Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009793.1 Kokia drynarioides strain JFW-HI SEQ_124514, 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: 56589
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:749 original size:13 final size:13
Alignment explanation
Indices: 731--765 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
721 TTTAATTTAA
731 TTTAATATTGAAT
1 TTTAATATTGAAT
744 TTTAATATTGAAT
1 TTTAATATTGAAT
*
757 TTTATTATT
1 TTTAATATT
766 ATTCTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (13 bp):
TTTAATATTGAAT
Found at i:2272 original size:23 final size:24
Alignment explanation
Indices: 2246--2297 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
2236 ATTAATCCCC
* *
2246 AATTTATTATATGA-TAAAAAACT
1 AATTAATTAAATGATTAAAAAACT
2269 AATTAATTAAATGATTAAAAAA--
1 AATTAATTAAATGATTAAAAAACT
2291 AATTAAT
1 AATTAAT
2298 GTATCTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 7 0.27
23 12 0.46
24 7 0.27
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (24 bp):
AATTAATTAAATGATTAAAAAACT
Found at i:11270 original size:14 final size:13
Alignment explanation
Indices: 11238--11269 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
11228 TTTTTTCTAG
11238 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
11251 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
11264 TTTTTT
1 TTTTTT
11270 TAAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:12907 original size:4 final size:4
Alignment explanation
Indices: 12876--12943 Score: 57
Period size: 4 Copynumber: 16.5 Consensus size: 4
12866 ATGAAAATTG
* * * *
12876 AAGA AAAA AAGA ATGA AAAA AGAGA AAGA AAGA AAGA AAG- AAGA AGGA
1 AAGA AAGA AAGA AAGA AAGA A-AGA AAGA AAGA AAGA AAGA AAGA AAGA
*
12924 AGGA GAAGA AAGA GAAGA AA
1 AAGA -AAGA AAGA -AAGA AA
12944 AAAAAAAGTA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
3 3 0.06
4 39 0.75
5 10 0.19
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (4 bp):
AAGA
Found at i:12907 original size:21 final size:21
Alignment explanation
Indices: 12877--12919 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12867 TGAAAATTGA
*
12877 AGAAAAAAAGAATGAAAAAAG
1 AGAAAAAAAGAAAGAAAAAAG
* *
12898 AGAAAGAAAGAAAGAAAGAAG
1 AGAAAAAAAGAAAGAAAAAAG
12919 A
1 A
12920 AGGAAGGAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (21 bp):
AGAAAAAAAGAAAGAAAAAAG
Found at i:12939 original size:19 final size:18
Alignment explanation
Indices: 12890--12940 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
12880 AAAAAAGAAT
*
12890 GAAA-AAAGAGAAAGAAA
1 GAAAGAAAGAGAAGGAAA
*
12907 GAAAGAAAGAAGAAGGAAG
1 GAAAGAAAG-AGAAGGAAA
12926 GAGAAGAAAGAGAAG
1 GA-AAGAAAGAGAAG
12941 AAAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 4 0.14
18 4 0.14
19 14 0.48
20 7 0.24
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
GAAAGAAAGAGAAGGAAA
Found at i:13326 original size:20 final size:21
Alignment explanation
Indices: 13285--13327 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
13275 TAATTTACTT
13285 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
13306 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
13326 TA
1 TA
13328 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:13854 original size:16 final size:16
Alignment explanation
Indices: 13809--13858 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
13799 TAAATCTAGC
*
13809 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
13825 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
13839 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
13855 TAAT
1 TAAT
13859 ATCCTCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:13925 original size:30 final size:30
Alignment explanation
Indices: 13891--13985 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
13881 AAATGGTACA
*
13891 AAATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATATATTTTGTACCATTTTAGT
** * * * *
13921 AAAT-AAT-GGT-GTGTGAATACTATTTTGGT
1 AAATAAATATATATTTTG--TACCATTTTAGT
*
13950 ATATAAATATATATTTTGTACCATTTTAGT
1 AAATAAATATATATTTTGTACCATTTTAGT
13980 AAATAA
1 AAATAA
13986 CTCATTTTGG
Statistics
Matches: 46, Mismatches: 14, Indels: 10
0.66 0.20 0.14
Matches are distributed among these distances:
27 3 0.07
28 1 0.02
29 16 0.35
30 22 0.48
31 1 0.02
32 3 0.07
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (30 bp):
AAATAAATATATATTTTGTACCATTTTAGT
Found at i:15236 original size:43 final size:43
Alignment explanation
Indices: 15154--15238 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
15144 ATTAACATGT
* * *
15154 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTACATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
15197 TAAATTACATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTACATTACTTGACTCGTATTAATATGCTTG-CATGTTA
15239 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (43 bp):
TAAATTACATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:18837 original size:4 final size:4
Alignment explanation
Indices: 18818--18893 Score: 73
Period size: 4 Copynumber: 19.0 Consensus size: 4
18808 ACACATTACT
* * * * * * *
18818 TTTC TTTC CTTC -TTC TTTC TTTCC TCTC CTTC TTCC TTCC TTCC TTCC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC
18866 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
18894 CCGTTTATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
3 3 0.05
4 57 0.90
5 3 0.05
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (4 bp):
TTTC
Found at i:19781 original size:23 final size:23
Alignment explanation
Indices: 19755--19807 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
19745 TATTTTACTC
*
19755 GCCAATGAGTATTGATCCATCTT
1 GCCAATGAGTACTGATCCATCTT
19778 GCCAATGAGTACTGATCCATCTT
1 GCCAATGAGTACTGATCCATCTT
*
19801 ACCAATG
1 GCCAATG
19808 GTCAAATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (23 bp):
GCCAATGAGTACTGATCCATCTT
Found at i:20124 original size:18 final size:18
Alignment explanation
Indices: 20101--20135 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20091 ATATTTTATG
*
20101 TAAAAAAAAATTTATAAT
1 TAAAAAAAAATTAATAAT
*
20119 TAAAAATAAATTAATAA
1 TAAAAAAAAATTAATAA
20136 AAATAATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAAAAAATTAATAAT
Found at i:21607 original size:18 final size:18
Alignment explanation
Indices: 21580--21618 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21570 TATTATCGTA
*
21580 TTTAATTTTATCAT-TATT
1 TTTAAATTTAT-ATATATT
21598 TTTAAATTTATATATATT
1 TTTAAATTTATATATATT
21616 TTT
1 TTT
21619 TATCTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTAAATTTATATATATT
Found at i:24188 original size:20 final size:20
Alignment explanation
Indices: 24165--24210 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
24155 ACTTTGTCCC
24165 ATACAAGTTCA-CGTCTATCA
1 ATACAA-TTCATCGTCTATCA
* *
24185 ATACAATTCATCTTCTATCG
1 ATACAATTCATCGTCTATCA
24205 ATACAA
1 ATACAA
24211 ATCGATACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.33
Consensus pattern (20 bp):
ATACAATTCATCGTCTATCA
Found at i:26640 original size:48 final size:48
Alignment explanation
Indices: 26586--26682 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
26576 TAGTTTTATG
*
26586 TTGATTAATTTAAATTATTAAAGAAATTATTTATAATCTTGAATTTCT
1 TTGATTAATATAAATTATTAAAGAAATTATTTATAATCTTGAATTTCT
*
26634 TTGATTAATATAAATTATTAAAGAAATTATTTATAATTTTGAATTTCT
1 TTGATTAATATAAATTATTAAAGAAATTATTTATAATCTTGAATTTCT
26682 T
1 T
26683 GAATATTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (48 bp):
TTGATTAATATAAATTATTAAAGAAATTATTTATAATCTTGAATTTCT
Found at i:26786 original size:21 final size:22
Alignment explanation
Indices: 26750--26796 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
26740 CTGGACTTTT
*
26750 ATAAAATAAGAAAGTGCACGAAG
1 ATAAAATAAGAAAGTGCA-GAAC
26773 ATAAAAT-A-AAAGTGCAGAAC
1 ATAAAATAAGAAAGTGCAGAAC
26793 ATAA
1 ATAA
26797 TGAAAAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 8 0.35
22 1 0.04
23 7 0.30
ACGTcount: A:0.60, C:0.09, G:0.17, T:0.15
Consensus pattern (22 bp):
ATAAAATAAGAAAGTGCAGAAC
Found at i:28277 original size:26 final size:27
Alignment explanation
Indices: 28248--28312 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 27
28238 ATTTAGCAAA
* * *
28248 AATAATAAATAAT-TTAATTATATTTT
1 AATAATAAATAATATTAAATACAATTT
*
28274 AAT-ATAATTAATATTAAATACAATTT
1 AATAATAAATAATATTAAATACAATTT
28300 AAT-A-AAATAATAT
1 AATAATAAATAATAT
28313 ATAATTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 16 0.48
26 17 0.52
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
AATAATAAATAATATTAAATACAATTT
Found at i:28339 original size:58 final size:57
Alignment explanation
Indices: 28209--28349 Score: 185
Period size: 58 Copynumber: 2.4 Consensus size: 57
28199 AGTAGATGAG
* * * *
28209 TATTTTAATAAAATTATTATTAGATTATAATTTAGCAAAAATAATAAATAATTTAATTA
1 TATTTTAATATAATTATTATTA-AATACAATTTA-CAAAAATAATAAATAATTTAATAA
* *
28268 TATTTTAATATAATTAATATTAAATACAATTTA-ATAAAATAATATATAATTTAATAA
1 TATTTTAATATAATTATTATTAAATACAATTTACA-AAAATAATAAATAATTTAATAA
28325 TATTTTTAATATAATTATTATTAAA
1 TA-TTTTAATATAATTATTATTAAA
28350 ATATGAATTA
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
56 1 0.01
57 22 0.30
58 30 0.41
59 20 0.27
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (57 bp):
TATTTTAATATAATTATTATTAAATACAATTTACAAAAATAATAAATAATTTAATAA
Found at i:28381 original size:58 final size:58
Alignment explanation
Indices: 28209--28374 Score: 194
Period size: 59 Copynumber: 2.8 Consensus size: 58
28199 AGTAGATGAG
* * * ** *
28209 TATTTTAATAAAATTATTATTAGATTATAATTTAGCAAAAATAATAAATAATTTAATTA
1 TATTTTAATATAATTATTATTAAAATATAATTTAATAAAAATAAT-AATAATTTAATAA
* *
28268 TATTTTAATATAATTAATATT-AAATACAATTTAAT-AAAATAATATATAATTTAATAA
1 TATTTTAATATAATTATTATTAAAATATAATTTAATAAAAATAATA-ATAATTTAATAA
*
28325 TATTTTTAATATAATTATTATTAAAATATGAA-TTAATAAAAATCATAATA
1 TA-TTTTAATATAATTATTATTAAAATAT-AATTTAATAAAAATAATAATA
28375 TATAATATTA
Statistics
Matches: 91, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
56 1 0.01
57 21 0.23
58 27 0.30
59 32 0.35
60 10 0.11
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (58 bp):
TATTTTAATATAATTATTATTAAAATATAATTTAATAAAAATAATAATAATTTAATAA
Found at i:30102 original size:89 final size:89
Alignment explanation
Indices: 29951--30128 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
29941 CTTCACAATG
29951 TTGTCCTCACCACCGGATACAACCCATCGACCATCTGGTGTGAACCTGATTGCATTGACTCCTCG
1 TTGTCCTCACCACCGGATACAACCCATCGACCATCTGGTGTGAACCTGATTGCATTGACTCCTCG
30016 AGTATGACCCTTGTAAGTGTGGAT
66 AGTATGACCCTTGTAAGTGTGGAT
30040 TTGTCCTCACCACCGGATACAACCCATCGACCATCTGGTGTGAACCTGATTGCATTGACTCCTCG
1 TTGTCCTCACCACCGGATACAACCCATCGACCATCTGGTGTGAACCTGATTGCATTGACTCCTCG
30105 AGTATGACCCTTGTAAGTGTGGAT
66 AGTATGACCCTTGTAAGTGTGGAT
30129 GCACTCTTTC
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.28
Consensus pattern (89 bp):
TTGTCCTCACCACCGGATACAACCCATCGACCATCTGGTGTGAACCTGATTGCATTGACTCCTCG
AGTATGACCCTTGTAAGTGTGGAT
Found at i:40391 original size:29 final size:32
Alignment explanation
Indices: 40342--40409 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 32
40332 TTTTAAAAAG
**
40342 TTCAAAAAATCAT-AACTAAAAA-T-TATAAT
1 TTCAAAAAATCATAAAAAAAAAACTCTATAAT
40371 TTCAAAAAAT-ATGAAAAAAAAAACTCTATAAT
1 TTCAAAAAATCAT-AAAAAAAAAACTCTATAAT
40403 TT-AAAAA
1 TTCAAAAA
40410 TAAATTCAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 2 0.06
29 10 0.30
30 7 0.21
31 6 0.18
32 8 0.24
ACGTcount: A:0.62, C:0.09, G:0.01, T:0.28
Consensus pattern (32 bp):
TTCAAAAAATCATAAAAAAAAAACTCTATAAT
Found at i:42239 original size:17 final size:17
Alignment explanation
Indices: 42219--42260 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
42209 GAAGAATAAG
* *
42219 AGAAGAAATGGAGAAGA
1 AGAAGAAACGAAGAAGA
42236 AGAAGAAACGAAGAAGA
1 AGAAGAAACGAAGAAGA
*
42253 GGAAGAAA
1 AGAAGAAA
42261 ATAACAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.62, C:0.02, G:0.33, T:0.02
Consensus pattern (17 bp):
AGAAGAAACGAAGAAGA
Found at i:43560 original size:29 final size:29
Alignment explanation
Indices: 43502--43560 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
43492 ATTATTAATC
*
43502 AGTGATTGTTTTATCATTTTGATAACATT
1 AGTGATTGTTTTATCATTTTGATAAAATT
* **
43531 AGTGATTGTTTTATTATTTTTTTAAAATT
1 AGTGATTGTTTTATCATTTTGATAAAATT
43560 A
1 A
43561 ACTGACTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.29, C:0.03, G:0.12, T:0.56
Consensus pattern (29 bp):
AGTGATTGTTTTATCATTTTGATAAAATT
Found at i:45995 original size:70 final size:70
Alignment explanation
Indices: 45881--46018 Score: 258
Period size: 70 Copynumber: 2.0 Consensus size: 70
45871 TTAAAACAGT
45881 AAGGTTAACCACTCATTTTATCTCAATGCAACAACAAGCATGTTATTCACCCACAAGTCCAAGCA
1 AAGGTTAACCACTCATTTTATCTCAATGCAACAACAAGCATGTTATTCACCCACAAGTCCAAGCA
45946 AAACG
66 AAACG
* *
45951 AAGGTTAACCGCTCATTTTATCTCAATGCAACAACAAGCGTGTTATTCACCCACAAGTCCAAGCA
1 AAGGTTAACCACTCATTTTATCTCAATGCAACAACAAGCATGTTATTCACCCACAAGTCCAAGCA
46016 AAA
66 AAA
46019 AGACGAAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.23
Consensus pattern (70 bp):
AAGGTTAACCACTCATTTTATCTCAATGCAACAACAAGCATGTTATTCACCCACAAGTCCAAGCA
AAACG
Found at i:49914 original size:5 final size:5
Alignment explanation
Indices: 49904--49930 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
49894 TCATCCCCTC
49904 TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT
49931 TACTCTACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:51312 original size:19 final size:19
Alignment explanation
Indices: 51271--51313 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
51261 TAAATCGTAT
*
51271 TAATTATATTTATTAATTA
1 TAATTTTATTTATTAATTA
51290 -AATTTTATTCTATT-ATTA
1 TAATTTTATT-TATTAATTA
51308 TAATTT
1 TAATTT
51314 ATAAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TAATTTTATTTATTAATTA
Found at i:51314 original size:32 final size:33
Alignment explanation
Indices: 51254--51315 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
51244 TAAATATAAT
51254 TTAAATTTAAATCGTATTAATTATATTTATTAA
1 TTAAATTTAAATCGTATTAATTATATTTATTAA
* *
51287 TTAAATTTTATTC-TATT-ATTATAATTTAT
1 TTAAATTTAAATCGTATTAATTAT-ATTTAT
51316 AAAAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 5 0.19
32 10 0.38
33 11 0.42
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (33 bp):
TTAAATTTAAATCGTATTAATTATATTTATTAA
Found at i:55337 original size:27 final size:26
Alignment explanation
Indices: 55289--55396 Score: 92
Period size: 27 Copynumber: 3.9 Consensus size: 26
55279 AATTTGATTT
* *
55289 TTTTTAATTTGTTATTTAAAATTT-TT
1 TTTTTAATTTGATATTT-AAATTTATA
*
55315 TTGGTTTAATATGATATTTAAATTTGATA
1 TT--TTTAATTTGATATTTAAATTT-ATA
55344 TTTTTAATTTGATATTTAAATTTGATA
1 TTTTTAATTTGATATTTAAATTT-ATA
* *
55371 TTTATTTTAAGTTGGTATTTAAATTT
1 --T-TTTTAATTTGATATTTAAATTT
55397 TTTGGAGTCT
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
26 2 0.03
27 30 0.43
28 13 0.19
29 4 0.06
30 20 0.29
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (26 bp):
TTTTTAATTTGATATTTAAATTTATA
Found at i:55354 original size:14 final size:13
Alignment explanation
Indices: 55326--55374 Score: 80
Period size: 13 Copynumber: 3.7 Consensus size: 13
55316 TGGTTTAATA
55326 TGATATTTAAATT
1 TGATATTTAAATT
*
55339 TGATATTTTTAATT
1 TGATA-TTTAAATT
55353 TGATATTTAAATT
1 TGATATTTAAATT
55366 TGATATTTA
1 TGATATTTA
55375 TTTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
13 21 0.64
14 12 0.36
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (13 bp):
TGATATTTAAATT
Found at i:55657 original size:31 final size:33
Alignment explanation
Indices: 55619--55682 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 33
55609 AAAAATTTAA
*
55619 ATATCAAATTAAG-AAAAAA-TATCAGTATCAT
1 ATATCAAATTAAGCAAAAAAGTATAAGTATCAT
*
55650 ATATCAAATTGAGTCAAAAAAGTATAAGTATCA
1 ATATCAAATTAAG-CAAAAAAGTATAAGTATCA
55683 AATTAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 12 0.43
33 6 0.21
34 10 0.36
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.28
Consensus pattern (33 bp):
ATATCAAATTAAGCAAAAAAGTATAAGTATCAT
Found at i:55714 original size:20 final size:19
Alignment explanation
Indices: 55689--55728 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
55679 ATCAAATTAA
55689 TAAATGTCAAATTCAAGTAT
1 TAAATGTCAAATT-AAGTAT
* *
55709 TAAATGTTATATTAAGTAT
1 TAAATGTCAAATTAAGTAT
55728 T
1 T
55729 TTTTAAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (19 bp):
TAAATGTCAAATTAAGTAT
Done.