Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015293.1 Kokia drynarioides strain JFW-HI SEQ_130338, 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: 258884
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 72 characters in sequence are not A, C, G, or T
Found at i:624 original size:59 final size:57
Alignment explanation
Indices: 555--926 Score: 265
Period size: 59 Copynumber: 6.3 Consensus size: 57
545 ACTCAGGGGC
* * *
555 AAAATGGTAATTTTT-ACAAGTTTCGGGATTAAAAATGTAATTTTTGGAAGTTTAGGGGTA
1 AAAAT-GTAATTTTTGA-AATTTTAGGG-TTAAAAATGGAATTTTTGGAAGTTT-GGGGTA
* * *
615 AAAATGTAATTTTTTGAAATTTTTGAGGTTAAAAATGGAATTTTTTGAAGTTTGGGGGTT
1 AAAATGTAA-TTTTTGAAATTTTAG-GGTTAAAAATGGAATTTTTGGAAGTTT-GGGGTA
675 AAAATGTAATTTTTGGAAATTTTAGGGTTAAAAATGGAA-TTTTGGAAAGTTTGGCGGTA
1 AAAATGTAATTTTT-GAAATTTTAGGGTTAAAAATGGAATTTTTGG-AAGTTTGG-GGTA
** ** * *
734 AAAATGCATTTTTTTGTGAAA--TCGGGGTCAAAAATGGAA-TTTTGGAATATTTAGGGGTA
1 AAAATG--TAATTTT-TGAAATTTTAGGGTTAAAAATGGAATTTTTGGAA-GTTT-GGGGTA
* * ** * * *
793 AAATTGTTATTTTTGGAAAAATTAGGGTCAAAAATAGAA-TTTTGGAAAGTTCGAGGGTA
1 AAAATGTAATTTTT-GAAATTTTAGGGTTAAAAATGGAATTTTTGG-AAGTTTG-GGGTA
* * * *
852 AAAATGTAATTTTTTGAAAGTTTAGGGGTCAAAAT--ATATTTTTGGAGAAGTTTAGGGGTT
1 AAAATGTAA-TTTTTGAAATTTTAGGGTTAAAAATGGA-ATTTTT-G-GAAGTTT-GGGGTA
*
912 AAAATATAATTTTTG
1 AAAATGTAATTTTTG
927 GACAATTTAG
Statistics
Matches: 258, Mismatches: 32, Indels: 45
0.77 0.10 0.13
Matches are distributed among these distances:
56 1 0.00
57 11 0.04
58 11 0.04
59 131 0.51
60 89 0.34
61 14 0.05
62 1 0.00
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (57 bp):
AAAATGTAATTTTTGAAATTTTAGGGTTAAAAATGGAATTTTTGGAAGTTTGGGGTA
Found at i:807 original size:118 final size:118
Alignment explanation
Indices: 645--938 Score: 316
Period size: 118 Copynumber: 2.5 Consensus size: 118
635 TTTTGAGGTT
* * * ** *
645 AAAAATGGAATTTTTTGAAGTTTGGGGGTTAAAATGTAATTTTTGGAAATTTTAGGGTTAAAAAT
1 AAAAATGGAATTTTTGGAAATTTAGGGGTTAAAATGTAATTTTTGGAAAAATTAGGGTCAAAAAT
* * *
710 GGAATTTTGGAAAGTTTG-GCGGTAAAAATGCATTTTTTTGTGAAATCGGGGTC
66 AGAATTTTGGAAAGTTCGAG-GGTAAAAATGCAATTTTTTGTGAAATCGGGGTC
*
763 AAAAATGGAA-TTTTGGAATATTTAGGGG-TAAAATTGTTATTTTTGGAAAAATTAGGGTCAAAA
1 AAAAATGGAATTTTTGGAA-ATTTAGGGGTTAAAA-TGTAATTTTTGGAAAAATTAGGGTCAAAA
* *
826 ATAGAATTTTGGAAAGTTCGAGGGTAAAAATGTAA-TTTTT-TGAAAGTTTAGGGGTC
64 ATAGAATTTTGGAAAGTTCGAGGGTAAAAATGCAATTTTTTGTGAAA---TCGGGGTC
* * *
882 -AAAAT--ATATTTTTGGAGAAGTTTAGGGGTTAAAATATAATTTTTGGACAATTTAGGG
1 AAAAATGGA-ATTTTTGGA-AA-TTTAGGGGTTAAAATGTAATTTTTGGAAAAATTAGGG
939 AACTTTAAGG
Statistics
Matches: 149, Mismatches: 16, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
116 6 0.04
117 18 0.12
118 84 0.56
119 36 0.24
120 5 0.03
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (118 bp):
AAAAATGGAATTTTTGGAAATTTAGGGGTTAAAATGTAATTTTTGGAAAAATTAGGGTCAAAAAT
AGAATTTTGGAAAGTTCGAGGGTAAAAATGCAATTTTTTGTGAAATCGGGGTC
Found at i:936 original size:30 final size:29
Alignment explanation
Indices: 586--938 Score: 176
Period size: 30 Copynumber: 11.9 Consensus size: 29
576 TTCGGGATTA
* * *
586 AAAATGTAATTTTTGGAAGTTTAGGGGTA
1 AAAATATAATTTTTGGAAATTTAGGGGTT
* * * *
615 AAAATGTAATTTTTTGAAATTTTTGAGGTT
1 AAAATATAATTTTTGGAAA-TTTAGGGGTT
* * *
645 AAAA-ATGGAATTTTTTGAAGTTTGGGGGTT
1 AAAATAT--AATTTTTGGAAATTTAGGGGTT
*
675 AAAATGTAATTTTTGGAAATTTTA-GGGTT
1 AAAATATAATTTTTGGAAA-TTTAGGGGTT
*
704 AAAA-ATGGAA-TTTTGGAAAGTTT-GGCGGTA
1 AAAATAT--AATTTTTGGAAA-TTTAGG-GGTT
* * *
734 AAAATGCAT-TTTTTTGTGAAA--TCGGGGTC
1 AAAAT--ATAATTTTTG-GAAATTTAGGGGTT
763 AAAA-ATGGAA-TTTTGGAATATTTAGGGG-T
1 AAAATAT--AATTTTTGGAA-ATTTAGGGGTT
* * * *
792 AAAATTGTTATTTTTGGAAAAATTA-GGGTC
1 AAAA-TATAATTTTTGG-AAATTTAGGGGTT
* * * *
822 AAAA-ATAGAATTTTGGAAAGTTCGAGGGTA
1 AAAATATA-ATTTTTGGAAATTTAG-GGGTT
* * *
852 AAAATGTAATTTTTTGAAAGTTTAGGGGTC
1 AAAATATAATTTTTGGAAA-TTTAGGGGTT
882 AAAATAT-ATTTTTGGAGAAGTTTAGGGGTT
1 AAAATATAATTTTTGGA-AA-TTTAGGGGTT
912 AAAATATAATTTTTGGACAATTTAGGG
1 AAAATATAATTTTTGGA-AATTTAGGG
939 AACTTTAAGG
Statistics
Matches: 250, Mismatches: 41, Indels: 65
0.70 0.12 0.18
Matches are distributed among these distances:
26 2 0.01
27 3 0.01
28 13 0.05
29 81 0.32
30 109 0.44
31 36 0.14
32 4 0.02
33 2 0.01
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.38
Consensus pattern (29 bp):
AAAATATAATTTTTGGAAATTTAGGGGTT
Found at i:2824 original size:6 final size:6
Alignment explanation
Indices: 2813--2862 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
2803 ATTTTGAAAA
*
2813 TAAATT TAAATT TAAATT T-AATT TAAATT TAAATT TAAA-A TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
2859 TAAA
1 TAAA
2863 AAGATCCGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 9 0.22
6 31 0.77
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
TAAATT
Found at i:2837 original size:11 final size:12
Alignment explanation
Indices: 2813--2862 Score: 77
Period size: 11 Copynumber: 4.3 Consensus size: 12
2803 ATTTTGAAAA
2813 TAAATTTAAATT
1 TAAATTTAAATT
2825 TAAATTT-AATT
1 TAAATTTAAATT
2836 TAAATTTAAATT
1 TAAATTTAAATT
*
2848 TAAA-ATAAATT
1 TAAATTTAAATT
2859 TAAA
1 TAAA
2863 AAGATCCGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
11 21 0.58
12 15 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TAAATTTAAATT
Found at i:2837 original size:17 final size:17
Alignment explanation
Indices: 2815--2862 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
2805 TTTGAAAATA
2815 AATTTAAATTTAAATTT
1 AATTTAAATTTAAATTT
2832 AATTTAAATTTAAATTT
1 AATTTAAATTTAAATTT
**
2849 AAAATAAATTTAAA
1 AATTTAAATTTAAA
2863 AAGATCCGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTAAATTTAAATTT
Found at i:4667 original size:35 final size:35
Alignment explanation
Indices: 4628--4698 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
4618 AATATAAGTC
4628 AAACCTTTTGTTCAATTGGATTAATTTCCAAATAT
1 AAACCTTTTGTTCAATTGGATTAATTTCCAAATAT
4663 AAACCTTTTGTTCAATTGGATTAATTTCCAAATAT
1 AAACCTTTTGTTCAATTGGATTAATTTCCAAATAT
4698 A
1 A
4699 TATACATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.42
Consensus pattern (35 bp):
AAACCTTTTGTTCAATTGGATTAATTTCCAAATAT
Found at i:9416 original size:8 final size:8
Alignment explanation
Indices: 9403--9436 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
9393 GAAAATATTT
9403 TTTTAAAA
1 TTTTAAAA
9411 TTTTAATAA
1 TTTTAA-AA
9420 TTATTAAAA
1 TT-TTAAAA
9429 TTTTAAAA
1 TTTTAAAA
9437 AATTAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 12 0.50
9 8 0.33
10 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTTTAAAA
Found at i:10927 original size:17 final size:17
Alignment explanation
Indices: 10895--10957 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
10885 AATTTGTTAA
10895 AATTTTTATCATAATTTTT
1 AATTTTTA--ATAATTTTT
10914 AATTTTTAATAATTTATATT
1 AATTTTTAATAA-TT-T-TT
* * *
10934 TATTTTTAAGATTTTTT
1 AATTTTTAATAATTTTT
10951 AATTTTT
1 AATTTTT
10958 TAGAATTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 12 0.32
18 3 0.08
19 11 0.30
20 11 0.30
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
AATTTTTAATAATTTTT
Found at i:11189 original size:2 final size:2
Alignment explanation
Indices: 11182--11210 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11172 GTTTTCCTAG
11182 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11211 TAATTTTCAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12556 original size:41 final size:41
Alignment explanation
Indices: 12499--12622 Score: 185
Period size: 41 Copynumber: 3.0 Consensus size: 41
12489 AAACCTTTAA
* **
12499 ATAGGGGGCAAAGTTCTACCGACATTAACTTCTCTACATAC
1 ATAGGGGGTAAAGTTCTACCGACATTATTTTCTCTACATAC
*
12540 ATAGGGGGTAAAGTTCTACCGATATTATTTTCTCTACATAC
1 ATAGGGGGTAAAGTTCTACCGACATTATTTTCTCTACATAC
* * *
12581 ATAGAGGGTAAATTTCTACCGACATTATTTTCTTTACATAC
1 ATAGGGGGTAAAGTTCTACCGACATTATTTTCTCTACATAC
12622 A
1 A
12623 AGACTCGAAC
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 75 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (41 bp):
ATAGGGGGTAAAGTTCTACCGACATTATTTTCTCTACATAC
Found at i:45299 original size:23 final size:23
Alignment explanation
Indices: 45179--45293 Score: 67
Period size: 23 Copynumber: 4.9 Consensus size: 23
45169 CAAAGTACTT
45179 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
* *
45205 AACAGTAAGCACACACAGTTC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * * *
45227 ATCAATAGGCGCACATAA-CGC-A
1 AACAGTAAGCACACA-AAGTGCGA
*
45249 AATCAGTAGGCACACAAAGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
*
45273 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
45294 TGAACAATAA
Statistics
Matches: 69, Mismatches: 15, Indels: 13
0.71 0.15 0.13
Matches are distributed among these distances:
22 17 0.25
23 31 0.45
24 3 0.04
26 14 0.20
27 4 0.06
ACGTcount: A:0.42, C:0.24, G:0.22, T:0.12
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:45304 original size:23 final size:23
Alignment explanation
Indices: 45258--45305 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
45248 AAATCAGTAG
*
45258 GCACACAAAGTGCGAAACAGTAA
1 GCACACAAAGTGCGAAACAATAA
*
45281 GCACACACAGTGCTG-AACAATAA
1 GCACACAAAGTGC-GAAACAATAA
45304 GC
1 GC
45306 GCGCTAACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.44, C:0.25, G:0.21, T:0.10
Consensus pattern (23 bp):
GCACACAAAGTGCGAAACAATAA
Found at i:45406 original size:24 final size:26
Alignment explanation
Indices: 45368--45415 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
45358 TCTACGTGGG
45368 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
45394 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
45416 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:46178 original size:16 final size:16
Alignment explanation
Indices: 46159--46199 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
46149 CCCTTCTCAT
*
46159 ATTTCCTTTGCACTAA
1 ATTTCATTTGCACTAA
46175 ATTTCATTTGCACTAA
1 ATTTCATTTGCACTAA
46191 ATTTCATTT
1 ATTTCATTT
46200 AATCACACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.49
Consensus pattern (16 bp):
ATTTCATTTGCACTAA
Found at i:51344 original size:16 final size:16
Alignment explanation
Indices: 51323--51354 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
51313 TAGGTTCTTC
51323 AAGAAGTTCATATGTT
1 AAGAAGTTCATATGTT
51339 AAGAAGTTCATATGTT
1 AAGAAGTTCATATGTT
51355 TGTTTTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (16 bp):
AAGAAGTTCATATGTT
Found at i:56085 original size:2 final size:2
Alignment explanation
Indices: 56078--56113 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
56068 TATCTGCACG
56078 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
56114 TACAAAATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:58286 original size:18 final size:18
Alignment explanation
Indices: 58252--58286 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58242 AAGCATAAAA
*
58252 TTCTTCATTTCCCTTATC
1 TTCTTCATTTCCATTATC
*
58270 TTCTTCATTTCTATTAT
1 TTCTTCATTTCCATTAT
58287 ACTCTAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.26, G:0.00, T:0.60
Consensus pattern (18 bp):
TTCTTCATTTCCATTATC
Found at i:58806 original size:2 final size:2
Alignment explanation
Indices: 58799--58824 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58789 AGCTGTCAAA
58799 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
58825 CTTTGAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59515 original size:13 final size:13
Alignment explanation
Indices: 59497--59521 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59487 TTGGGTCATA
59497 AATAAGAAAATAT
1 AATAAGAAAATAT
59510 AATAAGAAAATA
1 AATAAGAAAATA
59522 ATTAAAATTA
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:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (13 bp):
AATAAGAAAATAT
Found at i:60032 original size:33 final size:33
Alignment explanation
Indices: 59990--60057 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
59980 TTAAAAAATA
59990 ATAATACGAAAACAATGTATATAAGCTGTAATT
1 ATAATACGAAAACAATGTATATAAGCTGTAATT
* *
60023 ATAATACGAAAACAATGTATCTTAGCTGTAATT
1 ATAATACGAAAACAATGTATATAAGCTGTAATT
60056 AT
1 AT
60058 CTGTCCAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (33 bp):
ATAATACGAAAACAATGTATATAAGCTGTAATT
Found at i:60214 original size:17 final size:17
Alignment explanation
Indices: 60192--60262 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
60182 TCAACATCAA
* *
60192 ATTTTAAATTTTAATTT
1 ATTTTGAATTTAAATTT
60209 ATTTT-AATTTTAAATTT
1 ATTTTGAA-TTTAAATTT
* *
60226 ATGTTGAGTTTAAATTT
1 ATTTTGAATTTAAATTT
*
60243 ATTTTGAATTAAAATTT
1 ATTTTGAATTTAAATTT
60260 ATT
1 ATT
60263 ATTATTAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
16 2 0.04
17 43 0.93
18 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
ATTTTGAATTTAAATTT
Found at i:60269 original size:16 final size:16
Alignment explanation
Indices: 60204--60272 Score: 59
Period size: 17 Copynumber: 4.1 Consensus size: 16
60194 TTTAAATTTT
*
60204 AATTTATTTTAATTTTA
1 AATTTATTTTAA-TTAA
* * *
60221 AATTTATGTTGAGTTTA
1 AATTTAT-TTTAATTAA
60238 AATTTATTTTGAATTAA
1 AATTTATTTT-AATTAA
60255 AATTTATTATT-ATTAA
1 AATTTATT-TTAATTAA
60271 AA
1 AA
60273 GTCCAAAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
16 9 0.20
17 30 0.68
18 5 0.11
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
AATTTATTTTAATTAA
Found at i:62074 original size:29 final size:29
Alignment explanation
Indices: 62039--62202 Score: 113
Period size: 30 Copynumber: 5.5 Consensus size: 29
62029 CATTTCACCC
*
62039 TAAAAATTCCATTTTTTACCCCGAAACTTT
1 TAAAAATTCCATTTTTTACCCCAAAAC-TT
* * *
62069 TGAAATTTACCA--TTTTACCCTC-GAACTT
1 TAAAAATT-CCATTTTTTACCC-CAAAACTT
* *
62097 CCAAAAATTCCATTTTTGACCCCAAAACTTT
1 -TAAAAATTCCATTTTTTACCCCAAAAC-TT
* * *
62128 TGAAATATACCA--TTTTACCCCTAAACTT
1 T-AAAAATTCCATTTTTTACCCCAAAACTT
* *
62156 CCAAAAATTCCATTTTTAACCCCAAAACTT
1 -TAAAAATTCCATTTTTTACCCCAAAACTT
62186 TCAAAAATTACCATTTT
1 T-AAAAATT-CCATTTT
62203 ACCCTCGAAT
Statistics
Matches: 102, Mismatches: 19, Indels: 25
0.70 0.13 0.17
Matches are distributed among these distances:
28 15 0.15
29 29 0.28
30 38 0.37
31 20 0.20
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
TAAAAATTCCATTTTTTACCCCAAAACTT
Found at i:62107 original size:59 final size:59
Alignment explanation
Indices: 62040--62289 Score: 287
Period size: 59 Copynumber: 4.3 Consensus size: 59
62030 ATTTCACCCT
* *
62040 AAAAATTCCATTTTTTACCCCGAAACTTTTGAAATTTACCATTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTTAACCCCAAAACTTTTGAAATTTACCATTTTACCCTCGAACTTCC
* * *
62099 AAAAATTCCATTTTTGACCCCAAAACTTTTGAAATATACCATTTTACCC-CTAAACTTCC
1 AAAAATTCCATTTTTAACCCCAAAACTTTTGAAATTTACCATTTTACCCTC-GAACTTCC
** *
62158 AAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACCATTTTACCCTCGAA-TGTCC
1 AAAAATTCCATTTTTAACCCCAAAACTTTTGAAATTTACCATTTTACCCTCGAACT-TCC
* * * * *
62217 AAAAATTCCATTTTTGAA-CCTAAAA-TTTTCAAAAATTACAATTTTACCCCCGAA-TGT-C
1 AAAAATTCCATTTTT-AACCCCAAAACTTTT-GAAATTTACCATTTTACCCTCGAACT-TCC
*
62275 TAAAATTCCATTTTT
1 AAAAATTCCATTTTT
62290 GGCCCTAAAC
Statistics
Matches: 171, Mismatches: 15, Indels: 11
0.87 0.08 0.06
Matches are distributed among these distances:
58 20 0.12
59 148 0.87
60 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (59 bp):
AAAAATTCCATTTTTAACCCCAAAACTTTTGAAATTTACCATTTTACCCTCGAACTTCC
Found at i:62126 original size:30 final size:29
Alignment explanation
Indices: 62040--62303 Score: 164
Period size: 29 Copynumber: 9.0 Consensus size: 29
62030 ATTTCACCCT
* *
62040 AAAAATTCCATTTTTTACCCCGAAACTTTT
1 AAAAATTCCA-TTTTTACCCCAAAACTTTC
* * * *
62070 GAAATTTACCA-TTTTACCCTC-GAACTTCC
1 AAAAATT-CCATTTTTACCC-CAAAACTTTC
*
62099 AAAAATTCCATTTTTGACCCCAAAACTTTTG
1 AAAAATTCCATTTTT-ACCCCAAAAC-TTTC
* * * *
62130 AAATATACCA-TTTTACCCCTAAACTTCC
1 AAAAATTCCATTTTTACCCCAAAACTTTC
62158 AAAAATTCCATTTTTAACCCCAAAACTTTC
1 AAAAATTCCATTTTT-ACCCCAAAACTTTC
* *
62188 AAAAATTACCA-TTTTACCCTC-GAA-TGTCC
1 AAAAATT-CCATTTTTACCC-CAAAACT-TTC
* * *
62217 AAAAATTCCATTTTTGAACCTAAAATTTTC
1 AAAAATTCCATTTTT-ACCCCAAAACTTTC
* * ** *
62247 AAAAATTACAATTTTACCCCCGAA-TGTC
1 AAAAATTCCATTTTTACCCCAAAACTTTC
* ** *
62275 TAAAATTCCATTTTTGGCCCTAAACTTTC
1 AAAAATTCCATTTTTACCCCAAAACTTTC
62304 CCAAAATTAT
Statistics
Matches: 178, Mismatches: 40, Indels: 33
0.71 0.16 0.13
Matches are distributed among these distances:
28 37 0.21
29 63 0.35
30 61 0.34
31 17 0.10
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCCAAAACTTTC
Found at i:62229 original size:28 final size:29
Alignment explanation
Indices: 62187--62354 Score: 121
Period size: 28 Copynumber: 5.8 Consensus size: 29
62177 CCAAAACTTT
62187 CAAAAATTACCATTTTACCCTCGAATGTC
1 CAAAAATTACCATTTTACCCTCGAATGTC
* ** * *
62216 CAAAAATT-CCATTTTTGAACCTAAAATTTT
1 CAAAAATTACCA-TTTT-ACCCTCGAATGTC
* *
62246 CAAAAATTACAATTTTACCCCCGAATGT-
1 CAAAAATTACCATTTTACCCTCGAATGTC
* * * *
62274 CTAAAATT-CCATTTTTGGCCCT-AAACTTTC
1 CAAAAATTACCA-TTTT-ACCCTCGAA-TGTC
* * *
62304 CCAAAATTATCATTTTACCCTCGAGTGTC
1 CAAAAATTACCATTTTACCCTCGAATGTC
*
62333 C-AAAATTACCATTTTTCCCTCG
1 CAAAAATTACCATTTTACCCTCG
62355 GGTATAAAAA
Statistics
Matches: 105, Mismatches: 25, Indels: 19
0.70 0.17 0.13
Matches are distributed among these distances:
27 2 0.02
28 35 0.33
29 32 0.30
30 32 0.30
31 4 0.04
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.35
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCTCGAATGTC
Found at i:62310 original size:58 final size:56
Alignment explanation
Indices: 62040--62348 Score: 257
Period size: 59 Copynumber: 5.3 Consensus size: 56
62030 ATTTCACCCT
* * ** *
62040 AAAAATTCCATTTTTTACCCCGAAACTTTTGAAATTTACCATTTTACCCTCGAACT-TCC
1 AAAAATTCCATTTTTGA-CCCTAAACTTTCAAAAATTA-CATTTTACCCTCGAA-TGT-C
* ** *
62099 AAAAATTCCATTTTTGACCCCAAAACTTT-TGAAATATACCATTTTACCC-CTAAACT-TCC
1 AAAAATTCCATTTTTGA-CCCTAAACTTTCAAAAAT-TA-CATTTTACCCTC-GAA-TGT-C
* *
62158 AAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACCATTTTACCCTCGAATGTCC
1 AAAAATTCCATTTTTGA-CCCTAAACTTTCAAAAATTA-CATTTTACCCTCGAATGT-C
* * *
62217 AAAAATTCCATTTTTGAACCTAAAATTTTCAAAAATTACAATTTTACCCCCGAATGTC
1 AAAAATTCCATTTTTGACCCT-AAACTTTCAAAAATTAC-ATTTTACCCTCGAATGTC
* * * *
62275 TAAAATTCCATTTTTGGCCCTAAACTTTCCCAAAATTATCATTTTACCCTCGAGTGTC
1 AAAAATTCCATTTTTGACCCTAAACTTT-CAAAAATTA-CATTTTACCCTCGAATGTC
*
62333 CAAAATTACCATTTTT
1 AAAAATT-CCATTTTT
62349 CCCTCGGGTA
Statistics
Matches: 217, Mismatches: 23, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
57 6 0.03
58 57 0.26
59 149 0.69
60 5 0.02
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (56 bp):
AAAAATTCCATTTTTGACCCTAAACTTTCAAAAATTACATTTTACCCTCGAATGTC
Found at i:62333 original size:117 final size:118
Alignment explanation
Indices: 62040--62348 Score: 360
Period size: 118 Copynumber: 2.6 Consensus size: 118
62030 ATTTCACCCT
* * ** *
62040 AAAAATTCCATTTTTTACCCCGAAACTTTTGAAATTTACCATTTTACCCTCGAACT-TCCAAAAA
1 AAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACCATTTTACCCTCGAA-TGTCCAAAAA
* * * * *
62104 TTCCATTTTTGACCCCAAAACTTTTGAAATATACCATTTTACCCCTAAACTTCC
65 TTCCATTTTTGAACCCAAAACTTTTCAAAAATACAATTTTACCCCCAAACTTCC
62158 AAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACCATTTTACCCTCGAATGTCCAAAAAT
1 AAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACCATTTTACCCTCGAATGTCCAAAAAT
* *
62223 TCCATTTTTGAACCTAAAA-TTTTCAAAAATTACAATTTTACCCCCGAA-TGT-C
66 TCCATTTTTGAACCCAAAACTTTTCAAAAA-TACAATTTTACCCCCAAACT-TCC
* ** * * * *
62275 TAAAATTCCATTTTT-GGCCCTAAACTTTCCCAAAATTATCATTTTACCCTCGAGTGTCC-AAAA
1 AAAAATTCCATTTTTAACCCCAAAACTTT-CAAAAATTACCATTTTACCCTCGAATGTCCAAAAA
62338 TTACCATTTTT
65 TT-CCATTTTT
62349 CCCTCGGGTA
Statistics
Matches: 167, Mismatches: 19, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
116 16 0.10
117 60 0.36
118 91 0.54
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (118 bp):
AAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACCATTTTACCCTCGAATGTCCAAAAAT
TCCATTTTTGAACCCAAAACTTTTCAAAAATACAATTTTACCCCCAAACTTCC
Found at i:62365 original size:28 final size:28
Alignment explanation
Indices: 62306--62365 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
62296 AAACTTTCCC
* * **
62306 AAAATTATCATTTTACCCTCGAGTGTCC
1 AAAATTACCATTTTACCCTCGAGTATAA
* *
62334 AAAATTACCATTTTTCCCTCGGGTATAA
1 AAAATTACCATTTTACCCTCGAGTATAA
62362 AAAA
1 AAAA
62366 AGTCTTACTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (28 bp):
AAAATTACCATTTTACCCTCGAGTATAA
Found at i:63215 original size:3 final size:3
Alignment explanation
Indices: 63207--63236 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
63197 GGTTTCAACA
63207 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
63237 TAGATATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:63332 original size:29 final size:28
Alignment explanation
Indices: 63269--63323 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
63259 ATATAAACAA
*
63269 TATA-AAAATAATTAATTATGAAAATAG
1 TATAGAAAATAATTAAATATGAAAATAG
63296 TATAGAAAATAGATTAAATATGAAAATA
1 TATAGAAAATA-ATTAAATATGAAAATA
63324 TTGACGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 4 0.16
28 6 0.24
29 15 0.60
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (28 bp):
TATAGAAAATAATTAAATATGAAAATAG
Found at i:67877 original size:17 final size:17
Alignment explanation
Indices: 67852--67891 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
67842 CCTGACAACA
* *
67852 CCACGACCACTCGTCTG
1 CCACCACCACGCGTCTG
*
67869 CCACCACCACGCTTCTG
1 CCACCACCACGCGTCTG
67886 CCACCA
1 CCACCA
67892 TCGCATACGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.20, C:0.53, G:0.12, T:0.15
Consensus pattern (17 bp):
CCACCACCACGCGTCTG
Found at i:69047 original size:25 final size:26
Alignment explanation
Indices: 68999--69062 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
68989 GAACTTTATT
*
68999 TTTCTTTTAATTCAATCCTCTTTTTA
1 TTTCTTTTAAATCAATCCTCTTTTTA
69025 TTTCTTTTAAAT-AATCC-CTTTTTTA
1 TTTCTTTTAAATCAATCCTC-TTTTTA
*
69050 TGTTTTTTTAAAT
1 T-TTCTTTTAAAT
69063 TGGTCCATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 1 0.03
25 12 0.35
26 21 0.62
ACGTcount: A:0.22, C:0.14, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTCTTTTAAATCAATCCTCTTTTTA
Found at i:74083 original size:30 final size:29
Alignment explanation
Indices: 74049--74121 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
74039 TAAAAATTTT
74049 AAATTAATAAAGATCCTTTAAAAATGATAA
1 AAATTAATAAA-ATCCTTTAAAAATGATAA
** * *
74079 AAATTTAATTTAATCTTTTAAAAATTATAA
1 AAA-TTAATAAAATCCTTTAAAAATGATAA
74109 AAATATAA-AAAAT
1 AAAT-TAATAAAAT
74122 TTAATTTCAG
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
29 4 0.11
30 25 0.71
31 6 0.17
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.36
Consensus pattern (29 bp):
AAATTAATAAAATCCTTTAAAAATGATAA
Found at i:83648 original size:18 final size:18
Alignment explanation
Indices: 83617--83660 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
83607 CAGTTGAATC
*
83617 AATTTTATAATTTTTAAT
1 AATTTTTTAATTTTTAAT
83635 -ATTTTTTAATTTTTTAAT
1 AATTTTTTAA-TTTTTAAT
83653 AATTTTTT
1 AATTTTTT
83661 TGGTTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 8 0.35
18 8 0.35
19 7 0.30
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTTTTTAATTTTTAAT
Found at i:91008 original size:49 final size:49
Alignment explanation
Indices: 90952--91050 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
90942 TTTATAATAT
90952 TATAGAATACTTTAAATATAATTACCATATAATGAAAACAAATCAAATG
1 TATAGAATACTTTAAATATAATTACCATATAATGAAAACAAATCAAATG
*
91001 TATAGAATACTTTAAATATAATTACGATATAATGAAAACAAATCAAATG
1 TATAGAATACTTTAAATATAATTACCATATAATGAAAACAAATCAAATG
91050 T
1 T
91051 CTACTTCCAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (49 bp):
TATAGAATACTTTAAATATAATTACCATATAATGAAAACAAATCAAATG
Found at i:101801 original size:10 final size:11
Alignment explanation
Indices: 101782--101806 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
101772 ATTTATAGTT
101782 AAAATAAAAAA
1 AAAATAAAAAA
101793 AAAATAAAAAA
1 AAAATAAAAAA
101804 AAA
1 AAA
101807 GCTTTCATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAATAAAAAA
Found at i:110651 original size:2 final size:2
Alignment explanation
Indices: 110644--110674 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
110634 ACTTTGATTT
110644 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
110675 TCAAGTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:111127 original size:33 final size:35
Alignment explanation
Indices: 111071--111136 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
111061 ATCATTTATC
* *
111071 CAAATATATAATTATTTTCATA-TTACAATTTATTT
1 CAAATATATAATCATTATCATATTTA-AATTTATTT
111106 CAAATATATAA-CATTAT-ATATTTAAATTTAT
1 CAAATATATAATCATTATCATATTTAAATTTAT
111137 AATGGCTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 10 0.36
34 7 0.25
35 11 0.39
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (35 bp):
CAAATATATAATCATTATCATATTTAAATTTATTT
Found at i:116502 original size:28 final size:29
Alignment explanation
Indices: 116447--116503 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 29
116437 TTCTATTTTA
116447 AAATAATGATATTTATTATTCACAAAAAAAT
1 AAATAATGATATTTATTATT--CAAAAAAAT
116478 AAATAATGATATTTATTATT-AAAAAA
1 AAATAATGATATTTATTATTCAAAAAA
116504 GGAATAGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 6 0.23
31 20 0.77
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (29 bp):
AAATAATGATATTTATTATTCAAAAAAAT
Found at i:123856 original size:18 final size:18
Alignment explanation
Indices: 123831--123874 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
123821 ATATAAAATA
*
123831 ATTA-TAATTATAATTATT
1 ATTATTAATAATAATT-TT
123849 -TTATTAATAATAATTTT
1 ATTATTAATAATAATTTT
123866 ATTATTAAT
1 ATTATTAAT
123875 GTTATCGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTATTAATAATAATTTT
Found at i:123864 original size:15 final size:15
Alignment explanation
Indices: 123827--123874 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
123817 TAAAATATAA
*
123827 AATAATTATAATT-AT
1 AATAATT-TTATTAAT
*
123842 AATTATTTTATTAAT
1 AATAATTTTATTAAT
*
123857 AATAATTTTATTATT
1 AATAATTTTATTAAT
123872 AAT
1 AAT
123875 GTTATCGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATAATTTTATTAAT
Found at i:137446 original size:74 final size:74
Alignment explanation
Indices: 137356--138317 Score: 1470
Period size: 74 Copynumber: 13.1 Consensus size: 74
137346 GAATTACTCT
* * *
137356 ATTGTATGTTGTGTGTTTAGATAGTGAGTTAAGATTGTTAGCATGTAAAGTAGTTGATGGATTCT
1 ATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
* *
137421 AACTCATGG
66 AACACGTGG
* * *
137430 ATTTTATGTTGTGTGTTTAGATAGC-ACGTTAAGGTTGTTAGCATGTAAAGAAGTTGATGAATTC
1 ATTGTATGTTGTGTGTTTAGATAGCGA-GTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTC
137494 TAACACGTGG
65 TAACACGTGG
* *
137504 ATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGAAGTTGATGAATTCT
1 ATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
137569 AACACGTGG
66 AACACGTGG
* *
137578 ATTGCATGTTGCGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
1 ATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
* *
137643 AACATGCGG
66 AACACGTGG
**
137652 ATTGCGTGTTGTG-GTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
1 ATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
*
137716 AACATGTGG
66 AACACGTGG
* * * *
137725 ATTGTATGTTGTGTGTTTAGATAGCGCGTTAAGGTTGTTAGCACGTAAAGCAGTTGATGATTTCT
1 ATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
*
137790 AGCACGTGG
66 AACACGTGG
* * *
137799 ATTGTATATTGTGTGTTTAGATAGCGAGTTATGATTGTTAGCATGTAAAGAAGTTGATGAATTCT
1 ATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
*
137864 AACACATGG
66 AACACGTGG
* *
137873 ATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGAAGTTGATGAATTCT
1 ATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
* *
137938 AACACATGA
66 AACACGTGG
*
137947 ATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
1 ATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
138012 AACACGTGG
66 AACACGTGG
* *
138021 ATTGCATGTTGTG-GTTTAGATAGCTAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
1 ATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
138085 AACACGTGG
66 AACACGTGG
* *
138094 ATTGTATGTTGTGTGTTTAGATAGCGCGTTAAGGTTGTTAGCATGTAAAGCAGTTGAT---TTCT
1 ATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
138156 AACACGTGG
66 AACACGTGG
* * * * *
138165 ATTGTATATTATCTGTTTAGATAGC-ACGTTAAGGTTGTTAGCATGTAAAGCAGTTGATGATTTC
1 ATTGTATGTTGTGTGTTTAGATAGCGA-GTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTC
*
138229 TAACACTTGG
65 TAACACGTGG
*
138239 ATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCGGTTGATGAATTCT
1 ATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
*
138304 AACATGTGG
66 AACACGTGG
138313 ATTGT
1 ATTGT
138318 TGCCTTTGTC
Statistics
Matches: 820, Mismatches: 59, Indels: 18
0.91 0.07 0.02
Matches are distributed among these distances:
71 66 0.08
73 142 0.17
74 610 0.74
75 2 0.00
ACGTcount: A:0.28, C:0.09, G:0.27, T:0.37
Consensus pattern (74 bp):
ATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
AACACGTGG
Found at i:137900 original size:295 final size:295
Alignment explanation
Indices: 137356--138317 Score: 1499
Period size: 295 Copynumber: 3.3 Consensus size: 295
137346 GAATTACTCT
* * * *
137356 ATTGTATGTTGTGTGTTTAGATAGTGAGTTAAGATTGTTAGCATGTAAAGTAGTTGATGGATTCT
1 ATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
* * *
137421 AAC-TCATGGATTTTATGTTGTGTGTTTAGATAGCACGTTAAGGTTGTTAGCATGTAAAGAAGTT
66 AACAT-GTGGATTGTATGTTGTGTGTTTAGATAGCACGTTAAGGTTGTTAGCATGTAAAGCAGTT
*
137485 GATGAATTCTAACACGTGGATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGT
130 GATGAATTCTAACACGTGGATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGT
*
137550 AAAGAAGTTGATGAATTCTAACACGTGGATTGCATGTTGCGTGTTTAGATAGCGAGTTAAGATTG
195 AAAGAAGTTGATGAATTCTAACACGTGGATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTG
*
137615 TTAGCATGTAAAGCAGTTGATGAATTCTAACATGCGG
260 TTAGCATGTAAAGCAGTTGATGAATTCTAACAT-TGG
*
137652 ATTGCGTGTTGTG-GTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
1 ATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
* *
137716 AACATGTGGATTGTATGTTGTGTGTTTAGATAGCGCGTTAAGGTTGTTAGCACGTAAAGCAGTTG
66 AACATGTGGATTGTATGTTGTGTGTTTAGATAGCACGTTAAGGTTGTTAGCATGTAAAGCAGTTG
* * * *
137781 ATGATTTCTAGCACGTGGATTGTATATTGTGTGTTTAGATAGCGAGTTATGATTGTTAGCATGTA
131 ATGAATTCTAACACGTGGATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTA
*
137846 AAGAAGTTGATGAATTCTAACACATGGATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGT
196 AAGAAGTTGATGAATTCTAACACGTGGATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGT
* * *
137911 TAGCATGTAAAGAAGTTGATGAATTCTAACACATGA
261 TAGCATGTAAAGCAGTTGATGAATTCTAACA-TTGG
137947 ATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
1 ATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
* * *
138012 AACACGTGGATTGCATGTTGTG-GTTTAGATAGCTA-GTTAAGATTGTTAGCATGTAAAGCAGTT
66 AACATGTGGATTGTATGTTGTGTGTTTAGATAGC-ACGTTAAGGTTGTTAGCATGTAAAGCAGTT
* *
138075 GATGAATTCTAACACGTGGATTGTATGTTGTGTGTTTAGATAGCGCGTTAAGGTTGTTAGCATGT
130 GATGAATTCTAACACGTGGATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGT
* * * * * *
138140 AAAGCAGTTGAT---TTCTAACACGTGGATTGTATATTATCTGTTTAGATAGC-ACGTTAAGGTT
195 AAAGAAGTTGATGAATTCTAACACGTGGATTGCATGTTGTGTGTTTAGATAGCGA-GTTAAGATT
*
138201 GTTAGCATGTAAAGCAGTTGATGATTTCTAACACTTGG
259 GTTAGCATGTAAAGCAGTTGATGAATTCTAACA-TTGG
* *
138239 ATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCGGTTGATGAATTCT
1 ATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
138304 AACATGTGGATTGT
66 AACATGTGGATTGT
138318 TGCCTTTGTC
Statistics
Matches: 613, Mismatches: 48, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
291 1 0.00
292 150 0.24
295 379 0.62
296 83 0.14
ACGTcount: A:0.28, C:0.09, G:0.27, T:0.37
Consensus pattern (295 bp):
ATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCT
AACATGTGGATTGTATGTTGTGTGTTTAGATAGCACGTTAAGGTTGTTAGCATGTAAAGCAGTTG
ATGAATTCTAACACGTGGATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTA
AAGAAGTTGATGAATTCTAACACGTGGATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGT
TAGCATGTAAAGCAGTTGATGAATTCTAACATTGG
Found at i:138035 original size:369 final size:369
Alignment explanation
Indices: 137356--138307 Score: 1590
Period size: 369 Copynumber: 2.6 Consensus size: 369
137346 GAATTACTCT
* * * *
137356 ATTGTATGTTGTGTGTTTAGATAGTGAGTTAAGATTGTTAGCATGTAAAGTAGTTGATGGA-TTC
1 ATTGTATGTTGTGTGTTTAGATAGCGCGTTAAGGTTGTTAGCATGTAAAGCAGTTGAT-GATTTC
* * * *
137420 TAACTCATGGATTTTATGTTGTGTGTTTAGATAGCACGTTAAGGTTGTTAGCATGTAAAGAAGTT
65 TAACACGTGGATTGTATATTGTGTGTTTAGATAGCACGTTAAGGTTGTTAGCATGTAAAGAAGTT
*
137485 GATGAATTCTAACACGTGGATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGT
130 GATGAATTCTAACACATGGATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGT
* *
137550 AAAGAAGTTGATGAATTCTAACACGTGGATTGCATGTTGCGTGTTTAGATAGCGAGTTAAGATTG
195 AAAGAAGTTGATGAATTCTAACACATGAATTGCATGTTGCGTGTTTAGATAGCGAGTTAAGATTG
* *
137615 TTAGCATGTAAAGCAGTTGATGAATTCTAACATGCGGATTGCGTGTTGTGGTTTAGATAGCGAGT
260 TTAGCATGTAAAGCAGTTGATGAATTCTAACACGCGGATTGCATGTTGTGGTTTAGATAGCGAGT
*
137680 TAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCTAACATGTGG
325 TAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCTAACACGTGG
*
137725 ATTGTATGTTGTGTGTTTAGATAGCGCGTTAAGGTTGTTAGCACGTAAAGCAGTTGATGATTTCT
1 ATTGTATGTTGTGTGTTTAGATAGCGCGTTAAGGTTGTTAGCATGTAAAGCAGTTGATGATTTCT
* * *
137790 AGCACGTGGATTGTATATTGTGTGTTTAGATAGCGA-GTTATGATTGTTAGCATGTAAAGAAGTT
66 AACACGTGGATTGTATATTGTGTGTTTAGATAGC-ACGTTAAGGTTGTTAGCATGTAAAGAAGTT
137854 GATGAATTCTAACACATGGATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGT
130 GATGAATTCTAACACATGGATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGT
*
137919 AAAGAAGTTGATGAATTCTAACACATGAATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTG
195 AAAGAAGTTGATGAATTCTAACACATGAATTGCATGTTGCGTGTTTAGATAGCGAGTTAAGATTG
* *
137984 TTAGCATGTAAAGCAGTTGATGAATTCTAACACGTGGATTGCATGTTGTGGTTTAGATAGCTAGT
260 TTAGCATGTAAAGCAGTTGATGAATTCTAACACGCGGATTGCATGTTGTGGTTTAGATAGCGAGT
138049 TAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCTAACACGTGG
325 TAAGATTGTTAGCATGTAAAGCAGTTGATGAATTCTAACACGTGG
138094 ATTGTATGTTGTGTGTTTAGATAGCGCGTTAAGGTTGTTAGCATGTAAAGCAG-T--TGATTTCT
1 ATTGTATGTTGTGTGTTTAGATAGCGCGTTAAGGTTGTTAGCATGTAAAGCAGTTGATGATTTCT
* * *
138156 AACACGTGGATTGTATATTATCTGTTTAGATAGCACGTTAAGGTTGTTAGCATGTAAAGCAGTTG
66 AACACGTGGATTGTATATTGTGTGTTTAGATAGCACGTTAAGGTTGTTAGCATGTAAAGAAGTTG
* * *
138221 ATGATTTCTAACACTTGGATTGTATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTA
131 ATGAATTCTAACACATGGATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTA
**
138286 AAGCGGTTGATGAATTCTAACA
196 AAGAAGTTGATGAATTCTAACA
138308 TGTGGATTGT
Statistics
Matches: 547, Mismatches: 33, Indels: 9
0.93 0.06 0.02
Matches are distributed among these distances:
365 1 0.00
366 147 0.27
368 3 0.01
369 395 0.72
370 1 0.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.37
Consensus pattern (369 bp):
ATTGTATGTTGTGTGTTTAGATAGCGCGTTAAGGTTGTTAGCATGTAAAGCAGTTGATGATTTCT
AACACGTGGATTGTATATTGTGTGTTTAGATAGCACGTTAAGGTTGTTAGCATGTAAAGAAGTTG
ATGAATTCTAACACATGGATTGCATGTTGTGTGTTTAGATAGCGAGTTAAGATTGTTAGCATGTA
AAGAAGTTGATGAATTCTAACACATGAATTGCATGTTGCGTGTTTAGATAGCGAGTTAAGATTGT
TAGCATGTAAAGCAGTTGATGAATTCTAACACGCGGATTGCATGTTGTGGTTTAGATAGCGAGTT
AAGATTGTTAGCATGTAAAGCAGTTGATGAATTCTAACACGTGG
Found at i:140294 original size:115 final size:117
Alignment explanation
Indices: 140069--140333 Score: 405
Period size: 115 Copynumber: 2.3 Consensus size: 117
140059 TTAAGCATGA
* *
140069 ATTG-AGCTCAATTTCTTTCTTTTTTATTTATTTATTAATGATTTTAACTTTTTATTTTTTTTGG
1 ATTGAAGCCCAATTTCTTTC-TTTTTATTTATTTATTAATGATTTTAACTCTTTATTTTTTTTGG
*
140133 AAAAAAGAAAGAAATTTATAGTTGTTGACTTTTATTTTAGAAACTTCATTAAG
65 AAAAAAGAAAGAAATTTATAGTTGTTGACTTTTAATTTAGAAACTTCATTAAG
140186 ATTGAAGCCCAATTTCTTTCTTTTTATTTATTTATTAATGATTTTAACTCTTT-TTTTTTTT-GA
1 ATTGAAGCCCAATTTCTTTCTTTTTATTTATTTATTAATGATTTTAACTCTTTATTTTTTTTGGA
* *
140249 AGAAAA-AAAGAAATTTATATTTGTTGACTTTTAATTTAGAAACTTCATTCAG
66 A-AAAAGAAAGAAATTTATAGTTGTTGACTTTTAATTTAGAAACTTCATTAAG
* *
140301 ATAGAAGCCCAATTTCTTT-TTGTTTATCTATTT
1 ATTGAAGCCCAATTTCTTTCTT-TTTATTTATTT
140334 CTCTTGACAA
Statistics
Matches: 138, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
114 2 0.01
115 74 0.54
116 12 0.09
117 36 0.26
118 14 0.10
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.51
Consensus pattern (117 bp):
ATTGAAGCCCAATTTCTTTCTTTTTATTTATTTATTAATGATTTTAACTCTTTATTTTTTTTGGA
AAAAAGAAAGAAATTTATAGTTGTTGACTTTTAATTTAGAAACTTCATTAAG
Found at i:146980 original size:19 final size:19
Alignment explanation
Indices: 146952--146999 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
146942 ATGTATTATT
146952 TTATATTTATTTAAATATA
1 TTATATTTATTTAAATATA
*
146971 TTATACTTATTTAAATATA
1 TTATATTTATTTAAATATA
146990 TTATATTTAT
1 TTATATTTAT
147000 GGAGAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATATTTATTTAAATATA
Found at i:147512 original size:14 final size:14
Alignment explanation
Indices: 147493--147519 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
147483 ACACTAATTT
147493 TATTTTATTTTTTG
1 TATTTTATTTTTTG
147507 TATTTTATTTTTT
1 TATTTTATTTTTT
147520 TAGTTGTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (14 bp):
TATTTTATTTTTTG
Found at i:147526 original size:19 final size:19
Alignment explanation
Indices: 147489--147526 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
147479 GGTAACACTA
*
147489 ATTTTATTTTATTTTTTGT
1 ATTTTATTTTATTTGTTGT
147508 ATTTTATTTT-TTTAGTTGT
1 ATTTTATTTTATTT-GTTGT
147527 TGATTTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (19 bp):
ATTTTATTTTATTTGTTGT
Found at i:148821 original size:13 final size:13
Alignment explanation
Indices: 148803--148866 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
148793 AGTTTAGCAT
*
148803 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
148816 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
148829 TGC-TTTGAAAAAG
1 TGCTTTTG-AAAAG
*
148842 TGATTTTGAAAAG
1 TGCTTTTGAAAAG
*
148855 TACTTTTGAAAA
1 TGCTTTTGAAAA
148867 ATAAAATATC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
12 3 0.07
13 36 0.84
14 4 0.09
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:153202 original size:22 final size:22
Alignment explanation
Indices: 153177--153220 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
153167 CATCTAGTAG
153177 CTTTAATTTCATGAATGAGCAT
1 CTTTAATTTCATGAATGAGCAT
* *
153199 CTTTGATTTCATGAATTAGCAT
1 CTTTAATTTCATGAATGAGCAT
153221 ACAAACTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (22 bp):
CTTTAATTTCATGAATGAGCAT
Found at i:154979 original size:2 final size:2
Alignment explanation
Indices: 154972--155002 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
154962 AGATTTACCG
*
154972 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
155003 GCTACATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:159870 original size:21 final size:20
Alignment explanation
Indices: 159846--159895 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
159836 CAGATATCAT
159846 AATAAAACAAAT-TCAATTAAA
1 AATAAAA-AAATAT-AATTAAA
*
159867 AATAATAAAAATATAATTAAT
1 AATAA-AAAAATATAATTAAA
159888 AATAAAAA
1 AATAAAAA
159896 CTTTTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 20 0.77
22 3 0.12
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (20 bp):
AATAAAAAAATATAATTAAA
Found at i:167462 original size:29 final size:31
Alignment explanation
Indices: 167423--167484 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
167413 ATTTTAATAG
*
167423 TTTATAATTTT-AAAAAATTAAATTA-AATT
1 TTTATAATTTTAAAAAAATTAAAATACAATT
*
167452 TTTATATTTTTAAAAAAATTAAAATACAATT
1 TTTATAATTTTAAAAAAATTAAAATACAATT
167483 TT
1 TT
167485 ATTATTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 10 0.34
30 13 0.45
31 6 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (31 bp):
TTTATAATTTTAAAAAAATTAAAATACAATT
Found at i:167500 original size:36 final size:32
Alignment explanation
Indices: 167427--167502 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 32
167417 TAATAGTTTA
* *
167427 TAATTTTAAAAAATTAAATTAAATTTTTATAT
1 TAATTTAAAAAAATTAAAATAAATTTTTATAT
167459 T--TTTAAAAAAATTAAAATACAATTTTATTATTAT
1 TAATTTAAAAAAATTAAAATA-AA-TTT-TTA-TAT
167493 TAATTTAAAA
1 TAATTTAAAA
167503 TTTTAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
30 16 0.44
31 2 0.06
32 4 0.11
33 3 0.08
34 4 0.11
36 7 0.19
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (32 bp):
TAATTTAAAAAAATTAAAATAAATTTTTATAT
Found at i:169652 original size:3 final size:3
Alignment explanation
Indices: 169644--169683 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
169634 CTTACATAAC
169644 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
169684 AACCCAACCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:172253 original size:18 final size:20
Alignment explanation
Indices: 172230--172267 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
172220 TGAAAGATCT
172230 GTCCCATC-AAG-CATCCTC
1 GTCCCATCGAAGACATCCTC
172248 GTCCCATCGAAGACATCCTC
1 GTCCCATCGAAGACATCCTC
172268 TTCACGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 3 0.17
20 7 0.39
ACGTcount: A:0.24, C:0.42, G:0.13, T:0.21
Consensus pattern (20 bp):
GTCCCATCGAAGACATCCTC
Found at i:175687 original size:4 final size:4
Alignment explanation
Indices: 175671--175709 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
175661 AGGTATCATT
* *
175671 TATG TATG GATG TATG TATG CATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
175710 CTTTTCATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.46
Consensus pattern (4 bp):
TATG
Found at i:192449 original size:31 final size:31
Alignment explanation
Indices: 192414--192520 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 31
192404 TATCACTAAG
192414 AATATTTTTACAATTATATTGATACACTATT
1 AATATTTTTACAATTATATTGATACACTATT
* * * **
192445 AATATTTAT-CAATTTTTACAAGGTTAATTATCACTAAG
1 AATATTTTTACAA---TTA-TA--TTGA-TA-CACTATT
192483 AATATTTTTACAATTATATTGATACACTATT
1 AATATTTTTACAATTATATTGATACACTATT
192514 AATATTT
1 AATATTT
192521 ATCAATTTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
30 3 0.05
31 20 0.35
32 2 0.04
33 6 0.11
34 1 0.02
35 1 0.02
36 6 0.11
37 2 0.04
38 13 0.23
39 3 0.05
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (31 bp):
AATATTTTTACAATTATATTGATACACTATT
Found at i:192481 original size:69 final size:69
Alignment explanation
Indices: 192400--192541 Score: 284
Period size: 69 Copynumber: 2.1 Consensus size: 69
192390 AAGTGTGACA
192400 TAATTATCACTAAGAATATTTTTACAATTATATTGATACACTATTAATATTTATCAATTTTTACA
1 TAATTATCACTAAGAATATTTTTACAATTATATTGATACACTATTAATATTTATCAATTTTTACA
192465 AGGT
66 AGGT
192469 TAATTATCACTAAGAATATTTTTACAATTATATTGATACACTATTAATATTTATCAATTTTTACA
1 TAATTATCACTAAGAATATTTTTACAATTATATTGATACACTATTAATATTTATCAATTTTTACA
192534 AGGT
66 AGGT
192538 TAAT
1 TAAT
192542 ATTTGCAAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (69 bp):
TAATTATCACTAAGAATATTTTTACAATTATATTGATACACTATTAATATTTATCAATTTTTACA
AGGT
Found at i:193384 original size:21 final size:22
Alignment explanation
Indices: 193358--193399 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
193348 TTTCGGTTCC
193358 TTTAAAATCA-AAATTTTTTCA
1 TTTAAAATCATAAATTTTTTCA
*
193379 TTTAAATTCATTAAATTTTTT
1 TTTAAAATCA-TAAATTTTTT
193400 AAAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
23 9 0.50
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAAAATCATAAATTTTTTCA
Found at i:193981 original size:78 final size:78
Alignment explanation
Indices: 193823--193977 Score: 285
Period size: 77 Copynumber: 2.0 Consensus size: 78
193813 TAAGAGGTCT
193823 TTATAATCAAATTAGTCTCTCTATTATTAAATGAATCAATTTAGCATTTATATTATTAAAAAAAT
1 TTATAATCAAATTAGTCTCTCTATTATTAAATGAATCAATTTAGCATTTATATTATTAAAAAAAT
193888 CAAATAAAATTAA
66 CAAATAAAATTAA
*
193901 TTATAATCAAATTAGTC-CTCTATTATTAAATGAATCAATTTAGTATTTATATTATTAAAAAAAT
1 TTATAATCAAATTAGTCTCTCTATTATTAAATGAATCAATTTAGCATTTATATTATTAAAAAAAT
*
193965 CAAATAAAGTTAA
66 CAAATAAAATTAA
193978 ATTAGAACAG
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
77 58 0.77
78 17 0.23
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (78 bp):
TTATAATCAAATTAGTCTCTCTATTATTAAATGAATCAATTTAGCATTTATATTATTAAAAAAAT
CAAATAAAATTAA
Found at i:201895 original size:25 final size:25
Alignment explanation
Indices: 201863--201948 Score: 75
Period size: 25 Copynumber: 3.3 Consensus size: 25
201853 TTCTTAAATG
201863 ATTGATTAAAAATTTATTAAATATA
1 ATTGATTAAAAATTTATTAAATATA
* * *
201888 ATTGATTAAATTTAATATTTTTTTAA-ATG
1 ATTGATT-AA---AA-ATTTATTAAATATA
* *
201917 ATTAATTAAAAATTTATTAGATATA
1 ATTGATTAAAAATTTATTAAATATA
201942 ATTGATT
1 ATTGATT
201949 GAATTTAATA
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
24 7 0.15
25 17 0.37
26 2 0.04
28 2 0.04
29 10 0.22
30 8 0.17
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (25 bp):
ATTGATTAAAAATTTATTAAATATA
Found at i:201916 original size:54 final size:55
Alignment explanation
Indices: 201850--201963 Score: 194
Period size: 54 Copynumber: 2.1 Consensus size: 55
201840 GTAAAGATTT
*
201850 TTTTTCTTAAATGATTGATTAAAAATTTATTAAATATAATTGATTAAATTTAATA
1 TTTTTCTTAAATGATTAATTAAAAATTTATTAAATATAATTGATTAAATTTAATA
* *
201905 TTTTT-TTAAATGATTAATTAAAAATTTATTAGATATAATTGATTGAATTTAATA
1 TTTTTCTTAAATGATTAATTAAAAATTTATTAAATATAATTGATTAAATTTAATA
201959 TTTTT
1 TTTTT
201964 ATGATAATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
54 51 0.91
55 5 0.09
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (55 bp):
TTTTTCTTAAATGATTAATTAAAAATTTATTAAATATAATTGATTAAATTTAATA
Found at i:201947 original size:29 final size:29
Alignment explanation
Indices: 201867--201953 Score: 85
Period size: 30 Copynumber: 3.1 Consensus size: 29
201857 TAAATGATTG
201867 ATTAAAAATTTATTAAATATAATTGATTAA
1 ATTAAAAATTTATT-AATATAATTGATTAA
* * *
201897 ATTTAATATTT-TT--T-TAAATGATT-A
1 ATTAAAAATTTATTAATATAATTGATTAA
*
201921 ATTAAAAATTTATTAGATATAATTGATTGA
1 ATTAAAAATTTATTA-ATATAATTGATTAA
201951 ATT
1 ATT
201954 TAATATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
24 10 0.22
25 10 0.22
26 1 0.02
28 1 0.02
29 10 0.22
30 13 0.29
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (29 bp):
ATTAAAAATTTATTAATATAATTGATTAA
Found at i:205218 original size:24 final size:25
Alignment explanation
Indices: 205185--205235 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
205175 TTCGTAAGCC
*
205185 AAATAAATTATGCTAATAAATA-TA
1 AAATAAATTATACTAATAAATACTA
*
205209 AAATATATTATACTAATAAATACTA
1 AAATAAATTATACTAATAAATACTA
205234 AA
1 AA
205236 TCTTTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (25 bp):
AAATAAATTATACTAATAAATACTA
Found at i:205455 original size:3 final size:3
Alignment explanation
Indices: 205447--205481 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
205437 ATATATAGAT
205447 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
205482 TTGCTACTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:205488 original size:12 final size:12
Alignment explanation
Indices: 205449--205512 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
205439 ATATAGATTA
* *
205449 CTACTACTACTA
1 CTACTACTATTG
* *
205461 CTACTACTACTA
1 CTACTACTATTG
205473 CTACTACTATTG
1 CTACTACTATTG
*
205485 CTACTGCTATTG
1 CTACTACTATTG
* *
205497 TTGCTACTATTG
1 CTACTACTATTG
205509 CTAC
1 CTAC
205513 CCTAGTATAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.25, C:0.28, G:0.08, T:0.39
Consensus pattern (12 bp):
CTACTACTATTG
Found at i:208657 original size:23 final size:22
Alignment explanation
Indices: 208628--208756 Score: 123
Period size: 23 Copynumber: 5.5 Consensus size: 22
208618 GAACACTAGC
*
208628 GTGCTCTCTGTTTAGCACGTCT
1 GTGCTCTCTGTTTAGCACGTGT
208650 CGTGCTCTCTGTTATTAGCACTGTGT
1 -GTGCTCTCTG-T-TTAGCAC-GTGT
* * *
208676 GTGCTCTCTGATTAACACTTTGT
1 GTGCTCTCTGTTTAGCAC-GTGT
* * *
208699 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGTTTAGCAC-GTGT
*
208722 GTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGTTTAGCAC-GTGT
208745 GTGCTCTCTGTT
1 GTGCTCTCTGTT
208757 GCCCAGCACT
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
23 71 0.77
24 1 0.01
25 17 0.18
26 3 0.03
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (22 bp):
GTGCTCTCTGTTTAGCACGTGT
Found at i:208730 original size:46 final size:47
Alignment explanation
Indices: 208651--208755 Score: 140
Period size: 46 Copynumber: 2.2 Consensus size: 47
208641 AGCACGTCTC
* *
208651 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAACACTTTGT
1 GTGCTCTCTG-TATTAGCACTGTGTGTACTCTCTGATTAACACTGTGT
* * * *
208699 GTGCTCTCTG-ATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGTATTAGCACTGTGTGTACTCTCTGATTAACACTGTGT
208745 GTGCTCTCTGT
1 GTGCTCTCTGT
208756 TGCCCAGCAC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
46 40 0.80
48 10 0.20
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (47 bp):
GTGCTCTCTGTATTAGCACTGTGTGTACTCTCTGATTAACACTGTGT
Found at i:208799 original size:69 final size:69
Alignment explanation
Indices: 208654--208803 Score: 191
Period size: 69 Copynumber: 2.1 Consensus size: 69
208644 ACGTCTCGTG
*
208654 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAACACTTTGTGTGCTCTCTGATTAGTACTT
1 CTCTCTG-T-TTAGCACTGTGTGTGCTCTCTGATTAACACTTTATGTGCTCTCTGATTAGTACTT
208719 TGTGTA
64 TGTGTA
*
208725 CTCTCTGTTTAGCACTGTGTGTGCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTG-TTAGTAC
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATT----AACACTTTATGTGCTCTCTGATTAGTAC
208787 TTTG-GTA
62 TTTGTGTA
*
208794 TTCTCTGTTT
1 CTCTCTGTTT
208804 GTTCCGTATA
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
68 2 0.03
69 34 0.47
70 12 0.17
71 20 0.28
72 4 0.06
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (69 bp):
CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAACACTTTATGTGCTCTCTGATTAGTACTTTG
TGTA
Found at i:209629 original size:11 final size:11
Alignment explanation
Indices: 209613--209637 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
209603 ATCTCTGTCT
209613 CTTCACCCCAA
1 CTTCACCCCAA
209624 CTTCACCCCAA
1 CTTCACCCCAA
209635 CTT
1 CTT
209638 GGTGAATCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.52, G:0.00, T:0.24
Consensus pattern (11 bp):
CTTCACCCCAA
Found at i:212307 original size:16 final size:16
Alignment explanation
Indices: 212286--212320 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
212276 ATTATTTTAG
212286 TTATTTATTTAAATTT
1 TTATTTATTTAAATTT
* *
212302 TTATTTCTTTTAATTT
1 TTATTTATTTAAATTT
212318 TTA
1 TTA
212321 AATTTGTATT
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:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTATTTAAATTT
Found at i:214860 original size:22 final size:23
Alignment explanation
Indices: 214811--214860 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
214801 TATTTAAGCT
*
214811 CTTT-ATAATTTATAAAATTTTA
1 CTTTAATAATTTATAAAATTGTA
**
214833 AATTAATAA-TTATAAAATTGTA
1 CTTTAATAATTTATAAAATTGTA
214855 CTTTAA
1 CTTTAA
214861 CCTCTAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (23 bp):
CTTTAATAATTTATAAAATTGTA
Found at i:217264 original size:23 final size:21
Alignment explanation
Indices: 217212--217265 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
217202 AAATAATAGT
* *
217212 AAAAGCAACACCAAAACAATA
1 AAAAACAACACCAAAACAACA
*
217233 AAAAACAACACCAAAATAACA
1 AAAAACAACACCAAAACAACA
217254 ATCAAAACAACA
1 A--AAAACAACA
217266 AAATAAATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 19 0.68
23 9 0.32
ACGTcount: A:0.69, C:0.24, G:0.02, T:0.06
Consensus pattern (21 bp):
AAAAACAACACCAAAACAACA
Found at i:224393 original size:2 final size:2
Alignment explanation
Indices: 224386--224413 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
224376 AATACTGGAG
224386 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
224414 GATGTAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:244323 original size:62 final size:61
Alignment explanation
Indices: 244198--244331 Score: 148
Period size: 62 Copynumber: 2.1 Consensus size: 61
244188 GGGGTCCAAA
* **
244198 TTTTTTTTTTTTTAATTTAAGAGATTCAAAATTTTTTTTACCAACTTTTAAGAGGTCATAATT
1 TTTTTTTTTTTTTAATTTAAGAGACTCAAAATTTTTTTT--CAACTTTTAAGAACTCATAATT
* *
244261 TTTTTTTTTTTTTAAGTTTTAAG-GGCTCAAAATTTTTTATT-AACTTTTAAGACACTTA-AATT
1 TTTTTTTTTTTTTAA--TTTAAGAGACTCAAAATTTTTT-TTCAACTTTTAAGA-ACTCATAATT
244323 TTTTTTTTT
1 TTTTTTTTT
244332 CTAACTTTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
62 24 0.39
63 17 0.27
64 13 0.21
65 8 0.13
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.57
Consensus pattern (61 bp):
TTTTTTTTTTTTTAATTTAAGAGACTCAAAATTTTTTTTCAACTTTTAAGAACTCATAATT
Found at i:244351 original size:31 final size:31
Alignment explanation
Indices: 244293--244351 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
244283 GGGCTCAAAA
*
244293 TTTTTTATTAACTTTTAAGACACTTAAATTT
1 TTTTTTATTAACTTTTAAGACAATTAAATTT
*
244324 TTTTTTTTCTAACTTTTAAGA-AATTAAA
1 TTTTTTAT-TAACTTTTAAGACAATTAAA
244352 AACTTCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 13 0.52
32 12 0.48
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTTTTATTAACTTTTAAGACAATTAAATTT
Found at i:247116 original size:27 final size:27
Alignment explanation
Indices: 247049--247109 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
247039 CCTTTCAAAA
247049 TAGAAAGGGATGATAAAGTTAATTGAT
1 TAGAAAGGGATGATAAAGTTAATTGAT
*
247076 TAGAAAGGGATGATAAAGTTGATTGAT
1 TAGAAAGGGATGATAAAGTTAATTGAT
247103 TAGAAAG
1 TAGAAAG
247110 AGGTGATTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (27 bp):
TAGAAAGGGATGATAAAGTTAATTGAT
Found at i:253668 original size:17 final size:17
Alignment explanation
Indices: 253622--253671 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
253612 GAATTCTTGT
253622 TAAAATAAAATACAACAG
1 TAAAATAAAATA-AACAG
253640 TAAAATAAAATAAA-AG
1 TAAAATAAAATAAACAG
*
253656 TAAAGTCAAAATAAAC
1 TAAAAT-AAAATAAAC
253672 TAGACTTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 7 0.24
17 10 0.34
18 12 0.41
ACGTcount: A:0.68, C:0.08, G:0.06, T:0.18
Consensus pattern (17 bp):
TAAAATAAAATAAACAG
Found at i:257996 original size:32 final size:33
Alignment explanation
Indices: 257957--258030 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
257947 GTCAAAGTTG
* * *
257957 TTTATTTTATTAATTTTGTTTTGA-TTAAATT-
1 TTTATTTTACTAATTTCGTTTTGACTAAAATTA
*
257988 TGTTATTTTCCTAATTTCGTTTTGACTAAAATTA
1 T-TTATTTTACTAATTTCGTTTTGACTAAAATTA
258022 TTTATTTTA
1 TTTATTTTA
258031 AGTAAATAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 1 0.03
32 20 0.57
33 13 0.37
34 1 0.03
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.62
Consensus pattern (33 bp):
TTTATTTTACTAATTTCGTTTTGACTAAAATTA
Done.