Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015189.1 Kokia drynarioides strain JFW-HI SEQ_130233, 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: 64816
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 267 characters in sequence are not A, C, G, or T
Found at i:2458 original size:20 final size:18
Alignment explanation
Indices: 2410--2470 Score: 86
Period size: 18 Copynumber: 3.3 Consensus size: 18
2400 GCAAACATAA
*
2410 TTTTTCTTCTCTCTTTTC
1 TTTTTCTTCTCTCTTTCC
2428 TTTTTCTTCTCTCTTTCC
1 TTTTTCTTCTCTCTTTCC
*
2446 TTTTTCTTATCTCATTTTCC
1 TTTTTCTTCTCTC--TTTCC
2466 TTTTT
1 TTTTT
2471 ACGTGACTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
18 29 0.74
20 10 0.26
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTCTTCTCTCTTTCC
Found at i:5427 original size:25 final size:25
Alignment explanation
Indices: 5399--5448 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5389 CAAGTAAAAG
5399 TAAAACAAATAAAAGAAAAATTGAT
1 TAAAACAAATAAAAGAAAAATTGAT
5424 TAAAACAAATAAAAGAAAAATTGAT
1 TAAAACAAATAAAAGAAAAATTGAT
5449 AATGCGTCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.68, C:0.04, G:0.08, T:0.20
Consensus pattern (25 bp):
TAAAACAAATAAAAGAAAAATTGAT
Found at i:12042 original size:50 final size:50
Alignment explanation
Indices: 11969--12105 Score: 170
Period size: 50 Copynumber: 2.7 Consensus size: 50
11959 TGCATGACTT
*
11969 GATTTAATGATGCAAACTTAACTAACATGGGAGTTACATAATGCATGAT-AG
1 GATTT-ATGATGCAAACTTAACTAACATGAGAGTTACATAATGCATG-TCAG
* * * *
12020 GATTTATGATGCATATTTAACTAACATGTA-AGTTACTTAATGCATGTCAT
1 GATTTATGATGCAAACTTAACTAACATG-AGAGTTACATAATGCATGTCAG
*
12070 TATTTATGATGCAAACTTAACTAATCATGAGAGTTA
1 GATTTATGATGCAAACTTAACTAA-CATGAGAGTTA
12106 ATGGATGTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
49 1 0.01
50 59 0.80
51 14 0.19
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (50 bp):
GATTTATGATGCAAACTTAACTAACATGAGAGTTACATAATGCATGTCAG
Found at i:12331 original size:17 final size:17
Alignment explanation
Indices: 12300--12332 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12290 CAAACACTTA
12300 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
12317 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
12333 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:13752 original size:18 final size:18
Alignment explanation
Indices: 13716--13760 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
13706 CACTCTTTCT
13716 TTTCTTTCTTCATTCTCAA
1 TTTCTTT-TTCATTCTCAA
13735 TTTCTTTTTCAATT-TCAA
1 TTTCTTTTTC-ATTCTCAA
*
13753 TCTCTTTT
1 TTTCTTTT
13761 CTCACTCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTCTTTTTCATTCTCAA
Found at i:14766 original size:18 final size:18
Alignment explanation
Indices: 14745--14798 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
14735 TTCAATACTC
14745 GAATTTTTTTCTTCTTTT
1 GAATTTTTTTCTTCTTTT
** *
14763 GAATCTTTTTT-TTAATTC
1 GAAT-TTTTTTCTTCTTTT
*
14781 AAATTTTTTTCTTCTTTT
1 GAATTTTTTTCTTCTTTT
14799 TTTAAACTTC
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
17 6 0.22
18 15 0.56
19 6 0.22
ACGTcount: A:0.17, C:0.11, G:0.04, T:0.69
Consensus pattern (18 bp):
GAATTTTTTTCTTCTTTT
Found at i:16073 original size:51 final size:50
Alignment explanation
Indices: 16010--16147 Score: 154
Period size: 50 Copynumber: 2.7 Consensus size: 50
16000 TGCATGACTT
* *
16010 GATTTAATGATGCAAATTTTAACTAACATGGGAGTTACATAATGCATGAT-AG
1 GATTT-ATGATGCAAA-TTTAACTAACATGAGAGTTACATAATGCACG-TCAG
* * *
16062 GATTTATGATGCATATTTAACTAACATGTA-AGTTACTTAATGCACGTCAT
1 GATTTATGATGCAAATTTAACTAACATG-AGAGTTACATAATGCACGTCAG
* *
16112 TATTTATGATGCAAACTTAACTAATCATGAGAGTTA
1 GATTTATGATGCAAATTTAACTAA-CATGAGAGTTA
16148 ATGGATGTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
49 1 0.01
50 50 0.68
51 18 0.24
52 5 0.07
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.36
Consensus pattern (50 bp):
GATTTATGATGCAAATTTAACTAACATGAGAGTTACATAATGCACGTCAG
Found at i:16373 original size:17 final size:17
Alignment explanation
Indices: 16342--16374 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16332 CAAACACTTA
16342 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
16359 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
16375 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:17445 original size:18 final size:16
Alignment explanation
Indices: 17412--17447 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
17402 TTGATGCAAT
17412 TAGATAAAAGATTAAA
1 TAGATAAAAGATTAAA
17428 TAGATGAAAAGCATTAAA
1 TAGAT-AAAAG-ATTAAA
17446 TA
1 TA
17448 AGGATCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
18 8 0.44
ACGTcount: A:0.58, C:0.03, G:0.14, T:0.25
Consensus pattern (16 bp):
TAGATAAAAGATTAAA
Found at i:17797 original size:48 final size:48
Alignment explanation
Indices: 17718--17826 Score: 155
Period size: 48 Copynumber: 2.3 Consensus size: 48
17708 AGATCGTATC
*
17718 ATGCATCTTTGTTTAATAATCTACATCATTAAGTGTTTTGTTTGTTAA
1 ATGCATCTTTGTTTAATAATCTACATCATTAAATGTTTTGTTTGTTAA
* * * * *
17766 ATGCATCTTTTTTTAGTAATTTGCATTATTAAATGTTTTGTTTGTTAA
1 ATGCATCTTTGTTTAATAATCTACATCATTAAATGTTTTGTTTGTTAA
*
17814 ATGCATCTCTGTT
1 ATGCATCTTTGTT
17827 AAATGCCTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.52
Consensus pattern (48 bp):
ATGCATCTTTGTTTAATAATCTACATCATTAAATGTTTTGTTTGTTAA
Found at i:17838 original size:48 final size:48
Alignment explanation
Indices: 17718--17841 Score: 124
Period size: 48 Copynumber: 2.6 Consensus size: 48
17708 AGATCGTATC
* * * * *
17718 ATGCATCTTTGTTTAATAA-TCTACATCATTAAGTGTTTTGTTTGTTAA
1 ATGCATCTCTGTTAAATAACT-TGCATTATTAAATGTTTTGTTTGTTAA
* * * * *
17766 ATGCATCTTTTTTTAGTAATTTGCATTATTAAATGTTTTGTTTGTTAA
1 ATGCATCTCTGTTAAATAACTTGCATTATTAAATGTTTTGTTTGTTAA
**
17814 ATGCATCTCTGTTAAATGCCTTGCATTA
1 ATGCATCTCTGTTAAATAACTTGCATTA
17842 ACGCATCAGT
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
48 62 0.98
49 1 0.02
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (48 bp):
ATGCATCTCTGTTAAATAACTTGCATTATTAAATGTTTTGTTTGTTAA
Found at i:19829 original size:15 final size:15
Alignment explanation
Indices: 19811--19850 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
19801 GTGTTGCAAG
19811 CACTCATGTTACGAA
1 CACTCATGTTACGAA
* *
19826 CACTGATGTTTCGAA
1 CACTCATGTTACGAA
*
19841 CACTCGTGTT
1 CACTCATGTT
19851 GCGAGCATGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (15 bp):
CACTCATGTTACGAA
Found at i:21239 original size:16 final size:17
Alignment explanation
Indices: 21218--21251 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
21208 CTTCTCTCTC
21218 TTTTCTCAATTT-CTTT
1 TTTTCTCAATTTCCTTT
*
21234 TTTTCTCATTTTCCTTT
1 TTTTCTCAATTTCCTTT
21251 T
1 T
21252 CTCCATAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCTCAATTTCCTTT
Found at i:23889 original size:215 final size:215
Alignment explanation
Indices: 23491--27475 Score: 3765
Period size: 216 Copynumber: 18.6 Consensus size: 215
23481 TGTATAGAAA
* * * * * * * *
23491 AGAGAAATAATTTTCATGTAAATAAGTTTTTAATTAAAAGACCACAAGTTATTTACAAAATAACT
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACA
* * * * *
23556 AACTTTTTAGACCAAATGATGCTATTTCCTGAGCATGGAATGTTCTG-AAAATTTGACAAAGGAA
66 AACTATTTAGACCAAATGATGCGA-TTCCTGAGCATGGAATGTTC-GAAAAATTGGTCGAAGGAA
* * * * * * *
23620 TGGATCGTCTTGAACACT-TTAAGGAACCAAAGATATAAAAGATCTCGA-AAATGTTTAACAAGT
129 TGGATCGTCTTGAATACTCTCAA-GAATCGAAGTTATAAAAGAACTC-ATAAATGTTTGACAAGT
** *
23683 TCAAAAGTTCGTCCAAGAACCAAC
192 TCGGAAGTTCGTCCAAGAACCAAG
* * * * * * ** *
23707 AAAGAAACAATTCTCAGGTAAATAATTTTTTAATTTAAAAACCAAGAGTCATTTACCAAATGACA
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACA
** *
23772 AACTATTTAGACCAAATGATGTTATTCCTGAGCATGTAATGTTCGAAAAATTGGTCGAAGGAATG
66 AACTATTTAGACCAAATGATGCGATTCCTGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAATG
* * * * * * *
23837 GATCGCCTTGCATTCTCTCAAGAATCGAAGGTATAAAAGAACTCGTAAATGTTTGAAAAGTTTGG
131 GATCGTCTTGAATACTCTCAAGAATCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTTCGG
* *
23902 ATGTTCGTTCAAGAACCAAG
196 AAGTTCGTCCAAGAACCAAG
* * * *
23922 AGAGAAATAATTATCACATAAATAA----TTAATTCAAAGACCAAAAGTTGTTTACAAAATGAGA
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACA
* ** *
23983 AACTATTTAGACCAAATGATGCGACTTCCTGAGCATGGAATGCTCGAAAAATTACTCAAAGGAAT
66 AACTATTTAGACCAAATGATGCGA-TTCCTGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAAT
* * * * ** * * *
24048 GGATCATCTTAAATACT-TTAAGAATTGAAGTTATAAAAGAACTTGTAAATGTTTTACATGATCG
130 GGATCGTCTTGAATACTCTCAAGAATCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTTCG
*
24112 GAAGTTCGTCCAAGATCCAAG
195 GAAGTTCGTCCAAGAACCAAG
* * * * *
24133 AGAGAAACAATTCTCACGTAACTAAGTTTTTTATTCAAAAACCAAAAGTTGTTTACAAGATGAAA
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACA
* * * * *
24198 AACTACTTT-GACCAAATGATGCGATTTCTCAAGAATGGAATGTT-TAGAAAATTGGTCGAATGA
66 AACTA-TTTAGACCAAATGATGCGATTCCT-GAGCATGGAATGTTCGA-AAAATTGGTCGAAGGA
* * *
24261 ATGGATCGTCTTGAATACTCTCAGGAATCGAAGTTAGAAAAGAACTCATAAATGTTTAACAAGTT
128 ATGGATCGTCTTGAATACTCTCAAGAATCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTT
* * *
24326 CGGAAGTTCATCCAAGAACTAAT
193 CGGAAGTTCGTCCAAGAACCAAG
* * * * *
24349 AGAGAAATAATTTTCACGTAAATAAGTTTTTATTTCAAAGACCAAAAGTTGTTCACAGAATGACA
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACA
* ** * * *
24414 AACTTTTTTTACCAAATGATTCCATTTTACC-GAGAATGGAATGTTC-AGAAAATTGGTCGAAGG
66 AACTATTTAGACCAAATGATGCGA--TT-CCTGAGCATGGAATGTTCGA-AAAATTGGTCGAAGG
* * *
24477 AATGGATCGTCTTGAATACTCTCAAGAATCGAAGTTATAAAAGAACTCTTAAATGTTTGAGAGGT
127 AATGGATCGTCTTGAATACTCTCAAGAATCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGT
* * *
24542 TCAGAAGTTCGTCTAAGAACCAAA
192 TCGGAAGTTCGTCCAAGAACCAAG
* * * * *
24566 AGAGAAATAATTATCATGTAAATAAGTTTTTAATTCAAACACCATAAGTTGTTTACAAAATGACA
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACA
* * * * *** *
24631 AACTTTTTAGACCAAATAATGTGATTTCCTAAGCATGGAATGTTCGAAAAATTAAACGAAAGAAT
66 AACTATTTAGACCAAATGATGCGA-TTCCTGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAAT
* * * * * *
24696 GGTTCGTCTTGAATGCT-TTAAGGAA-CTAAAGTTATAAAAGAACTCAAAAATGTTTGACATGTT
130 GGATCGTCTTGAATACTCTCAA-GAATC-GAAGTTATAAAAGAACTCATAAATGTTTGACAAGTT
* *
24759 CGGAAGTTTGTCCAAGAACCAAC
193 CGGAAGTTCGTCCAAGAACCAAG
* * * * * *
24782 A-ATGAAACAATTCTCACGTAAAAAAAGTTTTTAATTCAAAAATCAAAAGTTTTTTTCAAAACGA
1 AGA-GAAACAATTCTCACGT-AAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGA
* * * * *
24846 CAAACTTTTTAGACCAAATGAAGCGATT-CTCGAGCATGGAATGTTCAAAAAATTTGTCAAAGGA
64 CAAACTATTTAGACCAAATGATGCGATTCCT-GAGCATGGAATGTTCGAAAAATTGGTCGAAGGA
* ** *
24910 ATGGATCATCTTGAATACTCTCAAGAATCGAAGTTATAAAAGAACTTGTAAATGTTTGACAAATT
128 ATGGATCGTCTTGAATACTCTCAAGAATCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTT
*** *
24975 TAAAAGTTCATCCAAGAACCAAG
193 CGGAAGTTCGTCCAAGAACCAAG
*
24998 AGAGAAACAATCCTCACGTAAATAA----TTAATTCAAAGACCAAAAGTTGTTTACAAAATGACA
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACA
* * * *
25059 AACTATTTAGACCAAATAATG-GAACTT-CTCGAGCATGGAATGTTCGAAAATTTGGTAGTAA-A
66 AACTATTTAGACCAAATGATGCG-A-TTCCT-GAGCATGGAATGTTCGAAAAATTGGTCG-AAGG
* * * *
25121 AATGGATCGTCTTG-A-ACTCTCAATAACCGAAGTTATAAAAGAACTCGTAAATGTTTGAAAAGT
127 AATGGATCGTCTTGAATACTCTCAAGAATCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGT
* * *
25184 TCAGAAGTTTGCCCAAGAA-CAAG
192 TCGGAAGTTCGTCCAAGAACCAAG
* * * *
25207 AGAGAAACAATTCTCACATAAATATGTTTTTAATTTAAAGACTAAAAGTTGTTTACAAAATGACA
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACA
* * * * *
25272 AACTATTTAGACCAAATGCTATG-GTTTACC-GAGAATGAAATGTTCAAAAAATTGGTCGAAGTA
66 AACTATTTAGACCAAATG--ATGCGATT-CCTGAGCATGGAATGTTCGAAAAATTGGTCGAAGGA
* * * * * * * *
25335 ATTGATTGTCTTGAATACTTTAAAGAACCGAAGTTTTAAAAGAACTCGTAAATGTTTGACATGTT
128 ATGGATCGTCTTGAATACTCTCAAGAATCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTT
*
25400 CGGAAGTTCGTCCAAGAACAAAG
193 CGGAAGTTCGTCCAAGAACCAAG
* *
25423 AGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGATCAAAAGTTG-TT------T-ACA
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACA
* * * *
25480 AA--A--T-GACCAAATGATGTGATTTCCCT-AGCATAGAATGTTCGGAAAATTGCTCGAAGGAA
66 AACTATTTAGACCAAATGATGCGA-TT-CCTGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAA
* * * * * * * * *
25539 TGGATTC-TATTGAATTCT-TTAGGGAACCAAAGTTGTAAAAGAACTCATAAAAGTTTGATAAGT
129 TGGA-TCGTCTTGAATACTCTCA-AGAATCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGT
* * **
25602 TTGAAAGCTT-G-GAAAGAACCAAG
192 TCGGAAG-TTCGTCCAAGAACCAAG
* *
25625 AGAGAAACAATTCTCACGTAAAT-A-TTTTTAATAT-AAAGACCAAAGGTTGATTACAAAATGAC
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAAT-TCAAAGACCAAAAGTTGTTTACAAAATGAC
** * * *
25687 AAACTATTTAGACCAAATGATGCGATTTTTCAAGCATGGAATGTTCGAAAAATTGCTCGAAGGAC
65 AAACTATTTAGACCAAATGATGCGATTCCT-GAGCATGGAATGTTCGAAAAATTGGTCGAAGGAA
* * * * * * *
25752 TGGATTGTCCTGAAT-GTTTTAAGGAA-CGAAAGTTATAAAAAAACTCATAAAAT-CTTGACAAG
129 TGGATCGTCTTGAATACTCTCAA-GAATCG-AAGTTATAAAAGAACTCAT-AAATGTTTGACAAG
** * * *
25814 CGCGAAAGTTCAG-CGAAGAA-CTA-
191 TTCGGAAGTTC-GTCCAAGAACCAAG
* * *
25837 AGAGAAACAATTCTAATGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTATTTACAAAATGACA
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACA
** * * *
25902 AACTATTTTTACCAAACGATGCGAATTCCCT-AGAATGGAATTTTCGAAAAATTGGTCGAAGGAA
66 AACTATTTAGACCAAATGATGCG-ATT-CCTGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAA
* * * * * * *
25966 T-GATCATCTTGAATATTCTCAAGAACCAAAGTTATAAAAGAACTCGTAATTGTTTGACAAGTTT
129 TGGATCGTCTTGAATACTCTCAAGAATCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTTC
* *
26030 GAAAGTTC--CCAAGAACCAAA
194 GGAAGTTCGTCCAAGAACCAAG
* * * *
26050 AGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGACCACAAGTTATTTACAAAATAACA
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACA
* * * * * * * *
26115 AACTTTTTGGACCAAGTGATACTATTTCCTGAGCATGGAATATTCTG-AAAATTGGACGAAGAAA
66 AACTATTTAGACCAAATGATGCGA-TTCCTGAGCATGGAATGTTC-GAAAAATTGGTCGAAGGAA
* * * * * *
26179 TGGATCATCTTGAACACT-TTAAGGAACCGAAGATATAAAAGAACTCAAAAATGTTTGACAAGTT
129 TGGATCGTCTTGAATACTCTCAA-GAATCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTT
* * *
26243 CGGAAGTTCATCCAAGATCCAAC
193 CGGAAGTTCGTCCAAGAACCAAG
* * * * **
26266 AAAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAAACCAAGAGTCATTTACAAAATGACA
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACA
* * * ** * *
26331 AACTTTTTAGACCAAATGATGCAAATCCTGAGCATATAATGTTCGGAAAATTGGTCGAGGGAATG
66 AACTATTTAGACCAAATGATGCGATTCCTGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAATG
* * * * * * *
26396 GATCGCCTTGAACT-CTCTCAGGAACCAAAGTTATAAAAGAACTCGTAAAATGTTTGACAATTTT
131 GATCGTCTTGAA-TACTCTCAAGAATCGAAGTTATAAAAGAACTCAT-AAATGTTTGACAAGTTC
** * *
26460 GGGTGTTCGTTCAAGAATCAAG
194 GGAAGTTCGTCCAAGAACCAAG
* * *
26482 AGAGAAACAATTATCACGTAAATAA----TTAATTCAAAGAACAAAAGTTGTTTACAAAATGAGA
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACA
* ** * * * *
26543 AACTATATAGACCAAATGATGCGACTTCCCAAGCATGGAATGATCGAAAAATTGCTCAAAGAAAT
66 AACTATTTAGACCAAATGATGCGA-TTCCTGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAAT
* * ** * *
26608 GGATCGTCATT-AATACT-TTAAGGTATTTAAGTTATAAAAGAACTCATAAATTTTTGACAAGAT
130 GGATCGTC-TTGAATACTCTCAA-GAATCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTT
* *
26671 CGAAAGTTTGTCCAAGATA-CAAG
193 CGGAAGTTCGTCCAAGA-ACCAAG
* * * * *
26694 AGAGAAATAATTCTCACGTAAATAAGTTTTAAATTCAAAAACCAAAAGTTGTTTACAAGATGAAA
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACA
* * * * * *
26759 AACTACTTT-GACCAAATGATGCGATTTCTCAAGAATGGAATGCTCAAAAAATTGGTCAAAGGAA
66 AACTA-TTTAGACCAAATGATGCGATTCCT-GAGCATGGAATGTTCGAAAAATTGGTCGAAGGAA
*
26823 TGGATCGTCTTGAATACTCTC-AGAAATCGAAGTTAGAAAAGAACTCATAAATGTTTGACAAGTT
129 TGGATCGTCTTGAATACTCTCAAG-AATCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTT
* * * *
26887 CAGAAATTTGTCCAAGAACCAAT
193 CGGAAGTTCGTCCAAGAACCAAG
* * * *
26910 AGAGAAACAATTCTCATGTAAATAAGTTTTAAATTCAAAGACGAAAAGTTGTTTAC-AGATGGA-
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAT-GAC
** * * * *
26973 AAACTATTTTTACCAAATGATTCCATTTTACC-GAGAATGGAATGTTCGAAAAATTGGTCAAAGG
65 AAACTATTTAGACCAAATGATGCGA--TT-CCTGAGCATGGAATGTTCGAAAAATTGGTCGAAGG
* * * * * * * * *
27037 AATGGATCTTCTTAAATATTCTCAGGAATCAAAGTTATAAACA-AACTCCTATATGTTTGAGAGG
127 AATGGATCGTCTTGAATACTCTCAAGAATCGAAGTTATAAA-AGAACTCATAAATGTTTGACAAG
* *
27101 TTCAGAAGTTCGTCCAAGAACCAAA
191 TTCGGAAGTTCGTCCAAGAACCAAG
* * * * *
27126 AAAGAAATAATTCTCATGTAAATAAGTTTTTAATT-GAAGCACCACAAGTTGTTTACAAAATGAC
1 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG-ACCAAAAGTTGTTTACAAAATGAC
* * * * *
27190 AAACTTTTTAGACCAAATGATGCGATTTCCTGATCATGGAATGTTCAAAAAACTAGAT-GAAGGA
65 AAACTATTTAGACCAAATGATGCGA-TTCCTGAGCATGGAATGTTCGAAAAA-TTGGTCGAAGGA
* * * * *
27254 ATGGTTCGTCTTGAATGCT-TTAAGGAATCGAAGTTATAAAAGAACTCAAAAATGTTTGACATGT
128 ATGGATCGTCTTGAATACTCTCAA-GAATCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGT
* * *
27318 TCGGAAGTTTGTCAAAGAACCAAT
192 TCGGAAGTTCGTCCAAGAACCAAG
* * *
27342 A-ATGAAACAATTCTCACGTAAA-AAGTTTTTAATTCAAAAACCAAAAGCTATTTACAAAATGAC
1 AGA-GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAC
* * *
27405 AAACTATTTAGACCAAATAATGCAACTTCCCGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAA
65 AAACTATTTAGACCAAATGATGCGA-TTCCTGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAA
27470 TGGATC
129 TGGATC
27476 NNNNNNNNNN
Statistics
Matches: 3102, Mismatches: 543, Indels: 249
0.80 0.14 0.06
Matches are distributed among these distances:
200 21 0.01
201 7 0.00
202 34 0.01
203 91 0.03
204 4 0.00
206 1 0.00
207 1 0.00
208 10 0.00
209 27 0.01
210 59 0.02
211 186 0.06
212 233 0.08
213 401 0.13
214 172 0.06
215 487 0.16
216 1082 0.35
217 282 0.09
218 3 0.00
219 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (215 bp):
AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACA
AACTATTTAGACCAAATGATGCGATTCCTGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAATG
GATCGTCTTGAATACTCTCAAGAATCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTTCGG
AAGTTCGTCCAAGAACCAAG
Found at i:30055 original size:7 final size:7
Alignment explanation
Indices: 30043--30075 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
30033 ATTATTTTTC
30043 AATATTG
1 AATATTG
30050 AATATTG
1 AATATTG
30057 AATATT-
1 AATATTG
30063 AATATTG
1 AATATTG
30070 AATATT
1 AATATT
30076 TTCAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (7 bp):
AATATTG
Found at i:30066 original size:13 final size:14
Alignment explanation
Indices: 30043--30075 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
30033 ATTATTTTTC
30043 AATATTGAATATTG
1 AATATTGAATATTG
30057 AATATT-AATATTG
1 AATATTGAATATTG
30070 AATATT
1 AATATT
30076 TTCAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (14 bp):
AATATTGAATATTG
Found at i:30575 original size:24 final size:24
Alignment explanation
Indices: 30547--30609 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
30537 AGAAATAATC
30547 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
30571 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
30595 TTTAAGTCAAACTCT
1 TTTCAGTTAAACTCT
30610 TGTTAGTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAATTG
Found at i:32620 original size:28 final size:24
Alignment explanation
Indices: 32539--32613 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
32529 AGAAATAATC
* *
32539 TTTCAGTTAAACTCTATTTAATTG
1 TTTCAATTAAACTCTATTTATTTG
32563 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
*
32587 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
32611 TTT
1 TTT
32614 AAGTCAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:35531 original size:14 final size:13
Alignment explanation
Indices: 35506--35540 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
35496 CATATTTTTT
35506 AAAAAT-AAATTA
1 AAAAATAAAATTA
35518 AAAACATAAAATTA
1 AAAA-ATAAAATTA
35532 AAAAATAAA
1 AAAAATAAA
35541 CAAATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.19
13 7 0.33
14 10 0.48
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAATAAAATTA
Found at i:38768 original size:24 final size:24
Alignment explanation
Indices: 38740--38802 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
38730 AGAAATAATC
*
38740 TTTCAGTTAAATTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
*
38764 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
*
38788 TTTGAGTTAAACTCT
1 TTTCAGTTAAACTCT
38803 TATTAGTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.54
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTG
Found at i:51336 original size:30 final size:30
Alignment explanation
Indices: 51290--51366 Score: 147
Period size: 30 Copynumber: 2.6 Consensus size: 30
51280 TCTAATCATA
51290 TAATAAATTA-TTAATATAGTTTATTATTT
1 TAATAAATTATTTAATATAGTTTATTATTT
51319 TAATAAATTATTTAATATAGTTTATTATTT
1 TAATAAATTATTTAATATAGTTTATTATTT
51349 TAATAAATTATTTAATAT
1 TAATAAATTATTTAATAT
51367 TTCAATTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 10 0.21
30 37 0.79
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (30 bp):
TAATAAATTATTTAATATAGTTTATTATTT
Found at i:51898 original size:22 final size:22
Alignment explanation
Indices: 51853--51898 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
51843 CCTAGTGTAA
*
51853 AAATATGAATATTGTATTATAT
1 AAATATGAATATTGTATTAAAT
*
51875 AAATATGAGTATTTGT-TTAAAT
1 AAATATGAATA-TTGTATTAAAT
51897 AA
1 AA
51899 TGTTTAGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (22 bp):
AAATATGAATATTGTATTAAAT
Found at i:52281 original size:32 final size:32
Alignment explanation
Indices: 52244--52308 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
52234 CTTTTATGAC
52244 ATATTTT-TAGGAAATCTATC-AAACAATAAAAA
1 ATATTTTATAGGAAATC-ATCTAAAC-ATAAAAA
* *
52276 ATATTTTATATGAATTCATCTAAACATAAAAA
1 ATATTTTATAGGAAATCATCTAAACATAAAAA
52308 A
1 A
52309 AATTATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (32 bp):
ATATTTTATAGGAAATCATCTAAACATAAAAA
Found at i:56137 original size:32 final size:31
Alignment explanation
Indices: 56043--56134 Score: 100
Period size: 31 Copynumber: 2.9 Consensus size: 31
56033 AAGGGGTTTA
* *
56043 ATTTTTTTCATCTTTTAAAGGGAT-CAAATT
1 ATTTTTTTCAACTTTTAAAGGGATAAAAATT
*
56073 -TTTTTTTACTAACTTTTAAAGGGCCTAAAAATT
1 ATTTTTTT-C-AACTTTTAAAGGG-ATAAAAATT
56106 ATTTTTTTCAACTTTT-AAGGGATTAAAAA
1 ATTTTTTTCAACTTTTAAAGGGA-TAAAAA
56135 ATTTAATTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
29 7 0.13
30 1 0.02
31 23 0.44
32 8 0.15
33 6 0.12
34 7 0.13
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.47
Consensus pattern (31 bp):
ATTTTTTTCAACTTTTAAAGGGATAAAAATT
Found at i:61502 original size:43 final size:43
Alignment explanation
Indices: 61455--61587 Score: 142
Period size: 43 Copynumber: 3.1 Consensus size: 43
61445 ATCATTAGCT
*
61455 AAACTAAAGTAAATATACTGGCAAATATAGTGCATCATCGGAC
1 AAACTAAAGCAAATATACTGGCAAATATAGTGCATCATCGGAC
* * * * *
61498 AAACTAAAGCAAATGTACTGACACATTTAGTGCATCATTTGGAC
1 AAACTAAAGCAAATATACTGGCAAATATAGTGCATCA-TCGGAC
* * * * * *
61542 TAGCTAAAGCAAATATACTAGC-ATTATAGTGCATTATCGAAC
1 AAACTAAAGCAAATATACTGGCAAATATAGTGCATCATCGGAC
61584 AAAC
1 AAAC
61588 CGAAGTATAA
Statistics
Matches: 70, Mismatches: 19, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
42 6 0.09
43 42 0.60
44 22 0.31
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (43 bp):
AAACTAAAGCAAATATACTGGCAAATATAGTGCATCATCGGAC
Done.