Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005571.1 Kokia drynarioides strain JFW-HI SEQ_119687, 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: 144606
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 37 characters in sequence are not A, C, G, or T
Found at i:1827 original size:11 final size:10
Alignment explanation
Indices: 1811--1860 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 10
1801 AAATAGAAAA
1811 AATTATTTATT
1 AATTA-TTATT
1822 AATTATTACTT
1 AATTATTA-TT
1833 AATTATTATT
1 AATTATTATT
1843 AAAATTATATATT
1 --AATTAT-TATT
1856 AATTA
1 AATTA
1861 AATTTAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 5 0.14
11 20 0.57
12 6 0.17
13 4 0.11
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (10 bp):
AATTATTATT
Found at i:3262 original size:21 final size:21
Alignment explanation
Indices: 3238--3289 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
3228 CGAGATGGTT
* *
3238 CTACCGATACATGTGACACTA
1 CTACCGATACAAGTCACACTA
* * *
3259 CTACCGAAACAAGTCATACTT
1 CTACCGATACAAGTCACACTA
3280 CTACCGATAC
1 CTACCGATAC
3290 TTAAAACTCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.31, G:0.12, T:0.23
Consensus pattern (21 bp):
CTACCGATACAAGTCACACTA
Found at i:4073 original size:24 final size:24
Alignment explanation
Indices: 4046--4176 Score: 217
Period size: 24 Copynumber: 5.5 Consensus size: 24
4036 TTTAGCTTAC
4046 ACGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
* *
4070 ACGAGCTCAGAATGGTTAGCTCTC
1 ACGAGCCCAGAATGGTTAGCTCTT
4094 ACGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
4118 ACGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
* * *
4142 ATGAGCCTAGAATGCTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
4166 ACGAGCCCAGA
1 ACGAGCCCAGA
4177 CAGAGTTTAA
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 98 1.00
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.24
Consensus pattern (24 bp):
ACGAGCCCAGAATGGTTAGCTCTT
Found at i:9695 original size:6 final size:6
Alignment explanation
Indices: 9684--9708 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9674 TGAAAGGGAG
9684 GCAGCT GCAGCT GCAGCT GCAGCT G
1 GCAGCT GCAGCT GCAGCT GCAGCT G
9709 GAGGAAGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (6 bp):
GCAGCT
Found at i:13014 original size:24 final size:24
Alignment explanation
Indices: 12987--13069 Score: 148
Period size: 24 Copynumber: 3.5 Consensus size: 24
12977 CAAAGGGAAG
*
12987 GAGCCAGGAAAGCCAGGAGCTGAA
1 GAGCCAGGAAAGCCAGGTGCTGAA
13011 GAGCCAGGAAAGCCAGGTGCTGAA
1 GAGCCAGGAAAGCCAGGTGCTGAA
*
13035 GAGCCAGGAAAACCAGGTGCTGAA
1 GAGCCAGGAAAGCCAGGTGCTGAA
13059 GAGCCAGGAAA
1 GAGCCAGGAAA
13070 ATTTGAAATA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.37, C:0.20, G:0.36, T:0.06
Consensus pattern (24 bp):
GAGCCAGGAAAGCCAGGTGCTGAA
Found at i:13844 original size:13 final size:13
Alignment explanation
Indices: 13822--13855 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
13812 TACTTAATCA
13822 TTCATTCATTAAT
1 TTCATTCATTAAT
*
13835 TTCGTTCATTAAT
1 TTCATTCATTAAT
13848 TTCATTCA
1 TTCATTCA
13856 GTGAGAGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.53
Consensus pattern (13 bp):
TTCATTCATTAAT
Found at i:14783 original size:2 final size:2
Alignment explanation
Indices: 14776--14803 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
14766 AAATAAATAA
14776 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14804 TTATTTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16144 original size:17 final size:19
Alignment explanation
Indices: 16103--16145 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
16093 TTAACTTGTC
16103 ATAATTT-TAATTATATAT
1 ATAATTTATAATTATATAT
*
16121 ATAATTTATAATTTTAT-T
1 ATAATTTATAATTATATAT
16139 AT-ATTTA
1 ATAATTTA
16146 AAAAAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 10 0.43
19 8 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATAATTTATAATTATATAT
Found at i:20413 original size:5 final size:5
Alignment explanation
Indices: 20403--20443 Score: 64
Period size: 5 Copynumber: 7.8 Consensus size: 5
20393 TTAGTGTCAT
20403 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAGA AGAAA CAGAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAA-A AGAAA -AGAA
20444 GCGTGAGCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 25 0.74
6 9 0.26
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:23589 original size:51 final size:52
Alignment explanation
Indices: 23523--23645 Score: 203
Period size: 52 Copynumber: 2.3 Consensus size: 52
23513 TTACTCTTTA
*
23523 AAATATAAAAAATATTTTTATATCAATATTTGTA-TTTTTTTATAATTAATTT
1 AAATA-AAAAAATATTTTTATATCAATATTTGTATTTTTTTTATAATTAATTC
23575 AAATAAAAAAATATTTTTATATCAATATTTGTATTTTTTTTATAATTAATTC
1 AAATAAAAAAATATTTTTATATCAATATTTGTATTTTTTTTATAATTAATTC
*
23627 AAATAAAATATATATTTTT
1 AAATAAAA-AAATATTTTT
23646 TCTTTAAATA
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 28 0.42
52 30 0.45
53 9 0.13
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (52 bp):
AAATAAAAAAATATTTTTATATCAATATTTGTATTTTTTTTATAATTAATTC
Found at i:29343 original size:4 final size:4
Alignment explanation
Indices: 29327--29356 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
29317 AAAAAATAAT
29327 TTAA TTCAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TT-AA TTAA TTAA TTAA TTAA TTAA T
29357 ATTTTGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:35522 original size:19 final size:19
Alignment explanation
Indices: 35462--35522 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
35452 AAACACTAGA
* *
35462 ATGCACTTCATGTGCCAGT
1 ATGCGCTTCATGCGCCAGT
** * *
35481 ATGCGCTTTGTGCGCTAGG
1 ATGCGCTTCATGCGCCAGT
*
35500 ATGCGCTTCATGCGCCAAT
1 ATGCGCTTCATGCGCCAGT
35519 ATGC
1 ATGC
35523 ACTTTATGTG
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (19 bp):
ATGCGCTTCATGCGCCAGT
Found at i:40810 original size:76 final size:71
Alignment explanation
Indices: 40657--40840 Score: 242
Period size: 76 Copynumber: 2.5 Consensus size: 71
40647 GTTCATCACT
*
40657 TGAAATATCTAAACCATGTATTTATCTTAATTTTATTTTCAAAACTTGATCAAATTTGCAGTTTT
1 TGAAA-ATCTAAACCATGTATTTATCTTAATTTTATTTTCAAAACTTGATCAAAATTGCAGTTTT
40722 CTACTTA
65 CTACTTA
* * * * * *
40729 CGAAAATCTTAACCATGTTTTCTTATCTTAATTTTATTTTCTAAACCTTATGGTCAAAATTGCTG
1 TGAAAATCTAAACCATG-TAT-TTATCTTAATTTTATTTTC-AAAAC-T-TGATCAAAATTGCAG
40794 TTTTCTACTTA
61 TTTTCTACTTA
*
40805 TGAAAATCTAAACCACGTATTTATCTTAATTTTATT
1 TGAAAATCTAAACCATGTATTTATCTTAATTTTATT
40841 CTCTTGAATT
Statistics
Matches: 96, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
71 11 0.11
72 6 0.06
73 19 0.20
74 20 0.21
75 3 0.03
76 37 0.39
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.46
Consensus pattern (71 bp):
TGAAAATCTAAACCATGTATTTATCTTAATTTTATTTTCAAAACTTGATCAAAATTGCAGTTTTC
TACTTA
Found at i:45898 original size:29 final size:27
Alignment explanation
Indices: 45844--45898 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
45834 TTTGGAATCG
*
45844 AGTCTCCTACTTTTATTCTAATAATTT
1 AGTCTCCTACTTTTATTCTAAAAATTT
45871 AGTCTCTCTACTTTTTAATT-TAAAAATT
1 AGTCTC-CTAC-TTTT-ATTCTAAAAATT
45899 CTTTCATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
28 4 0.17
29 11 0.46
30 3 0.12
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (27 bp):
AGTCTCCTACTTTTATTCTAAAAATTT
Found at i:66318 original size:35 final size:35
Alignment explanation
Indices: 66274--66369 Score: 183
Period size: 35 Copynumber: 2.7 Consensus size: 35
66264 AACCAACAAA
66274 ATTACATAGTATCAAAATACAATTTCGACTCTTCTG
1 ATTA-ATAGTATCAAAATACAATTTCGACTCTTCTG
66310 ATTAATAGTATCAAAATACAATTTCGACTCTTCTG
1 ATTAATAGTATCAAAATACAATTTCGACTCTTCTG
66345 ATTAATAGTATCAAAATACAATTTC
1 ATTAATAGTATCAAAATACAATTTC
66370 AAACCAGTCT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 56 0.93
36 4 0.07
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (35 bp):
ATTAATAGTATCAAAATACAATTTCGACTCTTCTG
Found at i:71314 original size:27 final size:28
Alignment explanation
Indices: 71283--71337 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
71273 GAGTCCCCCT
*
71283 CTATGTTTAGT-CAAATCGTATCCCAAA
1 CTATGTCTAGTCCAAATCGTATCCCAAA
*
71310 CTATGTCTAGTCCAAATCTTATCCCAAA
1 CTATGTCTAGTCCAAATCGTATCCCAAA
71338 TTAAGGTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (28 bp):
CTATGTCTAGTCCAAATCGTATCCCAAA
Found at i:72804 original size:25 final size:26
Alignment explanation
Indices: 72776--72839 Score: 62
Period size: 25 Copynumber: 2.5 Consensus size: 26
72766 TAGTTAATTT
72776 AATTAATTTCAATATTAT-AGTAACA
1 AATTAATTTCAATATTATAAGTAACA
* *
72801 AATTGA-TTC-ATATTATCAAGTAATA
1 AATTAATTTCAATATTAT-AAGTAACA
**
72826 AAAAAATTTCAATA
1 AATTAATTTCAATA
72840 ACTTATTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
23 7 0.23
24 3 0.10
25 14 0.47
26 3 0.10
27 3 0.10
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.38
Consensus pattern (26 bp):
AATTAATTTCAATATTATAAGTAACA
Found at i:73226 original size:18 final size:18
Alignment explanation
Indices: 73203--73240 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
73193 TAAACTTTAC
73203 AATTTGAATAACTCAAAT
1 AATTTGAATAACTCAAAT
*
73221 AATTTGAATAATTCAAAT
1 AATTTGAATAACTCAAAT
73239 AA
1 AA
73241 AAATTAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (18 bp):
AATTTGAATAACTCAAAT
Found at i:78536 original size:133 final size:135
Alignment explanation
Indices: 78295--78564 Score: 481
Period size: 133 Copynumber: 2.0 Consensus size: 135
78285 GCTAGAGACA
* *
78295 ATACGAACCCTATTTAAGAGTTTGATGATTCTAGACGAACAATATTTTGTAAATTTCTTTGGAAG
1 ATACGAACCCTATTTAAGAGTTT-ATGATTCTAGACGAACAATATTTTGTAAACTTCTTTGGAAA
78360 GAGTTAACCTTCCCTCAATAATATATTTTACTATCGTAAATAATTTAATATATTTTTAATATTTA
65 GAGTTAACCTTCCCTCAATAATATATTTTACTATCGTAAATAATTTAATATATTTTTAATATTTA
78425 TAATAT
130 TAATAT
*
78431 ATACGAACCCTATTTAAGAG-TT-TGATTCTAGACGAATAATATTTTGTAAACTTCTTTGGAAAG
1 ATACGAACCCTATTTAAGAGTTTATGATTCTAGACGAACAATATTTTGTAAACTTCTTTGGAAAG
*
78494 AGTTAACCTTCCCTCAATAATATATTTTACTATCGTACATAATTTAATATATTTTTAATATTTAT
66 AGTTAACCTTCCCTCAATAATATATTTTACTATCGTAAATAATTTAATATATTTTTAATATTTAT
78559 AATAT
131 AATAT
78564 A
1 A
78565 ATATATTATT
Statistics
Matches: 130, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
133 108 0.83
135 2 0.02
136 20 0.15
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (135 bp):
ATACGAACCCTATTTAAGAGTTTATGATTCTAGACGAACAATATTTTGTAAACTTCTTTGGAAAG
AGTTAACCTTCCCTCAATAATATATTTTACTATCGTAAATAATTTAATATATTTTTAATATTTAT
AATAT
Found at i:79156 original size:25 final size:25
Alignment explanation
Indices: 79122--79172 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
79112 GGGCCACAAC
79122 TTGGGGTTCAACTCATGCATGGCAT
1 TTGGGGTTCAACTCATGCATGGCAT
79147 TTGGGGTTCAACTCATGCATGGCAT
1 TTGGGGTTCAACTCATGCATGGCAT
79172 T
1 T
79173 AATACTACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (25 bp):
TTGGGGTTCAACTCATGCATGGCAT
Found at i:80115 original size:29 final size:30
Alignment explanation
Indices: 80075--80145 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
80065 AAATTATATC
80075 AAGGTTTTATTTAGATATAAATGAAAAG-CT
1 AAGG-TTTATTTAGATATAAATGAAAAGTCT
* *
80105 AAGGTTTATTT-GATATAATTTAAAAGTCT
1 AAGGTTTATTTAGATATAAATGAAAAGTCT
**
80134 AAGACTTATTTA
1 AAGGTTTATTTA
80146 AATGTAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 13 0.37
29 18 0.51
30 4 0.11
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.41
Consensus pattern (30 bp):
AAGGTTTATTTAGATATAAATGAAAAGTCT
Found at i:80119 original size:28 final size:31
Alignment explanation
Indices: 80075--80136 Score: 85
Period size: 28 Copynumber: 2.1 Consensus size: 31
80065 AAATTATATC
80075 AAGGTTTTATTTAGATATAAATGAAAAG-CT
1 AAGGTTTTATTTAGATATAAATGAAAAGTCT
* *
80105 AAGG-TTTATTT-GATATAATTTAAAAGTCT
1 AAGGTTTTATTTAGATATAAATGAAAAGTCT
80134 AAG
1 AAG
80137 ACTTATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 13 0.45
29 12 0.41
30 4 0.14
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (31 bp):
AAGGTTTTATTTAGATATAAATGAAAAGTCT
Found at i:83496 original size:16 final size:16
Alignment explanation
Indices: 83471--83504 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
83461 TTTAAAATAT
*
83471 ATATTTAATATATAAA
1 ATATTAAATATATAAA
*
83487 ATATTAAATATATCAA
1 ATATTAAATATATAAA
83503 AT
1 AT
83505 GAATTAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATTAAATATATAAA
Found at i:94219 original size:20 final size:22
Alignment explanation
Indices: 94180--94220 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
94170 GAAATGCAAG
*
94180 TTGAGTAAAAAATGGATTTAAC
1 TTGAGTAAAAAATAGATTTAAC
94202 TTGA-TAAAAAATAG-TTTAA
1 TTGAGTAAAAAATAGATTTAA
94221 AAATGGTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.49, C:0.02, G:0.15, T:0.34
Consensus pattern (22 bp):
TTGAGTAAAAAATAGATTTAAC
Found at i:95949 original size:3 final size:3
Alignment explanation
Indices: 95941--95968 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
95931 AAATCACAAT
95941 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
95969 AAGTATTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:109654 original size:17 final size:18
Alignment explanation
Indices: 109632--109671 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
109622 GATTTCATTT
109632 AAAATGAAAATTA-AAAA
1 AAAATGAAAATTATAAAA
* *
109649 AAAATGAATATTATGAAA
1 AAAATGAAAATTATAAAA
109667 AAAAT
1 AAAAT
109672 TTATCAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (18 bp):
AAAATGAAAATTATAAAA
Found at i:116870 original size:85 final size:85
Alignment explanation
Indices: 116727--116898 Score: 335
Period size: 85 Copynumber: 2.0 Consensus size: 85
116717 CACTTTTGGC
*
116727 ATCTAGAACTTGTCTTCCTCCAAAAACCTTCTAGGCACTTTCCCTTTCTGAATATAAATTGCATT
1 ATCTAAAACTTGTCTTCCTCCAAAAACCTTCTAGGCACTTTCCCTTTCTGAATATAAATTGCATT
116792 CTACAAAGATTAGTAGAAAT
66 CTACAAAGATTAGTAGAAAT
116812 ATCTAAAACTTGTCTTCCTCCAAAAACCTTCTAGGCACTTTCCCTTTCTGAATATAAATTGCATT
1 ATCTAAAACTTGTCTTCCTCCAAAAACCTTCTAGGCACTTTCCCTTTCTGAATATAAATTGCATT
116877 CTACAAAGATTAGTAGAAAT
66 CTACAAAGATTAGTAGAAAT
116897 AT
1 AT
116899 GACTATGGTG
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (85 bp):
ATCTAAAACTTGTCTTCCTCCAAAAACCTTCTAGGCACTTTCCCTTTCTGAATATAAATTGCATT
CTACAAAGATTAGTAGAAAT
Found at i:138857 original size:91 final size:90
Alignment explanation
Indices: 138698--138864 Score: 271
Period size: 91 Copynumber: 1.8 Consensus size: 90
138688 TTATGCCTCA
*
138698 TTAAACCCCTCAATTAGTCTTGAACAAATCAAACAAGACCATCACAAGAGACTCTTCATAAAAAT
1 TTAAACCCCTCAATTAATCTTGAACAAATCAAACAAGACCATCACAAGAGACTCTTCATAAAAAT
138763 CATTTGGTTTTCATCATGATCAGTC
66 CATTTGGTTTTCATCATGATCAGTC
* * ** *
138788 TTAATACCCCTTAATTAATCTTGAACAAATCAAATAAGGTCATCACAAGTGACTCTTCATAAAAA
1 TTAA-ACCCCTCAATTAATCTTGAACAAATCAAACAAGACCATCACAAGAGACTCTTCATAAAAA
138853 TCATTTGGTTTT
65 TCATTTGGTTTT
138865 ACCACGATTC
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 4 0.06
91 66 0.94
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.32
Consensus pattern (90 bp):
TTAAACCCCTCAATTAATCTTGAACAAATCAAACAAGACCATCACAAGAGACTCTTCATAAAAAT
CATTTGGTTTTCATCATGATCAGTC
Done.