Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007760.1 Hibiscus syriacus cultivar Beakdansim tig00110029_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: 2010226
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 8
Found at i:182 original size:10 final size:10
Alignment explanation
Indices: 163--208 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
153 ATTGGAGTGC
*
163 AAAAAGAAAG
1 AAAAAAAAAG
173 AAAAAAAAAG
1 AAAAAAAAAG
*
183 AAGAAGAAAAG
1 AA-AAAAAAAG
*
194 AAGAAAAAAG
1 AAAAAAAAAG
204 AAAAA
1 AAAAA
209 GAATTCAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:195 original size:21 final size:21
Alignment explanation
Indices: 163--211 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
153 ATTGGAGTGC
163 AAAAAG-AAAGAAAAAAAAAG
1 AAAAAGAAAAGAAAAAAAAAG
* *
183 AAGAAGAAAAGAAGAAAAAAG
1 AAAAAGAAAAGAAAAAAAAAG
204 AAAAAGAA
1 AAAAAGAA
212 TTCAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAGAAAAAAAAAG
Found at i:197 original size:24 final size:25
Alignment explanation
Indices: 164--211 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
154 TTGGAGTGCA
164 AAAAGAAAGAAAAAA-AAAGAAGAAG
1 AAAAGAAAGAAAAAAGAAA-AAGAAG
189 AAAAG-AAGAAAAAAGAAAAAGAA
1 AAAAGAAAGAAAAAAGAAAAAGAA
212 TTCAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (25 bp):
AAAAGAAAGAAAAAAGAAAAAGAAG
Found at i:9040 original size:19 final size:20
Alignment explanation
Indices: 8993--9043 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
8983 GAAACCCCTT
**
8993 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
9013 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
9032 TGAAGATACATG
1 TGAAAATACATG
9044 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:9863 original size:26 final size:25
Alignment explanation
Indices: 9833--9881 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
9823 ATAATATAAG
*
9833 CTAAGTATATGAATTATTATAAAGTA
1 CTAAGAATATGAA-TATTATAAAGTA
* *
9859 CTAAGAATGTGCATATTATAAAG
1 CTAAGAATATGAATATTATAAAG
9882 ATGTCAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (25 bp):
CTAAGAATATGAATATTATAAAGTA
Found at i:12490 original size:23 final size:25
Alignment explanation
Indices: 12464--12518 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
12454 AAATCCAGCA
*
12464 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAGAACTCAAAGAGG
* *
12487 AAGAAATTGAAAGAACTCAAAGAGG
1 AAGAAAATCAAAGAACTCAAAGAGG
12512 AAGAAAA
1 AAGAAAA
12519 AAAAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 18 0.69
24 1 0.04
25 7 0.27
ACGTcount: A:0.62, C:0.11, G:0.18, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGAACTCAAAGAGG
Found at i:18656 original size:19 final size:21
Alignment explanation
Indices: 18632--18683 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
18622 CGGCCAAGAG
*
18632 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
18651 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
18672 CATGTATTTTCA
1 CATGTATTTTCA
18684 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:22387 original size:20 final size:20
Alignment explanation
Indices: 22362--22399 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
22352 GAATCTGGTA
22362 CAAAATAGCT-TGGTACACGT
1 CAAAATAG-TATGGTACACGT
22382 CAAAATAGTATGGTACAC
1 CAAAATAGTATGGTACAC
22400 CATTATGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (20 bp):
CAAAATAGTATGGTACACGT
Found at i:23869 original size:35 final size:36
Alignment explanation
Indices: 23782--23869 Score: 124
Period size: 35 Copynumber: 2.5 Consensus size: 36
23772 TACAATCAGT
* *
23782 TCATCACCATCTTCCATCACCATTATCACGGCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
* *
23818 TCATCACCATAGTCCATCATCA-TATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
23853 TCATCACCAAATTCCAT
1 TCATCACCATATTCCAT
23870 TTCCATTTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 27 0.59
36 19 0.41
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
TCATCACCATATTCCATCACCATTATCACGCCTATA
Found at i:24266 original size:19 final size:19
Alignment explanation
Indices: 24244--24280 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
24234 CAAAAAAAGC
* *
24244 AACAAGAAAGAAGAAAAAA
1 AACAAAAAAAAAGAAAAAA
24263 AACAAAAAAAAAGAAAAA
1 AACAAAAAAAAAGAAAAA
24281 GACTCCTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (19 bp):
AACAAAAAAAAAGAAAAAA
Found at i:24489 original size:16 final size:15
Alignment explanation
Indices: 24463--24514 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
24453 GAGTTGTAAG
24463 TTATC-TTCATTTTT
1 TTATCTTTCATTTTT
*
24477 TTATCATTTCATTTCT
1 TTATC-TTTCATTTTT
24493 TTATTCTTTCATCTTTT
1 TTA-TCTTTCAT-TTTT
24510 CTTAT
1 -TTAT
24515 TTCATTACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 5 0.16
16 17 0.55
17 6 0.19
18 3 0.10
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATCTTTCATTTTT
Found at i:28347 original size:19 final size:20
Alignment explanation
Indices: 28297--28351 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 20
28287 CCATCACCAT
28297 TATCACGCCTATATCATCAC
1 TATCACGCCTATATCATCAC
28317 TAT-A-GTCC---ATCATCA-
1 TATCACG-CCTATATCATCAC
28332 TATCACGCCTATATCATCAC
1 TATCACGCCTATATCATCAC
28352 CAAATTCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 14
0.67 0.00 0.33
Matches are distributed among these distances:
15 3 0.11
16 10 0.36
17 1 0.04
18 1 0.04
19 10 0.36
20 3 0.11
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (20 bp):
TATCACGCCTATATCATCAC
Found at i:29754 original size:30 final size:29
Alignment explanation
Indices: 29718--29788 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 29
29708 ATTCATCTTG
29718 AAAAAAAAAGAATTCTGAAAATTAAAAAA
1 AAAAAAAAAGAATTCTGAAAATTAAAAAA
*
29747 AACAAAAACAA-AATTCTGAAAATTAAAAAG
1 AA-AAAAA-AAGAATTCTGAAAATTAAAAAA
*
29777 AAAAGAAAAGAA
1 AAAAAAAAAGAA
29789 AAGTTCTGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
28 2 0.05
29 8 0.22
30 25 0.68
31 2 0.05
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.14
Consensus pattern (29 bp):
AAAAAAAAAGAATTCTGAAAATTAAAAAA
Found at i:34321 original size:19 final size:21
Alignment explanation
Indices: 34297--34348 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
34287 CAGCCAAGAG
*
34297 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
34316 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
34337 CATGTATTTTCA
1 CATGTATTTTCA
34349 AAAGGGGTTT
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:38253 original size:19 final size:21
Alignment explanation
Indices: 38229--38280 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
38219 CAGCCAAGAG
*
38229 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
*
38248 CATGTATTTTTATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
38269 CATGTATTTTCA
1 CATGTATTTTCA
38281 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 6 0.21
21 12 0.43
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:44613 original size:5 final size:5
Alignment explanation
Indices: 44603--44628 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
44593 CTTCAACTTC
44603 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
44629 CTTTTTGAGC
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:56911 original size:13 final size:13
Alignment explanation
Indices: 56889--56918 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
56879 ACTGAACACC
56889 TTTC-ACATACCT
1 TTTCAACATACCT
56901 TTTCAACATACCT
1 TTTCAACATACCT
56914 TTTCA
1 TTTCA
56919 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:63082 original size:90 final size:91
Alignment explanation
Indices: 62927--63108 Score: 249
Period size: 90 Copynumber: 2.0 Consensus size: 91
62917 AGTAGTTGAT
* * **
62927 GCTTGGCCGAATAAGTAGAGAACTCTTTATCTTGGTGCCTAAATGAACCACATGCAAGGCACAT-
1 GCTTGGCCGAATAAGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
62991 GGGGCTGATCACATGCAAAACACATG
66 GGGGCTGATCACATGCAAAACACATG
* * * *
63017 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTTAATGATCCACATGCAAGGCGCATG
1 GCTTGGCCGAATAAGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
* * **
63082 GGGGCTGGTCATATGCAAGCCACATG
66 GGGGCTGATCACATGCAAAACACATG
63108 G
1 G
63109 GTGTTCTAGG
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
90 56 0.71
91 23 0.29
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (91 bp):
GCTTGGCCGAATAAGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
GGGGCTGATCACATGCAAAACACATG
Found at i:64839 original size:35 final size:37
Alignment explanation
Indices: 64770--64854 Score: 120
Period size: 35 Copynumber: 2.4 Consensus size: 37
64760 ATACTATTTC
*
64770 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
* *
64807 CATCACCATAGTCCATC-ACCA-TATCACTCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
64842 CATCACCAAAATC
1 CATCACCATAATC
64855 TCAAATTTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 24 0.56
36 3 0.07
37 16 0.37
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:69963 original size:31 final size:31
Alignment explanation
Indices: 69928--69986 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
69918 ATATATAATA
* *
69928 ATCATGCTTAATATGATTATAA-AACAATCCT
1 ATCATGCTTAACAT-ATTAAAATAACAATCCT
*
69959 ATCATGTTTAACATATTAAAATAACAAT
1 ATCATGCTTAACATATTAAAATAACAAT
69987 GTGCAAGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.36
Consensus pattern (31 bp):
ATCATGCTTAACATATTAAAATAACAATCCT
Found at i:76624 original size:15 final size:15
Alignment explanation
Indices: 76604--76654 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
76594 GATTAGAATA
76604 AAATAAATAAAAGAT
1 AAATAAATAAAAGAT
*
76619 AAATAAATGAAAGAT
1 AAATAAATAAAAGAT
76634 GAAATAAGATAATAA-AT
1 -AAATAA-ATAA-AAGAT
76651 AAAT
1 AAAT
76655 CAAAAGATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 14 0.45
16 10 0.32
17 5 0.16
18 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.22
Consensus pattern (15 bp):
AAATAAATAAAAGAT
Found at i:83422 original size:15 final size:14
Alignment explanation
Indices: 83402--83467 Score: 69
Period size: 15 Copynumber: 4.4 Consensus size: 14
83392 CTTGGCTTAC
83402 TTTCTTTTTGATTTT
1 TTTCTTTTTG-TTTT
*
83417 TTTCTTTTTTTTTT
1 TTTCTTTTTGTTTT
83431 TCTTCTTTTCTGTTTT
1 T-TTCTTTT-TGTTTT
*
83447 TTCTCTTTTTCTTTCT
1 TT-TCTTTTTGTTT-T
83463 TTTCT
1 TTTCT
83468 CACTCCAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
14 5 0.11
15 24 0.55
16 15 0.34
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (14 bp):
TTTCTTTTTGTTTT
Found at i:83425 original size:9 final size:9
Alignment explanation
Indices: 83413--83465 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 9
83403 TTCTTTTTGA
83413 TTTTTTTCT
1 TTTTTTTCT
*
83422 TTTTTTTTT
1 TTTTTTTCT
83431 TCTTCTTTTCT
1 T-TT-TTTTCT
83442 GTTTTTTCTCT
1 -TTTTTT-TCT
83453 TTTTCTTTCT
1 TTTT-TTTCT
83463 TTT
1 TTT
83466 CTCACTCCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
9 9 0.24
10 15 0.41
11 12 0.32
12 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:83430 original size:12 final size:13
Alignment explanation
Indices: 83413--83463 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 13
83403 TTCTTTTTGA
83413 TTTTTTTCTT-TT
1 TTTTTTTCTTCTT
83425 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
83438 TTCTGTTTT-TTCTCT
1 TT-T-TTTTCTTCT-T
83453 TTTTCTTTCTT
1 TTTT-TTTCTT
83464 TTCTCACTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 10 0.30
13 5 0.15
14 9 0.27
15 9 0.27
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (13 bp):
TTTTTTTCTTCTT
Found at i:83439 original size:29 final size:29
Alignment explanation
Indices: 83401--83463 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
83391 CCTTGGCTTA
* *
83401 CTTTCTT-TTTGAT-TTTTTTCTTTTTTT
1 CTTTCTTCTTTTATGTTTTTTCTCTTTTT
* *
83428 TTTTCTTCTTTTCTGTTTTTTCTCTTTTT
1 CTTTCTTCTTTTATGTTTTTTCTCTTTTT
83457 CTTTCTT
1 CTTTCTT
83464 TTCTCACTCC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 6 0.21
28 4 0.14
29 19 0.66
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (29 bp):
CTTTCTTCTTTTATGTTTTTTCTCTTTTT
Found at i:83456 original size:17 final size:17
Alignment explanation
Indices: 83419--83468 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
83409 TTGATTTTTT
83419 TCTTTT-TTTTTTTCT-
1 TCTTTTCTTTTTTTCTC
83434 TCTTTTCTGTTTTTTCTC
1 TCTTTTCT-TTTTTTCTC
83452 T-TTTTCTTTCTTTTCTC
1 TCTTTTCTTT-TTTTCTC
83469 ACTCCAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.19
16 3 0.10
17 21 0.68
18 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (17 bp):
TCTTTTCTTTTTTTCTC
Found at i:83466 original size:9 final size:8
Alignment explanation
Indices: 83402--83467 Score: 51
Period size: 8 Copynumber: 7.6 Consensus size: 8
83392 CTTGGCTTAC
83402 TTTCTTTT
1 TTTCTTTT
*
83410 TGATTTTTTT
1 T--TTCTTTT
*
83420 CTTTTTTTT
1 -TTTCTTTT
*
83429 TTTCTTCT
1 TTTCTTTT
83437 TTTCTGTTT
1 TTTCT-TTT
*
83446 TTTCTCTT
1 TTTCTTTT
83454 TTTCTTTCT
1 TTTCTTT-T
83463 TTTCT
1 TTTCT
83468 CACTCCAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
8 20 0.43
9 20 0.43
10 6 0.13
11 1 0.02
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (8 bp):
TTTCTTTT
Found at i:93894 original size:21 final size:21
Alignment explanation
Indices: 93870--93911 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
93860 AGTAGAAGAT
* *
93870 GAGGAAGGATTACCTTGGTAA
1 GAGGAAGAAGTACCTTGGTAA
*
93891 GAGGATGAAGTACCTTGGTAA
1 GAGGAAGAAGTACCTTGGTAA
93912 TGTTCACTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.33, T:0.24
Consensus pattern (21 bp):
GAGGAAGAAGTACCTTGGTAA
Found at i:95559 original size:11 final size:11
Alignment explanation
Indices: 95545--95583 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
95535 ATTTTGGTTT
95545 TTTTTTTTGCC
1 TTTTTTTTGCC
*
95556 TTTTTTTTTCC
1 TTTTTTTTGCC
95567 TTTTTTTTG--
1 TTTTTTTTGCC
95576 TTTTTTTT
1 TTTTTTTT
95584 AAATAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 8 0.31
11 18 0.69
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (11 bp):
TTTTTTTTGCC
Found at i:100115 original size:20 final size:20
Alignment explanation
Indices: 100090--100127 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
100080 GAATCTGGTA
100090 CAAAACAGCT-TGGTACACGT
1 CAAAACAG-TATGGTACACGT
100110 CAAAACAGTATGGTACAC
1 CAAAACAGTATGGTACAC
100128 CATTCTGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
CAAAACAGTATGGTACACGT
Found at i:106044 original size:25 final size:25
Alignment explanation
Indices: 106015--106071 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
106005 TCAATTAAAA
106015 ATAATGGTCTCCTTACAAATGAAAT
1 ATAATGGTCTCCTTACAAATGAAAT
106040 ATAATGGTCTCCTTACAAATGAAAT
1 ATAATGGTCTCCTTACAAATGAAAT
106065 ATAATGG
1 ATAATGG
106072 CCTATTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (25 bp):
ATAATGGTCTCCTTACAAATGAAAT
Found at i:112741 original size:8 final size:8
Alignment explanation
Indices: 112730--112754 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
112720 GAGAAAAATC
112730 AGAAAAGA
1 AGAAAAGA
112738 AGAAAAGA
1 AGAAAAGA
112746 AGAAAAGA
1 AGAAAAGA
112754 A
1 A
112755 AAGAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:112764 original size:16 final size:16
Alignment explanation
Indices: 112713--112764 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
112703 TTGGAGTGTA
112713 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGA-AAAAA--AG
*
112732 AAAAGAAGAAAAGAAG
1 AAAAGAAGAAAAAAAG
112748 AAAAGAA-AAGAAAAAG
1 AAAAGAAGAA-AAAAAG
112764 A
1 A
112765 GAAGTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.07
16 15 0.50
18 4 0.13
19 9 0.30
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (16 bp):
AAAAGAAGAAAAAAAG
Found at i:134730 original size:12 final size:12
Alignment explanation
Indices: 134713--134743 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
134703 TTAAGTGATG
134713 GAAACAAGGTAA
1 GAAACAAGGTAA
134725 GAAACAAGGTAA
1 GAAACAAGGTAA
*
134737 AAAACAA
1 GAAACAA
134744 TATTATAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.65, C:0.10, G:0.19, T:0.06
Consensus pattern (12 bp):
GAAACAAGGTAA
Found at i:140738 original size:20 final size:20
Alignment explanation
Indices: 140683--140731 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
140673 CTATTTTTTT
* *
140683 CAAAAAAAAAAACAAAAAAGG
1 CAAAAAAACAAA-AAAAAAGC
140704 CAAAAAAACAAAAAAAAAGC
1 CAAAAAAACAAAAAAAAAGC
140724 CAAAAAAA
1 CAAAAAAA
140732 GATAAAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.82, C:0.12, G:0.06, T:0.00
Consensus pattern (20 bp):
CAAAAAAACAAAAAAAAAGC
Found at i:148856 original size:19 final size:21
Alignment explanation
Indices: 148832--148883 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
148822 CAGCCAAGAG
148832 CATGTATCTTT-A-TTAAAA-T
1 CATGTAT-TTTCATTTAAAAGT
148851 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
148872 CATGTATTTTCA
1 CATGTATTTTCA
148884 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.10
19 8 0.27
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:149891 original size:17 final size:19
Alignment explanation
Indices: 149854--149891 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
149844 TTAGCTAGCC
149854 TTGAGCTTCTCCAACTGAG
1 TTGAGCTTCTCCAACTGAG
149873 TTGAGCTTC-CCAA-TGAG
1 TTGAGCTTCTCCAACTGAG
149890 TT
1 TT
149892 CCATGCTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (19 bp):
TTGAGCTTCTCCAACTGAG
Found at i:158609 original size:25 final size:26
Alignment explanation
Indices: 158555--158609 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 26
158545 AGATTAGAAC
**
158555 AAAATAAACAAAAGATAAAGAAATTG
1 AAAATAAACAAAAGATAAAGAAATAA
*
158581 AAAATAAA-ATAAGAT-AAGATAATAA
1 AAAATAAACAAAAGATAAAGA-AATAA
158606 AAAA
1 AAAA
158610 ATCATAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 4 0.16
25 13 0.52
26 8 0.32
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (26 bp):
AAAATAAACAAAAGATAAAGAAATAA
Found at i:164793 original size:20 final size:21
Alignment explanation
Indices: 164770--164814 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
164760 TTTTTTGAAA
164770 TTTTGGCTTTTTTGTTT-TTT
1 TTTTGGCTTTTTTGTTTGTTT
**
164790 TTTTGTTTTTTTTGTTTGTTT
1 TTTTGGCTTTTTTGTTTGTTT
164811 TTTT
1 TTTT
164815 TTAAAATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.84
Consensus pattern (21 bp):
TTTTGGCTTTTTTGTTTGTTT
Found at i:164800 original size:13 final size:13
Alignment explanation
Indices: 164784--164816 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
164774 GGCTTTTTTG
164784 TTTTTTTTTTGTT
1 TTTTTTTTTTGTT
*
164797 TTTTTTGTTTGTT
1 TTTTTTTTTTGTT
164810 TTTTTTT
1 TTTTTTT
164817 AAAATAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (13 bp):
TTTTTTTTTTGTT
Found at i:166325 original size:24 final size:24
Alignment explanation
Indices: 166288--166344 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
166278 TTTTCTTTGA
166288 TTTTC-TTCTTTTGAGTGCTGT-AT
1 TTTTCTTTCTTTTGAGTGCT-TCAT
166311 TTTTCTTTCTTTTGAGTGCTTCAT
1 TTTTCTTTCTTTTGAGTGCTTCAT
*
166335 TTTCCTTTCT
1 TTTTCTTTCT
166345 GATTTTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
23 6 0.19
24 25 0.81
ACGTcount: A:0.07, C:0.18, G:0.12, T:0.63
Consensus pattern (24 bp):
TTTTCTTTCTTTTGAGTGCTTCAT
Found at i:168765 original size:24 final size:24
Alignment explanation
Indices: 168730--168784 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
168720 TTCTTTTCTC
*
168730 TTTC-TTCTTTTGAGTGCTGGACT
1 TTTCTTTCTTTTGAGTGCTGCACT
*
168753 TTTCTTTCTTTTGAGTGCTTCACT
1 TTTCTTTCTTTTGAGTGCTGCACT
168777 TTT-TTTCT
1 TTTCTTTCT
168785 AAATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 9 0.31
24 20 0.69
ACGTcount: A:0.07, C:0.18, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTGCACT
Found at i:168827 original size:12 final size:12
Alignment explanation
Indices: 168810--168836 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
168800 CTTCTTTGAC
168810 TTTGCACTTCAT
1 TTTGCACTTCAT
168822 TTTGCACTTCAT
1 TTTGCACTTCAT
168834 TTT
1 TTT
168837 TGTATTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.56
Consensus pattern (12 bp):
TTTGCACTTCAT
Found at i:169128 original size:6 final size:6
Alignment explanation
Indices: 169117--169160 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
169107 GATGTAGGAG
*
169117 TCTTTT TC-TTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
169161 TGTTGCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:169140 original size:12 final size:12
Alignment explanation
Indices: 169117--169160 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
169107 GATGTAGGAG
169117 TCTTTTTC-TTT
1 TCTTTTTCTTTT
*
169128 TCTTTTTGTTTT
1 TCTTTTTCTTTT
169140 TCTTCTTTCTTTT
1 TCTT-TTTCTTTT
169153 TCTCTTTT
1 TCT-TTTT
169161 TGTTGCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.25
12 7 0.25
13 13 0.46
14 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:171770 original size:14 final size:14
Alignment explanation
Indices: 171751--171780 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
171741 TATCGACCAA
171751 ACAAGTAACTTGTT
1 ACAAGTAACTTGTT
171765 ACAAGTAACTTGTT
1 ACAAGTAACTTGTT
171779 AC
1 AC
171781 TTGTGGTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (14 bp):
ACAAGTAACTTGTT
Found at i:197700 original size:21 final size:20
Alignment explanation
Indices: 197660--197711 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
197650 TGGCCAAGAG
*
197660 CATGTATCTTC-TTTAAAAT
1 CATGTATTTTCATTTAAAAT
197679 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTT-AAAAT
197700 CATGTATTTTCA
1 CATGTATTTTCA
197712 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 10 0.33
20 3 0.10
21 17 0.57
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAAT
Found at i:198153 original size:17 final size:17
Alignment explanation
Indices: 198131--198167 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
198121 TATTTATTTC
198131 ATTTCATT-CTTATTATT
1 ATTTCATTACTTA-TATT
198148 ATTTCATTACTTATATT
1 ATTTCATTACTTATATT
198165 ATT
1 ATT
198168 ATTCCCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTCATTACTTATATT
Found at i:204006 original size:24 final size:21
Alignment explanation
Indices: 203972--204014 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
203962 TCCACAAGAT
*
203972 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
203994 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
204015 ATAATGAGCC
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:222322 original size:24 final size:24
Alignment explanation
Indices: 222271--222319 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
222261 TTTGATTTTA
*
222271 TTCTTTTGAGTGCTGGATTTTTCT
1 TTCTTTTGAGTGCTGCATTTTTCT
*
222295 TTCTTTTGAGTGCTTCA-TTTTCT
1 TTCTTTTGAGTGCTGCATTTTTCT
222318 TT
1 TT
222320 TCTGATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.08, C:0.14, G:0.16, T:0.61
Consensus pattern (24 bp):
TTCTTTTGAGTGCTGCATTTTTCT
Found at i:224781 original size:27 final size:24
Alignment explanation
Indices: 224720--224775 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
224710 TTCTTTGCTC
224720 TTTC-TTCTTTTAAGTGCTGAACT
1 TTTCTTTCTTTTAAGTGCTGAACT
* *
224743 TTTCTTTCTTTTGAGTGCTGCACT
1 TTTCTTTCTTTTAAGTGCTGAACT
*
224767 TTTTTTTCT
1 TTTCTTTCT
224776 AATTTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.11, C:0.18, G:0.12, T:0.59
Consensus pattern (24 bp):
TTTCTTTCTTTTAAGTGCTGAACT
Found at i:225463 original size:15 final size:15
Alignment explanation
Indices: 225443--225471 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
225433 GAAATGGAAG
225443 AAGAAAGGAAATGAT
1 AAGAAAGGAAATGAT
225458 AAGAAAGGAAATGA
1 AAGAAAGGAAATGA
225472 AAAAAAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (15 bp):
AAGAAAGGAAATGAT
Found at i:225651 original size:35 final size:35
Alignment explanation
Indices: 225612--225687 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
225602 ATGATAATGG
* *
225612 GATGGTGATTATATAGGCATGAAATAGCGATGCAA
1 GATGGTGATGATATAGGCATGAAATAGAGATGCAA
* * * *
225647 GATGGTGATGATATAGGCGTGATATGGAGATGGAA
1 GATGGTGATGATATAGGCATGAAATAGAGATGCAA
225682 GATGGT
1 GATGGT
225688 ATAGATAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.33, C:0.05, G:0.36, T:0.26
Consensus pattern (35 bp):
GATGGTGATGATATAGGCATGAAATAGAGATGCAA
Found at i:227352 original size:22 final size:22
Alignment explanation
Indices: 227312--227353 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
227302 AAATATGTGG
*
227312 TTCATAATAATATCTTCATACA
1 TTCATAATAATATCATCATACA
227334 TTCATAAT-ATCATCATCATA
1 TTCATAATAAT-ATCATCATA
227354 ACTATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATATCATCATACA
Found at i:229755 original size:18 final size:19
Alignment explanation
Indices: 229732--229785 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
229722 AATTGGAGTG
229732 CAAAAAGAAAGAAAAAGA-
1 CAAAAAGAAAGAAAAAGAT
229750 CAAAAAG-AAGAAAAA-ATT
1 CAAAAAGAAAGAAAAAGA-T
229768 CAGAAAAGAAA-AAAAAGA
1 CA-AAAAGAAAGAAAAAGA
229786 AATTTCAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.03
17 8 0.26
18 9 0.29
19 10 0.32
20 3 0.10
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.04
Consensus pattern (19 bp):
CAAAAAGAAAGAAAAAGAT
Found at i:239723 original size:6 final size:6
Alignment explanation
Indices: 239697--239743 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
239687 ATGCTGCAAC
*
239697 AAAAGA AACAA-A AAGAGA AAAAGAA AAAAGAA AAAAGA AAAAGA AAA
1 AAAAGA AA-AAGA AAAAGA AAAAG-A AAAAG-A AAAAGA AAAAGA AAA
239744 GACTCATACA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 1 0.03
6 20 0.56
7 15 0.42
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:239724 original size:7 final size:7
Alignment explanation
Indices: 239706--239743 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
239696 CAAAAGAAAC
239706 AAAAAGA
1 AAAAAGA
239713 GAAAAAGA
1 -AAAAAGA
239721 AAAAAGA
1 AAAAAGA
239728 AAAAAG-
1 AAAAAGA
239734 AAAAAGA
1 AAAAAGA
239741 AAA
1 AAA
239744 GACTCATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:239728 original size:13 final size:14
Alignment explanation
Indices: 239706--239743 Score: 60
Period size: 13 Copynumber: 2.7 Consensus size: 14
239696 CAAAAGAAAC
239706 AAAAAGAGAAAAAGA
1 AAAAAGA-AAAAAGA
239721 AAAAAGAAAAAAG-
1 AAAAAGAAAAAAGA
239734 AAAAAGAAAA
1 AAAAAGAAAA
239744 GACTCATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 10 0.43
14 6 0.26
15 7 0.30
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAGA
Found at i:239961 original size:16 final size:16
Alignment explanation
Indices: 239935--239992 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
239925 GAGTTGTAAG
239935 TTATCTTCATTTTCTTA
1 TTAT-TTCATTTTCTTA
*
239952 CTATTTCA-TTTCTTTA
1 TTATTTCATTTTC-TTA
* *
239968 TTCTTTCATCTT-TTA
1 TTATTTCATTTTCTTA
239983 TTATTTCATT
1 TTATTTCATT
239993 GCCATATGCT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
15 15 0.45
16 13 0.39
17 5 0.15
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTCATTTTCTTA
Found at i:243752 original size:14 final size:14
Alignment explanation
Indices: 243733--243769 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
243723 TAAGATACTA
243733 TTTCCATCACCATC
1 TTTCCATCACCATC
243747 TTTCCATCACCATC
1 TTTCCATCACCATC
*
243761 ATT-CATCAC
1 TTTCCATCAC
243770 TTTCACGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.35
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:245894 original size:20 final size:21
Alignment explanation
Indices: 245840--245894 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
245830 CACTTTCAGC
*
245840 TAGCTAAATT-TAGCTCACAT
1 TAGCTCAATTCTAGCTCACAT
**
245860 TAGCTCTGTTC-AGCTC-CAT
1 TAGCTCAATTCTAGCTCACAT
245879 TAGCTCAATTCTAGCT
1 TAGCTCAATTCTAGCT
245895 AACAAGTCCA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.36
Consensus pattern (21 bp):
TAGCTCAATTCTAGCTCACAT
Found at i:249451 original size:35 final size:36
Alignment explanation
Indices: 249395--249462 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
249385 ATACAATCTG
249395 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
249431 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
249463 ACTTATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:259599 original size:14 final size:14
Alignment explanation
Indices: 259580--259616 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
259570 TAAGATACTA
259580 TTTCCATCACCATC
1 TTTCCATCACCATC
259594 TTTCCATCACCATC
1 TTTCCATCACCATC
*
259608 ATT-CATCAC
1 TTTCCATCAC
259617 TTTCACGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.35
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:261733 original size:20 final size:21
Alignment explanation
Indices: 261679--261733 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
261669 CACTTTCAGC
*
261679 TAGCTAAATT-TAGCTCACAT
1 TAGCTCAATTCTAGCTCACAT
**
261699 TAGCTCCGTTC-AGCTC-CAT
1 TAGCTCAATTCTAGCTCACAT
261718 TAGCTCAATTCTAGCT
1 TAGCTCAATTCTAGCT
261734 AACAAGTCCA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (21 bp):
TAGCTCAATTCTAGCTCACAT
Found at i:265258 original size:35 final size:36
Alignment explanation
Indices: 265202--265269 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
265192 ATACAATCTG
265202 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
265238 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
265270 ACTTATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:276206 original size:27 final size:27
Alignment explanation
Indices: 276168--276227 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
276158 AGATGAACAT
*
276168 CCATTCATCAAAATTCATTCACCTAAG
1 CCATGCATCAAAATTCATTCACCTAAG
276195 CCATGCATCAAAATTCATTCACCTAAG
1 CCATGCATCAAAATTCATTCACCTAAG
276222 CCATGC
1 CCATGC
276228 TTTGTATCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.35, C:0.32, G:0.07, T:0.27
Consensus pattern (27 bp):
CCATGCATCAAAATTCATTCACCTAAG
Found at i:286004 original size:5 final size:5
Alignment explanation
Indices: 285994--286035 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
285984 CTTCAACTTC
* *
285994 TTTCT TTTCT TTTCT TTTCT TTGCT TTTCT TCT-T TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
286036 TGAGTGCTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 3 0.09
5 29 0.91
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:286015 original size:19 final size:19
Alignment explanation
Indices: 285991--286034 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
285981 GTGCTTCAAC
*
285991 TTCTTT-CTTTTCTTTTCTT
1 TTCTTTGCTTTTCTTCT-TT
286010 TTCTTTGCTTTTCTTCTTT
1 TTCTTTGCTTTTCTTCTTT
286029 TTCTTT
1 TTCTTT
286035 TTGAGTGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.77
Consensus pattern (19 bp):
TTCTTTGCTTTTCTTCTTT
Found at i:286036 original size:15 final size:13
Alignment explanation
Indices: 285991--286035 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
285981 GTGCTTCAAC
285991 TTCTTTCTTTTCTT
1 TTCTTT-TTTTCTT
286005 TTCTTTTCTTTGCTT
1 TTCTTTT-TTT-CTT
286020 TTCTTCTTTTTCTT
1 TTCTT-TTTTTCTT
286034 TT
1 TT
286036 TGAGTGCTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 1 0.04
14 14 0.50
15 11 0.39
16 2 0.07
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (13 bp):
TTCTTTTTTTCTT
Found at i:289358 original size:21 final size:18
Alignment explanation
Indices: 289324--289366 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
289314 CATAACACTG
*
289324 AAAAAAAATTAAAGTAAAAT
1 AAAAAAAATGAAAG--AAAT
289344 AAAAAATAATGAAAGAAAT
1 AAAAAA-AATGAAAGAAAT
289363 AAAA
1 AAAA
289367 TTCAACAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (18 bp):
AAAAAAAATGAAAGAAAT
Found at i:297441 original size:90 final size:89
Alignment explanation
Indices: 297288--297462 Score: 296
Period size: 90 Copynumber: 2.0 Consensus size: 89
297278 CCTAACACAC
* * *
297288 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
*
297353 ATTTAATTAATTAGAATTTAATAAT
66 ATTTAATTAATT-GAAATTAATAAT
*
297378 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
297443 ATTTAATTAATTGAAATTAA
66 ATTTAATTAATTGAAATTAA
297463 ATATTTAGGA
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 7 0.09
90 73 0.91
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAATAAT
Found at i:312961 original size:91 final size:91
Alignment explanation
Indices: 312782--312963 Score: 256
Period size: 91 Copynumber: 2.0 Consensus size: 91
312772 GTAGTTGATA
* * *
312782 CTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATGG
1 CTTGGCCGAATAGGGAGAGAACTCTTAATCTTAGCGCCTAAATGAACCACATGCAAGACACATGG
*
312847 GGGCTGATCACATGCAAAACACATGG
66 GGGCTGATCACATACAAAACACATGG
* * * *
312873 CTTGGCCGAATAGGGAGAGAACTCTTAATCTTAGCGCCTAATTGATCCACATGTAAGACGCATGG
1 CTTGGCCGAATAGGGAGAGAACTCTTAATCTTAGCGCCTAAATGAACCACATGCAAGACACATGG
* * **
312938 GGGCTGGTCATATACAAGGCACATGG
66 GGGCTGATCACATACAAAACACATGG
312964 GTGTTCTAGG
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
91 79 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.21
Consensus pattern (91 bp):
CTTGGCCGAATAGGGAGAGAACTCTTAATCTTAGCGCCTAAATGAACCACATGCAAGACACATGG
GGGCTGATCACATACAAAACACATGG
Found at i:317324 original size:91 final size:91
Alignment explanation
Indices: 317168--317350 Score: 285
Period size: 91 Copynumber: 2.0 Consensus size: 91
317158 GGTAGTTGAT
*
317168 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATATTGGCGCCTAAATGAACCACATGCAAGGCACATG
*
317233 GGGGCTGATCACATGCAAAACACATG
66 GGCGCTGATCACATGCAAAACACATG
* * *
317259 GCTTGGCCGAATAGGGAGAGAACTCTTCATATTGGCGCCTAAATTATCCACATGCAAGGCGCATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATATTGGCGCCTAAATGAACCACATGCAAGGCACATG
* * **
317324 GGCGCTGGTCATATGCAAGGCACATG
66 GGCGCTGATCACATGCAAAACACATG
317350 G
1 G
317351 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:0.28, C:0.23, G:0.28, T:0.20
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATATTGGCGCCTAAATGAACCACATGCAAGGCACATG
GGCGCTGATCACATGCAAAACACATG
Found at i:321089 original size:17 final size:17
Alignment explanation
Indices: 321067--321101 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
321057 GTACTCAAAG
321067 AAGAAAACAAAAAGAAA
1 AAGAAAACAAAAAGAAA
*
321084 AAGAAAAGAAAAAGAAA
1 AAGAAAACAAAAAGAAA
321101 A
1 A
321102 GTTGAAAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (17 bp):
AAGAAAACAAAAAGAAA
Found at i:321096 original size:11 final size:11
Alignment explanation
Indices: 321067--321102 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
321057 GTACTCAAAG
321067 AAGAAAACA-AA
1 AAGAAAA-AGAA
321078 AAGAAAAAGAA
1 AAGAAAAAGAA
321089 AAGAAAAAGAA
1 AAGAAAAAGAA
321100 AAG
1 AAG
321103 TTGAAAGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 1 0.04
11 23 0.96
ACGTcount: A:0.81, C:0.03, G:0.17, T:0.00
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:327060 original size:23 final size:24
Alignment explanation
Indices: 327025--327078 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
327015 AAATCCAACA
327025 AAGAAAATCAAAGCACTC-AAAAG
1 AAGAAAATCAAAGCACTCAAAAAG
* *
327048 AAGAAATTGAAAGCACTCAAAAAG
1 AAGAAAATCAAAGCACTCAAAAAG
327072 AAGAAAA
1 AAGAAAA
327079 AAGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.13, G:0.15, T:0.09
Consensus pattern (24 bp):
AAGAAAATCAAAGCACTCAAAAAG
Found at i:327094 original size:17 final size:17
Alignment explanation
Indices: 327072--327106 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
327062 ACTCAAAAAG
327072 AAGAAAAAAGA-AAAGAA
1 AAGAAAAAA-ATAAAGAA
327089 AAGAAAAAAATAAAGAA
1 AAGAAAAAAATAAAGAA
327106 A
1 A
327107 GTTGAAGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 16 0.94
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (17 bp):
AAGAAAAAAATAAAGAA
Found at i:340073 original size:83 final size:85
Alignment explanation
Indices: 339934--340104 Score: 229
Period size: 83 Copynumber: 2.0 Consensus size: 85
339924 GGCAAAGGGG
* * * *
339934 CATACACAGTAACAAATAAACATATTACAAGGCTCCAATGCCATTAAATTACTTGTTT-ATTTGC
1 CATACACAGTAACAAATAAACAGATTACAAGGATCCAATACCATTAAATTACTTGTTTAATTTCC
*
339998 ACTTGTAGGAACAT-AAGGA
66 ACTTGTAGGAACATCAAGAA
* * * * * *
340017 CATACACAGTAGCAAGTAATCAGATTATAAGGATTCAATATCATTAAATTACTTGTTTAATTTCC
1 CATACACAGTAACAAATAAACAGATTACAAGGATCCAATACCATTAAATTACTTGTTTAATTTCC
340082 ACTTGTAGGAACATCAAGAA
66 ACTTGTAGGAACATCAAGAA
340102 CAT
1 CAT
340105 GCCCCTAATG
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
83 49 0.65
84 19 0.25
85 7 0.09
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (85 bp):
CATACACAGTAACAAATAAACAGATTACAAGGATCCAATACCATTAAATTACTTGTTTAATTTCC
ACTTGTAGGAACATCAAGAA
Found at i:353202 original size:14 final size:14
Alignment explanation
Indices: 353183--353227 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
353173 ATGGTGATAG
353183 AAGATGGTAATGGA
1 AAGATGGTAATGGA
* *
353197 AAGATGGTATTAGA
1 AAGATGGTAATGGA
*
353211 AAGATGGTGATGGA
1 AAGATGGTAATGGA
353225 AAG
1 AAG
353228 GTAGAATCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.36, T:0.22
Consensus pattern (14 bp):
AAGATGGTAATGGA
Found at i:359034 original size:13 final size:13
Alignment explanation
Indices: 359016--359040 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
359006 AACACCTTTT
359016 ACATACCTTTTCA
1 ACATACCTTTTCA
359029 ACATACCTTTTC
1 ACATACCTTTTC
359041 TTCTTTGGCC
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:0.28, C:0.32, G:0.00, T:0.40
Consensus pattern (13 bp):
ACATACCTTTTCA
Found at i:361855 original size:23 final size:25
Alignment explanation
Indices: 361804--361857 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
361794 TTTTTTATCT
*
361804 TTTTCTTCTTTTTGATTGCTTTTCA
1 TTTTCTTCTTTTTGAGTGCTTTTCA
*
361829 -TTTCTTC-TTTTGAGTGC-TTTGA
1 TTTTCTTCTTTTTGAGTGCTTTTCA
361851 TTTTCTT
1 TTTTCTT
361858 TGCTGGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 4 0.15
23 15 0.58
24 7 0.27
ACGTcount: A:0.07, C:0.15, G:0.11, T:0.67
Consensus pattern (25 bp):
TTTTCTTCTTTTTGAGTGCTTTTCA
Found at i:364334 original size:25 final size:26
Alignment explanation
Indices: 364290--364347 Score: 100
Period size: 25 Copynumber: 2.3 Consensus size: 26
364280 CACATACAAG
*
364290 GCACATGGAGGTTGGTCATATGGCAT
1 GCACATGGAGGCTGGTCATATGGCAT
364316 GCACATGG-GGCTGGTCATATGGCAT
1 GCACATGGAGGCTGGTCATATGGCAT
364341 GCACATG
1 GCACATG
364348 AGTGTTCTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 23 0.74
26 8 0.26
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.24
Consensus pattern (26 bp):
GCACATGGAGGCTGGTCATATGGCAT
Found at i:371718 original size:2 final size:2
Alignment explanation
Indices: 371711--371741 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
371701 CTTTTAATTG
371711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
371742 ATTCAGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:372871 original size:22 final size:22
Alignment explanation
Indices: 372824--372875 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
372814 CACCATGAGG
* *
372824 CCATGCAAATTGTAACATTCGA
1 CCATGCATATTGTAACATACGA
* *
372846 CCATGCATATTGTAACCTACGT
1 CCATGCATATTGTAACATACGA
372868 CCATGCAT
1 CCATGCAT
372876 GCATTTTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (22 bp):
CCATGCATATTGTAACATACGA
Found at i:374843 original size:23 final size:23
Alignment explanation
Indices: 374817--374867 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
374807 ACTTTTCTTT
*
374817 ATTTTCTT-TTTTTAGTGCTTGCA
1 ATTTTCTTCTTTTGAGTGCTT-CA
374840 ATTTTCTTCTTTTGAGTGCTTCA
1 ATTTTCTTCTTTTGAGTGCTTCA
374863 ATTTT
1 ATTTT
374868 TTTGTTGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.61
Consensus pattern (23 bp):
ATTTTCTTCTTTTGAGTGCTTCA
Found at i:374857 original size:24 final size:22
Alignment explanation
Indices: 374817--374875 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
374807 ACTTTTCTTT
*
374817 ATTTTCTTTTTTTAGTGCTTGCA
1 ATTTTCTTTTTTGAGTGCTT-CA
374840 ATTTTCTTCTTTTGAGTGCTTCA
1 ATTTTCTT-TTTTGAGTGCTTCA
*
374863 ATTTT-TTTGTTGA
1 ATTTTCTTTTTTGA
374876 TTTTTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 5 0.15
22 2 0.06
23 15 0.45
24 11 0.33
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.61
Consensus pattern (22 bp):
ATTTTCTTTTTTGAGTGCTTCA
Found at i:381236 original size:8 final size:8
Alignment explanation
Indices: 381223--381247 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
381213 ATAATATAGT
381223 TATTTATA
1 TATTTATA
381231 TATTTATA
1 TATTTATA
381239 TATTTATA
1 TATTTATA
381247 T
1 T
381248 TATAGCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATTTATA
Found at i:385285 original size:12 final size:12
Alignment explanation
Indices: 385253--385297 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
385243 AAAAGCAACA
385253 AAAAGAGAAAAAG
1 AAAA-AGAAAAAG
*
385266 AAATAAGAAAAAC
1 AAA-AAGAAAAAG
385279 AAAAAG-AAAAG
1 AAAAAGAAAAAG
385290 AAAAAGAA
1 AAAAAGAA
385298 TCCTAAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 10 0.36
12 4 0.14
13 13 0.46
14 1 0.04
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:385294 original size:6 final size:6
Alignment explanation
Indices: 385253--385297 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
385243 AAAAGCAACA
*
385253 AAAAGAG AAAAAG AAATAAG AAAAAC AAAAAG -AAAAG AAAAAG AA
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AA
385298 TCCTAAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 19 0.56
7 10 0.29
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:401181 original size:23 final size:23
Alignment explanation
Indices: 401150--401281 Score: 136
Period size: 23 Copynumber: 6.0 Consensus size: 23
401140 ATATGGTATT
*
401150 GTAATAGTACTTTGTGTACTATG
1 GTAAGAGTACTTTGTGTACTATG
*
401173 GTAAGAGTACTTAGTGTACT-TG
1 GTAAGAGTACTTTGTGTACTATG
*
401195 G--AGTAGTACTTTGGGTACTATG
1 GTAAG-AGTACTTTGTGTACTATG
* *
401217 GTAATAGTACTTTGTGTA--ATT
1 GTAAGAGTACTTTGTGTACTATG
*
401238 GT---AGTACTTTGCGTACTATG
1 GTAAGAGTACTTTGTGTACTATG
*
401258 ATAAGAGTACTTTGTGTACTATG
1 GTAAGAGTACTTTGTGTACTATG
401281 G
1 G
401282 CACTTTGTGT
Statistics
Matches: 88, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
18 12 0.14
20 5 0.06
21 17 0.19
22 6 0.07
23 47 0.53
24 1 0.01
ACGTcount: A:0.26, C:0.09, G:0.25, T:0.40
Consensus pattern (23 bp):
GTAAGAGTACTTTGTGTACTATG
Found at i:401217 original size:44 final size:41
Alignment explanation
Indices: 401154--401277 Score: 167
Period size: 41 Copynumber: 3.0 Consensus size: 41
401144 GGTATTGTAA
* *
401154 TAGTACTTTGTGTACTATGGTAAGAGTACTTAGTGTACTTGGAG
1 TAGTACTTTGCGTACTATGGTAAGAGTACTTTGTGTACTT---G
* * *
401198 TAGTACTTTGGGTACTATGGTAATAGTACTTTGTGTAATTG
1 TAGTACTTTGCGTACTATGGTAAGAGTACTTTGTGTACTTG
*
401239 TAGTACTTTGCGTACTATGATAAGAGTACTTTGTGTACT
1 TAGTACTTTGCGTACTATGGTAAGAGTACTTTGTGTACT
401278 ATGGCACTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
41 36 0.50
44 36 0.50
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (41 bp):
TAGTACTTTGCGTACTATGGTAAGAGTACTTTGTGTACTTG
Found at i:401254 original size:41 final size:42
Alignment explanation
Indices: 401154--401275 Score: 165
Period size: 44 Copynumber: 2.9 Consensus size: 42
401144 GGTATTGTAA
* * *
401154 TAGTACTTTGTGTACTATGGTAAGAGTACTTAGTGTACTTGGAG
1 TAGTACTTTGCGTACTATGGTAAGAGTACTTTGTGTAATT-G-G
* *
401198 TAGTACTTTGGGTACTATGGTAATAGTACTTTGTGTAATT-G
1 TAGTACTTTGCGTACTATGGTAAGAGTACTTTGTGTAATTGG
*
401239 TAGTACTTTGCGTACTATGATAAGAGTACTTTGTGTA
1 TAGTACTTTGCGTACTATGGTAAGAGTACTTTGTGTA
401276 CTATGGCACT
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
41 35 0.49
44 36 0.51
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (42 bp):
TAGTACTTTGCGTACTATGGTAAGAGTACTTTGTGTAATTGG
Found at i:401834 original size:2 final size:2
Alignment explanation
Indices: 401827--401876 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
401817 ATGGATTTTA
*
401827 AT AT AT AT AT AT AT AT AT AT AT -T AT AG AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
401867 AT AT AT AT AT
1 AT AT AT AT AT
401877 TTGAAGAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:408055 original size:23 final size:23
Alignment explanation
Indices: 408024--408176 Score: 150
Period size: 23 Copynumber: 7.0 Consensus size: 23
408014 ATATGGTATT
*
408024 GTAATAGTACTTTGTGTACTATG
1 GTAAGAGTACTTTGTGTACTATG
408047 GTAAGAGTACTTTGTGTACT-TG
1 GTAAGAGTACTTTGTGTACTATG
408069 G--AGTAGTACTTTG-GATACTATG
1 GTAAG-AGTACTTTGTG-TACTATG
*
408091 GTAATAGTACTTTGTGTACT-T-
1 GTAAGAGTACTTTGTGTACTATG
*
408112 GT---AGTACTTTGCGTACTATG
1 GTAAGAGTACTTTGTGTACTATG
*
408132 ATAAGAGTACTTTGTGTACT-TG
1 GTAAGAGTACTTTGTGTACTATG
*
408154 G--AGTAGTACTGTGTGTACTATG
1 GTAAG-AGTACTTTGTGTACTATG
408176 G
1 G
408177 AACTTTGTGT
Statistics
Matches: 110, Mismatches: 7, Indels: 27
0.76 0.05 0.19
Matches are distributed among these distances:
18 14 0.13
19 1 0.01
20 6 0.05
21 29 0.26
22 12 0.11
23 46 0.42
24 2 0.02
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41
Consensus pattern (23 bp):
GTAAGAGTACTTTGTGTACTATG
Found at i:408091 original size:44 final size:44
Alignment explanation
Indices: 408028--408176 Score: 225
Period size: 44 Copynumber: 3.5 Consensus size: 44
408018 GGTATTGTAA
408028 TAGTACTTTGTGTACTATGGTAAGAGTACTTTGTGTACTTGGAG
1 TAGTACTTTGTGTACTATGGTAAGAGTACTTTGTGTACTTGGAG
*
408072 TAGTACTTTG-GATACTATGGTAATAGTACTTTGTGTACTT---G
1 TAGTACTTTGTG-TACTATGGTAAGAGTACTTTGTGTACTTGGAG
* *
408113 TAGTACTTTGCGTACTATGATAAGAGTACTTTGTGTACTTGGAG
1 TAGTACTTTGTGTACTATGGTAAGAGTACTTTGTGTACTTGGAG
*
408157 TAGTACTGTGTGTACTATGG
1 TAGTACTTTGTGTACTATGG
408177 AACTTTGTGT
Statistics
Matches: 94, Mismatches: 6, Indels: 10
0.85 0.05 0.09
Matches are distributed among these distances:
41 37 0.39
42 1 0.01
43 1 0.01
44 55 0.59
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.41
Consensus pattern (44 bp):
TAGTACTTTGTGTACTATGGTAAGAGTACTTTGTGTACTTGGAG
Found at i:408534 original size:2 final size:2
Alignment explanation
Indices: 408527--408573 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
408517 TTAAAATTAT
* *
408527 TA TA TA TA CA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
408569 TA TA T
1 TA TA T
408574 GTATTTGAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:413882 original size:23 final size:22
Alignment explanation
Indices: 413845--413996 Score: 127
Period size: 23 Copynumber: 6.9 Consensus size: 22
413835 ACATGGTATC
*
413845 GGAATAGTACTTTGTGTACTAT
1 GGAAGAGTACTTTGTGTACTAT
* *
413867 GGTAAGATTACTTTGTATACT-T
1 GG-AAGAGTACTTTGTGTACTAT
* *
413889 GG-AGTAATACTTTATGTACTAT
1 GGAAG-AGTACTTTGTGTACTAT
*
413911 GGTAAAAGTACTTTGTGTACT-T
1 GG-AAGAGTACTTTGTGTACTAT
*
413933 GG-AGTAGTACTTTGCGTACTAT
1 GGAAG-AGTACTTTGTGTACTAT
*
413955 GACAAGAGTACTTTGTGTACT-T
1 G-GAAGAGTACTTTGTGTACTAT
*
413977 GG-AGTAGTACTGTGTGTACT
1 GGAAG-AGTACTTTGTGTACT
413997 GTGGCACTTT
Statistics
Matches: 105, Mismatches: 15, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
20 5 0.05
21 40 0.38
22 15 0.14
23 42 0.40
24 3 0.03
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (22 bp):
GGAAGAGTACTTTGTGTACTAT
Found at i:413899 original size:21 final size:21
Alignment explanation
Indices: 413852--413996 Score: 98
Period size: 21 Copynumber: 6.6 Consensus size: 21
413842 ATCGGAATAG
*
413852 TACTTTGTGTACTATGGTAAG-AT
1 TACTTTGTGTACT-TGG--AGTAA
*
413875 TACTTTGTATACTTGGAGTAA
1 TACTTTGTGTACTTGGAGTAA
* *
413896 TACTTTATGTACTATGGTA-AAA
1 TACTTTGTGTACT-TGG-AGTAA
*
413918 GTACTTTGTGTACTTGGAGTAG
1 -TACTTTGTGTACTTGGAGTAA
* * *
413940 TACTTTGCGTACTATGACAAG-AG
1 TACTTTGTGTACT-TG--GAGTAA
*
413963 TACTTTGTGTACTTGGAGTAG
1 TACTTTGTGTACTTGGAGTAA
*
413984 TACTGTGTGTACT
1 TACTTTGTGTACT
413997 GTGGCACTTT
Statistics
Matches: 100, Mismatches: 13, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.04
21 39 0.39
22 16 0.16
23 39 0.39
24 2 0.02
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.41
Consensus pattern (21 bp):
TACTTTGTGTACTTGGAGTAA
Found at i:413915 original size:44 final size:44
Alignment explanation
Indices: 413849--413996 Score: 215
Period size: 44 Copynumber: 3.4 Consensus size: 44
413839 GGTATCGGAA
* *
413849 TAGTACTTTGTGTACTATGGTAAGATTACTTTGTATACTTGGAG
1 TAGTACTTTGTGTACTATGGTAAGAGTACTTTGTGTACTTGGAG
* * *
413893 TAATACTTTATGTACTATGGTAAAAGTACTTTGTGTACTTGGAG
1 TAGTACTTTGTGTACTATGGTAAGAGTACTTTGTGTACTTGGAG
* **
413937 TAGTACTTTGCGTACTATGACAAGAGTACTTTGTGTACTTGGAG
1 TAGTACTTTGTGTACTATGGTAAGAGTACTTTGTGTACTTGGAG
*
413981 TAGTACTGTGTGTACT
1 TAGTACTTTGTGTACT
413997 GTGGCACTTT
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 91 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.41
Consensus pattern (44 bp):
TAGTACTTTGTGTACTATGGTAAGAGTACTTTGTGTACTTGGAG
Found at i:422619 original size:29 final size:31
Alignment explanation
Indices: 422580--422643 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
422570 ATGGATTTAG
* *
422580 TTAGTGACCAAACTATATAT-TTTG-AAAGT
1 TTAGTGACCAAACTATAAATATTAGAAAAGT
*
422609 TTAGTGACCAAAGTATAAATATTAGAAAAGT
1 TTAGTGACCAAACTATAAATATTAGAAAAGT
422640 TTAG
1 TTAG
422644 GGAGCAAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 18 0.60
30 3 0.10
31 9 0.30
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (31 bp):
TTAGTGACCAAACTATAAATATTAGAAAAGT
Found at i:422639 original size:31 final size:29
Alignment explanation
Indices: 422580--422662 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 29
422570 ATGGATTTAG
* * *
422580 TTAGTGACCAAACTATATATTTTGAAAGT
1 TTAGTGACCAAAGTATAAATTTAGAAAGT
422609 TTAGTGACCAAAGTATAAATATTAGAAAAGT
1 TTAGTGACCAAAGTATAAAT-TTAG-AAAGT
* *
422640 TTAGGGAGCAAAGTGATAAATTT
1 TTAGTGACCAAAGT-ATAAATTT
422663 TTTTAAAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 18 0.39
30 3 0.07
31 19 0.41
32 6 0.13
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (29 bp):
TTAGTGACCAAAGTATAAATTTAGAAAGT
Found at i:425491 original size:16 final size:16
Alignment explanation
Indices: 425470--425502 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
425460 TACTGACCTA
425470 ACCCGACCCGACCGTT
1 ACCCGACCCGACCGTT
425486 ACCCGACCCGACCGTT
1 ACCCGACCCGACCGTT
425502 A
1 A
425503 ACCGTTGACC
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:0.21, C:0.48, G:0.18, T:0.12
Consensus pattern (16 bp):
ACCCGACCCGACCGTT
Found at i:432607 original size:17 final size:17
Alignment explanation
Indices: 432585--432623 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
432575 TGAACCAGTC
432585 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
432602 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
432619 TGACC
1 TGACC
432624 GTTGACTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:434039 original size:17 final size:17
Alignment explanation
Indices: 434017--434051 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
434007 GTATAATTTG
*
434017 TTTATAATTTCATTTTA
1 TTTATAATGTCATTTTA
*
434034 TTTATAATGTGATTTTA
1 TTTATAATGTCATTTTA
434051 T
1 T
434052 ATTGATGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.63
Consensus pattern (17 bp):
TTTATAATGTCATTTTA
Found at i:435692 original size:24 final size:25
Alignment explanation
Indices: 435659--435710 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
435649 ATCAACAAAG
*
435659 AAATTGAAGCACTCAAAAA-AAGAA
1 AAATTCAAGCACTCAAAAAGAAGAA
*
435683 AAATTCAAGCACTCAAAAAGAATAA
1 AAATTCAAGCACTCAAAAAGAAGAA
435708 AAA
1 AAA
435711 AATAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.63, C:0.13, G:0.10, T:0.13
Consensus pattern (25 bp):
AAATTCAAGCACTCAAAAAGAAGAA
Found at i:442444 original size:25 final size:26
Alignment explanation
Indices: 442387--442460 Score: 123
Period size: 25 Copynumber: 2.9 Consensus size: 26
442377 GTAGTGCTTG
*
442387 CACATAAGGTTGTGCCCACCATAGTA
1 CACATAAGGTCGTGCCCACCATAGTA
442413 CACATAAGGTCGTGCCCACCAT-GTA
1 CACATAAGGTCGTGCCCACCATAGTA
*
442438 CACATAAGGTCGTTCCCACCATA
1 CACATAAGGTCGTGCCCACCATA
442461 CACTTAGTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
25 24 0.53
26 21 0.47
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.22
Consensus pattern (26 bp):
CACATAAGGTCGTGCCCACCATAGTA
Found at i:444718 original size:48 final size:44
Alignment explanation
Indices: 444657--444774 Score: 121
Period size: 48 Copynumber: 2.6 Consensus size: 44
444647 TTCTTACCTT
*
444657 TTATCCCATAAGCTCATAAGCTTATTTTCACCAAAATACTTACCA
1 TTATTCCATAAGCTCATAAGCTTATTTT-ACCAAAATACTTACCA
* ** * *
444702 TTTAAATTCCATAAGCTCGTAAGCTT-TTTTTTCAATATACTTGCCA
1 -TT--ATTCCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCA
* *
444748 TTATTCCGTAAGCTCATAAGTTTATTT
1 TTATTCCATAAGCTCATAAGCTTATTT
444775 GCATGGTTAC
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
43 18 0.30
44 3 0.05
45 2 0.03
46 14 0.23
47 4 0.07
48 19 0.32
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.41
Consensus pattern (44 bp):
TTATTCCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCA
Found at i:451601 original size:58 final size:55
Alignment explanation
Indices: 451525--451633 Score: 137
Period size: 55 Copynumber: 1.9 Consensus size: 55
451515 GTTCATAAGC
*
451525 TTATTTTTACCAAAATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATT
1 TTATTTTTACCAAAATACTTACCA-TT--ATTCCATAAGCTCATAAGCTTATTTTATT
** * * *
451583 TTATTTTTTTCAATATACTTGCCATTATTCCGTAAGCTCATAAGCTTATTT
1 TTATTTTTACCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATTT
451634 GCATGGTTAC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
55 23 0.51
57 2 0.04
58 20 0.44
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.47
Consensus pattern (55 bp):
TTATTTTTACCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATTTTATT
Found at i:453055 original size:21 final size:22
Alignment explanation
Indices: 453015--453055 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
453005 GTTTGTTTTA
*
453015 AACAAAACTAGATCAATATATG
1 AACAAAACTAGATAAATATATG
*
453037 AACAAAA-TATATAAATATA
1 AACAAAACTAGATAAATATA
453056 AGCTCCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.24
Consensus pattern (22 bp):
AACAAAACTAGATAAATATATG
Found at i:454262 original size:30 final size:31
Alignment explanation
Indices: 454179--454268 Score: 128
Period size: 31 Copynumber: 2.9 Consensus size: 31
454169 AATTAACTTT
* *
454179 AAACCAAGATACCTCAACCTTATCATCTTCC
1 AAACCAATACACCTCAACCTTATCATCTTCC
* *
454210 AAACCAGTACACCTCAAGCTTATCATCTTCC
1 AAACCAATACACCTCAACCTTATCATCTTCC
*
454241 AAACCAATGCA-CTCAACCTTATCATCTT
1 AAACCAATACACCTCAACCTTATCATCTT
454269 TATTAAGTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
30 16 0.31
31 36 0.69
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.27
Consensus pattern (31 bp):
AAACCAATACACCTCAACCTTATCATCTTCC
Found at i:469476 original size:20 final size:20
Alignment explanation
Indices: 469417--469485 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
469407 CCGATTCCCG
469417 CACTATTCACGGGTACTGTT
1 CACTATTCACGGGTACTGTT
* ** *
469437 CACT-GTCATTGTTCACTGTT
1 CACTATTCACGGGT-ACTGTT
*
469457 CACTATTCACGGGTATTGTT
1 CACTATTCACGGGTACTGTT
469477 CACTATTCA
1 CACTATTCA
469486 TAAAAAAAAC
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
19 5 0.13
20 28 0.74
21 5 0.13
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (20 bp):
CACTATTCACGGGTACTGTT
Found at i:498784 original size:16 final size:18
Alignment explanation
Indices: 498753--498785 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
498743 ACTAATCCAA
498753 AAATACATCTTTTATTGT
1 AAATACATCTTTTATTGT
498771 AAATA-ATC-TTTATTG
1 AAATACATCTTTTATTG
498786 GGACAAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (18 bp):
AAATACATCTTTTATTGT
Found at i:501680 original size:35 final size:35
Alignment explanation
Indices: 501523--501818 Score: 307
Period size: 35 Copynumber: 8.5 Consensus size: 35
501513 AATATATATA
501523 TATATATATATTACGTTTTCAAAACTATTTTAAAAAC
1 TATATAT-TA-TACGTTTTCAAAACTATTTTAAAAAC
* * *
501560 --TATGTTATATGTTTTCAAAATTATTTTAAAAAAAC
1 TATATATTATACGTTTTCAAAACTATTTT--AAAAAC
* * * * *
501595 TATATACTATATGTTTTCAAAACCA-TTTCAGAAC
1 TATATATTATACGTTTTCAAAACTATTTTAAAAAC
* * **
501629 TATAT-TATATATGTTTTCAAAACCATTTTTTAAAC
1 TATATAT-TATACGTTTTCAAAACTATTTTAAAAAC
*
501664 TATATATTATACGTTTTTAAAACTATTTTAAAAA-
1 TATATATTATACGTTTTCAAAACTATTTTAAAAAC
* * *
501698 T-TATATTATATGTTTTCTAAATTATTTTAAAAAC
1 TATATATTATACGTTTTCAAAACTATTTTAAAAAC
* * **
501732 TATACACTATACGTTTTCAAAACCGTTTTAAAAAC
1 TATATATTATACGTTTTCAAAACTATTTTAAAAAC
* *
501767 TATATATTATAAGTTTTCAAAACTATTTTGAAAAC
1 TATATATTATACGTTTTCAAAACTATTTTAAAAAC
501802 TATATATTATACGTTTT
1 TATATATTATACGTTTT
501819 TTTAATAAGT
Statistics
Matches: 214, Mismatches: 36, Indels: 20
0.79 0.13 0.07
Matches are distributed among these distances:
33 46 0.21
34 31 0.14
35 114 0.53
36 4 0.02
37 19 0.09
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.45
Consensus pattern (35 bp):
TATATATTATACGTTTTCAAAACTATTTTAAAAAC
Found at i:501768 original size:103 final size:104
Alignment explanation
Indices: 501525--501818 Score: 321
Period size: 103 Copynumber: 2.8 Consensus size: 104
501515 TATATATATA
* * * *
501525 TATAT-ATATTACGTTTTCAAAACTATTTTAAAAAC--TATGTTATATGTTTTCAAAATTATTTT
1 TATATCATA-TACGTTTTCAAAACCATTTTAAAAACTATATATTATAAGTTTTCAAAACTATTTT
* * *
501587 AAAAAAACTATATACTATATGTTTTCAAAACCATTTCAGAAC
65 -AAAAAA-TATATATTATATGTTTTCAAAACCATTTAAAAAC
* * ** * *
501629 TATATTATATATGTTTTCAAAACCATTTTTTAAACTATATATTATACGTTTTTAAAACTATTTT-
1 TATATCATATACGTTTTCAAAACCATTTTAAAAACTATATATTATAAGTTTTCAAAACTATTTTA
* **
501693 AAAAAT-TATATTATATGTTTTCTAAATTATTTTAAAAAC
66 AAAAATATATATTATATGTTTTCAAAACCA-TTTAAAAAC
*
501732 TATA-CACTATACGTTTTCAAAACCGTTTTAAAAACTATATATTATAAGTTTTCAAAACTATTTT
1 TATATCA-TATACGTTTTCAAAACCATTTTAAAAACTATATATTATAAGTTTTCAAAACTATTTT
* * *
501796 GAAAACTATATATTATACGTTTT
65 AAAAAATATATATTATATGTTTT
501819 TTTAATAAGT
Statistics
Matches: 160, Mismatches: 23, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
102 20 0.12
103 63 0.39
104 37 0.23
105 17 0.11
106 23 0.14
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (104 bp):
TATATCATATACGTTTTCAAAACCATTTTAAAAACTATATATTATAAGTTTTCAAAACTATTTTA
AAAAATATATATTATATGTTTTCAAAACCATTTAAAAAC
Found at i:501843 original size:70 final size:68
Alignment explanation
Indices: 501523--501873 Score: 255
Period size: 70 Copynumber: 5.0 Consensus size: 68
501513 AATATATATA
* * * *
501523 TATATATATATTACGTTTTCAAAACTATTTTAAAAAC-TATGTTATAT-GTTTTCAAAATTATTT
1 TATATAT-TA-TACGTTTTTAAAA--GTTTTAAAAACATATATTATATAGTTTTCAAAACTATTT
*
501586 TAAAAAAAC
62 T--GAAAAC
* * * ** * * * *
501595 TATATACTATATGTTTTCAAAACCATTTCAGAAC-TATATTATATATGTTTTCAAAACCATTTTT
1 TATATATTATACGTTTTTAAAA-GTTTTAAAAACATATATTATATA-GTTTTCAAAACTATTTTG
*
501659 TAAAC
64 AAAAC
* * * * *
501664 TATATATTATACGTTTTTAAAACTATTTTAAAAA-TTATATTATAT-GTTTTCTAAATTATTTTA
1 TATATATTATACGTTTTTAAAA--GTTTTAAAAACATATATTATATAGTTTTCAAAACTATTTTG
501727 AAAAC
64 AAAAC
* * *
501732 TATACACTATACGTTTTCAAAACCGTTTTAAAAACTATATATTATA-AGTTTTCAAAACTATTTT
1 TATATATTATACGTTTTTAAAA--GTTTTAAAAAC-ATATATTATATAGTTTTCAAAACTATTTT
501796 GAAAAC
63 GAAAAC
* * *
501802 TATATATTATACGTTTTTTTAATAAGTTTCCAAAAACTATATATTATATATTTTTAAAAACTATA
1 TATATATTATACG--TTTTTAA-AAGTTT-TAAAAAC-ATATATTATATAGTTTTCAAAACTAT-
501867 TTTGAAA
60 TTTGAAA
501874 TTATTATATA
Statistics
Matches: 226, Mismatches: 40, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
68 47 0.21
69 39 0.17
70 68 0.30
71 21 0.09
72 29 0.13
73 15 0.07
74 7 0.03
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (68 bp):
TATATATTATACGTTTTTAAAAGTTTTAAAAACATATATTATATAGTTTTCAAAACTATTTTGAA
AAC
Found at i:502649 original size:31 final size:31
Alignment explanation
Indices: 502613--502678 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
502603 TTAGAAGCTA
*
502613 TAAAATGA-AAAATTATAAATTATTAAAAAAT
1 TAAAAT-ATAAAATTATAAAGTATTAAAAAAT
* *
502644 TAAAATATATATTTATAAAGTATTAAAAAAT
1 TAAAATATAAAATTATAAAGTATTAAAAAAT
502675 TAAA
1 TAAA
502679 CATGTCTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (31 bp):
TAAAATATAAAATTATAAAGTATTAAAAAAT
Found at i:502699 original size:32 final size:32
Alignment explanation
Indices: 502627--502699 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 32
502617 ATGAAAAATT
**
502627 ATAAAT-TATTAAAAAATTAAAATATATATTT
1 ATAAATGTATTAAAAAATTAAAATATATATCG
* *
502658 ATAAA-GTATTAAAAAATTAAACATGTCTATCG
1 ATAAATGTATTAAAAAATTAAA-ATATATATCG
502690 A-AAATGTATT
1 ATAAATGTATT
502700 GCATTGCATC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.37
Consensus pattern (32 bp):
ATAAATGTATTAAAAAATTAAAATATATATCG
Found at i:513591 original size:42 final size:42
Alignment explanation
Indices: 513529--513621 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
513519 ACTTAGTAAG
*
513529 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGTTTAAA
1 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
*
513571 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
513613 TCCTTCGGG
1 TCCTTCGGG
513622 TAATTTGTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.32
Consensus pattern (42 bp):
TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
Found at i:513707 original size:42 final size:42
Alignment explanation
Indices: 513660--513748 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
513650 TGAAGCAATC
* * * **
513660 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTTGGG
1 CCATCAGTAAGCCTTCCGAGAATGATGATGAAGTCCTCCGGG
*
513702 CCATCAGTAAGCCTTCCGAGAATGATGATTAAGTCCTCCGGG
1 CCATCAGTAAGCCTTCCGAGAATGATGATGAAGTCCTCCGGG
513744 CCATC
1 CCATC
513749 TTATGCCTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.27
Consensus pattern (42 bp):
CCATCAGTAAGCCTTCCGAGAATGATGATGAAGTCCTCCGGG
Found at i:513908 original size:53 final size:53
Alignment explanation
Indices: 513823--513977 Score: 222
Period size: 53 Copynumber: 2.9 Consensus size: 53
513813 AGAATCACAC
* *
513823 CAGAAGATTGTTCGAGTTCTACTCCCTAAAGCAAGAGGGAGCAAACCCGTAGG
1 CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCAAACCCGTAGG
* *
513876 CAGAAGATTATTCGAGTTCTACTCCTTGAAGCAAGAGGGAGAAAACCCGTAGG
1 CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCAAACCCGTAGG
* * * *
513929 CATAAGACTGA-TCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG
1 CAGAAGA-TTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCAAACCCG
513978 CTTGTAACCC
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
53 89 0.98
54 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.19
Consensus pattern (53 bp):
CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCAAACCCGTAGG
Done.