Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006207.1 Kokia drynarioides strain JFW-HI SEQ_120777, 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: 236596
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:97 original size:31 final size:30
Alignment explanation
Indices: 54--116 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
44 TTAACGCGGG
* *
54 TGACTAAATGATAAAAGTATCTAACAATAA
1 TGACTAAATGATAAAAATATATAACAATAA
84 TGACTAAAATGATAAAAATATATAACAATAA
1 TGACT-AAATGATAAAAATATATAACAATAA
115 TG
1 TG
117 CTTATATTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 5 0.17
31 25 0.83
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.27
Consensus pattern (30 bp):
TGACTAAATGATAAAAATATATAACAATAA
Found at i:651 original size:32 final size:27
Alignment explanation
Indices: 592--644 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
582 AGTATTTTTG
592 TTGGTGGCTTATATGAGATCGTATGTA
1 TTGGTGGCTTATATGAGATCGTATGTA
619 TTGGTGGCTTATATGAGATCGTATGT
1 TTGGTGGCTTATATGAGATCGTATGT
645 TTTGTATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.21, C:0.08, G:0.30, T:0.42
Consensus pattern (27 bp):
TTGGTGGCTTATATGAGATCGTATGTA
Found at i:16964 original size:20 final size:20
Alignment explanation
Indices: 16926--16964 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16916 CAATCTACAT
* *
16926 TTAGTACAAGGTCTCTACGA
1 TTAGAACAAGGCCTCTACGA
*
16946 TTAGAACAAGGCCTGTACG
1 TTAGAACAAGGCCTCTACG
16965 GTACTTTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (20 bp):
TTAGAACAAGGCCTCTACGA
Found at i:17285 original size:28 final size:30
Alignment explanation
Indices: 17230--17288 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
17220 CATGATTCGA
17230 ACCACAATCAAATTTTATATGCATAATTAT
1 ACCACAATCAAATTTTATATGCATAATTAT
17260 ACCA-AATCAAATTTATATAT-CA-AATTAT
1 ACCACAATCAAATTT-TATATGCATAATTAT
17288 A
1 A
17289 TATTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 7 0.25
29 12 0.43
30 9 0.32
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (30 bp):
ACCACAATCAAATTTTATATGCATAATTAT
Found at i:17818 original size:25 final size:24
Alignment explanation
Indices: 17770--17819 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
17760 TTAAAAGTGC
* * *
17770 ATAAAAGATTTAAAATTTATAAAA
1 ATAAAACATTTAAAATTAAAAAAA
17794 ATAAAACACTTTAAAATTAAAAAAA
1 ATAAAACA-TTTAAAATTAAAAAAA
17819 A
1 A
17820 AATTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (24 bp):
ATAAAACATTTAAAATTAAAAAAA
Found at i:18616 original size:23 final size:22
Alignment explanation
Indices: 18573--18617 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
18563 TTTCTTCAGT
*
18573 TATTAAAAACAATGCATTTTTA
1 TATTAAAAACAATACATTTTTA
* *
18595 TATTAAAAATATTACATCTTTTA
1 TATTAAAAACAATACAT-TTTTA
18618 ATATATATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (22 bp):
TATTAAAAACAATACATTTTTA
Found at i:21926 original size:16 final size:18
Alignment explanation
Indices: 21905--21938 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
21895 TAAGTAATGG
21905 TTCTTT-TTTT-TTTTTC
1 TTCTTTATTTTGTTTTTC
21921 TTCTTTATTTTGTTTTTC
1 TTCTTTATTTTGTTTTTC
21939 CATTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (18 bp):
TTCTTTATTTTGTTTTTC
Found at i:29081 original size:89 final size:89
Alignment explanation
Indices: 28930--29109 Score: 315
Period size: 89 Copynumber: 2.0 Consensus size: 89
28920 CACTGCTGCT
* *
28930 TTGGTATTTCTGACTCATGCAAAATGTCATACATGGAAGTCCTGCATGAAGCAAATTACTACAAA
1 TTGGTATTTCTGACTCATGCAAAATATCATACATAGAAGTCCTGCATGAAGCAAATTACTACAAA
* *
28995 AAATGACGAGCTTTAATCCCAAGG
66 AAATGACAAGCTTTAACCCCAAGG
*
29019 TTGGTATTTCTGACTCATGCAAAATATCATGCATAGAAGTCCTGCATGAAGCAAATTACTACAAA
1 TTGGTATTTCTGACTCATGCAAAATATCATACATAGAAGTCCTGCATGAAGCAAATTACTACAAA
29084 AAATGACAAGCTTTAACCCCAAGG
66 AAATGACAAGCTTTAACCCCAAGG
29108 TT
1 TT
29110 TCTGTTTCCG
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (89 bp):
TTGGTATTTCTGACTCATGCAAAATATCATACATAGAAGTCCTGCATGAAGCAAATTACTACAAA
AAATGACAAGCTTTAACCCCAAGG
Found at i:30681 original size:61 final size:61
Alignment explanation
Indices: 30529--30687 Score: 189
Period size: 61 Copynumber: 2.6 Consensus size: 61
30519 ATTTGGGACC
* * * *
30529 TGAACTTGGCAACTATTTTCACATTGGGGCCTGAA--TTTTTTTTGGTCCAAATTAAGCCT
1 TGAACTTGGCAATTGTTCTCACATTGGGGCTTGAACTTTTTTTTTGGTCCAAATTAAGCCT
** * * * *
30588 TGAACTTGGCAATTGTTCTCGTACTGGAGCTTGAACTTTTTTTTTTGTCCAAGTT-AGTCCT
1 TGAACTTGGCAATTGTTCTCACATTGGGGCTTGAACTTTTTTTTTGGTCCAAATTAAG-CCT
*
30649 TGAACTTGGCAATTGTTCCCACATTGGGGCTTGAACTTT
1 TGAACTTGGCAATTGTTCTCACATTGGGGCTTGAACTTT
30688 GGACCCCAAT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
59 27 0.33
60 2 0.02
61 53 0.65
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (61 bp):
TGAACTTGGCAATTGTTCTCACATTGGGGCTTGAACTTTTTTTTTGGTCCAAATTAAGCCT
Found at i:33019 original size:21 final size:19
Alignment explanation
Indices: 32995--33033 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
32985 ACCCGTTTTA
32995 TATGTTTATAGTATAATATAT
1 TATG-TTATA-TATAATATAT
*
33016 TATGTTATATATATTATA
1 TATGTTATATATAATATA
33034 ATTTATAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 5 0.29
21 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
TATGTTATATATAATATAT
Found at i:36443 original size:29 final size:28
Alignment explanation
Indices: 36411--36478 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 28
36401 ATTGAATTTG
*
36411 AATTTTAAAATATTAAAAATAGAGAGATT-
1 AATTTTAAAA-A-TAAAAATAGAAAGATTA
*
36440 AATTTTATGAAAATAAAAATATAAAGATTA
1 AATTTTA--AAAATAAAAATAGAAAGATTA
36470 AATTTTAAA
1 AATTTTAAA
36479 TCTGTGAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
28 2 0.06
29 21 0.62
30 8 0.24
31 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (28 bp):
AATTTTAAAAATAAAAATAGAAAGATTA
Found at i:38216 original size:3 final size:3
Alignment explanation
Indices: 38208--38240 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
38198 AGAATTACAC
38208 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
38241 ACCAACTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:43460 original size:12 final size:12
Alignment explanation
Indices: 43443--43470 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
43433 TGGTCACTAT
43443 CTACTCAACTCA
1 CTACTCAACTCA
43455 CTACTCAACTCA
1 CTACTCAACTCA
43467 CTAC
1 CTAC
43471 CTCCAAGGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.43, G:0.00, T:0.25
Consensus pattern (12 bp):
CTACTCAACTCA
Found at i:53168 original size:22 final size:21
Alignment explanation
Indices: 53138--53199 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 21
53128 TTTTTGCAAA
*
53138 TTTAAAATTTAAAATTTATTT
1 TTTATAATTTAAAATTTATTT
**
53159 TTTAGTAATTTAATTCTTTTATTT
1 TTTA-TAATTTAA--AATTTATTT
*
53183 TTTATATTTTAAAATTT
1 TTTATAATTTAAAATTT
53200 GAATTCAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
21 7 0.22
22 7 0.22
23 7 0.22
24 11 0.34
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTATAATTTAAAATTTATTT
Found at i:63728 original size:17 final size:17
Alignment explanation
Indices: 63690--63728 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
63680 CAATCAATCC
63690 CTTTAAATAATTTTTTT
1 CTTTAAATAATTTTTTT
*
63707 TTTTAAAT-ATTTTGTTT
1 CTTTAAATAATTTT-TTT
63724 CTTTA
1 CTTTA
63729 TCATGTTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (17 bp):
CTTTAAATAATTTTTTT
Found at i:64195 original size:6 final size:6
Alignment explanation
Indices: 64148--64222 Score: 59
Period size: 6 Copynumber: 13.0 Consensus size: 6
64138 CATTATTTAT
* * * *
64148 TTTAAA TTTATAA --TAAT TTTAAA TTCAAA CTTAAA -ATAAA TTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
64194 TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
64223 ACAAATTTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
4 1 0.02
5 10 0.19
6 41 0.76
7 2 0.04
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:64210 original size:17 final size:17
Alignment explanation
Indices: 64190--64246 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
64180 AAAATAAATT
64190 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
64207 TAAATCTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
64224 CAAATTT-AATATTAAAA
1 TAAATTTAAAT-TTAAAA
64241 TAAATT
1 TAAATT
64247 GAAAAGGGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 3 0.09
17 32 0.91
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:64219 original size:23 final size:23
Alignment explanation
Indices: 64148--64222 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 23
64138 CATTATTTAT
* *
64148 TTTAAATTTATAATAATTTTAAA
1 TTTAAATTTAAAATAAATTTAAA
* *
64171 TTCAAACTTAAAATAAATTTAAA
1 TTTAAATTTAAAATAAATTTAAA
*
64194 TTTAAATTTAAAATAAATCTAAA
1 TTTAAATTTAAAATAAATTTAAA
64217 TTTAAA
1 TTTAAA
64223 ACAAATTTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTAAATTTAAAATAAATTTAAA
Found at i:64943 original size:27 final size:27
Alignment explanation
Indices: 64885--64942 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
64875 TATACAAATA
*
64885 TAAATTTTTAAAACATAATAATTTTTT
1 TAAAATTTTAAAACATAATAATTTTTT
*
64912 TAAAATTTTAAAACATAA-CATTTTTT
1 TAAAATTTTAAAACATAATAATTTTTT
64938 TAAAA
1 TAAAA
64943 AATTAAGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (27 bp):
TAAAATTTTAAAACATAATAATTTTTT
Found at i:64948 original size:26 final size:27
Alignment explanation
Indices: 64892--64948 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
64882 ATATAAATTT
**
64892 TTAAAACATAATAATTTTTTTAAAATT
1 TTAAAACATAATAATTTTTTTAAAAAA
*
64919 TTAAAACATAA-CATTTTTTTAAAAAA
1 TTAAAACATAATAATTTTTTTAAAAAA
64945 TTAA
1 TTAA
64949 GATTACTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (27 bp):
TTAAAACATAATAATTTTTTTAAAAAA
Found at i:65266 original size:19 final size:20
Alignment explanation
Indices: 65236--65277 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
65226 TTACTTTTAC
*
65236 ATATTGTATATAAAATAATT
1 ATATTGTATATAAAATAAAT
*
65256 ATATT-TATATAATATAAAT
1 ATATTGTATATAAAATAAAT
65275 ATA
1 ATA
65278 AATATATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATATTGTATATAAAATAAAT
Found at i:65283 original size:19 final size:19
Alignment explanation
Indices: 65242--65284 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
65232 TTACATATTG
* **
65242 TATATAAAATAATTATATT
1 TATATAAAATAAATATAAA
*
65261 TATATAATATAAATATAAA
1 TATATAAAATAAATATAAA
65280 TATAT
1 TATAT
65285 TTATTTATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TATATAAAATAAATATAAA
Found at i:67086 original size:116 final size:113
Alignment explanation
Indices: 66911--67132 Score: 288
Period size: 116 Copynumber: 1.9 Consensus size: 113
66901 GGAGATAGCT
* * * *
66911 AAAATACAATTTTATCATTAGAGTAACACAAATTTTATAATTTTTCAATGAATTAAACTACA-AA
1 AAAATACAATGTTATCATTAGAGCAACACAAATTTTAAAATTTCTCAATGAATTAAACTACATAA
*
66975 CTTTTCACTTTTG-AAGGGATCAAAATTAAATTTTAAATTTTAAGAAGAG
66 -TTTTCACTTTTGAAAAGG-TCAAAATTAAATTTTAAATTTTAAGAAGAG
* *
67024 AAAATACAATGTTATCATT-GTAGCAACGCAAATTTTACGAAAATTTCTCAATGAATTAAACTAT
1 AAAATACAATGTTATCATTAG-AGCAACACAAATTTT---AAAATTTCTCAATGAATTAAACTAC
* *
67088 ATAATTTTCATTTTTGAAAAGGTCAAAATTAAATTTTAGATTTTA
62 ATAATTTTCACTTTTGAAAAGGTCAAAATTAAATTTTAAATTTTA
67133 GACAAACTAA
Statistics
Matches: 94, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
112 1 0.01
113 31 0.33
116 56 0.60
117 6 0.06
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (113 bp):
AAAATACAATGTTATCATTAGAGCAACACAAATTTTAAAATTTCTCAATGAATTAAACTACATAA
TTTTCACTTTTGAAAAGGTCAAAATTAAATTTTAAATTTTAAGAAGAG
Found at i:70244 original size:7 final size:7
Alignment explanation
Indices: 70227--70255 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
70217 TGCTGTTGTG
70227 TTTTC-T
1 TTTTCTT
70233 TTTTCTT
1 TTTTCTT
70240 TTTTCTT
1 TTTTCTT
70247 TTTTCTT
1 TTTTCTT
70254 TT
1 TT
70256 AAAGAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.23
7 17 0.77
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTCTT
Found at i:81989 original size:18 final size:18
Alignment explanation
Indices: 81900--81994 Score: 52
Period size: 18 Copynumber: 5.1 Consensus size: 18
81890 TGTTTTGTTT
*
81900 TGTTTTTA-TAAATAACA
1 TGTTTTTATTAAATAAAA
**
81917 -GTTTTTATTAAAATTTAA
1 TGTTTTTATT-AAATAAAA
*
81935 TATTATTCTAATT-AATAAATA
1 TGTT-TT-T-ATTAAATAAA-A
*
81956 TTTTATTTACTTAAATAAAA
1 TGTT-TTTA-TTAAATAAAA
*
81976 TGTTTTTATTAAATTAAA
1 TGTTTTTATTAAATAAAA
81994 T
1 T
81995 TTAAGTTAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
16 7 0.12
17 1 0.02
18 15 0.25
19 7 0.12
20 13 0.22
21 14 0.23
22 3 0.05
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (18 bp):
TGTTTTTATTAAATAAAA
Found at i:87756 original size:19 final size:19
Alignment explanation
Indices: 87728--87769 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
87718 TTCCTCCGGC
87728 TCTT-CTTCTTCTTCCTCG
1 TCTTGCTTCTTCTTCCTCG
*
87746 TCTTGCTTCTTCTTCCTCT
1 TCTTGCTTCTTCTTCCTCG
87765 TCTTG
1 TCTTG
87770 GATTCCGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.00, C:0.36, G:0.07, T:0.57
Consensus pattern (19 bp):
TCTTGCTTCTTCTTCCTCG
Found at i:90248 original size:20 final size:18
Alignment explanation
Indices: 90213--90252 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 18
90203 ACTCAATTAC
90213 AAAATATTTAATTAATTT
1 AAAATATTTAATTAATTT
90231 AAAATAATTTATATTAATTT
1 AAAAT-ATTTA-ATTAATTT
90251 AA
1 AA
90253 TTAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.25
19 5 0.25
20 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATATTTAATTAATTT
Found at i:137009 original size:63 final size:63
Alignment explanation
Indices: 136910--137035 Score: 225
Period size: 63 Copynumber: 2.0 Consensus size: 63
136900 AATACCCAAA
* *
136910 ATATTCCTTACCATCTCCTTTGCGACAAGCATAGACGATGGTAGTTGGTTTAGTCCTTGGATT
1 ATATTCCTTACCATCTCCTTGGCGACAAGCATAGACGATGGTAGTTGGTTTAGTACTTGGATT
*
136973 ATATTCCTTACCATCTCCTTGGCGACGAGCATAGACGATGGTAGTTGGTTTAGTACTTGGATT
1 ATATTCCTTACCATCTCCTTGGCGACAAGCATAGACGATGGTAGTTGGTTTAGTACTTGGATT
137036 CTTTTCAACA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (63 bp):
ATATTCCTTACCATCTCCTTGGCGACAAGCATAGACGATGGTAGTTGGTTTAGTACTTGGATT
Found at i:137778 original size:21 final size:21
Alignment explanation
Indices: 137737--137781 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
137727 AATATTGAGG
* *
137737 ATTAAGTTTTATATAATTATA
1 ATTAAGTTTGATAAAATTATA
137758 ATTAA-TTTGATAAAATATATA
1 ATTAAGTTTGATAAAAT-TATA
137779 ATT
1 ATT
137782 CTTTTGTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
ATTAAGTTTGATAAAATTATA
Found at i:140441 original size:14 final size:13
Alignment explanation
Indices: 140424--140484 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
140414 TTTTTATAAA
140424 TTTAAATTTAAATT
1 TTTAAATTT-AATT
* *
140438 TTTATATTTTATT
1 TTTAAATTTAATT
*
140451 TTTAAGAATTTATTT
1 TTT-A-AATTTAATT
* *
140466 TTTAATTTTTATT
1 TTTAAATTTAATT
140479 TTTAAA
1 TTTAAA
140485 AATTTAGTCT
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
13 17 0.47
14 10 0.28
15 9 0.25
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (13 bp):
TTTAAATTTAATT
Found at i:140461 original size:35 final size:34
Alignment explanation
Indices: 140414--140482 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
140404 AGTTTTTATT
140414 TTTTTATAAATTTAAATTTAAATTTTTATATTTTA
1 TTTTTATAAATTTAAATTTAAATTTTTAT-TTTTA
** *
140449 TTTTTA-AGAATTTATTTTTTAATTTTTATTTTTA
1 TTTTTATA-AATTTAAATTTAAATTTTTATTTTTA
140483 AAAATTTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
34 6 0.20
35 24 0.80
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (34 bp):
TTTTTATAAATTTAAATTTAAATTTTTATTTTTA
Found at i:140476 original size:28 final size:28
Alignment explanation
Indices: 140427--140490 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
140417 TTATAAATTT
*
140427 AAATTTAAATTTTTATATTTTATTTTTAA
1 AAATTT-ATTTTTTATATTTTATTTTTAA
*
140456 GAATTTATTTTTTA-ATTTTTATTTTTAA
1 AAATTTATTTTTTATA-TTTTATTTTTAA
140484 AAATTTA
1 AAATTTA
140491 GTCTATTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 1 0.03
28 25 0.81
29 5 0.16
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
AAATTTATTTTTTATATTTTATTTTTAA
Found at i:140490 original size:14 final size:14
Alignment explanation
Indices: 140445--140490 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
140435 ATTTTTATAT
*
140445 TTTATTTTTAAGAA
1 TTTATTTTTAAAAA
* **
140459 TTTATTTTTTAATT
1 TTTATTTTTAAAAA
140473 TTTATTTTTAAAAA
1 TTTATTTTTAAAAA
140487 TTTA
1 TTTA
140491 GTCTATTTAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
TTTATTTTTAAAAA
Found at i:141997 original size:7 final size:7
Alignment explanation
Indices: 141975--142009 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
141965 CCAAATATGA
141975 TTTTAA-
1 TTTTAAT
141981 TTTTAAT
1 TTTTAAT
*
141988 TTTTAGT
1 TTTTAAT
141995 TTTTAAT
1 TTTTAAT
142002 TTTTAAT
1 TTTTAAT
142009 T
1 T
142010 ATGTTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (7 bp):
TTTTAAT
Found at i:143840 original size:20 final size:20
Alignment explanation
Indices: 143817--143855 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
143807 ATTAATATAA
* * *
143817 TGTTAGAAATTTTTATATGG
1 TGTTAAAAAATTTGATATGG
143837 TGTTAAAAAATTTGATATG
1 TGTTAAAAAATTTGATATG
143856 TTTTTCTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (20 bp):
TGTTAAAAAATTTGATATGG
Found at i:153962 original size:25 final size:24
Alignment explanation
Indices: 153934--153989 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
153924 AAATATCTGT
* *
153934 AATTATTCCAAGCATGTCTTTATAA
1 AATTATT-CAAGCATGTATTCATAA
* *
153959 AATTAATTTAAGTATGTATTCATAA
1 AATT-ATTCAAGCATGTATTCATAA
153984 AATTAT
1 AATTAT
153990 CATTAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 2 0.08
25 21 0.81
26 3 0.12
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (24 bp):
AATTATTCAAGCATGTATTCATAA
Found at i:155425 original size:2 final size:2
Alignment explanation
Indices: 155418--155444 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
155408 TTATGCTGTT
155418 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 T
155445 GCACTAACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:160935 original size:16 final size:16
Alignment explanation
Indices: 160916--160947 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
160906 AACTTATAAT
*
160916 AAATTTATTAAAAAAA
1 AAATTTAATAAAAAAA
160932 AAATTTAATAAAAAAA
1 AAATTTAATAAAAAAA
160948 TTCGATAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATTTAATAAAAAAA
Found at i:173207 original size:18 final size:19
Alignment explanation
Indices: 173170--173207 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
173160 AAATTTATAA
* *
173170 TTAATGATAGCAATATTAT
1 TTAATAATAGCAAAATTAT
173189 TTAATAATA-CAAAATTAT
1 TTAATAATAGCAAAATTAT
173207 T
1 T
173208 CATAACTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (19 bp):
TTAATAATAGCAAAATTAT
Found at i:178712 original size:23 final size:23
Alignment explanation
Indices: 178686--178739 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
178676 AATTTAGAAT
*
178686 TTAATATTTTTTA-TTTTTAAAAA
1 TTAA-ATTTTTTACTTTCTAAAAA
**
178709 TTAAATTTTTTACTTTCTAAATT
1 TTAAATTTTTTACTTTCTAAAAA
178732 TTAAATTT
1 TTAAATTT
178740 CAAGTCAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (23 bp):
TTAAATTTTTTACTTTCTAAAAA
Found at i:191081 original size:15 final size:15
Alignment explanation
Indices: 191061--191116 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
191051 CATAAATTAC
191061 AAAAATAATTATAAA
1 AAAAATAATTATAAA
*
191076 AAAAATACTGATATTAAA
1 AAAAATAAT--TA-TAAA
191094 AATAAATAA-TATAAA
1 AA-AAATAATTATAAA
191109 AAACAATA
1 AAA-AATA
191117 CTGATGTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 1 0.03
15 18 0.53
16 2 0.06
17 2 0.06
18 6 0.18
19 5 0.15
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (15 bp):
AAAAATAATTATAAA
Found at i:192511 original size:6 final size:6
Alignment explanation
Indices: 192500--192524 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
192490 GTGCATCCAA
192500 TCCCAC TCCCAC TCCCAC TCCCAC T
1 TCCCAC TCCCAC TCCCAC TCCCAC T
192525 TAACTTTTAT
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:0.64, G:0.00, T:0.20
Consensus pattern (6 bp):
TCCCAC
Found at i:193572 original size:2 final size:2
Alignment explanation
Indices: 193565--193598 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
193555 CTCTAGGCTG
193565 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
193599 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:193603 original size:2 final size:2
Alignment explanation
Indices: 193598--193633 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
193588 ATATATATAT
193598 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
193634 GGGGAGTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:195202 original size:41 final size:41
Alignment explanation
Indices: 195110--195193 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 41
195100 ATAGCTTATT
* * * * *
195110 ACAGACCATGTGTCTCAAAACAATATACACACGCCCATGTC
1 ACAGCCCATGTGCCCCAAAACAATATACACACACCCATGAC
*
195151 TCAGCCCATGTGCCCCAAAACAATATACACACACCC-TGAC
1 ACAGCCCATGTGCCCCAAAACAATATACACACACCCATGAC
195191 ACA
1 ACA
195194 CACTCATGTC
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 5 0.14
41 31 0.86
ACGTcount: A:0.37, C:0.36, G:0.11, T:0.17
Consensus pattern (41 bp):
ACAGCCCATGTGCCCCAAAACAATATACACACACCCATGAC
Found at i:195216 original size:53 final size:53
Alignment explanation
Indices: 195136--195247 Score: 152
Period size: 53 Copynumber: 2.1 Consensus size: 53
195126 AAAACAATAT
*
195136 ACACACGCCCATGTCTCAGCCCATGTGCCCCAAAACAATATACACACACCCTG
1 ACACACACCCATGTCTCAGCCCATGTGCCCCAAAACAATATACACACACCCTG
* ** * * * *
195189 ACACACACTCATGTCTCAGCCTGTGTGCCCTAAAATATTATACACACACCTTG
1 ACACACACCCATGTCTCAGCCCATGTGCCCCAAAACAATATACACACACCCTG
195242 ACACAC
1 ACACAC
195248 GTTTGTATGC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.32, C:0.38, G:0.11, T:0.20
Consensus pattern (53 bp):
ACACACACCCATGTCTCAGCCCATGTGCCCCAAAACAATATACACACACCCTG
Found at i:195302 original size:31 final size:31
Alignment explanation
Indices: 195264--195364 Score: 121
Period size: 31 Copynumber: 3.3 Consensus size: 31
195254 ATGCCAAATA
195264 GTGTGCCTCCAAACAGTATACACACACGCCC
1 GTGTGCCTCCAAACAGTATACACACACGCCC
* * ***
195295 GTATGCCTCCAAACAGTATACGCACACGTTT
1 GTGTGCCTCCAAACAGTATACACACACGCCC
* * **
195326 TTGTGCCTCCAAATAGTATACACACGGGCCC
1 GTGTGCCTCCAAACAGTATACACACACGCCC
195357 GTGTGCCT
1 GTGTGCCT
195365 TCGAAAAGCA
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.23
Consensus pattern (31 bp):
GTGTGCCTCCAAACAGTATACACACACGCCC
Found at i:196200 original size:33 final size:36
Alignment explanation
Indices: 196163--196228 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 36
196153 TATTTACGTG
* *
196163 AAATTGAAGAGAAA-GAGAAGAA-AG-ACAAGGATC
1 AAATTGAAGACAAAGGAAAAGAATAGAACAAGGATC
196196 AAATTGAAGACAAAGGAAAAGAATAGAACAAGG
1 AAATTGAAGACAAAGGAAAAGAATAGAACAAGG
196229 GGTAAAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 13 0.46
34 7 0.25
35 2 0.07
36 6 0.21
ACGTcount: A:0.59, C:0.06, G:0.26, T:0.09
Consensus pattern (36 bp):
AAATTGAAGACAAAGGAAAAGAATAGAACAAGGATC
Found at i:197112 original size:23 final size:23
Alignment explanation
Indices: 197067--197192 Score: 80
Period size: 23 Copynumber: 5.4 Consensus size: 23
197057 ACGCTAGCGC
*
197067 GCTTACTGTTTCGCA-CTCCGTGT
1 GCTTACTGTTTCGCACCT-TGTGT
197090 GCTTACTGTTTCGCACCTTGTGT
1 GCTTACTGTTTCGCACCTTGTGT
* * * * *
197113 GCCTACTGATT-GC-GCTAAGTGC
1 GCTTACTGTTTCGCACCT-TGTGT
* * * *
197135 GCCTGCTGATT-GCACCGTGTGT
1 GCTTACTGTTTCGCACCTTGTGT
*
197157 GCTTACTGTTTCCCCAGCACTTGTGT
1 GCTTACTGTTT-CGCA-C-CTTGTGT
197183 GCTTACTGTT
1 GCTTACTGTT
197193 AAGTACTTGG
Statistics
Matches: 80, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
21 2 0.03
22 28 0.35
23 29 0.36
24 4 0.05
25 1 0.01
26 16 0.20
ACGTcount: A:0.11, C:0.28, G:0.24, T:0.37
Consensus pattern (23 bp):
GCTTACTGTTTCGCACCTTGTGT
Found at i:200168 original size:15 final size:15
Alignment explanation
Indices: 200148--200204 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
200138 ACACTACAAA
200148 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
200163 ATATTTATAACTATAAT
1 ATATTTATTA-T-TAAT
*
200180 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
200197 ATATTTAT
1 ATATTTAT
200205 ATTGTATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
15 17 0.49
16 1 0.03
17 7 0.20
18 1 0.03
19 9 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:201194 original size:12 final size:11
Alignment explanation
Indices: 201172--201201 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
201162 TTTGTGTACT
201172 TATTTTATTTA
1 TATTTTATTTA
201183 TATTTATATTTA
1 TATTT-TATTTA
201195 TATTTTA
1 TATTTTA
201202 ATTAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTTTATTTA
Found at i:216203 original size:63 final size:63
Alignment explanation
Indices: 216126--216263 Score: 240
Period size: 63 Copynumber: 2.2 Consensus size: 63
216116 CAAAATTCTA
* * *
216126 ATAATAATAAAATTAATGTAACTAATATAATTCAAATCTAAATTACATATGAAATTAACATCT
1 ATAATATTTAAATTAATATAACTAATATAATTCAAATCTAAATTACATATGAAATTAACATCT
*
216189 ATAATATTTAAATTAATATGACTAATATAATTCAAATCTAAATTACATATGAAATTAACATCT
1 ATAATATTTAAATTAATATAACTAATATAATTCAAATCTAAATTACATATGAAATTAACATCT
216252 ATAATATTTAAA
1 ATAATATTTAAA
216264 ACACTAAGTC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (63 bp):
ATAATATTTAAATTAATATAACTAATATAATTCAAATCTAAATTACATATGAAATTAACATCT
Found at i:223215 original size:12 final size:12
Alignment explanation
Indices: 223198--223223 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
223188 TTAAAGATAT
223198 AATAAAATATTA
1 AATAAAATATTA
223210 AATAAAATATTA
1 AATAAAATATTA
223222 AA
1 AA
223224 AGAAACACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAAAATATTA
Found at i:229755 original size:25 final size:25
Alignment explanation
Indices: 229708--229756 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
229698 TCCTAAATAG
* * *
229708 ATGTCCAAACTGTTGTCCCAACAAT
1 ATGTCCAAACAGATGTCCAAACAAT
*
229733 ATGTCCAAACAGATGTTCAAACAA
1 ATGTCCAAACAGATGTCCAAACAA
229757 GGCATAAAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (25 bp):
ATGTCCAAACAGATGTCCAAACAAT
Found at i:230043 original size:18 final size:18
Alignment explanation
Indices: 230020--230085 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
230010 ATTCTTCAGG
230020 TTATTGCTCAAAATGAGC
1 TTATTGCTCAAAATGAGC
** *
230038 TTATTGCTTCTAAGGTTGTGAGG
1 TTATTGC-TC-AA---AATGAGC
230061 TTATTGCTCAAAATGAGC
1 TTATTGCTCAAAATGAGC
230079 TTATTGC
1 TTATTGC
230086 GTCTAAGGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
18 18 0.49
19 2 0.05
20 2 0.05
21 2 0.05
22 2 0.05
23 11 0.30
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (18 bp):
TTATTGCTCAAAATGAGC
Found at i:230063 original size:41 final size:41
Alignment explanation
Indices: 230017--230098 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
230007 CGAATTCTTC
*
230017 AGGTTATTGCTCAAAATGAGCTTATTGCTTCTAAGGTTGTG
1 AGGTTATTGCTCAAAATGAGCTTATTGCGTCTAAGGTTGTG
230058 AGGTTATTGCTCAAAATGAGCTTATTGCGTCTAAGGTTGTG
1 AGGTTATTGCTCAAAATGAGCTTATTGCGTCTAAGGTTGTG
230099 CTTGAGAGTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (41 bp):
AGGTTATTGCTCAAAATGAGCTTATTGCGTCTAAGGTTGTG
Found at i:234684 original size:31 final size:31
Alignment explanation
Indices: 234641--234700 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
234631 AAATTTAGGT
*
234641 TCTAATATAGGAACAATTATCAAGTTCAAGC
1 TCTAATACAGGAACAATTATCAAGTTCAAGC
*
234672 TCTAATACAGGAACAATTGTCAAGTTCAA
1 TCTAATACAGGAACAATTATCAAGTTCAA
234701 ACCTCGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (31 bp):
TCTAATACAGGAACAATTATCAAGTTCAAGC
Found at i:236567 original size:2 final size:2
Alignment explanation
Indices: 236560--236596 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
236550 TTGGCATTAG
236560 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.