Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005041.1 Hibiscus syriacus cultivar Beakdansim tig00011314_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: 53687
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:289 original size:15 final size:16
Alignment explanation
Indices: 269--299 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
259 GTGTTTGTTG
269 AAGCTG-AGGCAAATA
1 AAGCTGCAGGCAAATA
284 AAGCTGCAGGCAAATA
1 AAGCTGCAGGCAAATA
300 TGATAATGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.45, C:0.16, G:0.26, T:0.13
Consensus pattern (16 bp):
AAGCTGCAGGCAAATA
Found at i:2450 original size:19 final size:21
Alignment explanation
Indices: 2406--2450 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
2396 CCTTTATAAT
2406 ATTTAATCATGAGAGGATAGCA
1 ATTTAATCATGAGA-GATAGCA
*
2428 ATTTAATCATG-GA-ATATCA
1 ATTTAATCATGAGAGATAGCA
2447 ATTT
1 ATTT
2451 TGCTTAGTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
21 2 0.09
22 11 0.50
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (21 bp):
ATTTAATCATGAGAGATAGCA
Found at i:6316 original size:106 final size:105
Alignment explanation
Indices: 6122--6320 Score: 260
Period size: 106 Copynumber: 1.9 Consensus size: 105
6112 TTCTGGTTAC
* *
6122 TTAATTTCTTAATTCACTGCCCAAGAACACTAATCCAATAAACTCTGGTTAAATAAGTTCCTAAT
1 TTAAATTCTAAATTCACTGCCCAAGAACACTAATCCAATAAACTCTGGTTAAATAAGTTCCTAAT
* *
6187 TTACTTCCCCAAAACCCTAAATCCAATATAGCCTGAAGAA
66 TCACTTCCACAAAACCCTAAATCCAATATAGCCTGAAGAA
* * * *
6227 TTAAATTCTAAATTCACTGCCCAAGAACTCTAAATCCAAT-AAC-CGTGGATTGATTAAGTTCTT
1 TTAAATTCTAAATTCACTGCCCAAGAACACT-AATCCAATAAACTC-TGG-TTAAATAAGTTCCT
*
6290 AATTCAC-TGCACATAAACCCTAAATCCAATA
63 AATTCACTTCCACA-AAACCCTAAATCCAATA
6321 ACCCAAAACC
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
104 1 0.01
105 38 0.47
106 42 0.52
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (105 bp):
TTAAATTCTAAATTCACTGCCCAAGAACACTAATCCAATAAACTCTGGTTAAATAAGTTCCTAAT
TCACTTCCACAAAACCCTAAATCCAATATAGCCTGAAGAA
Found at i:7887 original size:2 final size:2
Alignment explanation
Indices: 7880--7917 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
7870 CTTACTTCTA
7880 AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
7918 GTTTGACAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10184 original size:17 final size:17
Alignment explanation
Indices: 10162--10202 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
10152 CAAAATTATA
10162 AATTAAATATTTAATTT
1 AATTAAATATTTAATTT
10179 AATTAAATATTTAATTT
1 AATTAAATATTTAATTT
10196 AATTAAA
1 AATTAAA
10203 AAATAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTAAATATTTAATTT
Found at i:12120 original size:18 final size:18
Alignment explanation
Indices: 12059--12120 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
12049 TATATAAGTT
12059 TAATTTATTTTTATGTAA
1 TAATTTATTTTTATGTAA
* * *
12077 TAATTGATTAATAAT-T-A
1 TAATTTATT-TTTATGTAA
**
12094 TTTTTTATTTTTATGTAA
1 TAATTTATTTTTATGTAA
12112 TAATTTATT
1 TAATTTATT
12121 GATATTTTAA
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
16 3 0.10
17 8 0.26
18 17 0.55
19 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
TAATTTATTTTTATGTAA
Found at i:12143 original size:15 final size:16
Alignment explanation
Indices: 12123--12165 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
12113 AATTTATTGA
12123 TATTTTAAATA-TAAT
1 TATTTTAAATATTAAT
12138 TATTTTAAATATTAAT
1 TATTTTAAATATTAAT
*
12154 AATTTT-AATATT
1 TATTTTAAATATT
12166 TTATATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTTAAATATTAAT
Found at i:12384 original size:13 final size:13
Alignment explanation
Indices: 12366--12391 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12356 AGCCTAGTTA
12366 TAATATTATAAAT
1 TAATATTATAAAT
12379 TAATATTATAAAT
1 TAATATTATAAAT
12392 CTTTTTGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATATTATAAAT
Found at i:13689 original size:11 final size:11
Alignment explanation
Indices: 13673--13699 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
13663 ATTCGATATT
13673 GCTTGTAAAAA
1 GCTTGTAAAAA
13684 GCTTGTAAAAA
1 GCTTGTAAAAA
13695 GCTTG
1 GCTTG
13700 CTGCTACGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (11 bp):
GCTTGTAAAAA
Found at i:18425 original size:18 final size:16
Alignment explanation
Indices: 18395--18429 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
18385 AAACTATTAA
18395 AAAATTTGGTAACCGGT
1 AAAATTTGGTAA-CGGT
18412 AAAATTTGGTTAACGGT
1 AAAATTTGG-TAACGGT
18429 A
1 A
18430 GGTATCGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.31
Consensus pattern (16 bp):
AAAATTTGGTAACGGT
Found at i:19352 original size:73 final size:73
Alignment explanation
Indices: 19226--19723 Score: 741
Period size: 73 Copynumber: 6.8 Consensus size: 73
19216 CGATAGGTAA
* * * *
19226 TTTAATGTAATATGTAACGCCTA-TTTTTTTACCGTTTACATTATTAGCAACCTTCAAAAAACCA
1 TTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAACCG
* *
19290 GTAGGTAA
66 GTAGATAT
* * *
19298 TTGAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAATCA
1 TTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAACCG
*
19363 GTAGGTAT
66 GTAGATAT
* *
19371 TTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACATTCAAAAAAACC
1 TTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTT-AAAAAAACC
* *
19436 GATAGATAG
65 GGTAGATAT
*
19445 TTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACAATATTAGCAACCTTAAAAAAACCG
1 TTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAACCG
*
19510 GTAGATGT
66 GTAGATAT
* * * *
19518 TTTAATGTAATAGGTAACGCCTATTTTTTATACCATTTACATTATTAGCAACCTTAAAAAAACCG
1 TTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAACCG
19583 GTAGATAT
66 GTAGATAT
* * *
19591 TTTAATGTAATAGGTAGCGTCTATTTTTTTT-CCGTTTACATTATTAGCAACCTTAAAAAAAACG
1 TTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAACCG
19655 GTAGATAT
66 GTAGATAT
*
19663 TTTAATGTAAT-AGATAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACTTTAAAAAA
1 TTTAATGTAATAAG-TAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAA
19724 TCGATATTTT
Statistics
Matches: 388, Mismatches: 34, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
71 1 0.00
72 86 0.22
73 236 0.61
74 65 0.17
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (73 bp):
TTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAACCG
GTAGATAT
Found at i:19484 original size:147 final size:147
Alignment explanation
Indices: 19226--19723 Score: 756
Period size: 147 Copynumber: 3.4 Consensus size: 147
19216 CGATAGGTAA
*
19226 TTTAATGTAATATGTAACGCCTA-TTTTTTTACCGTTTACATTATTAGCAACCTTC-AAAAAACC
1 TTTAATGTAATAGGTAACGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTCAAAAAAACC
* *
19289 -AGTAGGTAATTGAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTT
66 GA-TAGATAATTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTT
* * *
19353 AAAAAAATCAGTAGGTAT
130 AAAAAAAACGGTAGATAT
* *
19371 TTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACATTCAAAAAAACC
1 TTTAATGTAATAGGTAACGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTCAAAAAAACC
* *
19436 GATAGATAGTTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACAATATTAGCAACCTTA
66 GATAGATAATTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
* *
19501 AAAAAACCGGTAGATGT
131 AAAAAAACGGTAGATAT
* *
19518 TTTAATGTAATAGGTAACGCCTATTTTTTATACCATTTACATTATTAGCAACCTT-AAAAAAACC
1 TTTAATGTAATAGGTAACGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTCAAAAAAACC
* * * *
19582 GGTAGATATTTTAATGTAATAGGTAGCGTCTATTTTTTTT-CCGTTTACATTATTAGCAACCTTA
66 GATAGATAATTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
19646 AAAAAAACGGTAGATAT
131 AAAAAAACGGTAGATAT
* * *
19663 TTTAATGTAATAGATAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAA-CTTTAAAAAA
1 TTTAATGTAATAGGTAACGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTCAAAAAA
19724 TCGATATTTT
Statistics
Matches: 323, Mismatches: 26, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
144 3 0.01
145 112 0.35
146 76 0.24
147 131 0.41
148 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (147 bp):
TTTAATGTAATAGGTAACGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTCAAAAAAACC
GATAGATAATTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
AAAAAAACGGTAGATAT
Found at i:19755 original size:16 final size:16
Alignment explanation
Indices: 19734--19764 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19724 TCGATATTTT
*
19734 TTTAACCGGTCACTTG
1 TTTAACCAGTCACTTG
19750 TTTAACCAGTCACTT
1 TTTAACCAGTCACTT
19765 TATTTTTTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.39
Consensus pattern (16 bp):
TTTAACCAGTCACTTG
Found at i:23895 original size:31 final size:31
Alignment explanation
Indices: 23860--23924 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
23850 TTTCTGTTTC
23860 TTCCAAAATATACTTTTAAGATTAATATTAA
1 TTCCAAAATATACTTTTAAGATTAATATTAA
23891 TTCCAAAATATACTTTTAAGATTAATATTAA
1 TTCCAAAATATACTTTTAAGATTAATATTAA
23922 TTC
1 TTC
23925 TCATACTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (31 bp):
TTCCAAAATATACTTTTAAGATTAATATTAA
Found at i:28031 original size:24 final size:24
Alignment explanation
Indices: 28004--28055 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
27994 AACGGATATA
*
28004 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
28028 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
28052 TCAA
1 TCAA
28056 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:28056 original size:24 final size:24
Alignment explanation
Indices: 28024--28141 Score: 159
Period size: 24 Copynumber: 4.9 Consensus size: 24
28014 AAACATAAAT
*
28024 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
28048 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
28072 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
28096 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
28120 CATGTCAAGTATCAGATCAGAA
1 CAGGTCAAGTATCAGATCAGAA
28142 ATCAAATCGA
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
23 5 0.06
24 79 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:28158 original size:48 final size:47
Alignment explanation
Indices: 28027--28158 Score: 151
Period size: 48 Copynumber: 2.7 Consensus size: 47
28017 CATAAATCAG
* *
28027 GTCAAGTATCATATCAGAAATCAGGTCAAGTAA-CAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAAATCAAGTCAA--AATCAGATCAGAATCCAA
* * *
28075 GTCAAGTATCAGATCAG-AATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAAT-CAAGTCA-AAATCAGATCAGAATCCAA
*
28123 GTCAAGTATCAGATCAGAAATCAAATCGAAAATCAG
1 GTCAAGTATCAGATCAGAAATCAAGTC-AAAATCAG
28159 GTAAAATATT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
47 4 0.06
48 63 0.88
49 5 0.07
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (47 bp):
GTCAAGTATCAGATCAGAAATCAAGTCAAAATCAGATCAGAATCCAA
Found at i:30584 original size:15 final size:15
Alignment explanation
Indices: 30564--30610 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
30554 GGTCAACTCC
30564 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
30579 GGTCAACAGTCAACG
1 GGTCAACGGTCAACG
*
30594 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
30607 GGTC
1 GGTC
30611 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 11 0.38
15 18 0.62
ACGTcount: A:0.23, C:0.26, G:0.36, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:30605 original size:13 final size:13
Alignment explanation
Indices: 30587--30646 Score: 66
Period size: 13 Copynumber: 4.2 Consensus size: 13
30577 CGGGTCAACA
30587 GTCAACGGGTCGG
1 GTCAACGGGTCGG
30600 GTCAACGGGTCGGGTCGG
1 GTCAA-----CGGGTCGG
30618 GTCAACGGGTCGG
1 GTCAACGGGTCGG
*
30631 GTAAACGGGTCGG
1 GTCAACGGGTCGG
30644 GTC
1 GTC
30647 GGGTTGTGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 27 0.68
18 13 0.32
ACGTcount: A:0.15, C:0.22, G:0.47, T:0.17
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:30625 original size:31 final size:31
Alignment explanation
Indices: 30587--30650 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
30577 CGGGTCAACA
*
30587 GTCAACGGGTCGGGTCAACGGGTCGGGTCGG
1 GTCAACGGGTCGGGTAAACGGGTCGGGTCGG
30618 GTCAACGGGTCGGGTAAACGGGTCGGGTCGG
1 GTCAACGGGTCGGGTAAACGGGTCGGGTCGG
30649 GT
1 GT
30651 TGTGACCGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.14, C:0.20, G:0.48, T:0.17
Consensus pattern (31 bp):
GTCAACGGGTCGGGTAAACGGGTCGGGTCGG
Found at i:30628 original size:8 final size:8
Alignment explanation
Indices: 30564--30610 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
30554 GGTCAACTCC
30564 GGTCAAC-
1 GGTCAACG
30571 GGTCAACG
1 GGTCAACG
30579 GGTCAAC-
1 GGTCAACG
*
30586 AGTCAACG
1 GGTCAACG
30594 GGT---CG
1 GGTCAACG
30599 GGTCAACG
1 GGTCAACG
30607 GGTC
1 GGTC
30611 GGGTCGGGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
5 5 0.15
7 13 0.39
8 15 0.45
ACGTcount: A:0.23, C:0.26, G:0.36, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:30650 original size:18 final size:18
Alignment explanation
Indices: 30592--30632 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
30582 CAACAGTCAA
30592 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
30610 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
30628 CGGGT
1 CGGGT
30633 AAACGGGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:34243 original size:20 final size:20
Alignment explanation
Indices: 34218--34269 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
34208 GTAAAAATAT
34218 GACAAAACCGGTCTCTAAAG
1 GACAAAACCGGTCTCTAAAG
* *
34238 GACAAAATCGATCTCTAAAG
1 GACAAAACCGGTCTCTAAAG
* *
34258 GATAAAAGCGGT
1 GACAAAACCGGT
34270 ATAGAGCGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.17
Consensus pattern (20 bp):
GACAAAACCGGTCTCTAAAG
Found at i:34427 original size:202 final size:202
Alignment explanation
Indices: 34081--34446 Score: 624
Period size: 202 Copynumber: 1.8 Consensus size: 202
34071 GCGCTACCGG
* * * *
34081 ATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATTTAAAAGATAAGCAG
1 ATATATTAAAAGTGTCGATACTTTAATATAAGTATCGACACATTATGAATTTAAAAGAAAAGCAG
* *
34146 TTTTAGCGCCTACAAAGTGTCGATACTTTATAACAATGTATCGATCCACAACGATATAAAAAGTA
66 TTTTAGCGCCTACAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAAAAAGCA
*
34211 AAAATATGACAAAACCGGTCTCTAAAGGACAAAATCGATCTCTAAAGGATAAAAGCGGTATAGAG
131 AAAATATGACAAAACCGGTCTCGAAAGGACAAAATCGATCTCTAAAGGATAAAAGCGGTATAGAG
34276 CGACTGA
196 CGACTGA
34283 ATATATTAAAAGTGTCGATACTTTAATATAAGTATCGACACATTATGAATTTAAAAGAAAAGCAG
1 ATATATTAAAAGTGTCGATACTTTAATATAAGTATCGACACATTATGAATTTAAAAGAAAAGCAG
* * * *
34348 TTTTAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACGATATAACAGGCA
66 TTTTAGCGCCTACAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAAAAAGCA
*
34413 AAAATATGACAAAACCGGTCTCGAAATGACAAAA
131 AAAATATGACAAAACCGGTCTCGAAAGGACAAAA
34447 CCGGTAAAGA
Statistics
Matches: 152, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
202 152 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (202 bp):
ATATATTAAAAGTGTCGATACTTTAATATAAGTATCGACACATTATGAATTTAAAAGAAAAGCAG
TTTTAGCGCCTACAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAAAAAGCA
AAAATATGACAAAACCGGTCTCGAAAGGACAAAATCGATCTCTAAAGGATAAAAGCGGTATAGAG
CGACTGA
Found at i:36911 original size:21 final size:21
Alignment explanation
Indices: 36887--36930 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
36877 ATGACAATCA
36887 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
*
36908 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
36929 AG
1 AG
36931 GCATAAGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.34, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:37218 original size:18 final size:18
Alignment explanation
Indices: 37195--37233 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
37185 GAAAAAATAT
37195 GAAGAAGAAAAGAGGGAG
1 GAAGAAGAAAAGAGGGAG
*
37213 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGAGGGAG
37231 GAA
1 GAA
37234 ATGAGGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.41, T:0.03
Consensus pattern (18 bp):
GAAGAAGAAAAGAGGGAG
Found at i:37925 original size:23 final size:20
Alignment explanation
Indices: 37877--37924 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
37867 CGTGTAATTG
37877 CAACAACAGGCGTTGGATGC
1 CAACAACAGGCGTTGGATGC
37897 CAACAACAGGCGTTGGATGC
1 CAACAACAGGCGTTGGATGC
37917 CAACAACA
1 CAACAACA
37925 AAGTAAGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.25, T:0.12
Consensus pattern (20 bp):
CAACAACAGGCGTTGGATGC
Found at i:39170 original size:15 final size:15
Alignment explanation
Indices: 39150--39187 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
39140 TCCAGTATGA
39150 TTCCCAAACATAAAG
1 TTCCCAAACATAAAG
*
39165 TTCCCAAACGTAAAG
1 TTCCCAAACATAAAG
*
39180 TTTCCAAA
1 TTCCCAAA
39188 AAATAGGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.26, G:0.08, T:0.24
Consensus pattern (15 bp):
TTCCCAAACATAAAG
Found at i:39559 original size:200 final size:199
Alignment explanation
Indices: 39204--40362 Score: 1214
Period size: 200 Copynumber: 5.7 Consensus size: 199
39194 GTAAGCAGAT
* *
39204 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* ** * * * *
39269 GATAATTTTGTAATATAACCGGTATAAGTATACCAGTTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAATTTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * * *
39334 ATCGACACTTTTGAAATTGGTGTCGATATTTTTTGTCCAGAATGAATGCCCAAAATGATGAACGC
131 ATCGACAC-TTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGCACGC
39399 ATAAA
195 ATAAA
* *
39404 GTGTCAATACATTTATAAAAAGTATCGATCCCAGAAATATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * * *
39469 GGTAAATTTACAATGTAACCGGTATAACTACACCGGTTTTATGAGAGAATATGTCTACATAATGT
66 GGTAATTTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * * * *
39534 ATCGACACTTCTGGAATTTGTGTCGATA-TTGTTTGTCCAGAATGAATGCTCAAAAGGGTTCACT
131 ATCGACACTT-TGAAATTTGTGTCGATACTT-TTTGTCCAGAATGAATGCCCAAAATGGTGCACG
39598 CATAAA
194 CATAAA
* * * ** *
39604 GTGTCGATACATTTTTTAAAAGTGTCGATACATTTTTTAAAAGTGTCGATCCCAGAGACATTGAA
1 GTGTCGATACATTTATAAAAAGTATCGAT-C---------------C---CAGA-A-ACATCGAA
* ** *** *
39669 ACCCGTAATTATAATGTAATAGGTAATTTTGTAATGTAACCGGTATAAATATATTAGTTTTATGT
45 ACCCATAATTATAATGTAATAGGTAATTTTACAATGTAACCGGTATAAATATACCGGTTTTATGA
* * * *
39734 GAGAATAGGTCTACATAATGTATCGACACAATTGAAATTAGTATCTATACTTTTTGTCCAGAATG
110 GAGAATAGGTCTACATAATGTATCGACAC-TTTGAAATTTGTGTCGATACTTTTTGTCCAGAATG
*
39799 AATGCCCAAAATGGTGAACGCATAAA
174 AATGCCCAAAATGGTGCACGCATAAA
* * * * * * *
39825 GTGTCGATACGTTTTTTAAAAGTGTCGATCCTAGAGACATCGAAACCCATAGTTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * *
39890 GGTAATTTTAAAATGTAACCGATATAAATATACCGGTTTTAT-ATGAGAGTAGGTCTACATAATG
66 GGTAATTTTACAATGTAACCGGTATAAATATACCGGTTTTATGA-GAGAATAGGTCTACATAATG
* * * *
39954 TATCGATACTTTTTAATTTTGTGTCGATACATTTTGTCCAGAATGAATGCCCAAAAAAATGGTGC
130 TATCGACAC-TTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCC---AAAATGGTGC
40019 ACGCATAAA
191 ACGCATAAA
* * * * *
40028 GTGTCGACACATTTATAAAAAATATCAATCCTAGAAACATCGAAACCCATGATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * * ** * * * *
40093 TGTAATTTTTCAATGTAACTGGTATAAATATATTGGTTTTATGCGAGCATAGGTCTAAAAAATGT
66 GGTAATTTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * * *
40158 ATCGACACTTATGGAATTTGTGTCGATACTTTTTGTCCAGAA-GGATG-CCAAAAGGGTGCACAC
131 ATCGACACTT-TGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGCACGC
*
40221 ATTAA
195 ATAAA
* * * *
40226 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * * * * *
40291 GGTAAATTT-CTAATGTAACCTGTATAAATATACCGATTTTATGAGAAAATAGGTC-AGCAAAAA
66 GGTAATTTTAC-AATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTA-CATAAT
40354 GTATCGACA
129 GTATCGACA
40363 ATTGTTAAAT
Statistics
Matches: 797, Mismatches: 129, Indels: 68
0.80 0.13 0.07
Matches are distributed among these distances:
197 2 0.00
198 128 0.16
199 4 0.01
200 321 0.40
201 3 0.00
202 7 0.01
203 159 0.20
205 1 0.00
216 1 0.00
219 2 0.00
220 2 0.00
221 164 0.21
222 3 0.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (199 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
ATCGACACTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGCACGCA
TAAA
Found at i:39625 original size:21 final size:21
Alignment explanation
Indices: 39601--39653 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
39591 GTTCACTCAT
39601 AAAGTGTCGATACATTTTTTA
1 AAAGTGTCGATACATTTTTTA
39622 AAAGTGTCGATACATTTTTTA
1 AAAGTGTCGATACATTTTTTA
39643 AAAGTGTCGAT
1 AAAGTGTCGAT
39654 CCCAGAGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (21 bp):
AAAGTGTCGATACATTTTTTA
Found at i:39792 original size:221 final size:221
Alignment explanation
Indices: 39401--39853 Score: 613
Period size: 221 Copynumber: 2.0 Consensus size: 221
39391 ATGAACGCAT
* *
39401 AAAGTGTCAATACATTTATAAAAAGTATCGATCCCAGAAATATCGAAACCCATAATTATAATGTA
1 AAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
* * *
39466 ATAGGTAAATTTACAATGTAACCGGTATAACTACACCGGTTTTATGAGAGAATATGTCTACATAA
66 ATAGGTAAATTTACAATGTAACCGGTATAAATACACCAGTTTTATGAGAGAATAGGTCTACATAA
* * * * * **
39531 TGTATCGACACTTCTGGAATTTGTGTCGATATTGTTTGTCCAGAATGAATGCTCAAAAGGGTTCA
131 TGTATCGACACATCTGAAATTAGTATCGATATTGTTTGTCCAGAATGAATGCCCAAAAGGGTGAA
*
39596 CTCATAAAGTGTCGATACATTTTTTA
196 CGCATAAAGTGTCGATACATTTTTTA
* * * * * *
39622 AAAGTGTCGATACATTTTTTAAAAGTGTCGATCCCAGAGACATTGAAACCCGTAATTATAATGTA
1 AAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
* ** * ** *
39687 ATAGGTAATTTTGTAATGTAACCGGTATAAATATATTAGTTTTATGTGAGAATAGGTCTACATAA
66 ATAGGTAAATTTACAATGTAACCGGTATAAATACACCAGTTTTATGAGAGAATAGGTCTACATAA
* *
39752 TGTATCGACACAAT-TGAAATTAGTATCTATACTT-TTTGTCCAGAATGAATGCCCAAAATGGTG
131 TGTATCGACAC-ATCTGAAATTAGTATCGATA-TTGTTTGTCCAGAATGAATGCCCAAAAGGGTG
*
39815 AACGCATAAAGTGTCGATACGTTTTTTA
194 AACGCATAAAGTGTCGATACATTTTTTA
39843 AAAGTGTCGAT
1 AAAGTGTCGAT
39854 CCTAGAGACA
Statistics
Matches: 201, Mismatches: 29, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
221 198 0.99
222 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (221 bp):
AAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
ATAGGTAAATTTACAATGTAACCGGTATAAATACACCAGTTTTATGAGAGAATAGGTCTACATAA
TGTATCGACACATCTGAAATTAGTATCGATATTGTTTGTCCAGAATGAATGCCCAAAAGGGTGAA
CGCATAAAGTGTCGATACATTTTTTA
Found at i:39992 original size:421 final size:401
Alignment explanation
Indices: 39204--40362 Score: 1378
Period size: 421 Copynumber: 2.8 Consensus size: 401
39194 GTAAGCAGAT
* *
39204 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * * **
39269 GATAATTTTGTAATATAACCGGTATAAGTATACCAGTTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATATTAGTTTTATGTGAGAATAGGTCTACATAATGT
* * *
39334 ATCGACACTTTTGAAATTGGTGTCGATATTTTTTGTCCAGAATGAATGCCCAAAATGATGAACGC
131 ATCGACAC-TTTGAAATTAGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGC
* * * *
39399 ATAAAGTGTCAATACATTTATAAAAAGTATCGATCCCAGAAATATCGAAACCCATAATTATAATG
195 ATAAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATG
* * * *
39464 TAATAGGTAAATTTACAATGTAACCGGTATAACTACACCGGTTTTATGAGAGAATATGTCTACAT
260 TAATAGGTAAATTTAAAATGTAACC-GTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAT
* *
39529 AATGTATCGACACTTCTGGAATTTGTGTCGATATTGTTTGTCCAGAATGAATGCTCAAAAGGGTT
324 AATGTATCGACACTTCTGGAATTTGTGTCGATAATGTTTGTCCAGAATGAATGCCCAAAA-----
*
39594 CACTCATAAAGTGTCGATACATTTTTTAAAA
384 -A---A-AAAGTG-C-ACACA-----T-AAA
* * * * * *
39625 GTGTCGATACATTTTTTAAAAGTGTCGATCCCAGAGACATTGAAACCCGTAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
39690 GGTAATTTTGTAATGTAACCGGTATAAATATATTAGTTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATATTAGTTTTATGTGAGAATAGGTCTACATAATGT
* * *
39755 ATCGACACAATTGAAATTAGTATCTATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGC
131 ATCGACAC-TTTGAAATTAGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGC
* * * * *
39820 ATAAAGTGTCGATACGTTTTTTAAAAGTGTCGATCCTAGAGACATCGAAACCCATAGTTATAATG
195 ATAAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATG
* *
39885 TAATAGGTAATTTTAAAATGTAACCGATATAAATATACCGGTTTTAT-ATGAGAGTAGGTCTACA
260 TAATAGGTAAATTTAAAATGTAACCG-TATAAATATACCGGTTTTATGA-GAGAATAGGTCTACA
* **
39949 TAATGTATCGATACTT-TTTAATTTTGTGTCGATACAT-TTTGTCCAGAATGAATGCCCAAAAAA
323 TAATGTATCGACACTTCTGGAA-TTTGTGTCGATA-ATGTTTGTCCAGAATGAATGCCCAAAAAA
** *
40012 ATGGTGCACGCATAAA
386 AAAGTGCACACATAAA
* * * * *
40028 GTGTCGACACATTTATAAAAAATATCAATCCTAGAAACATCGAAACCCATGATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * * * * * *
40093 TGTAATTTT-TCAATGTAACTGGTATAAATATATTGGTTTTATGCGAGCATAGGTCTAAAAAATG
66 GGTAATTTTGT-AATGTAACCGGTATAAATATATTAGTTTTATGTGAGAATAGGTCTACATAATG
* * * * * *
40157 TATCGACACTTATGGAATTTGTGTCGATACTTTTTGTCCAGAA-GGATG-CCAAAAGGGTGCACA
130 TATCGACACTT-TGAAATTAGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACG
* * *
40220 CATTAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCGATAATTATAAT
194 CATAAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAAT
** * *
40285 GTAATAGGTAAATTTCTAATGTAACCTGTATAAATATACCGATTTTATGAGAAAATAGGTC-AGC
259 GTAATAGGTAAATTTAAAATGTAACC-GTATAAATATACCGGTTTTATGAGAGAATAGGTCTA-C
* *
40349 AAAAAGTATCGACA
322 ATAATGTATCGACA
40363 ATTGTTAAAT
Statistics
Matches: 641, Mismatches: 88, Indels: 38
0.84 0.11 0.05
Matches are distributed among these distances:
400 1 0.00
401 132 0.21
402 8 0.01
403 148 0.23
404 1 0.00
409 3 0.00
410 1 0.00
411 4 0.01
412 1 0.00
415 1 0.00
420 5 0.01
421 335 0.52
422 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (401 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTGTAATGTAACCGGTATAAATATATTAGTTTTATGTGAGAATAGGTCTACATAATGT
ATCGACACTTTGAAATTAGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCA
TAAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGT
AATAGGTAAATTTAAAATGTAACCGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAA
TGTATCGACACTTCTGGAATTTGTGTCGATAATGTTTGTCCAGAATGAATGCCCAAAAAAAAAGT
GCACACATAAA
Found at i:41913 original size:6 final size:6
Alignment explanation
Indices: 41873--41912 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
41863 CAAGAGGTCA
* * *
41873 ATGAAG ATGAAG ATGACG ATGAAG ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
41913 TCCAATAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.42, C:0.03, G:0.33, T:0.23
Consensus pattern (6 bp):
ATGAAG
Found at i:43232 original size:24 final size:25
Alignment explanation
Indices: 43205--43259 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
43195 TTTCAAATTC
*
43205 ATTTCATATGT-AATTGGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
* *
43229 ATTT-AAATTTCAATTTGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
*
43253 GTTTCAA
1 ATTTCAA
43260 TATAAATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 4 0.16
24 19 0.76
25 2 0.08
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.47
Consensus pattern (25 bp):
ATTTCAAATGTCAATTGGAGTTTGA
Found at i:43267 original size:24 final size:24
Alignment explanation
Indices: 43216--43268 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
43206 TTTCATATGT
* * *
43216 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
* *
43240 AATTTGAGTTTGAGTTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
43264 AATTT
1 AATTT
43269 CGGCTCCACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:44930 original size:179 final size:180
Alignment explanation
Indices: 44615--45184 Score: 456
Period size: 179 Copynumber: 3.1 Consensus size: 180
44605 ACATGTTTAA
* *
44615 AAAGTATCGATCCCAAAAACATCGAAACCGAAAAATTATAATGTAATAGGTAAATTTACAATGTA
1 AAAGTATCGATCCCAAAAACATCGAAACCGAAAAATTATAATATAATAGGTAAATTTACAATATA
* *
44680 ACCGGTATAAATATATCAGTTTTTTGAGAAACTAGATACACATAATGCATCGACACTTGTGGAAA
66 ACAGATATAAATATATCAGTTTTTTGAGAAACTAGATACACATAATGCATCGACACTTGTGGAAA
* *
44745 TTGTGTCGATACTTTTTGTCCAAAATGAAT-GCCAAACGTGGTGCACACAT
131 TTGTGTCGATACTTTTTGTCCAAAATGAATGGCCAAA-ATGGTGAACACAT
* * * **
44795 AAAGTATCGATCCCAAAAACATCGAAACC-CATAATTATAATATAATAGGTAATTTTGTAATATA
1 AAAGTATCGATCCCAAAAACATCGAAACCGAAAAATTATAATATAATAGGTAAATTTACAATATA
* * * ** * *
44859 ACATATATAAATATATTAGTTTTATGTGAG-AA-TAGGT-CTACATAATGTGTCGACAGTT-TTG
66 ACAGATATAAATATATCAGTTTT-T-TGAGAAACTAGATAC-ACATAATGCATCGACACTTGTGG
* * * *
44920 AATTTTGTGTCGATACTTTTTGTCCAGAATGATTGGCCAAAATGGTGAACGCAT
128 AA-ATTGTGTCGATACTTTTTGTCCAAAATGAATGGCCAAAATGGTGAACACAT
* ** * * *
44974 AAAGTGTCGATACATTTATAAAAAGTATTGATCCCAGAAACATCAAAACCCATAATTATAATGTA
1 AAAGTATCGAT-C-----CCAAAA--A--CAT--C-GAAAC--C-GAA---A-AATTATAATATA
* * * * * * * *
45039 ATAGGTAAATTTACAATGTAACCGGTATAACTTTATCGGTTTTATGAGAGAA-TAGGT-CTACAT
46 ATAGGTAAATTTACAATATAACAGATATAAATATATCAGTTTTTTGAGA-AACTAGATAC-ACAT
* * * *
45102 AATGTATTGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAAAATGAAT-GCCAAAAGGGTT
109 AATGCATCGACACTTGTGGAAATTGTGTCGATACTTTTTGTCCAAAATGAATGGCCAAAATGG-T
*
45166 GCACACAT
173 GAACACAT
45174 AAAGTATCGAT
1 AAAGTATCGAT
45185 ACATTTTTAA
Statistics
Matches: 309, Mismatches: 51, Indels: 40
0.77 0.13 0.10
Matches are distributed among these distances:
178 5 0.02
179 115 0.37
180 39 0.13
181 4 0.01
185 4 0.01
187 1 0.00
189 2 0.01
191 1 0.00
192 5 0.02
194 1 0.00
196 1 0.00
198 4 0.01
199 9 0.03
200 114 0.37
201 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (180 bp):
AAAGTATCGATCCCAAAAACATCGAAACCGAAAAATTATAATATAATAGGTAAATTTACAATATA
ACAGATATAAATATATCAGTTTTTTGAGAAACTAGATACACATAATGCATCGACACTTGTGGAAA
TTGTGTCGATACTTTTTGTCCAAAATGAATGGCCAAAATGGTGAACACAT
Found at i:45138 original size:200 final size:197
Alignment explanation
Indices: 44795--45539 Score: 882
Period size: 200 Copynumber: 3.7 Consensus size: 197
44785 GTGCACACAT
* * * ** *
44795 AAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATATAATAGGTAATTTTGTAATATAA
1 AAAGTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
** ** * * * * *
44860 CATATATAAATATATTAGTTTTATGTGAGAATAGGTCTACATAATGTGTCGACAGTTTTGAATTT
66 CCGATATAAATATACCAATTTTATGAGAGAATAGGTCAACATAATGTATCGACACTTTTGAA-TT
* * * *
44925 TGTGTCGATACTTTTTGTCCAGAATGATTGGCCAAAATGGTGAACGCATAAAGTGTCGATACATT
130 TGTGTCGATACTTTTTGTCCAGAATGAAT-GCCAAAAGGGTGCACGCATAAAGTATCGATACATT
44990 TATAA
194 T-TAA
* *
44995 AAAGTATTGATCCCAGAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
1 AAAGTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
* * * * ** * * *
45060 CCGGTATAACTTTATCGGTTTTATGAGAGAATAGGTCTACATAATGTATTGACACTTGTGGAATT
66 CCGATATAAATATACCAATTTTATGAGAGAATAGGTCAACATAATGTATCGACACTT-TTGAATT
* *
45125 TGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGTTGCACACATAAAGTATCGATACATT
130 TGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAGGG-TGCACGCATAAAGTATCGATACA-T
45190 TTTAA
193 TTTAA
* * *
45195 AAAGTATCGATCCCAAAAACATCGAAACCGATCATTATAATGTAATAGGTAAATTTACAATGTAA
1 AAAGTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
* * * * *
45260 CCGGTATAAATTTACCGATTTTATGAGA-ACATATGTGAACATAATGTATCGACACGTTTT-AGA
66 CCGATATAAATATACCAATTTTATGAGAGA-ATAGGTCAACATAATGTATCGACAC-TTTTGA-A
* * * *
45323 TTTGTGTCGATACATTTTGTCCAGAATGAATGCCAAACGGGGTGCAGGCAGAAAGTATCGATACA
128 TTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAA-AGGGTGCACGCATAAAGTATCGATACA
45388 TTTTAA
192 TTTTAA
** * * * * * * *
45394 ATTGTATTGATCCAAAAAAATATCAAAACCGATAATTATAACGCAATAGATAAATTTACAATGTA
1 AAAGTATCGATCC-CAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTA
* *
45459 ACCGATATAAATATACCAATTTTATGAGAGAATATGTCAACATAATGTATCGACACTTTTAAATT
65 ACCGATATAAATATACCAATTTTATGAGAGAATAGGTCAACATAATGTATCGACACTTTTGAATT
45524 TGTGTCGATACTTTTT
130 TGTGTCGATACTTTTT
45540 AAATAACATG
Statistics
Matches: 475, Mismatches: 60, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
199 49 0.10
200 413 0.87
201 13 0.03
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (197 bp):
AAAGTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
CCGATATAAATATACCAATTTTATGAGAGAATAGGTCAACATAATGTATCGACACTTTTGAATTT
GTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAGGGTGCACGCATAAAGTATCGATACATTTT
AA
Found at i:47142 original size:19 final size:19
Alignment explanation
Indices: 47118--47166 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
47108 AATGTAGGAT
47118 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
** *
47137 TAATTTTACATACGATTTA
1 TAATTTTGTATAAGATTTA
47156 TAATTTTGTAT
1 TAATTTTGTAT
47167 GTGAATGTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:50079 original size:200 final size:197
Alignment explanation
Indices: 49646--50341 Score: 763
Period size: 200 Copynumber: 3.5 Consensus size: 197
49636 ACCTAAATAT
* *
49646 GTGTCGATACATTTTCTAAAAGTATCGA-CCCAAAAAACATCGAAACCAATAATTATAATGTAAT
1 GTGTCGATACATTTT-TAAAAGTATAGATCCCAAAAAACATCGAAACCGATAATTATAATGTAAT
* * * *
49710 AGGTAAATTAACAATGTAACCGATATAAATATACCGG-TTAATTAGAAAACATGTCAACATAATG
65 AGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATAAGAAAATATGTC-ACATAATG
* ** * *
49774 TATAGACACTTGTGCAATTTGTATCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCAC
129 TATCGACACTTGTTAAATTTGTGTCGATACTT-TTGTCCAGAATGAAT-ACCAAA-GAGGTGCAC
**
49839 AAATAAA
191 GCATAAA
* * *
49846 GTATCGATACATTTATTAAAAGTATCGATCCCAATAAA-ATCGAAACCGATAATTATAATGTAAT
1 GTGTCGATACATTT-TTAAAAGTATAGATCCCAAAAAACATCGAAACCGATAATTATAATGTAAT
* * * * *
49910 ATGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAGCATAAAG
65 AGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATAAGAAAATATGTCA-CATAATG
* * *
49975 TATCGACACTTGTTAAATTTGCGTCGATACATTTTGTCCATAATGAATACCAAAGGGGTGCACGC
129 TATCGACACTTGTTAAATTTGTGTCGATAC-TTTTGTCCAGAATGAATACCAAAGAGGTGCACGC
50040 ATAAA
193 ATAAA
* * *
50045 GTGTCGATACATTTATTAAAAGTATAGTATCCC-AAAAACATCGAAACTGATAATTACAATGTGA
1 GTGTCGATACATTT-TTAAAAGTATAG-ATCCCAAAAAACATCGAAACCGATAATTATAATGTAA
* * * *
50109 TAGG------TACAATGTACCCGATAGAAATATACCTGTTTTATAAGAAAATATGTCTAAATAAT
64 TAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATAAGAAAATATGTC-ACATAAT
* * * * * *
50168 GTATCAACACTTTTTAAGTTTGTGTCGATACTTTCT-TCTAGAATGAATGCGCAACGAGGTGCAC
128 GTATCGACACTTGTTAAATTTGTGTCGATACTTT-TGTCCAGAATGAATAC-CAAAGAGGTGCAC
50232 GCATAAA
191 GCATAAA
* *
50239 GTGTCGATACA-TTTCAAATTA-TATTGAT-CCAAAAAACATCGAAACCGATAATTATAATGTAA
1 GTGTCGATACATTTTTAAA--AGTATAGATCCCAAAAAACATCGAAACCGATAATTATAATGTAA
** * * *
50301 TAGGTAAATTTGTAATGTTACCGGTATAAATATACCAGTTT
64 TAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTT
50342 ACTTATAAAA
Statistics
Matches: 420, Mismatches: 57, Indels: 40
0.81 0.11 0.08
Matches are distributed among these distances:
191 2 0.00
192 38 0.09
193 20 0.05
194 103 0.25
195 1 0.00
198 24 0.06
199 42 0.10
200 120 0.29
201 68 0.16
202 2 0.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (197 bp):
GTGTCGATACATTTTTAAAAGTATAGATCCCAAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATAAGAAAATATGTCACATAATGTA
TCGACACTTGTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATACCAAAGAGGTGCACGCATA
AA
Found at i:50507 original size:83 final size:85
Alignment explanation
Indices: 50359--50517 Score: 250
Period size: 83 Copynumber: 1.9 Consensus size: 85
50349 AAATTGGTCA
* * *
50359 ATATAAGCGCTACCTATTACATTATATTAGCGCTGCCTAATATGTTATTGTACTTAATAATATTT
1 ATATAAGCACTACATATTACATTATATTAGCGCTACCTAATA--TTATTGTACTTAATAATATTT
50424 CCAGTTAAATGCCTATTTTATT
64 CCAGTTAAATGCCTATTTTATT
50446 ATATAAGCACTACATATTACATTATA-TAGCGCTACCTAATA-TATTGTACTTAATAATATTTCC
1 ATATAAGCACTACATATTACATTATATTAGCGCTACCTAATATTATTGTACTTAATAATATTTCC
*
50509 GGTTAAATG
66 AGTTAAATG
50518 ATATAACATA
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
83 30 0.44
86 14 0.21
87 24 0.35
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (85 bp):
ATATAAGCACTACATATTACATTATATTAGCGCTACCTAATATTATTGTACTTAATAATATTTCC
AGTTAAATGCCTATTTTATT
Done.