Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 4 of 279
Found at i:1005420 original size:49 final size:49
Alignment explanation
Indices: 1005346--1005572 Score: 251
Period size: 49 Copynumber: 4.6 Consensus size: 49
1005336 ATCTGGTACG
*
1005346 CATAGTAGCCTACACTTAGTACTACACATGCGACCAATTAT-GCAATACA
1 CATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCG-AATACA
* * * **
1005395 CGTAGTAGCCTGCACTTAATACTACACATGTGACCTAACCATCTG-ATACA
1 CATAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATC-GAATACA
* * * * * ** *
1005445 CGTAGTAACCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACG
1 CATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCGAATACA
* *
1005496 CATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACA
1 CATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCGAATACA
1005545 CATAGTAGCCTGCACTTAGTACTACACA
1 CATAGTAGCCTGCACTTAGTACTACACA
1005573 CGTGACCTCA
Statistics
Matches: 150, Mismatches: 22, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
49 68 0.45
50 45 0.30
51 36 0.24
52 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (49 bp):
CATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCGAATACA
Found at i:1005572 original size:26 final size:26
Alignment explanation
Indices: 1005496--1005572 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 26
1005486 ATCGGGTACG
1005496 CATAGTAGCCTGCACTTAGTACTACA
1 CATAGTAGCCTGCACTTAGTACTACA
* * * *
1005522 CAT-G-CGAC--CAATTA-TCCAGTACA
1 CATAGTAGCCTGCACTTAGT--ACTACA
1005545 CATAGTAGCCTGCACTTAGTACTACA
1 CATAGTAGCCTGCACTTAGTACTACA
1005571 CA
1 CA
1005573 CGTGACCTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
21 1 0.03
22 5 0.14
23 8 0.22
24 3 0.08
25 3 0.08
26 10 0.28
27 5 0.14
28 1 0.03
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (26 bp):
CATAGTAGCCTGCACTTAGTACTACA
Found at i:1005850 original size:27 final size:27
Alignment explanation
Indices: 1005820--1005873 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1005810 TCATACAACC
* *
1005820 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
1005847 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
1005874 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:1009228 original size:17 final size:18
Alignment explanation
Indices: 1009206--1009241 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1009196 CACATTGAAG
1009206 TGTTTT-ATCGAAAACCT
1 TGTTTTCATCGAAAACCT
*
1009223 TGTTTTCATTGAAAACCT
1 TGTTTTCATCGAAAACCT
1009241 T
1 T
1009242 TCTTTGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (18 bp):
TGTTTTCATCGAAAACCT
Found at i:1010535 original size:28 final size:28
Alignment explanation
Indices: 1010474--1010567 Score: 102
Period size: 28 Copynumber: 3.3 Consensus size: 28
1010464 GATCCATACT
* * *
1010474 TATTCATTTGGCCCCTTTAGGCCCAATC-
1 TATTCATATGG-CCCATCAGGCCCAATCA
*
1010502 TCATTCATATGGCCTATCAGGCCCAATCA
1 T-ATTCATATGGCCCATCAGGCCCAATCA
*
1010531 TATTCATATGGCCCATCAGGCCTAATCA
1 TATTCATATGGCCCATCAGGCCCAATCA
1010559 CT-TTCATAT
1 -TATTCATAT
1010568 CAGGCCCAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
28 46 0.81
29 11 0.19
ACGTcount: A:0.24, C:0.30, G:0.13, T:0.33
Consensus pattern (28 bp):
TATTCATATGGCCCATCAGGCCCAATCA
Found at i:1010571 original size:21 final size:21
Alignment explanation
Indices: 1010545--1010587 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1010535 CATATGGCCC
* *
1010545 ATCAGGCCTAATCACTTTCAT
1 ATCAGGCCCAATCACATTCAT
1010566 ATCAGGCCCAATCACATTCAT
1 ATCAGGCCCAATCACATTCAT
1010587 A
1 A
1010588 GTCATGCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.30, G:0.09, T:0.28
Consensus pattern (21 bp):
ATCAGGCCCAATCACATTCAT
Found at i:1014201 original size:21 final size:21
Alignment explanation
Indices: 1014177--1014216 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1014167 ATTTCTGACG
1014177 CTGACTTAGGTGTTTTCCAGT
1 CTGACTTAGGTGTTTTCCAGT
1014198 CTGACTTAGGTGTTTTCCA
1 CTGACTTAGGTGTTTTCCA
1014217 ATCTAACACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.42
Consensus pattern (21 bp):
CTGACTTAGGTGTTTTCCAGT
Found at i:1015954 original size:17 final size:18
Alignment explanation
Indices: 1015932--1015965 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1015922 CACATTGAAG
1015932 TGTTTT-ATCGAAAACCT
1 TGTTTTCATCGAAAACCT
*
1015949 TGTTTTCATTGAAAACC
1 TGTTTTCATCGAAAACC
1015966 CTTCTTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (18 bp):
TGTTTTCATCGAAAACCT
Found at i:1017262 original size:28 final size:28
Alignment explanation
Indices: 1017219--1017292 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
1017209 GGCCCCTTTT
*
1017219 GGCCCAATCTCATTCATATGGCCCATC-
1 GGCCCAATCACATTCATATGGCCCATCA
* * *
1017246 GAGCCCAATCACTTTCATGTGGCCCGTCA
1 G-GCCCAATCACATTCATATGGCCCATCA
*
1017275 GGCCCAATTACATTCATA
1 GGCCCAATCACATTCATA
1017293 GTCATGCAAC
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
27 1 0.03
28 36 0.95
29 1 0.03
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (28 bp):
GGCCCAATCACATTCATATGGCCCATCA
Found at i:1024577 original size:17 final size:19
Alignment explanation
Indices: 1024555--1024591 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1024545 TTGGGCTTAT
1024555 TGGG-CCACATGGG-CGTG
1 TGGGCCCACATGGGCCGTG
1024572 TGGGCCCACATGGGCCGTG
1 TGGGCCCACATGGGCCGTG
1024591 T
1 T
1024592 TATGGGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.11, C:0.27, G:0.43, T:0.19
Consensus pattern (19 bp):
TGGGCCCACATGGGCCGTG
Found at i:1025083 original size:33 final size:34
Alignment explanation
Indices: 1025014--1025087 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
1025004 TTGCATTTAA
1025014 GATACTGTTACTGTAATGAGCTAAGGCCCACACT
1 GATACTGTTACTGTAATGAGCTAAGGCCCACACT
*
1025048 GATACTGTTACTGTAATGGGCTAAGG-CCACACT
1 GATACTGTTACTGTAATGAGCTAAGGCCCACACT
1025081 GATACTG
1 GATACTG
1025088 GACTGTCACT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 14 0.36
34 25 0.64
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (34 bp):
GATACTGTTACTGTAATGAGCTAAGGCCCACACT
Found at i:1026234 original size:28 final size:27
Alignment explanation
Indices: 1026184--1026287 Score: 77
Period size: 26 Copynumber: 3.9 Consensus size: 27
1026174 ACTGTAAATG
** ** *
1026184 TGGAAGTCCATCAGGAGGATCTTAAATG
1 TGGAAGTCCGCCAGGACTATCTT-AATA
* *
1026212 TGGTAGTCCGCCAGGACTCTCTT-ATA
1 TGGAAGTCCGCCAGGACTATCTTAATA
* *
1026238 TGGAAGTCTGCCAGGACTATCTT-ATG
1 TGGAAGTCCGCCAGGACTATCTTAATA
* * *
1026264 TGAAAGTCCACCAAGACTATCTTA
1 TGGAAGTCCGCCAGGACTATCTTA
1026288 TTTCGAAAGT
Statistics
Matches: 60, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
26 43 0.72
28 17 0.28
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (27 bp):
TGGAAGTCCGCCAGGACTATCTTAATA
Found at i:1026252 original size:26 final size:26
Alignment explanation
Indices: 1026216--1026309 Score: 98
Period size: 26 Copynumber: 3.6 Consensus size: 26
1026206 TAAATGTGGT
* *
1026216 AGTCCGCCAGGACTCTCTTATATGGA
1 AGTCCGCCAGGACTATCTTATATGAA
* *
1026242 AGTCTGCCAGGACTATCTTATGTGAA
1 AGTCCGCCAGGACTATCTTATATGAA
* * *
1026268 AGTCCACCAAGACTATCTTATTTCGAA
1 AGTCCGCCAGGACTATCTTATAT-GAA
**
1026295 AGTTTGCCAGGACTA
1 AGTCCGCCAGGACTA
1026310 CTATTGTAAG
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
26 41 0.75
27 14 0.25
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (26 bp):
AGTCCGCCAGGACTATCTTATATGAA
Found at i:1030254 original size:29 final size:29
Alignment explanation
Indices: 1030170--1030410 Score: 150
Period size: 29 Copynumber: 8.3 Consensus size: 29
1030160 ATCTCTGAAT
* * *
1030170 GGATGCTTTTATGACTATCTCTATTATAA
1 GGATGCTTTTGTGGCTATCTCTATTAAAA
* * * * * *
1030199 GGAAGCCTTTGAGG-TGACCTTTGTTAAAA
1 GGATGCTTTTGTGGCT-ATCTCTATTAAAA
* *
1030228 GGATGCTTTTGTGGCTATCTCAATTAAAT
1 GGATGCTTTTGTGGCTATCTCTATTAAAA
* *
1030257 GAATG-TCTTTGTGGCTATCTCTATGAAAA
1 GGATGCT-TTTGTGGCTATCTCTATTAAAA
* * * * *
1030286 GGAAGCCTATGTGGCTATCTTTGTTAAAA
1 GGATGCTTTTGTGGCTATCTCTATTAAAA
* * * *
1030315 GGAT-ATCTTGTGGTTATCTCTATCAAAA
1 GGATGCTTTTGTGGCTATCTCTATTAAAA
* * *
1030343 AGATGCCTTTTGTGGTTATCTAT-TTCAAAA
1 GGATG-CTTTTGTGGCTATCTCTATT-AAAA
* * *
1030373 GGATGCCTTTGTGGCCATCTCTGTT-AAA
1 GGATGCTTTTGTGGCTATCTCTATTAAAA
1030401 GGAATGCTTT
1 GG-ATGCTTT
1030411 GTGACAAACT
Statistics
Matches: 155, Mismatches: 48, Indels: 18
0.70 0.22 0.08
Matches are distributed among these distances:
28 26 0.17
29 104 0.67
30 25 0.16
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.39
Consensus pattern (29 bp):
GGATGCTTTTGTGGCTATCTCTATTAAAA
Found at i:1030308 original size:87 final size:88
Alignment explanation
Indices: 1030171--1030410 Score: 222
Period size: 87 Copynumber: 2.8 Consensus size: 88
1030161 TCTCTGAATG
* * * * * *
1030171 GATG-CTTTTATGACTATCTCTATTATAAGGAAGCCTTTGAGG-TGACCTTTGTTAAAAGGATGC
1 GATGCCTTTTGTGGCTATCTCTATCAAAAGGAAGCCTTTGTGGCT-ATCTTTGTTAAAAGGATGC
* *
1030234 TTTTGTGGCTATCTCAAT-TAAAT
65 TTTTGTGGCTATCTCAATCAAAAA
* * * *
1030257 GAATGTC-TTTGTGGCTATCTCTATGAAAAGGAAGCCTATGTGGCTATCTTTGTTAAAAGGAT-A
1 G-ATGCCTTTTGTGGCTATCTCTATCAAAAGGAAGCCTTTGTGGCTATCTTTGTTAAAAGGATGC
* * *
1030320 TCTTGTGGTTATCTCTATCAAAAA
65 TTTTGTGGCTATCTCAATCAAAAA
* * * * * *
1030344 GATGCCTTTTGTGGTTATCTATTTCAAAAGGATGCCTTTGTGGCCATCTCTGTT-AAAGGAATGC
1 GATGCCTTTTGTGGCTATCTCTATCAAAAGGAAGCCTTTGTGGCTATCTTTGTTAAAAGG-ATGC
1030408 TTT
65 TTT
1030411 GTGACAAACT
Statistics
Matches: 123, Mismatches: 24, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
86 25 0.20
87 94 0.76
88 4 0.03
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.39
Consensus pattern (88 bp):
GATGCCTTTTGTGGCTATCTCTATCAAAAGGAAGCCTTTGTGGCTATCTTTGTTAAAAGGATGCT
TTTGTGGCTATCTCAATCAAAAA
Found at i:1030358 original size:30 final size:29
Alignment explanation
Indices: 1030322--1030386 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
1030312 AAAGGATATC
*
1030322 TTGTGGTTATCTCTATCAAAAAGATGCCTT
1 TTGTGGTTATCTATATCAAAAAGATGCC-T
* *
1030352 TTGTGGTTATCTATTTCAAAAGGATGCCT
1 TTGTGGTTATCTATATCAAAAAGATGCCT
1030381 TTGTGG
1 TTGTGG
1030387 CCATCTCTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.42
Consensus pattern (29 bp):
TTGTGGTTATCTATATCAAAAAGATGCCT
Found at i:1031300 original size:14 final size:13
Alignment explanation
Indices: 1031262--1031301 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
1031252 AAGAACTTCT
1031262 ATAGTAGCCATAA
1 ATAGTAGCCATAA
1031275 ATAGTAGCCATACA
1 ATAGTAGCCATA-A
1031289 AT-GTACGCCATAA
1 ATAGTA-GCCATAA
1031302 GAAATTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (13 bp):
ATAGTAGCCATAA
Found at i:1036839 original size:25 final size:25
Alignment explanation
Indices: 1036811--1036860 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1036801 CCTAATTCTT
1036811 CAAGAAATCAACAATGGTAACTTTC
1 CAAGAAATCAACAATGGTAACTTTC
1036836 CAAGAAATCAACAATGGTAACTTTC
1 CAAGAAATCAACAATGGTAACTTTC
1036861 TAAAGATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (25 bp):
CAAGAAATCAACAATGGTAACTTTC
Found at i:1036873 original size:25 final size:25
Alignment explanation
Indices: 1036812--1036866 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
1036802 CTAATTCTTC
*
1036812 AAGAAATCAACAATGGTAACTTTCC
1 AAGAAATCAACAATGGTAACTTTCA
1036837 AAGAAATCAACAATGGTAACTTTCTA
1 AAGAAATCAACAATGGTAACTTTC-A
1036863 AAGA
1 AAGA
1036867 TTTAACAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (25 bp):
AAGAAATCAACAATGGTAACTTTCA
Found at i:1037107 original size:24 final size:24
Alignment explanation
Indices: 1037080--1037151 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
1037070 CTATTTATAC
* *
1037080 TTTAGATTAACTTTATTAATTTAG
1 TTTAGATTAACTTAATTAATTTAA
1037104 TTTA-ACTTAACTTAATTAATTTAA
1 TTTAGA-TTAACTTAATTAATTTAA
*
1037128 TTTAG-TTAA-TTAAGATAATTTAA
1 TTTAGATTAACTTAA-TTAATTTAA
1037151 T
1 T
1037152 ATTATTAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 4 0.10
23 14 0.33
24 24 0.57
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (24 bp):
TTTAGATTAACTTAATTAATTTAA
Found at i:1037108 original size:19 final size:20
Alignment explanation
Indices: 1037080--1037138 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 20
1037070 CTATTTATAC
*
1037080 TTTAGATTAACTTTA-TTAA
1 TTTAGTTTAACTTTACTTAA
*
1037099 TTTAGTTTAACTTAACTTAA
1 TTTAGTTTAACTTTACTTAA
* *
1037119 -TTAATTTAA-TTTAGTTAA
1 TTTAGTTTAACTTTACTTAA
1037137 TT
1 TT
1037139 AAGATAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
18 7 0.21
19 22 0.67
20 4 0.12
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTAGTTTAACTTTACTTAA
Found at i:1037146 original size:18 final size:18
Alignment explanation
Indices: 1037115--1037149 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1037105 TTAACTTAAC
**
1037115 TTAATTAATTTAATTTAG
1 TTAATTAAGATAATTTAG
1037133 TTAATTAAGATAATTTA
1 TTAATTAAGATAATTTA
1037150 ATATTATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
TTAATTAAGATAATTTAG
Found at i:1042790 original size:66 final size:66
Alignment explanation
Indices: 1042715--1042910 Score: 261
Period size: 66 Copynumber: 3.0 Consensus size: 66
1042705 ATGAACTTGG
* * * *
1042715 CTATGGCAACATGTGGAGTTCGCTAGGACATTAAAGATTGGGTACATGTGTAAG-CCTTTAGCTC
1 CTATGGCAACATGTGGAGTCCGCCAGGACATTAAACATGGGGTACATGTGTAAGACC-TTAGCTC
1042779 GA
65 GA
*
1042781 CTATGGCAACGA-GTGGAGTCCACCAGGACATTAAACATGGGGTACATGTGTAAGACCTTAGCTC
1 CTATGGCAAC-ATGTGGAGTCCGCCAGGACATTAAACATGGGGTACATGTGTAAGACCTTAGCTC
1042845 GA
65 GA
** ** *
1042847 CTATGGCAATGTGTGGAGTCCGCCAGGACATTAAACATGGGGTTATGTGTGTAAGACCATAGCT
1 CTATGGCAACATGTGGAGTCCGCCAGGACATTAAACATGGGG-TACATGTGTAAGACCTTAGCT
1042911 TGGCTATGTT
Statistics
Matches: 115, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
66 94 0.82
67 21 0.18
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (66 bp):
CTATGGCAACATGTGGAGTCCGCCAGGACATTAAACATGGGGTACATGTGTAAGACCTTAGCTCG
A
Found at i:1042933 original size:67 final size:66
Alignment explanation
Indices: 1042715--1042933 Score: 217
Period size: 66 Copynumber: 3.3 Consensus size: 66
1042705 ATGAACTTGG
* * * * * * *
1042715 CTATGGCAACATGTGGAGTTCGCTAGGACATTAAAGATTGGGTACATGTGTAAG-CCTTTAGCTC
1 CTATGGCAACATGTAGAGTCCACCAGGACATTAAACATGGGGTACATGTGTAAGACC-ATAGCTC
1042779 GA
65 GA
* *
1042781 CTATGGCAACGA-GTGGAGTCCACCAGGACATTAAACATGGGGTACATGTGTAAGACCTTAGCTC
1 CTATGGCAAC-ATGTAGAGTCCACCAGGACATTAAACATGGGGTACATGTGTAAGACCATAGCTC
1042845 GA
65 GA
** * * ** *
1042847 CTATGGCAATGTGTGGAGTCCGCCAGGACATTAAACATGGGGTTATGTGTGTAAGACCATAGCTT
1 CTATGGCAACATGTAGAGTCCACCAGGACATTAAACATGGGG-TACATGTGTAAGACCATAGCTC
*
1042912 GG
65 GA
** *
1042914 CTATGTTAGCATGTAGAGTC
1 CTATGGCAACATGTAGAGTC
1042934 TGTAAATCAA
Statistics
Matches: 130, Mismatches: 19, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
66 94 0.72
67 36 0.28
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.26
Consensus pattern (66 bp):
CTATGGCAACATGTAGAGTCCACCAGGACATTAAACATGGGGTACATGTGTAAGACCATAGCTCG
A
Found at i:1043720 original size:18 final size:18
Alignment explanation
Indices: 1043693--1043739 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1043683 TGAGGGTACT
*
1043693 AGAAAGGGACCTTATTCA
1 AGAAAAGGACCTTATTCA
* *
1043711 AGAAATGGACCTTATTTA
1 AGAAAAGGACCTTATTCA
1043729 AGAAAAGGACC
1 AGAAAAGGACC
1043740 AAGCATAGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (18 bp):
AGAAAAGGACCTTATTCA
Found at i:1059711 original size:26 final size:24
Alignment explanation
Indices: 1059682--1059730 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
1059672 ATAAAAAAAG
*
1059682 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAACATAA-AAA-CAAATATA
1059708 TTTAAAAACATAAAAACAAATAT
1 TTTAAAAACATAAAAACAAATAT
1059731 TAAAACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
TTTAAAAACATAAAAACAAATATA
Found at i:1059750 original size:21 final size:21
Alignment explanation
Indices: 1059701--1059759 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
1059691 ATAATAAATC
*
1059701 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
1059721 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
1059743 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
1059760 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:1061867 original size:19 final size:19
Alignment explanation
Indices: 1061821--1061868 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1061811 GTATATATTT
1061821 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
1061839 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
1061858 TAAGTTTTATT
1 TAAATTTTATT
1061869 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:1061944 original size:42 final size:42
Alignment explanation
Indices: 1061885--1061969 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
1061875 CTAGGAATAT
* *
1061885 TTTTATTTTATCTTTTAGTAGTTTATTAGAGTAAGGGAACTA
1 TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGAGAACTA
* *
1061927 TTTTCTTTTATGTTTTAGTAGTTTATTAGAATAAGAGAACTA
1 TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGAGAACTA
1061969 T
1 T
1061970 CTTCCCAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (42 bp):
TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGAGAACTA
Found at i:1066537 original size:19 final size:19
Alignment explanation
Indices: 1066491--1066538 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1066481 GTATATATTT
1066491 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
1066509 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
1066528 TAAGTTTTATT
1 TAAATTTTATT
1066539 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:1066614 original size:42 final size:42
Alignment explanation
Indices: 1066555--1066639 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
1066545 CTAGGAATAT
1066555 TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
1 TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
* *
1066597 TTTTCTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAACTA
1 TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
1066639 T
1 T
1066640 CTTCCCAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (42 bp):
TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
Found at i:1077068 original size:42 final size:45
Alignment explanation
Indices: 1076943--1077110 Score: 105
Period size: 48 Copynumber: 3.6 Consensus size: 45
1076933 ATGCCAACGT
* * * * *
1076943 CATATCCCAAATATGGTCTTACATGAGATCACCA-CTCGATGCCAATGC
1 CATACCCCAGATATGGTCTTACA-GGGATCA-CATATCGATACC-A-GC
** * *
1076991 CATGTCCCAGACATGGTCTTACATGGGATCTCATATC-A-A-C-GC
1 CATACCCCAGATATGGTCTTACA-GGGATCACATATCGATACCAGC
1077033 CATACCCCAGATATGGTCTTACA-GGATAACACATATCGATACCGATGC
1 CATACCCCAGATATGGTCTTACAGGGAT--CACATATCGATACC-A-GC
* *
1077081 CATATCCCAGATATGGTCTTATACGGGATC
1 CATACCCCAGATATGGTCTTACA-GGGATC
1077111 TTGTTAACCC
Statistics
Matches: 96, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
40 4 0.04
42 29 0.30
43 1 0.01
44 1 0.01
45 2 0.02
47 3 0.03
48 52 0.54
50 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (45 bp):
CATACCCCAGATATGGTCTTACAGGGATCACATATCGATACCAGC
Found at i:1077090 original size:90 final size:90
Alignment explanation
Indices: 1076937--1077111 Score: 219
Period size: 90 Copynumber: 1.9 Consensus size: 90
1076927 AATAAGATGC
* * * * * *
1076937 CAACGTCATATCCCAAATATGGTCTTACATGAGATCACCACTCGATGCCAATGCCATGTCCCAGA
1 CAACGCCATACCCCAAATATGGTCTTACATGAGATAACCAATCGATACCAATGCCATATCCCAGA
*
1077002 CATGGTCTTACATGGGATCTCATAT
66 CATGGTCTTACACGGGATCTCATAT
* *
1077027 CAACGCCATACCCCAGATATGGTCTTACA-G-GATAACACATATCGATACCGATGCCATATCCCA
1 CAACGCCATACCCCAAATATGGTCTTACATGAGATAAC-CA-ATCGATACCAATGCCATATCCCA
* *
1077090 GATATGGTCTTATACGGGATCT
64 GACATGGTCTTACACGGGATCT
1077112 TGTTAACCCG
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
88 5 0.07
89 3 0.04
90 64 0.89
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (90 bp):
CAACGCCATACCCCAAATATGGTCTTACATGAGATAACCAATCGATACCAATGCCATATCCCAGA
CATGGTCTTACACGGGATCTCATAT
Found at i:1080289 original size:46 final size:46
Alignment explanation
Indices: 1080236--1080329 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
1080226 TTCAAATGTT
1080236 ATTGATTTATGCTACGCATTGTATTGTGTTGTATTTAGACCTGCTC
1 ATTGATTTATGCTACGCATTGTATTGTGTTGTATTTAGACCTGCTC
1080282 ATTGATTTATGCTACGCATTGTATTGTGTTGTATTTAGACCTGCTC
1 ATTGATTTATGCTACGCATTGTATTGTGTTGTATTTAGACCTGCTC
1080328 AT
1 AT
1080330 AGGTCGGGCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.20, C:0.15, G:0.19, T:0.46
Consensus pattern (46 bp):
ATTGATTTATGCTACGCATTGTATTGTGTTGTATTTAGACCTGCTC
Found at i:1080649 original size:15 final size:15
Alignment explanation
Indices: 1080629--1080658 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1080619 ATTGTATAAA
*
1080629 AATTATTTTATTATT
1 AATTATGTTATTATT
1080644 AATTATGTTATTATT
1 AATTATGTTATTATT
1080659 TTAAAGGAAT
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:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
AATTATGTTATTATT
Found at i:1080685 original size:30 final size:30
Alignment explanation
Indices: 1080642--1080700 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1080632 TATTTTATTA
*
1080642 TTAATTATGTTATTATTTTAAAGGAATTTG
1 TTAATTATATTATTATTTTAAAGGAATTTG
* * *
1080672 TTAATTTTATTATTATTTTAGAGGTATTT
1 TTAATTATATTATTATTTTAAAGGAATTT
1080701 ACTTGTTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.58
Consensus pattern (30 bp):
TTAATTATATTATTATTTTAAAGGAATTTG
Found at i:1083660 original size:133 final size:133
Alignment explanation
Indices: 1083438--1083890 Score: 340
Period size: 133 Copynumber: 3.4 Consensus size: 133
1083428 CGAAGGGATC
* * * * * * * *
1083438 TTCGATCGTTTTGAACAAATGAAAAAGCACAGCCCAACACGATAGGGCACGATTCTCGAATTGCC
1 TTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACGATTCCCAAATTGCC
* * *
1083503 AAACATCGAACATCGCATTTGTTTTAAAGGGTTTTCTTAAAACACAAGAGTGAAAACCTAAAGGA
66 AAACATCGAACATCGCATTCGTTTTAAAGGATTTTCTTAAAACACAAGACTGAAAACCTAAAGGA
1083568 ATA
131 ATA
* * *
1083571 TTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGTACGATAGGGCATGATTCCCAAATTGTC
1 TTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACGATTCCCAAATTGCC
* ** * * * * * * *** *
1083636 GAAC-TCCGAGTATTGCCTTCGTTTTAAAGGATTTTTTTAGAAGACATGACTGAAATTTTGAAGG
66 AAACAT-CGAACATCGCATTCGTTTTAAAGGATTTTCTTAAAACACAAGACTGAAAACCTAAAGG
*
1083700 GATA
130 AATA
* * ** * **
1083704 TTTGATTATTTT-AAGCAAACGAGAAATTGCAACCCAGCACGTTAGGGCACGATTCCGTGAATTG
1 TTCGATTGTTTTGAA-CAAACGAGAAATCACAACCCAGCACGATAGGGCACGATTCC-CAAATTG
* * * * * * * ** **
1083768 CCAAATATCGCACATCGCCTTCG-TTT-AAGGAATTT-TTAAAAGATATGGGTGAAATTCTAAAG
64 CCAAACATCGAACATCGCATTCGTTTTAAAGGATTTTCTTAAAACACAAGACTGAAAACCTAAAG
**
1083830 GAACC
129 GAATA
** * * ** * *
1083835 TTCGATTACTTTGAGCAAATGAGAAATTGCAACCCAACACGTTAGGGCACGATTCC
1 TTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACGATTCC
1083891 GCGAAATACC
Statistics
Matches: 256, Mismatches: 59, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
131 72 0.28
132 12 0.05
133 152 0.59
134 19 0.07
135 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (133 bp):
TTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACGATTCCCAAATTGCC
AAACATCGAACATCGCATTCGTTTTAAAGGATTTTCTTAAAACACAAGACTGAAAACCTAAAGGA
ATA
Found at i:1086548 original size:19 final size:19
Alignment explanation
Indices: 1086506--1086549 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1086496 TGGTTTGATT
* *
1086506 TTATTTTTTTATTTTTTTA
1 TTATTTATTTATTTTTATA
1086525 TTATTTATTTATTTTGTATA
1 TTATTTATTTATTTT-TATA
1086545 -TATTT
1 TTATTT
1086550 TGGTTTCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (19 bp):
TTATTTATTTATTTTTATA
Found at i:1090832 original size:393 final size:393
Alignment explanation
Indices: 1090107--1090879 Score: 1429
Period size: 393 Copynumber: 2.0 Consensus size: 393
1090097 GAAAATGGGG
1090107 GATGGAATGAATTATGATCATGAGACTATAGTAAATTTACATTTAATCATGTTATATTATTTGAA
1 GATGGAATGAATTATGATCATGAGACTATAGTAAATTTACATTTAATCATGTTATATTATTTGAA
*
1090172 TGTTATATGTATGGTAAGGTTGCTTATTTCTTGCATACGAGCTTACTAAGCTATATAGCTTACTC
66 CGTTATATGTATGGTAAGGTTGCTTATTTCTTGCATACGAGCTTACTAAGCTATATAGCTTACTC
* *
1090237 CGTTTATTTTCCATGTTTTATAGTACAGCCAAGCTAACTTAGATTAGAGATTGTCGAAGATTCGA
131 CGTTTATTTTCCATGTTTTATAGTACAGCCAAGCTAACTCAGATCAGAGATTGTCGAAGATTCGA
*
1090302 ATCACACTATTAAACTTTCATTTTGGGTAATTATGATCTTACTATTTTGAAAGTATGGCATGTAT
196 ATCACACTATCAAACTTTCATTTTGGGTAATTATGATCTTACTATTTTGAAAGTATGGCATGTAT
* *
1090367 AGGAACTTGGTCATTTTGTTATATGTGTTATTATGATTTTAGCCAAAGTATTGGCTTGTAATTTA
261 AGGAACTTGGTCATTTTGTTATATGTGTCATTATGATTTTAGCCAAAGTATTGGCTTGTAATGTA
*
1090432 TCAAAGGCTTTATTTGATATTTGGCCATGTAAATTGGCTTATTTTGGCTAACATGAGGTAAGTTT
326 TCAAAGGCTTGATTTGATATTTGGCCATGTAAATTGGCTTATTTTGGCTAACATGAGGTAAGTTT
1090497 GGT
391 GGT
1090500 GATGGAATGAATTATGATCATGAGACTATAGTAAATTTACATTTAATCATGTTATATTATTTGAA
1 GATGGAATGAATTATGATCATGAGACTATAGTAAATTTACATTTAATCATGTTATATTATTTGAA
*
1090565 CGTTATATGTATGGTAAGGTTGCTTATTTCTTGCATACGAGCTTACTAAGCTATATAGCTTACTT
66 CGTTATATGTATGGTAAGGTTGCTTATTTCTTGCATACGAGCTTACTAAGCTATATAGCTTACTC
* * *
1090630 CGTTTATTTTCCATGTTTTATAGTACTGCCAAGCTAACTCAGATCAGAGATTTTCGGAGATTCGA
131 CGTTTATTTTCCATGTTTTATAGTACAGCCAAGCTAACTCAGATCAGAGATTGTCGAAGATTCGA
*
1090695 ATCACACTATCAAACTTTCATTTTGGGTAATTATGATCTTAGTATTTTGAAAGTATGGCATGTAT
196 ATCACACTATCAAACTTTCATTTTGGGTAATTATGATCTTACTATTTTGAAAGTATGGCATGTAT
*
1090760 AGGAACTTGGTCATTTTGTTATATGTGTCATTATGATTTTATCCAAAGTATTGGCTTGTAATGTA
261 AGGAACTTGGTCATTTTGTTATATGTGTCATTATGATTTTAGCCAAAGTATTGGCTTGTAATGTA
1090825 TCAAAGGCTTGATTTGATATTTGGCCATGTAAATTGGCTTATTTTGGCTAACATG
326 TCAAAGGCTTGATTTGATATTTGGCCATGTAAATTGGCTTATTTTGGCTAACATG
1090880 GTTGTAAGCT
Statistics
Matches: 367, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
393 367 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (393 bp):
GATGGAATGAATTATGATCATGAGACTATAGTAAATTTACATTTAATCATGTTATATTATTTGAA
CGTTATATGTATGGTAAGGTTGCTTATTTCTTGCATACGAGCTTACTAAGCTATATAGCTTACTC
CGTTTATTTTCCATGTTTTATAGTACAGCCAAGCTAACTCAGATCAGAGATTGTCGAAGATTCGA
ATCACACTATCAAACTTTCATTTTGGGTAATTATGATCTTACTATTTTGAAAGTATGGCATGTAT
AGGAACTTGGTCATTTTGTTATATGTGTCATTATGATTTTAGCCAAAGTATTGGCTTGTAATGTA
TCAAAGGCTTGATTTGATATTTGGCCATGTAAATTGGCTTATTTTGGCTAACATGAGGTAAGTTT
GGT
Found at i:1097407 original size:47 final size:46
Alignment explanation
Indices: 1097333--1097461 Score: 147
Period size: 46 Copynumber: 2.8 Consensus size: 46
1097323 GGGATATTTG
* * *
1097333 GGCATCCGAACTCGTTGAGTGGAGTCCGAGTTC-GTGA-GATGTAACTA
1 GGCA-CCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAA--A
*
1097380 GGCAGCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAA
1 GGCA-CCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAA
*
1097428 TGC-CCGAACTCGTTGAGTTGAGTCCGAGTTCACT
1 GGCACCGAACTCGTTGAGTTGAGTCCGAGTTCACT
1097462 CATATTGAGT
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
46 31 0.42
47 31 0.42
48 5 0.07
50 6 0.08
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.26
Consensus pattern (46 bp):
GGCACCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAAA
Found at i:1102330 original size:30 final size:31
Alignment explanation
Indices: 1102285--1102344 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
1102275 AAAATGTAAA
*
1102285 TGATTACAGGGTATGAAAATGCAAATAAGAG
1 TGATTACAGGGTATGAAAATGAAAATAAGAG
*
1102316 TGATTACA-GGTATGATAATGAAAATAAGA
1 TGATTACAGGGTATGAAAATGAAAATAAGA
1102345 ATATTGATGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.47, C:0.05, G:0.23, T:0.25
Consensus pattern (31 bp):
TGATTACAGGGTATGAAAATGAAAATAAGAG
Found at i:1102705 original size:21 final size:21
Alignment explanation
Indices: 1102681--1102720 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1102671 CGAAACATTG
1102681 AAATCAAATC-TTGAAATCAGA
1 AAATCAAA-CATTGAAATCAGA
*
1102702 AAATGAAACATTGAAATCA
1 AAATCAAACATTGAAATCA
1102721 AATCTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.23
Consensus pattern (21 bp):
AAATCAAACATTGAAATCAGA
Found at i:1102715 original size:34 final size:34
Alignment explanation
Indices: 1102672--1102743 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
1102662 TCCGTTAGGC
1102672 GAAACATTGAAATCAAATCTTGAAATCAGAAAAT
1 GAAACATTGAAATCAAATCTTGAAATCAGAAAAT
1102706 GAAACATTGAAATCAAATCTTGAAATCAGAAAAT
1 GAAACATTGAAATCAAATCTTGAAATCAGAAAAT
1102740 GAAA
1 GAAA
1102744 TAAAACGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.54, C:0.11, G:0.12, T:0.22
Consensus pattern (34 bp):
GAAACATTGAAATCAAATCTTGAAATCAGAAAAT
Found at i:1108160 original size:482 final size:482
Alignment explanation
Indices: 1107255--1108218 Score: 1883
Period size: 482 Copynumber: 2.0 Consensus size: 482
1107245 GGCTGGTTGC
1107255 GATGAGGAAGTGATAAGAGATATGATCATTAACTTCATCATGGCAGGAAGGGATACAACTTCAGC
1 GATGAGGAAGTGATAAGAGATATGATCATTAACTTCATCATGGCAGGAAGGGATACAACTTCAGC
1107320 AGCAATGACATGGCTCTTCTGGTTGCTTTCATGCCATCCAGTTATAGAGCAAGAACTGCTGAAAG
66 AGCAATGACATGGCTCTTCTGGTTGCTTTCATGCCATCCAGTTATAGAGCAAGAACTGCTGAAAG
*
1107385 AGATACAGAAAAATGATAAAAGATTGTCAGATTATGAATCATTGGAGGGATTGAAATTGTTGAAA
131 AGATACAGAAAAATGATAAAAGATTGTCAGATTATGAATCATTGGAGGGACTGAAATTGTTGAAA
*
1107450 GCCTCTCTTTGTGAGTCCATGAGGCTCTACCCGCCGGTAGCTTGGGACTCAAAGCATGCCATGGT
196 GCCTCTCTTTGTGAGTCCATGAGGCTCTACCCGCCGGTAGCTTGGAACTCAAAGCATGCCATGGT
1107515 GGATGATATGTTACCTGATGGTACTTTAGTCCAGGCGGGGGATAGGGTAACCTATTTTCCCTATG
261 GGATGATATGTTACCTGATGGTACTTTAGTCCAGGCGGGGGATAGGGTAACCTATTTTCCCTATG
1107580 GAATGGGGAGGATGGAAGCGTTGTGGGGAAAGGACTGCATCGAGTTCAGACCGAGCCGGTGGTTT
326 GAATGGGGAGGATGGAAGCGTTGTGGGGAAAGGACTGCATCGAGTTCAGACCGAGCCGGTGGTTT
1107645 ATTGAACCAAGTCACCAGGGAGGATCACTAAAGAAGGTAAGTCCATACAAGTTTCCAGTTTTTCA
391 ATTGAACCAAGTCACCAGGGAGGATCACTAAAGAAGGTAAGTCCATACAAGTTTCCAGTTTTTCA
1107710 GGCAGGACCAAGAATTTGTCTTGGAAG
456 GGCAGGACCAAGAATTTGTCTTGGAAG
1107737 GATGAGGAAGTGATAAGAGATATGATCATTAACTTCATCATGGCAGGAAGGGATACAACTTCAGC
1 GATGAGGAAGTGATAAGAGATATGATCATTAACTTCATCATGGCAGGAAGGGATACAACTTCAGC
1107802 AGCAATGACATGGCTCTTCTGGTTGCTTTCATGCCATCCAGTTATAGAGCAAGAACTGCTGAAAG
66 AGCAATGACATGGCTCTTCTGGTTGCTTTCATGCCATCCAGTTATAGAGCAAGAACTGCTGAAAG
* *
1107867 AGATACAGAAAAATGATAAAATATTGTCGGATTATGAATCATTGGAGGGACTGAAATTGTTGAAA
131 AGATACAGAAAAATGATAAAAGATTGTCAGATTATGAATCATTGGAGGGACTGAAATTGTTGAAA
*
1107932 GCTTCTCTTTGTGAGTCCATGAGGCTCTACCCGCCGGTAGCTTGGAACTCAAAGCATGCCATGGT
196 GCCTCTCTTTGTGAGTCCATGAGGCTCTACCCGCCGGTAGCTTGGAACTCAAAGCATGCCATGGT
1107997 GGATGATATGTTACCTGATGGTACTTTAGTCCAGGCGGGGGATAGGGTAACCTATTTTCCCTATG
261 GGATGATATGTTACCTGATGGTACTTTAGTCCAGGCGGGGGATAGGGTAACCTATTTTCCCTATG
1108062 GAATGGGGAGGATGGAAGCGTTGTGGGGAAAGGACTGCATCGAGTTCAGACCGAGCCGGTGGTTT
326 GAATGGGGAGGATGGAAGCGTTGTGGGGAAAGGACTGCATCGAGTTCAGACCGAGCCGGTGGTTT
1108127 ATTGAACCAAGTCACCAGGGAGGATCACTAAAGAAGGTAAGTCCATACAAGTTTCCAGTTTTTCA
391 ATTGAACCAAGTCACCAGGGAGGATCACTAAAGAAGGTAAGTCCATACAAGTTTCCAGTTTTTCA
1108192 GGCAGGACCAAGAATTTGTCTTGGAAG
456 GGCAGGACCAAGAATTTGTCTTGGAAG
1108219 AGATATGGCC
Statistics
Matches: 477, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
482 477 1.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (482 bp):
GATGAGGAAGTGATAAGAGATATGATCATTAACTTCATCATGGCAGGAAGGGATACAACTTCAGC
AGCAATGACATGGCTCTTCTGGTTGCTTTCATGCCATCCAGTTATAGAGCAAGAACTGCTGAAAG
AGATACAGAAAAATGATAAAAGATTGTCAGATTATGAATCATTGGAGGGACTGAAATTGTTGAAA
GCCTCTCTTTGTGAGTCCATGAGGCTCTACCCGCCGGTAGCTTGGAACTCAAAGCATGCCATGGT
GGATGATATGTTACCTGATGGTACTTTAGTCCAGGCGGGGGATAGGGTAACCTATTTTCCCTATG
GAATGGGGAGGATGGAAGCGTTGTGGGGAAAGGACTGCATCGAGTTCAGACCGAGCCGGTGGTTT
ATTGAACCAAGTCACCAGGGAGGATCACTAAAGAAGGTAAGTCCATACAAGTTTCCAGTTTTTCA
GGCAGGACCAAGAATTTGTCTTGGAAG
Found at i:1111798 original size:64 final size:64
Alignment explanation
Indices: 1111719--1111848 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 64
1111709 TGGGTTAGTA
*
1111719 AGTGCTTCCTGAATATCAACTTCTTTTACGAGCTAACTCAAAATCAACTCGTTCCTAGAACTCC
1 AGTGCTTCCTGAATATCAACTTCTTTTACGAGCTAACTCAAAATCAACCCGTTCCTAGAACTCC
1111783 AGTGCTTCCTGAATATCAACTTCTTTTACGAGCTAACTCAAAATCAACCCGTTCCTAGAACTCC
1 AGTGCTTCCTGAATATCAACTTCTTTTACGAGCTAACTCAAAATCAACCCGTTCCTAGAACTCC
1111847 AG
1 AG
1111849 AAGTTGGGTA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (64 bp):
AGTGCTTCCTGAATATCAACTTCTTTTACGAGCTAACTCAAAATCAACCCGTTCCTAGAACTCC
Found at i:1112846 original size:11 final size:11
Alignment explanation
Indices: 1112830--1112854 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1112820 CCACCAGTAT
1112830 AAAATACTAAA
1 AAAATACTAAA
1112841 AAAATACTAAA
1 AAAATACTAAA
1112852 AAA
1 AAA
1112855 TCTAGAAAAA
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:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATACTAAA
Found at i:1112951 original size:9 final size:9
Alignment explanation
Indices: 1112937--1112993 Score: 73
Period size: 9 Copynumber: 6.6 Consensus size: 9
1112927 ATTTGTCAAG
*
1112937 TTTTTATTT
1 TTTTTACTT
1112946 TTTTTACTT
1 TTTTTACTT
1112955 TTTTTACTT
1 TTTTTACTT
1112964 TTTTTACTT
1 TTTTTACTT
*
1112973 TTTTAAC-T
1 TTTTTACTT
*
1112981 ATTTTA-TT
1 TTTTTACTT
1112989 TTTTT
1 TTTTT
1112994 CTTATATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
8 10 0.24
9 32 0.76
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTACTT
Found at i:1113071 original size:18 final size:18
Alignment explanation
Indices: 1113036--1113080 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1113026 TTTTTTAAGT
*
1113036 TTTATATTATTTACTTAA
1 TTTATATTACTTACTTAA
* *
1113054 TTTATTTTACTTATTTAA
1 TTTATATTACTTACTTAA
1113072 TTTATATTA
1 TTTATATTA
1113081 TTAATTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTATATTACTTACTTAA
Found at i:1113154 original size:22 final size:22
Alignment explanation
Indices: 1113112--1113155 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1113102 TATATATTTA
1113112 AAATGTTTTATAATATTTTTTT
1 AAATGTTTTATAATATTTTTTT
1113134 AAAT-TTTT-TAATTATTGTTTTT
1 AAATGTTTTATAA-TATT-TTTTT
1113156 TAAAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.15
21 8 0.40
22 9 0.45
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (22 bp):
AAATGTTTTATAATATTTTTTT
Found at i:1113259 original size:36 final size:37
Alignment explanation
Indices: 1113190--1113259 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 37
1113180 TATATTTGTG
**
1113190 AAATTAATTATTTATAAATTTTAAAAATGTAATTTTC
1 AAATTAATTATTTATAAATTTTAAAAAAATAATTTTC
*
1113227 AAATTAATTTTTTA-AAATTTTAAAAAAATAATT
1 AAATTAATTATTTATAAATTTTAAAAAAATAATT
1113260 ATTTTTTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 17 0.57
37 13 0.43
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (37 bp):
AAATTAATTATTTATAAATTTTAAAAAAATAATTTTC
Found at i:1113315 original size:17 final size:17
Alignment explanation
Indices: 1113295--1113341 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
1113285 TGAAGTCTAA
1113295 TTTTTTTCTTATTTTAT
1 TTTTTTTCTTATTTTAT
1113312 TTTTTTATC-TATTTTAT
1 TTTTTT-TCTTATTTTAT
*
1113329 TTATTTTTATTAT
1 TT-TTTTTCTTAT
1113342 ACATTTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTTCTTATTTTAT
Found at i:1113933 original size:10 final size:9
Alignment explanation
Indices: 1113914--1114021 Score: 67
Period size: 10 Copynumber: 11.6 Consensus size: 9
1113904 AAATTCTATG
1113914 TAAAAT-TT
1 TAAAATATT
*
1113922 AAAAATATT
1 TAAAATATT
1113931 TAAAATCATT
1 TAAAAT-ATT
1113941 TAAAATATT
1 TAAAATATT
*
1113950 AAAAAATATT
1 -TAAAATATT
*
1113960 TTAAATCATT
1 TAAAAT-ATT
*
1113970 TTAAATCATT
1 TAAAAT-ATT
* *
1113980 TTAAATGTTT
1 TAAAAT-ATT
*
1113990 TATAATATT
1 TAAAATATT
*
1113999 AAAAATATAT
1 TAAAATAT-T
*
1114009 T-TAATATT
1 TAAAATATT
1114017 TAAAA
1 TAAAA
1114022 AATAATTTGA
Statistics
Matches: 79, Mismatches: 15, Indels: 11
0.75 0.14 0.10
Matches are distributed among these distances:
8 7 0.09
9 29 0.37
10 43 0.54
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (9 bp):
TAAAATATT
Found at i:1113985 original size:29 final size:29
Alignment explanation
Indices: 1113914--1113975 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1113904 AAATTCTATG
*
1113914 TAAAAT-TT-AAAAATATTTAAAATCATT
1 TAAAATATTAAAAAATATTTTAAATCATT
1113941 TAAAATATTAAAAAATATTTTAAATCATT
1 TAAAATATTAAAAAATATTTTAAATCATT
*
1113970 TTAAAT
1 TAAAAT
1113976 CATTTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 6 0.19
28 2 0.06
29 23 0.74
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (29 bp):
TAAAATATTAAAAAATATTTTAAATCATT
Found at i:1114038 original size:31 final size:34
Alignment explanation
Indices: 1113991--1114079 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
1113981 TAAATGTTTT
1113991 ATAATATTAAAAATATA-TTTAATATTTA-AAAA
1 ATAATATTAAAAATATATTTTAATATTTATAAAA
*
1114023 ATAAT-TTGAAAATATATTTTTAATATTTATAAAA
1 ATAATATTAAAAATATA-TTTTAATATTTATAAAA
*
1114057 A-ATATATTATAAAACAT-TTTTAA
1 ATA-ATATTA-AAAATATATTTTAA
1114080 AAAATACATT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
31 10 0.21
32 5 0.10
33 12 0.25
34 13 0.27
35 2 0.04
36 6 0.12
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (34 bp):
ATAATATTAAAAATATATTTTAATATTTATAAAA
Found at i:1114070 original size:13 final size:13
Alignment explanation
Indices: 1114044--1114085 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
1114034 ATATATTTTT
1114044 AATATTTATAAAA
1 AATATTTATAAAA
1114057 AATATATTATAAAA
1 AATAT-TTATAAAA
*
1114071 CAT-TTT-TAAAA
1 AATATTTATAAAA
1114082 AATA
1 AATA
1114086 CATTTCAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 7 0.28
12 2 0.08
13 6 0.24
14 10 0.40
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATTTATAAAA
Found at i:1124318 original size:30 final size:30
Alignment explanation
Indices: 1124282--1124374 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 30
1124272 GGTCAAATGG
* *
1124282 ACTCGAACCGCCTATATCCGAGTGATATGA
1 ACTCGAACCACCTATGTCCGAGTGATATGA
* * *
1124312 ACTCGAACCACCCATGTTCGGGTGATATGA
1 ACTCGAACCACCTATGTCCGAGTGATATGA
* *
1124342 ACTCGCACCACCTATGTCC-AGGTTATATGA
1 ACTCGAACCACCTATGTCCGA-GTGATATGA
1124372 ACT
1 ACT
1124375 GCTCTGGGAC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (30 bp):
ACTCGAACCACCTATGTCCGAGTGATATGA
Found at i:1126622 original size:70 final size:68
Alignment explanation
Indices: 1126539--1126686 Score: 262
Period size: 70 Copynumber: 2.2 Consensus size: 68
1126529 TTCTAGTTAT
1126539 TTATAAATTAACTAGTAAATAATCAAATATATTCACTTTTATTATTATTGTTTTAATAATATATA
1 TTATAAATTAACTAGTAAATAATCAAATATATTCACTTTTATTATTATTGTTTT-ATAATATATA
1126604 TATTA
65 TA-TA
*
1126609 TTATAAATTAACTAGTAAATAATCAAATATATTCACTTTTATTATTATTGTTTTATTATATATAT
1 TTATAAATTAACTAGTAAATAATCAAATATATTCACTTTTATTATTATTGTTTTATAATATATAT
1126674 ATA
66 ATA
1126677 TTA-AAATTAA
1 TTATAAATTAA
1126687 AAGAATTTTT
Statistics
Matches: 77, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
67 7 0.09
68 5 0.06
69 11 0.14
70 54 0.70
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (68 bp):
TTATAAATTAACTAGTAAATAATCAAATATATTCACTTTTATTATTATTGTTTTATAATATATAT
ATA
Found at i:1127491 original size:18 final size:20
Alignment explanation
Indices: 1127451--1127495 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
1127441 AAAAAAAGAT
1127451 ATTTAATATATATATTTTAAA
1 ATTT-ATATATATATTTTAAA
*
1127472 ATTTATATTTATA-TTT-AA
1 ATTTATATATATATTTTAAA
1127490 ATTTAT
1 ATTTAT
1127496 TAATAGTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 3 0.13
20 8 0.35
21 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTATATATATATTTTAAA
Found at i:1127666 original size:23 final size:24
Alignment explanation
Indices: 1127615--1127666 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
1127605 TTTTAAATTG
* *
1127615 TAAAAAATATATTACAAAACATTT
1 TAAAATATACATTACAAAACATTT
*
1127639 T-AAATATACATTACAAAA-TTTT
1 TAAAATATACATTACAAAACATTT
1127661 TAAAAT
1 TAAAAT
1127667 TAATAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 4 0.17
23 19 0.79
24 1 0.04
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.37
Consensus pattern (24 bp):
TAAAATATACATTACAAAACATTT
Found at i:1127692 original size:13 final size:13
Alignment explanation
Indices: 1127668--1127713 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1127658 TTTTAAAATT
*
1127668 AATAATAAAAT-A
1 AATAAAAAAATAA
1127680 AATAAACAAAATAA
1 AATAAA-AAAATAA
1127694 AATAAAAAAA-AA
1 AATAAAAAAATAA
1127706 ACATAAAA
1 A-ATAAAA
1127714 TTTCAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 8 0.27
13 15 0.50
14 7 0.23
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAAAAAAATAA
Found at i:1127694 original size:18 final size:17
Alignment explanation
Indices: 1127671--1127714 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1127661 TAAAATTAAT
*
1127671 AATAAAATAAATAAACAA
1 AATAAAATAAA-AAAAAA
1127689 AATAAAATAAAAAAAAA
1 AATAAAATAAAAAAAAA
1127706 ACATAAAAT
1 A-ATAAAAT
1127715 TTCAAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (17 bp):
AATAAAATAAAAAAAAA
Found at i:1127788 original size:27 final size:28
Alignment explanation
Indices: 1127758--1127821 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 28
1127748 TTTTAAAAAA
* * *
1127758 TATTTAAAATATTATGATTTCTTATAT-
1 TATTTAAAAAATTATAATTTCTTAAATG
*
1127785 TA-TTAAAAAATTATAATTTTTTAAATG
1 TATTTAAAAAATTATAATTTCTTAAATG
1127812 TATTTAAAAA
1 TATTTAAAAA
1127822 TTGTATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 20 0.65
27 4 0.13
28 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (28 bp):
TATTTAAAAAATTATAATTTCTTAAATG
Found at i:1127829 original size:26 final size:26
Alignment explanation
Indices: 1127758--1127823 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
1127748 TTTTAAAAAA
* *
1127758 TATTTAAAATATTATGATTTCTTATAT
1 TATTTAAAA-ATTATAATTTCTTAAAT
* *
1127785 TATTAAAAAATTATAATTTTTTAAAT
1 TATTTAAAAATTATAATTTCTTAAAT
1127811 GTATTTAAAAATT
1 -TATTTAAAAATT
1127824 GTATTTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 14 0.42
27 19 0.58
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (26 bp):
TATTTAAAAATTATAATTTCTTAAAT
Found at i:1128041 original size:18 final size:18
Alignment explanation
Indices: 1127999--1128045 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 18
1127989 TTATAAAATA
*
1127999 ATATTT-AATATATATTT
1 ATATTTAAATTTATATTT
*
1128016 -T-TTAAAATTTATATTT
1 ATATTTAAATTTATATTT
1128032 ATATTTAAATTTAT
1 ATATTTAAATTTAT
1128046 TAATAGTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 2 0.08
16 11 0.46
17 1 0.04
18 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATTTAAATTTATATTT
Found at i:1128321 original size:21 final size:19
Alignment explanation
Indices: 1128296--1128360 Score: 76
Period size: 21 Copynumber: 3.2 Consensus size: 19
1128286 TAAAAAATAT
1128296 TTTTAAAAATAATAATTAAAA
1 TTTTAAAAAT-AT-ATTAAAA
*
1128317 TTTTAAAAATATTATAAAACA
1 TTTTAAAAATA-TATTAAA-A
*
1128338 TTTTAAATATATATTAAAA
1 TTTTAAAAATATATTAAAA
1128357 TTTT
1 TTTT
1128361 TTTAAAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 5 0.13
20 12 0.31
21 22 0.56
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTTAAAAATATATTAAAA
Found at i:1128362 original size:21 final size:21
Alignment explanation
Indices: 1128289--1128362 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 21
1128279 ATAAAGTTAA
*
1128289 AAAATATTTTTAAAAATAATAATT
1 AAAAT-TTTTTAAATAT-AT-ATT
**
1128313 AAAATTTTAAAAATAT-TA-T
1 AAAATTTTTTAAATATATATT
**
1128332 AAAACATTTTAAATATATATT
1 AAAATTTTTTAAATATATATT
1128353 AAAATTTTTT
1 AAAATTTTTT
1128363 TAAAATTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
19 13 0.33
20 3 0.08
21 10 0.26
23 8 0.21
24 5 0.13
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAATTTTTTAAATATATATT
Found at i:1128410 original size:36 final size:37
Alignment explanation
Indices: 1128370--1128443 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
1128360 TTTTAAAATT
*
1128370 AATAATAT-AAA-TTAAATAAGCAAAATAAAT-TAAGAA
1 AATAATATAAAACTTAAAAAAG-AAAA-AAATCTAAGAA
1128406 AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
1 AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
1128443 A
1 A
1128444 GAGACAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 12 0.35
37 14 0.41
38 8 0.24
ACGTcount: A:0.69, C:0.04, G:0.05, T:0.22
Consensus pattern (37 bp):
AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
Found at i:1128415 original size:18 final size:18
Alignment explanation
Indices: 1128365--1128416 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
1128355 AATTTTTTTA
*
1128365 AAATTAATAATATAAATT
1 AAATAAATAATATAAATT
** *
1128383 AAATAAGCAAAATAAATT
1 AAATAAATAATATAAATT
1128401 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
1128417 ACTTAAAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
AAATAAATAATATAAATT
Found at i:1129560 original size:34 final size:34
Alignment explanation
Indices: 1129509--1129574 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 34
1129499 ATAGTGTCTA
1129509 AAAAATAATTTATTAAAAATTATAAAAACTTTAT
1 AAAAATAATTTATTAAAAATTATAAAAACTTTAT
*
1129543 AAAAAT-ATTT-TTATAAAATTTATAAAATCTTT
1 AAAAATAATTTATTA-AAAA-TTATAAAAACTTT
1129575 TTATAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 3 0.10
33 8 0.28
34 18 0.62
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (34 bp):
AAAAATAATTTATTAAAAATTATAAAAACTTTAT
Found at i:1129575 original size:22 final size:24
Alignment explanation
Indices: 1129528--1129580 Score: 74
Period size: 22 Copynumber: 2.2 Consensus size: 24
1129518 TTATTAAAAA
1129528 TTATAAAAACTTTATAAAAATATTT
1 TTAT-AAAACTTTATAAAAATATTT
*
1129553 TTATAAAA-TTTAT-AAAATCTTT
1 TTATAAAACTTTATAAAAATATTT
1129575 TTATAA
1 TTATAA
1129581 TTTTAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 14 0.52
23 5 0.19
24 4 0.15
25 4 0.15
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TTATAAAACTTTATAAAAATATTT
Found at i:1137336 original size:43 final size:42
Alignment explanation
Indices: 1137288--1137425 Score: 181
Period size: 43 Copynumber: 3.2 Consensus size: 42
1137278 TATCTCAGGT
*
1137288 ATGGTCTTACATGTTATCTCATATCGATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATCTCATA-CGATGCCAATGTCCCAGAC
*
1137331 ATGGTCTTATACTG-AATCAT-ATAACGATGCCAATGTCCCAGAC
1 ATGGTCTTACA-TGTAATC-TCAT-ACGATGCCAATGTCCCAGAC
* *
1137374 ATGGTCTTACATGTAATCACAGTACGATGCCAATGTCCCAAAC
1 ATGGTCTTACATGTAATCTCA-TACGATGCCAATGTCCCAGAC
1137417 ATGGTCTTA
1 ATGGTCTTA
1137426 TGTGACAGCC
Statistics
Matches: 84, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
42 2 0.02
43 77 0.92
44 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (42 bp):
ATGGTCTTACATGTAATCTCATACGATGCCAATGTCCCAGAC
Found at i:1147586 original size:15 final size:15
Alignment explanation
Indices: 1147568--1147626 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 15
1147558 TAAAAAATAT
1147568 AATATATTAAATTAA
1 AATATATTAAATTAA
*
1147583 AATATA-TCAA-TAA
1 AATATATTAAATTAA
1147596 AATAT-TT-AATTAA
1 AATATATTAAATTAA
* *
1147609 ATTACATTAAATATAA
1 AATATATTAAAT-TAA
1147625 AA
1 AA
1147627 AAAATTCTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
12 2 0.06
13 15 0.43
14 5 0.14
15 9 0.26
16 4 0.11
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATATTAAATTAA
Found at i:1147589 original size:35 final size:35
Alignment explanation
Indices: 1147557--1147623 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
1147547 ACCTATATAT
*
1147557 ATAAAAAATATAA-TATATTAAATTAAAATATATCA
1 ATAAAAAATATAATTAAATTAAATT-AAATATATCA
* * *
1147592 ATAAAATATTTAATTAAATTACATTAAATATA
1 ATAAAAAATATAATTAAATTAAATTAAATATA
1147624 AAAAAAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 18 0.67
36 9 0.33
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (35 bp):
ATAAAAAATATAATTAAATTAAATTAAATATATCA
Found at i:1151724 original size:15 final size:16
Alignment explanation
Indices: 1151706--1151754 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
1151696 ATTTTTTTAA
1151706 AATT-ATCTTTTAATC
1 AATTGATCTTTTAATC
*
1151721 AATTGAT-TTCTAATC
1 AATTGATCTTTTAATC
*
1151736 AATTTGAGCTTTTAATC
1 AA-TTGATCTTTTAATC
1151753 AA
1 AA
1151755 CGTCTACAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 13 0.46
16 6 0.21
17 9 0.32
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (16 bp):
AATTGATCTTTTAATC
Found at i:1153237 original size:27 final size:26
Alignment explanation
Indices: 1153181--1153237 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1153171 CAACCTTAAC
* * *
1153181 CCTAGGGGTATATCAGTAATTTTGCT
1 CCTAGGGGTAAATCAGTAATTTTCCA
*
1153207 CCTAGGGGTAAATCTGTAAATTTTCCA
1 CCTAGGGGTAAATCAGT-AATTTTCCA
1153234 CCTA
1 CCTA
1153238 TAAAGGTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (26 bp):
CCTAGGGGTAAATCAGTAATTTTCCA
Found at i:1154147 original size:40 final size:39
Alignment explanation
Indices: 1154092--1154170 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 39
1154082 AGACTAGATC
*
1154092 TGAGGTGATGAGCACTTACCACTTATTCCTCTTTGATTT
1 TGAGGTGATGAGCACTTACCACTTATTCCTCTTTAATTT
*
1154131 NTGAGGTGATGAGCACTTACCACTTATTTCTCTTTAATTT
1 -TGAGGTGATGAGCACTTACCACTTATTCCTCTTTAATTT
1154171 CTATGCAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.42
Consensus pattern (39 bp):
TGAGGTGATGAGCACTTACCACTTATTCCTCTTTAATTT
Found at i:1157269 original size:27 final size:26
Alignment explanation
Indices: 1157213--1157269 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1157203 CAACCTTAAC
* * *
1157213 CCTAGGGGTATATCAGTAATTTTGCT
1 CCTAGGGGTAAATCAGTAATTTTCCA
*
1157239 CCTAGGGGTAAATCTGTAAATTTTCCA
1 CCTAGGGGTAAATCAGT-AATTTTCCA
1157266 CCTA
1 CCTA
1157270 TAAAGGTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (26 bp):
CCTAGGGGTAAATCAGTAATTTTCCA
Found at i:1159042 original size:46 final size:46
Alignment explanation
Indices: 1158970--1159061 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
1158960 TGCCAGAACC
*
1158970 TTCTCTCCCAAAATTAAAATTGAAGAATTGCCTCGAATTAAATTTA
1 TTCTCTCCCAAAATTAAAATTCAAGAATTGCCTCGAATTAAATTTA
1159016 TTCTCTCCCAAAATTAAAATTCAAGAATTGCCTCGAATTAAATTTA
1 TTCTCTCCCAAAATTAAAATTCAAGAATTGCCTCGAATTAAATTTA
1159062 CTCTTGGGCC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (46 bp):
TTCTCTCCCAAAATTAAAATTCAAGAATTGCCTCGAATTAAATTTA
Found at i:1165727 original size:12 final size:11
Alignment explanation
Indices: 1165699--1165726 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1165689 CACATATATA
1165699 AATTTTAAGAT
1 AATTTTAAGAT
1165710 AATTTTAAGAT
1 AATTTTAAGAT
1165721 AATTTT
1 AATTTT
1165727 TCTTATCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (11 bp):
AATTTTAAGAT
Found at i:1170726 original size:14 final size:14
Alignment explanation
Indices: 1170707--1170733 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1170697 GTTTTTAGTT
1170707 TAATTTTTGTTTTC
1 TAATTTTTGTTTTC
1170721 TAATTTTTGTTTT
1 TAATTTTTGTTTT
1170734 ATTTGCTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.04, G:0.07, T:0.74
Consensus pattern (14 bp):
TAATTTTTGTTTTC
Found at i:1174140 original size:9 final size:9
Alignment explanation
Indices: 1174120--1174195 Score: 50
Period size: 9 Copynumber: 8.2 Consensus size: 9
1174110 AGCCACCCCC
1174120 TTTTATTTTA
1 TTTTA-TTTA
1174130 TTTTATTTA
1 TTTTATTTA
*
1174139 TTATTATTTG
1 TT-TTATTTA
*
1174149 TTATA-TTA
1 TTTTATTTA
1174157 -TTTATTATCA
1 TTTTATT-T-A
* *
1174167 TTTTACTAA
1 TTTTATTTA
1174176 TTTTATTCTA
1 TTTTATT-TA
1174186 -TTTATTTA
1 TTTTATTTA
1174194 TT
1 TT
1174196 ATTCTTATAC
Statistics
Matches: 51, Mismatches: 8, Indels: 15
0.69 0.11 0.20
Matches are distributed among these distances:
7 3 0.06
8 5 0.10
9 23 0.45
10 15 0.29
11 5 0.10
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (9 bp):
TTTTATTTA
Found at i:1174157 original size:22 final size:22
Alignment explanation
Indices: 1174127--1174169 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1174117 CCCTTTTATT
* *
1174127 TTATTTTATTTATTATTATTTG
1 TTATATTATTTATTATCATTTG
1174149 TTATATTATTTATTATCATTT
1 TTATATTATTTATTATCATTT
1174170 TACTAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (22 bp):
TTATATTATTTATTATCATTTG
Found at i:1174222 original size:51 final size:49
Alignment explanation
Indices: 1174124--1174247 Score: 121
Period size: 51 Copynumber: 2.5 Consensus size: 49
1174114 ACCCCCTTTT
* *
1174124 ATTTTATTTTATTTATTATTATTTGTTATATTATTTATTATCATTTTACTA
1 ATTTTATTCTATTTATTATTATTTCTTATATTATTTATTATCATTTTA--A
*
1174175 ATTTTATTCTATTTATTTATTA-TTCTTATACTTATATT-TTAT-TTTTTAA
1 ATTTTATTCTATTTA-TTATTATTTCTTATA-TTAT-TTATTATCATTTTAA
* *
1174224 ATTTTTTTGCTATTT-CTATTATTT
1 ATTTTATT-CTATTTATTATTATTT
1174248 TTTGTATTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
48 5 0.08
49 10 0.16
50 6 0.10
51 26 0.41
52 14 0.22
53 2 0.03
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.68
Consensus pattern (49 bp):
ATTTTATTCTATTTATTATTATTTCTTATATTATTTATTATCATTTTAA
Found at i:1174346 original size:23 final size:22
Alignment explanation
Indices: 1174311--1174364 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 22
1174301 TATCATTGAG
*
1174311 TTTATTATTATTTTTTCTTTTCAT
1 TTTATT-TTATTTTTTATTTT-AT
1174335 TTTATTTTATTTTTTATTTTAT
1 TTTATTTTATTTTTTATTTTAT
1174357 TTCTATTT
1 TT-TATTT
1174365 ATCTTTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 4 0.14
23 18 0.64
24 6 0.21
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTATTTTATTTTTTATTTTAT
Found at i:1174349 original size:12 final size:12
Alignment explanation
Indices: 1174311--1174358 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
1174301 TATCATTGAG
1174311 TTTATTATTATTT
1 TTTATT-TTATTT
*
1174324 TTTCTTTTCA--T
1 TTTATTTT-ATTT
1174335 TTTATTTTATTT
1 TTTATTTTATTT
1174347 TTTATTTTATTT
1 TTTATTTTATTT
1174359 CTATTTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
10 1 0.03
11 8 0.27
12 15 0.50
13 6 0.20
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:1177173 original size:47 final size:47
Alignment explanation
Indices: 1177064--1177237 Score: 161
Period size: 47 Copynumber: 3.8 Consensus size: 47
1177054 CTTGTGTGAT
* *
1177064 CTAGTGTAAGA-CATGTTTGGGACATGA-ATTAGCCACATT-ATGAGA--G
1 CTAGTGTAAGACCATGTCTGGGACATGACATT-G--GCATTGA-GAGAGTG
*
1177110 CTAGTGTAAAACCATGTCTGGGACATGACATTGGCATTGAGACGAGTG
1 CTAGTGTAAGACCATGTCTGGGACATGACATTGGCATTGAGA-GAGTG
* *
1177158 CTAGTGTAAGA-CATGTCTGGGACATG-CATCGGC-TATGAGA-TGTG
1 CTAGTGTAAGACCATGTCTGGGACATGACATTGGCAT-TGAGAGAGTG
*
1177202 -TCAGTGTAAGACCATGTCTGGGACATGGCATTGGCA
1 CT-AGTGTAAGACCATGTCTGGGACATGACATTGGCA
1177238 CCTGACCCCA
Statistics
Matches: 110, Mismatches: 7, Indels: 21
0.80 0.05 0.15
Matches are distributed among these distances:
43 1 0.01
44 12 0.11
45 22 0.20
46 30 0.27
47 31 0.28
48 14 0.13
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.26
Consensus pattern (47 bp):
CTAGTGTAAGACCATGTCTGGGACATGACATTGGCATTGAGAGAGTG
Found at i:1184263 original size:46 final size:46
Alignment explanation
Indices: 1184109--1184278 Score: 173
Period size: 46 Copynumber: 3.7 Consensus size: 46
1184099 TCACTTGTGT
* * * ** *
1184109 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCTTCGGCCTCAAGACGA
* * **
1184155 GAGCCAGTGTAAGACCATGTCTGGGACATGGAATT-GGCATTGAGACGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-G-CTTCGGCCTCAAGACGA
* * *
1184203 GTGCTAGTGTAAGACATGTCTGGGACATGCTTCGACCTCAAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCTTCGGCCTCAAGACG-A
1184250 -AGCCAGTGTAAGACATGTCTGGGACATGC
1 GAGCCAGTGTAAGACATGTCTGGGACATGC
1184279 ATTGACTACG
Statistics
Matches: 100, Mismatches: 19, Indels: 10
0.78 0.15 0.08
Matches are distributed among these distances:
45 2 0.02
46 49 0.49
47 29 0.29
48 19 0.19
49 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCTTCGGCCTCAAGACGA
Found at i:1187818 original size:11 final size:11
Alignment explanation
Indices: 1187781--1187849 Score: 50
Period size: 11 Copynumber: 5.9 Consensus size: 11
1187771 GAAATAAAAC
*
1187781 AAAACAAAAGA
1 AAAAGAAAAGA
* *
1187792 ATAAGAATAGA
1 AAAAGAAAAGA
*
1187803 GAAAGAAAAGAA
1 AAAAGAAAAG-A
1187815 AAAGAGAAAAAGA
1 AAA-AG-AAAAGA
1187828 AATAA-AGAAAGA
1 AA-AAGA-AAAGA
1187840 AAAAGAAAAG
1 AAAAGAAAAG
1187850 GGAAATTTAG
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
11 22 0.49
12 11 0.24
13 6 0.13
14 6 0.13
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.04
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:1187840 original size:31 final size:31
Alignment explanation
Indices: 1187789--1187848 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1187779 ACAAAACAAA
* *
1187789 AGAATAAGAATAGAGAAAG-AAAAGAAAAAG
1 AGAAAAAGAATAAAGAAAGAAAAAGAAAAAG
1187819 AGAAAAAGAAATAAAGAAAGAAAAAGAAAA
1 AGAAAAAG-AATAAAGAAAGAAAAAGAAAA
1187849 GGGAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 7 0.27
31 10 0.38
32 9 0.35
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (31 bp):
AGAAAAAGAATAAAGAAAGAAAAAGAAAAAG
Found at i:1196783 original size:13 final size:13
Alignment explanation
Indices: 1196745--1196777 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1196735 AAGGGTTTGT
1196745 TTAT-TAAACTAA
1 TTATCTAAACTAA
1196757 TTATCTAAACTAA
1 TTATCTAAACTAA
1196770 TTATCTAA
1 TTATCTAA
1196778 TTTAATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:1204804 original size:13 final size:13
Alignment explanation
Indices: 1204782--1204814 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1204772 AAGGGTTTGT
1204782 TTAT-TAAACTAA
1 TTATCTAAACTAA
1204794 TTATCTAAACTAA
1 TTATCTAAACTAA
*
1204807 TTAACTAA
1 TTATCTAA
1204815 TTTAATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:1208698 original size:13 final size:13
Alignment explanation
Indices: 1208680--1208706 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1208670 GGAGTAATCG
1208680 CACACGGGCATGT
1 CACACGGGCATGT
1208693 CACACGGGCATGT
1 CACACGGGCATGT
1208706 C
1 C
1208707 CCTACCTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.33, G:0.30, T:0.15
Consensus pattern (13 bp):
CACACGGGCATGT
Found at i:1228133 original size:25 final size:25
Alignment explanation
Indices: 1228067--1228161 Score: 111
Period size: 25 Copynumber: 3.8 Consensus size: 25
1228057 GCTGTAAATT
* *
1228067 GTAAGCTCTTACGAGATGAATAACG
1 GTAAGCTCATACGAGCTGAATAACG
* *
1228092 GTAAGCTCCT-CTAAGCTGAATAACG
1 GTAAGCTCATAC-GAGCTGAATAACG
*
1228117 GTAAGCTCATACGAGCTGAGTAACG
1 GTAAGCTCATACGAGCTGAATAACG
* *
1228142 ATAAGCTCATAAGAGCTGAA
1 GTAAGCTCATACGAGCTGAA
1228162 ATCTTTAACC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
24 1 0.02
25 57 0.97
26 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (25 bp):
GTAAGCTCATACGAGCTGAATAACG
Found at i:1230199 original size:9 final size:10
Alignment explanation
Indices: 1230153--1230199 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
1230143 AACATGTTGC
*
1230153 ATTTTAATTA
1 ATTTTTATTA
1230163 ATTTTATAATTA
1 ATTTT-T-ATTA
*
1230175 ATTTTGATTA
1 ATTTTTATTA
1230185 ATTTTTATT-
1 ATTTTTATTA
1230194 ATTTTT
1 ATTTTT
1230200 GACATATTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 6 0.19
10 17 0.53
12 9 0.28
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (10 bp):
ATTTTTATTA
Found at i:1231200 original size:21 final size:21
Alignment explanation
Indices: 1231176--1231219 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1231166 ATTACAATTG
1231176 TAAGGTAAATAATGAATTAAT
1 TAAGGTAAATAATGAATTAAT
1231197 TAAGGTAAATAATGAATTAAT
1 TAAGGTAAATAATGAATTAAT
1231218 TA
1 TA
1231220 TTCAAATGAA
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:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (21 bp):
TAAGGTAAATAATGAATTAAT
Found at i:1238483 original size:25 final size:25
Alignment explanation
Indices: 1238427--1238510 Score: 91
Period size: 25 Copynumber: 3.4 Consensus size: 25
1238417 TATATCTCAT
* *
1238427 GTAAGCTCTTCC-AAGCTGAATAA-C
1 GTAAGCTCATCCGAA-CTGAATAATG
*
1238451 GTAAGCTCCTCCGAACTGAATAATG
1 GTAAGCTCATCCGAACTGAATAATG
* * *
1238476 GTAAGCTCATACGAGCTGAGTAATG
1 GTAAGCTCATCCGAACTGAATAATG
1238501 GTAAGCTCAT
1 GTAAGCTCAT
1238511 AAGAGCTAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
24 19 0.37
25 33 0.63
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (25 bp):
GTAAGCTCATCCGAACTGAATAATG
Found at i:1238511 original size:25 final size:25
Alignment explanation
Indices: 1238440--1238517 Score: 95
Period size: 25 Copynumber: 3.2 Consensus size: 25
1238430 AGCTCTTCCA
* * *
1238440 AGCTGAATAA-CGTAAGCTCCTCCG
1 AGCTGAATAATGGTAAGCTCATACG
*
1238464 AACTGAATAATGGTAAGCTCATACG
1 AGCTGAATAATGGTAAGCTCATACG
* *
1238489 AGCTGAGTAATGGTAAGCTCATAAG
1 AGCTGAATAATGGTAAGCTCATACG
1238514 AGCT
1 AGCT
1238518 AAAATCGGTA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
24 9 0.20
25 37 0.80
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (25 bp):
AGCTGAATAATGGTAAGCTCATACG
Found at i:1242550 original size:34 final size:34
Alignment explanation
Indices: 1242512--1242581 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
1242502 TTATGAAAAG
1242512 TTACAAAATTGTCATTTAACTATTCAAATTTATC
1 TTACAAAATTGTCATTTAACTATTCAAATTTATC
1242546 TTACAAAATTGTCATTTAACTATTCAAATTTATC
1 TTACAAAATTGTCATTTAACTATTCAAATTTATC
1242580 TT
1 TT
1242582 TTTTTGTTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (34 bp):
TTACAAAATTGTCATTTAACTATTCAAATTTATC
Found at i:1242574 original size:20 final size:20
Alignment explanation
Indices: 1242517--1242575 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
1242507 AAAAGTTACA
1242517 AAATTGTCATTTAACTATTC
1 AAATTGTCATTTAACTATTC
1242537 AAATT-T-ATCTT-AC-A---
1 AAATTGTCAT-TTAACTATTC
1242551 AAATTGTCATTTAACTATTC
1 AAATTGTCATTTAACTATTC
1242571 AAATT
1 AAATT
1242576 TATCTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 16
0.66 0.00 0.34
Matches are distributed among these distances:
14 5 0.16
15 3 0.10
16 4 0.13
17 2 0.06
18 4 0.13
19 3 0.10
20 10 0.32
ACGTcount: A:0.39, C:0.14, G:0.03, T:0.44
Consensus pattern (20 bp):
AAATTGTCATTTAACTATTC
Found at i:1242757 original size:18 final size:18
Alignment explanation
Indices: 1242736--1242770 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1242726 AAAATATGAA
1242736 AAGTAT-TTATTATATTTT
1 AAGTATGTTA-TATATTTT
1242754 AAGTATGTTATATATTT
1 AAGTATGTTATATATTT
1242771 CTATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (18 bp):
AAGTATGTTATATATTTT
Found at i:1244097 original size:31 final size:31
Alignment explanation
Indices: 1244062--1244131 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1244052 AAAATATCTC
* * * *
1244062 TATTATTTTTTTATATTATTTAAAATACCCT
1 TATTAATTATTTATACTACTTAAAATACCCT
1244093 TATTAATTATTTATACTACTTAAAATA-CCT
1 TATTAATTATTTATACTACTTAAAATACCCT
1244123 CTATTAATT
1 -TATTAATT
1244132 CTTAAACACT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 3 0.09
31 31 0.91
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (31 bp):
TATTAATTATTTATACTACTTAAAATACCCT
Found at i:1250407 original size:30 final size:30
Alignment explanation
Indices: 1250372--1250428 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
1250362 TGGGCATTTC
1250372 CACACGGGCTGGCCACACGCCCATGTGAGT
1 CACACGGGCTGGCCACACGCCCATGTGAGT
*
1250402 CACACGGGCTGGCCACATGCCCATGTG
1 CACACGGGCTGGCCACACGCCCATGTG
1250429 CTAGTCCGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.37, G:0.30, T:0.14
Consensus pattern (30 bp):
CACACGGGCTGGCCACACGCCCATGTGAGT
Found at i:1261339 original size:42 final size:43
Alignment explanation
Indices: 1261237--1261357 Score: 122
Period size: 42 Copynumber: 2.8 Consensus size: 43
1261227 ACAATGCTAA
* * * *
1261237 TGTCCCAGACATAGTCTTACATGTAATCAAATATCGATGCCAC
1 TGTCCCAGACGTGGTCTTACACGAAATCAAATATCGATGCCAC
* * *
1261280 TGTCCTAGACAG-GGTCTTACACGAAATCAAGTA-CGCTGCCAAC
1 TGTCCCAGAC-GTGGTCTTACACGAAATCAAATATCGATGCC-AC
* *
1261323 -GTCCCAGACGTGGTCTTACACGAAAACACATATCG
1 TGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
1261358 GATCCTATGT
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
41 1 0.02
42 32 0.51
43 30 0.48
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (43 bp):
TGTCCCAGACGTGGTCTTACACGAAATCAAATATCGATGCCAC
Found at i:1266698 original size:19 final size:19
Alignment explanation
Indices: 1266674--1266711 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1266664 TAAATTTGGA
1266674 TCTAGTATGAGATACTTTT
1 TCTAGTATGAGATACTTTT
1266693 TCTAGTATGAGATACTTTT
1 TCTAGTATGAGATACTTTT
1266712 ACTTTGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (19 bp):
TCTAGTATGAGATACTTTT
Found at i:1273560 original size:72 final size:71
Alignment explanation
Indices: 1273437--1273583 Score: 240
Period size: 72 Copynumber: 2.1 Consensus size: 71
1273427 CACTTTTTTG
* *
1273437 CTTTAGTTATTATTGTGATTATATCTGCTAATTGGGGTAAGTAAAGTTCAAACTTTGTAATATTC
1 CTTTAGTTATTATTGTGATTATATCTGCTAATTGGGGTAAGTAAAGGTCAAACCTTGTAATATTC
* *
1273502 CGCGAC
66 CACAAC
*
1273508 CTTTATGTTATTATTGTGATTATATCTGCTACTTGGGGTAAGTAAAGGTCAAACCTTGTAATATT
1 CTTTA-GTTATTATTGTGATTATATCTGCTAATTGGGGTAAGTAAAGGTCAAACCTTGTAATATT
1273573 CCACAAC
65 CCACAAC
1273580 CTTT
1 CTTT
1273584 TTGCATTGGT
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
71 5 0.07
72 65 0.93
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (71 bp):
CTTTAGTTATTATTGTGATTATATCTGCTAATTGGGGTAAGTAAAGGTCAAACCTTGTAATATTC
CACAAC
Found at i:1279475 original size:21 final size:21
Alignment explanation
Indices: 1279449--1279498 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1279439 TCAGAAGTAA
*
1279449 TAATACGACACACATGGTGCC
1 TAATACGACACACATAGTGCC
*
1279470 TAATACGACACATATAGTGCC
1 TAATACGACACACATAGTGCC
1279491 TAAT-CGAC
1 TAATACGAC
1279499 TCGAGGTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (21 bp):
TAATACGACACACATAGTGCC
Found at i:1280439 original size:16 final size:16
Alignment explanation
Indices: 1280418--1280451 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1280408 AAATCCCTAA
*
1280418 TTTCTCTTTTCTTTCT
1 TTTCTCCTTTCTTTCT
1280434 TTTCTCCTTTCTTTCT
1 TTTCTCCTTTCTTTCT
1280450 TT
1 TT
1280452 CCTATTTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTCCTTTCTTTCT
Found at i:1282442 original size:21 final size:21
Alignment explanation
Indices: 1282417--1282458 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1282407 TAAATTTAAC
1282417 TCAATTTAATAAAATTCACAT
1 TCAATTTAATAAAATTCACAT
* **
1282438 TCAATTTCATCCAATTCACAT
1 TCAATTTAATAAAATTCACAT
1282459 CTTAGGCAAA
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:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (21 bp):
TCAATTTAATAAAATTCACAT
Found at i:1293656 original size:26 final size:24
Alignment explanation
Indices: 1293617--1293675 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
1293607 TTATGTCATT
* *
1293617 AAATAAA-AAATTTAAAAATATAA
1 AAATAAATATATTTAAAAACATAA
1293640 TAAATCAAATATATTTAAAAACATAA
1 -AAAT-AAATATATTTAAAAACATAA
1293666 AAATAAATAT
1 AAATAAATAT
1293676 TAAAACAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 10 0.32
25 7 0.23
26 14 0.45
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATAAATATATTTAAAAACATAA
Found at i:1293687 original size:22 final size:22
Alignment explanation
Indices: 1293646--1293704 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
1293636 ATAATAAATC
* *
1293646 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
1293666 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
1293688 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
1293705 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
22 9 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:1293781 original size:15 final size:16
Alignment explanation
Indices: 1293751--1293783 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1293741 AAATGGTTAT
1293751 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
1293768 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
1293783 A
1 A
1293784 AAAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:1296433 original size:21 final size:21
Alignment explanation
Indices: 1296408--1296460 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1296398 AGCGGTGGCA
*
1296408 GTGAGATTAGTTACTGTAGCG
1 GTGAGATTAGATACTGTAGCG
*
1296429 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTGTAGCG
1296450 GTGAGATTAGA
1 GTGAGATTAGA
1296461 AACAGCGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.08, G:0.36, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCG
Found at i:1299177 original size:15 final size:15
Alignment explanation
Indices: 1299131--1299182 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 15
1299121 GGAAAAATAA
*
1299131 AAAATATTATTTGTT
1 AAAATATTATATGTT
* * *
1299146 -AAATGTTTTA-ATT
1 AAAATATTATATGTT
1299159 AAAATATTATATGTT
1 AAAATATTATATGTT
1299174 AAAATATTA
1 AAAATATTA
1299183 ATAAATGAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
13 2 0.07
14 15 0.54
15 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
AAAATATTATATGTT
Found at i:1308893 original size:161 final size:158
Alignment explanation
Indices: 1308628--1308939 Score: 459
Period size: 161 Copynumber: 2.0 Consensus size: 158
1308618 AAACCAAAGC
* *
1308628 TTTCTTTTAAAAAAAATACAATTTTTCTTAAAGATCAAAGCTTTATTTTGAAATAGTTGAAAAAG
1 TTTCTTTTAAAAAAAATACAACTTTTCTTAAAGATCAAAGCTTTATTTCGAAATAGTTGAAAAAG
* *
1308693 ATCGAAACTTTGTTTTAAAATTTTAAACTTTTCCTTTAAAATGACTAAAAAAAATAGATTTTTAT
66 ATCAAAACTTTATTTTAAAATTTTAAACTTTTCCTTTAAAATGACTAAAAAAAAT--ATTTTTAT
* *
1308758 TCTTAAAAATCTAAATTTTCTCTTCTTTTTT
129 T-TTAAAAATCTAAACTTCCTCTTCTTTTTT
* *
1308789 TTTCTTTT-AAAAAACTCACTACTTTTCTTAAAGATCAAAGCTTTTATTTCGAAATAGTTG-AAA
1 TTTCTTTTAAAAAAAAT-ACAACTTTTCTTAAAGATCAAAGC-TTTATTTCGAAATAGTTGAAAA
*
1308852 AGAATCAAAACTTTATTTTAAAATTTTAAAC-TTTCCTTTAAAATGACTAAAAAACATATTTTTA
64 AG-ATCAAAACTTTATTTTAAAATTTTAAACTTTTCCTTTAAAATGACTAAAAAAAATATTTTTA
*
1308916 TTTTTAAAATCTAAACTTCCTCTT
128 TTTTAAAAATCTAAACTTCCTCTT
1308940 TTAAAAAAAA
Statistics
Matches: 138, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
158 19 0.14
159 9 0.07
160 7 0.05
161 60 0.43
162 43 0.31
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (158 bp):
TTTCTTTTAAAAAAAATACAACTTTTCTTAAAGATCAAAGCTTTATTTCGAAATAGTTGAAAAAG
ATCAAAACTTTATTTTAAAATTTTAAACTTTTCCTTTAAAATGACTAAAAAAAATATTTTTATTT
TAAAAATCTAAACTTCCTCTTCTTTTTT
Found at i:1311562 original size:354 final size:354
Alignment explanation
Indices: 1310913--1311623 Score: 1332
Period size: 354 Copynumber: 2.0 Consensus size: 354
1310903 CAGGACTAAC
*
1310913 CAGGTTCGAAGTTGGAAAACATTGAAAAAGAGTAGTCCAAATTTGGACTATTTCTTCAAATTTTC
1 CAGGTTCGAAGTTGGAAAACATTGAAAAAAAGTAGTCCAAATTTGGACTATTTCTTCAAATTTTC
* *
1310978 TGTCAGAGATAACGGCTAAGCAGGAAGACGTGATAGCACATCAATGATAGAACCCGGACGAATTA
66 TGTCAGAGATAACGACTAAGCAGGAAGACGTGATAGCACATCAATGATAGAACCCGAACGAATTA
*
1311043 TGGGCAATGACACCTTAAGCATTTAAAAAGGAATCACTCTCATAACATTTCTACATTCATAATCA
131 TGGGCAATGACACCTTAAACATTTAAAAAGGAATCACTCTCATAACATTTCTACATTCATAATCA
*
1311108 TTCATCTAGTTAGGGATATTTGATTCATCTCGATCATAGCATCCTAGTTATTTGATATACGCAGA
196 TTCATCTAGTTAGGGACATTTGATTCATCTCGATCATAGCATCCTAGTTATTTGATATACGCAGA
1311173 TATAGGAAACCCATTCTACACATCATGTCTTTAGAAGACAGCGTAGCGACATTGCCAAATCCAGC
261 TATAGGAAACCCATTCTACACATCATGTCTTTAGAAGACAGCGTAGCGACATTGCCAAATCCAGC
1311238 AGATTTGGCATCTCTGTATTGGCGGAGAG
326 AGATTTGGCATCTCTGTATTGGCGGAGAG
1311267 CAGGTTCGAAGTTGGAAAACATTGAAAAAAAGTAGTCCAAATTTGGACTATTTCTTCAAATTTTC
1 CAGGTTCGAAGTTGGAAAACATTGAAAAAAAGTAGTCCAAATTTGGACTATTTCTTCAAATTTTC
*
1311332 TGTCAGAGATAACGACTAAGTAGGAAGACGTGATAGCACATCAATGATAGAACCCGAACGAATTA
66 TGTCAGAGATAACGACTAAGCAGGAAGACGTGATAGCACATCAATGATAGAACCCGAACGAATTA
1311397 TGGGCAATGACACCTTAAACATTTAAAAAGGAATCACTCTCATAACATTTCTACATTCATAATCA
131 TGGGCAATGACACCTTAAACATTTAAAAAGGAATCACTCTCATAACATTTCTACATTCATAATCA
*
1311462 TTCATCTAGTTAGGGACATTTGATTGATCTCGATCATAGCATCCTAGTTATTTGATATACGCAGA
196 TTCATCTAGTTAGGGACATTTGATTCATCTCGATCATAGCATCCTAGTTATTTGATATACGCAGA
***
1311527 TATAGGAAACCCATTCTACACATCATGTCTTTAGAAGACAGCGTAGCGACATTGGTGAATCCAGC
261 TATAGGAAACCCATTCTACACATCATGTCTTTAGAAGACAGCGTAGCGACATTGCCAAATCCAGC
1311592 AGATTTGGCATCTCTGTATTGGCGGAGAG
326 AGATTTGGCATCTCTGTATTGGCGGAGAG
1311621 CAG
1 CAG
1311624 ATCGAAGATA
Statistics
Matches: 347, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
354 347 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (354 bp):
CAGGTTCGAAGTTGGAAAACATTGAAAAAAAGTAGTCCAAATTTGGACTATTTCTTCAAATTTTC
TGTCAGAGATAACGACTAAGCAGGAAGACGTGATAGCACATCAATGATAGAACCCGAACGAATTA
TGGGCAATGACACCTTAAACATTTAAAAAGGAATCACTCTCATAACATTTCTACATTCATAATCA
TTCATCTAGTTAGGGACATTTGATTCATCTCGATCATAGCATCCTAGTTATTTGATATACGCAGA
TATAGGAAACCCATTCTACACATCATGTCTTTAGAAGACAGCGTAGCGACATTGCCAAATCCAGC
AGATTTGGCATCTCTGTATTGGCGGAGAG
Found at i:1311676 original size:44 final size:44
Alignment explanation
Indices: 1311589--1312520 Score: 1228
Period size: 44 Copynumber: 21.2 Consensus size: 44
1311579 TGGTGAATCC
* *
1311589 AGCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* * * * * *
1311633 AGTAGATTTGGCATCTCTGGATTGTCAGA-AGGCATATCAAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGA-GCAGATCAAAGAT
* **
1311677 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAAATTGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* *
1311721 AGTAGATTTGGCGTCTCTGTATTGGTGGAGAGCAGATCAAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
*
1311765 AGCAGATTTGGCATCTCTGTATTGGCAGG-GAGCAGATCAAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGC-GGAGAGCAGATCAAAGAT
* * * * *
1311809 AGCAGATTTGGCATCTCTGTATTGTCAGAGGGCAGATCGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* * *
1311853 AGCAGATTTGGCGTCTCTATATTAGCGGAGAGCAGATCGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* *
1311897 AGCAAATTTGGCATCTCTGTATTGGCAGG-GAGCAGATCAAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGC-GGAGAGCAGATCAAAGAT
* * * * * *
1311941 AGCAGATTTGGCGTATCTATATTGTCAGAGGGCAGATCGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
1311985 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* * * *
1312029 AGCAGATTTGGCGTCTCTGTATTGTCAGAGGGCAGATCGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
1312073 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* * *
1312117 AGCAGATTTGGCGTCTCTGTATTGGCAGAGGGCAGATCGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* * *
1312161 AGCAAATTTGGCGTATCTGTATTGGCGGAGAGCAGATCGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* * * *
1312205 AGCAGATTTGGCATCTCTGTATTGGTGGAGAGTAGATCGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* * * *
1312249 AACACATTTGGCGTCTCTGTATTGTCAGG-GGGCAGATCAAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGC-GGAGAGCAGATCAAAGAT
1312293 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
1312337 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* * *
1312381 AGCAGATTTGGCGTCTCTGTGTTGGCGGAGAGTAGATCGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* * * * * *
1312425 AGCAGATTTGACATCTCTGTGTTGACAGAGAGCAGATCAAGGAT
1 AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
* *
1312469 -GACAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAA-AT
1 AG-CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATC-AAAGAT
*
1312513 AACAGATT
1 AGCAGATT
1312521 GGTGCTCCCG
Statistics
Matches: 779, Mismatches: 98, Indels: 22
0.87 0.11 0.02
Matches are distributed among these distances:
43 6 0.01
44 764 0.98
45 9 0.01
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.26
Consensus pattern (44 bp):
AGCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT
Found at i:1314093 original size:47 final size:44
Alignment explanation
Indices: 1313986--1314076 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
1313976 TATTTCATTC
*
1313986 TTTAGGAAACTATTTTATTATTTATTTATTCAAAGCTTGTTTTT
1 TTTAGGAAACTATTTTATTATTCATTTATTCAAAGCTTGTTTTT
1314030 TTTAGGAAACTATTTTATTATTCATTTATTCAAAGCTTGTTTTT
1 TTTAGGAAACTATTTTATTATTCATTTATTCAAAGCTTGTTTTT
1314074 TTT
1 TTT
1314077 TTATATTATG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.26, C:0.08, G:0.09, T:0.57
Consensus pattern (44 bp):
TTTAGGAAACTATTTTATTATTCATTTATTCAAAGCTTGTTTTT
Found at i:1314504 original size:25 final size:26
Alignment explanation
Indices: 1314452--1314511 Score: 95
Period size: 25 Copynumber: 2.3 Consensus size: 26
1314442 GTTATTCACC
* *
1314452 TTTAAATTTCTTTTGTATTTATTTAT
1 TTTAAGTTTCTTTAGTATTTATTTAT
1314478 TTTAAGTTTCTTTAGTA-TTATTTAT
1 TTTAAGTTTCTTTAGTATTTATTTAT
1314503 TTTAAGTTT
1 TTTAAGTTT
1314512 TTATACATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 17 0.53
26 15 0.47
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (26 bp):
TTTAAGTTTCTTTAGTATTTATTTAT
Found at i:1314624 original size:22 final size:22
Alignment explanation
Indices: 1314598--1314642 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1314588 TATTTTTATG
*
1314598 TATTATTCATTTTAAATTGTTT
1 TATTATTCACTTTAAATTGTTT
* *
1314620 TATTATTTACTTTAAATTTTTT
1 TATTATTCACTTTAAATTGTTT
1314642 T
1 T
1314643 TCTCTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTCACTTTAAATTGTTT
Found at i:1334641 original size:14 final size:13
Alignment explanation
Indices: 1334607--1334647 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1334597 AAATATTAAC
1334607 TTTT-AAATCATT
1 TTTTAAAATCATT
*
1334619 TTTTAAAATAATT
1 TTTTAAAATCATT
1334632 TTTTAGAAATCATT
1 TTTTA-AAATCATT
1334646 TT
1 TT
1334648 CAGTCACACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 4 0.16
13 12 0.48
14 9 0.36
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (13 bp):
TTTTAAAATCATT
Done.