Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004315.1 Hibiscus syriacus cultivar Beakdansim tig00009460_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: 268930
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:8938 original size:1 final size:1
Alignment explanation
Indices: 8932--8986 Score: 56
Period size: 1 Copynumber: 55.0 Consensus size: 1
8922 CTCTTTAAAC
* * * * * *
8932 TTTTTTTTTTTATTTTTTTCTTTTCTTTTATTTTTTTTATTTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
8987 ACTAACCCGA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.07, C:0.04, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:8949 original size:9 final size:9
Alignment explanation
Indices: 8935--8986 Score: 79
Period size: 9 Copynumber: 5.8 Consensus size: 9
8925 TTTAAACTTT
8935 TTTTTTTTA
1 TTTTTTTTA
8944 TTTTTTTCT-
1 TTTTTTT-TA
*
8953 TTTCTTTTA
1 TTTTTTTTA
8962 TTTTTTTTA
1 TTTTTTTTA
8971 TTTTTTTTA
1 TTTTTTTTA
8980 TTTTTTT
1 TTTTTTT
8987 ACTAACCCGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
8 1 0.03
9 37 0.95
10 1 0.03
ACGTcount: A:0.08, C:0.04, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:9313 original size:17 final size:17
Alignment explanation
Indices: 9288--9330 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
9278 GTGAAGTATG
*
9288 AATGGTGTTGTCGTGGC
1 AATGTTGTTGTCGTGGC
*
9305 AATGTTGTTGTCGTGGT
1 AATGTTGTTGTCGTGGC
9322 AAGTGTTGT
1 AA-TGTTGT
9331 AAGGTTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.14, C:0.07, G:0.37, T:0.42
Consensus pattern (17 bp):
AATGTTGTTGTCGTGGC
Found at i:12058 original size:5 final size:5
Alignment explanation
Indices: 12048--12073 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12038 CTTCAACTTC
12048 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
12074 CTTTTTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:12096 original size:28 final size:29
Alignment explanation
Indices: 12062--12128 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
12052 TTTTCTTTTC
* *
12062 TTTTCTTTTCTTCTTTTTGAGTGC-TGGA
1 TTTTCTTTTCTTCTTTTGGAGTGCTTCGA
12090 TTTTC-TTTCTTTCTTTTGGAGTGCTTCGA
1 TTTTCTTTTC-TTCTTTTGGAGTGCTTCGA
12119 -TTTCTTTTCT
1 TTTTCTTTTCT
12129 GATTTTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 4 0.12
28 23 0.68
29 7 0.21
ACGTcount: A:0.06, C:0.16, G:0.15, T:0.63
Consensus pattern (29 bp):
TTTTCTTTTCTTCTTTTGGAGTGCTTCGA
Found at i:14055 original size:13 final size:12
Alignment explanation
Indices: 14036--14121 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
14026 ATATAGGCGT
14036 GATATGGTGATG
1 GATATGGTGATG
14048 GAATATGGTGAT-
1 G-ATATGGTGATG
*
14060 GATATAGGCG-T-
1 GATAT-GGTGATG
14071 GATAATGGTGATG
1 GAT-ATGGTGATG
14084 GACTATGGTGAT-
1 GA-TATGGTGATG
*
14096 GATATAGGCG-T-
1 GATAT-GGTGATG
14107 GATAATGGTGATG
1 GAT-ATGGTGATG
14120 GA
1 GA
14122 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:14091 original size:36 final size:36
Alignment explanation
Indices: 14018--14122 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
14008 ATTTATAAGT
* *
14018 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
14053 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
14089 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
14123 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:17538 original size:15 final size:15
Alignment explanation
Indices: 17505--17542 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
17495 CACTTTTCTT
17505 TTTCTTTTGATTTTC
1 TTTCTTTTGATTTTC
**
17520 -TTCTTTTTCTTTTC
1 TTTCTTTTGATTTTC
17534 TTTCTTTTG
1 TTTCTTTTG
17543 CACTCCAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTCTTTTGATTTTC
Found at i:18024 original size:13 final size:12
Alignment explanation
Indices: 18005--18090 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
17995 ATATAGGCGT
18005 GATATGGTGATG
1 GATATGGTGATG
18017 GAATATGGTGAT-
1 G-ATATGGTGATG
*
18029 GATATAGGCG-T-
1 GATAT-GGTGATG
18040 GATAATGGTGATG
1 GAT-ATGGTGATG
18053 GACTATGGTGAT-
1 GA-TATGGTGATG
*
18065 GATATAGGCG-T-
1 GATAT-GGTGATG
18076 GATAATGGTGATG
1 GAT-ATGGTGATG
18089 GA
1 GA
18091 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:18060 original size:36 final size:36
Alignment explanation
Indices: 17987--18091 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
17977 ATTTATAAGT
* *
17987 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
18022 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
18058 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
18092 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:21507 original size:15 final size:15
Alignment explanation
Indices: 21474--21511 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
21464 CACTTTTCTT
21474 TTTCTTTTGATTTTC
1 TTTCTTTTGATTTTC
**
21489 -TTCTTTTTCTTTTC
1 TTTCTTTTGATTTTC
21503 TTTCTTTTG
1 TTTCTTTTG
21512 CACTCCAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTCTTTTGATTTTC
Found at i:22003 original size:35 final size:36
Alignment explanation
Indices: 21956--22064 Score: 166
Period size: 36 Copynumber: 3.0 Consensus size: 36
21946 ATTTATAAGT
*
21956 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
21991 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* *
22027 AGGTGATGATATAGGCGTAATAATGGTGATGGACATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA-ATA
22064 T
1 T
22065 TGTATCTTAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 20 0.30
36 44 0.67
37 2 0.03
ACGTcount: A:0.31, C:0.05, G:0.34, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:24777 original size:28 final size:28
Alignment explanation
Indices: 24717--24783 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
24707 AACTTCTTTC
* *
24717 TTTTCTTTTCTTCTTTTTGAGTGCTGGA
1 TTTTCTTTTCTTCTTTTGGAGTGCTCGA
24745 TTTTC-TTTCTTTCTTTTGGAGTGCTTCGA
1 TTTTCTTTTC-TTCTTTTGGAGTGC-TCGA
24774 -TTTCTTTTCT
1 TTTTCTTTTCT
24784 GATTTTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 4 0.12
28 23 0.68
29 7 0.21
ACGTcount: A:0.06, C:0.16, G:0.15, T:0.63
Consensus pattern (28 bp):
TTTTCTTTTCTTCTTTTGGAGTGCTCGA
Found at i:25714 original size:91 final size:91
Alignment explanation
Indices: 25557--25730 Score: 294
Period size: 91 Copynumber: 1.9 Consensus size: 91
25547 GGTAGTTGAT
25557 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
25622 GGGGCTGATCACATGCAAAACACATG
66 GGGGCTGATCACATGCAAAACACATG
** * *
25648 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATGATCCACATGCAAGGCATATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
* *
25713 GGGGCTGGTCATATGCAA
66 GGGGCTGATCACATGCAA
25731 GGCAAATGGG
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 77 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.21
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
GGGGCTGATCACATGCAAAACACATG
Found at i:28755 original size:13 final size:13
Alignment explanation
Indices: 28733--28762 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28723 ACTAAACACC
28733 TTTC-ACATACCT
1 TTTCAACATACCT
28745 TTTCAACATACCT
1 TTTCAACATACCT
28758 TTTCA
1 TTTCA
28763 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:31529 original size:15 final size:15
Alignment explanation
Indices: 31494--31522 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31484 GTGCTTCAGC
31494 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
31508 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
31523 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:33592 original size:18 final size:17
Alignment explanation
Indices: 33543--33592 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
33533 AATTGGAGTG
33543 CAAAAAGAAAGAAAAAGA
1 CAAAAAGAAA-AAAAAGA
**
33561 CAAAAAGAAGAAAAAATT
1 CAAAAAGAA-AAAAAAGA
33579 CAGAAAAGAAAAAA
1 CA-AAAAGAAAAAA
33593 GAAATTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (17 bp):
CAAAAAGAAAAAAAAGA
Found at i:43179 original size:23 final size:23
Alignment explanation
Indices: 43134--43179 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
43124 TTATACCTAT
*
43134 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
43157 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
43180 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:45107 original size:166 final size:169
Alignment explanation
Indices: 44913--45251 Score: 614
Period size: 171 Copynumber: 2.0 Consensus size: 169
44903 ATATTATATC
*
44913 ATTCATACATCTATTCTCTCATAAGCATGCATTC-ATGTTATTAT-A-AATCATAATAATTTCAT
1 ATTCATACATCTATTCTATCATAAGCATGCATTCAATGTTATTATAATAATCATAATAATTTCAT
44975 CCTATGCCTAGTTGATCATGTCATTCATATCATTCAAATATATGCTATGATTACATATCATTTCT
66 CCTATGCCTAGTTGATCATGTCATTCATATCATTCAAATATATGCTATGATTACATATCATTTCT
45040 TAGGATATTATTA-TACATGTTTCCATTTATCATTTATT
131 TAGGATATTATTATTACATGTTTCCATTTATCATTTATT
45078 ATTCATACATTCTATTCTATCATAAGCATGCATTCATATGTTATTATAAATAATCATAATAATTT
1 ATTCATACA-TCTATTCTATCATAAGCATGCATTCA-ATGTTATTAT-AATAATCATAATAATTT
45143 CATCCTATGCCTAGTTGATCATGTCATTCATATCATTCAAATATATGCTATGATTACATATCATT
63 CATCCTATGCCTAGTTGATCATGTCATTCATATCATTCAAATATATGCTATGATTACATATCATT
45208 TCTTAGGATATTATTATTACATGTTTCCATTTATCATTTATT
128 TCTTAGGATATTATTATTACATGTTTCCATTTATCATTTATT
45250 AT
1 AT
45252 GAATACCATG
Statistics
Matches: 166, Mismatches: 1, Indels: 7
0.95 0.01 0.04
Matches are distributed among these distances:
165 9 0.05
166 24 0.14
168 10 0.06
170 1 0.01
171 95 0.57
172 27 0.16
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.45
Consensus pattern (169 bp):
ATTCATACATCTATTCTATCATAAGCATGCATTCAATGTTATTATAATAATCATAATAATTTCAT
CCTATGCCTAGTTGATCATGTCATTCATATCATTCAAATATATGCTATGATTACATATCATTTCT
TAGGATATTATTATTACATGTTTCCATTTATCATTTATT
Found at i:46970 original size:24 final size:23
Alignment explanation
Indices: 46941--46995 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
46931 AAAACCAGCA
*
46941 AAGAAAATCAAAGCACTCCAAAAG
1 AAGAAAATC-AAGCACTCAAAAAG
*
46965 AAGAAAAATCCAGCACTCAAAAAG
1 AAG-AAAATCAAGCACTCAAAAAG
46989 AAGAAAA
1 AAGAAAA
46996 GAAAAGAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 4 0.14
24 18 0.64
25 6 0.21
ACGTcount: A:0.62, C:0.18, G:0.13, T:0.07
Consensus pattern (23 bp):
AAGAAAATCAAGCACTCAAAAAG
Found at i:48329 original size:24 final size:21
Alignment explanation
Indices: 48295--48337 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
48285 TCCACAAGAC
*
48295 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
48317 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
48338 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:60938 original size:24 final size:24
Alignment explanation
Indices: 60911--60961 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
60901 ATCATAAAAC
60911 AAATTGAAAGCACTC-AAAAGAAAG
1 AAATTGAAAGCACTCAAAAAG-AAG
***
60935 AAATTTTCAGCACTCAAAAAGAAG
1 AAATTGAAAGCACTCAAAAAGAAG
60959 AAA
1 AAA
60962 AAGCAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.16
Consensus pattern (24 bp):
AAATTGAAAGCACTCAAAAAGAAG
Found at i:62414 original size:18 final size:19
Alignment explanation
Indices: 62391--62430 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
62381 TATTAGGGTT
62391 TTCATTTTATA-ACTTTGA
1 TTCATTTTATACACTTTGA
*
62409 TTCATTTTGTAGCACTTTGA
1 TTCATTTTATA-CACTTTGA
62429 TT
1 TT
62431 AGTATAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
20 9 0.47
ACGTcount: A:0.23, C:0.12, G:0.10, T:0.55
Consensus pattern (19 bp):
TTCATTTTATACACTTTGA
Found at i:69469 original size:18 final size:18
Alignment explanation
Indices: 69448--69483 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
69438 TTGATTCTTC
* *
69448 TTTTTCTTTTTTTTTGTT
1 TTTTTCTTCTTTCTTGTT
69466 TTTTTCTTCTTTCTTGTT
1 TTTTTCTTCTTTCTTGTT
69484 GCTTTTCGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (18 bp):
TTTTTCTTCTTTCTTGTT
Found at i:69472 original size:24 final size:23
Alignment explanation
Indices: 69423--69480 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
69413 TTTTGCTTTA
69423 CTTTTTCTATTCTTTTTGATTCTT
1 CTTTTTCT-TTCTTTTTGATTCTT
*
69447 CTTTTTCTTTTTTTTTG-TT-TT
1 CTTTTTCTTTCTTTTTGATTCTT
69468 -TTTCTTCTTTCTT
1 CTTT-TTCTTTCTT
69481 GTTGCTTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 3 0.10
21 10 0.32
22 2 0.06
23 8 0.26
24 8 0.26
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (23 bp):
CTTTTTCTTTCTTTTTGATTCTT
Found at i:75087 original size:25 final size:25
Alignment explanation
Indices: 75054--75122 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
75044 TTTGCTTCAC
75054 TTTTTCTTTTCTTTTTGATTCTTAT
1 TTTTTCTTTTCTTTTTGATTCTTAT
* * *
75079 TTTTTCTTTTCTTTTTGTTTTTTCT
1 TTTTTCTTTTCTTTTTGATTCTTAT
*
75104 TCTTTCTTGTTGCTTTTTG
1 TTTTTCTT-TT-CTTTTTG
75123 TTGTAGCACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 29 0.76
26 2 0.05
27 7 0.18
ACGTcount: A:0.03, C:0.13, G:0.07, T:0.77
Consensus pattern (25 bp):
TTTTTCTTTTCTTTTTGATTCTTAT
Found at i:78615 original size:13 final size:11
Alignment explanation
Indices: 78593--78658 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
78583 TATCACGCCT
78593 ATATCATCACC
1 ATATCATCACC
*
78604 ATAGTCCATCACT
1 ATA-T-CATCACC
78617 ATTATCA-CACC
1 A-TATCATCACC
78628 TATATCATCACC
1 -ATATCATCACC
78640 ATATTCCATCACC
1 ATA-T-CATCACC
78653 ATATCA
1 ATATCA
78659 CGCCTATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 10 0.22
13 18 0.39
14 2 0.04
ACGTcount: A:0.35, C:0.33, G:0.02, T:0.30
Consensus pattern (11 bp):
ATATCATCACC
Found at i:78621 original size:36 final size:35
Alignment explanation
Indices: 78571--78675 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 35
78561 GATACAATCT
78571 GTCCATCAGCATTATCACGCCTATATCATCACCATA
1 GTCCATCA-CATTATCACGCCTATATCATCACCATA
*
78607 GTCCATCACTATTATCACACCTATATCATCACCATA
1 GTCCATCAC-ATTATCACGCCTATATCATCACCATA
* *
78643 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCA-CATTATCACGCCTATATCATCACCA
78676 ACTTATAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
35 21 0.33
36 41 0.65
37 1 0.02
ACGTcount: A:0.31, C:0.34, G:0.05, T:0.30
Consensus pattern (35 bp):
GTCCATCACATTATCACGCCTATATCATCACCATA
Found at i:79141 original size:14 final size:15
Alignment explanation
Indices: 79107--79153 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
79097 AATTTGGAGT
79107 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
79122 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
79136 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
79153 G
1 G
79154 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:81312 original size:19 final size:21
Alignment explanation
Indices: 81288--81339 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
81278 CGGCCAAGAG
*
81288 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
81307 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
81328 CATGTATTTTCA
1 CATGTATTTTCA
81340 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:82090 original size:22 final size:24
Alignment explanation
Indices: 82047--82093 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
82037 TGGAGTGCAA
*
82047 AAAGAAGAGAAAAATCAGAAAGAAG
1 AAAGAAAAGAAAAA-CAGAAAGAAG
82072 AAAGAAAAGAAAAA-A-AAAGAAG
1 AAAGAAAAGAAAAACAGAAAGAAG
82094 TTCAAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 1 0.05
25 13 0.62
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (24 bp):
AAAGAAAAGAAAAACAGAAAGAAG
Found at i:85486 original size:19 final size:21
Alignment explanation
Indices: 85462--85513 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
85452 CGGCCAAGAG
*
85462 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
85481 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
85502 CATGTATTTTCA
1 CATGTATTTTCA
85514 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:90332 original size:36 final size:36
Alignment explanation
Indices: 90282--90386 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
90272 GATACAATCT
90282 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
90318 GTCCATCACTATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
90354 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
90387 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 21 0.32
36 44 0.68
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:91131 original size:24 final size:21
Alignment explanation
Indices: 91096--91138 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
91086 GGCTCATTCT
*
91096 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
91119 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
91139 ATCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:98473 original size:35 final size:37
Alignment explanation
Indices: 98427--98506 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
98417 TTTGAGAATT
*
98427 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
98462 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
98499 TGGTGATG
1 TGGTGATG
98507 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:101382 original size:15 final size:16
Alignment explanation
Indices: 101331--101383 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
101321 AGATAGTGAA
101331 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
101348 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
101365 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
101380 ATAA
1 ATAA
101384 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:103746 original size:35 final size:37
Alignment explanation
Indices: 103700--103779 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
103690 TTTGAGAATT
*
103700 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
103735 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
103772 TGGTGATG
1 TGGTGATG
103780 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:105126 original size:189 final size:189
Alignment explanation
Indices: 104806--105182 Score: 736
Period size: 189 Copynumber: 2.0 Consensus size: 189
104796 GACTCCCATG
104806 CTAGCTTTAAATCAGTTCCCAACATGTGGCCGAACATGCACCTACAAAAGAAAGCATAATATAAG
1 CTAGCTTTAAATCAGTTCCCAACATGTGGCCGAACATGCACCTACAAAAGAAAGCATAATATAAG
104871 CTAAGTATATGAATTACTATAAAGTAATAAGAATGTGCATATTATAAAGATGTGAACTATAGGTT
66 CTAAGTATATGAATTACTATAAAGTAATAAGAATGTGCATATTATAAAGATGTGAACTATAGGTT
104936 ATAATAATAACTCATGCATCATACGATAATGAATGAATATTATTATTACAACTATAGAC
131 ATAATAATAACTCATGCATCATACGATAATGAATGAATATTATTATTACAACTATAGAC
*
104995 CTAGCTTTAAATCAGTTCCCAACATGTGGCCGAATATGCACCTACAAAAGAAAGCATAATATAAG
1 CTAGCTTTAAATCAGTTCCCAACATGTGGCCGAACATGCACCTACAAAAGAAAGCATAATATAAG
*
105060 CTAAGTATATGAATTATTATAAAGTAATAAGAATGTGCATATTATAAAGATGTGAACTATAGGTT
66 CTAAGTATATGAATTACTATAAAGTAATAAGAATGTGCATATTATAAAGATGTGAACTATAGGTT
105125 ATAATAATAACTCATGCATCATACGATAATGAATGAATATTATTATTACAACTATAGA
131 ATAATAATAACTCATGCATCATACGATAATGAATGAATATTATTATTACAACTATAGA
105183 TTATATGCAT
Statistics
Matches: 186, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
189 186 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (189 bp):
CTAGCTTTAAATCAGTTCCCAACATGTGGCCGAACATGCACCTACAAAAGAAAGCATAATATAAG
CTAAGTATATGAATTACTATAAAGTAATAAGAATGTGCATATTATAAAGATGTGAACTATAGGTT
ATAATAATAACTCATGCATCATACGATAATGAATGAATATTATTATTACAACTATAGAC
Found at i:106693 original size:35 final size:37
Alignment explanation
Indices: 106647--106717 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 37
106637 TTAGAAGTTG
106647 GTGATAATATAGGCATGAT-ATGGTAATGGA-ATATA
1 GTGATAATATAGGCATGATAATGGTAATGGACATATA
* *
106682 GTGATGATATAGGCATGATAATGGTGATGGACATAT
1 GTGATAATATAGGCATGATAATGGTAATGGACATAT
106718 TGTATCTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 18 0.56
36 10 0.31
37 4 0.12
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.31
Consensus pattern (37 bp):
GTGATAATATAGGCATGATAATGGTAATGGACATATA
Found at i:110466 original size:22 final size:23
Alignment explanation
Indices: 110437--110480 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
110427 GTTGTAGGAG
110437 TCTTTTTCTT-TT-CTTTTTTTT
1 TCTTTTTCTTGTTACTTTTTTTT
110458 TCTTCTTTCTTGTTACTTTTTTT
1 TCTT-TTTCTTGTTACTTTTTTT
110481 GTTGTAGCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 6 0.30
23 2 0.10
24 8 0.40
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (23 bp):
TCTTTTTCTTGTTACTTTTTTTT
Found at i:112087 original size:35 final size:35
Alignment explanation
Indices: 112037--112134 Score: 148
Period size: 35 Copynumber: 2.9 Consensus size: 35
112027 GATTAAGCAA
112037 GCCAATATCATCACCATATTCCATTACCATATCAC
1 GCCAATATCATCACCATATTCCATTACCATATCAC
*
112072 GCCTATATCATCACCATATTCCATTACCATATCAC
1 GCCAATATCATCACCATATTCCATTACCATATCAC
*
112107 GCCAATAACATCATCC---TTCCATTACCAT
1 GCCAATATCATCA-CCATATTCCATTACCAT
112135 TTCATCACCA
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
33 12 0.20
35 45 0.76
36 2 0.03
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.30
Consensus pattern (35 bp):
GCCAATATCATCACCATATTCCATTACCATATCAC
Found at i:112132 original size:33 final size:33
Alignment explanation
Indices: 112055--112158 Score: 122
Period size: 35 Copynumber: 3.1 Consensus size: 33
112045 CATCACCATA
* *
112055 TTCCATTACCATATCACGCCTATATCATCA-CC
1 TTCCATTACCATATCACGCCAATAACATCATCC
112087 ATATTCCATTACCATATCACGCCAATAACATCATCC
1 ---TTCCATTACCATATCACGCCAATAACATCATCC
* *
112123 TTCCATTACCATTTCATCACCAATAA-ATCATCC
1 TTCCATTACCATATCA-CGCCAATAACATCATCC
112156 TTC
1 TTC
112159 ATTCATCAAC
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
33 25 0.40
34 8 0.13
35 28 0.44
36 2 0.03
ACGTcount: A:0.32, C:0.35, G:0.02, T:0.32
Consensus pattern (33 bp):
TTCCATTACCATATCACGCCAATAACATCATCC
Found at i:112533 original size:16 final size:16
Alignment explanation
Indices: 112512--112545 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
112502 AAAAAGCAAC
112512 AAGAAAGAAGAAAA-AA
1 AAGAAA-AAGAAAAGAA
112528 AAGAAAAAGAAAAGAA
1 AAGAAAAAGAAAAGAA
112544 AA
1 AA
112546 AGACTCCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGAAAAGAA
Found at i:112542 original size:11 final size:11
Alignment explanation
Indices: 112515--112548 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
112505 AAGCAACAAG
*
112515 AAAGAAGAAAAA
1 AAAGAA-AAAGA
112527 AAAGAAAAAGA
1 AAAGAAAAAGA
112538 AAAGAAAAAGA
1 AAAGAAAAAGA
112549 CTCCTACATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:112632 original size:24 final size:24
Alignment explanation
Indices: 112577--112625 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
112567 AGTGCAAAAG
* *
112577 AAAGAAAAGAAAAAGAAGAATCAA
1 AAAGCAAAGAAAAAGAAGAAACAA
*
112601 AAAGCAAAGAAAAAG-TGAAACAA
1 AAAGCAAAGAAAAAGAAGAAACAA
112624 AA
1 AA
112626 TTGCAAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.73, C:0.06, G:0.16, T:0.04
Consensus pattern (24 bp):
AAAGCAAAGAAAAAGAAGAAACAA
Found at i:117628 original size:36 final size:36
Alignment explanation
Indices: 117576--117688 Score: 158
Period size: 36 Copynumber: 3.2 Consensus size: 36
117566 GATACTATTT
117576 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCTCCATTATCACGCCTATA
* *
117612 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCTCCATTATCACGCCTATA
* *
117648 TCATCACCATATTCCAT-TACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCT-CCATTATCACGCCTATA
*
117683 ACATCA
1 TCATCA
117689 TCTTTCCATT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
35 17 0.24
36 53 0.76
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCTCCATTATCACGCCTATA
Found at i:117701 original size:33 final size:35
Alignment explanation
Indices: 117577--117703 Score: 134
Period size: 36 Copynumber: 3.6 Consensus size: 35
117567 ATACTATTTT
* * *
117577 CATCACCATAATCCATCT-CCATTATCACGCCTATAT
1 CATCACCATATTCCAT-TACCA-TATCACGCCAATAA
* * * *
117613 CATCACCATAGTCCATCACCATTATCACGCCTATAT
1 CATCACCATATTCCATTACCA-TATCACGCCAATAA
117649 CATCACCATATTCCATTACCATATCACGCCAATAA
1 CATCACCATATTCCATTACCATATCACGCCAATAA
*
117684 CATCATC-T-TTCCATTACCAT
1 CATCACCATATTCCATTACCAT
117704 TTCATCACCA
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
33 12 0.14
34 1 0.01
35 18 0.22
36 52 0.63
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.30
Consensus pattern (35 bp):
CATCACCATATTCCATTACCATATCACGCCAATAA
Found at i:117722 original size:33 final size:33
Alignment explanation
Indices: 117659--117723 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
117649 CATCACCATA
*
117659 TTCCATTACCATATCACGCCAATAACATCATCT
1 TTCCATTACCATATCACACCAATAACATCATCT
* *
117692 TTCCATTACCATTTCATCACCATTAA-ATCATC
1 TTCCATTACCATATCA-CACCAATAACATCATC
117724 CTTCATTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.34
Consensus pattern (33 bp):
TTCCATTACCATATCACACCAATAACATCATCT
Found at i:123360 original size:36 final size:36
Alignment explanation
Indices: 123308--123410 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
123298 ATACTATTTT
123308 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCTCCATTATCACGCCTATA
* *
123344 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCTCCATTATCACGCCTATA
*
123380 TCATCACCATATTCCAT-TACCA-TATCACGCC
1 TCATCACCATAATCCATCT-CCATTATCACGCC
123411 AATAACATTA
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 9 0.15
36 53 0.85
ACGTcount: A:0.30, C:0.37, G:0.04, T:0.29
Consensus pattern (36 bp):
TCATCACCATAATCCATCTCCATTATCACGCCTATA
Found at i:123457 original size:33 final size:33
Alignment explanation
Indices: 123391--123459 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
123381 CATCACCATA
* *
123391 TTCCATTACCATATCACGCCAATAACATTATCC
1 TTCCATTACCATATCACACCAATAACATCATCC
* *
123424 TTCCATTACCATTTCATCACCATTAA-ATCATCC
1 TTCCATTACCATATCA-CACCAATAACATCATCC
123457 TTC
1 TTC
123460 ATTCATCAAC
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:0.33, G:0.01, T:0.35
Consensus pattern (33 bp):
TTCCATTACCATATCACACCAATAACATCATCC
Found at i:129693 original size:35 final size:37
Alignment explanation
Indices: 129624--129703 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
129614 ATACTATTTC
* * *
129624 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCAGTATCACACCTATAT
*
129661 CATCACCATAGTCCATC-ACC-GTATCACACCTATAT
1 CATCACCATAATCCATCTACCAGTATCACACCTATAT
129696 CATCACCA
1 CATCACCA
129704 AATTCCCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 21 0.54
36 2 0.05
37 16 0.41
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCAGTATCACACCTATAT
Found at i:133835 original size:35 final size:37
Alignment explanation
Indices: 133766--133845 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
133756 ATACTATTTC
* *
133766 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
*
133803 CATCACCATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
133838 CATCACCA
1 CATCACCA
133846 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.33, C:0.38, G:0.03, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:133839 original size:11 final size:11
Alignment explanation
Indices: 133799--133845 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
133789 TATCACGCCT
133799 ATATCATCACC
1 ATATCATCACC
133810 ATAGTCCATCACC
1 ATA-T-CATCACC
133823 ATATCA-CACC
1 ATATCATCACC
133833 TATATCATCACC
1 -ATATCATCACC
133845 A
1 A
133846 AATTCTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 12 0.38
12 6 0.19
13 10 0.31
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (11 bp):
ATATCATCACC
Found at i:133843 original size:22 final size:24
Alignment explanation
Indices: 133799--133845 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
133789 TATCACGCCT
133799 ATATCATCACCATAGTCCATCACC
1 ATATCATCACCATAGTCCATCACC
133823 ATATCA-CACCTATA-T-CATCACC
1 ATATCATCACC-ATAGTCCATCACC
133845 A
1 A
133846 AATTCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (24 bp):
ATATCATCACCATAGTCCATCACC
Found at i:135720 original size:91 final size:91
Alignment explanation
Indices: 135536--135709 Score: 294
Period size: 91 Copynumber: 1.9 Consensus size: 91
135526 GGTAGTTGAT
*
135536 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGTCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
*
135601 GGGGCTGATCACATGCAAAACACATG
66 GGAGCTGATCACATGCAAAACACATG
* *
135627 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
* *
135692 GGAGCTGGTCATATGCAA
66 GGAGCTGATCACATGCAA
135710 GGAACATGGC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 77 1.00
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.21
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
GGAGCTGATCACATGCAAAACACATG
Found at i:139129 original size:26 final size:26
Alignment explanation
Indices: 139068--139129 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
139058 ACTTCTTCCT
* * *
139068 TTTCTTTTCTTCTTTTTGAGTGCTGGAT
1 TTTC-TTT-TTCTTTTGGAGTGCTGCAA
* *
139096 TTTTTTTTTCTTTTGGAGTGCTTCAA
1 TTTCTTTTTCTTTTGGAGTGCTGCAA
139122 TTTCTTTT
1 TTTCTTTT
139130 CTGATTTTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
26 22 0.79
27 3 0.11
28 3 0.11
ACGTcount: A:0.08, C:0.13, G:0.15, T:0.65
Consensus pattern (26 bp):
TTTCTTTTTCTTTTGGAGTGCTGCAA
Found at i:146337 original size:19 final size:20
Alignment explanation
Indices: 146290--146340 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
146280 GAAACCCCTT
**
146290 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
146310 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
146329 TGAATATACATG
1 TGAAAATACATG
146341 CTCTTGGCCG
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:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:149125 original size:19 final size:20
Alignment explanation
Indices: 149101--149156 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
149091 CTCTTTTTGA
149101 TTTTCTTTTTCTTTTCTTC-
1 TTTTCTTTTTCTTTTCTTCT
*
149120 TTTTCTGATTT-TTTTCTTCT
1 TTTTCT-TTTTCTTTTCTTCT
*
149140 TTTTGCCTTTTCTTTTC
1 TTTT-CTTTTTCTTTTC
149157 CTTTTGCACT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 14 0.47
20 10 0.33
21 6 0.20
ACGTcount: A:0.02, C:0.20, G:0.04, T:0.75
Consensus pattern (20 bp):
TTTTCTTTTTCTTTTCTTCT
Found at i:149139 original size:27 final size:25
Alignment explanation
Indices: 149088--149142 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 25
149078 CTCGGCTTGC
149088 TTTCTCTTTTTGATTTTCTTTTTCT
1 TTTCTCTTTTTGATTTTCTTTTTCT
149113 TTTCTTCTTTTCTGATTTT-TTTCTTCT
1 TTTC-TCTTTT-TGATTTTCTTT-TTCT
149140 TTT
1 TTT
149143 TGCCTTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 4 0.15
26 9 0.33
27 14 0.52
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (25 bp):
TTTCTCTTTTTGATTTTCTTTTTCT
Found at i:149149 original size:27 final size:27
Alignment explanation
Indices: 149088--149152 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
149078 CTCGGCTTGC
149088 TTTCT-CTTTT-TGATTTTCTTTTTCT
1 TTTCTCCTTTTCTGATTTTCTTTTTCT
*
149113 TTTCTTCTTTTCTGATTTT-TTTCTTCT
1 TTTCTCCTTTTCTGATTTTCTTT-TTCT
149140 TTT-TGCCTTTTCT
1 TTTCT-CCTTTTCT
149153 TTTCCTTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 5 0.14
26 9 0.26
27 21 0.60
ACGTcount: A:0.03, C:0.18, G:0.05, T:0.74
Consensus pattern (27 bp):
TTTCTCCTTTTCTGATTTTCTTTTTCT
Found at i:149150 original size:18 final size:18
Alignment explanation
Indices: 149112--149163 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
149102 TTTCTTTTTC
**
149112 TTTTCTTCTTTTCTGATTT
1 TTTTCTTCTTTT-TGCCTT
149131 TTTTCTTCTTTTTGCCTT
1 TTTTCTTCTTTTTGCCTT
*
149149 TTCTT-TTCCTTTTGC
1 TT-TTCTTCTTTTTGC
149164 ACTCAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.02, C:0.21, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTTCTTCTTTTTGCCTT
Found at i:149903 original size:19 final size:20
Alignment explanation
Indices: 149856--149906 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
149846 GAAACACCTT
**
149856 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
149876 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
149895 TGAAGATACATG
1 TGAAAATACATG
149907 CTCTTGGCCG
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:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:152004 original size:12 final size:12
Alignment explanation
Indices: 151987--152025 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
151977 ACCATTCAAT
151987 AAAAAGAAAATC
1 AAAAAGAAAATC
151999 AAAAAGAAAAGTGC
1 AAAAAGAAAA-T-C
*
152013 AAAAAAAAAATC
1 AAAAAGAAAATC
152025 A
1 A
152026 GCAAGTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 12 0.50
13 2 0.08
14 10 0.42
ACGTcount: A:0.74, C:0.08, G:0.10, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATC
Found at i:157560 original size:14 final size:14
Alignment explanation
Indices: 157537--157582 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
157527 TTTGGAGTGC
157537 AAAAGAAAGAAAAGA
1 AAAAG-AAGAAAAGA
*
157552 AAAAGAAGAATA-A
1 AAAAGAAGAAAAGA
*
157565 AAAA-AAGCAAAGA
1 AAAAGAAGAAAAGA
157578 AAAAG
1 AAAAG
157583 TGAAGCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
12 5 0.19
13 10 0.38
14 6 0.23
15 5 0.19
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (14 bp):
AAAAGAAGAAAAGA
Found at i:157592 original size:26 final size:27
Alignment explanation
Indices: 157535--157592 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
157525 AATTTGGAGT
*
157535 GCAAAAGAAAGAAAAGAAAAAGAAGAA
1 GCAAAAAAAAGAAAAGAAAAAGAAGAA
* * *
157562 -TAAAAAAAAGCAAAGAAAAAG-TGAA
1 GCAAAAAAAAGAAAAGAAAAAGAAGAA
157587 GCAAAA
1 GCAAAA
157593 TTGCAAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.72, C:0.05, G:0.19, T:0.03
Consensus pattern (27 bp):
GCAAAAAAAAGAAAAGAAAAAGAAGAA
Found at i:161080 original size:35 final size:36
Alignment explanation
Indices: 160969--161080 Score: 190
Period size: 36 Copynumber: 3.1 Consensus size: 36
160959 ATACAATCTG
*
160969 TCCATCACCATTATCACGCCTATATCATCACCATCT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
161005 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
161041 TCCATCACCA-TATCACGCCTATATCATCACCAAAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
161076 TCCAT
1 TCCAT
161081 TTCCATTTCT
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 28 0.39
36 44 0.61
ACGTcount: A:0.30, C:0.38, G:0.04, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:166476 original size:12 final size:13
Alignment explanation
Indices: 166446--166477 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
166436 TGGCCAAAGA
166446 TGAAAAGGTATGT
1 TGAAAAGGTATGT
166459 TGAAAAGGTATG-
1 TGAAAAGGTATGT
166471 TGAAAAG
1 TGAAAAG
166478 TGTTTAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.25
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:170412 original size:35 final size:37
Alignment explanation
Indices: 170343--170422 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
170333 ATACTATTTC
*
170343 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
170380 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
170415 CATCACCA
1 CATCACCA
170423 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:170902 original size:14 final size:15
Alignment explanation
Indices: 170868--170914 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
170858 AATTTGGAGT
170868 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
170883 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
170897 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
170914 G
1 G
170915 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:172715 original size:35 final size:37
Alignment explanation
Indices: 172646--172730 Score: 129
Period size: 35 Copynumber: 2.4 Consensus size: 37
172636 ATACTATTTC
* *
172646 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATATTCCATCTACCATTATCACGCCTATAT
172683 CATCACCATATTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATATTCCATCTACCATTATCACGCCTATAT
*
172718 CATCACCAAATTC
1 CATCACCATATTC
172731 TCAAATTTCC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
35 26 0.58
36 3 0.07
37 16 0.36
ACGTcount: A:0.32, C:0.36, G:0.02, T:0.29
Consensus pattern (37 bp):
CATCACCATATTCCATCTACCATTATCACGCCTATAT
Found at i:178190 original size:13 final size:13
Alignment explanation
Indices: 178168--178197 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
178158 ACTAAACACC
178168 TTTC-ACATACCT
1 TTTCAACATACCT
178180 TTTCAACATACCT
1 TTTCAACATACCT
178193 TTTCA
1 TTTCA
178198 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:184659 original size:19 final size:21
Alignment explanation
Indices: 184618--184666 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
184608 AAAATTTTGG
**
184618 TTTTTTTTGTTTTTTTAACTT
1 TTTTTTTTGCCTTTTTAACTT
184639 TTTTTTTTGCCTTTTT-A-TT
1 TTTTTTTTGCCTTTTTAACTT
184658 TTTTTTTTG
1 TTTTTTTTG
184667 GTTTTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 11 0.42
20 1 0.04
21 14 0.54
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.82
Consensus pattern (21 bp):
TTTTTTTTGCCTTTTTAACTT
Found at i:184672 original size:19 final size:21
Alignment explanation
Indices: 184618--184673 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 21
184608 AAAATTTTGG
*
184618 TTTTTTTTGTTTTTTTAACTT
1 TTTTTTTTGCTTTTTTAACTT
*
184639 TTTTTTTTGCCTTTTT-A-TT
1 TTTTTTTTGCTTTTTTAACTT
*
184658 TTTTTTTTGGTTTTTT
1 TTTTTTTTGCTTTTTT
184674 GAAAAATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.52
20 1 0.03
21 14 0.45
ACGTcount: A:0.05, C:0.05, G:0.07, T:0.82
Consensus pattern (21 bp):
TTTTTTTTGCTTTTTTAACTT
Found at i:186015 original size:14 final size:15
Alignment explanation
Indices: 185981--186027 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
185971 AATTTGGAGT
185981 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
185996 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
186010 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
186027 G
1 G
186028 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:190705 original size:10 final size:10
Alignment explanation
Indices: 190690--190760 Score: 78
Period size: 10 Copynumber: 7.5 Consensus size: 10
190680 ATTTTTGAAA
190690 TTTTGGCTTT
1 TTTTGGCTTT
190700 TTTTGGCTTT
1 TTTTGGCTTT
190710 TTTT-G-TTT
1 TTTTGGCTTT
*
190718 TTTTGCCTTT
1 TTTTGGCTTT
*
190728 TTTTTG--TT
1 TTTTGGCTTT
*
190736 TTTTGCCTTT
1 TTTTGGCTTT
*
190746 TTTTTGCTTT
1 TTTTGGCTTT
190756 TTTTG
1 TTTTG
190761 AATAAAAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
8 13 0.27
9 1 0.02
10 35 0.71
ACGTcount: A:0.00, C:0.10, G:0.14, T:0.76
Consensus pattern (10 bp):
TTTTGGCTTT
Found at i:190712 original size:19 final size:19
Alignment explanation
Indices: 190698--190758 Score: 90
Period size: 18 Copynumber: 3.3 Consensus size: 19
190688 AATTTTGGCT
* *
190698 TTTTTTGGC-TTTTTTTGT
1 TTTTTTGCCTTTTTTTTGC
190716 TTTTTTGCCTTTTTTTTG-
1 TTTTTTGCCTTTTTTTTGC
190734 TTTTTTGCCTTTTTTTTGC
1 TTTTTTGCCTTTTTTTTGC
190753 TTTTTT
1 TTTTTT
190759 TGAATAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
18 26 0.65
19 14 0.35
ACGTcount: A:0.00, C:0.10, G:0.11, T:0.79
Consensus pattern (19 bp):
TTTTTTGCCTTTTTTTTGC
Found at i:206226 original size:35 final size:37
Alignment explanation
Indices: 206157--206236 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
206147 ATACTATTTC
*
206157 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
206194 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
206229 CATCACCA
1 CATCACCA
206237 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:210643 original size:12 final size:13
Alignment explanation
Indices: 210619--210643 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
210609 CTTGAACTTC
210619 TTTTTGTATTTTT
1 TTTTTGTATTTTT
210632 TTTTTGTATTTT
1 TTTTTGTATTTT
210644 CGTTGTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (13 bp):
TTTTTGTATTTTT
Found at i:217633 original size:19 final size:19
Alignment explanation
Indices: 217609--217658 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
217599 GAAACCCCTT
217609 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
217628 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
217647 TGAAGATACATG
1 TGAAAATACATG
217659 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:226858 original size:15 final size:16
Alignment explanation
Indices: 226838--226867 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
226828 GTACTTCAAC
226838 TTTCTTTT-TTTTTCT
1 TTTCTTTTATTTTTCT
226853 TTTCTTTTATTTTTC
1 TTTCTTTTATTTTTC
226868 CTTCCTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTCTTTTATTTTTCT
Found at i:226902 original size:23 final size:23
Alignment explanation
Indices: 226875--226918 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
226865 TTCCTTCCTC
226875 TTTGAGTGCTTTCAATTTCTTCT
1 TTTGAGTGCTTTCAATTTCTTCT
* *
226898 TTTGAGTGCTTTGATTTTCTT
1 TTTGAGTGCTTTCAATTTCTT
226919 TGCTGGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.11, C:0.14, G:0.16, T:0.59
Consensus pattern (23 bp):
TTTGAGTGCTTTCAATTTCTTCT
Found at i:227050 original size:23 final size:24
Alignment explanation
Indices: 227011--227059 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
227001 TTCCACTAAA
*
227011 GCTCTGACTACCGCTTGATGTAAG
1 GCTCTGACTACCACTTGATGTAAG
227035 GCTCTGA-TACCACTTGATGTAAG
1 GCTCTGACTACCACTTGATGTAAG
227058 GC
1 GC
227060 ACTTGTACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (24 bp):
GCTCTGACTACCACTTGATGTAAG
Found at i:229240 original size:19 final size:20
Alignment explanation
Indices: 229199--229249 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
229189 GAAACCCCTT
* *
229199 TGAAAATGCTTGATTTCTAA
1 TGAAAATACATGATTTCTAA
229219 TGAAAATACATGATTT-TAA
1 TGAAAATACATGATTTCTAA
*
229238 TGAAGATACATG
1 TGAAAATACATG
229250 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTCTAA
Found at i:250122 original size:13 final size:13
Alignment explanation
Indices: 250098--250129 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
250088 ATACTAAACA
250098 CTTTTC-ACATAC
1 CTTTTCAACATAC
250110 CTTTTCAACATAC
1 CTTTTCAACATAC
250123 CTTTTCA
1 CTTTTCA
250130 TCTTTGGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (13 bp):
CTTTTCAACATAC
Found at i:255441 original size:20 final size:20
Alignment explanation
Indices: 255416--255461 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 20
255406 GCATAAAGCC
255416 TAAGAGC-TAAAATGAATGCA
1 TAAGAGCATAAAATGAATG-A
255436 TAAGAGCTGATAAAATGAATGA
1 TAAGAGC--ATAAAATGAATGA
255458 TAAG
1 TAAG
255462 TATGCTGCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.30
22 5 0.22
23 11 0.48
ACGTcount: A:0.50, C:0.07, G:0.22, T:0.22
Consensus pattern (20 bp):
TAAGAGCATAAAATGAATGA
Found at i:257809 original size:15 final size:15
Alignment explanation
Indices: 257770--257819 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
257760 ACTTTCTTCA
257770 CTTTTTCTTTTT-TT
1 CTTTTTCTTTTTCTT
***
257784 CTTTGAATTTTTCTT
1 CTTTTTCTTTTTCTT
257799 CTTTTTC-TTTTCTTT
1 CTTTTTCTTTTTC-TT
257814 CTTTTT
1 CTTTTT
257820 GATATAGTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 14 0.50
15 14 0.50
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (15 bp):
CTTTTTCTTTTTCTT
Found at i:259695 original size:15 final size:15
Alignment explanation
Indices: 259658--259705 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
259648 TGATAATTAA
*
259658 GAAATAGAAAGGAATT
1 GAAATGGAAA-GAATT
259674 GGAAATGGAAAGAATT
1 -GAAATGGAAAGAATT
*
259690 GAAATGGATAGAATT
1 GAAATGGAAAGAATT
259705 G
1 G
259706 TTATCAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 15 0.52
16 5 0.17
17 9 0.31
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (15 bp):
GAAATGGAAAGAATT
Found at i:259874 original size:35 final size:35
Alignment explanation
Indices: 259832--259898 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
259822 ATGGTTAAGG
259832 GATGGTGATGATATAGGCGTGAAATGGTGATGGAA
1 GATGGTGATGATATAGGCGTGAAATGGTGATGGAA
259867 GATGGTGATGATATAGGCGTGAAATGGTGATG
1 GATGGTGATGATATAGGCGTGAAATGGTGATG
259899 ATATAGGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.30, C:0.03, G:0.40, T:0.27
Consensus pattern (35 bp):
GATGGTGATGATATAGGCGTGAAATGGTGATGGAA
Found at i:259893 original size:22 final size:22
Alignment explanation
Indices: 259868--259938 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
259858 GTGATGGAAG
259868 ATGGTGATGATATAGGCGTGAA
1 ATGGTGATGATATAGGCGTGAA
*
259890 ATGGTGATGATATAGGCATGAA
1 ATGGTGATGATATAGGCGTGAA
* * * *
259912 ATGGTGATAAAATCGGTGTGAA
1 ATGGTGATGATATAGGCGTGAA
259934 ATGGT
1 ATGGT
259939 CATAGAAGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.34, C:0.04, G:0.34, T:0.28
Consensus pattern (22 bp):
ATGGTGATGATATAGGCGTGAA
Found at i:259951 original size:57 final size:57
Alignment explanation
Indices: 259832--259955 Score: 148
Period size: 57 Copynumber: 2.2 Consensus size: 57
259822 ATGGTTAAGG
* * * *
259832 GATGGTGATGATATAGGCGTGAAATGGTGATGGAAGATGGTGATGATATAGGCGTGAA
1 GATGGTGATGATATAGGCATGAAATGGTGAT-GAAAATGGTGATGAAATAGGCATGAA
259890 -ATGGTGATGATATAGGCATGAAATGGTGAT-AAAATCGGTG-TGAAAT-GGTCATAGAA
1 GATGGTGATGATATAGGCATGAAATGGTGATGAAAAT-GGTGATGAAATAGG-CAT-GAA
259946 GATGGTGATG
1 GATGGTGATG
259956 GACAGATAGT
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
54 2 0.03
55 11 0.19
56 7 0.12
57 38 0.66
ACGTcount: A:0.33, C:0.04, G:0.36, T:0.27
Consensus pattern (57 bp):
GATGGTGATGATATAGGCATGAAATGGTGATGAAAATGGTGATGAAATAGGCATGAA
Found at i:262816 original size:36 final size:36
Alignment explanation
Indices: 262768--262870 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
262758 GATACAAACT
*
262768 GTCCATCACCATTATCACGCCTATATCATCACCATC
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
262804 TTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
262840 GTCCATCACCA-TATCACGCC--TATCATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
262871 AATTCCATTT
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
33 11 0.17
35 9 0.14
36 44 0.69
ACGTcount: A:0.29, C:0.39, G:0.05, T:0.27
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:263375 original size:14 final size:15
Alignment explanation
Indices: 263341--263387 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
263331 AATTTGGAGT
263341 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
263356 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
263370 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
263387 G
1 G
263388 TGAAACAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:263553 original size:16 final size:15
Alignment explanation
Indices: 263520--263571 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
263510 GTAAGTTATC
263520 TTCATTTTTTATCAT
1 TTCATTTTTTATCAT
263535 TTCATTTCTTTATTC-T
1 TTCATTT-TTTA-TCAT
* * *
263551 TTCATCTTTTCTTAT
1 TTCATTTTTTATCAT
263566 TTCATT
1 TTCATT
263572 ACCATATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 11 0.37
17 2 0.07
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTCATTTTTTATCAT
Found at i:267285 original size:35 final size:36
Alignment explanation
Indices: 267191--267303 Score: 183
Period size: 36 Copynumber: 3.2 Consensus size: 36
267181 GATACAATCT
**
267191 GTCCATCACCATTATCACGCCTATATCATCACCATC
1 GTCCATCACCATTATCACGCCTATATCATCACCAAA
*
267227 TTCCATCACCATTATCACGCCTATATCATCACCAAA
1 GTCCATCACCATTATCACGCCTATATCATCACCAAA
267263 GTCCATCACCA-TATCACGCCTATATCATCACCAAA
1 GTCCATCACCATTATCACGCCTATATCATCACCAAA
*
267298 TTCCAT
1 GTCCAT
267304 TTTCCATTTC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 29 0.40
36 43 0.60
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.27
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCAAA
Found at i:268433 original size:22 final size:22
Alignment explanation
Indices: 268407--268449 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
268397 CCCGAGTGCA
268407 AACACGAGTGTGAGTGGAGTGT
1 AACACGAGTGTGAGTGGAGTGT
268429 AACACGAGTGTGAGTGGAGTG
1 AACACGAGTGTGAGTGGAGTG
268450 CAATCTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.09, G:0.42, T:0.21
Consensus pattern (22 bp):
AACACGAGTGTGAGTGGAGTGT
Done.