Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013642.1 Kokia drynarioides strain JFW-HI SEQ_128670, 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: 120740
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 117 characters in sequence are not A, C, G, or T
Found at i:890 original size:45 final size:45
Alignment explanation
Indices: 826--955 Score: 170
Period size: 45 Copynumber: 2.9 Consensus size: 45
816 GCATAGCTCA
* *
826 TCAAGCCAAAGATATCAACCCCAGTTTGACGAGCCACCGCAAAAC
1 TCAAGCCAAGGATATCAACCTCAGTTTGACGAGCCACCGCAAAAC
* *
871 TCAAGCCAAGGATATCAACCTCAATTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAACCTCAGTTTGACGAGCCACCGCAAAAC
** ** * *
916 TCAAGGGAAGGATATCAGGCTGAGTTTGACGAGCCCCCGC
1 TCAAGCCAAGGATATCAACCTCAGTTTGACGAGCCACCGC
956 GATATTCTAT
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.33, C:0.30, G:0.21, T:0.16
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAACCTCAGTTTGACGAGCCACCGCAAAAC
Found at i:1282 original size:28 final size:28
Alignment explanation
Indices: 1251--1311 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
1241 TAAACCCTAA
1251 ACTTGAAAC-CTTAAACAGATAACACTAG
1 ACTTGAAACTC-TAAACAGATAACACTAG
* *
1279 ACTTGAAACTCTAAACCGTTAACACTAG
1 ACTTGAAACTCTAAACAGATAACACTAG
1307 A-TTGA
1 ACTTGA
1312 TTAAGGAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 4 0.13
28 25 0.83
29 1 0.03
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (28 bp):
ACTTGAAACTCTAAACAGATAACACTAG
Found at i:4337 original size:19 final size:19
Alignment explanation
Indices: 4291--4338 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
4281 AATAAATCTG
*
4291 TTAAAAATTAAATAAAATT
1 TTAAAAATAAAATAAAATT
**
4310 TTAATAAATAAAATACGATT
1 TTAA-AAATAAAATAAAATT
4330 TTAAAAATA
1 TTAAAAATA
4339 TATCATACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
TTAAAAATAAAATAAAATT
Found at i:4396 original size:4 final size:4
Alignment explanation
Indices: 4376--4441 Score: 55
Period size: 4 Copynumber: 16.2 Consensus size: 4
4366 AACATATTAC
* * *
4376 CTTT CTTT CCTT C-TT CTTT CTTT C-CT CTGCTT CTTC CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT--TT CTTT CTTT CTTT CTTT
*
4424 CTTTT CTTT CTTT TTTT C
1 C-TTT CTTT CTTT CTTT C
4442 CTGTTTATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
3 5 0.10
4 38 0.76
5 4 0.08
6 3 0.06
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:4410 original size:17 final size:15
Alignment explanation
Indices: 4376--4436 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 15
4366 AACATATTAC
4376 CTTTCTTTCCTTCTT
1 CTTTCTTTCCTTCTT
*
4391 CTTTCTTTCC-TCTG
1 CTTTCTTTCCTTCTT
4405 C-TTC-TTCC-T-TT
1 CTTTCTTTCCTTCTT
4416 CTTTCTTT-CTT-TT
1 CTTTCTTTCCTTCTT
4429 CTTTCTTT
1 CTTTCTTT
4437 TTTTCCTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 2 0.05
12 9 0.22
13 16 0.39
14 4 0.10
15 10 0.24
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (15 bp):
CTTTCTTTCCTTCTT
Found at i:4434 original size:25 final size:24
Alignment explanation
Indices: 4376--4435 Score: 59
Period size: 29 Copynumber: 2.3 Consensus size: 24
4366 AACATATTAC
4376 CTTTCTTTCCTTCTTCTTTCTTTCCT
1 CTTTC-TTCCTTCTTCTTTCTTT-CT
4402 CTGCTTCTTCCTTTCTTTCTTTCTTT-T
1 CT--TTCTTCC-TTC-TTCTTTCTTTCT
4429 CTTTCTT
1 CTTTCTT
4436 TTTTTCCTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
25 5 0.17
26 2 0.07
27 7 0.23
28 6 0.20
29 10 0.33
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.67
Consensus pattern (24 bp):
CTTTCTTCCTTCTTCTTTCTTTCT
Found at i:24915 original size:26 final size:27
Alignment explanation
Indices: 24865--24926 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 27
24855 CTACATGCCA
24865 TTAAAAA-ATAATAGAAAATACAAATT
1 TTAAAAATATAATAGAAAATACAAATT
* *
24891 TTAAAAATATAATATATAATA-AAATT
1 TTAAAAATATAATAGAAAATACAAATT
* *
24917 ATATAAATAT
1 TTAAAAATAT
24927 TTTAATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (27 bp):
TTAAAAATATAATAGAAAATACAAATT
Found at i:34561 original size:30 final size:30
Alignment explanation
Indices: 34525--34584 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
34515 TATTGGGCAA
34525 GTGCAAGCTAACAAACTCCATGTTGTACCT
1 GTGCAAGCTAACAAACTCCATGTTGTACCT
34555 GTGCAAGCTAACAAACTCCATGTTGTACCT
1 GTGCAAGCTAACAAACTCCATGTTGTACCT
34585 TCGACTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (30 bp):
GTGCAAGCTAACAAACTCCATGTTGTACCT
Found at i:42201 original size:11 final size:11
Alignment explanation
Indices: 42187--42270 Score: 50
Period size: 11 Copynumber: 7.8 Consensus size: 11
42177 GTTTTGGTGC
42187 TGTTTTTTTAT
1 TGTTTTTTTAT
* *
42198 TGTTTTGATTGT
1 TGTTTT-TTTAT
42210 TG-TTTTTTAT
1 TGTTTTTTTAT
**
42220 TGTTTTGATAT
1 TGTTTTTTTAT
* *
42231 TG-TTTATTAC
1 TGTTTTTTTAT
*
42241 TGTTTTTGTA-
1 TGTTTTTTTAT
*
42251 -CTTTTTTTAT
1 TGTTTTTTTAT
42261 TGTTATTTTT
1 TGTT-TTTTT
42271 CTTGCTATTT
Statistics
Matches: 53, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
9 7 0.13
10 12 0.23
11 24 0.45
12 10 0.19
ACGTcount: A:0.12, C:0.02, G:0.13, T:0.73
Consensus pattern (11 bp):
TGTTTTTTTAT
Found at i:42203 original size:22 final size:22
Alignment explanation
Indices: 42175--42227 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
42165 ATATATATTG
42175 TTGTTTTG-GTGCTGTTTTTTTA
1 TTGTTTTGAGTGCTG-TTTTTTA
* *
42197 TTGTTTTGATTGTTGTTTTTTA
1 TTGTTTTGAGTGCTGTTTTTTA
42219 TTGTTTTGA
1 TTGTTTTGA
42228 TATTGTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.08, C:0.02, G:0.21, T:0.70
Consensus pattern (22 bp):
TTGTTTTGAGTGCTGTTTTTTA
Found at i:42233 original size:21 final size:21
Alignment explanation
Indices: 42190--42264 Score: 82
Period size: 22 Copynumber: 3.6 Consensus size: 21
42180 TTGGTGCTGT
*
42190 TTTTTTATTGTTTTGATTGTTG
1 TTTTTTATTGTTTTGA-TATTG
42212 TTTTTTATTGTTTTGATATTG
1 TTTTTTATTGTTTTGATATTG
* * *
42233 TTTATTACTGTTTTTG-TACT-
1 TTTTTTATTG-TTTTGATATTG
42253 TTTTTTATTGTT
1 TTTTTTATTGTT
42265 ATTTTTCTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
19 2 0.04
20 8 0.17
21 15 0.33
22 21 0.46
ACGTcount: A:0.12, C:0.03, G:0.13, T:0.72
Consensus pattern (21 bp):
TTTTTTATTGTTTTGATATTG
Found at i:42332 original size:12 final size:12
Alignment explanation
Indices: 42254--42328 Score: 62
Period size: 12 Copynumber: 6.3 Consensus size: 12
42244 TTTTGTACTT
*
42254 TTTTTATTGTTA
1 TTTTTGTTGTTA
* *
42266 TTTTTCTTGCTA
1 TTTTTGTTGTTA
*
42278 TTTTTGCTGTTA
1 TTTTTGTTGTTA
42290 TTTTTGTTGTT-
1 TTTTTGTTGTTA
* * * *
42301 GTTCTGCTGCTA
1 TTTTTGTTGTTA
*
42313 TTTTGGTTGTTA
1 TTTTTGTTGTTA
42325 TTTT
1 TTTT
42329 GGTTATTTGG
Statistics
Matches: 47, Mismatches: 15, Indels: 2
0.73 0.23 0.03
Matches are distributed among these distances:
11 7 0.15
12 40 0.85
ACGTcount: A:0.08, C:0.08, G:0.16, T:0.68
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:45534 original size:21 final size:21
Alignment explanation
Indices: 45508--45549 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
45498 TTTTTTATAC
*
45508 CGGTAGAAGCATGATTTGTTT
1 CGGTAGAAGCATCATTTGTTT
*
45529 CGGTAGAAGCTTCATTTGTTT
1 CGGTAGAAGCATCATTTGTTT
45550 AGATAGAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.40
Consensus pattern (21 bp):
CGGTAGAAGCATCATTTGTTT
Found at i:45564 original size:21 final size:21
Alignment explanation
Indices: 45511--45557 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
45501 TTTATACCGG
* * * *
45511 TAGAAGCATGATTTGTTTCGG
1 TAGAAGCTTCATTTGTTTAGA
45532 TAGAAGCTTCATTTGTTTAGA
1 TAGAAGCTTCATTTGTTTAGA
45553 TAGAA
1 TAGAA
45558 CTATCATAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (21 bp):
TAGAAGCTTCATTTGTTTAGA
Found at i:47587 original size:18 final size:18
Alignment explanation
Indices: 47564--47606 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
47554 GAATAGGTTT
47564 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
47582 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
47600 TTAATTA
1 TTAATTA
47607 CACATTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:51125 original size:7 final size:7
Alignment explanation
Indices: 51113--51142 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
51103 AGACAAATCA
51113 TGTGCAT
1 TGTGCAT
*
51120 TGTGCAC
1 TGTGCAT
51127 TGTGCAT
1 TGTGCAT
51134 TGTGCAT
1 TGTGCAT
51141 TG
1 TG
51143 CTGAACTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.13, C:0.17, G:0.30, T:0.40
Consensus pattern (7 bp):
TGTGCAT
Found at i:51859 original size:10 final size:9
Alignment explanation
Indices: 51846--51884 Score: 51
Period size: 10 Copynumber: 4.0 Consensus size: 9
51836 AAAATAATTT
51846 AAAAATTATA
1 AAAAATTA-A
51856 AAAAATTCAA
1 AAAAATT-AA
51866 AAAAATTAA
1 AAAAATTAA
51875 AAATAATTAA
1 AAA-AATTAA
51885 TGTAAAGTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 5 0.19
10 21 0.78
11 1 0.04
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (9 bp):
AAAAATTAA
Found at i:52818 original size:17 final size:18
Alignment explanation
Indices: 52786--52819 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52776 ACCATTCTCT
*
52786 TTTATTATATATTTTTAG
1 TTTATAATATATTTTTAG
52804 TTTATAATA-ATTTTTA
1 TTTATAATATATTTTTA
52820 AATGTTTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTATAATATATTTTTAG
Found at i:56723 original size:17 final size:17
Alignment explanation
Indices: 56703--56750 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
56693 CTATTAATGT
56703 TAAATTTTTTATTGAAA
1 TAAATTTTTTATTGAAA
* * *
56720 TAAAATTTTAATGTTAAA
1 TAAATTTTTTAT-TGAAA
*
56738 TAAATTTATTATT
1 TAAATTTTTTATT
56751 TAACTTTTAC
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
TAAATTTTTTATTGAAA
Found at i:63389 original size:17 final size:17
Alignment explanation
Indices: 63369--63415 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
63359 TTCATTGATA
*
63369 TTTAATTTTTTATCTTT
1 TTTAATTTTTTATATTT
*
63386 TTTAATTTTTCATATTT
1 TTTAATTTTTTATATTT
63403 TTGTAATTATTTT
1 TT-TAATT-TTTT
63416 TGCCTGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 17 0.68
18 5 0.20
19 3 0.12
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTAATTTTTTATATTT
Found at i:69053 original size:23 final size:23
Alignment explanation
Indices: 69020--69177 Score: 127
Period size: 23 Copynumber: 7.2 Consensus size: 23
69010 GCTGGGCAAC
69020 AGAGAGCACACAAAGTGCTAAAT
1 AGAGAGCACACAAAGTGCTAAAT
* *
69043 AGAGAGTACACAAA--G-T-ACT
1 AGAGAGCACACAAAGTGCTAAAT
** **
69062 ---GAGCACACAAAACGCTAATC
1 AGAGAGCACACAAAGTGCTAAAT
* *
69082 AGAGAGCACACGAAGTGCTAAAC
1 AGAGAGCACACAAAGTGCTAAAT
*
69105 AGAGAGCACACACAGTGCT-AAT
1 AGAGAGCACACAAAGTGCTAAAT
*
69127 CAGAGAGCACACGAAGTGCT-AAT
1 -AGAGAGCACACAAAGTGCTAAAT
* *
69150 CAGAGAGCACACGAAGTGCTAATT
1 -AGAGAGCACACAAAGTGCTAAAT
69174 AGAG
1 AGAG
69178 CATGCGCTAG
Statistics
Matches: 111, Mismatches: 15, Indels: 18
0.77 0.10 0.12
Matches are distributed among these distances:
16 10 0.09
18 1 0.01
19 3 0.03
20 2 0.02
21 1 0.01
22 2 0.02
23 90 0.81
24 2 0.02
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (23 bp):
AGAGAGCACACAAAGTGCTAAAT
Found at i:69079 original size:39 final size:39
Alignment explanation
Indices: 69023--69097 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
69013 GGGCAACAGA
** *
69023 GAGCACACAAAGTGCTAAAT-AGAGAGTACACAAAGTACT
1 GAGCACACAAAACGCT-AATCAGAGAGCACACAAAGTACT
*
69062 GAGCACACAAAACGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAACGCTAATCAGAGAGCACACAAAGT
69098 GCTAAACAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAACGCTAATCAGAGAGCACACAAAGTACT
Found at i:69129 original size:46 final size:46
Alignment explanation
Indices: 69075--69177 Score: 172
Period size: 46 Copynumber: 2.2 Consensus size: 46
69065 CACACAAAAC
69075 GCTAATCAGAGAGCACACGAAGTGCTAAACAGAGAGCACAC-ACAGT
1 GCTAATCAGAGAGCACACGAAGTGCTAAACAGAGAGCACACGA-AGT
*
69121 GCTAATCAGAGAGCACACGAAGTGCTAATCAGAGAGCACACGAAGT
1 GCTAATCAGAGAGCACACGAAGTGCTAAACAGAGAGCACACGAAGT
*
69167 GCTAATTAGAG
1 GCTAATCAGAG
69178 CATGCGCTAG
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
46 53 0.98
47 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.14
Consensus pattern (46 bp):
GCTAATCAGAGAGCACACGAAGTGCTAAACAGAGAGCACACGAAGT
Found at i:84512 original size:15 final size:15
Alignment explanation
Indices: 84494--84532 Score: 64
Period size: 13 Copynumber: 2.7 Consensus size: 15
84484 TTTGTATTAT
84494 TTATTTTTAATATAA
1 TTATTTTTAATATAA
84509 TTATTTTT--TATAA
1 TTATTTTTAATATAA
84522 TTATTTTTAAT
1 TTATTTTTAAT
84533 TTGTAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 13 0.59
15 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTTTTAATATAA
Found at i:96371 original size:63 final size:63
Alignment explanation
Indices: 96278--96397 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 63
96268 TACATATTAG
* * *
96278 CTGTAACACCCCTATACTCAGTTCACACGTATAAACCCGGTGT-AGAAGTATTACATATAGTAT
1 CTGTAACACCCCTAAACCCAGTTCACACGTATAAACCCGGTATAAG-AGTATTACATATAGTAT
* *
96341 CTGTAACACCCCTAAACCC-GATTCATACGTATAAATCCGGTATAAGAGTATTACATA
1 CTGTAACACCCCTAAACCCAG-TTCACACGTATAAACCCGGTATAAGAGTATTACATA
96398 CAGTGCCAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
62 1 0.02
63 47 0.94
64 2 0.04
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (63 bp):
CTGTAACACCCCTAAACCCAGTTCACACGTATAAACCCGGTATAAGAGTATTACATATAGTAT
Found at i:96895 original size:22 final size:22
Alignment explanation
Indices: 96868--96983 Score: 187
Period size: 22 Copynumber: 5.3 Consensus size: 22
96858 CTGCTGGGGA
*
96868 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAATGCTG
*
96890 AGCAGAAGCACACACAATGCTG
1 AACAGAAGCACACACAATGCTG
* * *
96912 AGCAGAAGCAAACACAGTGCTG
1 AACAGAAGCACACACAATGCTG
96934 AACAGAAGCACACACAATGCTG
1 AACAGAAGCACACACAATGCTG
96956 AACAGAAGCACACACAATGCTG
1 AACAGAAGCACACACAATGCTG
96978 AACAGA
1 AACAGA
96984 GAGCGCGCTA
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 87 1.00
ACGTcount: A:0.44, C:0.26, G:0.22, T:0.09
Consensus pattern (22 bp):
AACAGAAGCACACACAATGCTG
Found at i:100214 original size:35 final size:35
Alignment explanation
Indices: 100147--100214 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
100137 CTTTCATCTT
* * *
100147 CCTTGACTTTTAACCTTTCATCTTCTTTAACCTCC
1 CCTTGACTTTTAACCTTCCATCTTCCTCAACCTCC
100182 CCTTGACTTTTAACCTTCCATCTTCCTCAACCT
1 CCTTGACTTTTAACCTTCCATCTTCCTCAACCT
100215 TTCATATTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.18, C:0.37, G:0.03, T:0.43
Consensus pattern (35 bp):
CCTTGACTTTTAACCTTCCATCTTCCTCAACCTCC
Found at i:111041 original size:29 final size:30
Alignment explanation
Indices: 111009--111065 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
110999 TAGTTTAATG
*
111009 TGTAATTGTATATATG-AATTTTGATTTTT
1 TGTAATTGTATACATGAAATTTTGATTTTT
*
111038 TGTAATTTTATACATGAAATTTTGATTT
1 TGTAATTGTATACATGAAATTTTGATTT
111066 GATCAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (30 bp):
TGTAATTGTATACATGAAATTTTGATTTTT
Found at i:116485 original size:27 final size:27
Alignment explanation
Indices: 116452--116504 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
116442 TCAGCAAGTT
*
116452 TCAGCTTGCTTT-TTGTTTCGGATTTCC
1 TCAGCTTGCTTTGTTG-CTCGGATTTCC
*
116479 TCAGCTTTCTTTGTTGCTCGGATTTC
1 TCAGCTTGCTTTGTTGCTCGGATTTC
116505 AACTCCCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.08, C:0.23, G:0.19, T:0.51
Consensus pattern (27 bp):
TCAGCTTGCTTTGTTGCTCGGATTTCC
Found at i:118747 original size:6 final size:6
Alignment explanation
Indices: 118736--118765 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
118726 CTTTTGTTTT
*
118736 AGTCAC AGTCAC AGTCAC AGTCAC ACTCAC
1 AGTCAC AGTCAC AGTCAC AGTCAC AGTCAC
118766 TTTGCAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.33, C:0.37, G:0.13, T:0.17
Consensus pattern (6 bp):
AGTCAC
Done.