Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006469.1 Kokia drynarioides strain JFW-HI SEQ_121052, 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: 164225
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:413 original size:56 final size:56
Alignment explanation
Indices: 327--438 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
317 TATTCAACTT
327 TGCTTCACTTTTTCAAATGAGTAATAGACTATCCTATATCCCATCCATTATAATAG
1 TGCTTCACTTTTTCAAATGAGTAATAGACTATCCTATATCCCATCCATTATAATAG
383 TGCTTCACTTTTTCAAATGAGTAATAGACTATCCTATATCCCATCCATTATAATAG
1 TGCTTCACTTTTTCAAATGAGTAATAGACTATCCTATATCCCATCCATTATAATAG
439 AAACATTTTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (56 bp):
TGCTTCACTTTTTCAAATGAGTAATAGACTATCCTATATCCCATCCATTATAATAG
Found at i:7250 original size:25 final size:24
Alignment explanation
Indices: 7221--7267 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
7211 TTTCAAGTTA
7221 AAAAAAGTTTCACAAATTAATAAAT
1 AAAAAAGTTTCA-AAATTAATAAAT
* *
7246 AAAAATGTTTCAATATTAATAA
1 AAAAAAGTTTCAAAATTAATAA
7268 CACTATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (24 bp):
AAAAAAGTTTCAAAATTAATAAAT
Found at i:20079 original size:40 final size:39
Alignment explanation
Indices: 20035--20128 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 39
20025 AGTCTTACAA
* * *
20035 TGTTTACAATGTCACGGCTAGTACAGTAACAATGTTGTAG
1 TGTTTACAGTGTCACGGCTAGTACAGTAA-AATATTGCAG
* * * *
20075 TGTTTATAGTGTCACTGTTAGTCCAGTAAAATATTGCAG
1 TGTTTACAGTGTCACGGCTAGTACAGTAAAATATTGCAG
20114 TGTTTACAGTGTCAC
1 TGTTTACAGTGTCAC
20129 TGCCATTTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
39 22 0.48
40 24 0.52
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (39 bp):
TGTTTACAGTGTCACGGCTAGTACAGTAAAATATTGCAG
Found at i:20125 original size:39 final size:40
Alignment explanation
Indices: 20035--20131 Score: 124
Period size: 39 Copynumber: 2.5 Consensus size: 40
20025 AGTCTTACAA
* * * *
20035 TGTTTACAATGTCACGGCTAGTACAGTAACAATGTTGTAG
1 TGTTTACAGTGTCACTGCTAGTACAGTAACAATATTGCAG
* * *
20075 TGTTTATAGTGTCACTGTTAGTCCAGTAA-AATATTGCAG
1 TGTTTACAGTGTCACTGCTAGTACAGTAACAATATTGCAG
20114 TGTTTACAGTGTCACTGC
1 TGTTTACAGTGTCACTGC
20132 CATTTCAGTG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
39 24 0.50
40 24 0.50
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (40 bp):
TGTTTACAGTGTCACTGCTAGTACAGTAACAATATTGCAG
Found at i:22441 original size:54 final size:54
Alignment explanation
Indices: 22370--22478 Score: 193
Period size: 54 Copynumber: 2.0 Consensus size: 54
22360 TAAATACAGT
22370 AAAAAAACTACAGGTTTTCCAAAAGTAAGTTTATGGGTACAAGATATGGGTGAA
1 AAAAAAACTACAGGTTTTCCAAAAGTAAGTTTATGGGTACAAGATATGGGTGAA
*
22424 AAAAAAACTAC-GAGTTTTCTAAAAGTAAGTTTATGGGTACAAGATATGGGTGAA
1 AAAAAAACTACAG-GTTTTCCAAAAGTAAGTTTATGGGTACAAGATATGGGTGAA
22478 A
1 A
22479 TTTTAAGATA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
53 1 0.02
54 52 0.98
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (54 bp):
AAAAAAACTACAGGTTTTCCAAAAGTAAGTTTATGGGTACAAGATATGGGTGAA
Found at i:22877 original size:17 final size:16
Alignment explanation
Indices: 22847--22880 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
22837 ATAAATCATT
*
22847 AAAAATTAATAAAATA
1 AAAAATTAAAAAAATA
22863 AAAATATTAAAAAAATA
1 AAAA-ATTAAAAAAATA
22880 A
1 A
22881 TTAATTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAATTAAAAAAATA
Found at i:23902 original size:29 final size:29
Alignment explanation
Indices: 23860--23926 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
23850 TACTATGTTT
* * * *
23860 GCATATAACAGTTCGCACATAAATAGCTC
1 GCATACAATAGTTCACACATAAACAGCTC
* *
23889 GCATACAATAGTTCACATATAAACAGTTC
1 GCATACAATAGTTCACACATAAACAGCTC
*
23918 CCATACAAT
1 GCATACAAT
23927 CAGCTCACGC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.25
Consensus pattern (29 bp):
GCATACAATAGTTCACACATAAACAGCTC
Found at i:23964 original size:2 final size:2
Alignment explanation
Indices: 23959--23987 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23949 CACACACACG
23959 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23988 GGAAAACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41890 original size:15 final size:15
Alignment explanation
Indices: 41872--41958 Score: 81
Period size: 15 Copynumber: 5.9 Consensus size: 15
41862 TGAGCACTAG
41872 TGTTGCGAACACTCA
1 TGTTGCGAACACTCA
* *
41887 TGTTGAGAACACTGGA
1 TGTTGCGAACACT-CA
*
41903 -GTTGCGAACACTGA
1 TGTTGCGAACACTCA
*
41917 TGTTGTGAACACT-A
1 TGTTGCGAACACTCA
* *
41931 GTGTTGCCAGCACTCA
1 -TGTTGCGAACACTCA
41947 T-TTGCGAACACT
1 TGTTGCGAACACT
41959 GGAGCTGCAA
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
14 12 0.20
15 45 0.76
16 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (15 bp):
TGTTGCGAACACTCA
Found at i:41907 original size:30 final size:30
Alignment explanation
Indices: 41873--41988 Score: 128
Period size: 30 Copynumber: 3.9 Consensus size: 30
41863 GAGCACTAGT
*
41873 GTTGCGAACACTCATGTTGAGAACACTGGA
1 GTTGCGAACACTCATGTTGTGAACACTGGA
* * *
41903 GTTGCGAACACTGATGTTGTGAACACTAGT
1 GTTGCGAACACTCATGTTGTGAACACTGGA
* * *
41933 GTTGCCAGCACTCAT-TTGCGAACACTGGA
1 GTTGCGAACACTCATGTTGTGAACACTGGA
* *
41962 GCTGC-AACCACTAATGTTGTGAACACT
1 GTTGCGAA-CACTCATGTTGTGAACACT
41989 CGATCGAGCT
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
28 1 0.01
29 21 0.30
30 48 0.69
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (30 bp):
GTTGCGAACACTCATGTTGTGAACACTGGA
Found at i:41984 original size:59 final size:60
Alignment explanation
Indices: 41860--41988 Score: 181
Period size: 59 Copynumber: 2.2 Consensus size: 60
41850 AGATTGGAGA
* * * *
41860 TGTGAGCACTAGTGTTGCGAACACTCATGTTGAGAACACTGGAGTTGCGAACACTGATGT
1 TGTGAACACTAGTGTTGCCAACACTCATGTTGAGAACACTGGAGCTGCGAACACTAATGT
* *
41920 TGTGAACACTAGTGTTGCCAGCACTCAT-TTGCGAACACTGGAGCTGC-AACCACTAATGT
1 TGTGAACACTAGTGTTGCCAACACTCATGTTGAGAACACTGGAGCTGCGAA-CACTAATGT
41979 TGTGAACACT
1 TGTGAACACT
41989 CGATCGAGCT
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
58 2 0.03
59 35 0.56
60 25 0.40
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (60 bp):
TGTGAACACTAGTGTTGCCAACACTCATGTTGAGAACACTGGAGCTGCGAACACTAATGT
Found at i:49655 original size:23 final size:24
Alignment explanation
Indices: 49612--49657 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
49602 TGGGGTAGAT
49612 TGAAGATTTGAAGCTAAAATTTGC
1 TGAAGATTTGAAGCTAAAATTTGC
49636 TGAAGAGTTTGAA-C-AAAATTTG
1 TGAAGA-TTTGAAGCTAAAATTTG
49658 GATAAAACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.38
24 7 0.33
25 6 0.29
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (24 bp):
TGAAGATTTGAAGCTAAAATTTGC
Found at i:55314 original size:16 final size:16
Alignment explanation
Indices: 55295--55327 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
55285 TTTGAAGAGT
55295 ATTAATCTAAACTAAA
1 ATTAATCTAAACTAAA
*
55311 ATTAATCTAAATTAAA
1 ATTAATCTAAACTAAA
55327 A
1 A
55328 ATAAAATAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTAATCTAAACTAAA
Found at i:55419 original size:13 final size:13
Alignment explanation
Indices: 55401--55430 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
55391 AATGTGTTAG
55401 GTTAATCGTTTTA
1 GTTAATCGTTTTA
*
55414 GTTAATTGTTTTA
1 GTTAATCGTTTTA
55427 GTTA
1 GTTA
55431 CTTAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.17, T:0.57
Consensus pattern (13 bp):
GTTAATCGTTTTA
Found at i:57197 original size:25 final size:23
Alignment explanation
Indices: 57169--57214 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
57159 GTTGGATCCA
57169 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
57194 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
57215 CTCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:57866 original size:45 final size:45
Alignment explanation
Indices: 57817--57907 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
57807 CTTAGGTGTC
57817 TCCCCTTATCTAAATAATTACCTTAAATTCAAAATTAACAAGAAT
1 TCCCCTTATCTAAATAATTACCTTAAATTCAAAATTAACAAGAAT
57862 TCCCCTTATCTAAATAATTACCTTAAATTCAAAATTAACAAGAAT
1 TCCCCTTATCTAAATAATTACCTTAAATTCAAAATTAACAAGAAT
57907 T
1 T
57908 GACATCAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (45 bp):
TCCCCTTATCTAAATAATTACCTTAAATTCAAAATTAACAAGAAT
Found at i:58300 original size:18 final size:19
Alignment explanation
Indices: 58279--58320 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
58269 TGTCTTTTTC
58279 TTTTTTTTTTC-TCCAATT
1 TTTTTTTTTTCTTCCAATT
* *
58297 TTTTCTTTTTCTTTCAATT
1 TTTTTTTTTTCTTCCAATT
58316 TTTTT
1 TTTTT
58321 AGATTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTTTTTTCTTCCAATT
Found at i:58305 original size:19 final size:18
Alignment explanation
Indices: 58279--58320 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
58269 TGTCTTTTTC
58279 TTTTTTTTTTC-TCCAAT
1 TTTTTTTTTTCTTCCAAT
*
58296 TTTTTCTTTTTCTTTCAAT
1 TTTTT-TTTTTCTTCCAAT
58315 TTTTTT
1 TTTTTT
58321 AGATTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 7 0.32
19 10 0.45
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTTTTTCTTCCAAT
Found at i:58357 original size:23 final size:22
Alignment explanation
Indices: 58302--58365 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 22
58292 CAATTTTTTC
58302 TTTTTCTTTCAATTTTTTTAGAT
1 TTTTTCTTTC-ATTTTTTTAGAT
*
58325 TATTTT-TTTCATTTTTTTCGACT
1 T-TTTTCTTTCATTTTTTTAGA-T
*
58348 TTTTTCTTTCTTTTTTTT
1 TTTTTCTTTCATTTTTTT
58366 TCTTTTTCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
22 14 0.39
23 18 0.50
24 4 0.11
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.75
Consensus pattern (22 bp):
TTTTTCTTTCATTTTTTTAGAT
Found at i:63334 original size:25 final size:23
Alignment explanation
Indices: 63306--63351 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
63296 TTTGGATCCA
63306 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
63331 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
63352 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:65728 original size:31 final size:31
Alignment explanation
Indices: 65665--65728 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
65655 ACAATTAGTT
** *
65665 ATTTTAGTCACTATCATTAGGTATGTTATCA
1 ATTTTAGTCACTATCATTACATAAGTTATCA
* *
65696 ATTTTAGTCACTCTCATTACATAAGTTGTCA
1 ATTTTAGTCACTATCATTACATAAGTTATCA
65727 AT
1 AT
65729 ATTCGTCTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.44
Consensus pattern (31 bp):
ATTTTAGTCACTATCATTACATAAGTTATCA
Found at i:75040 original size:11 final size:11
Alignment explanation
Indices: 75013--75043 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
75003 AGATAATGCC
75013 CAAAGGAGACT
1 CAAAGGAGACT
75024 -AAAGGAGACT
1 CAAAGGAGACT
75034 CAAAGGAGAC
1 CAAAGGAGAC
75044 ACCTTTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.48, C:0.16, G:0.29, T:0.06
Consensus pattern (11 bp):
CAAAGGAGACT
Found at i:77797 original size:144 final size:143
Alignment explanation
Indices: 77629--78197 Score: 648
Period size: 145 Copynumber: 4.0 Consensus size: 143
77619 TTTTTTAAAG
*
77629 AAAGTTTAGATTTTTAAAAAATAAAAATTTATTTTTTAGTCATTTTACAA-GAAAAATTTTAAAT
1 AAAGTTTAGATTTTT-AAAAATAAAAATTTATTTTTTAGTCATTTTA-AAGGAAAAAGTTTAAAT
* *
77693 TTTTAAATAAAGTTTTGA-TTTTTTTTAACTATTTTGAAATAAAAAACTTTGATTTTTAAGAAAA
64 TTTTAAATAAA-TTTTGATTTTTTTTTAACTATTTTGAAAT-AAAAGCTTTAATTTTTAAGAAAA
77757 ATAGTGATTTAAAAAAA
127 ATAGTGATTTAAAAAAA
* * *
77774 AAAGTTTAGATTTTTAAAAATAAAAA--TAGCTTTTTAGTTATTTCAAAGGAAAAAGTTTAAATT
1 AAAGTTTAGATTTTTAAAAATAAAAATTTA-TTTTTTAGTCATTTTAAAGGAAAAAGTTTAAATT
* * *
77837 TTTAAATAACATTTTAAATTTTTTTTTACCTATTTTGAAATAAAAGTTTTAATTTTTAAGAAAAA
65 TTTAAATAA-ATTTT-GATTTTTTTTTAACTATTTTGAAATAAAAGCTTTAATTTTTAAGAAAAA
** ** *
77902 TAGTTTTTTTTTAAAAG
128 TAG-TGATTTAAAAAAA
* * *
77919 AAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGAAAAAGTTTAAAATT
1 AAAGTTTAGATTTTTAAAAATAAAAATTTATTTTTTAGTCATTTTAAAGGAAAAAGTTTAAATTT
* * * * * * * * *
77984 TTAAACAAATTTTTATTTTTTTTTAAATATTTTAAAATAAAAGTTTTGAGTTATAAGAAAAGTAG
66 TTAAATAAATTTTGATTTTTTTTTAACTATTTTGAAATAAAAGCTTTAATTTTTAAGAAAAATAG
*
78049 TGATTTTTTAAGAAAA
131 TGA---TTTAAAAAAA
* * * * **
78065 AAAGTTTAGATTTTTAATAATAAAAATTCA-TTTTTAGTCAATTTAAAAGAAAAAAATTAAATTT
1 AAAGTTTAGATTTTTAAAAATAAAAATTTATTTTTTAGTCATTTTAAAGGAAAAAGTTTAAATTT
* * * * *
78129 TTAAATGAAGTTTGA--TTTTTTTAACCATTTTGAAATAAAAGCTTTAATTTTTAAGAAAAGTAC
66 TTAAATAAATTTTGATTTTTTTTTAACTATTTTGAAATAAAAGCTTTAATTTTTAAGAAAAATAG
78192 TGATTT
131 TGATTT
78198 TGTTTAAAAA
Statistics
Matches: 358, Mismatches: 55, Indels: 27
0.81 0.12 0.06
Matches are distributed among these distances:
140 3 0.01
142 4 0.01
143 84 0.23
144 81 0.23
145 115 0.32
146 70 0.20
147 1 0.00
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (143 bp):
AAAGTTTAGATTTTTAAAAATAAAAATTTATTTTTTAGTCATTTTAAAGGAAAAAGTTTAAATTT
TTAAATAAATTTTGATTTTTTTTTAACTATTTTGAAATAAAAGCTTTAATTTTTAAGAAAAATAG
TGATTTAAAAAAA
Found at i:77901 original size:20 final size:20
Alignment explanation
Indices: 77868--77938 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
77858 TTTTTTACCT
* *
77868 ATTTTGAAATAAAAGTTTTA
1 ATTTTTAAAAAAAAGTTTTA
77888 ATTTTTAAGAAAAATAGTTTT-
1 ATTTTTAA-AAAAA-AGTTTTA
*
77909 -TTTTTAAAAGAAAG-TTTA
1 ATTTTTAAAAAAAAGTTTTA
77927 GATTTTTAAAAA
1 -ATTTTTAAAAA
77939 TAAAAATATG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
17 3 0.07
18 2 0.05
19 4 0.10
20 23 0.55
21 4 0.10
22 6 0.14
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (20 bp):
ATTTTTAAAAAAAAGTTTTA
Found at i:78788 original size:16 final size:15
Alignment explanation
Indices: 78764--78798 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
78754 TTATATATTC
78764 TTATTTTATCTTTAT
1 TTATTTTATCTTTAT
*
78779 TTATTGTTATGTTTAT
1 TTATT-TTATCTTTAT
78795 TTAT
1 TTAT
78799 ATATATGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.20, C:0.03, G:0.06, T:0.71
Consensus pattern (15 bp):
TTATTTTATCTTTAT
Found at i:78807 original size:21 final size:20
Alignment explanation
Indices: 78753--78813 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
78743 TTGTATAATT
*
78753 TTTATATAT-TCTTATTTTA
1 TTTATATATATGTTATTTTA
*
78772 TCTT-TATTTATTGTTATGTTTA
1 T-TTATATATA-TGTTAT-TTTA
*
78794 TTTATATATATGTTTTTTTA
1 TTTATATATATGTTATTTTA
78814 CACATTTCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
19 5 0.15
20 6 0.18
21 12 0.36
22 10 0.30
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTATATATATGTTATTTTA
Found at i:78898 original size:3 final size:3
Alignment explanation
Indices: 78890--78940 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
78880 GAATAAGGTG
*
78890 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
78938 TAT
1 TAT
78941 CATGTCTTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:80769 original size:40 final size:40
Alignment explanation
Indices: 80709--80813 Score: 176
Period size: 40 Copynumber: 2.6 Consensus size: 40
80699 ATTGTAGATA
* *
80709 TTCCCAAATCAAATGTTGGATAAATCATTTTCGATTTTCT
1 TTCCTAAATCAAATGTTGGATAAATCATTTTCAATTTTCT
80749 TTCCTAAATCAAATGTTGGATAAATCATTTTCAATTTTCT
1 TTCCTAAATCAAATGTTGGATAAATCATTTTCAATTTTCT
80789 TT-CTCAAATCAAATGTTGGATAAAT
1 TTCCT-AAATCAAATGTTGGATAAAT
80814 TTACTGGGCA
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
39 2 0.03
40 60 0.97
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (40 bp):
TTCCTAAATCAAATGTTGGATAAATCATTTTCAATTTTCT
Found at i:83523 original size:109 final size:110
Alignment explanation
Indices: 83391--83592 Score: 282
Period size: 110 Copynumber: 1.8 Consensus size: 110
83381 ATCGATTTTA
** * * *
83391 AAATAGGATGTTCAATTAATTAGGTTCCAAG-AAAAACCATACCCAATACGTTATGG-CACAATT
1 AAATAGGATACTCAATTAATTAGGGTCAAAGAAAAAACCATACCCAACACGTTA-GGACACAATT
*
83454 TCTCGAGTTCCCTAAAATAAAAGAAAATTAAGCGTTTATCAATTTC
65 TCTCGAATTCCCTAAAATAAAAGAAAATTAAGCGTTTATCAATTTC
* *** *
83500 AAATAGGATACTCAATTATTTAGGGTCAAAGAAAAAATTGTACCCAACATGTTAGGACACAATTT
1 AAATAGGATACTCAATTAATTAGGGTCAAAGAAAAAACCATACCCAACACGTTAGGACACAATTT
83565 CTCGAATTCCCTAAAATAAAAGAAAATT
66 CTCGAATTCCCTAAAATAAAAGAAAATT
83593 GCCTTGATTT
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
109 28 0.35
110 52 0.65
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (110 bp):
AAATAGGATACTCAATTAATTAGGGTCAAAGAAAAAACCATACCCAACACGTTAGGACACAATTT
CTCGAATTCCCTAAAATAAAAGAAAATTAAGCGTTTATCAATTTC
Found at i:83897 original size:31 final size:30
Alignment explanation
Indices: 83859--83938 Score: 97
Period size: 32 Copynumber: 2.6 Consensus size: 30
83849 AATAAAAGGT
*
83859 AATTTTAAAAGAAATAAAAATAAAAGGGTTA
1 AATTTTAAAA-AAATAAAAATAAAAGGATTA
* *
83890 AATTTTAACAAAAAAAACAAATAAAAGGATTT
1 AATTTTAA-AAAAATAA-AAATAAAAGGATTA
*
83922 AATTTAAAAAAAATAAA
1 AATTTTAAAAAAATAAA
83939 TGGGTGAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 20 0.48
32 21 0.50
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (30 bp):
AATTTTAAAAAAATAAAAATAAAAGGATTA
Found at i:83915 original size:32 final size:30
Alignment explanation
Indices: 83838--83934 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 30
83828 ATTAAAAAAT
*
83838 AAAAGAAACATAATAAAA-GG-TAATTTTAA
1 AAAAAAAACA-AATAAAAGGGTTAATTTTAA
*
83867 AAGAAATAA-AAATAAAAGGGTTAAATTTTAA
1 AA-AAAAAACAAATAAAAGGGTT-AATTTTAA
*
83898 CAAAAAAAACAAATAAAAGGATTTAA-TTTAA
1 -AAAAAAAACAAATAAAAGG-GTTAATTTTAA
83929 AAAAAA
1 AAAAAA
83935 TAAATGGGTG
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
28 7 0.12
29 5 0.09
30 11 0.19
31 18 0.32
32 14 0.25
33 2 0.04
ACGTcount: A:0.65, C:0.03, G:0.09, T:0.23
Consensus pattern (30 bp):
AAAAAAAACAAATAAAAGGGTTAATTTTAA
Found at i:83975 original size:55 final size:56
Alignment explanation
Indices: 83874--83984 Score: 145
Period size: 55 Copynumber: 2.0 Consensus size: 56
83864 TAAAAGAAAT
* *
83874 AAAAATAAAAGGGTTAAATTTTAACAAAAAAAACAAATAAAAGGATTTAATTTAAA
1 AAAAATAAAAGGGTGAAATTTTAACAAAAAAAACAAATAAAAGGATTAAATTTAAA
* * * *
83930 AAAAATAAATGGGTGAAA-TTTAATAGAGAAAAAC-AATAGAAGGATTAAATTTAAA
1 AAAAATAAAAGGGTGAAATTTTAACA-AAAAAAACAAATAAAAGGATTAAATTTAAA
83985 TTAAAACAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
55 25 0.52
56 23 0.48
ACGTcount: A:0.60, C:0.03, G:0.13, T:0.24
Consensus pattern (56 bp):
AAAAATAAAAGGGTGAAATTTTAACAAAAAAAACAAATAAAAGGATTAAATTTAAA
Found at i:85614 original size:39 final size:40
Alignment explanation
Indices: 85571--85649 Score: 151
Period size: 39 Copynumber: 2.0 Consensus size: 40
85561 CTATCTTCAA
85571 TATGCCCTCTGAAAAAGATTGGATGGTGTCTT-AATCTGC
1 TATGCCCTCTGAAAAAGATTGGATGGTGTCTTCAATCTGC
85610 TATGCCCTCTGAAAAAGATTGGATGGTGTCTTCAATCTGC
1 TATGCCCTCTGAAAAAGATTGGATGGTGTCTTCAATCTGC
85650 CTGATGATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
39 32 0.82
40 7 0.18
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (40 bp):
TATGCCCTCTGAAAAAGATTGGATGGTGTCTTCAATCTGC
Found at i:85721 original size:81 final size:80
Alignment explanation
Indices: 85625--86053 Score: 459
Period size: 81 Copynumber: 5.3 Consensus size: 80
85615 CCTCTGAAAA
* * * *
85625 AGATTGGATGGTGTCTTCAATCTGCCTGATGATTTGGGTAAGATATTGGATGACTTCAATCTGCC
1 AGATTGGATGATGTCTTCAATCTGCCTCATGATTGGGGTAAGAGATTGGATGACTTCAATCTGCC
85690 CCATGGTCTGGGTAAG
66 CCATGGTC-GGGTAAG
* * * * * * *
85706 AGATTGAATGATGTCTTCAATCTGCCTAATGGTTGGGGTAAGAGATTAGATGGCTTCAATCTTCT
1 AGATTGGATGATGTCTTCAATCTGCCTCATGATTGGGGTAAGAGATTGGATGACTTCAATCTGCC
*
85771 CTATGGTCGTGGTAAG
66 CCATGGTCG-GGTAAG
* * **
85787 AGATTGGATGATGTCTTCAATTTGCCCCATGATCAGGGTAAGAGATTGGAT-AGCTTCAATCTGC
1 AGATTGGATGATGTCTTCAATCTGCCTCATGATTGGGGTAAGAGATTGGATGA-CTTCAATCTGC
*
85851 CCCTTGGTCGGGGTAAG
65 CCCATGGTC-GGGTAAG
* * * * * *
85868 AGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTAGATGGCTTCAATATGCC
1 AGATTGGATGATGTCTTCAATCTGCCTCATGATTGGGGTAAGAGATTGGATGACTTCAATCTGCC
*
85933 TCATGGTCGGGGTAAG
66 CCATGGTC-GGGTAAG
* * * *
85949 AAATTGGATGATGTCTTCAATCTGCC-CTATGATCGGGCTAAGTGATTGGATGATGTCTTCAATC
1 AGATTGGATGATGTCTTCAATCTGCCTC-ATGATTGGGGTAAGAGATTGGATGA---CTTCAATC
* *
86013 TACCCCATGATCGAGGTGAA-
62 TGCCCCATGGTCG-GGT-AAG
*
86033 AGATTGGATGATATCTTCAAT
1 AGATTGGATGATGTCTTCAAT
86054 TTTCCACATG
Statistics
Matches: 294, Mismatches: 44, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
80 2 0.01
81 250 0.85
82 1 0.00
83 1 0.00
84 38 0.13
85 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (80 bp):
AGATTGGATGATGTCTTCAATCTGCCTCATGATTGGGGTAAGAGATTGGATGACTTCAATCTGCC
CCATGGTCGGGTAAG
Found at i:85728 original size:42 final size:41
Alignment explanation
Indices: 85625--86053 Score: 425
Period size: 42 Copynumber: 10.5 Consensus size: 41
85615 CCTCTGAAAA
* ** * *
85625 AGATTGGATGGTGTCTTCAATCTGCCTGATGATTTGGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATG-GTCGGGTAAG
*
85667 ATATTGGATGA---CTTCAATCTGCCCCATGGTCTGGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGGTC-GGGTAAG
* ** *
85706 AGATTGAATGATGTCTTCAATCTGCCTAATGGTTGGGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGG-TCGGGTAAG
* * * *
85748 AGATT--A-GATGGCTTCAATCTTCTCTATGGTCGTGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGGTCG-GGTAAG
* *
85787 AGATTGGATGATGTCTTCAATTTGCCCCATGATCAGGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGGTC-GGGTAAG
*
85829 AGATTGGAT-A-G-CTTCAATCTGCCCCTTGGTCGGGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGGTC-GGGTAAG
85868 AGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGGTC-GGGTAAG
* * *
85910 AGATT--A-GATGGCTTCAATATGCCTCATGGTCGGGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGGTC-GGGTAAG
* * *
85949 AAATTGGATGATGTCTTCAATCTGCCCTATGATCGGGCTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGG-TAAG
* * *
85991 TGATTGGATGATGTCTTCAATCTACCCCATGATCGAGGTGAA-
1 AGATTGGATGATGTCTTCAATCTGCCCCATGGTCG-GGT-AAG
*
86033 AGATTGGATGATATCTTCAAT
1 AGATTGGATGATGTCTTCAAT
86054 TTTCCACATG
Statistics
Matches: 325, Mismatches: 43, Indels: 38
0.80 0.11 0.09
Matches are distributed among these distances:
38 3 0.01
39 127 0.39
40 4 0.01
41 7 0.02
42 178 0.55
43 6 0.02
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (41 bp):
AGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGGTAAG
Found at i:85892 original size:162 final size:162
Alignment explanation
Indices: 85625--86053 Score: 560
Period size: 162 Copynumber: 2.6 Consensus size: 162
85615 CCTCTGAAAA
* ** * *
85625 AGATTGGATGGTGTCTTCAATCTGCCTGATGATTTGGGTAAGATATTGGAT-GACTTCAATCTGC
1 AGATTGGATGATGTCTTCAATCTGCCCCATGA-TCGGGTAAGAGATTGGATAGACTTCAATCTGC
* * * *
85689 CCCATGGTCTGGGTAAGAGATTGAATGATGTCTTCAATCTGCCTAATGGTTGGGGTAAGAGATTA
65 CCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCAATGGTCGGGGTAAGAGATTA
* * *
85754 GATGGCTTCAATCT-TCTCTATGGTCGTGGTAAG
130 GATGGCTTCAATATGCCTC-ATGGTCGGGGTAAG
*
85787 AGATTGGATGATGTCTTCAATTTGCCCCATGATCAGGGTAAGAGATTGGATAG-CTTCAATCTGC
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATC-GGGTAAGAGATTGGATAGACTTCAATCTGC
* *
85851 CCCTTGGTCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTA
65 CCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCAATGGTCGGGGTAAGAGATTA
85916 GATGGCTTCAATATGCCTCATGGTCGGGGTAAG
130 GATGGCTTCAATATGCCTCATGGTCGGGGTAAG
* * * *
85949 AAATTGGATGATGTCTTCAATCTGCCCTATGATCGGGCTAAGTGATTGGATGATGTCTTCAATCT
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGG-TAAGAGATTGGAT-A-GACTTCAATCT
* * * *
86014 ACCCCATGATCGAGGTGAA-AGATTGGATGATATCTTCAAT
63 GCCCCATGGTCGGGGT-AAGAGATTGGATGATGTCTTCAAT
86054 TTTCCACATG
Statistics
Matches: 235, Mismatches: 24, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
161 4 0.02
162 182 0.77
163 5 0.02
164 1 0.00
165 41 0.17
166 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (162 bp):
AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGTAAGAGATTGGATAGACTTCAATCTGCC
CCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCAATGGTCGGGGTAAGAGATTAG
ATGGCTTCAATATGCCTCATGGTCGGGGTAAG
Found at i:86255 original size:95 final size:95
Alignment explanation
Indices: 86117--86513 Score: 334
Period size: 95 Copynumber: 4.1 Consensus size: 95
86107 TAACTTTATA
* * * * * * *
86117 GAGATAAAAACTTGCTATTGTTTTAATCCGCTTCATTGTAACTTCAAGAAGATAAGATTTGGTGT
1 GAGATAAAGATTTGCTACTGCTTTAATTCGCTTCACTGTAACTTCAAGAAGATAGGATTTGGTGT
* * * *
86182 AGCTTAATCCTGCTCTACTGCAACTTCAAG
66 AGCTTCATCTTGCTCCACTGCAACTTCAGG
** * * *
86212 GAGATAAAGATTTGCTACTGCTTTAATTCGCTTCACTACAACTTCAAAAAGATAGGGTTTGATGT
1 GAGATAAAGATTTGCTACTGCTTTAATTCGCTTCACTGTAACTTCAAGAAGATAGGATTTGGTGT
* * * * *
86277 GGTTTCATCTTGCTCCATTGTAACTTTAGG
66 AGCTTCATCTTGCTCCACTGCAACTTCAGG
** ** * * * * *
86307 GAGATAAAGATCTACCAATGTTAGTTTTAATTCG-ATC-CTTGTAACTTCAAGGATATATGATTT
1 GAGATAAAGAT-TTGC--TACT-GCTTTAATTCGCTTCAC-TGTAACTTCAAGAAGATAGGATTT
*
86370 GGTGTTGTAGCTTCATCTTACTCCACTGCAACTTCAGG
61 -G-G-TGTAGCTTCATCTTGCTCCACTGCAACTTCAGG
* *
86408 GAGATAAAGATTTGGTACTGCTTTAA-TCAGCTTCACTGTAACTTCAAGAAGGTAGGATTTGGTG
1 GAGATAAAGATTTGCTACTGCTTTAATTC-GCTTCACTGTAACTTCAAGAAGATAGGATTTGGTG
* * *
86472 T-GACTTCATCTTCCTTCACTGCAACTTTAGG
65 TAG-CTTCATCTTGCTCCACTGCAACTTCAGG
* *
86503 AAGATTAAGAT
1 GAGATAAAGAT
86514 CTACCAATGT
Statistics
Matches: 233, Mismatches: 57, Indels: 24
0.74 0.18 0.08
Matches are distributed among these distances:
94 1 0.00
95 122 0.52
96 5 0.02
97 9 0.04
98 45 0.19
99 12 0.05
100 1 0.00
101 38 0.16
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (95 bp):
GAGATAAAGATTTGCTACTGCTTTAATTCGCTTCACTGTAACTTCAAGAAGATAGGATTTGGTGT
AGCTTCATCTTGCTCCACTGCAACTTCAGG
Found at i:86403 original size:101 final size:98
Alignment explanation
Indices: 86280--86566 Score: 266
Period size: 98 Copynumber: 2.9 Consensus size: 98
86270 TTGATGTGGT
* * *
86280 TTCATCTTGCTCCATTGTAACTTTAGGGAGATAAAGATCTACCAATGTTAGTTTTAATTCGATCC
1 TTCATCTTACTCCACTGCAACTTTAGGGAGATAAAGATCTACCAATGTTAGTTTTAATTCGATCC
*
86345 TTGTAACTTCAAGGATATATGATTTGGTGTTGTAGC
66 TTGTAACTTCAAGGATATAGGATTTGGTG-TG-A-C
* * *
86381 TTCATCTTACTCCACTGCAACTTCAGGGAGATAAAGAT-T-----TGGTACTGCTTTAA-TCAGC
1 TTCATCTTACTCCACTGCAACTTTAGGGAGATAAAGATCTACCAATGTTA--GTTTTAATTC-G-
* * **
86439 TTCAC-TGTAACTTCAAGAAGGTAGGATTTGGTGTGAC
62 ATC-CTTGTAACTTCAAGGATATAGGATTTGGTGTGAC
* * * * * *
86476 TTCATCTTCCTTCACTGCAACTTTAGGAAGATTAAGATCTACCAATGTTAGTTGTAATCCGATCC
1 TTCATCTTACTCCACTGCAACTTTAGGGAGATAAAGATCTACCAATGTTAGTTTTAATTCGATCC
** *
86541 TTACAACTTCAAGGATATGGGATTTG
66 TTGTAACTTCAAGGATATAGGATTTG
86567 TTGTTTCATT
Statistics
Matches: 146, Mismatches: 27, Indels: 29
0.72 0.13 0.14
Matches are distributed among these distances:
95 38 0.26
96 4 0.03
97 10 0.07
98 47 0.32
99 7 0.05
100 2 0.01
101 38 0.26
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (98 bp):
TTCATCTTACTCCACTGCAACTTTAGGGAGATAAAGATCTACCAATGTTAGTTTTAATTCGATCC
TTGTAACTTCAAGGATATAGGATTTGGTGTGAC
Found at i:86483 original size:196 final size:193
Alignment explanation
Indices: 86152--86558 Score: 528
Period size: 196 Copynumber: 2.1 Consensus size: 193
86142 ATCCGCTTCA
* * * *
86152 TTGTAACTTCAAGAAGATAAGATTTGGTGTAGCTTAATCCTGCTCTACTGCAACTTCAAGGAGAT
1 TTGTAACTTCAAGGATATAAGATTTGGTGTAGCTTAATCCTACTCCACTGCAACTTCAAGGAGAT
* **
86217 AAAGATTTGCTACTGCTTTAATTCGCTTCACTACAACTTCAAAAAGATAGGGTTTGATGTGGTTT
66 AAAGATTTGCTACTGCTTTAATTCGCTTCACTACAACTTCAAAAAGATAGGATTTGATGTGACTT
* * * * * *
86282 CATCTTGCTCCATTGTAACTTTAGGGAGATAAAGATCTACCAATGTTAGTTTTAATTCGATCC
131 CATCTTCCTCCACTGCAACTTTAGGAAGATAAAGATCTACCAATGTTAGTTGTAATCCGATCC
* * * *
86345 TTGTAACTTCAAGGATATATGATTTGGTGTTGTAGCTTCATCTTACTCCACTGCAACTTCAGGGA
1 TTGTAACTTCAAGGATATAAGATTT-G-G-TGTAGCTTAATCCTACTCCACTGCAACTTCAAGGA
* ** * * *
86410 GATAAAGATTTGGTACTGCTTTAA-TCAGCTTCACTGTAACTTCAAGAAGGTAGGATTTGGTGTG
63 GATAAAGATTTGCTACTGCTTTAATTC-GCTTCACTACAACTTCAAAAAGATAGGATTTGATGTG
* *
86474 ACTTCATCTTCCTTCACTGCAACTTTAGGAAGATTAAGATCTACCAATGTTAGTTGTAATCCGAT
127 ACTTCATCTTCCTCCACTGCAACTTTAGGAAGATAAAGATCTACCAATGTTAGTTGTAATCCGAT
86539 CC
192 CC
**
86541 TTACAACTTCAAGGATAT
1 TTGTAACTTCAAGGATAT
86559 GGGATTTGTT
Statistics
Matches: 183, Mismatches: 27, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
193 22 0.12
194 1 0.01
195 3 0.02
196 157 0.86
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (193 bp):
TTGTAACTTCAAGGATATAAGATTTGGTGTAGCTTAATCCTACTCCACTGCAACTTCAAGGAGAT
AAAGATTTGCTACTGCTTTAATTCGCTTCACTACAACTTCAAAAAGATAGGATTTGATGTGACTT
CATCTTCCTCCACTGCAACTTTAGGAAGATAAAGATCTACCAATGTTAGTTGTAATCCGATCC
Found at i:86549 original size:98 final size:97
Alignment explanation
Indices: 86248--86553 Score: 253
Period size: 98 Copynumber: 3.1 Consensus size: 97
86238 TTCGCTTCAC
* * * ** * * *
86248 TACAACTTCAAAAAGATAGGGTTTGATGTGGTTTCATCTTGCTCCATTGTAACTTTAGGGAGATA
1 TACAACTTCAAGAAGATAGGATTTGGTGTGACTTCATCTTACTCCACTGCAACTTTAGGGAGATA
*
86313 AAGATCTACCAATGTTAGTTTTAATTCGATCCT
66 AAGATCTACCAATGTTAG-TTTAATCCGATCCT
** * * * *
86346 TGTAACTTCAAGGATATATGATTTGGTGTTGTAGCTTCATCTTACTCCACTGCAACTTCAGGGAG
1 TACAACTTCAAGAAGATAGGATTTGGTG-TG-A-CTTCATCTTACTCCACTGCAACTTTAGGGAG
* *** * * * *
86411 ATAAAGATTTGGTACTG---CTTTAATCAGCTTCACT
63 ATAAAGATCTACCAATGTTAGTTTAATCCG-ATC-CT
* * * *
86445 GT--AACTTCAAGAAGGTAGGATTTGGTGTGACTTCATCTTCCTTCACTGCAACTTTAGGAAGAT
1 -TACAACTTCAAGAAGATAGGATTTGGTGTGACTTCATCTTACTCCACTGCAACTTTAGGGAGAT
*
86508 TAAGATCTACCAATGTTAGTTGTAATCCGATCCT
65 AAAGATCTACCAATGTTAGTT-TAATCCGATCCT
86542 TACAACTTCAAG
1 TACAACTTCAAG
86554 GATATGGGAT
Statistics
Matches: 156, Mismatches: 40, Indels: 24
0.71 0.18 0.11
Matches are distributed among these distances:
95 38 0.24
96 2 0.01
97 11 0.07
98 56 0.36
99 10 0.06
100 1 0.01
101 38 0.24
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (97 bp):
TACAACTTCAAGAAGATAGGATTTGGTGTGACTTCATCTTACTCCACTGCAACTTTAGGGAGATA
AAGATCTACCAATGTTAGTTTAATCCGATCCT
Found at i:106041 original size:17 final size:18
Alignment explanation
Indices: 105996--106041 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
105986 AGAATTTAAA
*
105996 AGAAAATAAAAAAAGATT
1 AGAAAATAATAAAAGATT
*
106014 AG-TAATCAATAAAAG-TT
1 AGAAAAT-AATAAAAGATT
106031 AGAAAATAATA
1 AGAAAATAATA
106042 GTAAATGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.22
Consensus pattern (18 bp):
AGAAAATAATAAAAGATT
Found at i:107812 original size:28 final size:28
Alignment explanation
Indices: 107771--107829 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
107761 CAAAGAAGTC
*
107771 ATCCATAAAAACCTCCTAC-GAATCCTTA
1 ATCCATAAAAACCTCC-ACTGAATCCTCA
*
107799 ATCCATAAATACCTCCACTGAATCCTCA
1 ATCCATAAAAACCTCCACTGAATCCTCA
107827 ATC
1 ATC
107830 ATATCGGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 26 0.93
ACGTcount: A:0.37, C:0.34, G:0.03, T:0.25
Consensus pattern (28 bp):
ATCCATAAAAACCTCCACTGAATCCTCA
Found at i:115331 original size:12 final size:12
Alignment explanation
Indices: 115314--115345 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
115304 ATTTCAAATA
*
115314 TTTATTTTCTAT
1 TTTATTTTCTAC
115326 TTTATTTTCTAC
1 TTTATTTTCTAC
115338 TTTATTTT
1 TTTATTTT
115346 ATTGTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTATTTTCTAC
Found at i:115702 original size:18 final size:18
Alignment explanation
Indices: 115679--115730 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
115669 TAGATTCAAT
115679 TTTATTTTATTTATTTAA
1 TTTATTTTATTTATTTAA
* *
115697 TTTATTTT-TCGTATTTCA
1 TTTATTTTAT-TTATTTAA
115715 TTT-TCTTTATTTATTT
1 TTTAT-TTTATTTATTT
115731 TTAATTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 2 0.07
18 25 0.89
19 1 0.04
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTATTTTATTTATTTAA
Found at i:119846 original size:65 final size:65
Alignment explanation
Indices: 119770--119909 Score: 244
Period size: 65 Copynumber: 2.2 Consensus size: 65
119760 AAAACACTAT
*
119770 TCTAATTTATTTCATTCTATTTCAACTCACAAAAATCTTTAAAATACCTAAAATTCATTTTTTTC
1 TCTAATTTATTTCATTCTATTTCAACTCACAAAAATCTTTAAAAAACCTAAAATTCATTTTTTTC
*
119835 TCTAATTTATTTCATTCTATTTCAACTCACAAAAATCTTTAAAAAACCTAAAATTCCTTTTTTTC
1 TCTAATTTATTTCATTCTATTTCAACTCACAAAAATCTTTAAAAAACCTAAAATTCATTTTTTTC
* *
119900 CCTATTTTAT
1 TCTAATTTAT
119910 CTTCTCACTT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 71 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.46
Consensus pattern (65 bp):
TCTAATTTATTTCATTCTATTTCAACTCACAAAAATCTTTAAAAAACCTAAAATTCATTTTTTTC
Found at i:123543 original size:48 final size:48
Alignment explanation
Indices: 123472--123569 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
123462 CAATTCGAGT
123472 TTCTTTTTCATTCTCTTATTCAAATAAATGTTCTTATATATTATTGTG
1 TTCTTTTTCATTCTCTTATTCAAATAAATGTTCTTATATATTATTGTG
* *
123520 TTCTTTTTCGTTCTCTTATTCAAATATATGTTCTTATATATTATTGTG
1 TTCTTTTTCATTCTCTTATTCAAATAAATGTTCTTATATATTATTGTG
123568 TT
1 TT
123570 TATAATGATC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.22, C:0.12, G:0.07, T:0.58
Consensus pattern (48 bp):
TTCTTTTTCATTCTCTTATTCAAATAAATGTTCTTATATATTATTGTG
Found at i:124010 original size:12 final size:12
Alignment explanation
Indices: 123992--124024 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
123982 CAAATCTTTC
123992 CTTTATTTTCTA
1 CTTTATTTTCTA
*
124004 TTTTATTTTCTA
1 CTTTATTTTCTA
124016 CTTTATTTT
1 CTTTATTTT
124025 ATGCTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTATTTTCTA
Found at i:126641 original size:14 final size:14
Alignment explanation
Indices: 126622--126650 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
126612 AGTAGTTCAC
126622 GTATATATATATAT
1 GTATATATATATAT
126636 GTATATATATATAT
1 GTATATATATATAT
126650 G
1 G
126651 CAAAATAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (14 bp):
GTATATATATATAT
Found at i:127729 original size:31 final size:31
Alignment explanation
Indices: 127693--127757 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
127683 GGATGCTAAG
* * *
127693 AAAATTGGAGACTGCAAAAAACTTTGATAGA
1 AAAATTAGAGAATGCAAAAAACTTTGAGAGA
*
127724 AAAATTAGAGAATGCAAAAACCTTTGAGAGA
1 AAAATTAGAGAATGCAAAAAACTTTGAGAGA
127755 AAA
1 AAA
127758 TACTAATTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.52, C:0.09, G:0.18, T:0.20
Consensus pattern (31 bp):
AAAATTAGAGAATGCAAAAAACTTTGAGAGA
Found at i:137162 original size:19 final size:19
Alignment explanation
Indices: 137140--137176 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
137130 CATTCCTGCA
137140 ACAGGATAACAATCCTCCC
1 ACAGGATAACAATCCTCCC
137159 ACAGGATAACAATCCTCC
1 ACAGGATAACAATCCTCC
137177 AGTGCAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.35, G:0.11, T:0.16
Consensus pattern (19 bp):
ACAGGATAACAATCCTCCC
Found at i:142582 original size:5 final size:5
Alignment explanation
Indices: 142572--142596 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
142562 ATGTCAACGC
142572 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
142597 TCAGTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:144472 original size:21 final size:22
Alignment explanation
Indices: 144446--144489 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
144436 CAAGTGACAG
144446 AGGAAGAAAAAGAGACTG-AGA
1 AGGAAGAAAAAGAGACTGTAGA
* *
144467 AGGAAGAAACAGAGCCTGTAGA
1 AGGAAGAAAAAGAGACTGTAGA
144489 A
1 A
144490 ATGCAGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.52, C:0.09, G:0.32, T:0.07
Consensus pattern (22 bp):
AGGAAGAAAAAGAGACTGTAGA
Found at i:153740 original size:18 final size:19
Alignment explanation
Indices: 153717--153761 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
153707 AAAGCATAGA
*
153717 AAGGAAGAGAAAA-AGAGG
1 AAGGAAGAGAAAAGAGAAG
*
153735 AAGGAAGATAAAAGAGAAG
1 AAGGAAGAGAAAAGAGAAG
*
153754 AAAGAAGA
1 AAGGAAGA
153762 AGCACCGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.02
Consensus pattern (19 bp):
AAGGAAGAGAAAAGAGAAG
Found at i:158592 original size:30 final size:29
Alignment explanation
Indices: 158536--158601 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
158526 ACAAAAAAAT
*
158536 AAAAACTAAAATAAAATAAAATAAAATGTA
1 AAAAAATAAAATAAAATAAAATAAAAT-TA
* *
158566 AAAAAATAAATTAAATTAAACA-AAAATTA
1 AAAAAATAAAATAAAATAAA-ATAAAATTA
158595 AACAAAA
1 AA-AAAA
158602 ATAAGGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 4 0.13
30 26 0.84
31 1 0.03
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.20
Consensus pattern (29 bp):
AAAAAATAAAATAAAATAAAATAAAATTA
Found at i:158596 original size:21 final size:18
Alignment explanation
Indices: 158565--158631 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
158555 AATAAAATGT
158565 AAAAAAA-TAAATTAAATTA
1 AAAAAAATTAAA--AAATTA
*
158584 AACAAAAATTAAACAAAAATA
1 AA-AAAAATT-AA-AAAATTA
*
158605 AGGAAAAATTAAAAAATTA
1 A-AAAAAATTAAAAAATTA
158624 AAAAAAAT
1 AAAAAAAT
158632 AAGAAAGGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
18 6 0.15
19 9 0.23
20 7 0.18
21 14 0.36
22 2 0.05
23 1 0.03
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (18 bp):
AAAAAAATTAAAAAATTA
Found at i:158630 original size:10 final size:10
Alignment explanation
Indices: 158536--158631 Score: 60
Period size: 10 Copynumber: 9.6 Consensus size: 10
158526 ACAAAAAAAT
*
158536 AAAAACTAAA
1 AAAAATTAAA
158546 ATAAAA-TAAA
1 A-AAAATTAAA
158556 ATAAAATGT-AA
1 A-AAAAT-TAAA
158567 AAAAA-TAAA
1 AAAAATTAAA
**
158576 TTAAATTAAA
1 AAAAATTAAA
158586 CAAAAATTAAA
1 -AAAAATTAAA
*
158597 CAAAAA-TAAGG
1 -AAAAATTAA-A
158608 AAAAATT--A
1 AAAAATTAAA
158616 AAAAATTAAA
1 AAAAATTAAA
158626 AAAAAT
1 AAAAAT
158632 AAGAAAGGGT
Statistics
Matches: 70, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
8 8 0.11
9 5 0.07
10 34 0.49
11 22 0.31
12 1 0.01
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:158630 original size:11 final size:11
Alignment explanation
Indices: 158578--158617 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
158568 AAAATAAATT
158578 AAATTAAACAA
1 AAATTAAACAA
158589 AAATTAAACAA
1 AAATTAAACAA
**
158600 AAA-TAAGGAA
1 AAATTAAACAA
158610 AAATTAAA
1 AAATTAAA
158618 AAATTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.17
Consensus pattern (11 bp):
AAATTAAACAA
Found at i:160494 original size:13 final size:13
Alignment explanation
Indices: 160478--160502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
160468 ATTTTTGGCA
160478 TATAGTTTTTATC
1 TATAGTTTTTATC
160491 TATAGTTTTTAT
1 TATAGTTTTTAT
160503 TTGCTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.64
Consensus pattern (13 bp):
TATAGTTTTTATC
Found at i:161000 original size:21 final size:21
Alignment explanation
Indices: 160968--161008 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
160958 ATCAAAAAGA
160968 AAAAGAAAATGAGT-AGAAAC
1 AAAAGAAAATGAGTAAGAAAC
*
160988 AAAAGAATCATGAGTAAGAAA
1 AAAAGAA-AATGAGTAAGAAA
161009 ACATGTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.63, C:0.05, G:0.20, T:0.12
Consensus pattern (21 bp):
AAAAGAAAATGAGTAAGAAAC
Done.