Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000363.1 Kokia drynarioides strain JFW-HI SEQ_111149, 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: 46467
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 124 characters in sequence are not A, C, G, or T
Found at i:8367 original size:50 final size:49
Alignment explanation
Indices: 8247--8371 Score: 119
Period size: 50 Copynumber: 2.5 Consensus size: 49
8237 GAACCGAAGA
* * * * *
8247 ACCATAAAGATATGAAGGGAAAAGTTGAGGTCGCAACGGCAAACTCGGT
1 ACCATGAAGATATGAAGGGAAAGGTTGAGGTCGAAACAGCAAACTCAGT
* * * * *
8296 ACCTTAGAAGATGTG-ATGGAAAGGATTGAGGTCGAAACATCGAA-TCTAGT
1 ACCAT-GAAGATATGAAGGGAAAGG-TTGAGGTCGAAACAGCAAACTC-AGT
8346 ACCATGAAGATATGAAGGGAAAGGTT
1 ACCATGAAGATATGAAGGGAAAGGTT
8372 AAGGCCGCAA
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
49 23 0.39
50 36 0.61
ACGTcount: A:0.38, C:0.13, G:0.29, T:0.20
Consensus pattern (49 bp):
ACCATGAAGATATGAAGGGAAAGGTTGAGGTCGAAACAGCAAACTCAGT
Found at i:8505 original size:99 final size:98
Alignment explanation
Indices: 8253--8510 Score: 272
Period size: 99 Copynumber: 2.6 Consensus size: 98
8243 AAGAACCATA
* * *
8253 AAGATATGAAGGGAAAAGTTGAGGTCGCAACGGCAAACTCGGTACCTTAGAAGATGTGAT-GGAA
1 AAGATATGAAGGGAAAA-TTGAGGCCGCAACGGCAAAC-CTGTACCTTAGAAGATGTGATAAGAA
* * *
8317 AGGATTGAGGTCGAAACATCGAATCTAGTACCATG
64 AGGATTAAGGCCGAAACATCGAATCTAGTACAATG
* * ** * *
8352 AAGATATGAAGGGAAAGGTTAAGGCCGCAACGATAAACCCTGTATCTTAAAAGATGTGATAAG-A
1 AAGATATGAAGGGAAA-ATTGAGGCCGCAACGGCAAA-CCTGTACCTTAGAAGATGTGATAAGAA
* * *
8416 AGGATTAAGGCCGTAACGA-CGAATCTGGTATAATG
64 AGGATTAAGGCCGAAAC-ATCGAATCTAGTACAATG
* *
8451 AAGATATGAAGGGAAATATTGAGGCCGAAACGGCAAACCTAATACCTTAGAAGAT-TGATA
1 AAGATATGAAGGGAAA-ATTGAGGCCGCAACGGCAAACCT-GTACCTTAGAAGATGTGATA
8511 TCGTAACGGT
Statistics
Matches: 130, Mismatches: 24, Indels: 11
0.79 0.15 0.07
Matches are distributed among these distances:
98 8 0.06
99 119 0.92
100 3 0.02
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.21
Consensus pattern (98 bp):
AAGATATGAAGGGAAAATTGAGGCCGCAACGGCAAACCTGTACCTTAGAAGATGTGATAAGAAAG
GATTAAGGCCGAAACATCGAATCTAGTACAATG
Found at i:8673 original size:99 final size:98
Alignment explanation
Indices: 8537--8716 Score: 245
Period size: 99 Copynumber: 1.8 Consensus size: 98
8527 GATACCAAGA
* * * * *
8537 AGATATGAAGGGAAAGGTTGATGCCGTAACGGTGAACC-CAGTACCTTAAAAGATATGATGGGAA
1 AGATATGAAGGGAAAGGTTGAAGCCGTAACGGCGAACCTCA-TACCAT-AAAGATATAAAGGGAA
8601 AGATTAAGGCCGCAACGGCGAATCTTGTACTATTG
64 AGATTAAGGCCGCAACGGCGAATCTTGTACTATTG
* * * *
8636 AGATATGGAGGGAAATGTTGAAGCCGTAACGGCGAACCTTATACCATAGAGATATAAAGGGAAAG
1 AGATATGAAGGGAAAGGTTGAAGCCGTAACGGCGAACCTCATACCATAAAGATATAAAGGGAAAG
*
8701 ATTAAGGCCGTAACGG
66 ATTAAGGCCGCAACGG
8717 TGGATCTCAT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
98 30 0.43
99 39 0.56
100 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (98 bp):
AGATATGAAGGGAAAGGTTGAAGCCGTAACGGCGAACCTCATACCATAAAGATATAAAGGGAAAG
ATTAAGGCCGCAACGGCGAATCTTGTACTATTG
Found at i:8729 original size:49 final size:49
Alignment explanation
Indices: 8512--8729 Score: 176
Period size: 49 Copynumber: 4.4 Consensus size: 49
8502 AGATTGATAT
* * *
8512 CGTAACGGTGAAT-TCGATACCA-AGAAGATATGAAGGGAAAGGTTGATGC
1 CGTAACGGTGAATCTC-ATACCATAG-AGATATGAAGGGAAAGATTAAGGC
* * * *
8561 CGTAACGGTGAA-CCCAGTACCTTAAAAGATATGATGGGAAAGATTAAGGC
1 CGTAACGGTGAATCTCA-TACCAT-AGAGATATGAAGGGAAAGATTAAGGC
* * ** * * *
8611 CGCAACGGCGAATCTTGTACTATTGAGATATGGAGGGAAATG-TTGAA-GC
1 CGTAACGGTGAATCTCATACCATAGAGATATGAAGGGAAA-GATT-AAGGC
* * * *
8660 CGTAACGGCGAACCTTATACCATAGAGATATAAAGGGAAAGATTAAGGC
1 CGTAACGGTGAATCTCATACCATAGAGATATGAAGGGAAAGATTAAGGC
*
8709 CGTAACGGTGGATCTCATACC
1 CGTAACGGTGAATCTCATACC
8730 CTAAATATGA
Statistics
Matches: 131, Mismatches: 29, Indels: 18
0.74 0.16 0.10
Matches are distributed among these distances:
48 4 0.03
49 88 0.67
50 37 0.28
51 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (49 bp):
CGTAACGGTGAATCTCATACCATAGAGATATGAAGGGAAAGATTAAGGC
Found at i:8854 original size:42 final size:42
Alignment explanation
Indices: 8805--9521 Score: 454
Period size: 40 Copynumber: 18.0 Consensus size: 42
8795 CGAAGCCGCA
* *
8805 CCAATCTCTTACCTCGACCATGGGGCAGATTGAAGACATAAT
1 CCAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCAT
* * *
8847 CTAATCTCTTACCTCGATCATGGGGTAGATTAAAGACATCAT
1 CCAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCAT
* * *
8889 CCAATCTCTTACCCCGATCATCGGCCAGATTGAAGACA-CAT
1 CCAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCAT
*
8930 CCAA--TC-T--CT---TCATGGGGCAGATTGAAGACATAAT
1 CCAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCAT
*
8964 CTAATCTCTTA-CTCCGATCATGGGGCAGATTGAAGACATCAT
1 CCAATCTCTTACCT-CGATCATGGGGCAGATTGAAGACATCAT
* * * *
9006 CCAATCTCTTACCCCGATCATGAGGCAGATTGAAGATATTAT
1 CCAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCAT
* * * *
9048 CCAATCTCTTACC-CTAATAATGGGGTAGATTGAAGAC-GCA-
1 CCAATCTCTTACCTC-GATCATGGGGCAGATTGAAGACATCAT
* *
9088 CTAATCTCTTACCCCGATCATGGGGCAGATTGAAG----CAT
1 CCAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCAT
* ** * * * *
9126 CCAATCTTTTACCTTAATCA-GAAGGTAGATTGAAAACA--AA
1 CCAATCTCTTACCTCGATCATG-GGGCAGATTGAAGACATCAT
* * *
9166 CCAATCTCTTACCCCGATCATGGGGCATATTGAAG---T-AC
1 CCAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCAT
* * **
9204 CCAATCTTTTACC-CTAATCAAAGGGCAGATTGAAGACA--AT
1 CCAATCTCTTACCTC-GATCATGGGGCAGATTGAAGACATCAT
* ** * *** * *
9244 CCAATCTCTTAACTTAATTAAAAGGCAAATTAAAGACA--AT
1 CCAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCAT
*
9284 CCAATCTCTTATCTCGATCATGGGGCAGATTGAAG----CAT
1 CCAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCAT
* ** * * *
9322 CCAATCTTTTA-CTTAATTA-GAAGGCAGATTGAAGACA--AA
1 CCAATCTCTTACCTCGATCATG-GGGCAGATTGAAGACATCAT
* * **
9361 CCAATCTCTTACCCCGATTATAAGGCAGATTGAAG-CATC-T
1 CCAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCAT
* *
9401 --AATCTTTTACC-CTAATCA-GAGGGCAGATTGAAGACA--AT
1 CCAATCTCTTACCTC-GATCATG-GGGCAGATTGAAGACATCAT
*
9439 CCAATCTCTTACC-CTAATCA-GAGGGCAGATTGAAGACA-CA-
1 CCAATCTCTTACCTC-GATCATG-GGGCAGATTGAAGACATCAT
* * *
9479 CCATTCTCTTACCCCGATCATGGGGTAGATTGAAG-CTATCAT
1 CCAATCTCTTACCTCGATCATGGGGCAGATTGAAGAC-ATCAT
9521 C
1 C
9522 ATATAGAAGT
Statistics
Matches: 536, Mismatches: 94, Indels: 90
0.74 0.13 0.12
Matches are distributed among these distances:
33 19 0.04
34 5 0.01
36 4 0.01
37 23 0.04
38 95 0.18
39 18 0.03
40 196 0.37
41 16 0.03
42 159 0.30
43 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (42 bp):
CCAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCAT
Found at i:8993 original size:75 final size:76
Alignment explanation
Indices: 8864--9015 Score: 234
Period size: 75 Copynumber: 2.0 Consensus size: 76
8854 CTTACCTCGA
* *
8864 TCATGGGGTAGATTAAAGACATCATCCAATCTCTTACCCCGATCATCGGCCAGATTGAAGACA-C
1 TCATGGGGCAGATTAAAGACATAATCCAATCTCTTACCCCGATCATCGGCCAGATTGAAGACATC
8928 ATCCAATCTCT
66 ATCCAATCTCT
* * * * *
8939 TCATGGGGCAGATTGAAGACATAATCTAATCTCTTACTCCGATCATGGGGCAGATTGAAGACATC
1 TCATGGGGCAGATTAAAGACATAATCCAATCTCTTACCCCGATCATCGGCCAGATTGAAGACATC
9004 ATCCAATCTCT
66 ATCCAATCTCT
9015 T
1 T
9016 ACCCCGATCA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 56 0.81
76 13 0.19
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (76 bp):
TCATGGGGCAGATTAAAGACATAATCCAATCTCTTACCCCGATCATCGGCCAGATTGAAGACATC
ATCCAATCTCT
Found at i:9035 original size:117 final size:118
Alignment explanation
Indices: 8822--9126 Score: 397
Period size: 117 Copynumber: 2.5 Consensus size: 118
8812 CTTACCTCGA
* *
8822 CCATGGGGCAGATTGAAGACATAATCTAATCTCTTACCTCGATCATGGGGTAGATTAAAGACATC
1 CCATGGGGCAGATTGAAGACATAATCTAATCTCTTACC-CGATCATGGGGCAGATTGAAGACATC
8887 ATCCAATCTCTTACCCCGATCATCGGCCAGATTGAAGACA-CATCCAATCTCTT
65 ATCCAATCTCTTACCCCGATCATCGGCCAGATTGAAGACATCATCCAATCTCTT
8940 -CATGGGGCAGATTGAAGACATAATCTAATCTCTTACTCCGATCATGGGGCAGATTGAAGACATC
1 CCATGGGGCAGATTGAAGACATAATCTAATCTCTTAC-CCGATCATGGGGCAGATTGAAGACATC
* * *
9004 ATCCAATCTCTTACCCCGATCAT-GAGGCAGATTGAAGATATTATCCAATCTCTT
65 ATCCAATCTCTTACCCCGATCATCG-GCCAGATTGAAGACATCATCCAATCTCTT
* **
9058 ACCCTAATAATGGGGTAGATTGAAGAC-GCA-CTAATCTCTTACCCCGATCATGGGGCAGATTGA
1 --CC-----ATGGGGCAGATTGAAGACATAATCTAATCTCTTA-CCCGATCATGGGGCAGATTGA
9121 AG-CATC
58 AGACATC
9127 CAATCTTTTA
Statistics
Matches: 167, Mismatches: 8, Indels: 19
0.86 0.04 0.10
Matches are distributed among these distances:
116 1 0.01
117 96 0.57
118 13 0.08
121 1 0.01
123 4 0.02
124 33 0.20
125 2 0.01
126 17 0.10
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (118 bp):
CCATGGGGCAGATTGAAGACATAATCTAATCTCTTACCCGATCATGGGGCAGATTGAAGACATCA
TCCAATCTCTTACCCCGATCATCGGCCAGATTGAAGACATCATCCAATCTCTT
Found at i:9357 original size:77 final size:77
Alignment explanation
Indices: 9204--9473 Score: 315
Period size: 77 Copynumber: 3.5 Consensus size: 77
9194 ATTGAAGTAC
* ** * * *
9204 CCAATCTTTTACCCTAATCAAAGGGCAGATTGAAGACAATCCAATCTCTTAACTTAATTAAAAGG
1 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAG-C-ATCCAATCT-TTTACTTAATTAGAAGG
* *
9269 CAAATTAAAGACAAT
63 CAGATTGAAGACAAT
* * *
9284 CCAATCTCTTATCTCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACTTAATTAGAAGGCAG
1 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAGCATCCAATCTTTTACTTAATTAGAAGGCAG
*
9349 ATTGAAGACAAA
66 ATTGAAGACAAT
* * * * * *
9361 CCAATCTCTTACCCCGATTATAAGGCAGATTGAAGCATCTAATCTTTTACCCTAATCAGAGGGCA
1 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAGCATCCAATCTTTTA-CTTAATTAGAAGGCA
9426 GATTGAAGACAAT
65 GATTGAAGACAAT
** *
9439 CCAATCTCTTACCCTAATCAGAGGGCAGATTGAAG
1 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAG
9474 ACACACCATT
Statistics
Matches: 162, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
77 70 0.43
78 63 0.39
79 1 0.01
80 28 0.17
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (77 bp):
CCAATCTCTTACCCCGATCATAGGGCAGATTGAAGCATCCAATCTTTTACTTAATTAGAAGGCAG
ATTGAAGACAAT
Found at i:9426 original size:195 final size:195
Alignment explanation
Indices: 8945--9514 Score: 714
Period size: 195 Copynumber: 2.9 Consensus size: 195
8935 CTCTTCATGG
* *
8945 GGCAGATTGAAGACATAATCTAATCTCTTACTCCGATCATGGGGCAGATTGAAGACATCATCCAA
1 GGCAGATTGAAGACA-AA-CCAATCTCTTACCCCGATCATGGGGCAGATTGAAG-CATC-T--AA
* ** * *
9010 TCTCTTACCCCGATCATGA-GGCAGATTGAAGATATTATCCAATCTCTTACCCTAA-TAATGGGG
60 TCTTTTACCCTAATCA-GAGGGCAGATTGAAGACA--ATCCAATCTCTTACCCTAATTAA-AGGG
* * *
9073 TAGATTGAAGACGCACTAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTAC
121 CAGATTGAAGAC-AACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTAC
9138 CTTAATCAGAA
185 CTTAATCAGAA
* * * * * *
9149 GGTAGATTGAAAACAAACCAATCTCTTACCCCGATCATGGGGCATATTGAAGTACCCAATCTTTT
1 GGCAGATTGAAGACAAACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCTAATCTTTT
* * * * * *
9214 ACCCTAATCAAAGGGCAGATTGAAGACAATCCAATCTCTTAACTTAATTAAAAGGCAAATTAAAG
66 ACCCTAATCAGAGGGCAGATTGAAGACAATCCAATCTCTTACCCTAATTAAAGGGCAGATTGAAG
* * *
9279 ACAATCCAATCTCTTATCTCGATCATGGGGCAGATTGAAGCATCCAATCTTTTA-CTTAATTAGA
131 ACAA-CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGA
9343 A
195 A
* **
9344 GGCAGATTGAAGACAAACCAATCTCTTACCCCGATTATAAGGCAGATTGAAGCATCTAATCTTTT
1 GGCAGATTGAAGACAAACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCTAATCTTTT
* *
9409 ACCCTAATCAGAGGGCAGATTGAAGACAATCCAATCTCTTACCCTAATCAGAGGGCAGATTGAAG
66 ACCCTAATCAGAGGGCAGATTGAAGACAATCCAATCTCTTACCCTAATTAAAGGGCAGATTGAAG
* *
9474 ACACACCATTCTCTTACCCCGATCATGGGGTAGATTGAAGC
131 ACA-ACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGC
9515 TATCATCATA
Statistics
Matches: 316, Mismatches: 46, Indels: 17
0.83 0.12 0.04
Matches are distributed among these distances:
195 159 0.50
196 75 0.24
197 4 0.01
198 29 0.09
201 2 0.01
202 32 0.10
203 2 0.01
204 13 0.04
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (195 bp):
GGCAGATTGAAGACAAACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCTAATCTTTT
ACCCTAATCAGAGGGCAGATTGAAGACAATCCAATCTCTTACCCTAATTAAAGGGCAGATTGAAG
ACAACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAA
Found at i:9450 original size:78 final size:79
Alignment explanation
Indices: 8939--9513 Score: 363
Period size: 78 Copynumber: 7.2 Consensus size: 79
8929 TCCAATCTCT
* * * **
8939 TCATG-GGGCAGATTGAAGACATAATCTAATCTCTTACTCCGATCATGGGGCAGATTGAAGACAT
1 TCATGAGGGCAGATTGAAGAC--AATCCAATCTCTTACCCCAATCATAAGGCAGATTGAAG----
*
9003 CATCCAATCTCTTACCCCGA
60 CATCCAATCTCTTACCCCAA
* * * ** *
9023 TCATGA-GGCAGATTGAAGATATTATCCAATCTCTTACCCTAATAATGGGGTAGATTGAAGACGC
1 TCATGAGGGCAGATTGAAGACA--ATCCAATCTCTTACCCCAATCATAAGGCAGATTG-A-A-GC
* *
9087 A-CTAATCTCTTACCCCGA
61 ATCCAATCTCTTACCCCAA
* ** * * * *
9105 TCATG-GGGCAGATTGAAG-C-ATCCAATCTTTTACCTTAATCAGAAGGTAGATTGAAAACAAAC
1 TCATGAGGGCAGATTGAAGACAATCCAATCTCTTACCCCAATCATAAGGCAGATTG-AAGC-ATC
*
9167 CAATCTCTTACCCCGA
64 CAATCTCTTACCCCAA
* * *
9183 TCATG-GGGCATATTGAAGTAC---CCAATCTTTTACCCTAATCA-AAGGGCAGATTGAAGACAA
1 TCATGAGGGCAGATTGAAG-ACAATCCAATCTCTTACCCCAATCATAA-GGCAGATTGAAG-C-A
* **
9243 TCCAATCTCTTAACTTAA
62 TCCAATCTCTTACCCCAA
* * * * * * * * **
9261 TTA-AAAGGCAAATTAAAGACAATCCAATCTCTTATCTCGATCATGGGGCAGATTGAAGCATCCA
1 TCATGAGGGCAGATTGAAGACAATCCAATCTCTTACCCCAATCATAAGGCAGATTGAAGCATCCA
* **
9325 ATCTTTTA-CTTAA
66 ATCTCTTACCCCAA
* * * * * *
9338 TTA-GAAGGCAGATTGAAGACAAACCAATCTCTTACCCCGATTATAAGGCAGATTGAAGCATCTA
1 TCATGAGGGCAGATTGAAGACAATCCAATCTCTTACCCCAATCATAAGGCAGATTGAAGCATCCA
* *
9402 ATCTTTTACCCTAA
66 ATCTCTTACCCCAA
* * * *
9416 TCA-GAGGGCAGATTGAAGACAATCCAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACACAC
1 TCATGAGGGCAGATTGAAGACAATCCAATCTCTTACCCCAATCATAAGGCAGATTGAAG-CA-TC
* *
9480 CATTCTCTTACCCCGA
64 CAATCTCTTACCCCAA
*
9496 TCATG-GGGTAGATTGAAG
1 TCATGAGGGCAGATTGAAG
9514 CTATCATCAT
Statistics
Matches: 404, Mismatches: 65, Indels: 48
0.78 0.13 0.09
Matches are distributed among these distances:
76 1 0.00
77 75 0.19
78 184 0.46
79 3 0.01
80 55 0.14
81 1 0.00
82 34 0.08
83 2 0.00
84 46 0.11
85 1 0.00
86 1 0.00
87 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (79 bp):
TCATGAGGGCAGATTGAAGACAATCCAATCTCTTACCCCAATCATAAGGCAGATTGAAGCATCCA
ATCTCTTACCCCAA
Found at i:11502 original size:16 final size:17
Alignment explanation
Indices: 11470--11502 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11460 ATGAAAGGCT
*
11470 TTTATTCTTTCTATTTA
1 TTTATTCTTTATATTTA
11487 TTTATT-TTTATATTTA
1 TTTATTCTTTATATTTA
11503 AAAAAAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTCTTTATATTTA
Found at i:11820 original size:2 final size:2
Alignment explanation
Indices: 11815--11859 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
11805 TAAAAAAAAA
11815 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
11857 AT A
1 AT A
11860 AATTACTTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24645 original size:15 final size:16
Alignment explanation
Indices: 24612--24645 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
24602 ACCCATAATC
*
24612 AAAACCCAGAATTCAA
1 AAAACCCAAAATTCAA
*
24628 AAAACCCAAAATTGAA
1 AAAACCCAAAATTCAA
24644 AA
1 AA
24646 CAATTCTTCA
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:0.62, C:0.21, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAACCCAAAATTCAA
Found at i:25063 original size:20 final size:21
Alignment explanation
Indices: 25037--25083 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
25027 ATCGTTACAA
25037 AATTATTATAATATTTA-ATT
1 AATTATTATAATATTTACATT
* *
25057 TATTATTATTATATTTACATT
1 AATTATTATAATATTTACATT
25078 AATTAT
1 AATTAT
25084 AAATAAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTATTATAATATTTACATT
Found at i:26480 original size:14 final size:16
Alignment explanation
Indices: 26445--26490 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
26435 AAATAAAAAA
*
26445 TCATTATATTAAT-AT
1 TCATTATATAAATAAT
*
26460 TCATTATTTAAA-AAT
1 TCATTATATAAATAAT
26475 TC-TTATATAAATAAT
1 TCATTATATAAATAAT
26490 T
1 T
26491 TGTATAATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (16 bp):
TCATTATATAAATAAT
Found at i:29942 original size:3 final size:3
Alignment explanation
Indices: 29934--29959 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29924 CCTTCCTCTT
29934 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
29960 CTTTCACCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:35140 original size:133 final size:135
Alignment explanation
Indices: 34900--35150 Score: 461
Period size: 133 Copynumber: 1.9 Consensus size: 135
34890 TTAAAGTTTT
*
34900 ACTCATTTCTTGTAATTCACCAAAAAATAAATAAATTAAAGATACGATATCATTTATAAAAATTT
1 ACTCATCTCTTGTAATTCACCAAAAAATAAATAAATTAAAGATACGATATCATTTATAAAAATTT
34965 AGAATAATAACAAAATAAATATGAAAGTAACTCGTAACTTTTAGATATTACTCGTAATTTTAGAA
66 AGAATAATAACAAAATAAATATGAAAGTAACTCGTAACTTTTAGATATTACTCGTAATTTTAGAA
35030 TAATA
131 TAATA
* *
35035 ACTCATCTCTTGTAATTCACCAAAAAA-AAA-AAATTAAATATACGATATCATTTGTAAAAATTT
1 ACTCATCTCTTGTAATTCACCAAAAAATAAATAAATTAAAGATACGATATCATTTATAAAAATTT
35098 AGAATAATAACAAAATAAATATGAAAGTAACTCGTAACTTTTAGATATTACTC
66 AGAATAATAACAAAATAAATATGAAAGTAACTCGTAACTTTTAGATATTACTC
35151 CAAAACATAA
Statistics
Matches: 113, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
133 84 0.74
134 3 0.03
135 26 0.23
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (135 bp):
ACTCATCTCTTGTAATTCACCAAAAAATAAATAAATTAAAGATACGATATCATTTATAAAAATTT
AGAATAATAACAAAATAAATATGAAAGTAACTCGTAACTTTTAGATATTACTCGTAATTTTAGAA
TAATA
Found at i:36866 original size:2 final size:2
Alignment explanation
Indices: 36852--36905 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
36842 TGTTACATTT
36852 TC TC TC T- TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
36892 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
36906 ACACACACAC
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:41398 original size:29 final size:29
Alignment explanation
Indices: 41366--41462 Score: 88
Period size: 29 Copynumber: 3.2 Consensus size: 29
41356 GATTTTGCCT
*
41366 TTTAGGTATTAAATTGGATAAAAAAAAAC
1 TTTAGGTATTAAATTGGATAAAAAAAAAG
* *
41395 TTTAGGTGTCAAATTAGGA-AAAAAGTATAAAG
1 TTTAGGTATTAAATT-GGATAAAAA--A-AAAG
* * * *
41427 TTTAAGTACTAATTTGAATAAAAAAAAAG
1 TTTAGGTATTAAATTGGATAAAAAAAAAG
41456 TTTAGGT
1 TTTAGGT
41463 GCCAAATTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
29 28 0.53
30 4 0.08
31 3 0.06
32 18 0.34
ACGTcount: A:0.48, C:0.03, G:0.16, T:0.32
Consensus pattern (29 bp):
TTTAGGTATTAAATTGGATAAAAAAAAAG
Found at i:41478 original size:29 final size:29
Alignment explanation
Indices: 41385--41482 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 29
41375 TAAATTGGAT
* * *
41385 AAAAAAAAACTTTAGGTGTCAAATTAGGA
1 AAAAAAAAAGTTTAGGTGCCAAATTAAGA
* * * * *
41414 AAAAAGTATAAAGTTTAAGTACTAATTTGAA-T
1 AAAAA--A-AAAGTTTAGGTGCCAAATT-AAGA
41446 AAAAAAAAAGTTTAGGTGCCAAATTAAGA
1 AAAAAAAAAGTTTAGGTGCCAAATTAAGA
41475 AAAAAAAA
1 AAAAAAAA
41483 TGTCAAGTTC
Statistics
Matches: 51, Mismatches: 13, Indels: 10
0.69 0.18 0.14
Matches are distributed among these distances:
28 2 0.04
29 28 0.55
30 1 0.02
31 1 0.02
32 18 0.35
33 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.24
Consensus pattern (29 bp):
AAAAAAAAAGTTTAGGTGCCAAATTAAGA
Found at i:46435 original size:2 final size:2
Alignment explanation
Indices: 46424--46467 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
46414 TTATTTTAAA
46424 AT AT -T AT AT AT AT 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 AT AT AT AT AT AT AT
46465 AT A
1 AT A
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.