTATATATG
54132271 AGTTATGTA
1 AGTTATGTA
54132280 AGTTATGATA
1 AGTTATG-TA
* * *
54132290 TGATATAT-
1 AGTTATGTA
*
54132298 ATTTATGT-
1 AGTTATGTA
*
54132306 A-TTACGTA
1 AGTTATGTA
*
54132314 AATTATGTA
1 AGTTATGTA
*
54132323 AATTATGTA
1 AGTTATGTA
54132332 AGTTATGTA
1 AGTTATGTA
* *
54132341 AGTAATAT-
1 AGTTATGTA
54132349 A-TTATGTA
1 AGTTATGTA
*
54132357 AGTTGTGTATA
1 AGTTATG--TA
*
54132368 ATGTAAT-TA
1 A-GTTATGTA
54132377 AGTTATGTA
1 AGTTATGTA
*
54132386 AG-T-TGCA
1 AGTTATGTA
54132393 AGTTATGT-
1 AGTTATGTA
54132401 A-TTATGTA
1 AGTTATGTA
*
54132409 AGTTATTTA
1 AGTTATGTA
*
54132418 AGTTATATA
1 AGTTATGTA
*
54132427 AGTTGTGT-
1 AGTTATGTA
*
54132435 A-TTATGTG
1 AGTTATGTA
*
54132443 AGTTATGCA
1 AGTTATGTA
*
54132452 ATTTATGTA
1 AGTTATGTA
* * *
54132461 GGCTATAT-
1 AGTTATGTA
54132469 A-TTATGTA
1 AGTTATGTA
54132477 AGTTAT-TA
1 AGTTATGTA
*
54132485 TGTTATTATGTA
1 AG---TTATGTA
*
54132497 AGTTATGCA
1 AGTTATGTA
54132506 AGTT
1 AGTT
54132510 TAATTATATA
Statistics
Matches: 170, Mismatches: 39, Indels: 42
0.68 0.16 0.17
Matches are distributed among these distances:
7 29 0.17
8 22 0.13
9 100 0.59
10 6 0.04
11 7 0.04
12 6 0.04
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (9 bp):
AGTTATGTA
Found at i:54132352 original size:25 final size:25
Alignment explanation
Indices: 54132324--54132388 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
54132314 AATTATGTAA
54132324 ATTATGTAAGTTATGTAAGTAATAT
1 ATTATGTAAGTTATGTAAGTAATAT
* *
54132349 ATTATGTAAGTTGTGT-A-TAATGT
1 ATTATGTAAGTTATGTAAGTAATAT
54132372 A--AT-TAAGTTATGTAAGT
1 ATTATGTAAGTTATGTAAGT
54132389 TGCAAGTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 9 0.26
21 3 0.09
22 1 0.03
23 6 0.17
24 1 0.03
25 15 0.43
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (25 bp):
ATTATGTAAGTTATGTAAGTAATAT
Found at i:54132440 original size:41 final size:42
Alignment explanation
Indices: 54132305--54132441 Score: 125
Period size: 41 Copynumber: 3.2 Consensus size: 42
54132295 TATATTTATG
* * **
54132305 TATTACGTAAATTATGTAAATTATGTAAGTTATGTAAGTAATA
1 TATTATGT-AATTATGTAAATTATTTAAGTTATGTAAGTTGTA
* * *
54132348 TATTATGTAAGTTGTGTATAATGTAATTAAGTTATGTAAGTTGCA
1 TATTATGTAA-TTATGTA-AAT-TATTTAAGTTATGTAAGTTGTA
* * *
54132393 -AGTTATGT-ATTATGTAAGTTATTTAAGTTATATAAGTTGTG
1 TA-TTATGTAATTATGTAAATTATTTAAGTTATGTAAGTTGTA
54132434 TATTATGT
1 TATTATGT
54132442 GAGTTATGCA
Statistics
Matches: 76, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
41 24 0.32
42 5 0.07
43 19 0.25
44 5 0.07
45 23 0.30
ACGTcount: A:0.35, C:0.01, G:0.18, T:0.46
Consensus pattern (42 bp):
TATTATGTAATTATGTAAATTATTTAAGTTATGTAAGTTGTA
Found at i:54132572 original size:29 final size:29
Alignment explanation
Indices: 54132536--54132697 Score: 126
Period size: 29 Copynumber: 5.8 Consensus size: 29
54132526 TCTATATAAT
54132536 TAAGTTTATTTTACTTACTTCATTATATAG
1 TAAGTTTATTTTACTTACTT-ATTATATAG
* * *
54132566 TCA-TTTATTTTACATACTTA-TATA-AT
1 TAAGTTTATTTTACTTACTTATTATATAG
* * * *
54132592 TAAGTTTA-TATA-TAAGTT-TCTATATAAT
1 TAAGTTTATTTTACTTACTTAT-TATAT-AG
54132620 TAAGTTTATTTTACTTACTTAATTATATAG
1 TAAGTTTATTTTACTTACTT-ATTATATAG
* *
54132650 TCA-TTTATTTTACTTACTTA-TATA-AT
1 TAAGTTTATTTTACTTACTTATTATATAG
* *
54132676 TAAGTTTAATTTACTTAATTAT
1 TAAGTTTATTTTACTTACTTAT
54132698 ATAGTTATTT
Statistics
Matches: 104, Mismatches: 17, Indels: 24
0.72 0.12 0.17
Matches are distributed among these distances:
25 3 0.03
26 13 0.12
27 27 0.26
28 12 0.12
29 34 0.33
30 9 0.09
31 5 0.05
32 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (29 bp):
TAAGTTTATTTTACTTACTTATTATATAG
Found at i:54132605 original size:16 final size:15
Alignment explanation
Indices: 54132583--54132626 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
54132573 TTTTACATAC
54132583 TTATATAATTAAG-T
1 TTATATAATTAAGTT
54132597 TTATAT-A-TAAGTT
1 TTATATAATTAAGTT
54132610 TCTATATAATTAAGTT
1 T-TATATAATTAAGTT
54132626 T
1 T
54132627 ATTTTACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.15
13 3 0.12
14 11 0.42
15 1 0.04
16 7 0.27
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (15 bp):
TTATATAATTAAGTT
Found at i:54132608 original size:84 final size:84
Alignment explanation
Indices: 54132513--54132683 Score: 324
Period size: 84 Copynumber: 2.0 Consensus size: 84
54132503 GCAAGTTTAA
*
54132513 TTATATATAAGTTTCTATATAATTAAGTTTATTTTACTTACTTCATTATATAGTCATTTATTTTA
1 TTATATATAAGTTTCTATATAATTAAGTTTATTTTACTTACTTAATTATATAGTCATTTATTTTA
54132578 CATACTTATATAATTAAGT
66 CATACTTATATAATTAAGT
54132597 TTATATATAAGTTTCTATATAATTAAGTTTATTTTACTTACTTAATTATATAGTCATTTATTTTA
1 TTATATATAAGTTTCTATATAATTAAGTTTATTTTACTTACTTAATTATATAGTCATTTATTTTA
*
54132662 CTTACTTATATAATTAAGT
66 CATACTTATATAATTAAGT
54132681 TTA
1 TTA
54132684 ATTTACTTAA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.53
Consensus pattern (84 bp):
TTATATATAAGTTTCTATATAATTAAGTTTATTTTACTTACTTAATTATATAGTCATTTATTTTA
CATACTTATATAATTAAGT
Found at i:54134268 original size:21 final size:22
Alignment explanation
Indices: 54134244--54134297 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
54134234 AAACTTAAAT
*
54134244 TAAACCCTAAACCC-TAAATTA
1 TAAACCCTAAACCCGTAAACTA
*
54134265 TAAA--CTATAACCCGTAAACTG
1 TAAACCCTA-AACCCGTAAACTA
54134286 TAAACCCTAAAC
1 TAAACCCTAAAC
54134298 TATAAACAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
19 3 0.11
20 5 0.19
21 13 0.48
22 3 0.11
23 3 0.11
ACGTcount: A:0.46, C:0.28, G:0.04, T:0.22
Consensus pattern (22 bp):
TAAACCCTAAACCCGTAAACTA
Found at i:54134310 original size:14 final size:14
Alignment explanation
Indices: 54134265--54134326 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
54134255 CCCTAAATTA
*
54134265 TAAACTATAACCCG
1 TAAACTATAAACCG
* *
54134279 TAAACTGTAAACCC
1 TAAACTATAAACCG
*
54134293 TAAACTATAAACAG
1 TAAACTATAAACCG
*
54134307 TAAACCTGTAAACCG
1 TAAA-CTATAAACCG
*
54134322 CAAAC
1 TAAAC
54134327 ACCAACCACC
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
14 27 0.71
15 11 0.29
ACGTcount: A:0.47, C:0.26, G:0.08, T:0.19
Consensus pattern (14 bp):
TAAACTATAAACCG
Found at i:54134341 original size:22 final size:22
Alignment explanation
Indices: 54134316--54134360 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
54134306 GTAAACCTGT
54134316 AAACCGCAAACA-CCAACCACCA
1 AAACCGCAAA-ATCCAACCACCA
* *
54134338 AAACCTCAAAATCCAACCCCCA
1 AAACCGCAAAATCCAACCACCA
54134360 A
1 A
54134361 TATACCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.49, C:0.44, G:0.02, T:0.04
Consensus pattern (22 bp):
AAACCGCAAAATCCAACCACCA
Found at i:54134476 original size:15 final size:15
Alignment explanation
Indices: 54134436--54134477 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54134426 ATTGTAAATT
*
54134436 GTAAACCCTAAA-CC
1 GTAAACCATAAACCC
54134450 GTAAA-CATTAAACCC
1 GTAAACCA-TAAACCC
54134465 GTAAACCATAAAC
1 GTAAACCATAAAC
54134478 ACCAATCAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.04
14 9 0.38
15 12 0.50
16 2 0.08
ACGTcount: A:0.48, C:0.29, G:0.07, T:0.17
Consensus pattern (15 bp):
GTAAACCATAAACCC
Found at i:54134476 original size:22 final size:21
Alignment explanation
Indices: 54134437--54134478 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
54134427 TTGTAAATTG
*
54134437 TAAACCCTAAACCGTAAACAT
1 TAAACCCTAAACCATAAACAT
54134458 TAAACCCGTAAACCATAAACA
1 TAAACCC-TAAACCATAAACA
54134479 CCAATCAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.50, C:0.29, G:0.05, T:0.17
Consensus pattern (21 bp):
TAAACCCTAAACCATAAACAT
Found at i:54135109 original size:72 final size:71
Alignment explanation
Indices: 54135006--54135504 Score: 446
Period size: 72 Copynumber: 6.9 Consensus size: 71
54134996 TCAAGAAAAA
* * * * * *
54135006 CGCCGCTAATACCACTGCATCTCAAATCAAAATGATGCGTTTTAATTATTTTTTGCGGCGTTTTT
1 CGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGATT-TTTTTTGTGGCGCTTTT
54135071 ACAGAAG
65 ACAGAAG
* * * * *
54135078 CACCGCTAATGCCACTAAATCTGAAACCAAAACGATGCGTTTTGGTTTTTTTTGGTGGCGCTTTT
1 CGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGATTTTTTTT-GTGGCGCTTTT
54135143 ACAGAAG
65 ACAGAAG
* * *
54135150 CGCCGCTAATGCCACTACATCTCATATCAAAACGATGCGTTTTGGTTTGTTTTTTGTGGCGCTTA
1 CGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTT-GATT-TTTTTTGTGGCGCTTT
54135215 TACAGAAG
64 TACAGAAG
* * * * **
54135223 CGCCACTAATGCCACTACATCTCAAATCAAAACGATGTGTTTTGGTTATTCCTTACT-GCGCTTT
1 CGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGATT-TT-TTTTGTGGCGCTTT
**
54135287 TATGGAAG
64 TACAGAAG
* * * * * *
54135295 CGCCGCTAATGCAACTACATCCCAAATAAAAACGATGTGTTTTGATTATTATTTG-CGCTGCTTT
1 CGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGATT-TTTTTTGTGGC-GCTTT
*** *
54135359 TGTGGAAT
64 TACAGAAG
* * * * *
54135367 CGCCGCTAATGCCACAACATCTCAAATCAAAACGAAGCGTTTGGGTTATTTTTTGTTGCGGCGTT
1 CGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTT---TGATTTTTT-TTGTGGCGCT
*
54135432 TTTAC-GGAG
62 TTTACAGAAG
* * * * * * * *
54135441 TAGTCACTAATCCCACTACAACTCAAATCAAAACGATGCGTTTGGATTTTTTTTGCGGTGCTTT
1 -CGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGATTTTTTTTGTGGCGCTTT
54135505 ATCGAAAATG
Statistics
Matches: 351, Mismatches: 64, Indels: 25
0.80 0.15 0.06
Matches are distributed among these distances:
71 20 0.06
72 208 0.59
73 63 0.18
74 11 0.03
75 47 0.13
76 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (71 bp):
CGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGATTTTTTTTGTGGCGCTTTTA
CAGAAG
Found at i:54135268 original size:145 final size:143
Alignment explanation
Indices: 54135006--54135504 Score: 500
Period size: 145 Copynumber: 3.4 Consensus size: 143
54134996 TCAAGAAAAA
* * * * *
54135006 CGCCGCTAATACCACTGCATCTCAAATCAAAATGATGCGTTTTAATTATTTTTTGCGGCGTTTTT
1 CGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGATTATTTTTTG-GGCGCTTTT
* * * *
54135071 ACAGAAGCACCGCTAATGCCACTAAATCTGAAACCAAAACGATGCGTTTTGGTT-TTTTTTGGTG
65 ACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTATTTTTTGGTG
54135135 GCGCTTTTACAGAAG
130 GCGCTTTTAC-GAAG
* * * *
54135150 CGCCGCTAATGCCACTACATCTCATATCAAAACGATGCGTTTTGGTTTGTTTTTTGTGGCGCTTA
1 CGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTT-GATTATTTTTTG-GGCGCTTT
* * ** **
54135215 TACAGAAGCGCCACTAATGCCACTACATCTCAAATCAAAACGATGTGTTTTGGTTATTCCTTACT
64 TACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTATTTTTTGGT
*
54135280 -GCGCTTTTATGGAAG
129 GGCGCTTTTA-CGAAG
* * * * * *
54135295 CGCCGCTAATGCAACTACATCCCAAATAAAAACGATGTGTTTTGATTATTATTTGCGCTGCTTTT
1 CGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGATTATTTTTTGGGC-GCTTTT
*** * * * *
54135360 GTGGAATCGCCGCTAATGCCACAACATCTCAAATCAAAACGAAGCGTTTGGGTTATTTTTTGTTG
65 ACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTATTTTTTG--G
* * *
54135425 CGGCGTTTTTACGGAG
128 TGGCGCTTTTACGAAG
* * * * * * *
54135441 TAGTCACTAATCCCACTACAACTCAAATCAAAACGATGCGTTTGGATT-TTTTTTGCGGTGCTTT
1 -CGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGATTATTTTTTG-GGCGCTTT
54135505 ATCGAAAATG
Statistics
Matches: 285, Mismatches: 61, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
143 2 0.01
144 103 0.36
145 115 0.40
146 19 0.07
147 46 0.16
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (143 bp):
CGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGATTATTTTTTGGGCGCTTTTA
CAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGGTTATTTTTTGGTGG
CGCTTTTACGAAG
Found at i:54135614 original size:41 final size:40
Alignment explanation
Indices: 54135569--54135660 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 40
54135559 GGTTTTTTGT
*
54135569 GGCGTTTTCTCCAGATTCGCCGCTAAAT-TCATATTATTAGC
1 GGCGTTTTCTCCAGAATCGCCG-TAAATCTC-TATTATTAGC
* * * *
54135610 GGCGTTTACT-TAGAATCGCCGTTAATGCTCTATTTTTAGC
1 GGCGTTTTCTCCAGAATCGCCGTAAAT-CTCTATTATTAGC
54135650 GGCGTTTTCTC
1 GGCGTTTTCTC
54135661 TGATGCGCCG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
39 4 0.10
40 27 0.64
41 11 0.26
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (40 bp):
GGCGTTTTCTCCAGAATCGCCGTAAATCTCTATTATTAGC
Found at i:54135670 original size:40 final size:40
Alignment explanation
Indices: 54135600--54135694 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
54135590 GCTAAATTCA
* *
54135600 TATTATTAGCGGCGTTTACTTAGAATCGCCGTTAATGCTC
1 TATTTTTAGCGGCGTTTACTTAGAATCGCCGTTAATACTC
*
54135640 TATTTTTAGCGGCGTTTTCTCT-G-ATGCGCCGTTAATACTC
1 TATTTTTAGCGGCGTTTACT-TAGAAT-CGCCGTTAATACTC
* *
54135680 GATTTTTACCGGCGT
1 TATTTTTAGCGGCGT
54135695 CTGTTATCCA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.04
40 45 0.94
41 1 0.02
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (40 bp):
TATTTTTAGCGGCGTTTACTTAGAATCGCCGTTAATACTC
Found at i:54141304 original size:40 final size:40
Alignment explanation
Indices: 54141232--54141351 Score: 116
Period size: 40 Copynumber: 3.0 Consensus size: 40
54141222 CATACGTGTA
* * * *
54141232 TATATATATTCATATATTTTAA-TTCATGTACATATATATG
1 TATATATATACATATTTTTTAACTT-GTATACATATATATG
* * * *
54141272 TATATATATACTTATTTTTTAACTTGTATACATGTCTATA
1 TATATATATACATATTTTTTAACTTGTATACATATATATG
* * * *
54141312 TATTTATGTACATATTTTTTAACTTTTATAAATATATATG
1 TATATATATACATATTTTTTAACTTGTATACATATATATG
54141352 CATACTTGAA
Statistics
Matches: 63, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 61 0.97
41 2 0.03
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (40 bp):
TATATATATACATATTTTTTAACTTGTATACATATATATG
Found at i:54141387 original size:24 final size:24
Alignment explanation
Indices: 54141323--54141394 Score: 72
Period size: 28 Copynumber: 2.8 Consensus size: 24
54141313 ATTTATGTAC
* * *
54141323 ATATTTTTTAACTTTTATAAATAT
1 ATATCTTTTAATTTTTATATATAT
*
54141347 ATATGCATACTTGAATTTTTATATATAT
1 ATAT-C-T--TTTAATTTTTATATATAT
54141375 ATATCTTTTAATTTTTATAT
1 ATATCTTTTAATTTTTATAT
54141395 GTGTGTACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
24 17 0.44
26 2 0.05
27 1 0.03
28 19 0.49
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.57
Consensus pattern (24 bp):
ATATCTTTTAATTTTTATATATAT
Found at i:54141527 original size:12 final size:13
Alignment explanation
Indices: 54141510--54141538 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
54141500 GTTTTAATAT
54141510 TATTTG-TTTGTA
1 TATTTGTTTTGTA
54141522 TATTTGTTTTGTA
1 TATTTGTTTTGTA
54141535 TATT
1 TATT
54141539 ATGGGTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (13 bp):
TATTTGTTTTGTA
Found at i:54143429 original size:23 final size:23
Alignment explanation
Indices: 54143383--54143429 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
54143373 CACCTATATA
*
54143383 AGCATATAAGCAATCAGAACATT
1 AGCATATAAGCAATCAGAAAATT
54143406 AGCATATAAGCAATCA-AATAATT
1 AGCATATAAGCAATCAGAA-AATT
54143429 A
1 A
54143430 AATGTAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.51, C:0.15, G:0.11, T:0.23
Consensus pattern (23 bp):
AGCATATAAGCAATCAGAAAATT
Found at i:54145656 original size:12 final size:13
Alignment explanation
Indices: 54145639--54145699 Score: 63
Period size: 13 Copynumber: 4.6 Consensus size: 13
54145629 AAAAGGTATT
54145639 TAATAATATTAGTAA
1 TAATAATA-TA-TAA
**
54145654 TAATAAT-GCTAA
1 TAATAATATATAA
54145666 TAATAATATATAA
1 TAATAATATATAA
54145679 TAATAATA-ATAA
1 TAATAATATATAA
54145691 TAAATAATA
1 T-AATAATA
54145700 GCACACATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 15 0.38
13 18 0.45
15 7 0.17
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (13 bp):
TAATAATATATAA
Found at i:54145657 original size:3 final size:3
Alignment explanation
Indices: 54145639--54145699 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
54145629 AAAAGGTATT
* * **
54145639 TAA TAA TAT TAG TAA TAA TAA TGC TAA TAA TAA TATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
54145685 TAA TAA TAAA TAA TA
1 TAA TAA T-AA TAA TA
54145700 GCACACATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:54145684 original size:16 final size:16
Alignment explanation
Indices: 54145663--54145699 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
54145653 ATAATAATGC
54145663 TAATAATAAT-ATATAA
1 TAATAATAATAATA-AA
54145679 TAATAATAATAATAAA
1 TAATAATAATAATAAA
54145695 TAATA
1 TAATA
54145700 GCACACATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATAATAATAATAAA
Found at i:54146216 original size:2 final size:2
Alignment explanation
Indices: 54146211--54146239 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
54146201 AAAAAAAAAC
54146211 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
54146240 TGCTCTCTCA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:54146494 original size:16 final size:17
Alignment explanation
Indices: 54146468--54146499 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
54146458 CAAGTAAGGC
54146468 TTTTCCTTTTCTTTTTG
1 TTTTCCTTTTCTTTTTG
54146485 TTTT-CTTTTCTTTTT
1 TTTTCCTTTTCTTTTT
54146500 AGTATGAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (17 bp):
TTTTCCTTTTCTTTTTG
Found at i:54155379 original size:3 final size:3
Alignment explanation
Indices: 54155366--54155396 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
54155356 CAACATCCAT
54155366 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
54155397 AATATGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:54162259 original size:3 final size:3
Alignment explanation
Indices: 54162251--54162287 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
54162241 CCGTATGAAC
54162251 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
54162288 GCTCCTGCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:54163930 original size:21 final size:21
Alignment explanation
Indices: 54163904--54163948 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
54163894 ACAAGGAAAC
*
54163904 AAAACAACAAGGAAAGAAATA
1 AAAACAACAAGGAAAGAAAGA
* *
54163925 AAAACAGCAAGGATAGAAAGA
1 AAAACAACAAGGAAAGAAAGA
54163946 AAA
1 AAA
54163949 TCAAAGATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.69, C:0.09, G:0.18, T:0.04
Consensus pattern (21 bp):
AAAACAACAAGGAAAGAAAGA
Found at i:54164172 original size:23 final size:23
Alignment explanation
Indices: 54164128--54164173 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
54164118 TACTTGTATT
*
54164128 TCTATTTTATTTTTTCCGTTATA
1 TCTATTTTATTTTTTCAGTTATA
*
54164151 TCTA-TTTATTTTTATCATTTATA
1 TCTATTTTATTTTT-TCAGTTATA
54164174 AATAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.65
Consensus pattern (23 bp):
TCTATTTTATTTTTTCAGTTATA
Found at i:54167528 original size:23 final size:22
Alignment explanation
Indices: 54167485--54167530 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
54167475 TGTTTGTTTA
54167485 TATAAAAATGATATATATTATT
1 TATAAAAATGATATATATTATT
*
54167507 TATAAATAAT-ATAATATTTTATT
1 TATAAA-AATGAT-ATATATTATT
54167530 T
1 T
54167531 TGAGACCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TATAAAAATGATATATATTATT
Found at i:54177185 original size:28 final size:26
Alignment explanation
Indices: 54177140--54177213 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 26
54177130 TTCAGTTTAC
* * * *
54177140 ACTAACTAAAGTATTTTCAGTACAGTTT
1 ACTATCTATAGTAGTTTCAGTA-A-TAT
54177168 ACTATCTATAGTAGTTTCAG-AATAT
1 ACTATCTATAGTAGTTTCAGTAATAT
* *
54177193 ACTATCCATAATAGTTTCAGT
1 ACTATCTATAGTAGTTTCAGT
54177214 TTAAAACAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 20 0.51
26 1 0.03
27 1 0.03
28 17 0.44
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (26 bp):
ACTATCTATAGTAGTTTCAGTAATAT
Found at i:54181479 original size:3 final size:3
Alignment explanation
Indices: 54181471--54181497 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
54181461 AACAAGCTTA
54181471 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
54181498 TCGCATGGTG
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:54186926 original size:17 final size:17
Alignment explanation
Indices: 54186900--54186935 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
54186890 TAATATCCAT
*
54186900 AATTTGAATTAAATTTA
1 AATTTAAATTAAATTTA
*
54186917 AATTTAAATTAAGTTTA
1 AATTTAAATTAAATTTA
54186934 AA
1 AA
54186936 ATATTTAACA
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:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
AATTTAAATTAAATTTA
Found at i:54191618 original size:50 final size:50
Alignment explanation
Indices: 54191466--54191752 Score: 236
Period size: 50 Copynumber: 5.6 Consensus size: 50
54191456 GATAATAACA
* * * * * * * *
54191466 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTTC-TGT-AC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGA-CTTCTCATCTCAG
* * * * * * * *
54191515 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACTTCTCATCTCAG
* * * * *
54191565 TGCCCATGCCATGTCTCAGACATGGTCTTACGGGGGACTTTTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACTTCTCATCTCAG
* * * *
54191615 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACTTCTCATCTCAG
* * *
54191665 TGCCAACGTCATGTCCCAGACATGGTCTTACAGGGGGCCTCTCATAATCTCAATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACA-GGGGACT-TC-TCATCTC-A-G
*
54191720 ATGCCAATGCCATGTCCCAGACATGGTCTTACA
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACA
54191753 CTGGCTCACA
Statistics
Matches: 191, Mismatches: 39, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
48 5 0.03
49 33 0.17
50 110 0.58
51 4 0.02
52 2 0.01
53 6 0.03
55 1 0.01
56 30 0.16
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.29
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACTTCTCATCTCAG
Found at i:54191648 original size:100 final size:106
Alignment explanation
Indices: 54191528--54191800 Score: 294
Period size: 100 Copynumber: 2.7 Consensus size: 106
54191518 CAATGTCATA
* ** * * *
54191528 TCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCTCAGACATGGTCT
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGACATGGTCT
* *
54191593 TAC-GGGGGACT-T-TTCATCTC-A-G-TGCCAACGCCATG
66 TACAGGGGGACTCTCATAATCTCAATGATGCCAACGCCATG
* * *
54191628 TCCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGTCATGTCCCAGACATGGTCT
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGACATGGTCT
* *
54191693 TACAGGGGGCCTCTCATAATCTCAATGATGCCAATGCCATG
66 TACAGGGGGACTCTCATAATCTCAATGATGCCAACGCCATG
* * * * * * *
54191734 TCCCAGACATGGTCTTACACT-GG--CTCACATACCGATGTCGATGCCATGTCCCAAACATGGTC
1 TCCCAGACATGGTCTTACA-TGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGACATGGTC
54191796 TTACA
65 TTACA
54191801 CTAGCTCACA
Statistics
Matches: 143, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
100 59 0.41
101 7 0.05
102 1 0.01
103 6 0.04
104 36 0.25
105 1 0.01
106 32 0.22
107 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (106 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGACATGGTCT
TACAGGGGGACTCTCATAATCTCAATGATGCCAACGCCATG
Found at i:54191797 original size:48 final size:48
Alignment explanation
Indices: 54191726--54191846 Score: 206
Period size: 48 Copynumber: 2.5 Consensus size: 48
54191716 AATGATGCCA
* *
54191726 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATACCGATGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATACCGATCTCG
* *
54191774 ATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGATCTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATACCGATCTCG
54191822 ATGCCATGTCCCAGACATGGTCTTA
1 ATGCCATGTCCCAGACATGGTCTTA
54191847 TATGAGATCG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 68 1.00
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATACCGATCTCG
Found at i:54192568 original size:22 final size:22
Alignment explanation
Indices: 54192537--54192609 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 22
54192527 TAATTTAAAA
*
54192537 TGAAATCCCAATTTGTCGTAAT
1 TGAAAGCCCAATTTGTCGTAAT
*
54192559 TGAAAGCCCAA-TT-AC--AA-
1 TGAAAGCCCAATTTGTCGTAAT
**
54192576 -GAAATTCCAATTTGTCGTAAT
1 TGAAAGCCCAATTTGTCGTAAT
54192597 TGAAAGCCCAATT
1 TGAAAGCCCAATT
54192610 ACAAGAAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
16 8 0.21
17 2 0.05
18 3 0.08
20 3 0.08
21 2 0.05
22 20 0.53
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (22 bp):
TGAAAGCCCAATTTGTCGTAAT
Found at i:54192580 original size:38 final size:38
Alignment explanation
Indices: 54192538--54192630 Score: 177
Period size: 38 Copynumber: 2.4 Consensus size: 38
54192528 AATTTAAAAT
*
54192538 GAAATCCCAATTTGTCGTAATTGAAAGCCCAATTACAA
1 GAAATTCCAATTTGTCGTAATTGAAAGCCCAATTACAA
54192576 GAAATTCCAATTTGTCGTAATTGAAAGCCCAATTACAA
1 GAAATTCCAATTTGTCGTAATTGAAAGCCCAATTACAA
54192614 GAAATTCCAATTTGTCG
1 GAAATTCCAATTTGTCG
54192631 AATCCATTGG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (38 bp):
GAAATTCCAATTTGTCGTAATTGAAAGCCCAATTACAA
Found at i:54195977 original size:29 final size:29
Alignment explanation
Indices: 54195920--54195978 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
54195910 CAATGTTTAC
* *
54195920 TTTTCAAAATGAATCATTTACGTACATAA
1 TTTTCAAAATGAATCATTTACATAAATAA
* * *
54195949 TTTTCAAAGTGGATCATTTTCATAAATAA
1 TTTTCAAAATGAATCATTTACATAAATAA
54195978 T
1 T
54195979 CAAAATTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (29 bp):
TTTTCAAAATGAATCATTTACATAAATAA
Found at i:54196894 original size:29 final size:29
Alignment explanation
Indices: 54196828--54196893 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
54196818 GTAATTTACC
**
54196828 AATATATATACATTTATTATCTGTTTTAA
1 AATATATATACATTTATTATCTGTGATAA
*
54196857 AAAATATATACATTTATTAT-TG-GATAA
1 AATATATATACATTTATTATCTGTGATAA
*
54196884 AATTTATATA
1 AATATATATA
54196894 TTTAATTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 11 0.34
28 2 0.06
29 19 0.59
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (29 bp):
AATATATATACATTTATTATCTGTGATAA
Found at i:54200057 original size:52 final size:52
Alignment explanation
Indices: 54199953--54200057 Score: 124
Period size: 52 Copynumber: 2.0 Consensus size: 52
54199943 CTGACTTGCT
* * * *
54199953 AACATGCATTAAGTCTATCCGAATTATAACATATTTAATAAGAATGACTCAA
1 AACATGCATTAAGTCTATCCGAATTAGAACATACTTAATAAGAATAAATCAA
* *
54200005 AACATGCATTGA-TGCTATCCTAATTAGAACATACTTAAT-AGACATAAATCAA
1 AACATGCATTAAGT-CTATCCGAATTAGAACATACTTAATAAGA-ATAAATCAA
54200057 A
1 A
54200058 GTAAAATACC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 4 0.09
52 41 0.91
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.30
Consensus pattern (52 bp):
AACATGCATTAAGTCTATCCGAATTAGAACATACTTAATAAGAATAAATCAA
Found at i:54219616 original size:22 final size:23
Alignment explanation
Indices: 54219585--54219633 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
54219575 CTTTATGAAA
54219585 TTTTCAAAAAATTTAACTAATT-
1 TTTTCAAAAAATTTAACTAATTC
* *
54219607 TTTTCTAAAATTTTAACTAATTC
1 TTTTCAAAAAATTTAACTAATTC
54219630 TTTT
1 TTTT
54219634 TATATTTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTCAAAAAATTTAACTAATTC
Found at i:54219925 original size:12 final size:12
Alignment explanation
Indices: 54219908--54219937 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
54219898 AATTTTATTC
*
54219908 CATATATATATA
1 CATATATATAAA
54219920 CATATATATAAA
1 CATATATATAAA
54219932 CATATA
1 CATATA
54219938 ACCAATTAAA
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:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (12 bp):
CATATATATAAA
Found at i:54220273 original size:22 final size:22
Alignment explanation
Indices: 54220247--54220292 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
54220237 ATTTTCACAC
54220247 CAAAATTTGGACAGCATATATA
1 CAAAATTTGGACAGCATATATA
* *
54220269 CAAAATTTGGACTGCATTTATA
1 CAAAATTTGGACAGCATATATA
54220291 CA
1 CA
54220293 TCAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (22 bp):
CAAAATTTGGACAGCATATATA
Found at i:54220411 original size:95 final size:93
Alignment explanation
Indices: 54220247--54220457 Score: 332
Period size: 95 Copynumber: 2.2 Consensus size: 93
54220237 ATTTTCACAC
* * *
54220247 CAAAATTTGGACAGCATATATACAAAATTTGGACTGCATTTATACATCAAAATTTAACAGCATAT
1 CAAAATTT-GACAGCATATACATAAAAATTGGACTGCATTTATACATCAAAATTTAACAGCATAT
54220312 ACATATATAATTGGACTGCATTTATACAT
65 ACATATATAATTGGACTGCATTTATACAT
* * *
54220341 CAAAATTTGACAGCATATACATAAATAATTGGATTGCATTTTGTACATCAAAATTTGACAGCATA
1 CAAAATTTGACAGCATATACATAAA-AATTGGACTGCA-TTTATACATCAAAATTTAACAGCATA
*
54220406 TACATATATAATTGGACTGCATTTGTACAT
64 TACATATATAATTGGACTGCATTTATACAT
54220436 CAAAATTTGACAGCATATACAT
1 CAAAATTTGACAGCATATACAT
54220458 TCATTTACTC
Statistics
Matches: 108, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
93 15 0.14
94 18 0.17
95 75 0.69
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (93 bp):
CAAAATTTGACAGCATATACATAAAAATTGGACTGCATTTATACATCAAAATTTAACAGCATATA
CATATATAATTGGACTGCATTTATACAT
Found at i:54220455 original size:47 final size:47
Alignment explanation
Indices: 54220247--54220457 Score: 318
Period size: 47 Copynumber: 4.5 Consensus size: 47
54220237 ATTTTCACAC
* *
54220247 CAAAATTTGGACAGCATAT--ATACAAAATTTGGACTGCATTTATACAT
1 CAAAATTT-GACAGCATATACATATATAA-TTGGACTGCATTTATACAT
*
54220294 CAAAATTTAACAGCATATACATATATAATTGGACTGCATTTATACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* * *
54220341 CAAAATTTGACAGCATATACATAAATAATTGGATTGCATTTTGTACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCA-TTTATACAT
*
54220389 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
54220436 CAAAATTTGACAGCATATACAT
1 CAAAATTTGACAGCATATACAT
54220458 TCATTTACTC
Statistics
Matches: 152, Mismatches: 9, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
46 9 0.06
47 93 0.61
48 50 0.33
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (47 bp):
CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
Found at i:54220743 original size:15 final size:15
Alignment explanation
Indices: 54220709--54220740 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
54220699 TATATACATT
54220709 ACCATATAAATACTA
1 ACCATATAAATACTA
54220724 ACCATA-AAATACTA
1 ACCATATAAATACTA
54220738 ACC
1 ACC
54220741 CATGATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:54221473 original size:43 final size:43
Alignment explanation
Indices: 54221426--54221508 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
54221416 AATCACATAC
54221426 CGATGCC-ACTATCCCAAACAG-GGTCTTACACGAAAACACAAGT
1 CGATGCCGAC-ATCCCAAAC-GTGGTCTTACACGAAAACACAAGT
* * *
54221469 CGATGCCGACGTCCCAGACGTGGTCTTACATGAAAACACA
1 CGATGCCGACATCCCAAACGTGGTCTTACACGAAAACACA
54221509 TATCGGAGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 1 0.03
43 32 0.91
44 2 0.06
ACGTcount: A:0.34, C:0.30, G:0.19, T:0.17
Consensus pattern (43 bp):
CGATGCCGACATCCCAAACGTGGTCTTACACGAAAACACAAGT
Found at i:54222450 original size:12 final size:12
Alignment explanation
Indices: 54222433--54222463 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
54222423 TATTAACCTT
54222433 TATATAAATATA
1 TATATAAATATA
*
54222445 TATATACATATA
1 TATATAAATATA
54222457 TATATAA
1 TATATAA
54222464 GGCTATACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATAAATATA
Found at i:54223525 original size:15 final size:16
Alignment explanation
Indices: 54223499--54223528 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54223489 GATTCAGTTG
54223499 ATTTTGAATTGGATCC
1 ATTTTGAATTGGATCC
54223515 ATTTT-AATTGGATC
1 ATTTTGAATTGGATC
54223529 AACATAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.47
Consensus pattern (16 bp):
ATTTTGAATTGGATCC
Found at i:54225213 original size:14 final size:13
Alignment explanation
Indices: 54225184--54225218 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
54225174 AATTCTCTCT
*
54225184 TAAAATTTTTTAC
1 TAAATTTTTTTAC
54225197 TAAATTTTTTTATC
1 TAAATTTTTTTA-C
54225211 TAAATTTT
1 TAAATTTT
54225219 ATTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATTTTTTTAC
Done.