Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011735.1 Kokia drynarioides strain JFW-HI SEQ_126729, 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: 123511
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 66 characters in sequence are not A, C, G, or T
Found at i:939 original size:6 final size:6
Alignment explanation
Indices: 928--972 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
918 TGATCAAAAT
* * * *
928 TGAAAG TGAAAG TGAAAG TAAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
973 TATGAATTGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:969 original size:18 final size:18
Alignment explanation
Indices: 924--972 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
914 TTTGTGATCA
924 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* * *
942 AAAGTAAAAGTGAAATTG
1 AAATTGAAAGTGAAAGTG
*
960 GAATTGAAAGTGA
1 AAATTGAAAGTGA
973 TATGAATTGC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:2711 original size:27 final size:27
Alignment explanation
Indices: 2681--2760 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
2671 AAAATCCATG
2681 TATTCACATTACACTAATCGTTTCAAC
1 TATTCACATTACACTAATCGTTTCAAC
* * **
2708 TATTTA-ATTACTA-AAATC----CATG
1 TATTCACATTAC-ACTAATCGTTTCAAC
*
2730 TATTCACATTACCCTAATCGTTTCAAC
1 TATTCACATTACACTAATCGTTTCAAC
2757 TATT
1 TATT
2761 TAATTAATGA
Statistics
Matches: 37, Mismatches: 9, Indels: 14
0.62 0.15 0.23
Matches are distributed among these distances:
22 7 0.19
23 9 0.24
26 9 0.24
27 12 0.32
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.40
Consensus pattern (27 bp):
TATTCACATTACACTAATCGTTTCAAC
Found at i:2725 original size:49 final size:49
Alignment explanation
Indices: 2671--2766 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
2661 TTCTAACCTA
2671 AAAATCCATGTATTCACATTACACTAATCGTTTCAACTATTTAATTACT
1 AAAATCCATGTATTCACATTACACTAATCGTTTCAACTATTTAATTACT
*
2720 AAAATCCATGTATTCACATTACCCTAATCGTTTCAACTATTTAATTA
1 AAAATCCATGTATTCACATTACACTAATCGTTTCAACTATTTAATTA
2767 ATGAACTCTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.39
Consensus pattern (49 bp):
AAAATCCATGTATTCACATTACACTAATCGTTTCAACTATTTAATTACT
Found at i:2849 original size:21 final size:20
Alignment explanation
Indices: 2823--2877 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
2813 CCACAAATTA
**
2823 TTTATTACAATTATCTTTAGT
1 TTTATTACAATTATAGTTA-T
2844 TTTATTA-AATTTATAGTTAT
1 TTTATTACAA-TTATAGTTAT
2864 TTTAGTTACAATTA
1 TTTA-TTACAATTA
2878 ATGTAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 7 0.24
21 20 0.69
22 2 0.07
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTATTACAATTATAGTTAT
Found at i:3359 original size:8 final size:8
Alignment explanation
Indices: 3346--3370 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3336 AGGGTTTTTT
3346 GTTTTCGG
1 GTTTTCGG
3354 GTTTTCGG
1 GTTTTCGG
3362 GTTTTCGG
1 GTTTTCGG
3370 G
1 G
3371 ATTTAGTTTT
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:0.00, C:0.12, G:0.40, T:0.48
Consensus pattern (8 bp):
GTTTTCGG
Found at i:10518 original size:31 final size:30
Alignment explanation
Indices: 10483--10545 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
10473 TTGTTTTAAT
* *
10483 AAAATATATGGTTAATTTACTAAAATAATCC
1 AAAATATATGATT-ATTTACGAAAATAATCC
* * *
10514 AAAATTTTTGATTATTTACGAAAATGATCC
1 AAAATATATGATTATTTACGAAAATAATCC
10544 AA
1 AA
10546 GTTAAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.37
Consensus pattern (30 bp):
AAAATATATGATTATTTACGAAAATAATCC
Found at i:10885 original size:105 final size:103
Alignment explanation
Indices: 10751--10947 Score: 265
Period size: 105 Copynumber: 1.9 Consensus size: 103
10741 CGACAACCCT
* * *
10751 TTTTCTCGAAAAAAAATATATTTTTGGGTGTTGGCCATTGCATGGTCGATACCCC-CTTT-TTGA
1 TTTTCTCGAAAAAAAATATATTTTTGGGTGTTAGCCATTGCATGGCCGACACCCCTCTTTCTTGA
* *
10814 GAAAAAAAATTTTCAAATTTTTTTGGTGTCGATCATCCCC
66 G-AAAAAAA-TTTCAAAATTTTTTAGTGTCGATCATCCCC
* *
10854 TTTTCTCGAAACAAAAAT-TGCATTTTTGGGTGTTAGTCATTGCATGGCCGACACCCCTTTTTCT
1 TTTTCTCGAAA-AAAAATAT--ATTTTTGGGTGTTAGCCATTGCATGGCCGACACCCCTCTTTCT
10918 TGAGAAAAAAATTTCAAAATTTTTTAGTGT
63 TGAGAAAAAAATTTCAAAATTTTTTAGTGT
10948 TGGCCATCAA
Statistics
Matches: 82, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
103 12 0.15
104 6 0.07
105 49 0.60
106 10 0.12
107 5 0.06
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (103 bp):
TTTTCTCGAAAAAAAATATATTTTTGGGTGTTAGCCATTGCATGGCCGACACCCCTCTTTCTTGA
GAAAAAAATTTCAAAATTTTTTAGTGTCGATCATCCCC
Found at i:10967 original size:61 final size:60
Alignment explanation
Indices: 10841--11373 Score: 455
Period size: 61 Copynumber: 8.9 Consensus size: 60
10831 TTTTTTTGGT
* * * * * ***
10841 GTCGATCATCCCCTTTTCTCGAAACAAAAATTGC---ATTTTTGGGTGTTAGTCATTGCATG
1 GTCGA-CACCCCCTTTTCTCGAAA-AAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATG
* * * *
10900 GCCGACACCCCTTTTTCTTGAGAAAAAAATTTCAAAATTTTTTAGTGTTGGCCATCAAATG
1 GTCGACACCCCCTTTTCTCGA-AAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATG
* * *
10961 GTCGACACCCCCTGTTCTCAAAAAAAAAATTT--TAATTTTTTGGTGTTGGCCATCAAATG
1 GTCGACACCCCCTTTTCTC-GAAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATG
* *
11020 GTCGACA-CCCCTTTTCTCGAGAAAAAATTTCAAAATTTTTTTTGTGTTGGCCATCAAATG
1 GTCGACACCCCCTTTTCTCGAAAAAAAATTTCAAAA-TTTTTTGGTGTTGGCCATCAAATG
* * ** *
11080 G-CTGACATCCCCTTTTCTCGAAAAAAATTTTCAAAA-TTTTTGGTGTTAACCATGAAATG
1 GTC-GACACCCCCTTTTCTCGAAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATG
* * * *
11139 GTCGACACCCCCCATTTCTCGAAAAAAAATTTCAAATTTTTTTTGTGTTGGCTATCAAATG
1 GTCGACA-CCCCCTTTTCTCGAAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATG
* * * *
11200 GTCGACACCCCCTATTCTCCAAAAAAAAAAATTCAAAATTTTTT-GTGTAGGCCATCAAATG
1 GTCGACACCCCCTTTTCT-C-GAAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATG
* * * * * * ***
11261 G-CTAACACCTCCTGTTCTCGAAAAAAAATTGC---ATTTTTGGGTGTTGGTCATTGCATG
1 GTC-GACACCCCCTTTTCTCGAAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATG
* * * * *
11318 GTCGACACCCCCTTCTCTTGGATAAAAAAATTGT-AAATTTTTTTGCTGTTGACCAT
1 GTCGACACCCCCTTTTC-TCGA-AAAAAAATT-TCAAAATTTTTTGGTGTTGGCCAT
11374 GTAACAGTCA
Statistics
Matches: 381, Mismatches: 69, Indels: 45
0.77 0.14 0.09
Matches are distributed among these distances:
56 6 0.02
57 33 0.09
58 35 0.09
59 84 0.22
60 65 0.17
61 123 0.32
62 35 0.09
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (60 bp):
GTCGACACCCCCTTTTCTCGAAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATG
Found at i:10990 original size:119 final size:117
Alignment explanation
Indices: 10841--11234 Score: 420
Period size: 119 Copynumber: 3.3 Consensus size: 117
10831 TTTTTTTGGT
* * * * * * *
10841 GTCGATCATCCCCTTTTCTCGAAACAAAAATTGCATTTTTGGGTGTTAGTCATTGCATGGCCGAC
1 GTCGA-CACCCCCTTTTCTCAAAAAAAAAATTTCATTTTT-GGTGTTAGCCATTGAATGGTCGAC
* *
10906 ACCCCTTTTTCTTGAGAAAAAAATTTCAAAATTTTTTAGTGTTGGCCATCAAATG
64 ACCCC-TTTTCTCGAGAAAAAAATTTCAAAATTTTTTTGTGTTGGCCATCAAATG
* * * **
10961 GTCGACACCCCCTGTTCTCAAAAAAAAAATTTTAATTTTTTGGTGTTGGCCATCAAATGGTCGAC
1 GTCGACACCCCCTTTTCTCAAAAAAAAAA-TTTCA-TTTTTGGTGTTAGCCATTGAATGGTCGAC
11026 ACCCCTTTTCTCGAG-AAAAAATTTCAAAATTTTTTTTGTGTTGGCCATCAAATG
64 ACCCCTTTTCTCGAGAAAAAAATTTCAAAA-TTTTTTTGTGTTGGCCATCAAATG
* * * *
11080 G-CTGACATCCCCTTTTCTC-GAAAAAAATTTTCAAAATTTTTGGTGTTAACCA-TGAAATGGTC
1 GTC-GACACCCCCTTTTCTCAAAAAAAAAATTTC---ATTTTTGGTGTTAGCCATTG-AATGGTC
* * *
11142 GACACCCCCCATTTCTCGA-AAAAAAATTTCAAATTTTTTTTGTGTTGGCTATCAAATG
61 GACA--CCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTTGTGTTGGCCATCAAATG
* *
11200 GTCGACACCCCCTATTCTCCAAAAAAAAAAATTCA
1 GTCGACACCCCCTTTTCT-CAAAAAAAAAATTTCA
11235 AAATTTTTTG
Statistics
Matches: 229, Mismatches: 31, Indels: 29
0.79 0.11 0.10
Matches are distributed among these distances:
117 3 0.01
118 22 0.10
119 93 0.41
120 69 0.30
121 32 0.14
122 10 0.04
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.34
Consensus pattern (117 bp):
GTCGACACCCCCTTTTCTCAAAAAAAAAATTTCATTTTTGGTGTTAGCCATTGAATGGTCGACAC
CCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTTGTGTTGGCCATCAAATG
Found at i:22999 original size:20 final size:21
Alignment explanation
Indices: 22963--23004 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
22953 TAAAGTAGTG
*
22963 ATTTTGTTATAATAAAA-AAA
1 ATTTTGTTATAAAAAAAGAAA
22983 ATTTTGATT-TAAAAAAAGAAA
1 ATTTTG-TTATAAAAAAAGAAA
23004 A
1 A
23005 AGAAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (21 bp):
ATTTTGTTATAAAAAAAGAAA
Found at i:23609 original size:16 final size:17
Alignment explanation
Indices: 23576--23623 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
23566 TATAATTTTT
*
23576 TATTTATTCTTATTTCA
1 TATTTATTCATATTTCA
23593 TATTTATTCAT-TTTCA
1 TATTTATTCATATTTCA
* *
23609 TATCTATTTATATTT
1 TATTTATTCATATTT
23624 ATGTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTATTCATATTTCA
Found at i:24733 original size:20 final size:21
Alignment explanation
Indices: 24703--24741 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
24693 ATTTTTGCAT
*
24703 ATTAGATTTATTTATTTGTGC
1 ATTAGATTTATTTAATTGTGC
24724 ATTA-ATTTATTTAATTGT
1 ATTAGATTTATTTAATTGT
24742 CTAATGTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (21 bp):
ATTAGATTTATTTAATTGTGC
Found at i:31441 original size:20 final size:19
Alignment explanation
Indices: 31418--31486 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 19
31408 TGTTTAAATC
31418 AAGAAAAAGTACAAAAAAAG
1 AAGAAAAAG-ACAAAAAAAG
*
31438 AAGAAAAAAGA-AAAAAGAG
1 AAG-AAAAAGACAAAAAAAG
* *
31457 AAAAAAAAAAACAACAAAAGAG
1 -AAGAAAAAGACAA-AAAA-AG
31479 AAGAAAAA
1 AAGAAAAA
31487 AATAGAAAGC
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 13 0.33
20 8 0.21
21 16 0.41
22 2 0.05
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.01
Consensus pattern (19 bp):
AAGAAAAAGACAAAAAAAG
Found at i:31451 original size:17 final size:15
Alignment explanation
Indices: 31430--31467 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 15
31420 GAAAAAGTAC
31430 AAAAAAAGAAGAAAAA
1 AAAAAAAG-AGAAAAA
31446 AGAAAAAAGAGAAAAA
1 A-AAAAAAGAGAAAAA
31462 AAAAAA
1 AAAAAA
31468 CAACAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.24
16 9 0.43
17 7 0.33
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAGAAAAA
Found at i:31466 original size:22 final size:22
Alignment explanation
Indices: 31441--31494 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
31431 AAAAAAGAAG
31441 AAAAAAGAAAAAAGAGAAAAAA
1 AAAAAAGAAAAAAGAGAAAAAA
* *
31463 AAAAACA-ACAAAAGAGAAGAAA
1 AAAAA-AGAAAAAAGAGAAAAAA
*
31485 AAAATAGAAA
1 AAAAAAGAAA
31495 GCGAGAGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.04
22 24 0.92
23 1 0.04
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (22 bp):
AAAAAAGAAAAAAGAGAAAAAA
Found at i:31475 original size:14 final size:13
Alignment explanation
Indices: 31430--31488 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
31420 GAAAAAGTAC
*
31430 AAAAAAAGAAGAA
1 AAAAAAAAAAGAA
31443 AAAAGAAAAAAGAGA
1 AAAA-AAAAAAGA-A
*
31458 AAAAAAAAAACAA
1 AAAAAAAAAAGAA
* * *
31471 CAAAAGAGAAGAA
1 AAAAAAAAAAGAA
31484 AAAAA
1 AAAAA
31489 TAGAAAGCGA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
13 18 0.49
14 14 0.38
15 5 0.14
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:31487 original size:20 final size:19
Alignment explanation
Indices: 31418--31487 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 19
31408 TGTTTAAATC
31418 AAGAAAAAGTACAAAAAA-AG
1 AAGAAAAA--ACAAAAAAGAG
*
31438 AAGAAAAAAGAAAAAAGAG
1 AAGAAAAAACAAAAAAGAG
*
31457 AAAAAAAAAAACAACAAAAGAG
1 --AAGAAAAAACAA-AAAAGAG
31479 AAGAAAAAA
1 AAGAAAAAA
31488 ATAGAAAGCG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
18 7 0.17
19 2 0.05
20 16 0.38
21 10 0.24
22 7 0.17
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.01
Consensus pattern (19 bp):
AAGAAAAAACAAAAAAGAG
Found at i:32010 original size:42 final size:42
Alignment explanation
Indices: 31895--32386 Score: 671
Period size: 42 Copynumber: 11.7 Consensus size: 42
31885 AAGGAAAACA
* * * *
31895 TTCATTGCATTTAGAGGCCCAAGTGTGGATGTCCATTTAC-T
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * * * *
31936 TTCATCACATTCAGAAGCTCAAGTGTGGAGGCCCATTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* *
31978 TTTATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* *
32020 TTCATCGCATTTAGAGGTCCAGGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
*
32062 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* *
32104 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGCCCATTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * *
32146 TTCATCGAATTTAGAGGCCTAGGTGTGGAGGCCTATTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * *
32188 TTCATCGCATTTATAGGCCTAAGTGTGGAGGCCCATTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * *
32230 TTCATCGCATTTAGAGACCTAGGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * *
32272 TTCATCGCATTTAGAGACCTAGGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * * *
32314 TTCATGGCATTTAGAGGCCCAAGTGTAGAGGCCCATTTAATT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* *
32356 TTCATGGCATTTAGAGACCCAGGTGTGGAGG
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGG
32387 TGTGGAGGTG
Statistics
Matches: 405, Mismatches: 45, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
41 33 0.08
42 372 0.92
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.34
Consensus pattern (42 bp):
TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
Found at i:32389 original size:8 final size:8
Alignment explanation
Indices: 32376--32401 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
32366 TTAGAGACCC
32376 AGGTGTGG
1 AGGTGTGG
32384 AGGTGTGG
1 AGGTGTGG
32392 AGGTGTGG
1 AGGTGTGG
32400 AG
1 AG
32402 ATCCATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.62, T:0.23
Consensus pattern (8 bp):
AGGTGTGG
Found at i:32487 original size:100 final size:100
Alignment explanation
Indices: 32292--32487 Score: 248
Period size: 100 Copynumber: 2.0 Consensus size: 100
32282 TTAGAGACCT
* *
32292 AGGTGTGGAGGTCCATTTACTTTTCATGGCATTTAGAGGCCCAAGTGTAGAGGCCCATTTAATTT
1 AGGTGTGGAGATCCATTTACTTTTCATGGCATTCAGAGGCCCAAGTGTAGAGGCCCATTTAATTT
* **** *
32357 TCATGGCATTTAGAGACCCAGGTGTGGAGGTGTGG
66 TCATGGCAATTAGAGACCCAACCATAGAGGTGTGG
* * * * *
32392 AGGTGTGGAGATCCATTTACTTTTCATTGCATTCAGAGGCCCAGGTGTGGAGGTCCATTTACTTT
1 AGGTGTGGAGATCCATTTACTTTTCATGGCATTCAGAGGCCCAAGTGTAGAGGCCCATTTAATTT
* * *
32457 TCATTGCAATTAGATACCTAACCATAGAGGT
66 TCATGGCAATTAGAGACCCAACCATAGAGGT
32488 CCATTTATTT
Statistics
Matches: 80, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
100 80 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.32
Consensus pattern (100 bp):
AGGTGTGGAGATCCATTTACTTTTCATGGCATTCAGAGGCCCAAGTGTAGAGGCCCATTTAATTT
TCATGGCAATTAGAGACCCAACCATAGAGGTGTGG
Found at i:32820 original size:10 final size:10
Alignment explanation
Indices: 32805--32834 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
32795 AAATAGAGGT
32805 TTTTTTTTTC
1 TTTTTTTTTC
32815 TTTTTTTTTC
1 TTTTTTTTTC
32825 TTTTCTTTTT
1 TTTT-TTTTT
32835 GGGCTTGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:32828 original size:15 final size:14
Alignment explanation
Indices: 32804--32834 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
32794 CAAATAGAGG
32804 TTTTTTTTTTCTTT
1 TTTTTTTTTTCTTT
32818 TTTTTTCTTTTCTTT
1 TTTTTT-TTTTCTTT
32833 TT
1 TT
32835 GGGCTTGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTTCTTT
Found at i:32865 original size:3 final size:3
Alignment explanation
Indices: 32859--32926 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
32849 CCAAATTATT
*
32859 ATC ATC ACC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
32907 ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC AT
32927 TATTATTATT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:32931 original size:3 final size:3
Alignment explanation
Indices: 32925--32969 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
32915 CATCATCATC
32925 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
32970 TAGGGTTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:33676 original size:147 final size:146
Alignment explanation
Indices: 33434--33862 Score: 549
Period size: 147 Copynumber: 2.9 Consensus size: 146
33424 TTGGGAAAAA
* *
33434 TTTTGGTTTTTTTAAATAATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTTCTT
1 TTTTGATTTTTTTAACT-ATTTCGAAATAAAAG-TTTGATTTTTAAGTAAAATAGTGATTTTCTT
* * *
33499 TAAAAAAGTGAAAGTTTATATTTTTAAAAATAAAATTATATTTTTTAGTTATTTTAA-AAAAAAG
64 TAAAAAAGAGAAAATTTATATTTTTAAAAATAAAAATATATTTTTTAGTTATTTTAAGAAAAAA-
33563 TTTAAATTTTTAAACAAAG
128 TTTAAATTTTTAAACAAAG
* *
33582 TTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGAATTTTTAAGTAAAATAATAATTTTCTTT
1 TTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTG-ATTTTTAAGTAAAATAGTGATTTTCTTT
* *
33647 AAAAAAGAGAAAATTTATATTTTTGAAAATAAAAATCTATTTTTTAGTTATTTTAAGGAAAAAAT
65 AAAAAAGAGAAAATTTATATTTTTAAAAATAAAAATATATTTTTTAGTTATTTTAA-GAAAAAAT
33712 TTAAATTTTTAAACAAAG
129 TTAAATTTTTAAACAAAG
* * *
33730 TTTTTATTTTTTTAAACTATTTCGAAATAAAA-TTTGGATTTTTAAGTAAAATTGCGATTTTCTT
1 TTTTGATTTTTTT-AACTATTTCGAAATAAAAGTTT-GATTTTTAAGTAAAATAGTGATTTTCTT
* * * * * * *
33794 TAAAAAAAAAAAGAAAAAGTTTAGATTTTTAAAAGTAAAAGTAT-GTTTTTAATGATTTTAAAGA
64 T---AAAAAAGAG-AAAA-TTTATATTTTTAAAAATAAAAATATATTTTTTAGTTATTTT-AAGA
33858 AAAAA
123 AAAAA
33863 GTTTTGATTT
Statistics
Matches: 247, Mismatches: 23, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
146 4 0.02
147 92 0.37
148 73 0.30
149 25 0.10
151 8 0.03
152 23 0.09
153 22 0.09
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (146 bp):
TTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGATTTTTAAGTAAAATAGTGATTTTCTTTA
AAAAAGAGAAAATTTATATTTTTAAAAATAAAAATATATTTTTTAGTTATTTTAAGAAAAAATTT
AAATTTTTAAACAAAG
Found at i:33776 original size:148 final size:148
Alignment explanation
Indices: 33434--33800 Score: 562
Period size: 147 Copynumber: 2.5 Consensus size: 148
33424 TTGGGAAAAA
* *
33434 TTTTGGTTTTTTTAAA-TAATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTTCT
1 TTTTGATTTTTTTAAACT-ATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCT
* * *
33498 TTAAAAAAGTGAAAGTTTATATTTTTAAAAATAAAATTATATTTTTTAGTTATTTTAAAAAAAAG
65 TTAAAAAAGAGAAAATTTATATTTTTAAAAATAAAAATATATTTTTTAGTTATTTTAAAAAAAAG
33563 TTTAAATTTTTAAACAAAG
130 TTTAAATTTTTAAACAAAG
* * *
33582 TTTTGATTTTTTT-AACTATTTCGAAATAAAAGTTTGAATTTTTAAGTAAAATAATAATTTTCTT
1 TTTTGATTTTTTTAAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCTT
* *
33646 TAAAAAAGAGAAAATTTATATTTTTGAAAATAAAAATCTATTTTTTAGTTATTTTAAGGAAAAAA
66 TAAAAAAGAGAAAATTTATATTTTTAAAAATAAAAATATATTTTTTAGTTATTTTAA--AAAAAA
33711 -TTTAAATTTTTAAACAAAG
129 GTTTAAATTTTTAAACAAAG
* * *
33730 TTTTTATTTTTTTAAACTATTTCGAAATAAAA-TTTGGATTTTTAAGTAAAATTGCGATTTTCTT
1 TTTTGATTTTTTTAAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCTT
33794 TAAAAAA
66 TAAAAAA
33801 AAAAAGAAAA
Statistics
Matches: 199, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
147 97 0.49
148 78 0.39
149 24 0.12
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (148 bp):
TTTTGATTTTTTTAAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCTT
TAAAAAAGAGAAAATTTATATTTTTAAAAATAAAAATATATTTTTTAGTTATTTTAAAAAAAAGT
TTAAATTTTTAAACAAAG
Found at i:33878 original size:34 final size:33
Alignment explanation
Indices: 33839--33906 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
33829 TAAAAGTATG
*
33839 TTTTTAA-TGATTTTAAAGAAAAAAGTTTTGATTT
1 TTTTTAACT-ATTTCAAA-AAAAAAGTTTTGATTT
* *
33873 TTTTTAACTATTTCGAAATAAAAGTTTTGATTT
1 TTTTTAACTATTTCAAAAAAAAAGTTTTGATTT
33906 T
1 T
33907 GAAGTAAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 16 0.53
34 13 0.43
35 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.51
Consensus pattern (33 bp):
TTTTTAACTATTTCAAAAAAAAAGTTTTGATTT
Found at i:42905 original size:17 final size:15
Alignment explanation
Indices: 42863--42915 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 15
42853 AAGTTAATTC
42863 TATTACTATATTATATAA
1 TATTA-TATA-TATAT-A
*
42881 TGTTATATCATATCATA
1 TATTATAT-ATAT-ATA
42898 TATTATATATATATA
1 TATTATATATATATA
42913 TAT
1 TAT
42916 CAATGATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 6 0.19
16 4 0.13
17 14 0.45
18 7 0.23
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.51
Consensus pattern (15 bp):
TATTATATATATATA
Found at i:42985 original size:24 final size:24
Alignment explanation
Indices: 42958--43015 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
42948 TATATATTTT
* *
42958 GTTATGATATATA-ATATAATAATA
1 GTTAT-ATATATATATAAAAAAATA
*
42982 GTTATATATATATTTAAAAAAATA
1 GTTATATATATATATAAAAAAATA
43006 GTTATATATA
1 GTTATATATA
43016 ATAGTAGTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 7 0.23
24 23 0.77
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (24 bp):
GTTATATATATATATAAAAAAATA
Found at i:43258 original size:16 final size:17
Alignment explanation
Indices: 43232--43282 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 17
43222 GATTATAATA
43232 TATATTATAATAATAGT
1 TATATTATAATAATAGT
*
43249 TATA-TATAATAGTAG-
1 TATATTATAATAATAGT
* *
43264 TAAATTAT-ATATTAGT
1 TATATTATAATAATAGT
43280 TAT
1 TAT
43283 TATATATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 9 0.32
16 15 0.54
17 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (17 bp):
TATATTATAATAATAGT
Found at i:43385 original size:7 final size:7
Alignment explanation
Indices: 43374--43410 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
43364 ATATTATATC
43374 ATATAAT
1 ATATAAT
*
43381 TTATAAT
1 ATATAAT
43388 ATATAAT
1 ATATAAT
43395 ATATAAT
1 ATATAAT
43402 ATATTAAT
1 ATA-TAAT
43410 A
1 A
43411 ACGTATGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 22 0.81
8 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
ATATAAT
Found at i:43538 original size:17 final size:17
Alignment explanation
Indices: 43516--43548 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43506 AGTAGTACAT
43516 TATATATTACATATTAC
1 TATATATTACATATTAC
*
43533 TATATATTATATATTA
1 TATATATTACATATTA
43549 TTGTTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATTACATATTAC
Found at i:43571 original size:18 final size:18
Alignment explanation
Indices: 43537--43586 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
43527 TATTACTATA
* *
43537 TATTA-TATATTATTGTT
1 TATTATTATACTAGTGTT
43554 TATTATTATACTAGTGTT
1 TATTATTATACTAGTGTT
*
43572 TATTATTATTCTAGT
1 TATTATTATACTAGT
43587 TGAAATATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 5 0.17
18 24 0.83
ACGTcount: A:0.28, C:0.04, G:0.08, T:0.60
Consensus pattern (18 bp):
TATTATTATACTAGTGTT
Found at i:43911 original size:10 final size:10
Alignment explanation
Indices: 43896--43946 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
43886 CTCTCCTATT
43896 ATATTATATA
1 ATATTATATA
*
43906 ATATTATATC
1 ATATTATATA
*
43916 ATATCATATA
1 ATATTATATA
43926 ATA-TAT-TA
1 ATATTATATA
43934 ATAGCTTATATA
1 ATA--TTATATA
43946 A
1 A
43947 ATATCGATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 5 0.15
9 2 0.06
10 20 0.61
11 3 0.09
12 3 0.09
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (10 bp):
ATATTATATA
Found at i:44071 original size:30 final size:29
Alignment explanation
Indices: 44004--44071 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
43994 TTATAATAGA
*
44004 ATATTATAGTAATAGTTATATATGTATTAAT
1 ATATTTTAGTAATAGTTATATAT-TA-TAAT
44035 AT-TTTTAGTAATAGTTATATATTATAAT
1 ATATTTTAGTAATAGTTATATATTATAAT
44063 ATCATTTTA
1 AT-ATTTTA
44072 TGTATTAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
28 6 0.18
29 2 0.06
30 24 0.71
31 2 0.06
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.51
Consensus pattern (29 bp):
ATATTTTAGTAATAGTTATATATTATAAT
Found at i:44216 original size:16 final size:17
Alignment explanation
Indices: 44197--44229 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44187 AATTTTATAG
44197 ATTTTA-ATAATTATTA
1 ATTTTATATAATTATTA
*
44213 ATTTTATATATTTATTA
1 ATTTTATATAATTATTA
44230 TATATATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTATATAATTATTA
Found at i:44814 original size:14 final size:14
Alignment explanation
Indices: 44797--44826 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
44787 ACTTAATAAG
44797 TTAGGACACAACAA
1 TTAGGACACAACAA
44811 TTAGGACACAACAA
1 TTAGGACACAACAA
44825 TT
1 TT
44827 CGAATTTTTG
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:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (14 bp):
TTAGGACACAACAA
Found at i:44876 original size:22 final size:22
Alignment explanation
Indices: 44811--44876 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 22
44801 GACACAACAA
44811 TTAGGACACAACAATTCGAATT
1 TTAGGACACAACAATTCGAATT
* * * * *
44833 TTTGAACATAATAAGTT---TTT
1 TTAGGACACAACAA-TTCGAATT
44853 TTAGGACACAACAATTCGAATT
1 TTAGGACACAACAATTCGAATT
44875 TT
1 TT
44877 CGAACATAAC
Statistics
Matches: 30, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
19 2 0.07
20 12 0.40
22 14 0.47
23 2 0.07
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (22 bp):
TTAGGACACAACAATTCGAATT
Found at i:44887 original size:22 final size:22
Alignment explanation
Indices: 44811--44888 Score: 54
Period size: 22 Copynumber: 3.6 Consensus size: 22
44801 GACACAACAA
* *
44811 TTAGGACACAACAATTCGAATT
1 TTAGAACATAACAATTCGAATT
* * *
44833 TTTGAACATAATAAGTT---TTT
1 TTAGAACATAACAA-TTCGAATT
* *
44853 TTAGGACACAACAATTCGAATT
1 TTAGAACATAACAATTCGAATT
*
44875 TTCGAACATAACAA
1 TTAGAACATAACAA
44889 GCATTTTTAA
Statistics
Matches: 39, Mismatches: 13, Indels: 8
0.65 0.22 0.13
Matches are distributed among these distances:
19 2 0.05
20 12 0.31
22 23 0.59
23 2 0.05
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (22 bp):
TTAGAACATAACAATTCGAATT
Found at i:44896 original size:42 final size:42
Alignment explanation
Indices: 44811--44897 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 42
44801 GACACAACAA
* * **
44811 TTAGGACACAACAATTCGAATTTTTGAACATAATAAGTTTTT
1 TTAGGACACAACAATTCGAATTTTCGAACATAACAAGCATTT
44853 TTAGGACACAACAATTCGAATTTTCGAACATAACAAGCATTT
1 TTAGGACACAACAATTCGAATTTTCGAACATAACAAGCATTT
44895 TTA
1 TTA
44898 ATTGTTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.34
Consensus pattern (42 bp):
TTAGGACACAACAATTCGAATTTTCGAACATAACAAGCATTT
Found at i:45404 original size:13 final size:13
Alignment explanation
Indices: 45388--45412 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45378 TTAATGAATA
45388 AAATAAAAATAAT
1 AAATAAAAATAAT
45401 AAATAAAAATAA
1 AAATAAAAATAA
45413 ATAATGAATA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAAATAAT
Found at i:45416 original size:17 final size:18
Alignment explanation
Indices: 45374--45428 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
45364 AGTAACAAGC
*
45374 AAAATTAATGAATAAAAT
1 AAAAATAATGAATAAAAT
*
45392 AAAAATAATAAATAAAA-
1 AAAAATAATGAATAAAAT
*
45409 ATAAATAATGAATAAAAT
1 AAAAATAATGAATAAAAT
45427 AA
1 AA
45429 TATGAACATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 15 0.48
18 16 0.52
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (18 bp):
AAAAATAATGAATAAAAT
Found at i:45444 original size:35 final size:36
Alignment explanation
Indices: 45379--45449 Score: 85
Period size: 35 Copynumber: 2.0 Consensus size: 36
45369 CAAGCAAAAT
*
45379 TAATGAATAAAATAAAAATAA-TAAATAAAAATAAA
1 TAATGAATAAAATAAAAATAACAAAATAAAAATAAA
*
45414 TAATGAATAAAAT-AATATGAACATAAA-AAAAATAAA
1 TAATGAATAAAATAAAAAT-AACA-AAATAAAAATAAA
45450 AAAATTAGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
34 4 0.13
35 15 0.48
36 9 0.29
37 3 0.10
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (36 bp):
TAATGAATAAAATAAAAATAACAAAATAAAAATAAA
Found at i:51105 original size:3 final size:3
Alignment explanation
Indices: 51097--51130 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
51087 AGCCATGTCG
51097 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
51131 TATTTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:55763 original size:54 final size:54
Alignment explanation
Indices: 55700--55810 Score: 222
Period size: 54 Copynumber: 2.1 Consensus size: 54
55690 GTCTTGATTT
55700 TACAAGGGGTATCAATATTTTAGAAATTATCGATACTTAACCAAAAAGTATCGA
1 TACAAGGGGTATCAATATTTTAGAAATTATCGATACTTAACCAAAAAGTATCGA
55754 TACAAGGGGTATCAATATTTTAGAAATTATCGATACTTAACCAAAAAGTATCGA
1 TACAAGGGGTATCAATATTTTAGAAATTATCGATACTTAACCAAAAAGTATCGA
55808 TAC
1 TAC
55811 TTTTTGGCCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (54 bp):
TACAAGGGGTATCAATATTTTAGAAATTATCGATACTTAACCAAAAAGTATCGA
Found at i:58478 original size:19 final size:19
Alignment explanation
Indices: 58454--58490 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
58444 AAGACAGTAA
*
58454 TAATGTAAAGTTAAAGAAG
1 TAATGTAAAATTAAAGAAG
58473 TAATGTAAAATTAAAGAA
1 TAATGTAAAATTAAAGAA
58491 ATAAAACTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.16, T:0.27
Consensus pattern (19 bp):
TAATGTAAAATTAAAGAAG
Found at i:60988 original size:24 final size:24
Alignment explanation
Indices: 60936--60990 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
60926 ATTTGCCTTG
*
60936 ACTTCTTTTCCTTCCTCTCTTTTT
1 ACTTCTTTTCCTTCCTCTCTTTTC
*
60960 TCTTCTTTTCCTT-CT-TCTTCTTCC
1 ACTTCTTTTCCTTCCTCTCTT-TT-C
60984 ACTTCTT
1 ACTTCTT
60991 CCACTTGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 18 0.69
ACGTcount: A:0.04, C:0.35, G:0.00, T:0.62
Consensus pattern (24 bp):
ACTTCTTTTCCTTCCTCTCTTTTC
Found at i:60991 original size:15 final size:12
Alignment explanation
Indices: 60937--60983 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
60927 TTTGCCTTGA
60937 CTTCTTTTCCTT
1 CTTCTTTTCCTT
60949 CCTCTCTTTT--TT
1 -CT-TCTTTTCCTT
60961 CTTCTTTTCCTT
1 CTTCTTTTCCTT
60973 CTTCTTCTTCC
1 CTTCTT-TTCC
60984 ACTTCTTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 6 0.20
11 2 0.07
12 10 0.33
13 6 0.20
14 6 0.20
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (12 bp):
CTTCTTTTCCTT
Found at i:76090 original size:18 final size:19
Alignment explanation
Indices: 76063--76119 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
76053 AAGTAACAAG
76063 AAAAATTAATGAATAAAAC
1 AAAAATTAATGAATAAAAC
* *
76082 AAAAA-TAATAAATAAAAAT
1 AAAAATTAATGAAT-AAAAC
76101 AAATAATTAATGAATAAAA
1 AAA-AATTAATGAATAAAA
76120 TAATATGAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 7 0.22
19 12 0.38
20 6 0.19
21 7 0.22
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.23
Consensus pattern (19 bp):
AAAAATTAATGAATAAAAC
Found at i:76113 original size:39 final size:38
Alignment explanation
Indices: 76046--76119 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
76036 ATATACAATT
* *
76046 AAATAATAAGTAACAAGAAAAATTAATGAATAAAACAA
1 AAATAATAAATAAAAAGAAAAATTAATGAATAAAACAA
*
76084 AAATAATAAATAAAAATAAATAATTAATGAATAAAA
1 AAATAATAAATAAAAAGAAA-AATTAATGAATAAAA
76120 TAATATGAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 17 0.53
39 15 0.47
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (38 bp):
AAATAATAAATAAAAAGAAAAATTAATGAATAAAACAA
Found at i:76148 original size:39 final size:39
Alignment explanation
Indices: 76063--76144 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
76053 AAGTAACAAG
*
76063 AAAAATTAATGAATAAAACAAAAATAATAAATAAAAATA
1 AAAAATTAATGAATAAAACAAAAATAACAAATAAAAATA
* * *
76102 AATAATTAATGAATAAAA-TAATATGAACAAA-AAAAATA
1 AAAAATTAATGAATAAAACAAAAAT-AACAAATAAAAATA
76140 AAAAA
1 AAAAA
76145 ATTAGGGTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
38 15 0.41
39 22 0.59
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (39 bp):
AAAAATTAATGAATAAAACAAAAATAACAAATAAAAATA
Found at i:77573 original size:40 final size:40
Alignment explanation
Indices: 77518--77624 Score: 133
Period size: 40 Copynumber: 2.7 Consensus size: 40
77508 CAAAAATGCC
* * * *
77518 GCAAAAAGTAAAGCAATAGCGATATTTTTCCTTAGACGCT
1 GCAAAAGGTAAAGCAATAGCGACATTTTTCCATAAACGCT
* *
77558 GCAAAAGGTAAAGCAATAGCGGCGTTTTTCCATAAACGCT
1 GCAAAAGGTAAAGCAATAGCGACATTTTTCCATAAACGCT
* * *
77598 ACAAAAGGTAAAGCAATAACGGCATTT
1 GCAAAAGGTAAAGCAATAGCGACATTT
77625 ATGAGAAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (40 bp):
GCAAAAGGTAAAGCAATAGCGACATTTTTCCATAAACGCT
Found at i:77687 original size:82 final size:81
Alignment explanation
Indices: 77599--77847 Score: 245
Period size: 82 Copynumber: 3.0 Consensus size: 81
77589 ATAAACGCTA
* * *
77599 CAAAAGGTAAAGCAATAACGGCATTTATGAGAAAAACGCCACAAAAAGTAAGAGCATTAGCGGCG
1 CAAAAGGTAAAGCAATAGCGGCGTTTATGAG-AAAACGCCGCAAAAAGTAAGAGCATTAGCGGCG
* *
77664 TTTATGGGAAAATGCCG
65 TTTATGAGAAAACGCCG
* * * *
77681 CGAAAGGT-AAG-AATATTGGCGGCGTTTATG-GTAAAATGTCGCAAAAGGTAAGAGCATTAGCG
1 CAAAAGGTAAAGCAATA---GCGGCGTTTATGAG-AAAACGCCGCAAAAAGTAAGAGCATTAGCG
*
77743 GCGTTTATGAGAAAACGCCA
62 GCGTTTATGAGAAAACGCCG
* ** * * * * *
77763 CAAAAGGCATAAA-CATTAGTTGCGTTTATGAGAAAACACTGTAAAAAGTAAGAGCATTAGTGAC
1 CAAAAGG--TAAAGCAATAGCGGCGTTTATGAGAAAACGCCGCAAAAAGTAAGAGCATTAGCGGC
77827 GTTTATGAGAAAACGCCG
64 GTTTATGAGAAAACGCCG
77845 CAA
1 CAA
77848 CAGATAAGAG
Statistics
Matches: 135, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
80 4 0.03
81 3 0.02
82 111 0.82
83 11 0.08
84 1 0.01
85 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.20
Consensus pattern (81 bp):
CAAAAGGTAAAGCAATAGCGGCGTTTATGAGAAAACGCCGCAAAAAGTAAGAGCATTAGCGGCGT
TTATGAGAAAACGCCG
Found at i:77703 original size:41 final size:41
Alignment explanation
Indices: 77599--77880 Score: 190
Period size: 41 Copynumber: 6.9 Consensus size: 41
77589 ATAAACGCTA
* * * * * * *
77599 CAAAAGGTAA-AGCAATAACGGCATTTATGAGAAAAACGCCA
1 CAAAAGGTAAGAACATTAGCGGCGTTTATG-GGAAAATGCCG
* *
77640 CAAAAAGTAAGAGCATTAGCGGCGTTTATGGGAAAATGCCG
1 CAAAAGGTAAGAACATTAGCGGCGTTTATGGGAAAATGCCG
* * * * *
77681 CGAAAGGTAAGAATATTGGCGGCGTTTATGGTAAAATGTCG
1 CAAAAGGTAAGAACATTAGCGGCGTTTATGGGAAAATGCCG
* * * *
77722 CAAAAGGTAAGAGCATTAGCGGCGTTTATGAGAAAACGCCA
1 CAAAAGGTAAGAACATTAGCGGCGTTTATGGGAAAATGCCG
* ** * ** *
77763 CAAAAGGCATA-AACATTAGTTGCGTTTATGAGAAAACACTG
1 CAAAAGGTA-AGAACATTAGCGGCGTTTATGGGAAAATGCCG
* * * * * * *
77804 TAAAAAGTAAGAGCATTAGTGACGTTTATGAGAAAACGCCG
1 CAAAAGGTAAGAACATTAGCGGCGTTTATGGGAAAATGCCG
* * * * * *
77845 CAACAGATAAGAGCATTAGTGACATTTATGGGAAAA
1 CAAAAGGTAAGAACATTAGCGGCGTTTATGGGAAAA
77881 CGTCGCTGAA
Statistics
Matches: 194, Mismatches: 44, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
40 1 0.01
41 176 0.91
42 17 0.09
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (41 bp):
CAAAAGGTAAGAACATTAGCGGCGTTTATGGGAAAATGCCG
Found at i:77814 original size:123 final size:123
Alignment explanation
Indices: 77599--77882 Score: 279
Period size: 123 Copynumber: 2.3 Consensus size: 123
77589 ATAAACGCTA
* *
77599 CAAAAGGTAA-AGCAATAACGGCATTTATGAGAAAAACGCCACAAAAAGTAAGAGCATTAGCGGC
1 CAAAAGGTAAGAGCATTAGCGGCATTTATGAG-AAAACGCCACAAAAAGTAAGAGCATTAGCGGC
* ** * * * * * * *
77663 GTTTATGGGAAAATGCCGCGAAAGGTAAGAATATTGGCGGCGTTTATG-GTAAAATGTCG
65 GTTTATGAGAAAACACCGCAAAAAGTAAGAACATTAGCGACGTTTATGAG-AAAACGCCG
* * **
77722 CAAAAGGTAAGAGCATTAGCGGCGTTTATGAGAAAACGCCACAAAAGGCATAA-A-CATTAGTTG
1 CAAAAGGTAAGAGCATTAGCGGCATTTATGAGAAAACGCCACAAAAAG--TAAGAGCATTAGCGG
* * * *
77785 CGTTTATGAGAAAACACTGTAAAAAGTAAGAGCATTAGTGACGTTTATGAGAAAACGCCG
64 CGTTTATGAGAAAACACCGCAAAAAGTAAGAACATTAGCGACGTTTATGAGAAAACGCCG
* * * * *
77845 CAACAGATAAGAGCATTAGTGACATTTATGGGAAAACG
1 CAAAAGGTAAGAGCATTAGCGGCATTTATGAGAAAACG
77883 TCGCTGAAGG
Statistics
Matches: 131, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
123 108 0.82
124 20 0.15
125 3 0.02
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (123 bp):
CAAAAGGTAAGAGCATTAGCGGCATTTATGAGAAAACGCCACAAAAAGTAAGAGCATTAGCGGCG
TTTATGAGAAAACACCGCAAAAAGTAAGAACATTAGCGACGTTTATGAGAAAACGCCG
Found at i:77862 original size:82 final size:78
Alignment explanation
Indices: 77640--77881 Score: 220
Period size: 82 Copynumber: 2.9 Consensus size: 78
77630 AAAAACGCCA
* * * * * *
77640 CAAAAAGTAAGAGCATTAGCGGCGTTTATGGGAAAATGCCGCGAAAGGTAAGAATATTGGCGGCG
1 CAAAAAGTAAGAGCATTAGCGGCGTTTATGAGAAAACGCCGC-AAAGATAAG-ACATTAG-TGCG
*
77705 TTTATGGTAAA-ATGT
63 TTTATGGAAAACATGT
* *
77720 CGCAAAAGGTAAGAGCATTAGCGGCGTTTATGAGAAAACGCCACAAAAGGCATAA-ACATTAGTT
1 --CAAAAAGTAAGAGCATTAGCGGCGTTTATGAGAAAACGCCGC-AAA-G-ATAAGACATTAG-T
77784 GCGTTTATGAGAAAACACTGT
60 GCGTTTATG-GAAAACA-TGT
* * *
77805 -AAAAAGTAAGAGCATTAGTGACGTTTATGAGAAAACGCCGCAACAGATAAGAGCATTAGTGACA
1 CAAAAAGTAAGAGCATTAGCGGCGTTTATGAGAAAACGCCGCAA-AGATAAGA-CATTAGTG-CG
77869 TTTATGGGAAAAC
63 TTTAT-GGAAAAC
77882 GTCGCTGAAG
Statistics
Matches: 134, Mismatches: 16, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
80 4 0.03
81 6 0.04
82 111 0.83
83 6 0.04
84 4 0.03
85 3 0.02
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.22
Consensus pattern (78 bp):
CAAAAAGTAAGAGCATTAGCGGCGTTTATGAGAAAACGCCGCAAAGATAAGACATTAGTGCGTTT
ATGGAAAACATGT
Found at i:79268 original size:41 final size:41
Alignment explanation
Indices: 79216--79312 Score: 119
Period size: 40 Copynumber: 2.4 Consensus size: 41
79206 AAACGTCGTA
* *
79216 AAAAG-TAAAGCAATAACAACGTTTATCGGAAAAACACCGC-
1 AAAAGATAAAGCAATAACAACATTTAT-GAAAAAACACCGCT
* * *
79256 AATAGATAAAGCAATAGCAATATTTATGAAAAAACACCGCT
1 AAAAGATAAAGCAATAACAACATTTATGAAAAAACACCGCT
79297 AAAAGAT-AAGCAATAA
1 AAAAGATAAAGCAATAA
79313 TGGTGTTTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
40 24 0.50
41 24 0.50
ACGTcount: A:0.54, C:0.15, G:0.13, T:0.18
Consensus pattern (41 bp):
AAAAGATAAAGCAATAACAACATTTATGAAAAAACACCGCT
Found at i:84763 original size:51 final size:49
Alignment explanation
Indices: 84673--84771 Score: 117
Period size: 51 Copynumber: 2.0 Consensus size: 49
84663 CTTTCAACCA
* *** *
84673 GTCATTCACCAACTATTTCCCCAAATTTGTCAAGTCTTGTGTCACCTACTG
1 GTCACTCACCAACTATTTCCCCAAATTACCCAAGCCTTGTG--ACCTACTG
* *
84724 GTCACTCACCAACTGTTTCCTCAAATTACCCAAGCCTTGTGACCTACT
1 GTCACTCACCAACTATTTCCCCAAATTACCCAAGCCTTGTGACCTACT
84772 ATCTCATTGC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 7 0.17
51 34 0.83
ACGTcount: A:0.24, C:0.32, G:0.11, T:0.32
Consensus pattern (49 bp):
GTCACTCACCAACTATTTCCCCAAATTACCCAAGCCTTGTGACCTACTG
Found at i:87072 original size:16 final size:16
Alignment explanation
Indices: 87051--87086 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
87041 CTATTTTCAA
87051 TTTCTTTTAATTCTGT
1 TTTCTTTTAATTCTGT
* *
87067 TTTCTTTTATTTTTGT
1 TTTCTTTTAATTCTGT
87083 TTTC
1 TTTC
87087 CCCAGATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.08, C:0.11, G:0.06, T:0.75
Consensus pattern (16 bp):
TTTCTTTTAATTCTGT
Found at i:87581 original size:45 final size:45
Alignment explanation
Indices: 87517--87612 Score: 183
Period size: 45 Copynumber: 2.1 Consensus size: 45
87507 CCAAGGAGTT
*
87517 GATCCATCGACGGGAGTGTCAATCACTAGGGTTGACGAAAATCGA
1 GATCCATCGACGAGAGTGTCAATCACTAGGGTTGACGAAAATCGA
87562 GATCCATCGACGAGAGTGTCAATCACTAGGGTTGACGAAAATCGA
1 GATCCATCGACGAGAGTGTCAATCACTAGGGTTGACGAAAATCGA
87607 GATCCA
1 GATCCA
87613 CCACTACCTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.20
Consensus pattern (45 bp):
GATCCATCGACGAGAGTGTCAATCACTAGGGTTGACGAAAATCGA
Found at i:88684 original size:21 final size:21
Alignment explanation
Indices: 88660--88721 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
88650 ATCAATCTAT
88660 AGATTTTCAAAAGCAAACTGC
1 AGATTTTCAAAAGCAAACTGC
* *
88681 AGATTTTCAATAGCAAACTGT
1 AGATTTTCAAAAGCAAACTGC
*
88702 AGATTTTCAAAAGAAAACTG
1 AGATTTTCAAAAGCAAACTG
88722 AGGCATCTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (21 bp):
AGATTTTCAAAAGCAAACTGC
Found at i:92784 original size:27 final size:26
Alignment explanation
Indices: 92748--92805 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
92738 CAATATTTTT
* * *
92748 TTTATTTTTATTTTTTAGTTTTATTTA
1 TTTATATTTATTTATT-GATTTATTTA
*
92775 TTTATATTTATTTATTGATTTGTTTA
1 TTTATATTTATTTATTGATTTATTTA
92801 TTTAT
1 TTTAT
92806 TATATGTCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (26 bp):
TTTATATTTATTTATTGATTTATTTA
Found at i:92788 original size:14 final size:13
Alignment explanation
Indices: 92748--92806 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 13
92738 CAATATTTTT
92748 TTTATTTTTATTT-
1 TTTA-TTTTATTTA
92761 TTTAGTTTTATTTA
1 TTTA-TTTTATTTA
92775 TTTATATTTATTTA
1 TTTAT-TTTATTTA
* *
92789 TTGA-TTTGTTTA
1 TTTATTTTATTTA
92801 TTTATT
1 TTTATT
92807 ATATGTCCAG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 10 0.26
13 14 0.36
14 15 0.38
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:95182 original size:16 final size:16
Alignment explanation
Indices: 95161--95195 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
95151 CTATTTTCTA
95161 TTTCTTTTAATTCTGT
1 TTTCTTTTAATTCTGT
* *
95177 TTTCTTTTATTTTTGT
1 TTTCTTTTAATTCTGT
95193 TTT
1 TTT
95196 TCCCCAGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTCTTTTAATTCTGT
Found at i:96679 original size:19 final size:18
Alignment explanation
Indices: 96649--96688 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
96639 AACTAAATTA
96649 ACAAAAAGAAATGCAATG
1 ACAAAAAGAAATGCAATG
*
96667 ACAAAATAGAAATGTAATG
1 ACAAAA-AGAAATGCAATG
96686 ACA
1 ACA
96689 GTAAAATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.60, C:0.10, G:0.15, T:0.15
Consensus pattern (18 bp):
ACAAAAAGAAATGCAATG
Found at i:98975 original size:15 final size:14
Alignment explanation
Indices: 98952--98989 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
98942 GCAAAGAAAT
98952 TAAAATGAAACAAA
1 TAAAATGAAACAAA
*
98966 TAAAATTGAAATAAA
1 TAAAA-TGAAACAAA
98981 TAAAA-GAAA
1 TAAAATGAAA
98990 ATGTGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 5 0.23
15 13 0.59
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (14 bp):
TAAAATGAAACAAA
Found at i:114147 original size:24 final size:23
Alignment explanation
Indices: 114114--114176 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
114104 TTGTTAACAT
*
114114 TGTTCGTGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCAATTA-A
*
114138 TGTTCATGAACATGTTCGATTAA
1 TGTTCATGAACATGTTCAATTAA
*
114161 -GTTAAATGAACATGTT
1 TGTT-CATGAACATGTT
114177 TGTAAACATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
22 3 0.09
23 12 0.34
24 20 0.57
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (23 bp):
TGTTCATGAACATGTTCAATTAA
Found at i:115353 original size:57 final size:58
Alignment explanation
Indices: 115285--115404 Score: 172
Period size: 58 Copynumber: 2.1 Consensus size: 58
115275 AAAAGAGTTA
*
115285 TTTATGAGTGTTATTT-AGGAAT-AAATTATATTTGAGTTTAAAAATATTTAAGTTTAG
1 TTTATGAGTGTT-TTTGAAGAATAAAATTATATTTGAGTTTAAAAATATTTAAGTTTAG
* * **
115342 TTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTACAAATATTTGGGTTTAG
1 TTTATGAGTGTTTTTGAAGAATAAAATTATATTTGAGTTTAAAAATATTTAAGTTTAG
115400 TTTAT
1 TTTAT
115405 TGATGGGTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
56 3 0.05
57 17 0.30
58 36 0.64
ACGTcount: A:0.33, C:0.01, G:0.17, T:0.48
Consensus pattern (58 bp):
TTTATGAGTGTTTTTGAAGAATAAAATTATATTTGAGTTTAAAAATATTTAAGTTTAG
Found at i:116453 original size:26 final size:26
Alignment explanation
Indices: 116432--116481 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
116422 TTAAATTTTT
* *
116432 TTCGAATCGAGTCGAGTGAAATAAAA
1 TTCGAATCGAATCGAGTGAAATTAAA
*
116458 TTCGAGTCGAATCGAGTGAAATTA
1 TTCGAATCGAATCGAGTGAAATTA
116482 TTCGAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (26 bp):
TTCGAATCGAATCGAGTGAAATTAAA
Found at i:116790 original size:19 final size:18
Alignment explanation
Indices: 116738--116790 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
116728 TTAAAAATAT
* *
116738 AATATTTGAATTTTTTATA
1 AATATTTTAA-TTTTTAAA
*
116757 AATATTTTAAATTTTAAA
1 AATATTTTAATTTTTAAA
*
116775 AATTATTTTTATTTTT
1 AA-TATTTTAATTTTT
116791 TTTAATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
AATATTTTAATTTTTAAA
Found at i:121030 original size:59 final size:59
Alignment explanation
Indices: 120946--121080 Score: 198
Period size: 59 Copynumber: 2.3 Consensus size: 59
120936 ACATTTTATG
* * * * * *
120946 AAAGTGCAAGCACCATAATAAAGCATATTAATAGTTTAGGTATCACATTGGGTATTTTC
1 AAAGTACAAGTACCACAATAAAGCATATTAATAATTCAGGTATCACATTGAGTATTTTC
121005 AAAGTACAAGTACCACAATAAAGCATATTAATAATTCAGGTATCACATTGAGTATTTTC
1 AAAGTACAAGTACCACAATAAAGCATATTAATAATTCAGGTATCACATTGAGTATTTTC
* *
121064 AAAATATAAGTACCACA
1 AAAGTACAAGTACCACA
121081 TTGGACATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 68 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (59 bp):
AAAGTACAAGTACCACAATAAAGCATATTAATAATTCAGGTATCACATTGAGTATTTTC
Done.