Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014808.1 Kokia drynarioides strain JFW-HI SEQ_129850, 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: 421509
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 247 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:269453 original size:43 final size:43
Alignment explanation
Indices: 269372--269453 Score: 96
Period size: 43 Copynumber: 1.9 Consensus size: 43
269362 TTAGATAATG
* * * *
269372 TTATTAACAATAAAATATATCAAAATTATATATTAAATAAATA
1 TTATTAAAAATAAAATATATAAAAATTATAAATAAAATAAATA
269415 TTATTAAAAATAAAA-ATATGAAAAATTA-ACAATAAAATA
1 TTATTAAAAATAAAATATAT-AAAAATTATA-AATAAAATA
269454 TTTATAACGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
42 5 0.15
43 28 0.85
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (43 bp):
TTATTAAAAATAAAATATATAAAAATTATAAATAAAATAAATA
Found at i:274653 original size:6 final size:6
Alignment explanation
Indices: 274613--274652 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
274603 CAAATCAAGA
* *
274613 GCCAAT GCCAAT GCCAAT GCCAAT GCCATT GCCATT GCCA
1 GCCAAT GCCAAT GCCAAT GCCAAT GCCAAT GCCAAT GCCA
274653 TCGCCATCGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.28, C:0.35, G:0.17, T:0.20
Consensus pattern (6 bp):
GCCAAT
Found at i:279283 original size:41 final size:41
Alignment explanation
Indices: 279238--279331 Score: 152
Period size: 41 Copynumber: 2.3 Consensus size: 41
279228 TTATTTTATT
* * *
279238 TTAACAAGAATTCTAGTCATTCAATTCTAACAATCTTCACC
1 TTAACAAGAATTCTAGTCACTCAATTCTAACAATCTCCACA
279279 TTAACAAGAATTCTAGTCACTCAATTCTAACAATCTCCACA
1 TTAACAAGAATTCTAGTCACTCAATTCTAACAATCTCCACA
*
279320 TTGACAAGAATT
1 TTAACAAGAATT
279332 TTCTATGAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.32
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACTCAATTCTAACAATCTCCACA
Found at i:279730 original size:25 final size:25
Alignment explanation
Indices: 279696--279747 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
279686 AGCTTCTTTA
279696 CAAGCCTCGGTAATCGTCATGTACT
1 CAAGCCTCGGTAATCGTCATGTACT
279721 CAAGCCTCGGTAATCGTCATGTACT
1 CAAGCCTCGGTAATCGTCATGTACT
279746 CA
1 CA
279748 GCTTCAGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (25 bp):
CAAGCCTCGGTAATCGTCATGTACT
Found at i:293178 original size:25 final size:25
Alignment explanation
Indices: 293150--293198 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
293140 AAGATTACCC
* *
293150 AATAAGATA-ATTACATGTGAAAAAT
1 AATAAAATACATTAAAT-TGAAAAAT
293175 AATAAAATACATTAAATTGAAAAA
1 AATAAAATACATTAAATTGAAAAA
293199 ATAACTCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.61, C:0.04, G:0.08, T:0.27
Consensus pattern (25 bp):
AATAAAATACATTAAATTGAAAAAT
Found at i:294703 original size:11 final size:11
Alignment explanation
Indices: 294687--294801 Score: 55
Period size: 11 Copynumber: 10.4 Consensus size: 11
294677 CTTAATCACT
294687 TTAATATTAAA
1 TTAATATTAAA
294698 TTAATA-T-AA
1 TTAATATTAAA
*
294707 -TAATTATCAAGA
1 TTAA-TATTAA-A
*
294719 TAAATATTAAA
1 TTAATATTAAA
294730 TTAA-ATTTAATA
1 TTAATA-TTAA-A
* *
294742 TTAGAATAATCACA
1 TT--AAT-ATTAAA
294756 TTAATATTAAA
1 TTAATATTAAA
294767 TTAATA--AAA
1 TTAATATTAAA
*
294776 -TACTATTAAA
1 TTAATATTAAA
*
294786 ATAATTATTAAA
1 TTAA-TATTAAA
294798 TTAA
1 TTAA
294802 ATTTTTATAA
Statistics
Matches: 78, Mismatches: 11, Indels: 29
0.66 0.09 0.25
Matches are distributed among these distances:
8 7 0.09
9 7 0.09
10 5 0.06
11 27 0.35
12 22 0.28
13 2 0.03
14 5 0.06
15 2 0.03
16 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:303054 original size:59 final size:58
Alignment explanation
Indices: 302987--303515 Score: 301
Period size: 59 Copynumber: 9.1 Consensus size: 58
302977 TTGGGTATTA
* * *
302987 GCCATGCAATGACCGACACCCTTTTTAATCTGATAAAAAAATCAAAATTTTGGGTGTTG
1 GCCATGCAATGACCGACACCCTTTTT-ATCAGATAAAAAAATCAAATTTTTTGGTGTTG
* * *
303046 GCCATGCAATGGCCGACACTCCTTTTTTGTCAGAT-AAAAAAT-ACAATTTTTTTGTGTTG
1 GCCATGCAATGACCGACAC-CC-TTTTTATCAGATAAAAAAATCA-AATTTTTTGGTGTTG
* * * * **
303105 GCCATACAATGGCCGACACCCCTATTTATCTGATAAAAAAATCAAA-TTTTT-G-CATG
1 GCCATGCAATGACCGACA-CCCTTTTTATCAGATAAAAAAATCAAATTTTTTGGTGTTG
* * **
303161 G---T-C---GA-C-ACCCCTTTTTTTATCAGAT-AAAAAATTTAATTTTTTGGTGTTG
1 GCCATGCAATGACCGACACC-CTTTTTATCAGATAAAAAAATCAAATTTTTTGGTGTTG
* * *
303210 GTCATACAATGACCGACACCCCTATTTT-TCTGATAAAAAAAAATCAAATTTTTTGGTGTTG
1 GCCATGCAATGACCGACA-CCCT-TTTTATCAGAT--AAAAAAATCAAATTTTTTGGTGTTG
* ** * ** *
303271 GTCATTGC-ATGGTCAACATCTCCTTTTTTATCAGAT-AAAAAAT-TTATTTTTTAGTGTTG
1 GCCA-TGCAATGACCGACA-C-CC-TTTTTATCAGATAAAAAAATCAAATTTTTTGGTGTTG
* *
303330 GCCATGCAAT-ATCCGACACTTCTATTTATCTA-ATAAAAAAATCAAA-TTTTTGAGTGTTG
1 GCCATGCAATGA-CCGACAC-CCTTTTTATC-AGATAAAAAAATCAAATTTTTTG-GTGTTG
* * * * * * *
303389 GTCATGCAATGGCCGACATCCTTTTTCTCAGATAAAAAAATTTCAATTTTTTTTAGTGTTA
1 GCCATGCAATGACCGACACCCTTTTTATCAGATAAAAAAA--TCAA-ATTTTTTGGTGTTG
* *** * ** *
303450 GTCATGCAATGGTTGACACCCCTATTTATTTGATAAAAAAATTTCAAATTTTTTGGTGTCG
1 GCCATGCAATGACCGACA-CCCTTTTTATCAGATAAAAAAA--TCAAATTTTTTGGTGTTG
303511 GCCAT
1 GCCAT
303516 TGTATGGCCA
Statistics
Matches: 364, Mismatches: 65, Indels: 80
0.72 0.13 0.16
Matches are distributed among these distances:
46 11 0.03
47 17 0.05
48 2 0.01
49 4 0.01
52 2 0.01
53 2 0.01
56 5 0.01
57 12 0.03
58 58 0.16
59 115 0.32
60 20 0.05
61 74 0.20
62 36 0.10
63 6 0.02
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (58 bp):
GCCATGCAATGACCGACACCCTTTTTATCAGATAAAAAAATCAAATTTTTTGGTGTTG
Found at i:303187 original size:105 final size:105
Alignment explanation
Indices: 303054--303262 Score: 312
Period size: 105 Copynumber: 2.0 Consensus size: 105
303044 TGGCCATGCA
* * * *
303054 ATGGCCGACACTCCTTTTTTGTCAGATAAAAAATACAATTTTTTTGTGTTGGCCATACAATGGCC
1 ATGGCCGACACCCCTTTTTTATCAGATAAAAAATACAATTTTTTGGTGTTGGCCATACAATGACC
303119 GACACCCCTATTTATCTGAT-AAAAAAATCAAATTTTTGC
66 GACACCCCTATTTATCTGATAAAAAAAATCAAATTTTTGC
* ** *
303158 ATGGTCGACACCCCTTTTTTTATCAGATAAAAAATTTAATTTTTTGGTGTTGGTCATACAATGAC
1 ATGGCCGACACCCC-TTTTTTATCAGATAAAAAATACAATTTTTTGGTGTTGGCCATACAATGAC
*
303223 CGACACCCCTATTTTTCTGATAAAAAAAAATCAAATTTTT
65 CGACACCCCTATTTATCTGAT-AAAAAAAATCAAATTTTT
303263 TGGTGTTGGT
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
104 12 0.13
105 64 0.69
107 17 0.18
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (105 bp):
ATGGCCGACACCCCTTTTTTATCAGATAAAAAATACAATTTTTTGGTGTTGGCCATACAATGACC
GACACCCCTATTTATCTGATAAAAAAAATCAAATTTTTGC
Found at i:303268 original size:61 final size:61
Alignment explanation
Indices: 303186--303508 Score: 245
Period size: 61 Copynumber: 5.4 Consensus size: 61
303176 TTTATCAGAT
** * * *
303186 AAAAAATTTAATTTTTTGGTGTTGGTCATACAATGACCGACACCCCTATTTTTCTGATAAA
1 AAAAAATCAAATTTTTTGGTGTTGGTCATGCAATGGCCGACACTCCTATTTTTCTGATAAA
* * * *
303247 AAAAAATCAAATTTTTTGGTGTTGGTCATTGC-ATGGTCAACATCTCCTTTTTTATCAGAT---
1 AAAAAATCAAATTTTTTGGTGTTGGTCA-TGCAATGGCCGACA-CTCCTATTTT-TCTGATAAA
** * * ** * * *
303307 AAAAAAT-TTATTTTTTAGTGTTGGCCATGCAATATCCGACACTTCTATTTATCT-A-ATA
1 AAAAAATCAAATTTTTTGGTGTTGGTCATGCAATGGCCGACACTCCTATTTTTCTGATAAA
*
303365 AAAAAATCAAA-TTTTTGAGTGTTGGTCATGCAATGGCCGACA-TCCT-TTTTCTCAGATAAA
1 AAAAAATCAAATTTTTTG-GTGTTGGTCATGCAATGGCCGACACTCCTATTTT-TCTGATAAA
** * * * ** *
303425 AAAATTTCAATTTTTTTTAGTGTTAGTCATGCAATGGTTGACACCCCTATTTATT-TGATAAA
1 AAAAAATCAA-ATTTTTTGGTGTTGGTCATGCAATGGCCGACACTCCTATTT-TTCTGATAAA
**
303487 AAAATTTCAAATTTTTTGGTGT
1 AAAAAATCAAATTTTTTGGTGT
303509 CGGCCATTGT
Statistics
Matches: 203, Mismatches: 42, Indels: 34
0.73 0.15 0.12
Matches are distributed among these distances:
56 1 0.00
57 5 0.02
58 27 0.13
59 45 0.22
60 17 0.08
61 64 0.32
62 34 0.17
63 9 0.04
64 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.40
Consensus pattern (61 bp):
AAAAAATCAAATTTTTTGGTGTTGGTCATGCAATGGCCGACACTCCTATTTTTCTGATAAA
Found at i:303368 original size:120 final size:121
Alignment explanation
Indices: 303154--303529 Score: 412
Period size: 120 Copynumber: 3.1 Consensus size: 121
303144 AATCAAATTT
* * * * *
303154 TTGCATGGTCGACACCCCTTTTTTTATCAGATAAAAAATTTAATTTTTTGGTGTTGGTCATACAA
1 TTGCATGGCCAACACTCC-TTTTTTATCAGATAAAAAATTTAATTTTTTAGTGTTGGTCATGCAA
*
303219 TGA-CCGACACCCCTATTTTTCTGATAAAAAAAAATCAAATTTTTTGGTGTTGGTCA
65 TGATCCGACACCCCTATTTATCTGATAAAAAAAAATCAAATTTTTTGGTGTTGGTCA
* *
303275 TTGCATGGTCAACATCTCCTTTTTTATCAGATAAAAAATTT-ATTTTTTAGTGTTGGCCATGCAA
1 TTGCATGGCCAACA-CTCCTTTTTTATCAGATAAAAAATTTAATTTTTTAGTGTTGGTCATGCAA
** *
303339 T-ATCCGACACTTCTATTTATCT-A-ATAAAAAAATCAAA-TTTTTGAGTGTTGGTCA
65 TGATCCGACACCCCTATTTATCTGATAAAAAAAAATCAAATTTTTTG-GTGTTGGTCA
* * *
303393 -TGCAATGGCCGACA-TCC-TTTTTCTCAGATAAAAAAATTTCAATTTTTTTTAGTGTTAGTCAT
1 TTGC-ATGGCCAACACTCCTTTTTTATCAGAT-AAAAAATTT-AA--TTTTTTAGTGTTGGTCAT
* * * ** * *
303455 GCAATGGT-TGACACCCCTATTTATTTGATAAAAAAATTTCAAATTTTTTGGTGTCGGCCA
61 GCAATGATCCGACACCCCTATTTATCTGATAAAAAAAAATCAAATTTTTTGGTGTTGGTCA
*
303515 TTGTATGGCCAACAC
1 TTGCATGGCCAACAC
303530 AAAAAAATTA
Statistics
Matches: 214, Mismatches: 26, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
115 11 0.05
116 12 0.06
117 9 0.04
118 32 0.15
119 2 0.01
120 72 0.34
121 37 0.17
122 31 0.14
123 8 0.04
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (121 bp):
TTGCATGGCCAACACTCCTTTTTTATCAGATAAAAAATTTAATTTTTTAGTGTTGGTCATGCAAT
GATCCGACACCCCTATTTATCTGATAAAAAAAAATCAAATTTTTTGGTGTTGGTCA
Found at i:317463 original size:17 final size:17
Alignment explanation
Indices: 317441--317473 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
317431 ATATTGCCGC
*
317441 ATATTTCATTTTTTTTA
1 ATATTTAATTTTTTTTA
317458 ATATTTAATTTTTTTT
1 ATATTTAATTTTTTTT
317474 TTTTACTATA
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:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
ATATTTAATTTTTTTTA
Found at i:319596 original size:19 final size:20
Alignment explanation
Indices: 319574--319618 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
319564 TTTTATTAGG
319574 ATTTAAT-ATTTAAGATAT-T
1 ATTTAATCATTTAA-ATATGT
*
319593 ATTT-ATCATTTAAATTTGT
1 ATTTAATCATTTAAATATGT
319612 ATTTAAT
1 ATTTAAT
319619 TCATGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 5 0.23
19 15 0.68
20 2 0.09
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
ATTTAATCATTTAAATATGT
Found at i:329420 original size:4 final size:4
Alignment explanation
Indices: 329413--329439 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
329403 TACATACATA
329413 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
329440 TGGTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:333800 original size:120 final size:119
Alignment explanation
Indices: 333583--333820 Score: 325
Period size: 120 Copynumber: 2.0 Consensus size: 119
333573 TGTCAACAAT
* *
333583 GGCCTTTACAAAACTAAATACACTTCGTTTAACCTAGCATTAGGGTTCCTAAGTTTCTATATTTC
1 GGCCTTTACAAAACTAAATACACTTCGTTTAACCTAGCATGAGGGTTCCTAAGTTTCTACATTTC
* * * *
333648 AGCAGCTAACTCTCCCACCCCCTCCCGAAAATTTATCTACATGGTATCTTTGAC
66 AGCAGCTAACTCTACCACCCCCTCCCGAAAATTTAGCAACATGGTAACTTTGAC
* * * *
333702 GGCCTTTTCAAAACTAAATACACTTTCGTTTAACCTAGTATGAGGGTTCCTACGTTTCTGCATTT
1 GGCCTTTACAAAACTAAATACAC-TTCGTTTAACCTAGCATGAGGGTTCCTAAGTTTCTACATTT
* * * *
333767 TAGCAGCTTACTCTACCACCCTCTCTCTG-AAATTTAGCAACATGGTAACTTTGA
65 CAGCAGCTAACTCTACCACCCCCTC-CCGAAAATTTAGCAACATGGTAACTTTGA
333821 TGGAAGGTTA
Statistics
Matches: 103, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
119 22 0.21
120 79 0.77
121 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (119 bp):
GGCCTTTACAAAACTAAATACACTTCGTTTAACCTAGCATGAGGGTTCCTAAGTTTCTACATTTC
AGCAGCTAACTCTACCACCCCCTCCCGAAAATTTAGCAACATGGTAACTTTGAC
Found at i:338791 original size:19 final size:20
Alignment explanation
Indices: 338767--338804 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
338757 TTACAAAAAG
338767 AAAAA-TCAAAATAATTTTA
1 AAAAATTCAAAATAATTTTA
338786 AAAAATTCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
338805 TTATATTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTA
Found at i:346032 original size:11 final size:11
Alignment explanation
Indices: 346016--346044 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
346006 GTTTAGATAT
346016 TAAAATCCACC
1 TAAAATCCACC
346027 TAAAATCCACC
1 TAAAATCCACC
346038 TAAAATC
1 TAAAATC
346045 TACTGTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (11 bp):
TAAAATCCACC
Found at i:356625 original size:13 final size:14
Alignment explanation
Indices: 356607--356636 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
356597 GCCAATGCAA
356607 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
356620 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
356634 TCA
1 TCA
356637 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:358887 original size:40 final size:40
Alignment explanation
Indices: 358806--358948 Score: 153
Period size: 40 Copynumber: 3.5 Consensus size: 40
358796 TTTGGACAGA
* * * * * * **
358806 AAACGCTGCAAAAAGTAAATCAATAGCGGCATTTTTTCAT
1 AAACGCCGCAAAAGGTAAAGCAACAGCGACGTTTTCCCAT
*
358846 AAATGCCGCAAAAGGTAAAGCAACAGC-AGCGTTTTCCCAT
1 AAACGCCGCAAAAGGTAAAGCAACAGCGA-CGTTTTCCCAT
* * *
358886 AAACACTGCAAAAGGTAAAGCAATAGCGACGTTTTCCCAT
1 AAACGCCGCAAAAGGTAAAGCAACAGCGACGTTTTCCCAT
358926 AAACGCCGCAAAAGGTAAGAGCA
1 AAACGCCGCAAAAGGTAA-AGCA
358949 TTAGCGGTGT
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
40 80 0.94
41 5 0.06
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (40 bp):
AAACGCCGCAAAAGGTAAAGCAACAGCGACGTTTTCCCAT
Found at i:358980 original size:41 final size:41
Alignment explanation
Indices: 358926--359178 Score: 240
Period size: 41 Copynumber: 6.1 Consensus size: 41
358916 GTTTTCCCAT
* * *
358926 AAACGCCGCAAAAGGTAAGAGCATTAGCGGTGTTTATGAGA
1 AAACGCTGTAAAAGGTAAGAGCATTAGCGGCGTTTATGAGA
* * * * *
358967 AAAC-ATAATAAAAGGTCATAGCATTAACGGCGTTTATGAGA
1 AAACGCT-GTAAAAGGTAAGAGCATTAGCGGCGTTTATGAGA
* * * *
359008 AAACGCT-TCAAAAGGTCAGAGCATTAGCGACATTTGTGAGA
1 AAACGCTGT-AAAAGGTAAGAGCATTAGCGGCGTTTATGAGA
* * * **
359049 AAATGCCGCAAAAGGTAAGAGCATTAGTAGCGTTTATGAGA
1 AAACGCTGTAAAAGGTAAGAGCATTAGCGGCGTTTATGAGA
* ** * *
359090 AAACGCTGTAAAAGGTCAGAGCATTAGTAGTGTTTGTGAGA
1 AAACGCTGTAAAAGGTAAGAGCATTAGCGGCGTTTATGAGA
* * *
359131 AAACGCTGCAAAAGGTAAGAGCATTAGCGACGTTTATGGGA
1 AAACGCTGTAAAAGGTAAGAGCATTAGCGGCGTTTATGAGA
359172 AGAACGC
1 A-AACGC
359179 CGCTAAAGGT
Statistics
Matches: 170, Mismatches: 37, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
40 1 0.01
41 163 0.96
42 6 0.04
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (41 bp):
AAACGCTGTAAAAGGTAAGAGCATTAGCGGCGTTTATGAGA
Found at i:359194 original size:123 final size:122
Alignment explanation
Indices: 358886--359188 Score: 349
Period size: 123 Copynumber: 2.5 Consensus size: 122
358876 GTTTTCCCAT
* * ***
358886 AAACACTGCAAAAGGTAA-AGCAATAGCGACGTTTTCCCATAAACGCCGCAAAAGGTAAGAGCAT
1 AAACGCTGCAAAAGGTAAGAGCATTAGCGACGTTTTGAGA-AAACGCCGCAAAAGGTAAGAGCAT
* * * *
358950 TAGCGGTGTTTATGAGAAAACATAATAAAAGGTCATAGCATTAACGGCGTTTATGAGA
65 TAGCAGCGTTTATGAGAAAACATAATAAAAGGTCAGAGCATTAACAGCGTTTATGAGA
* * * *
359008 AAACGCTTCAAAAGGTCAGAGCATTAGCGACATTTGTGAGAAAATGCCGCAAAAGGTAAGAGCAT
1 AAACGCTGCAAAAGGTAAGAGCATTAGCGACGTTT-TGAGAAAACGCCGCAAAAGGTAAGAGCAT
* * * ** * *
359073 TAGTAGCGTTTATGAGAAAACGCT-GTAAAAGGTCAGAGCATTAGTAGTGTTTGTGAGA
65 TAGCAGCGTTTATGAGAAAAC-ATAATAAAAGGTCAGAGCATTAACAGCGTTTATGAGA
* *
359131 AAACGCTGCAAAAGGTAAGAGCATTAGCGACGTTTATGGGAAGAACGCCGCTAAAGGT
1 AAACGCTGCAAAAGGTAAGAGCATTAGCGACGTTT-TGAGAA-AACGCCGCAAAAGGT
359189 TGAGCAATAG
Statistics
Matches: 150, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
122 15 0.10
123 119 0.79
124 16 0.11
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.21
Consensus pattern (122 bp):
AAACGCTGCAAAAGGTAAGAGCATTAGCGACGTTTTGAGAAAACGCCGCAAAAGGTAAGAGCATT
AGCAGCGTTTATGAGAAAACATAATAAAAGGTCAGAGCATTAACAGCGTTTATGAGA
Found at i:360610 original size:41 final size:41
Alignment explanation
Indices: 360568--360753 Score: 171
Period size: 41 Copynumber: 4.5 Consensus size: 41
360558 GGTTAAGCAA
*
360568 TAACGACGTTTATGAGAAAAACACCGCAAAAGGTAA-AACAA
1 TAACGACGTTTATG-GAAAAACACCGCAAAAGGTAAGAACAT
* ** *
360609 TAACGGCGTTTATGGAAAGAACGTCGCAAAAGGTAAGAGCAT
1 TAACGACGTTTATGGAAA-AACACCGCAAAAGGTAAGAACAT
* ** *
360651 TAACG-CGTTTATGGGAAAACGTCGCAAAAAGTAA-AAGCAT
1 TAACGACGTTTATGGAAAAACACCGCAAAAGGTAAGAA-CAT
* * * * * *
360691 TAACAACGTTTATGGGACAACACCGTAAAAGATAAGAGCAT
1 TAACGACGTTTATGGAAAAACACCGCAAAAGGTAAGAACAT
**
360732 TAACGACGTTTAAAGAAAAACA
1 TAACGACGTTTATGGAAAAACA
360754 TCGTTAAAGG
Statistics
Matches: 119, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
39 1 0.01
40 27 0.23
41 82 0.69
42 9 0.08
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (41 bp):
TAACGACGTTTATGGAAAAACACCGCAAAAGGTAAGAACAT
Found at i:360742 original size:82 final size:83
Alignment explanation
Indices: 360563--360753 Score: 210
Period size: 81 Copynumber: 2.3 Consensus size: 83
360553 TTAGAGGTTA
* * ** *
360563 AGCAATAACGACGTTTATGAGAAAAACACCGCAAAAGGTAAAACAATAACGGCGTTTATGGAAAG
1 AGCATTAACGACGTTTATGAGAAAAACACCGCAAAAAGTAAAACAATAACAACGTTTATGGAAAC
** *
360628 AACGTCGCAAAAGGTAAG
66 AACACCGCAAAAGATAAG
* ** * *
360646 AGCATTAACG-CGTTTATG-GGAAAACGTCGCAAAAAGTAAAAGCATTAACAACGTTTATGG-GA
1 AGCATTAACGACGTTTATGAGAAAAACACCGCAAAAAGTAAAA-CAATAACAACGTTTATGGAAA
*
360708 CAACACCGTAAAAGATAAG
65 CAACACCGCAAAAGATAAG
*
360727 AGCATTAACGACGTTTA-AAGAAAAACA
1 AGCATTAACGACGTTTATGAGAAAAACA
360754 TCGTTAAAGG
Statistics
Matches: 88, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
81 44 0.50
82 35 0.40
83 9 0.10
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.18
Consensus pattern (83 bp):
AGCATTAACGACGTTTATGAGAAAAACACCGCAAAAAGTAAAACAATAACAACGTTTATGGAAAC
AACACCGCAAAAGATAAG
Found at i:362734 original size:2 final size:2
Alignment explanation
Indices: 362727--362755 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
362717 TATTCTACAT
362727 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
362756 TATATACATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:363854 original size:43 final size:43
Alignment explanation
Indices: 363773--363879 Score: 117
Period size: 43 Copynumber: 2.5 Consensus size: 43
363763 TTTGGATTTG
***
363773 ACATGATCTTTAGCGGTGTTTGTGGAAAAAGTGTCGTTAAAGA
1 ACATGATCTTTAGCGGTGTTTGTGGAAAAAGCACCGTTAAAGA
* * * *
363816 ACATGGTCTTTAGTGGTGTTTGTGGGAAAAGCACCGTTAAATA
1 ACATGATCTTTAGCGGTGTTTGTGGAAAAAGCACCGTTAAAGA
* *
363859 TCATG-TTTTATAGCGGTGTTT
1 ACATGATCTT-TAGCGGTGTTT
363880 TTTCACATAA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 3 0.06
43 50 0.94
ACGTcount: A:0.26, C:0.10, G:0.27, T:0.36
Consensus pattern (43 bp):
ACATGATCTTTAGCGGTGTTTGTGGAAAAAGCACCGTTAAAGA
Found at i:364648 original size:27 final size:27
Alignment explanation
Indices: 364617--364672 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
364607 ACATCAATTA
364617 AGCTTCCGGCAAACAAAAATGTTTTAT
1 AGCTTCCGGCAAACAAAAATGTTTTAT
364644 AGCTTCCGGCAAACAAAAATGTTTTAT
1 AGCTTCCGGCAAACAAAAATGTTTTAT
364671 AG
1 AG
364673 TAATAAGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (27 bp):
AGCTTCCGGCAAACAAAAATGTTTTAT
Found at i:370959 original size:48 final size:50
Alignment explanation
Indices: 370895--370991 Score: 180
Period size: 48 Copynumber: 2.0 Consensus size: 50
370885 ATTATTCCAG
370895 TTTTTTTGTGTGTGTATATAAATAAACTAAATTATAATAAAGTCATAATC
1 TTTTTTTGTGTGTGTATATAAATAAACTAAATTATAATAAAGTCATAATC
370945 TTTTTTT-T-TGTGTATATAAATAAACTAAATTATAATAAAGTCATAAT
1 TTTTTTTGTGTGTGTATATAAATAAACTAAATTATAATAAAGTCATAAT
370992 AAAATATGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 39 0.83
49 1 0.02
50 7 0.15
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.45
Consensus pattern (50 bp):
TTTTTTTGTGTGTGTATATAAATAAACTAAATTATAATAAAGTCATAATC
Found at i:371528 original size:75 final size:75
Alignment explanation
Indices: 371392--371538 Score: 213
Period size: 75 Copynumber: 2.0 Consensus size: 75
371382 GAAAATCGGA
** * * * *
371392 ATTATTCTTTTATTATTAGAGAAGGCAAATGGAAAGTTAGAAAAATGAATTATATTTTTTCCAAA
1 ATTATTCACTTATTAATAGAGAAGGCAAATGGAAAGTTAGAAAAATGAATCATACTCTTTCCAAA
*
371457 AGAATATATG
66 AAAATATATG
* *
371467 ATTATTCACTTATTAATAGATAAGGCAAATGGAAAGTTAGAAAAATGAATCATGCTCTTTCCAAA
1 ATTATTCACTTATTAATAGAGAAGGCAAATGGAAAGTTAGAAAAATGAATCATACTCTTTCCAAA
371532 AAAATAT
66 AAAATAT
371539 TAATTTCCAT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 63 1.00
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (75 bp):
ATTATTCACTTATTAATAGAGAAGGCAAATGGAAAGTTAGAAAAATGAATCATACTCTTTCCAAA
AAAATATATG
Found at i:374757 original size:15 final size:15
Alignment explanation
Indices: 374737--374782 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
374727 TATCATAATT
374737 TTTTTCTTCTTTTTC
1 TTTTTCTTCTTTTTC
374752 TTTTTCTTCCTTTTTC
1 TTTTTCTT-CTTTTTC
*
374768 TCATTT-TTCTTTTTC
1 T-TTTTCTTCTTTTTC
374783 AAGTGTCTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 15 0.54
16 10 0.36
17 3 0.11
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTCTTCTTTTTC
Found at i:375387 original size:18 final size:20
Alignment explanation
Indices: 375364--375407 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
375354 TAACAAAATG
*
375364 AATGCAGTGAC-A-AAATAA
1 AATGCAGAGACAATAAATAA
375382 AATGCAGAGACAATAAATAA
1 AATGCAGAGACAATAAATAA
375402 AATGCA
1 AATGCA
375408 TGAAAATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.43
19 1 0.04
20 12 0.52
ACGTcount: A:0.57, C:0.11, G:0.16, T:0.16
Consensus pattern (20 bp):
AATGCAGAGACAATAAATAA
Found at i:384309 original size:138 final size:138
Alignment explanation
Indices: 384128--384544 Score: 610
Period size: 138 Copynumber: 3.0 Consensus size: 138
384118 ACATAGATAA
* * *
384128 AATTAATATATGAATTTGTTTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
1 AATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
384193 TAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAAAATATGGAAATTAATATTCTTTTGG
66 TAAACAATTATATTAATTAATTTC-GTCAAAATATAAAAAAATATGGAAATTAATATTCTTTTGG
384258 AAAGAATAT
130 AAAGAATAT
* * *
384267 AATTAA-ATATAAATTTGATTCATATAAAATATTAATTGTATATATTTTTCTGAATTTATTAATA
1 AATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
* * * *
384331 TAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGAA-ATGAAAATTAGTATTCTTTTGG
66 TAAACAATTATATTAATTAATTTCG-TCAAAATATAAAAAAATATGGAAATTAATATTCTTTTGG
*
384395 AAAGAATAA
130 AAAGAATAT
384404 AATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
1 AATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
* * * * *
384469 TAAACAATTATATTAATTAATTTTGGTTAAATTATAAAAGACATA--GAAA-TAATATTCTTTTA
66 TAAACAATTATATTAATTAA-TTTCGTCAAAATATAAAA-AAATATGGAAATTAATATTCTTTTG
*
384531 GAAAAAATAT
129 GAAAGAATAT
384541 AATT
1 AATT
384545 CATTTTTCTA
Statistics
Matches: 248, Mismatches: 25, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
137 58 0.23
138 178 0.72
139 11 0.04
140 1 0.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (138 bp):
AATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
TAAACAATTATATTAATTAATTTCGTCAAAATATAAAAAAATATGGAAATTAATATTCTTTTGGA
AAGAATAT
Found at i:390085 original size:23 final size:23
Alignment explanation
Indices: 390055--390098 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
390045 GTATGAGATA
390055 TCACACTTATTTGTTTATTGTGG
1 TCACACTTATTTGTTTATTGTGG
390078 TCACACTTATTTGTTTATTGT
1 TCACACTTATTTGTTTATTGT
390099 AGTATGCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.55
Consensus pattern (23 bp):
TCACACTTATTTGTTTATTGTGG
Found at i:390657 original size:138 final size:138
Alignment explanation
Indices: 390476--391031 Score: 850
Period size: 138 Copynumber: 4.0 Consensus size: 138
390466 ACATAGACAA
* * * *
390476 AATTAATATATGAATTTAATCCATACAAAGTATTAATTTTATATATTTTACCGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
*
390541 TAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATAGAAATTAATATTCTTTTGGA
66 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATAGAAATTAATATTCTTTTGGA
390606 AAGAATAT
131 AAGAATAT
* * *
390614 AATTAATATATGAATTTGATTCTTATAAAATATTAATTGTATATATTTTACTGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
* *
390679 TAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATAAAAATTAATATTCTTTTGGA
66 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATAGAAATTAATATTCTTTTGGA
*
390744 ATGAATAT
131 AAGAATAT
*
390752 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATACATTTTACCGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
* * * *
390817 TAAAGAGTTATTTTAATTAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
66 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATAGAAATTAATATTCTTTTGGA
390882 AAGAATAT
131 AAGAATAT
* *
390890 AATTAATATATGAATTTGATTCATACAAAATGTTAATTGTATATATATTTTACTGAA-TTATTAA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTG--TATATATTTTACCGAATTTATTAA
* *
390954 TATAAATAGTTATATGT--TTAATTTCGGTCAAAATATAAAAGATAT-GAAAATTAATATTCTTT
64 TATAAACAGTTATAT-TAATTAATTTCGGTCAAAATATAAAAGACATAG-AAATTAATATTCTTT
**
391016 TAAAAAGAATAT
127 TGGAAAGAATAT
391028 AATT
1 AATT
391032 CCTTTTTCTA
Statistics
Matches: 383, Mismatches: 31, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
137 1 0.00
138 347 0.91
139 20 0.05
140 15 0.04
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (138 bp):
AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATAGAAATTAATATTCTTTTGGA
AAGAATAT
Found at i:390781 original size:71 final size:71
Alignment explanation
Indices: 390568--390784 Score: 168
Period size: 71 Copynumber: 3.1 Consensus size: 71
390558 TAATTTCGGT
* *
390568 CAAAATATAAAAGACATAGAAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGA
1 CAAAATATAAAAGACATAAAAATTAATATTCTTTTGGAATGAATATAATTAATATATGAATTTGA
*
390633 TTCTTA
66 TTCATA
* ** * * ** * * *
390639 TAAAATATTAATTG-TATATATTTTACTGAATT-TATT--AAT--ATAAACAGTT-ATAT-T-AA
1 CAAAATA-TAAAAGACATAAAAATTAAT--ATTCTTTTGGAATGAATATA-A-TTAATATATGAA
*
390695 -TTAATTTCAGT-
61 TTTGA-TTCA-TA
390706 CAAAATATAAAAGACATAAAAATTAATATTCTTTTGGAATGAATATAATTAATATATGAATTTGA
1 CAAAATATAAAAGACATAAAAATTAATATTCTTTTGGAATGAATATAATTAATATATGAATTTGA
390771 TTCATA
66 TTCATA
390777 CAAAATAT
1 CAAAATAT
390785 TAATTGTATA
Statistics
Matches: 104, Mismatches: 24, Indels: 36
0.63 0.15 0.22
Matches are distributed among these distances:
65 3 0.03
66 10 0.10
67 19 0.18
68 11 0.11
69 10 0.10
70 10 0.10
71 28 0.27
72 10 0.10
73 3 0.03
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (71 bp):
CAAAATATAAAAGACATAAAAATTAATATTCTTTTGGAATGAATATAATTAATATATGAATTTGA
TTCATA
Found at i:391144 original size:73 final size:74
Alignment explanation
Indices: 391007--391150 Score: 227
Period size: 73 Copynumber: 2.0 Consensus size: 74
390997 ATGAAAATTA
* * *
391007 ATATTCTTTTAAAAAGAATATAATTCCTTTTTCTAACTTTCATTTGTCTTCTATATTAATAAGGG
1 ATATTCTTTTAAAAAGAATATAATTCATTTTTCTAACTTCCATTTGCCTTCTATATTAATAAGGG
391072 AATAATACT
66 AATAATACT
** *
391081 ATATTCTTTTGGAAAGAATATAATTCATTTTT-TAACTTCCATTTGCCTTCTCTATTAATAAGGG
1 ATATTCTTTTAAAAAGAATATAATTCATTTTTCTAACTTCCATTTGCCTTCTATATTAATAAGGG
391145 AATAAT
66 AATAAT
391151 CATGGTTTCT
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
73 35 0.55
74 29 0.45
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.45
Consensus pattern (74 bp):
ATATTCTTTTAAAAAGAATATAATTCATTTTTCTAACTTCCATTTGCCTTCTATATTAATAAGGG
AATAATACT
Found at i:393802 original size:57 final size:57
Alignment explanation
Indices: 393734--393884 Score: 189
Period size: 57 Copynumber: 2.6 Consensus size: 57
393724 AAAAATGGGG
* * *
393734 TTAAAATGAGTAAGACCATAGATGAAAGATGTTATGGAATCAAAAGATGAATTGACA
1 TTAAAAAGAGTAAGACCATAGATAAAAGATGCTATGGAATCAAAAGATGAATTGACA
* **
393791 TTAAAAAGAGTAAGACCATA-ACTAAAAGATACTATGGCGTCAAAAGATGAATTGACA
1 TTAAAAAGAGTAAGACCATAGA-TAAAAGATGCTATGGAATCAAAAGATGAATTGACA
* **
393848 ATAAAACTAGTAAGACCATATG-TAAAAGATGCTATGG
1 TTAAAAAGAGTAAGACCATA-GATAAAAGATGCTATGG
393885 CGCCAAAGAT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
56 1 0.01
57 80 0.99
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.23
Consensus pattern (57 bp):
TTAAAAAGAGTAAGACCATAGATAAAAGATGCTATGGAATCAAAAGATGAATTGACA
Found at i:397972 original size:25 final size:26
Alignment explanation
Indices: 397934--398185 Score: 219
Period size: 25 Copynumber: 9.7 Consensus size: 26
397924 GGACAAAGTA
* *
397934 ATTCTGATTCTGGCTCATAAGGGTAAT
1 ATTCTGATT-TGGCTCGTAAGAGTAAT
* **
397961 ATTCTG-TTTGGCTCATAAGAGCGAT
1 ATTCTGATTTGGCTCGTAAGAGTAAT
* * *
397986 ATTATGATTCTAGCTTGTAAGAGTAAT
1 ATTCTGATT-TGGCTCGTAAGAGTAAT
* * * **
398013 ATTTTG-TATGCCTCGTAAGAGGGAT
1 ATTCTGATTTGGCTCGTAAGAGTAAT
*
398038 ATTCTGATTCAGGCTCGTAAGAGTAAT
1 ATTCTGATT-TGGCTCGTAAGAGTAAT
* *
398065 ATTCT-ATTTAGCTCGTAAGAGTGAT
1 ATTCTGATTTGGCTCGTAAGAGTAAT
*
398090 ATTCTGATTTAGGCTCGTAAGAGCAAT
1 ATTCTGATTT-GGCTCGTAAGAGTAAT
*
398117 ATGT-TG-TTTGGCTCGTAAGAGTGAT
1 AT-TCTGATTTGGCTCGTAAGAGTAAT
*
398142 ATTCTGATTCTAGCTCGTAAGAGTAAT
1 ATTCTGATT-TGGCTCGTAAGAGTAAT
* *
398169 ATTCCG-TCTGGCTCGTA
1 ATTCTGATTTGGCTCGTA
398186 TGAGCGATAT
Statistics
Matches: 180, Mismatches: 35, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
24 1 0.01
25 81 0.45
26 19 0.11
27 78 0.43
28 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (26 bp):
ATTCTGATTTGGCTCGTAAGAGTAAT
Found at i:398012 original size:52 final size:53
Alignment explanation
Indices: 397934--398209 Score: 334
Period size: 52 Copynumber: 5.3 Consensus size: 53
397924 GGACAAAGTA
* * *
397934 ATTCTGATTCT-GGCTCATAAGGGTAATATTCTGTTTGGCTCATAAGAGCGAT
1 ATTCTGATTCTAGGCTCGTAAGAGTAATATTCTGTTTGGCTCGTAAGAGCGAT
* * * * * *
397986 ATTATGATTCTA-GCTTGTAAGAGTAATATTTTGTATGCCTCGTAAGAGGGAT
1 ATTCTGATTCTAGGCTCGTAAGAGTAATATTCTGTTTGGCTCGTAAGAGCGAT
* * *
398038 ATTCTGATTC-AGGCTCGTAAGAGTAATATTCTATTTAGCTCGTAAGAGTGAT
1 ATTCTGATTCTAGGCTCGTAAGAGTAATATTCTGTTTGGCTCGTAAGAGCGAT
* *
398090 ATTCTGATT-TAGGCTCGTAAGAGCAATATGT-TGTTTGGCTCGTAAGAGTGAT
1 ATTCTGATTCTAGGCTCGTAAGAGTAATAT-TCTGTTTGGCTCGTAAGAGCGAT
* * *
398142 ATTCTGATTCTA-GCTCGTAAGAGTAATATTCCGTCTGGCTCGTATGAGCGAT
1 ATTCTGATTCTAGGCTCGTAAGAGTAATATTCTGTTTGGCTCGTAAGAGCGAT
398194 ATTCT-A-TCTAGGCTCG
1 ATTCTGATTCTAGGCTCG
398210 CTTGAGTCAA
Statistics
Matches: 192, Mismatches: 25, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
50 4 0.02
51 8 0.04
52 177 0.92
53 3 0.02
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (53 bp):
ATTCTGATTCTAGGCTCGTAAGAGTAATATTCTGTTTGGCTCGTAAGAGCGAT
Found at i:400806 original size:25 final size:26
Alignment explanation
Indices: 400762--400816 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
400752 ATAAAATATG
400762 TTCTCTTTTACTCTCCTA-TTTGTTA
1 TTCTCTTTTACTCTCCTATTTTGTTA
* ** *
400787 TTCTCTTTTGCTCTTTTATTTTTTTA
1 TTCTCTTTTACTCTCCTATTTTGTTA
400813 TTCT
1 TTCT
400817 TTTACTTTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.09, C:0.20, G:0.04, T:0.67
Consensus pattern (26 bp):
TTCTCTTTTACTCTCCTATTTTGTTA
Found at i:400817 original size:16 final size:17
Alignment explanation
Indices: 400798--400831 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
400788 TCTCTTTTGC
*
400798 TCTTTTA-TTTTTTTAT
1 TCTTTTACTTTCTTTAT
400814 TCTTTTACTTTCTTTAT
1 TCTTTTACTTTCTTTAT
400831 T
1 T
400832 ATTTATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (17 bp):
TCTTTTACTTTCTTTAT
Found at i:400831 original size:17 final size:16
Alignment explanation
Indices: 400798--400840 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
400788 TCTCTTTTGC
*
400798 TCTTTTATTTTTTTAT
1 TCTTTTATTTCTTTAT
400814 TCTTTTACTTTCTTTAT
1 TCTTTTA-TTTCTTTAT
*
400831 T-ATTTATTTC
1 TCTTTTATTTC
400841 ATAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.17
16 11 0.46
17 9 0.38
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (16 bp):
TCTTTTATTTCTTTAT
Found at i:400893 original size:26 final size:26
Alignment explanation
Indices: 400864--400916 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
400854 TTTTACTTAA
400864 ATTT-GATAAAATAAAACATTAAATAT
1 ATTTCGATAAAA-AAAACATTAAATAT
** *
400890 ATTTCTTTAAAAAATACATTAAATAT
1 ATTTCGATAAAAAAAACATTAAATAT
400916 A
1 A
400917 AAATAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (26 bp):
ATTTCGATAAAAAAAACATTAAATAT
Found at i:400928 original size:18 final size:18
Alignment explanation
Indices: 400897--400932 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
400887 TATATTTCTT
400897 TAAAAAATACATTAAATA
1 TAAAAAATACATTAAATA
400915 TAAAATAATA-ATTAAATA
1 TAAAA-AATACATTAAATA
400933 AAATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAAATACATTAAATA
Found at i:403720 original size:17 final size:17
Alignment explanation
Indices: 403696--403730 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
403686 ATATTGATAT
403696 ATATATATATATATATTTA
1 ATATAT-TAT-TATATTTA
403715 ATATATTATTATATTT
1 ATATATTATTATATTT
403731 CTATACGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATATTATTATATTTA
Found at i:405921 original size:21 final size:20
Alignment explanation
Indices: 405895--405939 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
405885 CTATAGGGGT
*
405895 CACACGGCTGTATGGCTCTCC
1 CACACGGCTATATGGC-CTCC
* *
405916 CACACGTCTATATGGCCTTC
1 CACACGGCTATATGGCCTCC
405936 CACA
1 CACA
405940 TGCCCTTGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.20, C:0.38, G:0.18, T:0.24
Consensus pattern (20 bp):
CACACGGCTATATGGCCTCC
Found at i:407158 original size:109 final size:109
Alignment explanation
Indices: 406975--407299 Score: 373
Period size: 109 Copynumber: 3.0 Consensus size: 109
406965 TATCACCCAT
* ** * * * * * *
406975 TCACGATGCTGCTCACATAAGCTGTTAAGAATGCACAATATATGCAGGATCTCAACCATTGTGAC
1 TCACGATGCTGCTCACACAAGCTACTGAGAATCCACAACATATGCAGGATCTCAGCCATCGCGAC
*
407040 AGTGTGTATCACCAGAACATAGTATCCATTTAGTATTCACCACC
66 AGTGTGTATCATCAGAACATAGTATCCATTTAGTATTCACCACC
* * * *
407084 TCACGATACTGCTCACACAAGCTACTGAGAATCCATAACATATGCAGGACCTCAGTCATCGCGAC
1 TCACGATGCTGCTCACACAAGCTACTGAGAATCCACAACATATGCAGGATCTCAGCCATCGCGAC
* * * **
407149 GGTGTGTATCATCAGAACATAGTATCCATTCAGTATTCATCGGC
66 AGTGTGTATCATCAGAACATAGTATCCATTTAGTATTCACCACC
* ** * * * *
407193 TCACGATGCTGCTCAAACAAG-TTGTCGAGAATTCGCAACATATGCAGGATCTTAGCCATCGCAA
1 TCACGATGCTGCTCACACAAGCTACT-GAGAATCCACAACATATGCAGGATCTCAGCCATCGCGA
* * *
407257 CAATGTGTATCATTAGAACATAATATCCATTTAGTATTCACCA
65 CAGTGTGTATCATCAGAACATAGTATCCATTTAGTATTCACCA
407300 ACTTAAGGCC
Statistics
Matches: 178, Mismatches: 37, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
108 2 0.01
109 176 0.99
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (109 bp):
TCACGATGCTGCTCACACAAGCTACTGAGAATCCACAACATATGCAGGATCTCAGCCATCGCGAC
AGTGTGTATCATCAGAACATAGTATCCATTTAGTATTCACCACC
Found at i:413498 original size:19 final size:19
Alignment explanation
Indices: 413462--413497 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
413452 TAGTTTAGTT
*
413462 GATTTTGATGTTATTTTTG
1 GATTTTGATATTATTTTTG
413481 GATTTTGATA-TATTTTT
1 GATTTTGATATTATTTTT
413498 TTCTGATGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.64
Consensus pattern (19 bp):
GATTTTGATATTATTTTTG
Found at i:414328 original size:12 final size:12
Alignment explanation
Indices: 414311--414449 Score: 69
Period size: 11 Copynumber: 11.9 Consensus size: 12
414301 ATAACATCCA
414311 AACAACCAAAAT
1 AACAACCAAAAT
414323 AACAACCAAAAT
1 AACAACCAAAAT
* *
414335 AGC-AGCACAAAT
1 AACAACCA-AAAT
*
414347 AACAA-CAAAAC
1 AACAACCAAAAT
414358 AACAA-C-AAA-
1 AACAACCAAAAT
*
414367 AACAACAAAAAT
1 AACAACCAAAAT
*
414379 AGCAGCAACAAAAAT
1 A--A-CAACCAAAAT
* *
414394 AGCAA-AAAAAT
1 AACAACCAAAAT
* * *
414405 AACAGCAAAAAC
1 AACAACCAAAAT
*
414417 AAC-ACAAAAAT
1 AACAACCAAAAT
*
414428 AGC-ACCAAAAT
1 AACAACCAAAAT
*
414439 AGCAACCAAAA
1 AACAACCAAAA
414450 CAGTAAAAAA
Statistics
Matches: 104, Mismatches: 13, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
9 5 0.05
10 3 0.03
11 42 0.40
12 41 0.39
13 1 0.01
14 1 0.01
15 11 0.11
ACGTcount: A:0.66, C:0.22, G:0.06, T:0.06
Consensus pattern (12 bp):
AACAACCAAAAT
Found at i:414393 original size:15 final size:15
Alignment explanation
Indices: 414369--414397 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
414359 ACAACAAAAA
414369 CAACAAAAATAGCAG
1 CAACAAAAATAGCAG
414384 CAACAAAAATAGCA
1 CAACAAAAATAGCA
414398 AAAAAATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.21, G:0.10, T:0.07
Consensus pattern (15 bp):
CAACAAAAATAGCAG
Found at i:414394 original size:47 final size:46
Alignment explanation
Indices: 414297--414451 Score: 142
Period size: 44 Copynumber: 3.4 Consensus size: 46
414287 AAAAACGCAT
* * * *
414297 AAAAATAACATCCAAACAACCAA-AATAACAACCAAAATAGCAGCAC
1 AAAAATAACAACAAAACAA-CAACAAAAACAACAAAAATAGCAGCAC
414343 --AAATAACAACAAAACAACAACAAAAACAACAAAAATAGCAGCAAC
1 AAAAATAACAACAAAACAACAACAAAAACAACAAAAATAGCAGC-AC
* * * *
414388 AAAAATAGCAAAAAAATAACAGCAAAAACAACACAAAAATAGCA-C-C
1 AAAAATAACAACAAAACAACAACAAAAAC-A-ACAAAAATAGCAGCAC
*
414434 -AAAATAGCAACCAAAACA
1 AAAAATAACAA-CAAAACA
414452 GTAAAAAAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
43 3 0.03
44 34 0.37
45 12 0.13
46 6 0.07
47 23 0.25
48 2 0.02
49 12 0.13
ACGTcount: A:0.66, C:0.23, G:0.05, T:0.06
Consensus pattern (46 bp):
AAAAATAACAACAAAACAACAACAAAAACAACAAAAATAGCAGCAC
Found at i:414438 original size:34 final size:34
Alignment explanation
Indices: 414367--414478 Score: 100
Period size: 34 Copynumber: 3.1 Consensus size: 34
414357 CAACAACAAA
**
414367 AACAACAAAAATAGCAGCAACAAAAATAGCAAAAAAAT
1 AACAAC-AAAA-A-CAG-AACAAAAATAGCACCAAAAT
*
414405 AACAGCAAAAACA-ACACAAAAATAGCACCAAAAT
1 AACAACAAAAACAGA-ACAAAAATAGCACCAAAAT
* * * *
414439 AGCAACCAAAACAGTAAAAAAAATAGCACCAAAAC
1 AACAACAAAAACAG-AACAAAAATAGCACCAAAAT
414474 AACAA
1 AACAA
414479 TATAATTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
33 1 0.02
34 27 0.44
35 23 0.37
36 2 0.03
37 4 0.06
38 5 0.08
ACGTcount: A:0.66, C:0.21, G:0.07, T:0.06
Consensus pattern (34 bp):
AACAACAAAAACAGAACAAAAATAGCACCAAAAT
Found at i:414449 original size:23 final size:22
Alignment explanation
Indices: 414315--414449 Score: 71
Period size: 23 Copynumber: 5.8 Consensus size: 22
414305 CATCCAAACA
414315 ACCAAAATAACAACCAAAATAGC
1 ACCAAAAT-ACAACCAAAATAGC
* * *
414338 AGCACAAATAACAA-CAAAACAAC
1 ACCA-AAAT-ACAACCAAAATAGC
* *
414361 AACAAAA-ACAACAAAAATAGC
1 ACCAAAATACAACCAAAATAGC
* *
414382 AGCAACAAAAATAGCAA-AAAAATAAC
1 A-C--C-AAAATA-CAACCAAAATAGC
*
414408 AGCAAAA-ACAACACAAAAATAGC
1 ACCAAAATACAAC-C-AAAATAGC
414431 ACCAAAATAGCAACCAAAA
1 ACCAAAATA-CAACCAAAA
414450 CAGTAAAAAA
Statistics
Matches: 86, Mismatches: 13, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
20 7 0.08
21 8 0.09
22 7 0.08
23 31 0.36
24 12 0.14
25 8 0.09
26 10 0.12
27 3 0.03
ACGTcount: A:0.66, C:0.22, G:0.06, T:0.06
Consensus pattern (22 bp):
ACCAAAATACAACCAAAATAGC
Found at i:414472 original size:12 final size:12
Alignment explanation
Indices: 414372--414472 Score: 57
Period size: 12 Copynumber: 8.4 Consensus size: 12
414362 ACAAAAACAA
414372 CAAAAATAGCAGC
1 CAAAAATAGCA-C
414385 AACAAAAATAGCA-
1 --CAAAAATAGCAC
* * *
414398 AAAAAATAACAG
1 CAAAAATAGCAC
* *
414410 CAAAAACAACA-
1 CAAAAATAGCAC
414421 CAAAAATAGCAC
1 CAAAAATAGCAC
414433 C-AAAATAGCAAC
1 CAAAAATAGC-AC
* * *
414445 C-AAAACAGTAA
1 CAAAAATAGCAC
*
414456 AAAAAATAGCAC
1 CAAAAATAGCAC
414468 CAAAA
1 CAAAA
414473 CAACAATATA
Statistics
Matches: 68, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
11 27 0.40
12 30 0.44
15 11 0.16
ACGTcount: A:0.65, C:0.20, G:0.08, T:0.07
Consensus pattern (12 bp):
CAAAAATAGCAC
Done.