Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011627.1 Kokia drynarioides strain JFW-HI SEQ_126618, 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: 128154
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 59 characters in sequence are not A, C, G, or T
Found at i:354 original size:26 final size:26
Alignment explanation
Indices: 302--355 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
292 TAAATTTAAA
* **
302 AAATTATTTAGAATTAAAATTTTATT
1 AAATTATTTAAAATTAAAATTAAATT
*
328 AAATTATTTAAAATTAAGATTAAATT
1 AAATTATTTAAAATTAAAATTAAATT
354 AA
1 AA
356 TAAAATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (26 bp):
AAATTATTTAAAATTAAAATTAAATT
Found at i:3257 original size:29 final size:32
Alignment explanation
Indices: 3216--3296 Score: 87
Period size: 33 Copynumber: 2.6 Consensus size: 32
3206 AATTGAATCA
* *
3216 AAACAAAATTTCATGTATA-G-AATTACACA-
1 AAACCAAAGTTCATGTATATGCAATTACACAT
* *
3245 AAATCAAAGTTCATGTATATGCAATTGCACATT
1 AAACCAAAGTTCATGTATATGCAATTACACA-T
*
3278 AAACCATAGTTCATGTATA
1 AAACCAAAGTTCATGTATA
3297 ATTTTGAGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
29 16 0.38
30 1 0.02
31 8 0.19
33 17 0.40
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (32 bp):
AAACCAAAGTTCATGTATATGCAATTACACAT
Found at i:4603 original size:21 final size:21
Alignment explanation
Indices: 4579--4650 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
4569 CTTTTATGGA
4579 TTGTGATTTCATTTGTGCTTG
1 TTGTGATTTCATTTGTGCTTG
* ** ** *
4600 TTGTTATTTTGTTT-TTATGG
1 TTGTGATTTCATTTGTGCTTG
4620 ATTGTGATTTCATTTGTGCTTG
1 -TTGTGATTTCATTTGTGCTTG
*
4642 TTGTTATTT
1 TTGTGATTT
4651 TGTTTTTTAG
Statistics
Matches: 36, Mismatches: 13, Indels: 4
0.68 0.25 0.08
Matches are distributed among these distances:
20 3 0.08
21 30 0.83
22 3 0.08
ACGTcount: A:0.11, C:0.06, G:0.21, T:0.62
Consensus pattern (21 bp):
TTGTGATTTCATTTGTGCTTG
Found at i:4621 original size:42 final size:42
Alignment explanation
Indices: 4570--4657 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
4560 TTTCGTTTTC
4570 TTTTATGGATTGTGATTTCATTTGTGCTTGTTGTTATTTTGT
1 TTTTATGGATTGTGATTTCATTTGTGCTTGTTGTTATTTTGT
4612 TTTTATGGATTGTGATTTCATTTGTGCTTGTTGTTATTTTGT
1 TTTTATGGATTGTGATTTCATTTGTGCTTGTTGTTATTTTGT
4654 TTTT
1 TTTT
4658 TAGGCATGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.11, C:0.05, G:0.20, T:0.64
Consensus pattern (42 bp):
TTTTATGGATTGTGATTTCATTTGTGCTTGTTGTTATTTTGT
Found at i:9332 original size:82 final size:82
Alignment explanation
Indices: 9195--9359 Score: 321
Period size: 82 Copynumber: 2.0 Consensus size: 82
9185 GAAAATGATG
*
9195 TATTGGACCTCGTTTTTGAAATTAAGGGCCGTAAATATTTTTATTAAATATTTATAGAGTCTTAT
1 TATTGGACCTCGTTTTTGAAATTAAGGGCCATAAATATTTTTATTAAATATTTATAGAGTCTTAT
9260 TATATGTGAATTGAAGT
66 TATATGTGAATTGAAGT
9277 TATTGGACCTCGTTTTTGAAATTAAGGGCCATAAATATTTTTATTAAATATTTATAGAGTCTTAT
1 TATTGGACCTCGTTTTTGAAATTAAGGGCCATAAATATTTTTATTAAATATTTATAGAGTCTTAT
9342 TATATGTGAATTGAAGT
66 TATATGTGAATTGAAGT
9359 T
1 T
9360 CGATTGAGTA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.44
Consensus pattern (82 bp):
TATTGGACCTCGTTTTTGAAATTAAGGGCCATAAATATTTTTATTAAATATTTATAGAGTCTTAT
TATATGTGAATTGAAGT
Found at i:11301 original size:52 final size:52
Alignment explanation
Indices: 11222--11357 Score: 193
Period size: 52 Copynumber: 2.6 Consensus size: 52
11212 ATAAATGGAA
11222 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT-CCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCCTTTACGGATT-T
* * * * *
11274 GAGGTCCGATGACTATGAGTCATCGTGAGCATATGGATCCCTTTTCGGATTT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCCTTTACGGATTT
* *
11326 AAAGTCCGATGACTTTGTGTCATCGTGAGTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTAT
11358 TAAATGGGAA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
52 62 0.85
53 11 0.15
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCCTTTACGGATTT
Found at i:12668 original size:12 final size:12
Alignment explanation
Indices: 12651--12677 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12641 TCGGAATATC
12651 CTTTTTCTTCTT
1 CTTTTTCTTCTT
12663 CTTTTTCTTCTT
1 CTTTTTCTTCTT
12675 CTT
1 CTT
12678 CTTAAACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:17794 original size:27 final size:27
Alignment explanation
Indices: 17750--17818 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 27
17740 TTATGAATAA
* * *
17750 ATTATTATAAAGTGGATGTCCGTTAAG
1 ATTAATATAAATTGGATGTACGTTAAG
* *
17777 ATTAATATAAATTTGATGTACTTTAAG
1 ATTAATATAAATTGGATGTACGTTAAG
*
17804 ACTTGAATATTAATT
1 A-TT-AATATAAATT
17819 AAAAATAAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 23 0.68
28 2 0.06
29 9 0.26
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (27 bp):
ATTAATATAAATTGGATGTACGTTAAG
Found at i:18019 original size:12 final size:12
Alignment explanation
Indices: 17976--18023 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
17966 ATTTCATAAC
17976 ACTTTTATAATT
1 ACTTTTATAATT
* *
17988 ATTTATTAATAATA
1 ACTT-TT-ATAATT
*
18002 ATTTTTATAATT
1 ACTTTTATAATT
18014 ACTTTTATAA
1 ACTTTTATAA
18024 AATTGAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 17 0.57
13 4 0.13
14 9 0.30
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (12 bp):
ACTTTTATAATT
Found at i:23708 original size:29 final size:30
Alignment explanation
Indices: 23661--23717 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
23651 ATCGGAGTTC
*
23661 AAAATGAGACTTTTCGGATTCCCGGGGGCA
1 AAAATGAGAATTTTCGGATTCCCGGGGGCA
* *
23691 AAAATGATAATTTT-GGATTCTCGGGGG
1 AAAATGAGAATTTTCGGATTCCCGGGGG
23718 TGAAACGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (30 bp):
AAAATGAGAATTTTCGGATTCCCGGGGGCA
Found at i:23819 original size:30 final size:30
Alignment explanation
Indices: 23778--24113 Score: 177
Period size: 30 Copynumber: 11.4 Consensus size: 30
23768 ATCCGGGGGT
*
23778 AAAATGTAATTTTAGGAAGTTTTGGAGTCA
1 AAAATGGAATTTTAGGAAGTTTTGGAGTCA
* *
23808 AAAATGGAATTTTGGGAAG-TTT-GAGGCTA
1 AAAATGGAATTTTAGGAAGTTTTGGAGTC-A
* *
23837 AAAATGGAATTTTTA-GAAG-TTTCGAGGTTA
1 AAAATGGAA-TTTTAGGAAGTTTTGGA-GTCA
* *
23867 AAAATGGAATTTT-GGAAGTTCT-AAGGTCA
1 AAAATGGAATTTTAGGAAGTTTTGGA-GTCA
* * *
23896 AAAATGGGATTTTTA-GAAGTTTGGGGGT-A
1 AAAAT-GGAATTTTAGGAAGTTTTGGAGTCA
*
23925 AAAACTGG-ATTTTTGGAAGTTTTGG-GATCA
1 AAAA-TGGAATTTTAGGAAGTTTTGGAG-TCA
* *
23955 AAAATGGGATTTTTA-GAAG-TTTGGGGT-A
1 AAAAT-GGAATTTTAGGAAGTTTTGGAGTCA
* * *
23983 AAAATGGAATTTTTGG-AGGTTTCGAGGTCA
1 AAAATGGAATTTTAGGAAGTTTTGGA-GTCA
* * * * * *
24013 AAAATGGGATTTTTGAAAGTTTAGGGGT-T
1 AAAATGGAATTTTAGGAAGTTTTGGAGTCA
* *
24042 AAAATGGGATTTTTA-GAAGTTTT-GAGGTTA
1 AAAAT-GGAATTTTAGGAAGTTTTGGA-GTCA
* * * * *
24072 AAAATGGGATTTTTGGATGTTTCGGGGTC-
1 AAAATGGAATTTTAGGAAGTTTTGGAGTCA
*
24101 AAAATGGGATTTT
1 AAAATGGAATTTT
24114 TAGAAGCTTC
Statistics
Matches: 236, Mismatches: 44, Indels: 53
0.71 0.13 0.16
Matches are distributed among these distances:
27 9 0.04
28 21 0.09
29 96 0.41
30 99 0.42
31 11 0.05
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (30 bp):
AAAATGGAATTTTAGGAAGTTTTGGAGTCA
Found at i:23840 original size:29 final size:29
Alignment explanation
Indices: 23743--24181 Score: 292
Period size: 29 Copynumber: 15.0 Consensus size: 29
23733 GGGAAAATGA
* * **
23743 GAGGTTAAAAATGGATTTTTTGGACA-TCC
1 GAGGGTAAAAATGGAATTTTTGGA-AGTTT
* * *
23772 GGGGGT-AAAATGTAATTTTAGGAAGTTTT
1 GAGGGTAAAAATGGAATTTTTGGAAG-TTT
* *
23801 G-GAGTCAAAAATGGAATTTTGGGAAGTTT
1 GAGGGT-AAAAATGGAATTTTTGGAAGTTT
* *
23830 GAGGCTAAAAATGGAATTTTTAGAAGTTT
1 GAGGGTAAAAATGGAATTTTTGGAAGTTT
*
23859 CGAGGTTAAAAATGGAA-TTTTGGAAGTTCT
1 -GAGGGTAAAAATGGAATTTTTGGAAGTT-T
* * *
23889 -AAGGTCAAAAATGGGATTTTTAGAAGTTT
1 GAGGGT-AAAAATGGAATTTTTGGAAGTTT
*
23918 GGGGGTAAAAACTGG-ATTTTTGGAAGTTTT
1 GAGGGTAAAAA-TGGAATTTTTGGAAG-TTT
* * *
23948 G-GGATCAAAAATGGGATTTTTAGAAGTTT
1 GAGGGT-AAAAATGGAATTTTTGGAAGTTT
*
23977 G-GGGTAAAAATGGAATTTTTGGAGGTTT
1 GAGGGTAAAAATGGAATTTTTGGAAGTTT
* *
24005 CGA-GGTCAAAAATGGGATTTTTGAAAGTTT
1 -GAGGGT-AAAAATGGAATTTTTGGAAGTTT
* * *
24035 -AGGGGTTAAAATGGGATTTTTAGAAGTTTT
1 GA-GGGTAAAAATGGAATTTTTGGAAG-TTT
* * *
24065 GAGGTTAAAAATGGGATTTTTGGATGTTT
1 GAGGGTAAAAATGGAATTTTTGGAAGTTT
* * * *
24094 CG-GGGTCAAAATGGGATTTTTAGAAGCTTC
1 -GAGGGTAAAAATGGAATTTTTGGAAG-TTT
** *
24124 GA-GGTCAAAAATAGG-ATTTTTAAAAGTTC
1 GAGGGT-AAAAAT-GGAATTTTTGGAAGTTT
* * *
24153 GGGGGTAAAAACGGGATTTTTGGAAGTTT
1 GAGGGTAAAAATGGAATTTTTGGAAGTTT
24182 CGGGACCCTC
Statistics
Matches: 331, Mismatches: 51, Indels: 56
0.76 0.12 0.13
Matches are distributed among these distances:
27 1 0.00
28 43 0.13
29 147 0.44
30 137 0.41
31 3 0.01
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (29 bp):
GAGGGTAAAAATGGAATTTTTGGAAGTTT
Found at i:23848 original size:59 final size:57
Alignment explanation
Indices: 23778--24181 Score: 341
Period size: 59 Copynumber: 6.9 Consensus size: 57
23768 ATCCGGGGGT
* * *
23778 AAAATGTAATTTTAGGAAGTTTTGGAGTCAAAAATGGAATTTTGGGAAGTTTGAGG-CTA
1 AAAATGGAATTTTA-GAAGTTTTGGGGT-AAAAATGGAATTTTTGGAAGTTTGAGGTC-A
* * *
23837 AAAATGGAATTTTTAGAAGTTTCGAGGTTAAAAATGGAA-TTTTGGAAGTTCTAAGGTCA
1 AAAATGGAA-TTTTAGAAGTTTTG-GGGTAAAAATGGAATTTTTGGAAGTT-TGAGGTCA
* *
23896 AAAATGGGATTTTTAGAAGTTTGGGGGTAAAAACTGG-ATTTTTGGAAGTTTTG-GGATCA
1 AAAAT-GGAATTTTAGAAGTTTTGGGGTAAAAA-TGGAATTTTTGGAAG-TTTGAGG-TCA
* *
23955 AAAATGGGATTTTTAGAAG-TTTGGGGTAAAAATGGAATTTTTGGAGGTTTCGAGGTCA
1 AAAAT-GGAATTTTAGAAGTTTTGGGGTAAAAATGGAATTTTTGGAAGTTT-GAGGTCA
* * * * * * *
24013 AAAATGGGATTTTTGAAAGTTTAGGGGTTAAAATGGGATTTTTAGAAGTTTTGAGGTTA
1 AAAATGGAATTTTAG-AAGTTTTGGGGTAAAAATGGAATTTTTGGAAG-TTTGAGGTCA
* * * * * * * *
24072 AAAATGGGATTTTTGGATGTTTCGGGGTCAAAATGGGATTTTTAGAAGCTTCGAGGTCA
1 AAAAT-GGAATTTTAGAAGTTTTGGGGTAAAAATGGAATTTTTGGAAG-TTTGAGGTCA
* * ** * *
24131 AAAATAGGATTTTTAAAAGTTCGGGGGTAAAAACGGGATTTTTGGAAGTTT
1 AAAAT-GGAATTTTAGAAGTTTTGGGGTAAAAATGGAATTTTTGGAAGTTT
24182 CGGGACCCTC
Statistics
Matches: 289, Mismatches: 40, Indels: 33
0.80 0.11 0.09
Matches are distributed among these distances:
57 13 0.04
58 57 0.20
59 196 0.68
60 23 0.08
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (57 bp):
AAAATGGAATTTTAGAAGTTTTGGGGTAAAAATGGAATTTTTGGAAGTTTGAGGTCA
Found at i:24141 original size:30 final size:30
Alignment explanation
Indices: 23787--24183 Score: 338
Period size: 29 Copynumber: 13.5 Consensus size: 30
23777 TAAAATGTAA
* *
23787 TTTTAGGAAGTTTTG-GAGTCAAAAATGGAAT
1 TTTTA-GAAGTTTCGAG-GTCAAAAATGGGAT
** *
23818 TTTGGGAAGTTT-GAGG-CTAAAAATGGAAT
1 TTTTAGAAGTTTCGAGGTC-AAAAATGGGAT
* *
23847 TTTTAGAAGTTTCGAGGTTAAAAAT-GGAA
1 TTTTAGAAGTTTCGAGGTCAAAAATGGGAT
* *
23876 TTTTGGAAG-TTCTAAGGTCAAAAATGGGAT
1 TTTTAGAAGTTTC-GAGGTCAAAAATGGGAT
* *
23906 TTTTAGAAGTTTGGGGGT-AAAAACT-GGAT
1 TTTTAGAAGTTTCGAGGTCAAAAA-TGGGAT
* *
23935 TTTTGGAAGTTTTG-GGATCAAAAATGGGAT
1 TTTTAGAAGTTTCGAGG-TCAAAAATGGGAT
* *
23965 TTTTAGAAGTTT-GGGGT-AAAAATGGAAT
1 TTTTAGAAGTTTCGAGGTCAAAAATGGGAT
* *
23993 TTTTGGAGGTTTCGAGGTCAAAAATGGGAT
1 TTTTAGAAGTTTCGAGGTCAAAAATGGGAT
* * *
24023 TTTT-GAAAGTTTAGGGGT-TAAAATGGGAT
1 TTTTAG-AAGTTTCGAGGTCAAAAATGGGAT
* *
24052 TTTTAGAAGTTTTGAGGTTAAAAATGGGAT
1 TTTTAGAAGTTTCGAGGTCAAAAATGGGAT
* * *
24082 TTTTGGATGTTTCGGGGTC-AAAATGGGAT
1 TTTTAGAAGTTTCGAGGTCAAAAATGGGAT
* *
24111 TTTTAGAAGCTTCGAGGTCAAAAATAGGAT
1 TTTTAGAAGTTTCGAGGTCAAAAATGGGAT
* * *
24141 TTTTAAAAG-TTCGGGGGT-AAAAACGGGAT
1 TTTTAGAAGTTTC-GAGGTCAAAAATGGGAT
*
24170 TTTTGGAAGTTTCG
1 TTTTAGAAGTTTCG
24184 GGACCCTCGG
Statistics
Matches: 300, Mismatches: 46, Indels: 42
0.77 0.12 0.11
Matches are distributed among these distances:
28 26 0.09
29 142 0.47
30 127 0.42
31 5 0.02
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (30 bp):
TTTTAGAAGTTTCGAGGTCAAAAATGGGAT
Found at i:25426 original size:20 final size:20
Alignment explanation
Indices: 25401--25447 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
25391 CAAACCTGTG
* * *
25401 TGCTTTGGTTGTTTGGCAAT
1 TGCTTTGATTGTCTAGCAAT
25421 TGCTTTGATTGTCTAGCAAT
1 TGCTTTGATTGTCTAGCAAT
25441 TGCTTTG
1 TGCTTTG
25448 CCTTTTCGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.49
Consensus pattern (20 bp):
TGCTTTGATTGTCTAGCAAT
Found at i:25935 original size:11 final size:11
Alignment explanation
Indices: 25921--25991 Score: 72
Period size: 11 Copynumber: 6.4 Consensus size: 11
25911 TGGACTTTTT
25921 AATTTAAATTA
1 AATTTAAATTA
* *
25932 AATTCAATTTA
1 AATTTAAATTA
*
25943 AATTT-AATATC
1 AATTTAAAT-TA
25954 AATTTAAATTTA
1 AATTTAAA-TTA
*
25966 AATTTAAATCA
1 AATTTAAATTA
*
25977 AATTTAAAATA
1 AATTTAAATTA
25988 AATT
1 AATT
25992 AAAAAAAACC
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
10 2 0.04
11 34 0.71
12 11 0.23
13 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:25946 original size:6 final size:6
Alignment explanation
Indices: 25921--25984 Score: 64
Period size: 6 Copynumber: 11.3 Consensus size: 6
25911 TGGACTTTTT
* * *
25921 AATTTA AA-TTA AA-TTC AATTTA AATTT- AATATC AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
25966 AATTTA AA-TCA AATTTA AA
1 AATTTA AATTTA AATTTA AA
25985 ATAAATTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
5 17 0.35
6 31 0.65
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:25955 original size:17 final size:16
Alignment explanation
Indices: 25921--25966 Score: 74
Period size: 17 Copynumber: 2.8 Consensus size: 16
25911 TGGACTTTTT
*
25921 AATTTAAATTAAATTC
1 AATTTAAATTTAATTC
25937 AATTTAAATTTAATATC
1 AATTTAAATTTAAT-TC
25954 AATTTAAATTTAA
1 AATTTAAATTTAA
25967 ATTTAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTTAAATTTAATTC
Found at i:25967 original size:23 final size:23
Alignment explanation
Indices: 25921--25984 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
25911 TGGACTTTTT
* *
25921 AATTTAAATTAAA-TTCAATTTA
1 AATTTAAATCAAATTTAAATTTA
25943 AATTTAATATC-AATTTAAATTTA
1 AATTTAA-ATCAAATTTAAATTTA
25966 AATTTAAATCAAATTTAAA
1 AATTTAAATCAAATTTAAA
25985 ATAAATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
22 12 0.32
23 25 0.68
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTTAAATCAAATTTAAATTTA
Found at i:28128 original size:15 final size:15
Alignment explanation
Indices: 28110--28152 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
28100 ATAATAAAAG
28110 TAATATTAATTAATA
1 TAATATTAATTAATA
*
28125 TAATATTATATTAATG
1 TAATATTA-ATTAATA
28141 TGAA-ATTAATTA
1 T-AATATTAATTA
28153 GTTTAGTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 12 0.48
16 11 0.44
17 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (15 bp):
TAATATTAATTAATA
Found at i:29734 original size:44 final size:44
Alignment explanation
Indices: 29671--29760 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
29661 GGTTTTAAGA
29671 AGGATCGTTTGTGACCCCTCGAATCTTTCTTCAGAATTAAATCC
1 AGGATCGTTTGTGACCCCTCGAATCTTTCTTCAGAATTAAATCC
29715 AGGATCGTTTGTGACCCCTCGAATCTTTCTTCAGAATTAAATCC
1 AGGATCGTTTGTGACCCCTCGAATCTTTCTTCAGAATTAAATCC
29759 AG
1 AG
29761 TATGGTTTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (44 bp):
AGGATCGTTTGTGACCCCTCGAATCTTTCTTCAGAATTAAATCC
Found at i:32531 original size:29 final size:29
Alignment explanation
Indices: 32488--32554 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
32478 GTATTTTTTT
* *
32488 ATCATCTAATTATGAAAAATTATAAAATG
1 ATCATTTAATTATGAAAAATTACAAAATG
* *
32517 GTCATTTAATTATGAAAAGTTACAAAATG
1 ATCATTTAATTATGAAAAATTACAAAATG
*
32546 ATCACTTAA
1 ATCATTTAA
32555 CTATTCAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (29 bp):
ATCATTTAATTATGAAAAATTACAAAATG
Found at i:33547 original size:2 final size:2
Alignment explanation
Indices: 33542--33582 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
33532 TATATATATA
33542 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
33583 AAGAATTGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:36610 original size:32 final size:31
Alignment explanation
Indices: 36553--36612 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
36543 AAACTATTAT
*
36553 AATAAAGTTTAGAATGATTTTTAATTTTAAA
1 AATAAAGTTTAGAAAGATTTTTAATTTTAAA
36584 AATAAAGTTTA-AAAGACATTTTTAATTTT
1 AATAAAGTTTAGAAAG--ATTTTTAATTTT
36613 TTTTATTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 3 0.12
31 11 0.42
32 12 0.46
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (31 bp):
AATAAAGTTTAGAAAGATTTTTAATTTTAAA
Found at i:43054 original size:3 final size:3
Alignment explanation
Indices: 43046--43071 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43036 GAGATGGAGA
43046 TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TG
43072 ACACATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:43877 original size:10 final size:10
Alignment explanation
Indices: 43862--43903 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
43852 TCTTAACAAC
43862 TTTTTAATGA
1 TTTTTAATGA
43872 TTTTT-ATG-
1 TTTTTAATGA
*
43880 TTTTTAATAA
1 TTTTTAATGA
43890 TTTTTAATTGA
1 TTTTTAA-TGA
43901 TTT
1 TTT
43904 GCTTACGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 5 0.19
9 5 0.19
10 12 0.44
11 5 0.19
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (10 bp):
TTTTTAATGA
Found at i:43886 original size:29 final size:29
Alignment explanation
Indices: 43845--43903 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
43835 TACAAAATAA
43845 TTTATATTCTTAACAACTTTTTAA-TGATT
1 TTTATATTCTTAACAA-TTTTTAATTGATT
* * *
43874 TTTATGTTTTTAATAATTTTTAATTGATT
1 TTTATATTCTTAACAATTTTTAATTGATT
43903 T
1 T
43904 GCTTACGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (29 bp):
TTTATATTCTTAACAATTTTTAATTGATT
Found at i:44065 original size:19 final size:19
Alignment explanation
Indices: 43973--44065 Score: 55
Period size: 19 Copynumber: 4.9 Consensus size: 19
43963 ATTCCTAGCC
* *
43973 AATACCAAAATTTCTAACG
1 AATATCAAAATTTCTAACA
* ***
43992 AGTATCAAAGCCTCTAACA
1 AATATCAAAATTTCTAACA
* *
44011 TATATC-AAATTTCTTAACG
1 AATATCAAAATTTC-TAACA
* **
44030 AATA-CTAGAATCCCTAACA
1 AATATC-AAAATTTCTAACA
44049 AATATCAAAATTTCTAA
1 AATATCAAAATTTCTAA
44066 TGAAAGATGT
Statistics
Matches: 50, Mismatches: 20, Indels: 8
0.64 0.26 0.10
Matches are distributed among these distances:
18 5 0.10
19 40 0.80
20 5 0.10
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.29
Consensus pattern (19 bp):
AATATCAAAATTTCTAACA
Found at i:44239 original size:19 final size:19
Alignment explanation
Indices: 44215--44253 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
44205 CCTAACATCC
*
44215 TCCATTAAAAATTTTGATA
1 TCCATTAAAAACTTTGATA
44234 TCCATTAAAAACTTTGATA
1 TCCATTAAAAACTTTGATA
44253 T
1 T
44254 TTGGTATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (19 bp):
TCCATTAAAAACTTTGATA
Found at i:47720 original size:222 final size:221
Alignment explanation
Indices: 47301--47737 Score: 615
Period size: 222 Copynumber: 2.0 Consensus size: 221
47291 AAAAAAGTCT
* *
47301 AACGAAATAAACCAAAAATCGAAAAATAAGTCCAAAAGTACCAACAATCCAAAAAGTCCATATTA
1 AACGAAATAAACCAAAAACCGAAAAACAAGTCCAAAAGTACCAACAATCCAAAAAGTCCATATTA
* * * * * *
47366 AAAAATAAGTATCTTAAAACTGTTTTATTATTAAGAATTCAACCCGAGCTCCCACACGTCGTCCC
66 AAAAATAAGTATCTTAAAACTGTTTTATTACTAAAAATCCAACCCGAGCTCCCACACGCCATCCA
* * * * * *
47431 TTCCTAAGTTTGCTAATTACCCGAGAAGTTAAAAAATATAGGGTGAGCTAACAAAGTTCAGTGTG
131 ATCCTAAGTTTGCTAATTACCCGAAAAGATAAAAAATATAGGATGAGCTAACAAAGCTAAGTGTG
47496 CAACTCAGCCCTCATGCATAACAGGC
196 CAACTCAGCCCTCATGCATAACAGGC
* * *
47522 AACGAAATAAGCCAAAAACCGAAAAACAAGTCCAAAAGTATCAACAGTCCAAAAAGTCCATATTA
1 AACGAAATAAACCAAAAACCGAAAAACAAGTCCAAAAGTACCAACAATCCAAAAAGTCCATATTA
* * *** * *
47587 AACAATAAGTCTCTTAAAAACTGTTTTATTACTAAAAATCCAACCCGAGCTCTTGCATGCCATTC
66 AAAAATAAGTATCTT-AAAACTGTTTTATTACTAAAAATCCAACCCGAGCTCCCACACGCCATCC
* *
47652 AATCCTAAGTTT-CTTGATTACCTGAAAAGATAAAAAATATAGGATGAGCTAACAAAGCTAAGTG
130 AATCCTAAGTTTGC-TAATTACCCGAAAAGATAAAAAATATAGGATGAGCTAACAAAGCTAAGTG
47716 TGCAACTCAGCCCTCATGCATA
194 TGCAACTCAGCCCTCATGCATA
47738 TATAACAAAT
Statistics
Matches: 188, Mismatches: 26, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
221 74 0.39
222 114 0.61
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.24
Consensus pattern (221 bp):
AACGAAATAAACCAAAAACCGAAAAACAAGTCCAAAAGTACCAACAATCCAAAAAGTCCATATTA
AAAAATAAGTATCTTAAAACTGTTTTATTACTAAAAATCCAACCCGAGCTCCCACACGCCATCCA
ATCCTAAGTTTGCTAATTACCCGAAAAGATAAAAAATATAGGATGAGCTAACAAAGCTAAGTGTG
CAACTCAGCCCTCATGCATAACAGGC
Found at i:53228 original size:23 final size:26
Alignment explanation
Indices: 53187--53234 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
53177 TTAGATATCA
*
53187 ATTTTAATAAAATATA-TTTAAAAAT
1 ATTTTAATAAAATAAATTTTAAAAAT
53212 ATTTT-AT-AAATAAATTTTAAAAA
1 ATTTTAATAAAATAAATTTTAAAAA
53235 ATCACATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 10 0.48
25 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTTTAATAAAATAAATTTTAAAAAT
Found at i:55582 original size:21 final size:21
Alignment explanation
Indices: 55552--55594 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
55542 GTTTTTATAA
* *
55552 ATATTCAAAATTCAATATTTG
1 ATATTAAAAAATCAATATTTG
55573 ATATTAAAAAATCAATATTTG
1 ATATTAAAAAATCAATATTTG
55594 A
1 A
55595 ACAAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (21 bp):
ATATTAAAAAATCAATATTTG
Found at i:56647 original size:135 final size:137
Alignment explanation
Indices: 56404--56675 Score: 419
Period size: 136 Copynumber: 2.0 Consensus size: 137
56394 CTAAACCTAT
*
56404 TTCCACACACCTTTCTTCTTCATCTTCATCTTCTTCCCTTTTGATTCCAATATCTTTAGTTACAA
1 TTCCACACACCTTTCTTCTTAATCTTCATCTTCTTCCCTTTTGATTCCAATATCTTTAGTTACAA
** *
56469 TCTGTCTCAAAGCTTGAATCTTTGAAAGCCATTAACTC-AAAAAAACTTAACGGGAAGAAGATAT
66 TCTGTCTCAAAGCTTGAATAATTGAAACCCATTAACTCAAAAAAAACTTAACGGGAAGAAGATAT
56533 T-GAATC
131 TGGAATC
*
56539 TTCCACACACCTCTT-TTCTTAATCTTCATCTTCTTCCCTTTTGATTCCAATATATTTTA-TTAC
1 TTCCACACACCT-TTCTTCTTAATCTTCATCTTCTTCCCTTTTGATTCCAATAT-CTTTAGTTAC
* *
56602 AAATTTGTCTCAAAGCTTGAATAATTGAAACCCATTAAC-CCAAAAAAACTTAACGGGAAGAAGA
64 -AATCTGTCTCAAAGCTTGAATAATTGAAACCCATTAACTCAAAAAAAACTTAACGGGAAGAAGA
56666 TATTGGAATC
128 TATTGGAATC
56676 AAAGATATTG
Statistics
Matches: 126, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
135 54 0.43
136 67 0.53
137 5 0.04
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (137 bp):
TTCCACACACCTTTCTTCTTAATCTTCATCTTCTTCCCTTTTGATTCCAATATCTTTAGTTACAA
TCTGTCTCAAAGCTTGAATAATTGAAACCCATTAACTCAAAAAAAACTTAACGGGAAGAAGATAT
TGGAATC
Found at i:57119 original size:18 final size:20
Alignment explanation
Indices: 57077--57124 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
57067 TTGATTACTC
*
57077 ATTTTATTTTTTAAAAATTA
1 ATTTTAGTTTTTAAAAATTA
*
57097 A-TTTA-TTTTT-AGAATTA
1 ATTTTAGTTTTTAAAAATTA
57114 ATTTTAGTTTT
1 ATTTTAGTTTT
57125 CTTCCAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 7 0.28
18 9 0.36
19 8 0.32
20 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
ATTTTAGTTTTTAAAAATTA
Found at i:58091 original size:19 final size:18
Alignment explanation
Indices: 58049--58092 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
58039 ATGGAAAACC
58049 AATTTAACTTTTTAAATT
1 AATTTAACTTTTTAAATT
**
58067 GCTTTAACTTTTTAAAATT
1 AATTTAACTTTTT-AAATT
58086 AATTTAA
1 AATTTAA
58093 GATTTGTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (18 bp):
AATTTAACTTTTTAAATT
Found at i:71510 original size:30 final size:31
Alignment explanation
Indices: 71447--71510 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
71437 TATCGATTTA
* * *
71447 TTTCGTTTGTTTTTTTTCTTTCTTTATTTAT
1 TTTCGTTTGTTTTTTATCTTTCTTAATCTAT
71478 TTTCGTTAT-TTTTTTAT-TTTCTTAATCTAT
1 TTTCGTT-TGTTTTTTATCTTTCTTAATCTAT
71508 TTT
1 TTT
71511 ATGGTTCATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 14 0.48
31 14 0.48
32 1 0.03
ACGTcount: A:0.11, C:0.09, G:0.05, T:0.75
Consensus pattern (31 bp):
TTTCGTTTGTTTTTTATCTTTCTTAATCTAT
Found at i:74612 original size:20 final size:20
Alignment explanation
Indices: 74576--74621 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
74566 TCATTAAGCT
*
74576 TTAATTAATCATTTTTA-ATC
1 TTAATTAATCATATTTATA-C
74596 TTAATTAAATC-TATTTATAC
1 TTAATT-AATCATATTTATAC
74616 TTAATT
1 TTAATT
74622 TAAACCATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTAATCATATTTATAC
Found at i:83000 original size:12 final size:13
Alignment explanation
Indices: 82977--83011 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
82967 TTTCTATTCT
82977 CCTTCCCTCTTCC
1 CCTTCCCTCTTCC
*
82990 CTTTCCC-CTTCC
1 CCTTCCCTCTTCC
83002 CCTTCCCTCT
1 CCTTCCCTCT
83012 CTCCTTCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (13 bp):
CCTTCCCTCTTCC
Found at i:83008 original size:18 final size:19
Alignment explanation
Indices: 82977--83019 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
82967 TTTCTATTCT
*
82977 CCTTCCCTCTTCCCTTTCC
1 CCTTCCCTCTTCCCTCTCC
*
82996 CCTTCCC-CTTCCCTCTCT
1 CCTTCCCTCTTCCCTCTCC
83014 CCTTCC
1 CCTTCC
83020 AAGAATTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (19 bp):
CCTTCCCTCTTCCCTCTCC
Found at i:83904 original size:10 final size:11
Alignment explanation
Indices: 83874--83914 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
83864 TTATATTTAA
83874 AAAATAATTTT
1 AAAATAATTTT
*
83885 AAATTAATTTT
1 AAAATAATTTT
83896 AAAAT-ATTTT
1 AAAATAATTTT
83906 AAAA-AATTT
1 AAAATAATTT
83915 ATGTTTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 13 0.48
11 14 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:84603 original size:19 final size:18
Alignment explanation
Indices: 84572--84619 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
84562 TTTTTTGAAT
84572 TTTTAAGAAAATTATTT-TA
1 TTTTAA-AAAATT-TTTGTA
*
84591 TTTTAAAACAATTTTTGTG
1 TTTTAAAA-AATTTTTGTA
84610 TTTTAAAAAA
1 TTTTAAAAAA
84620 CAGTGTACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (18 bp):
TTTTAAAAAATTTTTGTA
Found at i:85648 original size:40 final size:40
Alignment explanation
Indices: 85589--86098 Score: 441
Period size: 40 Copynumber: 12.9 Consensus size: 40
85579 TCACAACCTA
* * *
85589 TCTTCAATTTGCCCAATGATCGGGGTAAGAGATTGAAT-TA
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTG-ATGTG
* *
85629 TCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGATGTG
** * * *
85669 TCTTCAATCTATCCTATGATTGGGGAAAGAGATTGGAT-TG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATT-GATGTG
* * * *
85709 TCTTCAATCTGCTCCATGATTGAGGTAAGAGATTGGTGTG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGATGTG
*
85749 TCTTCAATCTGCCCCATGATC-GAGTAAGAGATTGATGTG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGATGTG
*
85788 TTTTCAATCTGCCCCATGATCGGGGTAAGAGATTTG-TGTG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGA-TTGATGTG
* * *
85828 T-TTGCAATCTGCCCCATGATCGAGGTTAGAGATTGGTGTG
1 TCTT-CAATCTGCCCCATGATCGGGGTAAGAGATTGATGTG
* *** **** *
85868 TCTTCAATCTACCTTTTGATTAATGTAAAAGATTG--GATG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGATG-TG
* *** *** * *
85907 -ATTCAATCTGCCTTTTGATTAAGGTAAAACATTG--GATG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGATG-TG
* **
85945 -ATTCAATCTGCCCCATGATCAAGGTAAGAGATTGATGTG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGATGTG
85984 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT-TG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATT-GATGTG
* ** ** *
86024 TCTTCAATCTACTTCATGATTAGGGTAAGAGATTGGTGTG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGATGTG
* *
86064 TCTTCAATCTGCCACATGATCGGGTTAAGAGATTG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
86099 GTGAGTTTTA
Statistics
Matches: 396, Mismatches: 60, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
38 63 0.16
39 49 0.12
40 274 0.69
41 10 0.03
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (40 bp):
TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGATGTG
Found at i:85726 original size:80 final size:80
Alignment explanation
Indices: 85589--86099 Score: 507
Period size: 80 Copynumber: 6.5 Consensus size: 80
85579 TCACAACCTA
* * * * **
85589 TCTTCAATTTGCCCAATGATCGGGGTAAGAGATTGAATTATCTTCAATCTACCCCATGATCGGGG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATTGTCTTCAATCTACCCCATGATCAAGG
85654 TAAGAGATTGGTGTG
66 TAAGAGATTGGTGTG
** * * * * * **
85669 TCTTCAATCTATCCTATGATTGGGGAAAGAGATTGGATTGTCTTCAATCTGCTCCATGATTGAGG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATTGTCTTCAATCTACCCCATGATCAAGG
85734 TAAGAGATTGGTGTG
66 TAAGAGATTGGTGTG
* * * **
85749 TCTTCAATCTGCCCCATGATC-GAGTAAGAGATT-GATGTGTTTTCAATCTGCCCCATGATCGGG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT-TGTCTTCAATCTACCCCATGATCAAG
*
85812 GTAAGAGATTTGTGTG
65 GTAAGAGATTGGTGTG
* * *** *
85828 T-TTGCAATCTGCCCCATGATCGAGGTTAGAGATTGG-TGTGTCTTCAATCTACCTTTTGATTAA
1 TCTT-CAATCTGCCCCATGATCGGGGTAAGAGATTGGAT-TGTCTTCAATCTACCCCATGATCAA
* * *
85891 TGTAAAAGATTGG-ATG
64 GGTAAGAGATTGGTGTG
* *** *** * * * *
85907 -ATTCAATCTGCCTTTTGATTAAGGTAAAACATTGGA-TG-ATTCAATCTGCCCCATGATCAAGG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATTGTCTTCAATCTACCCCATGATCAAGG
*
85969 TAAGAGATTGATGTG
66 TAAGAGATTGGTGTG
** * *
85984 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATTGTCTTCAATCTACTTCATGATTAGGG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATTGTCTTCAATCTACCCCATGATCAAGG
86049 TAAGAGATTGGTGTG
66 TAAGAGATTGGTGTG
* *
86064 TCTTCAATCTGCCACATGATCGGGTTAAGAGATTGG
1 TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
86100 TGAGTTTTAT
Statistics
Matches: 347, Mismatches: 74, Indels: 20
0.79 0.17 0.05
Matches are distributed among these distances:
76 26 0.07
77 4 0.01
78 56 0.16
79 71 0.20
80 189 0.54
81 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33
Consensus pattern (80 bp):
TCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATTGTCTTCAATCTACCCCATGATCAAGG
TAAGAGATTGGTGTG
Found at i:85921 original size:38 final size:38
Alignment explanation
Indices: 85870--85956 Score: 147
Period size: 38 Copynumber: 2.3 Consensus size: 38
85860 TTGGTGTGTC
* * *
85870 TTCAATCTACCTTTTGATTAATGTAAAAGATTGGATGA
1 TTCAATCTGCCTTTTGATTAAGGTAAAACATTGGATGA
85908 TTCAATCTGCCTTTTGATTAAGGTAAAACATTGGATGA
1 TTCAATCTGCCTTTTGATTAAGGTAAAACATTGGATGA
85946 TTCAATCTGCC
1 TTCAATCTGCC
85957 CCATGATCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (38 bp):
TTCAATCTGCCTTTTGATTAAGGTAAAACATTGGATGA
Found at i:89964 original size:22 final size:21
Alignment explanation
Indices: 89911--89964 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
89901 TTTTGACAAG
89911 GGTAAAAATACTTGTCAAATT
1 GGTAAAAATACTTGTCAAATT
* * *
89932 GAATAATAATATTTGTCAAACTT
1 G-GTAAAAATACTTGTCAAA-TT
89955 GGTAAAAATA
1 GGTAAAAATA
89965 AATAGAATTC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.04
22 22 0.85
23 3 0.12
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.33
Consensus pattern (21 bp):
GGTAAAAATACTTGTCAAATT
Found at i:98446 original size:8 final size:9
Alignment explanation
Indices: 98432--98458 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
98422 TTTTAAAAAT
98432 TTTTTTTTG
1 TTTTTTTTG
98441 TTTTTTTTG
1 TTTTTTTTG
98450 TTTTTTTTG
1 TTTTTTTTG
98459 GGGGGGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:99279 original size:12 final size:12
Alignment explanation
Indices: 99262--99293 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
99252 ATAAATAAAA
99262 TTTTTTATTTAT
1 TTTTTTATTTAT
99274 TTTTTTATTTAT
1 TTTTTTATTTAT
99286 TTTATTTA
1 TTT-TTTA
99294 GTTTGCGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTATTTAT
Found at i:103069 original size:42 final size:42
Alignment explanation
Indices: 103010--103094 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
103000 AGTTACGTGT
103010 AAGGAAGGATTAGCACCCTCATACACCCAAAATTGGTACCTA
1 AAGGAAGGATTAGCACCCTCATACACCCAAAATTGGTACCTA
103052 AAGGAAGGATTAGCACCCTCATACACCCAAAATTGGTACCTA
1 AAGGAAGGATTAGCACCCTCATACACCCAAAATTGGTACCTA
103094 A
1 A
103095 TCGATTATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (42 bp):
AAGGAAGGATTAGCACCCTCATACACCCAAAATTGGTACCTA
Found at i:105318 original size:18 final size:18
Alignment explanation
Indices: 105285--105342 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
105275 GGAAATGAGG
*
105285 GATCTTGGGCAGAGGAGC
1 GATCTCGGGCAGAGGAGC
* *
105303 GGTCTCGGGGAGAGGAGC
1 GATCTCGGGCAGAGGAGC
*
105321 AATCTCGGGCAGAGGAGC
1 GATCTCGGGCAGAGGAGC
105339 GATC
1 GATC
105343 AATGGTCAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.22, C:0.19, G:0.45, T:0.14
Consensus pattern (18 bp):
GATCTCGGGCAGAGGAGC
Found at i:106274 original size:49 final size:48
Alignment explanation
Indices: 106204--106496 Score: 274
Period size: 49 Copynumber: 6.0 Consensus size: 48
106194 TTCCCTCCAT
* *
106204 ATCTTC-GTGGTAC-TGGATTCACCATTGCGGCTTAAATCTTTCCCTTC
1 ATCTTCTGTGGTACAAGG-TTCACCGTTGCGGCTTAAATCTTTCCCTTC
* * ** * * *
106251 ATACTTCTGAGGTACAAGGTTCACCATTGCAACTTAAATGTTTCTCTTT
1 AT-CTTCTGTGGTACAAGGTTCACCGTTGCGGCTTAAATCTTTCCCTTC
* * *
106300 ATATCCTTGTGGTAC-TGGATTCACCGTTGCGGCTTAAATCTTTCCCTTC
1 ATCTTC-TGTGGTACAAGG-TTCACCGTTGCGGCTTAAATCTTTCCCTTC
** **
106349 ATGCTTCTAAGGTACAAGGTTTGCCGTTGTC-GCTTAAATCTTTCCCTTTGC
1 AT-CTTCTGTGGTACAAGGTTCACCGTTG-CGGCTTAAATCTTTCCC-TT-C
* * *
106400 ATCTTC-GTGGTAC-TGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTC
1 ATCTTCTGTGGTACAAGG-TTCACCGTTGCGGCTTAAATCTTTCCCTTC
* *
106447 ATTTTCTGTGGTACAAGGTTCACCGTTACGGCTTAAATCTTTCCCTTC
1 ATCTTCTGTGGTACAAGGTTCACCGTTGCGGCTTAAATCTTTCCCTTC
106495 AT
1 AT
106497 GTCTTCATGG
Statistics
Matches: 198, Mismatches: 34, Indels: 27
0.76 0.13 0.10
Matches are distributed among these distances:
47 8 0.04
48 49 0.25
49 125 0.63
50 13 0.07
51 3 0.02
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (48 bp):
ATCTTCTGTGGTACAAGGTTCACCGTTGCGGCTTAAATCTTTCCCTTC
Found at i:106334 original size:98 final size:97
Alignment explanation
Indices: 106192--106508 Score: 370
Period size: 98 Copynumber: 3.2 Consensus size: 97
106182 TGGTCGTAAC
** *
106192 CTTTCCCTCCATATCTTCGTGGTACTGGATTCACCATTGCGGCTTAAATCTTTCCCTTCATACTT
1 CTTTCCCTTTATATCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCAT-CTT
106257 CTGAGGTACAAGGTTCACCATTG-CAACTTAAAT
65 CTGAGGTACAAGGTTCACCATTGTC-ACTTAAAT
* *
106290 GTTTCTCTTTATATCCTT-GTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCT
1 CTTTCCCTTTATAT-CTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCAT-CT
* ** * *
106354 TCTAAGGTACAAGGTTTGCCGTTGTCGCTTAAAT
64 TCTGAGGTACAAGGTTCACCATTGTCACTTAAAT
** * * *
106388 CTTTCCCTTTGCATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATTTTC
1 CTTTCCCTTTATATCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATCTTC
* * * *
106453 TGTGGTACAAGGTTCACCGTT-ACGGCTTAAAT
66 TGAGGTACAAGGTTCACCATTGTC-ACTTAAAT
* * *
106485 CTTTCCCTTCATGTCTTCATGGTA
1 CTTTCCCTTTATATCTTCGTGGTA
106509 ATGAGACCTG
Statistics
Matches: 187, Mismatches: 28, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
96 1 0.01
97 50 0.27
98 132 0.71
99 4 0.02
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.39
Consensus pattern (97 bp):
CTTTCCCTTTATATCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATCTTC
TGAGGTACAAGGTTCACCATTGTCACTTAAAT
Found at i:119441 original size:18 final size:18
Alignment explanation
Indices: 119416--119462 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
119406 GAGGGATCTT
*
119416 GGGCAGAGGAGTGGTCTC
1 GGGCAGAGGAGTAGTCTC
119434 AGGG-AGAGGAGTAGTCTC
1 -GGGCAGAGGAGTAGTCTC
119452 GGGCAGAGGAG
1 GGGCAGAGGAG
119463 CAATCAATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.23, C:0.13, G:0.51, T:0.13
Consensus pattern (18 bp):
GGGCAGAGGAGTAGTCTC
Found at i:125700 original size:21 final size:21
Alignment explanation
Indices: 125673--125726 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
125663 CTTGTGTTAG
*
125673 ATCTACCGATACAAGT-ATGGT
1 ATCTACCGATACAAGTCAT-GC
* *
125694 TTCTACCGGTACAAGTCATGC
1 ATCTACCGATACAAGTCATGC
125715 ATCTACCGATAC
1 ATCTACCGATAC
125727 CAAAAACTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (21 bp):
ATCTACCGATACAAGTCATGC
Done.