Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014490.1 Kokia drynarioides strain JFW-HI SEQ_129529, 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: 189920
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:1687 original size:2 final size:2
Alignment explanation
Indices: 1680--1704 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1670 GTATGTTCTT
1680 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 T
1705 CATCAAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1923 original size:17 final size:17
Alignment explanation
Indices: 1892--1925 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1882 TATTTTGACT
**
1892 TTTTAAATTTTTAAAAA
1 TTTTAAATTAGTAAAAA
1909 TTTTAAATTAGTAAAAA
1 TTTTAAATTAGTAAAAA
1926 GAAAATTTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTTAAATTAGTAAAAA
Found at i:3885 original size:122 final size:123
Alignment explanation
Indices: 3662--4149 Score: 662
Period size: 123 Copynumber: 4.0 Consensus size: 123
3652 GATTTCACTA
* * * * *
3662 AATATT-AAAACATAGATA-TTAATATCCTTTTGGAAATGATATAACGTTTTAAT-AACTTTACA
1 AATATTAAAAACATGGA-AGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCA
* * * *
3724 TATATTTTTCTAAAGGAATAATTCTATTTTAATATGAGATATTAAATAAAAAGAAATTG
65 TATATTTCTGTAAAGGAATATTTCTATTTTAATATGAGATATTAAATAAAAGGAAATTG
*
3783 AATATTAAAAACAT-GTAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCAT
*
3847 ATATTTCTATAAAGGAATATTTCTATTTTAATATGAGATATTAAATAAAAGGAAATTG
66 ATATTTCTGTAAAGGAATATTTCTATTTTAATATGAGATATTAAATAAAAGGAAATTG
** * * * *
3905 AATATTAAAAACATGGAAGTTAATATCCTTTTATAAAAAATATAATATTTTAATAAATCTTTCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCAT
* * * *
3970 ATATTTCTGTAAAAGAATATTTTTGTTTTAATATGAGATATTAAATAAAAGGAAATTA
66 ATATTTCTGTAAAGGAATATTTCTATTTTAATATGAGATATTAAATAAAAGGAAATTG
* * *
4028 AATATTAAAAACATGGAAGTTAATATCCTTTAGGAAAGGATATAATGATTTTAATGAACCTTCCA
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAAGATATAATG-TTTTAATAAACCTTCCA
* * * *
4093 AATATTTTTGTAAAGGAATAATTT-TGTTTTAATATGAGATATTAAATAAAATGAAAT
65 TATATTTCTGTAAAGGAAT-ATTTCTATTTTAATATGAGATATTAAATAAAAGGAAAT
4150 GTAGTAGAAT
Statistics
Matches: 327, Mismatches: 34, Indels: 9
0.88 0.09 0.02
Matches are distributed among these distances:
120 1 0.00
121 40 0.12
122 83 0.25
123 137 0.42
124 62 0.19
125 4 0.01
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (123 bp):
AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCAT
ATATTTCTGTAAAGGAATATTTCTATTTTAATATGAGATATTAAATAAAAGGAAATTG
Found at i:3922 original size:22 final size:21
Alignment explanation
Indices: 3884--3930 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
3874 TTAATATGAG
3884 ATATTAAATAAAAGGAAATTGA
1 ATATTAAATAAAAGGAAATT-A
* *
3906 ATATTAAA-AACATGGAAGTTA
1 ATATTAAATAA-AAGGAAATTA
3927 ATAT
1 ATAT
3931 CCTTTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.55, C:0.02, G:0.13, T:0.30
Consensus pattern (21 bp):
ATATTAAATAAAAGGAAATTA
Found at i:6237 original size:30 final size:29
Alignment explanation
Indices: 6203--6285 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 29
6193 AAGAATTTAA
6203 GGTCAAAATGTAATTTTGGAAAAAATCGAG
1 GGTCAAAATGTAATTTTGGAAAAAATCG-G
****
6233 GGTCAAAATGTAATTTTAGGAATGTTTCGG
1 GGTCAAAATGTAATTTT-GGAAAAAATCGG
*
6263 GGTCAAAAATGTGATTTTGGAAA
1 GGTC-AAAATGTAATTTTGGAAA
6286 GGTTTGAGGG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
30 26 0.58
31 19 0.42
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.31
Consensus pattern (29 bp):
GGTCAAAATGTAATTTTGGAAAAAATCGG
Found at i:6295 original size:61 final size:59
Alignment explanation
Indices: 6198--6516 Score: 233
Period size: 61 Copynumber: 5.4 Consensus size: 59
6188 TTTCAAAGAA
* * ** * * * *
6198 TTTAAGGTC-AAAATGTAATTTTGGAAAAAATCGAGGGTCAAAATGTAATTTTAGGAATG
1 TTTAGGGTCAAAAATGTGATTTTGGAAAAGTTTGAGGGTTAAAATATAATTTT-GGAAAG
* * *
6257 TTTCGGGGTCAAAAATGTGATTTTGGAAAGGTTTGAGGGTTAAAATATGATTTTGGAAAAG
1 TTT-AGGGTCAAAAATGTGATTTTGGAAAAGTTTGAGGGTTAAAATATAATTTTGG-AAAG
* * * *
6318 TTTGAGGG--ATAAAATTTGATTTTGGAAAGGTTTG-GGGTT-AAATATGATTTTGGGAAG
1 TTT-AGGGTCA-AAAATGTGATTTTGGAAAAGTTTGAGGGTTAAAATATAATTTTGGAAAG
* * * * *
6375 TTAAAGGT-TAAAATGTGATTTTAGAAAAGTTT-AGGGGTTAAAATATAATTTTTTGAAAG
1 TTTAGGGTCAAAAATGTGATTTTGGAAAAGTTTGA-GGGTTAAAATATAA-TTTTGGAAAG
* * * * * *
6434 TTTAGGGTACAAAAATGTAATTTTAGAAAA-TTTAAGGGTCAAAATAAAATTTTGAAAAAG
1 TTTAGGGT-CAAAAATGTGATTTTGGAAAAGTTTGAGGGTTAAAATATAATTTTG-GAAAG
* *
6494 CTTGAGGGT-TAAAATGTGATTTT
1 -TTTAGGGTCAAAAATGTGATTTT
6517 TAAATAAAAT
Statistics
Matches: 211, Mismatches: 35, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
56 23 0.11
57 10 0.05
58 21 0.10
59 39 0.18
60 48 0.23
61 70 0.33
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.36
Consensus pattern (59 bp):
TTTAGGGTCAAAAATGTGATTTTGGAAAAGTTTGAGGGTTAAAATATAATTTTGGAAAG
Found at i:6308 original size:30 final size:29
Alignment explanation
Indices: 6268--6516 Score: 186
Period size: 30 Copynumber: 8.4 Consensus size: 29
6258 TTCGGGGTCA
*
6268 AAAATGTGATTTTGGAAAGGTTTGAGGGTT
1 AAAATATGATTTTGGAAA-GTTTGAGGGTT
*
6298 AAAATATGATTTTGGAAAAGTTTGAGGGAT
1 AAAATATGATTTTGG-AAAGTTTGAGGGTT
*
6328 AAAATTTGATTTTGGAAAGGTTTG-GGGTT
1 AAAATATGATTTTGGAAA-GTTTGAGGGTT
* * *
6357 -AAATATGATTTTGGGAAG-TTAAAGGTT
1 AAAATATGATTTTGGAAAGTTTGAGGGTT
* *
6384 AAAATGTGATTTTAGAAAAGTTT-AGGGGTT
1 AAAATATGATTTT-GGAAAGTTTGA-GGGTT
* *
6414 AAAATATAATTTTTTGAAAGTTT-AGGG-T
1 AAAATATGA-TTTTGGAAAGTTTGAGGGTT
* * * * *
6442 ACAAAAATGTAATTTTAGAAAATTTAAGGGTC
1 A-AAATATG--ATTTTGGAAAGTTTGAGGGTT
** * *
6474 AAAATAAAATTTTGAAAAAGCTTGAGGGTT
1 AAAATATGATTTTG-GAAAGTTTGAGGGTT
*
6504 AAAATGTGATTTT
1 AAAATATGATTTT
6517 TAAATAAAAT
Statistics
Matches: 172, Mismatches: 33, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
26 2 0.01
27 5 0.03
28 28 0.16
29 25 0.15
30 95 0.55
31 16 0.09
32 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.37
Consensus pattern (29 bp):
AAAATATGATTTTGGAAAGTTTGAGGGTT
Found at i:6346 original size:60 final size:59
Alignment explanation
Indices: 6268--6516 Score: 222
Period size: 60 Copynumber: 4.2 Consensus size: 59
6258 TTCGGGGTCA
* *
6268 AAAATGTGATTTTGGAAAGGTTTGAGGGTTAAAATATGATTTTGGAAAAGTTTGAGGGAT
1 AAAATGTGATTTTAGAAAGGTTTGAGGGTTAAAATATAATTTTGG-AAAGTTTGAGGGAT
* * * * * * *
6328 AAAATTTGATTTTGGAAAGGTTTG-GGGTT-AAATATGATTTTGGGAAG-TTAAAGGTT
1 AAAATGTGATTTTAGAAAGGTTTGAGGGTTAAAATATAATTTTGGAAAGTTTGAGGGAT
* * *
6384 AAAATGTGATTTTAGAAAAGTTT-AGGGGTTAAAATATAATTTTTTGAAAGTTT-AGGGTACA
1 AAAATGTGATTTTAGAAAGGTTTGA-GGGTTAAAATATAA-TTTTGGAAAGTTTGAGGG-A-T
* * * * * * * *
6445 AAAATGTAATTTTAGAAA-ATTTAAGGGTCAAAATAAAATTTTGAAAAAGCTTGAGGGTT
1 AAAATGTGATTTTAGAAAGGTTTGAGGGTTAAAATATAATTTTG-GAAAGTTTGAGGGAT
6504 AAAATGTGATTTT
1 AAAATGTGATTTT
6517 TAAATAAAAT
Statistics
Matches: 155, Mismatches: 24, Indels: 21
0.77 0.12 0.10
Matches are distributed among these distances:
56 26 0.17
57 8 0.05
58 21 0.14
59 32 0.21
60 46 0.30
61 22 0.14
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.37
Consensus pattern (59 bp):
AAAATGTGATTTTAGAAAGGTTTGAGGGTTAAAATATAATTTTGGAAAGTTTGAGGGAT
Found at i:6449 original size:31 final size:30
Alignment explanation
Indices: 6393--6486 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 30
6383 TAAAATGTGA
* *
6393 TTTTAGAAAAGTTTAGGGGTTAAAATATAAT
1 TTTTAGAAAA-TTTAAGGGTCAAAATATAAT
* * *
6424 TTTTTGAAAGTTT-AGGGTACAAAAATGTAA-
1 TTTTAGAAAATTTAAGGGT-C-AAAATATAAT
*
6454 TTTTAGAAAATTTAAGGGTCAAAATAAAAT
1 TTTTAGAAAATTTAAGGGTCAAAATATAAT
6484 TTT
1 TTT
6487 GAAAAAGCTT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
29 11 0.22
30 18 0.36
31 21 0.42
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.38
Consensus pattern (30 bp):
TTTTAGAAAATTTAAGGGTCAAAATATAAT
Found at i:6983 original size:89 final size:86
Alignment explanation
Indices: 6827--7002 Score: 325
Period size: 89 Copynumber: 2.0 Consensus size: 86
6817 TTGAAAATCT
6827 CATTTTTCATTTTGTTTTTTCAAAAAAAAAAACTCTTTTTTTCCTCGTTCTCTCTCAACTCTCCT
1 CATTTTTCATTTTGTTTTTTCAAAAAAAAAAACTCTTTTTTTCCTCGTTCTCTCTCAACTCTCCT
6892 TCTCCGATCCCCTCTTCGACC
66 TCTCCGATCCCCTCTTCGACC
6913 CNATTTTTCATTTTGTTTTTTCAAAAAAAAAAACTTTCTTTTTTTCCTCGTTCTCTCTCAACTCT
1 C-ATTTTTCATTTTGTTTTTTCAAAAAAAAAAAC--TCTTTTTTTCCTCGTTCTCTCTCAACTCT
6978 CCTTCTCCGATCCCCTCTTCGACC
63 CCTTCTCCGATCCCCTCTTCGACC
7002 C
1 C
7003 TAGGGTTCCA
Statistics
Matches: 87, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
86 1 0.01
87 32 0.37
89 54 0.62
ACGTcount: A:0.19, C:0.31, G:0.05, T:0.44
Consensus pattern (86 bp):
CATTTTTCATTTTGTTTTTTCAAAAAAAAAAACTCTTTTTTTCCTCGTTCTCTCTCAACTCTCCT
TCTCCGATCCCCTCTTCGACC
Found at i:9058 original size:20 final size:20
Alignment explanation
Indices: 9035--9086 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
9025 GTAGTATTTT
*
9035 ATTAATTTAATATTAAAGTG
1 ATTAATTTAATATTAAAGTA
9055 ATT-ATCTTAATATTAAAGTA
1 ATTAAT-TTAATATTAAAGTA
9075 ATTAAGTTTAAT
1 ATTAA-TTTAAT
9087 CATAGTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 19 0.68
21 6 0.21
22 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (20 bp):
ATTAATTTAATATTAAAGTA
Found at i:16658 original size:6 final size:6
Alignment explanation
Indices: 16647--16703 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
16637 TGATCAAAAT
* * * * * *
16647 TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGAAAG TGAAAT TGGAAT
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
16695 TGAAAG TGA
1 TGAAAG TGA
16704 TATGAATTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.46, C:0.00, G:0.30, T:0.25
Consensus pattern (6 bp):
TGAAAG
Found at i:16666 original size:18 final size:18
Alignment explanation
Indices: 16647--16703 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
16637 TGATCAAAAT
* *
16647 TGAAAGTGAAAGTGAAAT
1 TGAAATTGAAAGTGAAAG
*
16665 TGGAATTGAAAGTGAAAG
1 TGAAATTGAAAGTGAAAG
* *
16683 TGAAATTGGAATTGAAAG
1 TGAAATTGAAAGTGAAAG
16701 TGA
1 TGA
16704 TATGAATTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.30, T:0.25
Consensus pattern (18 bp):
TGAAATTGAAAGTGAAAG
Found at i:16676 original size:24 final size:24
Alignment explanation
Indices: 16644--16703 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
16634 TTGTGATCAA
16644 AATTGAAAGTGAAAGTGAAATTGG
1 AATTGAAAGTGAAAGTGAAATTGG
16668 AATTGAAAGTGAAAGTGAAATTGG
1 AATTGAAAGTGAAAGTGAAATTGG
16692 AATTGAAAGTGA
1 AATTGAAAGTGA
16704 TATGAATTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.25
Consensus pattern (24 bp):
AATTGAAAGTGAAAGTGAAATTGG
Found at i:16853 original size:41 final size:39
Alignment explanation
Indices: 16805--16905 Score: 98
Period size: 38 Copynumber: 2.6 Consensus size: 39
16795 TCGACCTTGA
** *
16805 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACT-GGTGTCACCACTTTACTTCGGATAG
* ** *
16845 ATTCGATGAGGTACTGG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGTGTCACCACTTTACTTCGGATAG
16883 GTCGATGAGACACTAGGTGTCAC
1 GTCGATGAGACACT-GGTGTCAC
16906 TTTATTGCTT
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
37 11 0.23
38 17 0.36
39 4 0.09
40 4 0.09
41 11 0.23
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.31
Consensus pattern (39 bp):
GTCGATGAGACACTGGTGTCACCACTTTACTTCGGATAG
Found at i:16907 original size:37 final size:38
Alignment explanation
Indices: 16803--16909 Score: 108
Period size: 37 Copynumber: 2.8 Consensus size: 38
16793 CTTCGACCTT
*
16803 GAGTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATA
1 GAGTCGATGAGACACTGGGTGTC---ACTTTACTTCGGATA
* ** ** *
16844 GATTCGATGAGGTACTGGGTACCACTTTACTTCGGCTA
1 GAGTCGATGAGACACTGGGTGTCACTTTACTTCGGATA
*
16882 G-GTCGATGAGACACTAGGTGTCACTTTA
1 GAGTCGATGAGACACTGGGTGTCACTTTA
16910 TTGCTTCGAA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
37 21 0.40
38 14 0.26
41 18 0.34
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (38 bp):
GAGTCGATGAGACACTGGGTGTCACTTTACTTCGGATA
Found at i:22102 original size:7 final size:7
Alignment explanation
Indices: 22090--22114 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
22080 CTTTATAATA
22090 ACATTAT
1 ACATTAT
22097 ACATTAT
1 ACATTAT
22104 ACATTAT
1 ACATTAT
22111 ACAT
1 ACAT
22115 ATGTGCATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (7 bp):
ACATTAT
Found at i:22914 original size:19 final size:20
Alignment explanation
Indices: 22878--22919 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
22868 ATATAATTTT
*
22878 TAAAAAATATATATAATAAA
1 TAAAAAATATATAAAATAAA
22898 TAAAAAATAT-TAAAATAAA
1 TAAAAAATATATAAAATAAA
22917 TAA
1 TAA
22920 TTCACAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAAAATATATAAAATAAA
Found at i:23505 original size:60 final size:61
Alignment explanation
Indices: 23405--23523 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 61
23395 ATAGTTAATT
23405 ATTTTATGACTTTTTAAAAGTTAACTAATTAAAACTTAAATTTACTA-ATAATTTAATGATC
1 ATTTTATGACTTTTTAAAAGTTAACTAATTAAAACTTAAATTTAC-ACATAATTTAATGATC
* * * * *
23466 ATTTTATTATTTTTTAAAATTTAA-TGATTAAAA-TATAAATTTTCACATAATTTAATGA
1 ATTTTATGACTTTTTAAAAGTTAACTAATTAAAACT-TAAATTTACACATAATTTAATGA
23524 AGTTGAGTAG
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
59 2 0.04
60 28 0.55
61 21 0.41
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (61 bp):
ATTTTATGACTTTTTAAAAGTTAACTAATTAAAACTTAAATTTACACATAATTTAATGATC
Found at i:29005 original size:9 final size:9
Alignment explanation
Indices: 28987--29023 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
28977 AGAGTCCATA
28987 TCATTCGTT
1 TCATTCGTT
*
28996 TCATTTGTT
1 TCATTCGTT
29005 TCATTCGTT
1 TCATTCGTT
*
29014 TCATCCGTT
1 TCATTCGTT
29023 T
1 T
29024 TCCTTTGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.11, C:0.22, G:0.11, T:0.57
Consensus pattern (9 bp):
TCATTCGTT
Found at i:31413 original size:32 final size:32
Alignment explanation
Indices: 31377--31450 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
31367 CTATTTACTT
* *
31377 AAAATAA-ATAATTTTGTCAAAATAAAATTAAG
1 AAAATAACA-AATTTAGTCAAAACAAAATTAAG
* *
31409 AAAATAACAAATTTAGTCAACACAAAATTAAT
1 AAAATAACAAATTTAGTCAAAACAAAATTAAG
31441 AAAATAACAA
1 AAAATAACAA
31451 CTTTGAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 36 0.97
33 1 0.03
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (32 bp):
AAAATAACAAATTTAGTCAAAACAAAATTAAG
Found at i:37993 original size:18 final size:18
Alignment explanation
Indices: 37970--38082 Score: 165
Period size: 18 Copynumber: 6.3 Consensus size: 18
37960 CGATCTAGTA
*
37970 ATGCTCTTACGAGCCAGT
1 ATGCTCTAACGAGCCAGT
*
37988 ATGCTCAAACGAGCCAGT
1 ATGCTCTAACGAGCCAGT
*
38006 ATGCT-TAAGCGAGCAAGT
1 ATGCTCTAA-CGAGCCAGT
38024 ATGCTCTAACGAGCCAGT
1 ATGCTCTAACGAGCCAGT
* *
38042 ATGCTCAAACGAGCCAAT
1 ATGCTCTAACGAGCCAGT
38060 ATGCTCTAACGAGCCAGT
1 ATGCTCTAACGAGCCAGT
38078 ATGCT
1 ATGCT
38083 ATTCCTTTCG
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
17 2 0.02
18 79 0.94
19 3 0.04
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (18 bp):
ATGCTCTAACGAGCCAGT
Found at i:38036 original size:54 final size:54
Alignment explanation
Indices: 37970--38082 Score: 183
Period size: 54 Copynumber: 2.1 Consensus size: 54
37960 CGATCTAGTA
* *
37970 ATGCTCTTACGAGCCAGTATGCTCAAACGAGCCAGTATGCT-TAAGCGAGCAAGT
1 ATGCTCTAACGAGCCAGTATGCTCAAACGAGCCAATATGCTCTAA-CGAGCAAGT
*
38024 ATGCTCTAACGAGCCAGTATGCTCAAACGAGCCAATATGCTCTAACGAGCCAGT
1 ATGCTCTAACGAGCCAGTATGCTCAAACGAGCCAATATGCTCTAACGAGCAAGT
38078 ATGCT
1 ATGCT
38083 ATTCCTTTCG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
54 52 0.95
55 3 0.05
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (54 bp):
ATGCTCTAACGAGCCAGTATGCTCAAACGAGCCAATATGCTCTAACGAGCAAGT
Found at i:42371 original size:77 final size:79
Alignment explanation
Indices: 42273--42455 Score: 244
Period size: 77 Copynumber: 2.3 Consensus size: 79
42263 CACTTTCGCG
* * ** * *
42273 GTTTATCTGATAAGCACTGGGTGTTATGATTTGACGGATATTTGTTGGTTAAACCAACTAGAGCT
1 GTTTATCCGATAGGCACTGGGTGCCAGGAATTGACGGATATTTGTTGGTTAAACCAACTAGAGCT
*
42338 -GG-CACATTTACG
66 GGGCCACATTTACA
* * *
42350 GTTTCTTCGCTAGGCACTGGGTGCCAGGAATTGACGGATATTTGTTGGTTAAACCAACTAGAGCT
1 GTTTATCCGATAGGCACTGGGTGCCAGGAATTGACGGATATTTGTTGGTTAAACCAACTAGAGCT
*
42415 GGGCTCACATTTGCA
66 GGGC-CACATTTACA
42430 GTTTATCCGATAGGCACTGGGTGCCA
1 GTTTATCCGATAGGCACTGGGTGCCA
42456 TAATCGTCGG
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
77 56 0.63
78 2 0.02
80 31 0.35
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (79 bp):
GTTTATCCGATAGGCACTGGGTGCCAGGAATTGACGGATATTTGTTGGTTAAACCAACTAGAGCT
GGGCCACATTTACA
Found at i:48704 original size:80 final size:80
Alignment explanation
Indices: 48599--48765 Score: 228
Period size: 80 Copynumber: 2.1 Consensus size: 80
48589 TGTTTATTTT
* * ** * *
48599 CTAGGCACTGGGTGTCAGGATTTGACGGATATTTGTTGGTTAAAGTAACTAGAGTTGAGCTCACA
1 CTAGGCACTGGGTGTCAGGAATTGACAGATATTTGTTGGTTAAACCAACAAGAGCTGAGCTCACA
48664 TTTGCGGTTTATCCA
66 TTTGCGGTTTATCCA
* *
48679 CTAGGCACTGGGTG-CTAGGAATTGACAGATATTTGTTGGTTAAACCAACAATAGCTGGGCTCAC
1 CTAGGCACTGGGTGTC-AGGAATTGACAGATATTTGTTGGTTAAACCAACAAGAGCTGAGCTCAC
**
48743 ATTTGCGGTTTATCTG
65 ATTTGCGGTTTATCCA
48759 CTAGGCA
1 CTAGGCA
48766 TTGGATGCAA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
79 1 0.01
80 75 0.99
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.32
Consensus pattern (80 bp):
CTAGGCACTGGGTGTCAGGAATTGACAGATATTTGTTGGTTAAACCAACAAGAGCTGAGCTCACA
TTTGCGGTTTATCCA
Found at i:57234 original size:21 final size:21
Alignment explanation
Indices: 57182--57235 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
57172 TTAAAGTGTG
57182 TTGTAGCTGCATCTGGCTCTA
1 TTGTAGCTGCATCTGGCTCTA
* * *
57203 ATGTGGCTGCATCTGGCTTTA
1 TTGTAGCTGCATCTGGCTCTA
*
57224 TTGTAGATGCAT
1 TTGTAGCTGCAT
57236 TTGAGTATGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.39
Consensus pattern (21 bp):
TTGTAGCTGCATCTGGCTCTA
Found at i:77371 original size:32 final size:32
Alignment explanation
Indices: 77335--77397 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
77325 GCCATCCATA
* *
77335 CATGTACCTGAAATATATTAATCAGCTAATTG
1 CATGTACCTGAAACATATTAATCAACTAATTG
77367 CATGTACCTGAAACATATTAATCAACTAATT
1 CATGTACCTGAAACATATTAATCAACTAATT
77398 AATTTCAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (32 bp):
CATGTACCTGAAACATATTAATCAACTAATTG
Found at i:77546 original size:37 final size:38
Alignment explanation
Indices: 77432--77539 Score: 155
Period size: 37 Copynumber: 2.8 Consensus size: 38
77422 CAAACATGAA
* * * *
77432 ATTAATTTGTCTCAAACTTAGACACCTTAAAAACAACT
1 ATTAATATGTATCAAACTAAGACACATTAAAAACAACT
*
77470 ATT-ATATGTATCAAAATAAGACACATTAAAAACAACT
1 ATTAATATGTATCAAACTAAGACACATTAAAAACAACT
77507 ATTAAATATGTATCAAACTAAGACACATTAAAA
1 ATT-AATATGTATCAAACTAAGACACATTAAAA
77540 CCCTATTTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
37 32 0.52
38 3 0.05
39 27 0.44
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.29
Consensus pattern (38 bp):
ATTAATATGTATCAAACTAAGACACATTAAAAACAACT
Found at i:79878 original size:31 final size:28
Alignment explanation
Indices: 79843--79899 Score: 78
Period size: 31 Copynumber: 1.9 Consensus size: 28
79833 TTCATATTTT
*
79843 TCTTTTCTCTCTTTCTTTTCACTTTCTTTGC
1 TCTTTTCTCTC-AT-TTTTC-CTTTCTTTGC
79874 TCTTTTCTCTCATTTTTCCTTTCTTT
1 TCTTTTCTCTCATTTTTCCTTTCTTT
79900 TTTTCAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 5 0.20
30 1 0.04
31 11 0.44
ACGTcount: A:0.04, C:0.28, G:0.02, T:0.67
Consensus pattern (28 bp):
TCTTTTCTCTCATTTTTCCTTTCTTTGC
Found at i:79900 original size:21 final size:20
Alignment explanation
Indices: 79874--79922 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
79864 CTTTCTTTGC
*
79874 TCTTTTCTCTCATTTTTCCTT
1 TCTTTT-TCTCAATTTTCCTT
* *
79895 TCTTTTTTTCAATTTTCTTT
1 TCTTTTTCTCAATTTTCCTT
79915 TCTTTTTC
1 TCTTTTTC
79923 ATTCTCACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.71
Consensus pattern (20 bp):
TCTTTTTCTCAATTTTCCTT
Found at i:81329 original size:21 final size:21
Alignment explanation
Indices: 81312--81376 Score: 130
Period size: 21 Copynumber: 3.1 Consensus size: 21
81302 CCACTCGTTC
81312 TCACTCTCGAGGACCTCGGTT
1 TCACTCTCGAGGACCTCGGTT
81333 TCACTCTCGAGGACCTCGGTT
1 TCACTCTCGAGGACCTCGGTT
81354 TCACTCTCGAGGACCTCGGTT
1 TCACTCTCGAGGACCTCGGTT
81375 TC
1 TC
81377 TTTGGCCTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.14, C:0.34, G:0.23, T:0.29
Consensus pattern (21 bp):
TCACTCTCGAGGACCTCGGTT
Found at i:84588 original size:31 final size:28
Alignment explanation
Indices: 84553--84609 Score: 78
Period size: 31 Copynumber: 1.9 Consensus size: 28
84543 TTCATATTTT
*
84553 TCTTTTCTCTCTTTCTTTTCACTTTCTTTGC
1 TCTTTTCTCTC-AT-TTTTC-CTTTCTTTGC
84584 TCTTTTCTCTCATTTTTCCTTTCTTT
1 TCTTTTCTCTCATTTTTCCTTTCTTT
84610 TTTTCAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 5 0.20
30 1 0.04
31 11 0.44
ACGTcount: A:0.04, C:0.28, G:0.02, T:0.67
Consensus pattern (28 bp):
TCTTTTCTCTCATTTTTCCTTTCTTTGC
Found at i:84610 original size:21 final size:20
Alignment explanation
Indices: 84584--84632 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
84574 CTTTCTTTGC
*
84584 TCTTTTCTCTCATTTTTCCTT
1 TCTTTT-TCTCAATTTTCCTT
* *
84605 TCTTTTTTTCAATTTTCTTT
1 TCTTTTTCTCAATTTTCCTT
84625 TCTTTTTC
1 TCTTTTTC
84633 ATTCTCACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.71
Consensus pattern (20 bp):
TCTTTTTCTCAATTTTCCTT
Found at i:86039 original size:21 final size:21
Alignment explanation
Indices: 86022--86086 Score: 130
Period size: 21 Copynumber: 3.1 Consensus size: 21
86012 CCACTCGTTC
86022 TCACTCTCGAGGACCTCGGTT
1 TCACTCTCGAGGACCTCGGTT
86043 TCACTCTCGAGGACCTCGGTT
1 TCACTCTCGAGGACCTCGGTT
86064 TCACTCTCGAGGACCTCGGTT
1 TCACTCTCGAGGACCTCGGTT
86085 TC
1 TC
86087 TTTGGCCTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.14, C:0.34, G:0.23, T:0.29
Consensus pattern (21 bp):
TCACTCTCGAGGACCTCGGTT
Found at i:87550 original size:10 final size:10
Alignment explanation
Indices: 87535--87567 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
87525 AATTAAGTTA
87535 GGAGCTGAAT
1 GGAGCTGAAT
87545 GGAGCTGAAT
1 GGAGCTGAAT
87555 GGAGCTGAAT
1 GGAGCTGAAT
87565 GGA
1 GGA
87568 CTAGGCTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.42, T:0.18
Consensus pattern (10 bp):
GGAGCTGAAT
Found at i:87921 original size:32 final size:32
Alignment explanation
Indices: 87860--87922 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
87850 GCCATCCATA
* * * *
87860 CATGTACCTGAAATATAGTAATTAGCTAATTG
1 CATGTACCTAAAACATAGTAATCAACTAATTG
*
87892 CATGTACCTAAAACATATTAATCAACTAATT
1 CATGTACCTAAAACATAGTAATCAACTAATT
87923 AATTTCAGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (32 bp):
CATGTACCTAAAACATAGTAATCAACTAATTG
Found at i:88011 original size:39 final size:39
Alignment explanation
Indices: 87968--88066 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
87958 TTAATTTGTC
* *
87968 TCAAACTTAGACACCTTAAAAACAACTATTAAATATGTA
1 TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA
* *
88007 TCAAAATAAGACACATTAAAACCAACTATTAAATATGTA
1 TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA
*
88046 TCAAACAAAGACACATTAAAA
1 TCAAACTAAGACACATTAAAA
88067 CCCTATTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.54, C:0.17, G:0.05, T:0.24
Consensus pattern (39 bp):
TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA
Found at i:88233 original size:24 final size:24
Alignment explanation
Indices: 88206--88254 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
88196 AGTTCAATGA
88206 GCTATGAATGAGCTAGATGAACTT
1 GCTATGAATGAGCTAGATGAACTT
*
88230 GCTATGAATTAGCTAGATGAACTT
1 GCTATGAATGAGCTAGATGAACTT
88254 G
1 G
88255 TAGGAGGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (24 bp):
GCTATGAATGAGCTAGATGAACTT
Found at i:92412 original size:21 final size:21
Alignment explanation
Indices: 92386--92432 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
92376 ATCCAATGTG
92386 TCTTGGCTATAAGATTCGGTT
1 TCTTGGCTATAAGATTCGGTT
*
92407 TCTTGGCTGTAAGATTCGGTT
1 TCTTGGCTATAAGATTCGGTT
92428 TCTTG
1 TCTTG
92433 ATTTTCTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.45
Consensus pattern (21 bp):
TCTTGGCTATAAGATTCGGTT
Found at i:100155 original size:26 final size:26
Alignment explanation
Indices: 100103--100156 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
100093 CACCTAGGAA
*
100103 TGTCACTGCATGAACATGTACAGAAT
1 TGTCACTGCATGAACATGTACAAAAT
* * *
100129 TGTCGCTGCATGAACGTGTCCAAAAT
1 TGTCACTGCATGAACATGTACAAAAT
100155 TG
1 TG
100157 CACCCATAAT
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:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (26 bp):
TGTCACTGCATGAACATGTACAAAAT
Found at i:104024 original size:165 final size:165
Alignment explanation
Indices: 103830--104160 Score: 626
Period size: 165 Copynumber: 2.0 Consensus size: 165
103820 AATAAATCTA
*
103830 AATAAAACTCTTAATTAAACTATAACTCTAACTAATCTAAACAAGAAGTAGTTTTAAACTAAACT
1 AATAAAACTCTTAATTAAACTAGAACTCTAACTAATCTAAACAAGAAGTAGTTTTAAACTAAACT
103895 TTCTTGTTGACATAAAACTCCTAAAAACTTAAACTACTTAATAATTATTCAAAATTCGGAATAAA
66 TTCTTGTTGACATAAAACTCCTAAAAACTTAAACTACTTAATAATTATTCAAAATTCGGAATAAA
103960 AATAACAATAAAATAATAAGAGCTGATAATACAAT
131 AATAACAATAAAATAATAAGAGCTGATAATACAAT
103995 AATAAAACTCTTAATTAAACTAGAACTCTAACTAATCTAAACAAGAAGTAGTTTTAAACTAAACT
1 AATAAAACTCTTAATTAAACTAGAACTCTAACTAATCTAAACAAGAAGTAGTTTTAAACTAAACT
*
104060 TTCTTGTTGACATTAAACTCCTAAAAACTTAAACTACTTAATAATTATTCAAAATTCGGAATAAA
66 TTCTTGTTGACATAAAACTCCTAAAAACTTAAACTACTTAATAATTATTCAAAATTCGGAATAAA
* *
104125 AATAACAATAAAATAATAAGAGTTGATAATATAAT
131 AATAACAATAAAATAATAAGAGCTGATAATACAAT
104160 A
1 A
104161 TTGGGCTCAT
Statistics
Matches: 162, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
165 162 1.00
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.31
Consensus pattern (165 bp):
AATAAAACTCTTAATTAAACTAGAACTCTAACTAATCTAAACAAGAAGTAGTTTTAAACTAAACT
TTCTTGTTGACATAAAACTCCTAAAAACTTAAACTACTTAATAATTATTCAAAATTCGGAATAAA
AATAACAATAAAATAATAAGAGCTGATAATACAAT
Found at i:112330 original size:17 final size:17
Alignment explanation
Indices: 112301--112333 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
112291 CATTGAACTC
112301 AACTTCAGCTTATTTTT
1 AACTTCAGCTTATTTTT
112318 AACTT-AGCATTATTTT
1 AACTTCAGC-TTATTTT
112334 GCTGGAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (17 bp):
AACTTCAGCTTATTTTT
Found at i:112537 original size:38 final size:39
Alignment explanation
Indices: 112428--112526 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
112418 TTAAATAGGG
*
112428 TTTTAATGTGTCTTAGTTTGATACATATTTAACAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
* *
112467 TTTTAATGTGTCTTATTTTGATACATATTTAATAGTTTT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
* *
112506 TTTTAAGGTGTCTAAGTTTGA
1 TTTTAATGTGTCTTAGTTTGA
112527 GACAAATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.25, C:0.06, G:0.15, T:0.54
Consensus pattern (39 bp):
TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
Found at i:112608 original size:32 final size:32
Alignment explanation
Indices: 112572--112634 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
112562 AGCTAAAATT
*
112572 AATTAGCTGATTAATATGTTTCAGGTACATGC
1 AATTAGCTGATTAATATATTTCAGGTACATGC
*
112604 AATTAGCTGATTAATATATTTTAGGTACATG
1 AATTAGCTGATTAATATATTTCAGGTACATG
112635 TATGGATGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (32 bp):
AATTAGCTGATTAATATATTTCAGGTACATGC
Found at i:118995 original size:39 final size:39
Alignment explanation
Indices: 118949--119047 Score: 162
Period size: 39 Copynumber: 2.5 Consensus size: 39
118939 TTAAATAGGG
118949 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
* *
118988 TTTTAATGTATCTTATTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
* *
119027 TTTTAAGGTGTCTAAGTTTGA
1 TTTTAATGTGTCTTAGTTTGA
119048 GACAAATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.26, C:0.05, G:0.15, T:0.54
Consensus pattern (39 bp):
TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
Found at i:119129 original size:32 final size:32
Alignment explanation
Indices: 119093--119155 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
119083 AGCTGAAATT
*
119093 AATTAGCTGATTAATATGTTTCAGGCACATGC
1 AATTAGCTGATTAATATATTTCAGGCACATGC
*
119125 AATTAGCTGATTAATATATTTCAGGTACATG
1 AATTAGCTGATTAATATATTTCAGGCACATG
119156 TATGGATGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
AATTAGCTGATTAATATATTTCAGGCACATGC
Found at i:147265 original size:30 final size:28
Alignment explanation
Indices: 147208--147265 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
147198 TCTTTATGAC
* *
147208 GATCTCTATTAAAGGAAGCCTTTGTGGA
1 GATCTCTATTAAAAGAAGCCCTTGTGGA
*
147236 GATCTCTGTTAAAAGAATGGCCCTTGTGGA
1 GATCTCTATTAAAAGAA--GCCCTTGTGGA
147266 AATCAATTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 15 0.60
30 10 0.40
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (28 bp):
GATCTCTATTAAAAGAAGCCCTTGTGGA
Found at i:148757 original size:36 final size:36
Alignment explanation
Indices: 148717--148799 Score: 112
Period size: 36 Copynumber: 2.3 Consensus size: 36
148707 CCTGCTGATT
* * *
148717 CAAAGGTCGTGATGCTCATTTTACTCCCAATTGACC
1 CAAAGGTCATGATGCTCAATTAACTCCCAATTGACC
* * *
148753 CAAAGGTCATTATGCTCAATTAACTCCCTATTGACT
1 CAAAGGTCATGATGCTCAATTAACTCCCAATTGACC
148789 CAAAGGTCATG
1 CAAAGGTCATG
148800 CTTGTTACTA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (36 bp):
CAAAGGTCATGATGCTCAATTAACTCCCAATTGACC
Found at i:155977 original size:36 final size:36
Alignment explanation
Indices: 155889--155980 Score: 112
Period size: 36 Copynumber: 2.6 Consensus size: 36
155879 TCGTTTAACT
* * * * * *
155889 CCTGTTGACTCAAAGGCCGTGATGCTCATTTTACTC
1 CCTGTTGACCCAAAGGTCATAATCCTCAATTTACTC
* *
155925 CCTATTAACCCAAAGGTCATAATCCTCAATTTACTC
1 CCTGTTGACCCAAAGGTCATAATCCTCAATTTACTC
155961 CCTGTTGACCCAAAGGTCAT
1 CCTGTTGACCCAAAGGTCAT
155981 GCCTATTACC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.30
Consensus pattern (36 bp):
CCTGTTGACCCAAAGGTCATAATCCTCAATTTACTC
Found at i:157078 original size:20 final size:21
Alignment explanation
Indices: 157053--157094 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
157043 ACTTTAATGA
*
157053 TTAACT-TACTTAATCATATT
1 TTAACTCTAATTAATCATATT
*
157073 TTAACTCTAATTAATCCTATT
1 TTAACTCTAATTAATCATATT
157094 T
1 T
157095 ATAAGTCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAACTCTAATTAATCATATT
Found at i:161102 original size:31 final size:30
Alignment explanation
Indices: 161058--161121 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
161048 TATAGAAAAT
* * *
161058 AAATTAATAAAATTTAAGTTTTTTCTTTTA
1 AAATTAATAAAATTTAAATATTTTCTCTTA
*
161088 AAATTTATATAAATTTAAATATTTTCTCTTA
1 AAATTAATA-AAATTTAAATATTTTCTCTTA
161119 AAA
1 AAA
161122 AATACAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (30 bp):
AAATTAATAAAATTTAAATATTTTCTCTTA
Found at i:161153 original size:29 final size:28
Alignment explanation
Indices: 161114--161183 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
161104 AAATATTTTC
161114 TCTT-AAA-AAATACAAACGTATTTAAGT
1 TCTTGAAAGAAATAC-AACGTATTTAAGT
* * *
161141 TCTTGAAAGAAATACTATGTTTTTAAGT
1 TCTTGAAAGAAATACAACGTATTTAAGT
161169 TCTTGAAAGAAATAC
1 TCTTGAAAGAAATAC
161184 TATGTTTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.11
28 28 0.74
29 6 0.16
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (28 bp):
TCTTGAAAGAAATACAACGTATTTAAGT
Found at i:161171 original size:28 final size:28
Alignment explanation
Indices: 161134--161191 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
161124 TACAAACGTA
161134 TTTAAGTTCTTGAAAGAAATACTATGTT
1 TTTAAGTTCTTGAAAGAAATACTATGTT
161162 TTTAAGTTCTTGAAAGAAATACTATGTT
1 TTTAAGTTCTTGAAAGAAATACTATGTT
161190 TT
1 TT
161192 AGTGACTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (28 bp):
TTTAAGTTCTTGAAAGAAATACTATGTT
Found at i:163824 original size:17 final size:17
Alignment explanation
Indices: 163802--163836 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
163792 TAGGGAAATT
163802 CTTACAAAATTTCTTTC
1 CTTACAAAATTTCTTTC
163819 CTTACAAAATTTCTTTC
1 CTTACAAAATTTCTTTC
163836 C
1 C
163837 CATCAGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.46
Consensus pattern (17 bp):
CTTACAAAATTTCTTTC
Found at i:169037 original size:531 final size:531
Alignment explanation
Indices: 168034--169095 Score: 1971
Period size: 531 Copynumber: 2.0 Consensus size: 531
168024 TTAGCCCCGA
* *
168034 TATTTGTCGATTTCGTTTTCTTTATCGCGATAACAGGGTGTCCATGTTACGACGTCGATTTCAGT
1 TATTTGTCGATTTCGTTTTCTTTATCACGACAACAGGGTGTCCATGTTACGACGTCGATTTCAGT
168099 CTTGCTCTTTCTGGATTCTGTCACCTTTGTTACGTCATAGCTGATAGTATGTCATAACATGCCCT
66 CTTGCTCTTTCTGGATTCTGTCACCTTTGTTACGTCATAGCTGATAGTATGTCATAACATGCCCT
*
168164 TATTTTCTATTAAATACTAAAAGAAAAACATGTTAGAATGATATACAGAAATATACATAAGTTAG
131 TATTTTCTATTAAATACTAAAAGAAAAACATGTTAGAATGATATACAGAAACATACATAAGTTAG
**
168229 TTCCACCTCTTTACCTTTAACTCTTACTACCGAAATCATTCTTTATGCTTACCCTTATCGAGCAA
196 TTCCACCTCTTTACCTTTAACTCCCACTACCGAAATCATTCTTTATGCTTACCCTTATCGAGCAA
*
168294 ATCCAACTTTGTTCACCTTTTTTCCACTTCTCATGAGATCTTGCTAACTCCTTCAATTGATCCCT
261 ATCCAACTTTGTTCACCTTTTTTCCACTTCTCATGAGATCTTGCTAACTCCTTCAATCGATCCCT
* *
168359 TTCATTGAATCATTAATTCTTTCCTTATTCATGAATGGAATTTGATTGTGCCCTTCTTCCTTATT
326 TTCATTGAATCATTAATTCTTTCCGTATTCATGAAAGGAATTTGATTGTGCCCTTCTTCCTTATT
168424 TAATTCTAGCAGATGGCATCGCTCTTTGTGCTCTTGGATTTCATCACTTTTGTCCCCACACTTGA
391 TAATTCTAGCAGATGGCATCGCTCTTTGTGCTCTTGGATTTCATCACTTTTGTCCCCACACTTGA
* *
168489 AGATTTCCACCTCACCATTGATTCTCATAGTAAGCTCGTTATTGTTCAAATCGATGGTGGATTGA
456 ACATTTCCACCTCACCATTGATTCTCATAGTAAGCTCGTTATTGTTCAAATCGATGGTGGATCGA
168554 TATGTATCTAG
521 TATGTATCTAG
*
168565 TATTTGTCGATTTTGTTTTCTTTATCACGACAACAGGGTGTCCATGTTACGACGTCGATTTCAGT
1 TATTTGTCGATTTCGTTTTCTTTATCACGACAACAGGGTGTCCATGTTACGACGTCGATTTCAGT
*
168630 CTTGCTCTTTCTGGATTCTGTCACCTTTGTTACGTCATAGCTGATAGTGTGTCATAACATGCCCT
66 CTTGCTCTTTCTGGATTCTGTCACCTTTGTTACGTCATAGCTGATAGTATGTCATAACATGCCCT
168695 TATTTTCTATTAAATACTAAAAGAAAAACATGTTAGAATGATATACAGAAACATACATAAGTTAG
131 TATTTTCTATTAAATACTAAAAGAAAAACATGTTAGAATGATATACAGAAACATACATAAGTTAG
* * *
168760 TTCCACCTCTTTACCTTTAACTCCCACTACCGGACTCATTCTTTATGCTTACCCTTATCGAGCAG
196 TTCCACCTCTTTACCTTTAACTCCCACTACCGAAATCATTCTTTATGCTTACCCTTATCGAGCAA
*
168825 ATCCAACTTTGTTCACCTTTTTTCCAGTTCTCATGAGATCTTGCTAACTCCTTCAATCGATCCCT
261 ATCCAACTTTGTTCACCTTTTTTCCACTTCTCATGAGATCTTGCTAACTCCTTCAATCGATCCCT
168890 TTCATTGAATCATTAATTCTTTCCGTATTCATGAAAGGAATTTGATTGTGCCCTTCTTCCTTATT
326 TTCATTGAATCATTAATTCTTTCCGTATTCATGAAAGGAATTTGATTGTGCCCTTCTTCCTTATT
*
168955 TAATTCTAGCAGATGTCATCGCTCTTTGTGCTCTTGGATTTCATCACTTTTGTCCCCACACTTGA
391 TAATTCTAGCAGATGGCATCGCTCTTTGTGCTCTTGGATTTCATCACTTTTGTCCCCACACTTGA
169020 ACATTTCCACCTCACCATTGATTCTCATAGTAAGCTCGTTATTGTTCAAATCGATGGTGGATCGA
456 ACATTTCCACCTCACCATTGATTCTCATAGTAAGCTCGTTATTGTTCAAATCGATGGTGGATCGA
169085 TATGTATCTAG
521 TATGTATCTAG
169096 GAATGGTCTT
Statistics
Matches: 514, Mismatches: 17, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
531 514 1.00
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.39
Consensus pattern (531 bp):
TATTTGTCGATTTCGTTTTCTTTATCACGACAACAGGGTGTCCATGTTACGACGTCGATTTCAGT
CTTGCTCTTTCTGGATTCTGTCACCTTTGTTACGTCATAGCTGATAGTATGTCATAACATGCCCT
TATTTTCTATTAAATACTAAAAGAAAAACATGTTAGAATGATATACAGAAACATACATAAGTTAG
TTCCACCTCTTTACCTTTAACTCCCACTACCGAAATCATTCTTTATGCTTACCCTTATCGAGCAA
ATCCAACTTTGTTCACCTTTTTTCCACTTCTCATGAGATCTTGCTAACTCCTTCAATCGATCCCT
TTCATTGAATCATTAATTCTTTCCGTATTCATGAAAGGAATTTGATTGTGCCCTTCTTCCTTATT
TAATTCTAGCAGATGGCATCGCTCTTTGTGCTCTTGGATTTCATCACTTTTGTCCCCACACTTGA
ACATTTCCACCTCACCATTGATTCTCATAGTAAGCTCGTTATTGTTCAAATCGATGGTGGATCGA
TATGTATCTAG
Found at i:172846 original size:23 final size:23
Alignment explanation
Indices: 172819--172865 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
172809 ATCTGCTAGG
172819 TATGAAATCGACAGATCAATGGC
1 TATGAAATCGACAGATCAATGGC
172842 TATGAAATCGACAGATCAATGGC
1 TATGAAATCGACAGATCAATGGC
172865 T
1 T
172866 CATGGTGGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (23 bp):
TATGAAATCGACAGATCAATGGC
Found at i:174546 original size:18 final size:19
Alignment explanation
Indices: 174517--174552 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
174507 GCAATTATTC
*
174517 TTTCTTTCTTACTTATCTT
1 TTTCTTTCTTACTAATCTT
174536 TTTCTTT-TTACTAATCT
1 TTTCTTTCTTACTAATCT
174553 GTTTAACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTCTTTCTTACTAATCTT
Found at i:181333 original size:21 final size:21
Alignment explanation
Indices: 181307--181350 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
181297 GGTTGGTTCG
*
181307 AAGGACAAGAAA-AGGAAGCAC
1 AAGGACAA-AAAGAAGAAGCAC
181328 AAGGACAAAAAGAAGAAGCAC
1 AAGGACAAAAAGAAGAAGCAC
181349 AA
1 AA
181351 AGAGGAAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.61, C:0.14, G:0.25, T:0.00
Consensus pattern (21 bp):
AAGGACAAAAAGAAGAAGCAC
Done.