Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002812.1 Kokia drynarioides strain JFW-HI SEQ_115166, 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: 63959
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:8178 original size:22 final size:22
Alignment explanation
Indices: 8150--8195 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
8140 GCGTGAGTCA
8150 AAACGCATTGAGAATCCAAACT
1 AAACGCATTGAGAATCCAAACT
8172 AAACGCATTGAGAATCCAAACT
1 AAACGCATTGAGAATCCAAACT
8194 AA
1 AA
8196 CCCTTACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.48, C:0.22, G:0.13, T:0.17
Consensus pattern (22 bp):
AAACGCATTGAGAATCCAAACT
Found at i:12203 original size:18 final size:16
Alignment explanation
Indices: 12143--12226 Score: 80
Period size: 16 Copynumber: 5.1 Consensus size: 16
12133 GAGCAACATA
12143 TTATATTATGTTATTT
1 TTATATTATGTTATTT
* ** *
12159 TTAAAGTTCATAATA-CT
1 TTATA-TT-ATGTTATTT
12176 TTATATTATGTTATTT
1 TTATATTATGTTATTT
*
12192 TTATACATTATGTAATTT
1 TTAT--ATTATGTTATTT
12210 TTATATTATGTTATTT
1 TTATATTATGTTATTT
12226 T
1 T
12227 GAGAATCACG
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
15 4 0.08
16 23 0.43
17 7 0.13
18 19 0.36
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.61
Consensus pattern (16 bp):
TTATATTATGTTATTT
Found at i:15845 original size:97 final size:97
Alignment explanation
Indices: 15670--15863 Score: 266
Period size: 97 Copynumber: 2.0 Consensus size: 97
15660 AACTTTGGAA
* *
15670 AAGGATATTCGATTATCTCGATTTAAAGAAAAGTCGCACCTAGTAAGTTAAGGCAAAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTAAAGAAAAATCACACCTAGTAAGTTAAGGCAAAAATTTTCA
* *
15735 GAATCAGAGAT-AAAGAAACATTGCCTCGATTT
66 AAATCAGAAATAAAAG-AACATTGCCTCGATTT
* * * *
15767 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATCACACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTAAAGAAAAATCACACCTAGTAAGTTAAGGCAAAAATTTTCA
* *
15832 AAACTC-GAAATAAAAGAATATTGCCTTGATTT
66 AAA-TCAGAAATAAAAGAACATTGCCTCGATTT
15864 TAAAGTTTTC
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
97 79 0.93
98 6 0.07
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.29
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTAAAGAAAAATCACACCTAGTAAGTTAAGGCAAAAATTTTCA
AAATCAGAAATAAAAGAACATTGCCTCGATTT
Found at i:16110 original size:27 final size:28
Alignment explanation
Indices: 16080--16141 Score: 99
Period size: 27 Copynumber: 2.2 Consensus size: 28
16070 AAAATGAGAT
16080 TTTTGGATGCTCGGGGGT-AAATGGTAA
1 TTTTGGATGCTCGGGGGTAAAATGGTAA
*
16107 TTTTGGATGCTTGGGGGTAAAAATGGTAA
1 TTTTGGATGCTCGGGGGT-AAAATGGTAA
16136 TTTTGG
1 TTTTGG
16142 GGTTAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 17 0.53
29 15 0.47
ACGTcount: A:0.23, C:0.05, G:0.35, T:0.37
Consensus pattern (28 bp):
TTTTGGATGCTCGGGGGTAAAATGGTAA
Found at i:16160 original size:21 final size:21
Alignment explanation
Indices: 16117--16159 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
16107 TTTTGGATGC
*
16117 TTGGGGGTAAAAATGGTAATT
1 TTGGGGGTAAAAATGGAAATT
*
16138 TTGGGGTTAAAAAT-GAAATT
1 TTGGGGGTAAAAATGGAAATT
16158 TT
1 TT
16160 TAGACATTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.28, T:0.37
Consensus pattern (21 bp):
TTGGGGGTAAAAATGGAAATT
Found at i:16274 original size:29 final size:29
Alignment explanation
Indices: 16235--16340 Score: 92
Period size: 29 Copynumber: 3.6 Consensus size: 29
16225 GTTCGAGGGT
*
16235 AAATGGTAATTTTTGGGAAATTTGGGGTCA
1 AAATGG-AATTTTTGGAAAATTTGGGGTCA
*
16265 AAATGGAA-TTTT-GAAAAGTTTAGGGGTAA
1 AAATGGAATTTTTGGAAAA-TTT-GGGGTCA
* * **
16294 AAAAGTAATTTTTGGAAAATTTAAGGTCAA
1 AAATGGAATTTTTGGAAAATTTGGGGTC-A
*
16324 AAATAGAA-TTTTGGAAA
1 AAATGGAATTTTTGGAAA
16341 GTTCGAGGGC
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
27 4 0.07
28 7 0.11
29 26 0.43
30 19 0.31
31 5 0.08
ACGTcount: A:0.42, C:0.02, G:0.24, T:0.33
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAAATTTGGGGTCA
Found at i:16355 original size:29 final size:29
Alignment explanation
Indices: 16271--16364 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
16261 GTCAAAATGG
* * * *
16271 AATTTTGAAAAGTTTAGGGGTAAAAAAGT
1 AATTTTGGAAAGTTAAGGGCTAAAATAGT
* * *
16300 AATTTTTGGAAAATTTAAGGTCAAAAATAG-
1 AA-TTTTGG-AAAGTTAAGGGCTAAAATAGT
*
16330 AATTTTGGAAAGTTCGAGGGCTAAAAT-GT
1 AATTTTGGAAAGTT-AAGGGCTAAAATAGT
16359 AATTTT
1 AATTTT
16365 CAGATAGTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
28 6 0.12
29 23 0.46
30 7 0.14
31 14 0.28
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.34
Consensus pattern (29 bp):
AATTTTGGAAAGTTAAGGGCTAAAATAGT
Found at i:16361 original size:59 final size:58
Alignment explanation
Indices: 16166--16364 Score: 201
Period size: 59 Copynumber: 3.4 Consensus size: 58
16156 TTTTTAGACA
* * * *
16166 TTCGAGGGTAAAATGGTAATTTTTGGAAAGAATCAAGTTTAAAAATGAAATTTTTGG-AAG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAA-ATTTAAGGTCAAAAATG-AA-TTTTGGAAAG
* ** *
16226 TTCGAGGGT-AAATGGTAATTTTTGGGAAATTTGGGGTC-AAAATGGAATTTTGAAAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAAATTTAAGGTCAAAAAT-GAATTTTGGAAAG
* **
16283 TT-TAGGGGTAAAAAAGTAATTTTTGGAAAATTTAAGGTCAAAAATAGAATTTTGGAAAG
1 TTCGA-GGGTAAAATGGTAATTTTTGGAAAATTTAAGGTCAAAAAT-GAATTTTGGAAAG
16342 TTCGAGGGCTAAAAT-GTAATTTT
1 TTCGAGGG-TAAAATGGTAATTTT
16365 CAGATAGTTT
Statistics
Matches: 114, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
56 6 0.05
57 16 0.14
58 29 0.25
59 48 0.42
60 15 0.13
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.34
Consensus pattern (58 bp):
TTCGAGGGTAAAATGGTAATTTTTGGAAAATTTAAGGTCAAAAATGAATTTTGGAAAG
Found at i:17138 original size:18 final size:19
Alignment explanation
Indices: 17097--17140 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
17087 CAACTCTTTT
* *
17097 TTATTATTAATAATATTTA
1 TTATTATAAATAATATTCA
17116 TTATTATAAATAA-ATTCA
1 TTATTATAAATAATATTCA
17134 TTATTAT
1 TTATTAT
17141 TGTTATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATTATAAATAATATTCA
Found at i:17844 original size:17 final size:17
Alignment explanation
Indices: 17824--17886 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
17814 AAACCCAATT
*
17824 TAAAATTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* * *
17841 TAAATTTTAGTTTAAAT
1 TAAATTTAAATTTAAAA
*
17858 TAAATTTGAATTTAAAA
1 TAAATTTAAATTTAAAA
17875 TAAATTTAAATT
1 TAAATTTAAATT
17887 CAAACTTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:17846 original size:23 final size:22
Alignment explanation
Indices: 17820--17911 Score: 80
Period size: 23 Copynumber: 4.1 Consensus size: 22
17810 TTCTAAACCC
*
17820 AATTTAAAATTAAATTTAAAATA
1 AATTTAAAA-TAAATTTAAATTA
*** *
17843 AATTTTAGTTTAAA-TTAAATTTG
1 AA-TTTAAAATAAATTTAAA-TTA
17866 AATTTAAAATAAATTTAAATTCA
1 AATTTAAAATAAATTTAAATT-A
*
17889 AACTTAAAATAAATTT-AATTA
1 AATTTAAAATAAATTTAAATTA
17910 AA
1 AA
17912 GATTGGGCTT
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
21 3 0.05
22 19 0.35
23 29 0.53
24 4 0.07
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
AATTTAAAATAAATTTAAATTA
Found at i:17904 original size:34 final size:33
Alignment explanation
Indices: 17823--17906 Score: 96
Period size: 34 Copynumber: 2.5 Consensus size: 33
17813 TAAACCCAAT
* * *
17823 TTAAAATTAAATTTAAAATAAATTTTAGTTTAAA
1 TTAAAA-TAAATTTAAAATAAATTTAAATTCAAA
* *
17857 TTAAATTTGAATTTAAAATAAATTTAAATTCAAA
1 TTAAA-ATAAATTTAAAATAAATTTAAATTCAAA
17891 CTTAAAATAAATTTAA
1 -TTAAAATAAATTTAA
17907 TTAAAGATTG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
34 36 0.88
35 5 0.12
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (33 bp):
TTAAAATAAATTTAAAATAAATTTAAATTCAAA
Found at i:18926 original size:49 final size:49
Alignment explanation
Indices: 18873--19192 Score: 208
Period size: 49 Copynumber: 6.6 Consensus size: 49
18863 AGGTATAGGG
* * *
18873 TTCGCCATTGCGACTTAAACCTTTCCCCTTGCATCTTCGCGATACTAGA
1 TTCGCCATTGCGGCTTAAACCTTTCCCCTTGCATCTTCGAGGTACTAGA
* * * * * *
18922 TTCGCCGTTGTGGCTTAAATCTTT-CCCTT-CATGTCTCTGAGGTATTAGG
1 TTCGCCATTGCGGCTTAAACCTTTCCCCTTGCATCT-TC-GAGGTACTAGA
* * * * *
18971 TTCGCCATTGCGACTTAAACCTTTCCCATGTG--TCCTCGTGGTACTGGA
1 TTCGCCATTGCGGCTTAAACCTTTCCCCT-TGCATCTTCGAGGTACTAGA
* * * * *
19019 TTAGCCGTTACGGCTTAAATCTTT-CCCTT-CA-CGTCTCTGAGGTACTAGG
1 TTCGCCATTGCGGCTTAAACCTTTCCCCTTGCATC-T-TC-GAGGTACTAGA
* * * ** *
19068 TTCGCCATTGAGACTTAAACCTTTCCCTTTTGTGTCTTCGAGGTA-TAAGG
1 TTCGCCATTGCGGCTTAAACCTTTCCC-CTTGCATCTTCGAGGTACT-AGA
* ** *
19118 TTCGCCATTACGGCTTAAACCTTT-CCCTTGTGTCTTCGTGGTACTAGA
1 TTCGCCATTGCGGCTTAAACCTTTCCCCTTGCATCTTCGAGGTACTAGA
** * *
19166 TTCATCGTTGCGGCTTAAATCTTTCCC
1 TTCGCCATTGCGGCTTAAACCTTTCCC
19193 TTCACGTCTC
Statistics
Matches: 204, Mismatches: 50, Indels: 34
0.71 0.17 0.12
Matches are distributed among these distances:
46 2 0.01
47 7 0.03
48 71 0.35
49 81 0.40
50 36 0.18
51 5 0.02
52 1 0.00
53 1 0.00
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (49 bp):
TTCGCCATTGCGGCTTAAACCTTTCCCCTTGCATCTTCGAGGTACTAGA
Found at i:19062 original size:97 final size:96
Alignment explanation
Indices: 18860--19146 Score: 346
Period size: 97 Copynumber: 2.9 Consensus size: 96
18850 TTTAATGCCG
* * * *
18860 CTGAGGTATAGGGTTCGCCATTGCGACTTAAACCTTTCCCCT-TGCATCTTCGCGATACTAGATT
1 CTGAGGTATA-GGTTCGCCATTGCGACTTAAACCTTTCCCATGTG--TCTTCGAGGTACTGGATT
** *
18924 CGCCGTTGTGGCTTAAATCTTTCCCTTCATGTCT
63 CGCCGTTACGGCTTAAATCTTTCCCTTCACGTCT
* * *
18958 CTGAGGTATTAGGTTCGCCATTGCGACTTAAACCTTTCCCATGTGTCCTCGTGGTACTGGATTAG
1 CTGAGGTA-TAGGTTCGCCATTGCGACTTAAACCTTTCCCATGTGTCTTCGAGGTACTGGATTCG
19023 CCGTTACGGCTTAAATCTTTCCCTTCACGTCT
65 CCGTTACGGCTTAAATCTTTCCCTTCACGTCT
* *
19055 CTGAGGTACTAGGTTCGCCATTGAGACTTAAACCTTTCCCTTTTGTGTCTTCGAGGTA-TAAGG-
1 CTGAGGTA-TAGGTTCGCCATTGCGACTTAAACCTTTCCC--ATGTGTCTTCGAGGTACT--GGA
* *
19118 TTCGCCATTACGGCTTAAACCTTTCCCTT
61 TTCGCCGTTACGGCTTAAATCTTTCCCTT
19147 GTGTCTTCGT
Statistics
Matches: 166, Mismatches: 17, Indels: 11
0.86 0.09 0.06
Matches are distributed among these distances:
97 82 0.49
98 39 0.23
99 43 0.26
100 2 0.01
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.36
Consensus pattern (96 bp):
CTGAGGTATAGGTTCGCCATTGCGACTTAAACCTTTCCCATGTGTCTTCGAGGTACTGGATTCGC
CGTTACGGCTTAAATCTTTCCCTTCACGTCT
Found at i:19141 original size:147 final size:147
Alignment explanation
Indices: 18915--19248 Score: 428
Period size: 147 Copynumber: 2.3 Consensus size: 147
18905 ATCTTCGCGA
* * * *
18915 TACTAGATTCGCCGTTGTGGCTTAAATCTTTCCC-TTCATGTCTCTGAGGTATTAGGTTCGCCAT
1 TACTAGGTTCGCCATTGAGGCTTAAATCTTTCCCTTTCATGTCTCTGAGGTATAAGGTTCGCCAT
* *
18979 TGCGACTTAAACCTTTCCCATGTGTCCTCGTGGTACTGGATT-AGCCGTTACGGCTTAAATCTTT
66 TACGACTTAAACCTTTCCCATGTGTCCTCGTGGTACTAGATTCA-CCGTTACGGCTTAAATCTTT
19043 CCCTTCACGTCTCTGAGG
130 CCCTTCACGTCTCTGAGG
* * **
19061 TACTAGGTTCGCCATTGAGACTTAAACCTTTCCCTTTTGTGTCT-TCGAGGTATAAGGTTCGCCA
1 TACTAGGTTCGCCATTGAGGCTTAAATCTTTCCCTTTCATGTCTCT-GAGGTATAAGGTTCGCCA
* * * * *
19125 TTACGGCTTAAACCTTTCCCTTGTGTCTTCGTGGTACTAGATTCATCGTTGCGGCTTAAATCTTT
65 TTACGACTTAAACCTTTCCCATGTGTCCTCGTGGTACTAGATTCACCGTTACGGCTTAAATCTTT
*
19190 CCCTTCACGTCTCTGTGG
130 CCCTTCACGTCTCTGAGG
* *
19208 TA-TTGGATTCG-CAGTTGCGGCTTAAATCTTTCCC-TTCATGT
1 TACTAGG-TTCGCCA-TTGAGGCTTAAATCTTTCCCTTTCATGT
19249 TTCATGGTAC
Statistics
Matches: 161, Mismatches: 22, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
146 40 0.25
147 120 0.75
148 1 0.01
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (147 bp):
TACTAGGTTCGCCATTGAGGCTTAAATCTTTCCCTTTCATGTCTCTGAGGTATAAGGTTCGCCAT
TACGACTTAAACCTTTCCCATGTGTCCTCGTGGTACTAGATTCACCGTTACGGCTTAAATCTTTC
CCTTCACGTCTCTGAGG
Found at i:19227 original size:49 final size:50
Alignment explanation
Indices: 18920--19248 Score: 229
Period size: 49 Copynumber: 6.7 Consensus size: 50
18910 CGCGATACTA
* *
18920 GATTCGCCGTTGTGGCTTAAATCTTTCCCTTCATGTCTCT-GAGGTATTAG
1 GATTCGCAGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTCGAGGTATT-G
* * * * * *
18970 G-TTCGCCA-TTGCGACTTAAACCTTTCCCAT-GTGTC-CTCGTGGTACTG
1 GATTCG-CAGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTCGAGGTATTG
* * * * *
19017 GATTAGCCGTTACGGCTTAAATCTTTCCCTTCACGTCTCT-GAGGTACTAG
1 GATTCGCAGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTCGAGGTA-TTG
* * * * * *
19067 G-TTCGCCA-TTGAGACTTAAACCTTTCCCTT-TTGTGTCTTCGAGGTATAAG
1 GATTCG-CAGTTGCGGCTTAAATCTTTCCCTTCATGTCTC-TCGAGGTAT-TG
* * * * * *
19117 G-TTCGCCA-TTACGGCTTAAACCTTTCCCTT-GTGTCT-TCGTGGTACTA
1 GATTCG-CAGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTCGAGGTATTG
* * *
19164 GATTCATC-GTTGCGGCTTAAATCTTTCCCTTCACGTCTCT-GTGGTATTG
1 GATTC-GCAGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTCGAGGTATTG
19213 GATTCGCAGTTGCGGCTTAAATCTTTCCCTTCATGT
1 GATTCGCAGTTGCGGCTTAAATCTTTCCCTTCATGT
19249 TTCATGGTAC
Statistics
Matches: 216, Mismatches: 46, Indels: 35
0.73 0.15 0.12
Matches are distributed among these distances:
47 6 0.03
48 67 0.31
49 96 0.44
50 47 0.22
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (50 bp):
GATTCGCAGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTCGAGGTATTG
Found at i:19708 original size:18 final size:18
Alignment explanation
Indices: 19682--19716 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19672 AAAATTGCTG
*
19682 AATATTTACAAGGAACAA
1 AATAATTACAAGGAACAA
19700 AATAATTACAAGGAACA
1 AATAATTACAAGGAACA
19717 GTATTAGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (18 bp):
AATAATTACAAGGAACAA
Found at i:24004 original size:18 final size:18
Alignment explanation
Indices: 23962--24005 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
23952 GCCAGTCGTG
23962 CTTTTCTCATCTCTGGCTT
1 CTTTTC-CATCTCTGGCTT
* **
23981 CCTTTCCATCTCTTTCTT
1 CTTTTCCATCTCTGGCTT
23999 CTTTTCC
1 CTTTTCC
24006 TTCACATTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.05, C:0.36, G:0.05, T:0.55
Consensus pattern (18 bp):
CTTTTCCATCTCTGGCTT
Found at i:32921 original size:37 final size:37
Alignment explanation
Indices: 32878--33037 Score: 214
Period size: 37 Copynumber: 4.3 Consensus size: 37
32868 TCGGGTTATC
*
32878 TGCCTAGCAGGCTTCGTGTCGGTGTATTCAGGTTATG
1 TGCCTAGCAGGCTTCGTGTCGGTGTATTCAGGCTATG
* * * * *
32915 TGCCTAGCAGGCTTCATGCCAGTGCATTCGGGCTATG
1 TGCCTAGCAGGCTTCGTGTCGGTGTATTCAGGCTATG
* *
32952 TGCCTAGAAGGCTTCGTG-CTGGTGTATTCAGGCTACG
1 TGCCTAGCAGGCTTCGTGTC-GGTGTATTCAGGCTATG
* *
32989 TGCCTAGCAGGCTTCGTGTTGGTGTATTCAGGCTATA
1 TGCCTAGCAGGCTTCGTGTCGGTGTATTCAGGCTATG
33026 TGCCTAGCAGGC
1 TGCCTAGCAGGC
33038 CTTGGTGCTG
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
36 1 0.01
37 104 0.99
ACGTcount: A:0.16, C:0.23, G:0.31, T:0.31
Consensus pattern (37 bp):
TGCCTAGCAGGCTTCGTGTCGGTGTATTCAGGCTATG
Found at i:32984 original size:21 final size:21
Alignment explanation
Indices: 32960--33022 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
32950 TGTGCCTAGA
32960 AGGCTTCGTGCTGGTGTATTC
1 AGGCTTCGTGCTGGTGTATTC
* * *
32981 AGGCTACGTGC----CTA-GC
1 AGGCTTCGTGCTGGTGTATTC
*
32997 AGGCTTCGTGTTGGTGTATTC
1 AGGCTTCGTGCTGGTGTATTC
33018 AGGCT
1 AGGCT
33023 ATATGCCTAG
Statistics
Matches: 30, Mismatches: 7, Indels: 10
0.64 0.15 0.21
Matches are distributed among these distances:
16 10 0.33
17 2 0.07
20 2 0.07
21 16 0.53
ACGTcount: A:0.13, C:0.21, G:0.33, T:0.33
Consensus pattern (21 bp):
AGGCTTCGTGCTGGTGTATTC
Found at i:32992 original size:74 final size:74
Alignment explanation
Indices: 32866--33050 Score: 228
Period size: 74 Copynumber: 2.5 Consensus size: 74
32856 CATCTTAATA
* * * *
32866 ATTCGGGTTATCTGCCTAGCAGGCTTCGTG-TCGGTGTATTCAGGTTATGTGCCTAGCAGGCTTC
1 ATTCGGGCTATATGCCTAGCAGGCTTCGTGCT-GGTGTATTCAGGCTACGTGCCTAGCAGGCTTC
32930 ATGCCAGTGC
65 ATGCCAGTGC
* * *
32940 ATTCGGGCTATGTGCCTAGAAGGCTTCGTGCTGGTGTATTCAGGCTACGTGCCTAGCAGGCTTCG
1 ATTCGGGCTATATGCCTAGCAGGCTTCGTGCTGGTGTATTCAGGCTACGTGCCTAGCAGGCTTCA
*** *
33005 TGTTGGTGT
66 TGCCAGTGC
* *
33014 ATTCAGGCTATATGCCTAGCAGGCCTTGGTGCTGGTG
1 ATTCGGGCTATATGCCTAGCAGG-CTTCGTGCTGGTG
33051 ATTAGAAGAC
Statistics
Matches: 95, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
74 82 0.86
75 13 0.14
ACGTcount: A:0.15, C:0.22, G:0.32, T:0.32
Consensus pattern (74 bp):
ATTCGGGCTATATGCCTAGCAGGCTTCGTGCTGGTGTATTCAGGCTACGTGCCTAGCAGGCTTCA
TGCCAGTGC
Found at i:36843 original size:30 final size:30
Alignment explanation
Indices: 36772--36850 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 30
36762 ACTCGCTCAA
* ** *
36772 AAATAGTTCGCATACAAT-AGTTCGTATAT
1 AAATAGTTCGCATACAATCAGCTCACATAC
* * *
36801 AAACAATTCGCATACCATCAGCTCACATAC
1 AAATAGTTCGCATACAATCAGCTCACATAC
36831 AAATAGTTCGCATACAATCA
1 AAATAGTTCGCATACAATCA
36851 ATTTAGTGAT
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 15 0.38
30 24 0.62
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.27
Consensus pattern (30 bp):
AAATAGTTCGCATACAATCAGCTCACATAC
Found at i:36844 original size:15 final size:15
Alignment explanation
Indices: 36772--36847 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
36762 ACTCGCTCAA
36772 AAATAGTTCGCATAC
1 AAATAGTTCGCATAC
* *
36787 -AATAGTTCGTATAT
1 AAATAGTTCGCATAC
* *
36801 AAACAATTCGCATAC
1 AAATAGTTCGCATAC
* * *
36816 -CATCAGCTCACATAC
1 AAAT-AGTTCGCATAC
36831 AAATAGTTCGCATAC
1 AAATAGTTCGCATAC
36846 AA
1 AA
36848 TCAATTTAGT
Statistics
Matches: 44, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
14 13 0.30
15 29 0.66
16 2 0.05
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.26
Consensus pattern (15 bp):
AAATAGTTCGCATAC
Found at i:36902 original size:15 final size:15
Alignment explanation
Indices: 36859--36902 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
36849 CAATTTAGTG
*
36859 ATATAAACAATTCGC
1 ATATAAACAATTCAC
** *
36874 ATATATGCAGTTCAC
1 ATATAAACAATTCAC
36889 ATATAAACAATTCA
1 ATATAAACAATTCA
36903 GTGATATATT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (15 bp):
ATATAAACAATTCAC
Found at i:37563 original size:21 final size:21
Alignment explanation
Indices: 37505--37564 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
37495 ATGTAAGAGC
* * *
37505 TCGCACAGCATGTGAAAGTGT
1 TCGCATAGCATATAAAAGTGT
* ***
37526 TCGCATAACACCCAAAAGTGT
1 TCGCATAGCATATAAAAGTGT
37547 TCGCATAGCATATAAAAG
1 TCGCATAGCATATAAAAG
37565 AGTTTGCAAC
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (21 bp):
TCGCATAGCATATAAAAGTGT
Found at i:38994 original size:10 final size:9
Alignment explanation
Indices: 38959--38995 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
38949 GGGTTTACCC
38959 ACAATTAAA
1 ACAATTAAA
38968 ACAATTAAA
1 ACAATTAAA
*
38977 AAAATTAAA
1 ACAATTAAA
38986 ACAAGTTAAA
1 ACAA-TTAAA
38996 CACTAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 20 0.80
10 5 0.20
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.22
Consensus pattern (9 bp):
ACAATTAAA
Found at i:45000 original size:24 final size:24
Alignment explanation
Indices: 44952--45000 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
44942 TTTTATGGTA
* * *
44952 ATGGTAATGAAGGTGGAGAGGGTG
1 ATGGTAATAAAGATGGAGAGAGTG
*
44976 ATGGTAATAAAGATGGTGAGAGTG
1 ATGGTAATAAAGATGGAGAGAGTG
45000 A
1 A
45001 GGGTGGTGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.43, T:0.22
Consensus pattern (24 bp):
ATGGTAATAAAGATGGAGAGAGTG
Found at i:45041 original size:15 final size:15
Alignment explanation
Indices: 44989--45041 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
44979 GTAATAAAGA
*
44989 TGGTGAGAGTGAGGG
1 TGGTGAGGGTGAGGG
* *
45004 TGGTGAAGGTG-GTGA
1 TGGTGAGGGTGAG-GG
*
45019 AGGTGAGGGTGAGGG
1 TGGTGAGGGTGAGGG
45034 TGGTGAGG
1 TGGTGAGG
45042 TTGTTGGCAA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 1 0.03
15 27 0.93
16 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.60, T:0.21
Consensus pattern (15 bp):
TGGTGAGGGTGAGGG
Found at i:47438 original size:160 final size:158
Alignment explanation
Indices: 47156--47617 Score: 522
Period size: 160 Copynumber: 2.9 Consensus size: 158
47146 AACAAAAGAT
* ** * * *
47156 CATGCATTCAACCTAACACAACGGGAGCACGAGTATAT-GTAAACACT-TTTTCATTGTCAATTC
1 CATGCATTCAGCCTAACACAACTAGATCACAAGTATATCGTAAACACTATTTT-AATGTCAATTC
* * ** * *
47219 CAAAATATAAAAATCTAATTTGGGTTTTGATTTTTTTGGTCTAAGTCTGGTACGAGTACGAGAAC
65 AAAAACATTTAAATCTAATTGGGGTTTTGATTTTTTTGGTCTAAGTCTAGTACGAGTACGAGAAC
*
47284 TAGAAGCCCAAAAAATAACAACATAACAC
130 TAGAAGCCCAAAAAATAACAACAGAACAC
* *** *
47313 CATGCATTCAGCCTAATACAACTAGATCATGGGTATATCGTATACACTATTTTAATGTCAAATTC
1 CATGCATTCAGCCTAACACAACTAGATCACAAGTATATCGTAAACACTATTTTAATGTC-AATTC
* *
47378 AAAAACATTTTAATCTAATTCGGGGTTTTGATTTTTTTGGTCTTAGTCTAGTACGAGTACGAGAA
65 AAAAACATTTAAATCTAATT-GGGGTTTTGATTTTTTTGGTCTAAGTCTAGTACGAGTACGAGAA
* * * *
47443 CTAGAAGCCAAAAAAAGAACAACAGGACAT
129 CTAGAAGCCCAAAAAATAACAACAGAACAC
* * * *
47473 CATGCTTTCAGCCTAACACAACTGGATCACAAGTATATCGTAAACACTTTTTTAATGTCAATTCC
1 CATGCATTCAGCCTAACACAACTAGATCACAAGTATATCGTAAACACTATTTTAATGTCAATTCA
** ** * *
47538 AAATTATTTAAAT-TCAATTTGGGGTTTTGATTTTTTT--TCCCATTCTAGTACGAGTATGAGAA
66 AAAACATTTAAATCT-AA-TTGGGGTTTTGATTTTTTTGGTCTAAGTCTAGTACGAGTACGAGAA
47600 CTAGAAG-CCAAATAAATA
129 CTAGAAGCCCAAA-AAATA
47618 TGACATATCA
Statistics
Matches: 258, Mismatches: 40, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
156 4 0.02
157 63 0.24
158 14 0.05
159 58 0.22
160 119 0.46
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (158 bp):
CATGCATTCAGCCTAACACAACTAGATCACAAGTATATCGTAAACACTATTTTAATGTCAATTCA
AAAACATTTAAATCTAATTGGGGTTTTGATTTTTTTGGTCTAAGTCTAGTACGAGTACGAGAACT
AGAAGCCCAAAAAATAACAACAGAACAC
Found at i:47827 original size:82 final size:82
Alignment explanation
Indices: 47691--47892 Score: 363
Period size: 82 Copynumber: 2.5 Consensus size: 82
47681 TTGAGATGGT
47691 TAACATA-TTTGTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGAGTAACATCTTACTGCTATA
1 TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGAGTAACATCTTACTGCTATA
47755 GGATCATTTTGTTAGTA
66 GGATCATTTTGTTAGTA
*
47772 TAACATATTTTGTTTGTTTTTTGAAACGATTTGTTGAAATGGTTG-GTTAACATCTTACTGCTAT
1 TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGAG-TAACATCTTACTGCTAT
47836 AGGATCATTTTGTTAGTA
65 AGGATCATTTTGTTAGTA
*
47854 TAACATATTTTATTTGTTTTTTGAAATGATTTGTTGAAA
1 TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAA
47893 GATGTATACC
Statistics
Matches: 116, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
81 8 0.07
82 108 0.93
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (82 bp):
TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGAGTAACATCTTACTGCTATA
GGATCATTTTGTTAGTA
Found at i:49701 original size:18 final size:18
Alignment explanation
Indices: 49658--49701 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
49648 ACTTAGGGGT
*
49658 TTTAAATTTTTTTATTAA
1 TTTAAATTATTTTATTAA
*
49676 TTTTAATTATTTT-TTAA
1 TTTAAATTATTTTATTAA
49693 GTTTAAATT
1 -TTTAAATT
49702 CATTAGTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTAAATTATTTTATTAA
Found at i:50000 original size:26 final size:27
Alignment explanation
Indices: 49971--50030 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
49961 TATAATGACT
*
49971 ATATAAAAATT-TTCAATAAATAAAA-A
1 ATATAAAAATTATTAAAT-AATAAAATA
*
49997 ATATATAAAATTATTAAATATTAAAATA
1 ATATA-AAAATTATTAAATAATAAAATA
50025 ATATAA
1 ATATAA
50031 TATAAATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 5 0.17
27 13 0.45
28 11 0.38
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (27 bp):
ATATAAAAATTATTAAATAATAAAATA
Found at i:50016 original size:28 final size:28
Alignment explanation
Indices: 49970--50029 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
49960 TTATAATGAC
*
49970 TATATAAAAATTTTCAATAAATAAAA-AA
1 TATATAAAAATTTTAAAT-AATAAAATAA
*
49998 TATAT-AAAATTATTAAATATTAAAATAA
1 TATATAAAAATT-TTAAATAATAAAATAA
50026 TATA
1 TATA
50030 ATATAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
TATATAAAAATTTTAAATAATAAAATAA
Found at i:56798 original size:16 final size:17
Alignment explanation
Indices: 56774--56813 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
56764 GAAACTAAAT
*
56774 AACTAAAATAAATAAAC
1 AACTAAAATAAACAAAC
56791 AA-TAAAATAAACAAAC
1 AACTAAAATAAACAAAC
56807 AACTAAA
1 AACTAAA
56814 CCTATTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.15
Consensus pattern (17 bp):
AACTAAAATAAACAAAC
Found at i:60013 original size:27 final size:26
Alignment explanation
Indices: 59977--60047 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
59967 GGGTGGTCAA
59977 ATTTGGGGATTTTGGGTACGGGTTTTG
1 ATTTGGGGATTTTGGGTA-GGGTTTTG
** *
60004 ATTTGGGGATTTTTGTTTAGGTTTTTG
1 ATTTGGGGA-TTTTGGGTAGGGTTTTG
*
60031 ATTTTGGAGATTTTGGG
1 A-TTTGGGGATTTTGGG
60048 GATTGCTCAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.13, C:0.01, G:0.35, T:0.51
Consensus pattern (26 bp):
ATTTGGGGATTTTGGGTAGGGTTTTG
Found at i:60674 original size:13 final size:14
Alignment explanation
Indices: 60663--60718 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
60653 AAACGTTAAA
60663 AATAGATTTTAATAT
1 AATA-ATTTTAATAT
*
60678 AATAATTTTATATTT
1 AATAATTTTA-ATAT
*
60693 CAA-AA-TATAATAT
1 -AATAATTTTAATAT
60706 AATAATTTTAATA
1 AATAATTTTAATA
60719 ATTTTATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
12 2 0.06
13 5 0.15
14 15 0.45
15 9 0.27
16 2 0.06
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (14 bp):
AATAATTTTAATAT
Found at i:60724 original size:37 final size:38
Alignment explanation
Indices: 60677--60754 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 38
60667 GATTTTAATA
*
60677 TAATAATTTTATATTTCAAAATATAA-TATAATAATTT
1 TAATAATTTTATATTTCAAAAAATAAGTATAATAATTT
*
60714 TAATAATTTTATATTTCAAAAAATAAGTTTAATAATTT
1 TAATAATTTTATATTTCAAAAAATAAGTATAATAATTT
60752 TAA
1 TAA
60755 AATCATTTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 25 0.66
38 13 0.34
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (38 bp):
TAATAATTTTATATTTCAAAAAATAAGTATAATAATTT
Found at i:60738 original size:20 final size:20
Alignment explanation
Indices: 60678--60744 Score: 52
Period size: 20 Copynumber: 3.5 Consensus size: 20
60668 ATTTTAATAT
60678 AATAATTTTATATTTCAAAA
1 AATAATTTTATATTTCAAAA
* * * *
60698 TATAATATAATAATTT----T
1 AATAATTTTAT-ATTTCAAAA
60715 AATAATTTTATATTTCAAAA
1 AATAATTTTATATTTCAAAA
*
60735 AATAAGTTTA
1 AATAATTTTA
60745 ATAATTTTAA
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
16 4 0.12
17 8 0.24
20 17 0.52
21 4 0.12
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (20 bp):
AATAATTTTATATTTCAAAA
Done.