Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000431.1 Hibiscus syriacus cultivar Beakdansim tig00000790_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: 66465
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2263 original size:20 final size:19
Alignment explanation
Indices: 2221--2263 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2211 AAAAAATTGA
* *
2221 TTTTGTTTTAAATTGTTGT
1 TTTTGATTTAAATTGTTGG
*
2240 TTTTGATTTAATTATGTTGG
1 TTTTGATTTAAAT-TGTTGG
2260 TTTT
1 TTTT
2264 ATGAAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.67
Consensus pattern (19 bp):
TTTTGATTTAAATTGTTGG
Found at i:4149 original size:19 final size:20
Alignment explanation
Indices: 4107--4150 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
4097 AATAAAATAT
* *
4107 TATTGAATTTTAAGATTTTA
1 TATTCAATTTTAAGATTATA
4127 TATTCAATTTTAA-ATTATA
1 TATTCAATTTTAAGATTATA
4146 TATTC
1 TATTC
4151 GATTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
TATTCAATTTTAAGATTATA
Found at i:6698 original size:64 final size:65
Alignment explanation
Indices: 6619--6783 Score: 187
Period size: 64 Copynumber: 2.6 Consensus size: 65
6609 AAAGAAGCCT
* * * **
6619 GGAGTGCATCAATGCATGGTCTGTGCATCGGTACATAAAATGCATTCGATGTTCAAA-ATATTC-
1 GGAGTGCATCGATGCATGGTCTGTGCATCGGTACACAAAATGCATTCAAAATTCAAATA-ATTCA
6682 A
65 A
* *
6683 GGAGTGCATCGATGCAT-GCCTTGTGCATCGGTACACAAAATGCATTCAAAATTCAATTAATTCA
1 GGAGTGCATCGATGCATGGTC-TGTGCATCGGTACACAAAATGCATTCAAAATTCAAATAATTCA
6747 A
65 A
*
6748 GG-GTGCATCGATGCATTGAT-TGGTGCATCGGTACAC
1 GGAGTGCATCGATGCA-TGGTCT-GTGCATCGGTACAC
6784 TACTTTGAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
63 2 0.02
64 65 0.76
65 19 0.22
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (65 bp):
GGAGTGCATCGATGCATGGTCTGTGCATCGGTACACAAAATGCATTCAAAATTCAAATAATTCAA
Found at i:7447 original size:23 final size:23
Alignment explanation
Indices: 7418--7463 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
7408 CAAAGCATCC
7418 AACGCATAAATCCAAACATTCAA
1 AACGCATAAATCCAAACATTCAA
7441 AACGCATAAATCCAAACATTCAA
1 AACGCATAAATCCAAACATTCAA
7464 TTATTCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.04, T:0.17
Consensus pattern (23 bp):
AACGCATAAATCCAAACATTCAA
Found at i:9433 original size:23 final size:23
Alignment explanation
Indices: 9403--9484 Score: 105
Period size: 23 Copynumber: 3.7 Consensus size: 23
9393 TGCACAACAT
9403 AGTGCATCGATGCACATTCAAGG
1 AGTGCATCGATGCACATTCAAGG
* * *
9426 AGTGCATCGGTGCACCTTC-ATG
1 AGTGCATCGATGCACATTCAAGG
*
9448 -GTGTATCGATGCACATTCAAGG
1 AGTGCATCGATGCACATTCAAGG
*
9470 AATGCATCGATGCAC
1 AGTGCATCGATGCAC
9485 TAGCTAGTGT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
21 15 0.31
22 4 0.08
23 29 0.60
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (23 bp):
AGTGCATCGATGCACATTCAAGG
Found at i:15429 original size:64 final size:64
Alignment explanation
Indices: 15331--15454 Score: 146
Period size: 64 Copynumber: 1.9 Consensus size: 64
15321 GTGCATGGTC
* * * * *
15331 TGTGTATCGGTACATAAAATGCATTCGGTGTTCAAA-ATATTC-AGGAGTGCATTGATGCATGCC
1 TGTGCATCAGTACACAAAATGCATTCGATGTTCAAATA-ATTCAAGG-GTGCATCGATGCATGCC
15394 T
64 T
*
15395 TGTGCATCAGTACACAAAATGCATTCGAAT-TTCAATTAATTCAAGGGTGCATCGATGCAT
1 TGTGCATCAGTACACAAAATGCATTCG-ATGTTCAAATAATTCAAGGGTGCATCGATGCAT
15455 TGTACACTAC
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
64 46 0.90
65 5 0.10
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (64 bp):
TGTGCATCAGTACACAAAATGCATTCGATGTTCAAATAATTCAAGGGTGCATCGATGCATGCCT
Found at i:16826 original size:12 final size:12
Alignment explanation
Indices: 16809--16838 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16799 CATTGTTTTG
16809 TCTTTAATATTT
1 TCTTTAATATTT
16821 TCTTTAATATTT
1 TCTTTAATATTT
16833 T-TTTAA
1 TCTTTAA
16839 ATCTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (12 bp):
TCTTTAATATTT
Found at i:17725 original size:7 final size:7
Alignment explanation
Indices: 17706--17772 Score: 57
Period size: 7 Copynumber: 9.4 Consensus size: 7
17696 GCGAGAACAC
*
17706 AAAGCAA
1 AAAGAAA
17713 AAAGAAA
1 AAAGAAA
*
17720 AGAGAAA
1 AAAGAAA
17727 AAAG-AA
1 AAAGAAA
17733 AAAGAAA
1 AAAGAAA
**
17740 TGAGAAA
1 AAAGAAA
17747 AAA-ATAA
1 AAAGA-AA
17754 AAGAGAAA
1 AA-AGAAA
17762 AAAGAAGA
1 AAAGAA-A
17770 AAA
1 AAA
17773 AAGGAAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
6 7 0.15
7 31 0.65
8 9 0.19
9 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (7 bp):
AAAGAAA
Found at i:17736 original size:20 final size:20
Alignment explanation
Indices: 17706--17772 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 20
17696 GCGAGAACAC
17706 AAAGCAAAAAGAAAAGAGAAA
1 AAAG-AAAAAGAAAAGAGAAA
*
17727 AAAGAAAAAGAAATGAGAAAA
1 AAAGAAAAAGAAAAGAG-AAA
* *
17748 AAATAAAAGAGAAAAAAGAAGA
1 AAAGAAAA-AGAAAAGAGAA-A
17770 AAA
1 AAA
17773 AAGGAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
20 12 0.31
21 16 0.41
22 11 0.28
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGAAAAGAGAAA
Found at i:17750 original size:35 final size:33
Alignment explanation
Indices: 17711--17782 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 33
17701 AACACAAAGC
17711 AAAAAGAAAAGAGAAAAAAGAA-AAAGAAATGAGAA
1 AAAAAGAAAAGAGAAAAAAGAAGAAA-AAA-G-GAA
*
17746 AAAAATAAAAGAGAAAAAAGAAGAAAAAAGGAA
1 AAAAAGAAAAGAGAAAAAAGAAGAAAAAAGGAA
17779 AAAA
1 AAAA
17783 TTGATCAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
33 7 0.20
34 1 0.03
35 24 0.69
36 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (33 bp):
AAAAAGAAAAGAGAAAAAAGAAGAAAAAAGGAA
Found at i:17772 original size:10 final size:9
Alignment explanation
Indices: 17717--17782 Score: 59
Period size: 9 Copynumber: 7.4 Consensus size: 9
17707 AAGCAAAAAG
17717 AAAAGAGAA
1 AAAAGAGAA
*
17726 AAAAGAAAA
1 AAAAGAGAA
17735 AGAAATGAG-A
1 A-AAA-GAGAA
*
17745 AAAA-A-AT
1 AAAAGAGAA
17752 AAAAGAGAA
1 AAAAGAGAA
17761 AAAAGAAGAA
1 AAAAG-AGAA
17771 AAAAG-GAA
1 AAAAGAGAA
17779 AAAA
1 AAAA
17783 TTGATCAAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
7 5 0.11
8 8 0.17
9 18 0.38
10 14 0.30
11 2 0.04
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (9 bp):
AAAAGAGAA
Found at i:21641 original size:104 final size:104
Alignment explanation
Indices: 21325--21655 Score: 378
Period size: 104 Copynumber: 3.2 Consensus size: 104
21315 TTCATCAATG
* * * * * * * * *
21325 AGAATGAACAACGTCATATGAAAGTGGCCATAACTCTCCAA-ATTGGATGAGTAATGTCATCTTT
1 AGAAGGAACAACGTCATCTGAAAGCGACCATAACTTTTCAACA-TGGATGAGCAGTGTCATCTTC
* * *
21389 AACACCATATTATCTCCAAATTAACTCAACTTCCTCAACA
65 AACACCAAATTATCTCTAAATTGACTCAACTTCCTCAACA
** * * *
21429 AGAAAAAACAACATCATCTGAAAGTGGA-CATAACTTTTCAACATGGATGAACAGTGTCATCTTC
1 AGAAGGAACAACGTCATCTGAAAG-CGACCATAACTTTTCAACATGGATGAGCAGTGTCATCTTC
* *
21493 AACACCAGATTATCTCTAGATTGACTCAACTTCCTCAACA
65 AACACCAAATTATCTCTAAATTGACTCAACTTCCTCAACA
* * *
21533 AGAAGGAACAACGTCATCTGAAAGCGACCAAAACTTTTCAACATGGATCAGCAGTGTCGTCTTCA
1 AGAAGGAACAACGTCATCTGAAAGCGACCATAACTTTTCAACATGGATGAGCAGTGTCATCTTCA
* * * *
21598 ATACCAAATTATCTCTAAATTGACTCGACTTCTTCAACG
66 ACACCAAATTATCTCTAAATTGACTCAACTTCCTCAACA
**
21637 AGAAGGAACATTGTCATCT
1 AGAAGGAACAACGTCATCT
21656 TCAACAAGTA
Statistics
Matches: 192, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
103 2 0.01
104 188 0.98
105 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (104 bp):
AGAAGGAACAACGTCATCTGAAAGCGACCATAACTTTTCAACATGGATGAGCAGTGTCATCTTCA
ACACCAAATTATCTCTAAATTGACTCAACTTCCTCAACA
Found at i:25525 original size:18 final size:18
Alignment explanation
Indices: 25487--25525 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
25477 TTATGTTGAG
* **
25487 AAAAAATATGACGAATTA
1 AAAAAATATGAAGAAGAA
25505 AAAAAATATGAAGAAGAA
1 AAAAAATATGAAGAAGAA
25523 AAA
1 AAA
25526 TTGGATGAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.69, C:0.03, G:0.13, T:0.15
Consensus pattern (18 bp):
AAAAAATATGAAGAAGAA
Found at i:26503 original size:19 final size:19
Alignment explanation
Indices: 26443--26506 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
26433 GGTTCCACTA
* *
26443 GACCTGAACTGTTTGACCC
1 GACCCGAACTGTTTGATCC
**
26462 GACTTGAACTGTTTGGCAT--
1 GACCCGAACTGTTT-G-ATCC
26481 GACCCGAACTGTTTGATCC
1 GACCCGAACTGTTTGATCC
26500 GACCCGA
1 GACCCGA
26507 CCCGTTGACT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 2 0.05
18 1 0.03
19 32 0.86
20 1 0.03
21 1 0.03
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (19 bp):
GACCCGAACTGTTTGATCC
Found at i:26733 original size:138 final size:137
Alignment explanation
Indices: 26527--26781 Score: 345
Period size: 138 Copynumber: 1.9 Consensus size: 137
26517 TTGACCATAA
* *
26527 TTGACTTTGACCCAAAAAGTCATATTTTCTAAAAAGTCATATTTTATGTTTTTCGATGTCCTGAG
1 TTGACTTTGACCCAAAAAGTCAAATTTTCTAAAAAGTCATATTTTATGTTTTTCAATGTCCTGAG
* * *
26592 TCCGAATCCGAGAAGT-TCGTTATTCCAAATTCGAACCCGAAAGCCTCCAAATTGTCAGTCAAAC
66 TCCGAATCC--GAAGTCT-ATTATTCCAAAATCAAACCCGAAAGCCTCCAAATTGTCAGTCAAAC
26656 CCGTTGACTT
128 CCGTTGACTT
* **
26666 TTGACTTTGA-CCAAAAAGTCAAATTTT-TCAAAAAGTTATATTTTATGTTTTTCAATGTTTTGA
1 TTGACTTTGACCCAAAAAGTCAAATTTTCT-AAAAAGTCATATTTTATGTTTTTCAATGTCCTGA
* * * *
26729 GTCCGATTTCGAAGTCTATTTTTCCAAAATCAAACCCGAAAGCCTCCGAATTG
65 GTCCGAATCCGAAGTCTATTATTCCAAAATCAAACCCGAAAGCCTCCAAATTG
26782 ACCCGTAAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
136 36 0.35
137 2 0.02
138 54 0.53
139 10 0.10
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (137 bp):
TTGACTTTGACCCAAAAAGTCAAATTTTCTAAAAAGTCATATTTTATGTTTTTCAATGTCCTGAG
TCCGAATCCGAAGTCTATTATTCCAAAATCAAACCCGAAAGCCTCCAAATTGTCAGTCAAACCCG
TTGACTT
Found at i:30555 original size:71 final size:72
Alignment explanation
Indices: 30480--30661 Score: 267
Period size: 71 Copynumber: 2.5 Consensus size: 72
30470 AAATAATCGT
* * * *
30480 TACCTATTACGTTAAAATAGATACCGGTTTCTTTAACGGATAATAATAATGTAAACGA-AAAAAA
1 TACCTATTACGTTAAACTAGCTACCGATTTCTTTAAAGGATAATAATAATGTAAACGATAAAAAA
30544 TAGGCTC
66 TAGGCTC
* * * *
30551 TACCTATTACGTTAAACTAGCTAACGATTTGTTTAAAGGTTAATAATAATGTAAACGATTTAAAA
1 TACCTATTACGTTAAACTAGCTACCGATTTCTTTAAAGGATAATAATAATGTAAACGA-TAAAAA
30616 ATAGGCTC
65 ATAGGCTC
*
30624 TACCTATTACGTTAAACTACCTACCGATTTCTTTAAAG
1 TACCTATTACGTTAAACTAGCTACCGATTTCTTTAAAG
30662 ATATATTTTT
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
71 51 0.52
73 47 0.48
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (72 bp):
TACCTATTACGTTAAACTAGCTACCGATTTCTTTAAAGGATAATAATAATGTAAACGATAAAAAA
TAGGCTC
Found at i:30757 original size:12 final size:12
Alignment explanation
Indices: 30742--30766 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30732 TTAATACTTA
30742 AATTTCAATTTG
1 AATTTCAATTTG
30754 AATTTCAATTTG
1 AATTTCAATTTG
30766 A
1 A
30767 GCTCCACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (12 bp):
AATTTCAATTTG
Found at i:31985 original size:75 final size:73
Alignment explanation
Indices: 31840--32000 Score: 216
Period size: 75 Copynumber: 2.2 Consensus size: 73
31830 CTTAAGCTGT
* * * *
31840 TAAAATAAAATAGGCGCTACCTTTACGTTAATCATCTACCGGTTTGTTTAAAGGTTACTAATAAT
1 TAAAATAAAATAGGCGCTACCTTTACGTTAATCACCTACAGGTTTGTTTAAAGATGACTAATAAT
31905 ATAAACGG
66 ATAAACGG
* *
31913 TAAAATAAAATAGGTGCTACCTATTACGTTAAAAT-ACCTATAGGTTTGTTTAAAGATGACTAAT
1 TAAAATAAAATAGGCGCTACCT-TTACGTT--AATCACCTACAGGTTTGTTTAAAGATGACTAAT
* *
31977 TATGTAAACGG
63 AATATAAACGG
31988 TAAAATAAAATAG
1 TAAAATAAAATAG
32001 ACGTAAATTT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
73 21 0.27
74 7 0.09
75 46 0.60
76 3 0.04
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (73 bp):
TAAAATAAAATAGGCGCTACCTTTACGTTAATCACCTACAGGTTTGTTTAAAGATGACTAATAAT
ATAAACGG
Found at i:32393 original size:199 final size:198
Alignment explanation
Indices: 32042--32647 Score: 793
Period size: 199 Copynumber: 3.0 Consensus size: 198
32032 GCTCGTACCA
* * ** *
32042 ATACTTTTATTTCAGTATGCTTCTCAAACAATTTGCACCCAAAATATATCGATACACATATA-AT
1 ATACTTTTATTCCAATATGCTTCTCAAACAATTTGCATGCAAAATGTATCGATACACATATATA-
*
32106 AAGTATCGGTACTTAGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAA
65 AAGTATCGATACTTAGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAA
* * * *
32171 CGGTAAAAGTTTATCGGTATATTGATAATAGGTGTAAATACCAAATATCGATATTTTTATATATG
130 CGGTAAAAATCTATCGGTATATTGATAATAGGCGTAAATACCAAGTATCGATATTTTTATATA-G
32236 TATCG
194 TATCG
32241 ATACTTTTATTCCAATATGCTTCTCAAACAATTTGCATGCAAAATGTATCGATACACATATATAA
1 ATACTTTTATTCCAATATGCTTCTCAAACAATTTGCATGCAAAATGTATCGATACACATATATAA
* * * *
32306 ATTATTGTTACTTAGAATTTCAAAACCTATTACTTTAAAGTAATAGGTTAATTAACAATGTAAAC
66 AGTATCGATACTTAGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAAC
* * * * * *
32371 GGTAAAAATCTACCGATATATTGATAATAGACGTAAATACCAAGTATCAACACTTTTATATAGAT
131 GGTAAAAATCTATCGGTATATTGATAATAGGCGTAAATACCAAGTATCGATATTTTTATATAG-T
*
32436 ATGG
195 ATCG
* *
32440 ATACTTTTATTCCAATATGTTTCTCAAACAATTTGCATGCAAAATGTATCGATACACATACATAA
1 ATACTTTTATTCCAATATGCTTCTCAAACAATTTGCATGCAAAATGTATCGATACACATATATAA
* * * * * *
32505 AGTATCAATACTAATAATTTCGAAACCTATTACTTTAAAGTAATATGTAAATTAACAATGTACAC
66 AGTATCGATACTTAGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAAC
* ** * * * * *
32570 GATAAACGTTTCTATCGGTATCATT-AAAATAGGGGTAAATGTCCAAGTATCGATATTGTCATAT
131 GGTAAA--AATCTATCGGTAT-ATTGATAATAGGCGTAAAT-ACCAAGTATCGATATTTTTATAT
32634 AAGTATCG
192 -AGTATCG
32642 ATACTT
1 ATACTT
32648 ATAATTTCAA
Statistics
Matches: 353, Mismatches: 47, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
198 1 0.00
199 298 0.84
200 1 0.00
201 21 0.06
202 30 0.08
203 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (198 bp):
ATACTTTTATTCCAATATGCTTCTCAAACAATTTGCATGCAAAATGTATCGATACACATATATAA
AGTATCGATACTTAGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAAC
GGTAAAAATCTATCGGTATATTGATAATAGGCGTAAATACCAAGTATCGATATTTTTATATAGTA
TCG
Found at i:33125 original size:226 final size:226
Alignment explanation
Indices: 32708--33185 Score: 588
Period size: 226 Copynumber: 2.1 Consensus size: 226
32698 ACGGTAATAT
* *
32708 AACAATTTAAGTAATTAACATATTTTGCTATCGTCGGATTTCTAAAACCCTATCAGTTTTGAACA
1 AACAAATTAAGTAATTAACATATTTTGCTATCGTCGGATTTCTAAAACCCTATCAGTTTTAAACA
* * * * *
32773 GATACTACCTATTACATTAAATAAACACTATTTGTTATGTTATTATGGTTGATAATGTTTTCAGT
66 GACACTACCTATTACATTAAATAAACACTATTTATTATGTTAATATGGTTGATAATATTTTCAAT
** ** ** *
32838 AATTATGTCATTTTGTTATCGTTGGATTTCTAAGGCTTTATCAGCTTAAACTTTGGTAACATTTT
131 AATTACCTCATTTTGTTATCGTCAGATTTCTAAGGCTCAATCAGCTTAAACTTTAGTAACATTTT
*
32903 AGGCGTTACCAAATATGTTGATAATATTGAA
196 AGACGTTACCAAATATGTTGATAATATTGAA
* * * ** *
32934 AACAAATTAAGTAATTAACATATTTTGTTATCGTCTGATTT-TTAAGGCATCATC-GATTTTAAA
1 AACAAATTAAGTAATTAACATATTTTGCTATCGTCGGATTTCTAAAACCCT-ATCAG-TTTTAAA
* * * **
32997 CAGGCGCTACCTATTACATTAAATAAGCGTTACTTTATTATGTTAATATGGTTGA-AACTATTTT
64 CAGACACTACCTATTACATTAAATAAACACTA-TTTATTATGTTAATATGGTTGATAA-TATTTT
* *
33061 CAATAATTAACCT-ATTTTGTTATTGTCAGATTTTTAAGGCTCAATCAGCTTAAA-TTTAGTAAC
127 CAATAATT-ACCTCATTTTGTTATCGTCAGATTTCTAAGGCTCAATCAGCTTAAACTTTAGTAAC
* *
33124 ATTTTAGACGTTACCTAATATGTTGATAATATTGAT
191 ATTTTAGACGTTACCAAATATGTTGATAATATTGAA
* *
33160 AACTAATTAAGTAATTAACTTATTTT
1 AACAAATTAAGTAATTAACATATTTT
33186 ATTAATATCA
Statistics
Matches: 215, Mismatches: 32, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
225 6 0.03
226 140 0.65
227 67 0.31
228 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (226 bp):
AACAAATTAAGTAATTAACATATTTTGCTATCGTCGGATTTCTAAAACCCTATCAGTTTTAAACA
GACACTACCTATTACATTAAATAAACACTATTTATTATGTTAATATGGTTGATAATATTTTCAAT
AATTACCTCATTTTGTTATCGTCAGATTTCTAAGGCTCAATCAGCTTAAACTTTAGTAACATTTT
AGACGTTACCAAATATGTTGATAATATTGAA
Found at i:33237 original size:226 final size:227
Alignment explanation
Indices: 32779--33284 Score: 569
Period size: 226 Copynumber: 2.2 Consensus size: 227
32769 AACAGATACT
* ** * * * *
32779 ACCTATTACATTAAATAAACACTA-TTTGTTATGTTATTATGGTTGATAATGTTTTCAGTAATTA
1 ACCTATTACATTAAATAAGCGTTACTTTATTATGTTAATATGGTTGATAATATTTTCAATAATTA
** ** ** * *
32843 TGTCATTTTGTTATCGTTGGATTTCTAAGGCTTTATCAGCTTAAACTTTGGTAACATTTTAGGCG
66 CCTCATTTTGTTATCGTCAGATTTCTAAGGCTCAATCAGCTTAAACTTTAGTAACATTTTAGACG
* *
32908 TTACCAAATATGTTGATAATATTGAAAACAAATTAAGTAATTAACATATTTTGTTATCGTCTGAT
131 TTACCAAATATGTTGATAATATTGAAAACAAATTAAGTAATTAACATATTTTATTATCATCTGAT
* * * * * * * *
32973 TTTTAAGGCATCATCGATTTTAAACAGGCGCT
196 TTCTAAGGCACCAACAACTTTAAAAAGACGCA
33005 ACCTATTACATTAAATAAGCGTTACTTTATTATGTTAATATGGTTGA-AACTATTTTCAATAATT
1 ACCTATTACATTAAATAAGCGTTACTTTATTATGTTAATATGGTTGATAA-TATTTTCAATAATT
* *
33069 AACCT-ATTTTGTTATTGTCAGATTTTTAAGGCTCAATCAGCTTAAA-TTTAGTAACATTTTAGA
65 -ACCTCATTTTGTTATCGTCAGATTTCTAAGGCTCAATCAGCTTAAACTTTAGTAACATTTTAGA
* * * *
33132 CGTTACCTAATATGTTGATAATATTGATAACTAATTAAGTAATTAACTTATTTTATTAAT-ATCA
129 CGTTACCAAATATGTTGATAATATTGAAAACAAATTAAGTAATTAACATATTTTATT-ATCATC-
*
33196 T-ATTTCTAAGG-ACCCAACAACTTTAAAAAGATGCA
192 TGATTTCTAAGGCA-CCAACAACTTTAAAAAGACGCA
* * * * * *
33231 ACCTATTACATTAAATAAGTGTTAC-ATGTTATATTATTATGATTGATAATATTT
1 ACCTATTACATTAAATAAGCGTTACTTTATTATGTTAATATGGTTGATAATATTT
33285 CTAGTAATTA
Statistics
Matches: 235, Mismatches: 38, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
225 22 0.09
226 141 0.60
227 70 0.30
228 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (227 bp):
ACCTATTACATTAAATAAGCGTTACTTTATTATGTTAATATGGTTGATAATATTTTCAATAATTA
CCTCATTTTGTTATCGTCAGATTTCTAAGGCTCAATCAGCTTAAACTTTAGTAACATTTTAGACG
TTACCAAATATGTTGATAATATTGAAAACAAATTAAGTAATTAACATATTTTATTATCATCTGAT
TTCTAAGGCACCAACAACTTTAAAAAGACGCA
Found at i:34024 original size:32 final size:33
Alignment explanation
Indices: 33983--34060 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
33973 TTTAAATAGT
* *
33983 TATTATTTTTTA-TATTAAT-ATATTTATGTAAA
1 TATTATTTTTTATTA-AAATAATATTTATATAAA
*
34015 TATTATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATTAAAATAATATTTATATAAA
34048 TATTATTTATTTA
1 TATTATTT-TTTA
34061 GAATTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.38
33 21 0.52
34 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTATTTTTTATTAAAATAATATTTATATAAA
Found at i:34222 original size:17 final size:17
Alignment explanation
Indices: 34200--34253 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
34190 AATGTTAATA
34200 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
34217 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
34234 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
34251 TTT
1 TTT
34254 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:35814 original size:21 final size:21
Alignment explanation
Indices: 35784--35831 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
35774 GCAGGGGTAC
* *
35784 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
35805 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
35826 ATGCCA
1 ATGCCA
35832 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:35861 original size:21 final size:21
Alignment explanation
Indices: 35835--35928 Score: 138
Period size: 21 Copynumber: 4.5 Consensus size: 21
35825 TATGCCATCT
*
35835 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
*
35856 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
35877 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
35898 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
35919 CCGCAGGGTT
1 CCGCAGGGTT
35929 TTATACCATA
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
20 2 0.03
21 66 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.26, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:36496 original size:40 final size:39
Alignment explanation
Indices: 36452--36535 Score: 132
Period size: 39 Copynumber: 2.1 Consensus size: 39
36442 AAATGTTTTT
* *
36452 AAAATACAAATTATATTATTCGAAATTTAAATTTAAAATA
1 AAAATAAAAATAATATTATTC-AAATTTAAATTTAAAATA
36492 AAAATAAAAATAATATTATTCAAATTTAAATTTAAAATA
1 AAAATAAAAATAATATTATTCAAATTTAAATTTAAAATA
*
36531 TAAAT
1 AAAAT
36536 TATAGTATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 22 0.54
40 19 0.46
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (39 bp):
AAAATAAAAATAATATTATTCAAATTTAAATTTAAAATA
Found at i:36521 original size:33 final size:34
Alignment explanation
Indices: 36480--36554 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
36470 TTCGAAATTT
*
36480 AAATTTAAAATAAAAATAAAAATAATATTATTC-
1 AAATTTAAAATAAAAATAAAAATAATAGTATTCA
* * * *
36513 AAATTTAAATTTAAAATATAAATTATAGTATTCA
1 AAATTTAAAATAAAAATAAAAATAATAGTATTCA
36547 AAATTTAA
1 AAATTTAA
36555 CATTAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 28 0.78
34 8 0.22
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (34 bp):
AAATTTAAAATAAAAATAAAAATAATAGTATTCA
Found at i:37186 original size:128 final size:128
Alignment explanation
Indices: 36955--38215 Score: 2218
Period size: 128 Copynumber: 9.9 Consensus size: 128
36945 TTACCTGATT
36955 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
37020 TGATGAAATAATGGAAGGCGCGCCCCCAGGAACACGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
37083 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
37148 TGACGAAATAATGGAAGGCGCGCCCCCTGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
37211 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
37276 TGACGAAATAATGGAA-GCGTGCCCCCGGGAACGCGCCTTCATGTGAATAATGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
37338 TACTGATATATCTAGTGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*** *
37402 TGACGAAATAATGGAAGGCGCG-CCCC-GGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
37463 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
37528 TGACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
37590 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*** *
37655 TGACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
37716 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
37781 TGACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAACTAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
37843 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
37908 TGATGAAATAATGGAAGGCGTGCCCCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
37971 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
38036 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
38099 TACTGATATATCTAGTGTCCCCAAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
38164 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
38216 ACTCCGATTA
Statistics
Matches: 1082, Mismatches: 42, Indels: 18
0.95 0.04 0.02
Matches are distributed among these distances:
125 46 0.04
126 263 0.24
127 294 0.27
128 478 0.44
129 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:37796 original size:253 final size:256
Alignment explanation
Indices: 36955--38206 Score: 2299
Period size: 253 Copynumber: 4.9 Consensus size: 256
36945 TTACCTGATT
36955 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
37020 TGATGAAATAATGGAAGGCGCGCCCCCAGGAACACGCCTTCATGTGAATAGTGAAATAATAGGTA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
37085 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
*
37150 ACGAAATAATGGAAGGCGCGCCCCCTGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
196 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
37211 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
37276 TGACGAAATAATGGAA-GCGTGCCCCCGGGAACGCGCCTTCATGTGAATAATGAAATAATAGGTA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
37340 CTGATATATCTAGTGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
37404 ACGAAATAATGGAAGGCGCG-CCCC-GGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
196 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
37463 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
37528 TGACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
37592 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
37657 ACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGT-CCCTGAGAAATAATAGG
196 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
37716 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
37781 TGACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAACTAATAGGTA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
37845 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
* * ***
37910 ATGAAATAATGGAAGGCGTGCCCCCGGGAACGCGCCTTCATGT-GAAT-AGTAAAATAATAGG
196 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAG--AAATAATAGG
37971 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
38036 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
*
38101 CTGATATATCTAGTGTCCCCAAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
38166 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAT
196 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAT
38207 ATGAATAGTA
Statistics
Matches: 972, Mismatches: 17, Indels: 14
0.97 0.02 0.01
Matches are distributed among these distances:
252 173 0.18
253 310 0.32
254 108 0.11
255 157 0.16
256 224 0.23
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (256 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
Found at i:42438 original size:56 final size:56
Alignment explanation
Indices: 42352--42460 Score: 209
Period size: 56 Copynumber: 1.9 Consensus size: 56
42342 TTGGAAAGAA
*
42352 CAAATATTTCTAAATTATATGGATGTGTATATGAACAACTAAAATTAATATAATAC
1 CAAATATTTCTAAATTATATCGATGTGTATATGAACAACTAAAATTAATATAATAC
42408 CAAATATTTCTAAATTATATCGATGTGTATATGAACAACTAAAATTAATATAA
1 CAAATATTTCTAAATTATATCGATGTGTATATGAACAACTAAAATTAATATAA
42461 CACAGAGACA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (56 bp):
CAAATATTTCTAAATTATATCGATGTGTATATGAACAACTAAAATTAATATAATAC
Found at i:45368 original size:32 final size:32
Alignment explanation
Indices: 45301--45379 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
45291 TCATTTTGTT
* *
45301 AAAATAAAATCGAAGTTGAAACTAAATATTAAA
1 AAAATAAAA-CGAAATTGAAAATAAATATTAAA
*
45334 AAAATAAAACGAAATT-AAAATAGATAATTAAA
1 AAAATAAAACGAAATTGAAAATAAAT-ATTAAA
*
45366 AAAATCAAA-GAAAT
1 AAAATAAAACGAAAT
45380 CAGATAAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 12 0.29
32 20 0.49
33 9 0.22
ACGTcount: A:0.66, C:0.05, G:0.08, T:0.22
Consensus pattern (32 bp):
AAAATAAAACGAAATTGAAAATAAATATTAAA
Found at i:46959 original size:2 final size:2
Alignment explanation
Indices: 46952--46986 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
46942 TAAGACAGGA
46952 AG AG AG AG ACG -G AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG A-G AG AG AG AG AG AG AG AG AG AG AG AG A
46987 CCTTTCTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.94
3 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52022 original size:16 final size:16
Alignment explanation
Indices: 52003--52036 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
51993 CAATATACGA
52003 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
52019 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
52035 AT
1 AT
52037 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:52110 original size:16 final size:18
Alignment explanation
Indices: 52078--52111 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
52068 TATTAATGTA
52078 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
52096 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
52112 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:52346 original size:24 final size:25
Alignment explanation
Indices: 52304--52367 Score: 112
Period size: 24 Copynumber: 2.6 Consensus size: 25
52294 ACAATTTATC
*
52304 AAATATAATATTTTTTATTGTAAAA
1 AAATATAATATTTTCTATTGTAAAA
52329 AAATAT-ATATTTTCTATTGTAAAA
1 AAATATAATATTTTCTATTGTAAAA
52353 AAATATAATATTTTC
1 AAATATAATATTTTC
52368 CCATCATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
24 23 0.62
25 14 0.38
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (25 bp):
AAATATAATATTTTCTATTGTAAAA
Found at i:52822 original size:130 final size:129
Alignment explanation
Indices: 52607--52853 Score: 413
Period size: 130 Copynumber: 1.9 Consensus size: 129
52597 AATTTTATTC
* *
52607 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATATGTGTTAACACATGTCAGATC
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATATGTGCTAACACATGTCAGATC
** *
52672 CTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
52736 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGAT-ATGTGCTAACACATGTCAGAT
52801 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
65 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
52854 TATATAAATA
Statistics
Matches: 109, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
129 39 0.36
130 70 0.64
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (129 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATATGTGCTAACACATGTCAGATC
CTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:53300 original size:35 final size:35
Alignment explanation
Indices: 53250--53325 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
53240 AATTGAATTT
* *
53250 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
53285 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
53320 AATTGA
1 AATTGA
53326 GGTATGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:57756 original size:24 final size:25
Alignment explanation
Indices: 57724--57773 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
57714 GGTCCACATT
57724 TATGTTCCAAAAGACCA-ATATATG
1 TATGTTCCAAAAGACCACATATATG
* *
57748 TATGTTCCAAAGGATCACATATATG
1 TATGTTCCAAAAGACCACATATATG
57773 T
1 T
57774 CCCGGAGGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (25 bp):
TATGTTCCAAAAGACCACATATATG
Found at i:64712 original size:21 final size:21
Alignment explanation
Indices: 64688--64811 Score: 79
Period size: 21 Copynumber: 5.8 Consensus size: 21
64678 TATCCCGAAT
*
64688 GACCACATATATGTCCCATCG
1 GACCACATATATGTCCCATAG
* * *
64709 GACCCCATAGAATTGTCCCGTAG
1 GACCACATA-TA-TGTCCCATAG
* * *
64732 GACCACATATATGTTCCAAAT
1 GACCACATATATGTCCCATAG
* * * *
64753 GACCAAATATATGTCCAAAAAA
1 GACCACATATATGTCC-CATAG
* *
64775 GACCGA-ATATATGTTCCAAAG
1 GACC-ACATATATGTCCCATAG
*
64796 GATCACATATATGTCC
1 GACCACATATATGTCC
64812 TGAAGGACCA
Statistics
Matches: 79, Mismatches: 19, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
20 1 0.01
21 43 0.54
22 18 0.23
23 17 0.22
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (21 bp):
GACCACATATATGTCCCATAG
Found at i:66107 original size:52 final size:52
Alignment explanation
Indices: 66035--66138 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
66025 GTTTCTATAA
*
66035 ACTTTTCTAATGCTTCATCAATCAAAAGCACTCATGAATTGCAAGAATAAAC
1 ACTTTCCTAATGCTTCATCAATCAAAAGCACTCATGAATTGCAAGAATAAAC
66087 ACTTTCCTAATGCTTCATCAATCAAAAGCACTCATGAATTGCAAGAATAAAC
1 ACTTTCCTAATGCTTCATCAATCAAAAGCACTCATGAATTGCAAGAATAAAC
66139 CAGCTGTAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (52 bp):
ACTTTCCTAATGCTTCATCAATCAAAAGCACTCATGAATTGCAAGAATAAAC
Found at i:66232 original size:7 final size:7
Alignment explanation
Indices: 66220--66248 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
66210 AGAAATATAT
66220 CTTTTCC
1 CTTTTCC
66227 CTTTTCC
1 CTTTTCC
66234 CTTTTCC
1 CTTTTCC
66241 CTTTTCC
1 CTTTTCC
66248 C
1 C
66249 CTAGCTCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (7 bp):
CTTTTCC
Done.