Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007814.1 Hibiscus syriacus cultivar Beakdansim tig00110146_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 367404
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:620 original size:7 final size:6
Alignment explanation
Indices: 578--619 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
568 GTGCTGCAAC
*
578 AAAAGA AAAAGA GAAAGA AAGAAGAA AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AA-AAG-A AAAAGA AAAAGA AAAA
620 AAAGACTCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 23 0.72
7 6 0.19
8 3 0.09
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:622 original size:15 final size:16
Alignment explanation
Indices: 580--624 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 16
570 GCTGCAACAA
580 AAGAAAAAGAGAAAGAAAG
1 AAGAAAAA-AG-AA-AAAG
599 AAGAAAAAAGAAAAAG
1 AAGAAAAAAGAAAAAG
615 AA-AAAAAAGA
1 AAGAAAAAAGA
625 CTCCTACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.31
16 6 0.23
17 2 0.08
18 2 0.08
19 8 0.31
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAGAAAAAG
Found at i:13966 original size:30 final size:31
Alignment explanation
Indices: 13908--13967 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
13898 TCTATCTTTA
** *
13908 TATTATGTTTTACATATGTTTTATATTCATT
1 TATTATGTTTTACATATCATTTACATTCATT
*
13939 TATTATG-TTTGCATATCATTTACATTCAT
1 TATTATGTTTTACATATCATTTACATTCAT
13968 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.57
Consensus pattern (31 bp):
TATTATGTTTTACATATCATTTACATTCATT
Found at i:20168 original size:13 final size:13
Alignment explanation
Indices: 20146--20175 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
20136 ACTCAACACC
20146 TTTC-ACATACCT
1 TTTCAACATACCT
20158 TTTCAACATACCT
1 TTTCAACATACCT
20171 TTTCA
1 TTTCA
20176 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:25821 original size:91 final size:91
Alignment explanation
Indices: 25666--25847 Score: 274
Period size: 91 Copynumber: 2.0 Consensus size: 91
25656 GTAGTTTATT
* * *
25666 CTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCATATGCAAGGCACATGG
1 CTTGGCCGAATAGGGAGAGAACTCTTCATCTAGCCGCCTAAATGAACCACATGCAAGGCACATGG
25731 GGGCTGATCACATGCAAAACACATGG
66 GGGCTGATCACATGCAAAACACATGG
* *
25757 CTTGGCTGAATAGGGAGAGAACTCTTCATCTAGCCGCCTAAATGATCCACATGCAAGGCACATGG
1 CTTGGCCGAATAGGGAGAGAACTCTTCATCTAGCCGCCTAAATGAACCACATGCAAGGCACATGG
* * * **
25822 GGGTTGGTCATATGCAAGGCACATGG
66 GGGCTGATCACATGCAAAACACATGG
25848 GTGTTCTATG
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 81 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (91 bp):
CTTGGCCGAATAGGGAGAGAACTCTTCATCTAGCCGCCTAAATGAACCACATGCAAGGCACATGG
GGGCTGATCACATGCAAAACACATGG
Found at i:29334 original size:8 final size:8
Alignment explanation
Indices: 29311--29340 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
29301 ATTAGAGTGC
29311 AAAAAGAA
1 AAAAAGAA
29319 AGAAAAGAA
1 A-AAAAGAA
29328 AAAAAGAA
1 AAAAAGAA
29336 AAAAA
1 AAAAA
29341 TCAGAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:29370 original size:24 final size:24
Alignment explanation
Indices: 29311--29371 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
29301 ATTAGAGTGC
* *
29311 AAAAAGAAAGAAAAGAAAAAAAGA
1 AAAAAAAAAGAATAGAAAAAAAGA
** * *
29335 AAAAAATCAGAATATAAGAAAAGA
1 AAAAAAAAAGAATAGAAAAAAAGA
29359 AAAAAAAAAGAAT
1 AAAAAAAAAGAAT
29372 TTCAAAAAGA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.07
Consensus pattern (24 bp):
AAAAAAAAAGAATAGAAAAAAAGA
Found at i:33135 original size:8 final size:8
Alignment explanation
Indices: 33112--33141 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
33102 ATTAGAGTGC
33112 AAAAAGAA
1 AAAAAGAA
33120 AGAAAAGAA
1 A-AAAAGAA
33129 AAAAAGAA
1 AAAAAGAA
33137 AAAAA
1 AAAAA
33142 TCAGAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:33147 original size:24 final size:24
Alignment explanation
Indices: 33120--33165 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
33110 GCAAAAAGAA
33120 AGAAAAGAAAAAAAGAAAAAAATC
1 AGAAAAGAAAAAAAGAAAAAAATC
* * *
33144 AGAATATAAGAAAAGAAAAAAA
1 AGAAAAGAAAAAAAGAAAAAAA
33166 AAGAATTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (24 bp):
AGAAAAGAAAAAAAGAAAAAAATC
Found at i:36110 original size:25 final size:24
Alignment explanation
Indices: 36053--36111 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
36043 ATTCTTTGTT
* *
36053 TTTTTTTCTTTTTGAGTGCTGGAA
1 TTTTTTTCTTTTGGAGTGCTGCAA
*
36077 TTTTCTTTCTTTTGGAGTGCTTCAA
1 TTTT-TTTCTTTTGGAGTGCTGCAA
36102 TTTCTTTTCT
1 TTT-TTTTCT
36112 GATTTCTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.13
25 25 0.83
26 1 0.03
ACGTcount: A:0.10, C:0.14, G:0.15, T:0.61
Consensus pattern (24 bp):
TTTTTTTCTTTTGGAGTGCTGCAA
Found at i:38524 original size:27 final size:26
Alignment explanation
Indices: 38478--38533 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
38468 GAAATATGAA
38478 ATAAGAAATGGAAGAAGAAAGGAAATG
1 ATAAGAAATGGAAGAAGAAAGG-AATG
***
38505 ATAAGAAATGGAATTGGAAAGGAATG
1 ATAAGAAATGGAAGAAGAAAGGAATG
38531 ATA
1 ATA
38534 TCAAAGTAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.16
Consensus pattern (26 bp):
ATAAGAAATGGAAGAAGAAAGGAATG
Found at i:39097 original size:19 final size:19
Alignment explanation
Indices: 39073--39109 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39063 TACATGATTT
39073 TTTTAATGAAAATACATGA
1 TTTTAATGAAAATACATGA
*
39092 TTTTAATGAAGATACATG
1 TTTTAATGAAAATACATG
39110 CTCTTGGCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (19 bp):
TTTTAATGAAAATACATGA
Found at i:40726 original size:19 final size:20
Alignment explanation
Indices: 40704--40741 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
40694 CATTTCTTTA
40704 TTTTCATTTCATT-CTTATT
1 TTTTCATTTCATTACTTATT
*
40723 TTTTCCTTTCATTACTTAT
1 TTTTCATTTCATTACTTAT
40742 ATTATTACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTCATTTCATTACTTATT
Found at i:41045 original size:13 final size:12
Alignment explanation
Indices: 40998--41045 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 12
40988 ATTAGAGTGC
*
40998 AAAAAGAAGAGA
1 AAAAAGAAAAGA
41010 AAAATCAGAAAAGA
1 AAAA--AGAAAAGA
41024 ATAAAAGAAAAGA
1 A-AAAAGAAAAGA
41037 AAAAGAGAA
1 AAAA-AGAA
41046 GTTCAAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 7 0.23
13 13 0.42
14 8 0.26
15 3 0.10
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:45298 original size:19 final size:20
Alignment explanation
Indices: 45276--45313 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
45266 CATTTCTTTA
45276 TTTTCATTTCATT-CTTATT
1 TTTTCATTTCATTACTTATT
*
45295 TTTTCCTTTCATTACTTAT
1 TTTTCATTTCATTACTTAT
45314 ATTATTACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTCATTTCATTACTTATT
Found at i:49857 original size:19 final size:20
Alignment explanation
Indices: 49829--49866 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
49819 TATTTCATTA
49829 TTTTCATTTCATT-CTTATT
1 TTTTCATTTCATTACTTATT
*
49848 TTTTCCTTTCATTACTTAT
1 TTTTCATTTCATTACTTAT
49867 ATTATTTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTCATTTCATTACTTATT
Found at i:59265 original size:13 final size:11
Alignment explanation
Indices: 59224--59308 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
59214 ACAATCTATC
59224 CATCACCATTAT
1 CATCACCA-TAT
*
59236 CA-CGCCTATAT
1 CATCACC-ATAT
59247 CATCACCATAGT
1 CATCACCATA-T
59259 CCATCACCATTAT
1 -CATCACCA-TAT
*
59272 CA-CGCCTATAT
1 CATCACC-ATAT
59283 CATCACCATATT
1 CATCACCATA-T
59295 CCATCACCATAT
1 -CATCACCATAT
59307 CA
1 CA
59309 CGCCCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:59269 original size:36 final size:36
Alignment explanation
Indices: 59222--59325 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
59212 ATACAATCTA
59222 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
59258 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
59294 TCCATCACCA-TATCACGCCCATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
59326 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:64981 original size:13 final size:11
Alignment explanation
Indices: 64940--65024 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
64930 ACAATCTGTC
64940 CATCACCATTAT
1 CATCACCA-TAT
*
64952 CA-CGACTATAT
1 CATC-ACCATAT
64963 CATCACCATAGT
1 CATCACCATA-T
64975 CCATCACCATTAT
1 -CATCACCA-TAT
*
64988 CA-CGCCTATAT
1 CATCACC-ATAT
64999 CATCACCATATT
1 CATCACCATA-T
65011 CCATCACCATAT
1 -CATCACCATAT
65023 CA
1 CA
65025 CGCCCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:64984 original size:36 final size:36
Alignment explanation
Indices: 64937--65041 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
64927 GATACAATCT
*
64937 GTCCATCACCATTATCACGACTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
64973 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
65009 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
65042 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.31, C:0.36, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:69179 original size:11 final size:11
Alignment explanation
Indices: 69165--69221 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
69155 AGGATGATTT
69165 AATGGTGATGA
1 AATGGTGATGA
69176 AATGGTGATGGA
1 AATGGTGAT-GA
69188 ATATGGTGATGA
1 A-ATGGTGATGA
* *
69200 TATAGGCG-TGA
1 AAT-GGTGATGA
69211 TAATGGTGATG
1 -AATGGTGATG
69222 GACAGATTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
11 17 0.46
12 12 0.32
13 8 0.22
ACGTcount: A:0.32, C:0.02, G:0.37, T:0.30
Consensus pattern (11 bp):
AATGGTGATGA
Found at i:74425 original size:12 final size:13
Alignment explanation
Indices: 74408--74437 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
74398 GTTGTAGGAG
74408 TCTTTTCTTTTC-
1 TCTTTTCTTTTCT
74420 TCTTTTCTTTTCT
1 TCTTTTCTTTTCT
74433 TCTTT
1 TCTTT
74438 CTTGTTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTTCTTTTCT
Found at i:74819 original size:11 final size:11
Alignment explanation
Indices: 74805--74861 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
74795 AGGATGATTT
74805 AATGGTGATGA
1 AATGGTGATGA
74816 AATGGTGATGGA
1 AATGGTGAT-GA
74828 ATATGGTGATGA
1 A-ATGGTGATGA
* *
74840 TATAGGCG-TGA
1 AAT-GGTGATGA
74851 TAATGGTGATG
1 -AATGGTGATG
74862 GACAGATTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
11 17 0.46
12 12 0.32
13 8 0.22
ACGTcount: A:0.32, C:0.02, G:0.37, T:0.30
Consensus pattern (11 bp):
AATGGTGATGA
Found at i:112539 original size:23 final size:24
Alignment explanation
Indices: 112513--112571 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
112503 AAAATCTGCA
112513 AAGAAAATAAAAGCACT-AAAAAG
1 AAGAAAATAAAAGCACTCAAAAAG
* * *
112536 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCAAAAAG
112560 AAGAAAAATAAA
1 AAG-AAAATAAA
112572 GAAAGAAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
23 15 0.52
24 8 0.28
25 6 0.21
ACGTcount: A:0.66, C:0.08, G:0.15, T:0.10
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCAAAAAG
Found at i:121712 original size:23 final size:24
Alignment explanation
Indices: 121670--121722 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
121660 TTTCTTTCTT
121670 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
121694 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
121717 TTTCTT
1 TTTCTT
121723 TACTGTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:125325 original size:14 final size:15
Alignment explanation
Indices: 125308--125336 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
125298 GAACATTCAG
125308 AAAAGAAGA-AGAAA
1 AAAAGAAGAGAGAAA
125322 AAAAGAAGAGAGAAA
1 AAAAGAAGAGAGAAA
125337 GCAAGCCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAGAGAAA
Found at i:127947 original size:13 final size:12
Alignment explanation
Indices: 127928--128013 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
127918 AAATAGGCGT
127928 GATATGGTGATG
1 GATATGGTGATG
127940 GAATATGGTGAT-
1 G-ATATGGTGATG
*
127952 GATATAGGCG-T-
1 GATAT-GGTGATG
127963 GATAATGGTGATG
1 GAT-ATGGTGATG
127976 GACTATGGTGAT-
1 GA-TATGGTGATG
*
127988 GATATAGGCG-T-
1 GATAT-GGTGATG
127999 GATAATGGTGATG
1 GAT-ATGGTGATG
128012 GA
1 GA
128014 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:127983 original size:36 final size:36
Alignment explanation
Indices: 127910--128014 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
127900 ATTTATAAGT
* * *
127910 TGGTGATAAAATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
127945 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
127981 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
128015 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:133695 original size:36 final size:36
Alignment explanation
Indices: 133632--133726 Score: 156
Period size: 36 Copynumber: 2.7 Consensus size: 36
133622 TGGTGATAAA
* *
133632 ATAGGCATGAT-ATGGTGATGGAATATGGTGAAGAT
1 ATAGGCGTGATAATGGTGATGGACTATGGTGAAGAT
*
133667 ATAGGCGTGATAATGGTGATGGACTATGGTGATGAT
1 ATAGGCGTGATAATGGTGATGGACTATGGTGAAGAT
133703 ATAGGCGTGATAATGGTGATGGAC
1 ATAGGCGTGATAATGGTGATGGAC
133727 AGATTGTATC
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 10 0.18
36 46 0.82
ACGTcount: A:0.31, C:0.05, G:0.36, T:0.28
Consensus pattern (36 bp):
ATAGGCGTGATAATGGTGATGGACTATGGTGAAGAT
Found at i:138754 original size:5 final size:5
Alignment explanation
Indices: 138744--138774 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
138734 CTTCAACTTG
*
138744 TTTCT TTTCT TTTCT TTTCT TTGCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
138775 CTTTTTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:158322 original size:18 final size:17
Alignment explanation
Indices: 158273--158323 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
158263 AATTGGAGTG
158273 CAAAAAGAAAGAAAAAGA
1 CAAAAAGAAA-AAAAAGA
**
158291 CAAAAAGAAGAAAAAATT
1 CAAAAAGAA-AAAAAAGA
158309 CAGAAAAGAAAAAAA
1 CA-AAAAGAAAAAAA
158324 GAAATTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 21 0.72
19 8 0.28
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (17 bp):
CAAAAAGAAAAAAAAGA
Found at i:163596 original size:38 final size:39
Alignment explanation
Indices: 163545--163622 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
163535 TCCTTCCTAG
*
163545 ATCCACAATCAA-TTGTTAAGGTACAAGTGCCTTACATC
1 ATCCACAATCAATTTGTTAAGGTACAAATGCCTTACATC
*
163583 ATCCACAATCAATTTGTTGAGGTACAAATGCCTTACATC
1 ATCCACAATCAATTTGTTAAGGTACAAATGCCTTACATC
163622 A
1 A
163623 AGTGGCAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 12 0.32
39 25 0.68
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (39 bp):
ATCCACAATCAATTTGTTAAGGTACAAATGCCTTACATC
Found at i:163760 original size:23 final size:24
Alignment explanation
Indices: 163739--163788 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
163729 TCAGAAAAGG
*
163739 AAATGAAGCACTCAAAATAAAGAA
1 AAATCAAGCACTCAAAATAAAGAA
* *
163763 AAATCCAGCACTCAAAA-GAAGAA
1 AAATCAAGCACTCAAAATAAAGAA
163786 AAA
1 AAA
163789 AAGAAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.62, C:0.16, G:0.12, T:0.10
Consensus pattern (24 bp):
AAATCAAGCACTCAAAATAAAGAA
Found at i:168623 original size:11 final size:11
Alignment explanation
Indices: 168609--168635 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
168599 TATTTTCTTT
168609 ATCTTATTTTA
1 ATCTTATTTTA
168620 ATCTTATTTTA
1 ATCTTATTTTA
168631 ATCTT
1 ATCTT
168636 GTTTCCAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (11 bp):
ATCTTATTTTA
Found at i:169026 original size:12 final size:12
Alignment explanation
Indices: 168982--169009 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
168972 AACAAAAAAC
168982 AAAAAAAGGCAA
1 AAAAAAAGGCAA
168994 AAAAAAAGGCAA
1 AAAAAAAGGCAA
169006 AAAA
1 AAAA
169010 CAAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAAGGCAA
Found at i:169038 original size:20 final size:19
Alignment explanation
Indices: 168965--169026 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
168955 GCTATTTTTT
*
168965 AAAAAA-AAACAAAAAA-CA
1 AAAAAACAAA-AAAAAAGCC
*
168983 AAAAAAGGCAAAAAAAAAGGC
1 AAAAAA--CAAAAAAAAAGCC
169004 AAAAAACAAAAAAAAAGCC
1 AAAAAACAAAAAAAAAGCC
169023 AAAA
1 AAAA
169027 TTTCAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 6 0.16
19 16 0.43
20 6 0.16
21 9 0.24
ACGTcount: A:0.81, C:0.11, G:0.08, T:0.00
Consensus pattern (19 bp):
AAAAAACAAAAAAAAAGCC
Found at i:173355 original size:22 final size:22
Alignment explanation
Indices: 173330--173371 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
173320 CAATTCATTT
173330 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
173352 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
173372 CCAGCACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:187031 original size:33 final size:33
Alignment explanation
Indices: 186952--187055 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
186942 ATACAATCTG
* *
186952 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
186988 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
187021 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
187054 TC
1 TC
187056 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:187497 original size:15 final size:15
Alignment explanation
Indices: 187462--187509 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
187452 AATTTGGAGT
*
187462 GCAAAAGAAAGAAAA
1 GCAAAAGAAAAAAAA
*
187477 GAAAAAGAAAAAAAA
1 GCAAAAGAAAAAAAA
*
187492 TCAAAAGCAAAAGAAAA
1 GCAAAAG-AAAA-AAAA
187509 G
1 G
187510 TGAAGCAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 18 0.69
16 4 0.15
17 4 0.15
ACGTcount: A:0.75, C:0.06, G:0.17, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAAAAAA
Found at i:190982 original size:33 final size:33
Alignment explanation
Indices: 190903--191006 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
190893 ATACAATCTG
* *
190903 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
190939 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
190972 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
191005 TC
1 TC
191007 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:192684 original size:11 final size:11
Alignment explanation
Indices: 192628--192684 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
192618 ACAATCTGTC
192628 CATCACCATTAT
1 CATCACCATT-T
* *
192640 CA-CGCCTATAT
1 CATCACC-ATTT
192651 CATCACCATATT
1 CATCACCAT-TT
192663 CCATCACCATTT
1 -CATCACCATTT
192675 CATCACCATT
1 CATCACCATT
192685 AAATCATCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
11 18 0.49
12 10 0.27
13 9 0.24
ACGTcount: A:0.30, C:0.37, G:0.02, T:0.32
Consensus pattern (11 bp):
CATCACCATTT
Found at i:193137 original size:15 final size:15
Alignment explanation
Indices: 193102--193149 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
193092 AATTTGGAGT
*
193102 GCAAAAGAAAGAAAA
1 GCAAAAGAAAAAAAA
*
193117 GAAAAAGAAAAAAAA
1 GCAAAAGAAAAAAAA
*
193132 TCAAAAGCAAAAGAAAA
1 GCAAAAG-AAAA-AAAA
193149 G
1 G
193150 TGAAGCAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 18 0.69
16 4 0.15
17 4 0.15
ACGTcount: A:0.75, C:0.06, G:0.17, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAAAAAA
Found at i:198294 original size:11 final size:11
Alignment explanation
Indices: 198238--198294 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
198228 ACAATCTGTC
198238 CATCACCATTAT
1 CATCACCATT-T
* *
198250 CA-CGCCTATAT
1 CATCACC-ATTT
198261 CATCACCATATT
1 CATCACCAT-TT
198273 CCATCACCATTT
1 -CATCACCATTT
198285 CATCACCATT
1 CATCACCATT
198295 AAATCATCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
11 18 0.49
12 10 0.27
13 9 0.24
ACGTcount: A:0.30, C:0.37, G:0.02, T:0.32
Consensus pattern (11 bp):
CATCACCATTT
Found at i:208316 original size:11 final size:11
Alignment explanation
Indices: 208302--208343 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
208292 AATTTTGGCT
208302 TTTTTTTTTGG
1 TTTTTTTTTGG
*
208313 TTTTGTTTTTGC
1 TTTT-TTTTTGG
*
208325 ATTTTTTTT-G
1 TTTTTTTTTGG
208335 TTTTTTTTT
1 TTTTTTTTT
208344 AAATAGCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 8 0.31
11 9 0.35
12 9 0.35
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTGG
Found at i:208699 original size:11 final size:12
Alignment explanation
Indices: 208669--208714 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
208659 TTGGTGCTAG
208669 AAACAAGATAAA
1 AAACAAGATAAA
* *
208681 AAATAAGAT-TA
1 AAACAAGATAAA
208692 AAACAAGATAAA
1 AAACAAGATAAA
*
208704 GAA-AAGATAAA
1 AAACAAGATAAA
208715 GCAATTGCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:208699 original size:23 final size:22
Alignment explanation
Indices: 208669--208711 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
208659 TTGGTGCTAG
208669 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
*
208692 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
208712 AAAGCAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Found at i:213808 original size:19 final size:20
Alignment explanation
Indices: 213784--213826 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
213774 AGCATTTATC
*
213784 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
213803 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
213823 TTCA
1 TTCA
213827 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:214181 original size:14 final size:14
Alignment explanation
Indices: 214162--214189 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
214152 TAAGATACTA
214162 TTTCCATCACCATC
1 TTTCCATCACCATC
214176 TTTCCATCACCATC
1 TTTCCATCACCATC
214190 AATCCTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:224550 original size:16 final size:16
Alignment explanation
Indices: 224529--224561 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
224519 TAGTTAGCTC
224529 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
224545 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
224561 A
1 A
224562 GGTGGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:228150 original size:16 final size:16
Alignment explanation
Indices: 228129--228161 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
228119 TAGTTAGCTC
228129 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
*
228145 ATTTGCATTGTAACAT
1 ATTTGCATTCTAACAT
228161 A
1 A
228162 GGTGGCAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:231771 original size:16 final size:16
Alignment explanation
Indices: 231750--231782 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
231740 TAGTTAGCTC
231750 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
*
231766 ATTTGCATTGTAACAT
1 ATTTGCATTCTAACAT
231782 A
1 A
231783 GGTGGCAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:241119 original size:14 final size:11
Alignment explanation
Indices: 241086--241118 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
241076 AAGGAAGTAT
241086 CTCAAAGAAGA
1 CTCAAAGAAGA
241097 CTCAAAGAAGA
1 CTCAAAGAAGA
241108 CTCAAAGAAGA
1 CTCAAAGAAGA
241119 ACCAATGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.55, C:0.18, G:0.18, T:0.09
Consensus pattern (11 bp):
CTCAAAGAAGA
Found at i:242947 original size:22 final size:22
Alignment explanation
Indices: 242919--242960 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
242909 AACAAAGTGA
242919 AGCACTC-AAAAGAAAGAAAATC
1 AGCACTCAAAAAG-AAGAAAATC
242941 AGCACTCAAAAAGAAGAAAA
1 AGCACTCAAAAAGAAGAAAA
242961 GCAAAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.62, C:0.17, G:0.14, T:0.07
Consensus pattern (22 bp):
AGCACTCAAAAAGAAGAAAATC
Found at i:243011 original size:13 final size:13
Alignment explanation
Indices: 242993--243025 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
242983 AGTTGAAGCA
242993 CTCATCAACAATT
1 CTCATCAACAATT
243006 CTCATCAACAATT
1 CTCATCAACAATT
243019 CTCATCA
1 CTCATCA
243026 CCAAGCATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (13 bp):
CTCATCAACAATT
Found at i:249927 original size:25 final size:25
Alignment explanation
Indices: 249899--249949 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
249889 ACATTAGAAT
249899 CGTTTAATGATTCATTCACATTATA
1 CGTTTAATGATTCATTCACATTATA
249924 CGTTTAATGATTCATTCACATTATA
1 CGTTTAATGATTCATTCACATTATA
249949 C
1 C
249950 TTACCGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (25 bp):
CGTTTAATGATTCATTCACATTATA
Found at i:253301 original size:9 final size:9
Alignment explanation
Indices: 253289--253322 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
253279 AAATTTTGGC
253289 TTTTTTGTT
1 TTTTTTGTT
253298 TTTTTGTGTT
1 TTTTT-TGTT
253308 TTTTTTGTT
1 TTTTTTGTT
253317 TTTTTT
1 TTTTTT
253323 TGAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:253312 original size:11 final size:10
Alignment explanation
Indices: 253289--253324 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
253279 AAATTTTGGC
253289 TTTTTTGTTT
1 TTTTTTGTTT
*
253299 TTTTGTG-TT
1 TTTTTTGTTT
253308 TTTTTTGTTT
1 TTTTTTGTTT
253318 TTTTTTG
1 TTTTTTG
253325 AAAAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:253874 original size:21 final size:21
Alignment explanation
Indices: 253850--253897 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
253840 GAAATTTTGA
253850 TTTTTTG-TTTTTTTCTTCTTT
1 TTTTTTGCTTTTTTTCTT-TTT
*
253871 TTTTTTGCCTTTTTTTGTTTTT
1 TTTTTTG-CTTTTTTTCTTTTT
253893 TTTTT
1 TTTTT
253898 AAAATAGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 8 0.33
23 9 0.38
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.85
Consensus pattern (21 bp):
TTTTTTGCTTTTTTTCTTTTT
Found at i:254261 original size:11 final size:10
Alignment explanation
Indices: 254226--254268 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 10
254216 TGCTGGAAAC
254226 AAGATAAGAAA
1 AAGATAA-AAA
254237 TAAGATTAAAAA
1 -AAGA-TAAAAA
254249 AAGATAAAGAA
1 AAGATAAA-AA
254260 AAGATAAAA
1 AAGATAAAA
254269 GAATTGCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.17
11 14 0.48
12 7 0.24
13 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (10 bp):
AAGATAAAAA
Found at i:263164 original size:12 final size:12
Alignment explanation
Indices: 263149--263173 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
263139 CCTCTTTGCA
263149 TTTTTCTTTCTT
1 TTTTTCTTTCTT
263161 TTTTTCTTTCTT
1 TTTTTCTTTCTT
263173 T
1 T
263174 CGTTTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:266241 original size:33 final size:33
Alignment explanation
Indices: 266197--266265 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
266187 CATCACCATA
*
266197 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
266230 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
266263 TTC
1 TTC
266266 ATTTATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:268113 original size:11 final size:11
Alignment explanation
Indices: 268057--268113 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
268047 ACAATCTGTC
268057 CATCACCATTAT
1 CATCACCATT-T
* *
268069 CA-CGCCTATAT
1 CATCACC-ATTT
268080 CATCACCATATT
1 CATCACCAT-TT
268092 CCATCACCATTT
1 -CATCACCATTT
268104 CATCACCATT
1 CATCACCATT
268114 AAATCATCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
11 18 0.49
12 10 0.27
13 9 0.24
ACGTcount: A:0.30, C:0.37, G:0.02, T:0.32
Consensus pattern (11 bp):
CATCACCATTT
Found at i:270777 original size:33 final size:33
Alignment explanation
Indices: 270698--270801 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
270688 ATACAATCTA
* *
270698 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
270734 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
270767 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
270800 TC
1 TC
270802 ATTTATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:273852 original size:15 final size:15
Alignment explanation
Indices: 273832--273870 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
273822 CAATATTTAT
273832 CTTTCTATTTCATTA
1 CTTTCTATTTCATTA
273847 CTTTCTATTTCATTA
1 CTTTCTATTTCATTA
273862 CTTTC-ATTT
1 CTTTCTATTT
273871 AACCATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.62
Consensus pattern (15 bp):
CTTTCTATTTCATTA
Found at i:278821 original size:22 final size:23
Alignment explanation
Indices: 278796--278845 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
278786 AATGGAAGGA
* *
278796 TGATGTTATTGGCGTGAT-ATGG
1 TGATGATATAGGCGTGATAATGG
278818 TGATGATATAGGCGTGATAATGG
1 TGATGATATAGGCGTGATAATGG
278841 TGATG
1 TGATG
278846 GACAGATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.24, C:0.04, G:0.36, T:0.36
Consensus pattern (23 bp):
TGATGATATAGGCGTGATAATGG
Found at i:281436 original size:11 final size:11
Alignment explanation
Indices: 281422--281478 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
281412 AGGATGATTT
281422 AATGGTGATGA
1 AATGGTGATGA
281433 AATGGTGATGGA
1 AATGGTGAT-GA
281445 ATATGGTGATGA
1 A-ATGGTGATGA
* *
281457 TATAGGCG-TGA
1 AAT-GGTGATGA
281468 TAATGGTGATG
1 -AATGGTGATG
281479 GACAGATTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
11 17 0.46
12 12 0.32
13 8 0.22
ACGTcount: A:0.32, C:0.02, G:0.37, T:0.30
Consensus pattern (11 bp):
AATGGTGATGA
Found at i:283573 original size:23 final size:23
Alignment explanation
Indices: 283547--283593 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
283537 TCCTATTTAT
283547 AGGAAATGGAAAGACATGGCTGA
1 AGGAAATGGAAAGACATGGCTGA
283570 AGGAAATGGAAAGACATGGCTGA
1 AGGAAATGGAAAGACATGGCTGA
283593 A
1 A
283594 TAATTACAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.09, G:0.34, T:0.13
Consensus pattern (23 bp):
AGGAAATGGAAAGACATGGCTGA
Found at i:294501 original size:91 final size:91
Alignment explanation
Indices: 294341--294523 Score: 285
Period size: 91 Copynumber: 2.0 Consensus size: 91
294331 GGTAGTTAAT
* *
294341 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCATATGCAAGGAACATG
1 GCTTAGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGAACATG
294406 GGGGCTGATCACATGCAAAACACATG
66 GGGGCTGATCACATGCAAAACACATG
* * *
294432 GCTTAGCCGAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATGATCCACATGCAAGGCACATG
1 GCTTAGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGAACATG
* * **
294497 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGATCACATGCAAAACACATG
294523 G
1 G
294524 GTGTTCTAGG
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 83 1.00
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.21
Consensus pattern (91 bp):
GCTTAGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGAACATG
GGGGCTGATCACATGCAAAACACATG
Found at i:301777 original size:19 final size:20
Alignment explanation
Indices: 301753--301792 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
301743 TATCCCATCC
301753 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
301772 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
301792 T
1 T
301793 ATTATTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:302115 original size:25 final size:24
Alignment explanation
Indices: 302058--302116 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
302048 ATTGGAGTGC
302058 AAAA-AGAAAAGAAAAAAAATCAG
1 AAAAGAGAAAAGAAAAAAAATCAG
*
302081 AAAAGAAGAAAAGAAAAAGAAGTTCA-
1 AAAAG-AGAAAAGAAAAA-AA-ATCAG
302107 AAAAGAGAAA
1 AAAAGAGAAA
302117 GCAAGCCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 4 0.13
25 17 0.55
26 7 0.23
27 3 0.10
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.05
Consensus pattern (24 bp):
AAAAGAGAAAAGAAAAAAAATCAG
Found at i:302577 original size:22 final size:21
Alignment explanation
Indices: 302547--302588 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
302537 CTTATCTTTT
302547 CTTTGGAGTGAACTTGTAAGA
1 CTTTGGAGTGAACTTGTAAGA
**
302568 CTTTGTGAGTGTGCTTGTAAG
1 CTTTG-GAGTGAACTTGTAAG
302589 GTTTATTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.21, C:0.10, G:0.31, T:0.38
Consensus pattern (21 bp):
CTTTGGAGTGAACTTGTAAGA
Found at i:306199 original size:13 final size:13
Alignment explanation
Indices: 306181--306249 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
306171 CTACCTATAA
*
306181 CATCACCATTTTC
1 CATCACCATATTC
*
306194 CATCACCAT-TTT
1 CATCACCATATTC
* **
306206 CA-CGCC-TATAA
1 CATCACCATATTC
*
306217 CATCACCATCTTC
1 CATCACCATATTC
*
306230 CATCACCATAGTC
1 CATCACCATATTC
306243 CATCACC
1 CATCACC
306250 TTCACGCCAA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
10 1 0.02
11 6 0.14
12 7 0.16
13 29 0.67
ACGTcount: A:0.28, C:0.41, G:0.03, T:0.29
Consensus pattern (13 bp):
CATCACCATATTC
Found at i:306712 original size:19 final size:20
Alignment explanation
Indices: 306684--306723 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
306674 GGATAATAAT
306684 ATAAGTAATGACAAT-AAATA
1 ATAAGTAATGA-AATGAAATA
306704 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAATGAAATA
306723 A
1 A
306724 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.16
19 11 0.58
20 5 0.26
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAATGAAATA
Found at i:311261 original size:35 final size:35
Alignment explanation
Indices: 311222--311326 Score: 111
Period size: 35 Copynumber: 3.0 Consensus size: 35
311212 ATTGGTGGTT
* * *
311222 ATATAGGTTTGAAATGGTGATAGAAGTTGATGATA
1 ATATAGGCTTGAAATGGTGATGGAAGATGATGATA
* * * *
311257 ATATAGGCGTGCAATGGTGATGGAAGATGGTGATG
1 ATATAGGCTTGAAATGGTGATGGAAGATGATGATA
* * *
311292 TTATAGGCGTTAAAATGGTGATGGAAGATGGTGAT
1 ATATAGGC-TTGAAATGGTGATGGAAGATGATGAT
311327 GAACAGATAG
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
35 35 0.60
36 23 0.40
ACGTcount: A:0.32, C:0.03, G:0.34, T:0.30
Consensus pattern (35 bp):
ATATAGGCTTGAAATGGTGATGGAAGATGATGATA
Found at i:311313 original size:36 final size:35
Alignment explanation
Indices: 311233--311328 Score: 120
Period size: 35 Copynumber: 2.7 Consensus size: 35
311223 TATAGGTTTG
* * * * *
311233 AAATGGTGATAGAAGTTGATGATAATATAGGCGTG
1 AAATGGTGATGGAAGATGGTGATGATATAGGCGTA
* *
311268 CAATGGTGATGGAAGATGGTGATGTTATAGGCGTTA
1 AAATGGTGATGGAAGATGGTGATGATATAGGCG-TA
311304 AAATGGTGATGGAAGATGGTGATGA
1 AAATGGTGATGGAAGATGGTGATGA
311329 ACAGATAGTA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
35 27 0.53
36 24 0.47
ACGTcount: A:0.33, C:0.03, G:0.35, T:0.28
Consensus pattern (35 bp):
AAATGGTGATGGAAGATGGTGATGATATAGGCGTA
Found at i:311716 original size:19 final size:20
Alignment explanation
Indices: 311669--311719 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
311659 GAAACCCCTT
**
311669 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
311689 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
311708 TGAAGATACATG
1 TGAAAATACATG
311720 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:314676 original size:12 final size:13
Alignment explanation
Indices: 314642--314674 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
314632 AGGGGTAGGA
314642 AAGAAAAAGGTTT
1 AAGAAAAAGGTTT
314655 AAGAAAAAGGTTT
1 AAGAAAAAGGTTT
314668 AAGAAAA
1 AAGAAAA
314675 GGATAAGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18
Consensus pattern (13 bp):
AAGAAAAAGGTTT
Found at i:314871 original size:5 final size:5
Alignment explanation
Indices: 314861--314897 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
314851 TTTTACAACT
*
314861 TTTTC TTTTC TTTTA TTTTC --TTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
314898 TGCACTCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
3 3 0.11
5 25 0.89
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:314886 original size:18 final size:18
Alignment explanation
Indices: 314863--314897 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
314853 TTACAACTTT
314863 TTCTTTTCTTTTATTTTC
1 TTCTTTTCTTTTATTTTC
*
314881 TTCTTTTCTTTTCTTTT
1 TTCTTTTCTTTTATTTT
314898 TGCACTCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (18 bp):
TTCTTTTCTTTTATTTTC
Found at i:314943 original size:6 final size:6
Alignment explanation
Indices: 314924--314963 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
314914 TGTAGGAGTC
*
314924 TTTT-T TTTTCT TTTTGT TTTTCT TCTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTT
314964 TGTTGCAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
5 4 0.13
6 21 0.68
7 6 0.19
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:314956 original size:13 final size:13
Alignment explanation
Indices: 314922--314960 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
314912 GATGTAGGAG
*
314922 TCTTTTTTTTTCT
1 TCTTTCTTTTTCT
*
314935 T-TTTGTTTTTCT
1 TCTTTCTTTTTCT
314947 TCTTTCTTTTTCT
1 TCTTTCTTTTTCT
314960 T
1 T
314961 TTTTGTTGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (13 bp):
TCTTTCTTTTTCT
Found at i:315440 original size:36 final size:35
Alignment explanation
Indices: 315342--315443 Score: 114
Period size: 35 Copynumber: 2.9 Consensus size: 35
315332 ATTGGTGGTT
* ** *
315342 ATATAGGCGTGAAATGGTGATAGAATTTGATGATA
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTGATA
* * * *
315377 ATATAGGCGTGCAACGGCGATGGAAGATGGTGATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTGATA
*
315412 TTATAGGCGTGAAAATGGTGATGGAAGATGGT
1 ATATAGGCGTG-AAATGGTGATGGAAGATGGT
315444 AATGAACAGA
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
35 37 0.69
36 17 0.31
ACGTcount: A:0.32, C:0.06, G:0.35, T:0.26
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATGGAAGATGGTGATA
Found at i:331388 original size:13 final size:12
Alignment explanation
Indices: 331369--331454 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
331359 AAATAGGCGT
331369 GATATGGTGATG
1 GATATGGTGATG
331381 GAATATGGTGAT-
1 G-ATATGGTGATG
*
331393 GATATAGGCG-T-
1 GATAT-GGTGATG
331404 GATAATGGTGATG
1 GAT-ATGGTGATG
331417 GACTATGGTGAT-
1 GA-TATGGTGATG
*
331429 GATATAGGCG-T-
1 GATAT-GGTGATG
331440 GATAATGGTGATG
1 GAT-ATGGTGATG
331453 GA
1 GA
331455 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:331424 original size:36 final size:36
Alignment explanation
Indices: 331351--331455 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
331341 ATTTATAAGT
* * *
331351 TGGTGATAAAATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
331386 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
331422 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
331456 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:334315 original size:24 final size:23
Alignment explanation
Indices: 334252--334315 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
334242 AACAAAGTGA
*
334252 AGCACTCTAAAG--AAAAAAAAC
1 AGCACTCAAAAGAAAAAAAAAAC
334273 AGCACTCAAAAGAAAAAAAAAAC
1 AGCACTCAAAAGAAAAAAAAAAC
*
334296 AGCACTCAAAACGAAGAAAA
1 AGCACTCAAAA-GAAAAAAA
334316 GCAAAGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 11 0.29
23 20 0.53
24 7 0.18
ACGTcount: A:0.64, C:0.19, G:0.11, T:0.06
Consensus pattern (23 bp):
AGCACTCAAAAGAAAAAAAAAAC
Found at i:338998 original size:33 final size:33
Alignment explanation
Indices: 338956--339024 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
338946 GTTGATGAAT
*
338956 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
338989 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
339022 GAA
1 GAA
339025 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:343470 original size:33 final size:33
Alignment explanation
Indices: 343428--343496 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
343418 GTTGATGAAT
*
343428 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
343461 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
343494 GAA
1 GAA
343497 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:345160 original size:19 final size:19
Alignment explanation
Indices: 345121--345174 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
345111 GAAACCCCTT
*
345121 TGAAAATAAATGACTTTTTAA
1 TGAAAATACATG-C-TTTTAA
345142 TGAAAATACATGCTTTTAA
1 TGAAAATACATGCTTTTAA
*
345161 TGAAGATACATGCT
1 TGAAAATACATGCT
345175 CTTGGCCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 19 0.61
20 1 0.03
21 11 0.35
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (19 bp):
TGAAAATACATGCTTTTAA
Found at i:349729 original size:36 final size:36
Alignment explanation
Indices: 349682--349752 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
349672 GATACAATCT
349682 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
349718 GTCCATCACCATTATCACGCCTATATCATCACCAT
1 GTCCATCACCATTATCACGCCTATATCATCACCAT
349753 CACCATATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.30, C:0.37, G:0.06, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:349767 original size:28 final size:29
Alignment explanation
Indices: 349720--349779 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
349710 TCACCATAGT
349720 CCATCACCATTATCACGCCTATATCATCA
1 CCATCACCATTATCACGCCTATATCATCA
* *
349749 CCATCACCA-TATCACGCCTATTTTATCA
1 CCATCACCATTATCACGCCTATATCATCA
349777 CCA
1 CCA
349780 ACTTATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.30, C:0.38, G:0.03, T:0.28
Consensus pattern (29 bp):
CCATCACCATTATCACGCCTATATCATCA
Found at i:360683 original size:19 final size:20
Alignment explanation
Indices: 360659--360708 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
360649 GGCCAAGAGA
* *
360659 ATGTATCTTCATC-TAAATC
1 ATGTATTTTCATCAAAAATC
360678 ATGTATTTTCATCAAAAATC
1 ATGTATTTTCATCAAAAATC
360698 ATGTATTTTCA
1 ATGTATTTTCA
360709 AAAGGGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (20 bp):
ATGTATTTTCATCAAAAATC
Found at i:361893 original size:13 final size:11
Alignment explanation
Indices: 361852--361936 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
361842 ACAATCTGTC
361852 CATCACCATTAT
1 CATCACCA-TAT
*
361864 CA-CGCCTATAT
1 CATCACC-ATAT
361875 CATCACCATAGT
1 CATCACCATA-T
361887 CCATCACCATTAT
1 -CATCACCA-TAT
*
361900 CA-CGCCTATAT
1 CATCACC-ATAT
361911 CATCACCATATT
1 CATCACCATA-T
361923 CCATCACCATAT
1 -CATCACCATAT
361935 CA
1 CA
361937 CGCCTATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:361896 original size:36 final size:36
Alignment explanation
Indices: 361849--361953 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
361839 GATACAATCT
361849 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
361885 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
361921 TTCCATCACCA-TATCACGCCTATTTTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
361954 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:364227 original size:22 final size:22
Alignment explanation
Indices: 364202--364244 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
364192 CAATTCATTT
364202 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
364224 ATCTTATTTTTATCTTGTTTT
1 ATCTTATTTTTATCTTGTTTT
364245 CAGCACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Done.