Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008166.1 Kokia drynarioides strain JFW-HI SEQ_122825, 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: 93761
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:8232 original size:13 final size:13
Alignment explanation
Indices: 8214--8241 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
8204 ATTTTAATTA
8214 TTATAGTTTAAAT
1 TTATAGTTTAAAT
8227 TTATAGTTTAAAT
1 TTATAGTTTAAAT
8240 TT
1 TT
8242 GAAATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (13 bp):
TTATAGTTTAAAT
Found at i:8786 original size:14 final size:15
Alignment explanation
Indices: 8758--8790 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
8748 GGTATTTAAA
8758 TATTATTTTAATTAT
1 TATTATTTTAATTAT
*
8773 TATTA-TTTAGTTAT
1 TATTATTTTAATTAT
8787 TATT
1 TATT
8791 TATATTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TATTATTTTAATTAT
Found at i:8787 original size:26 final size:27
Alignment explanation
Indices: 8740--8791 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
8730 TATTATATAT
8740 ATTATTATGGTATTTAAATATTATTTTA
1 ATTATTAT-GTATTTAAATATTATTTTA
**
8768 ATTATTAT-TATTTAGTTATTATTT
1 ATTATTATGTATTTAAATATTATTT
8792 ATATTTAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 14 0.64
28 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.62
Consensus pattern (27 bp):
ATTATTATGTATTTAAATATTATTTTA
Found at i:8844 original size:8 final size:8
Alignment explanation
Indices: 8831--8881 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
8821 TATTAAAATT
8831 AAAATTAA
1 AAAATTAA
*
8839 AAAATTCA
1 AAAATTAA
**
8847 AAGTTTAA
1 AAAATTAA
8855 AAAA-T-A
1 AAAATTAA
*
8861 AAATTTAA
1 AAAATTAA
8869 AAAATTAA
1 AAAATTAA
8877 AAAAT
1 AAAAT
8882 GAACTTCAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
6 4 0.12
7 2 0.06
8 27 0.82
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (8 bp):
AAAATTAA
Found at i:8865 original size:21 final size:20
Alignment explanation
Indices: 8839--8899 Score: 52
Period size: 22 Copynumber: 3.0 Consensus size: 20
8829 TTAAAATTAA
8839 AAAATTCAAAGTTTAAAAAAT
1 AAAATTCAAA-TTTAAAAAAT
* *
8860 AAAATTTAAAAAATTAAAAAAT
1 AAAA-TT-CAAATTTAAAAAAT
* *
8882 GAACTTCAAA-TTAAAAAA
1 AAAATTCAAATTTAAAAAA
8900 AATTATAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
19 8 0.24
20 3 0.09
21 6 0.18
22 13 0.39
23 3 0.09
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAATTCAAATTTAAAAAAT
Found at i:8871 original size:15 final size:15
Alignment explanation
Indices: 8825--8878 Score: 76
Period size: 14 Copynumber: 3.7 Consensus size: 15
8815 TAATAATATT
8825 AAAATTAAAA-TTAA
1 AAAATTAAAATTTAA
*
8839 AAAATTCAAAGTTTAA
1 AAAATT-AAAATTTAA
8855 AAAA-TAAAATTTAA
1 AAAATTAAAATTTAA
8869 AAAATTAAAA
1 AAAATTAAAA
8879 AATGAACTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 18 0.51
15 9 0.26
16 8 0.23
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
AAAATTAAAATTTAA
Found at i:8899 original size:29 final size:29
Alignment explanation
Indices: 8867--8931 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
8857 AATAAAATTT
8867 AAAAAATTAAAAAATGAACTTCAAATTAA
1 AAAAAATTAAAAAATGAACTTCAAATTAA
* ** * *
8896 AAAAAATTATAATTTGAATTTTAAATTAA
1 AAAAAATTAAAAAATGAACTTCAAATTAA
8925 AAAAAAT
1 AAAAAAT
8932 ACAGGTTAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAAAATTAAAAAATGAACTTCAAATTAA
Found at i:9216 original size:22 final size:22
Alignment explanation
Indices: 9165--9216 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
9155 AACAATTTAT
* *
9165 ATTATATATATTTAAAATTATA
1 ATTAAATATATTTAAAATGATA
*
9187 TTTAAA-ATAATTTAAAAATGATA
1 ATTAAATAT-ATTT-AAAATGATA
9210 ATTAAAT
1 ATTAAAT
9217 TAAAATAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
21 2 0.09
22 8 0.35
23 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTAAATATATTTAAAATGATA
Found at i:9231 original size:10 final size:12
Alignment explanation
Indices: 9171--9203 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
9161 TTATATTATA
9171 TATATTTAAAAT
1 TATATTTAAAAT
9183 TATATTTAAAA-
1 TATATTTAAAAT
9194 TA-ATTTAAAA
1 TATATTTAAAA
9204 ATGATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
11 2 0.10
12 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TATATTTAAAAT
Found at i:9232 original size:11 final size:12
Alignment explanation
Indices: 9170--9215 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
9160 TTTATATTAT
9170 ATATATTTAAAA
1 ATATATTTAAAA
*
9182 TTATATTT-AAA
1 ATATATTTAAAA
9193 ATA-ATTTAAAA
1 ATATATTTAAAA
*
9204 ATGATAATTAAA
1 AT-ATATTTAAA
9216 TTAAAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
10 4 0.14
11 10 0.36
12 8 0.29
13 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (12 bp):
ATATATTTAAAA
Found at i:9317 original size:21 final size:21
Alignment explanation
Indices: 9292--9351 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
9282 TTTCAAATTA
9292 AAATAATTAAAAAACCTATTT
1 AAATAATTAAAAAACCTATTT
**
9313 AAATAA--AACTAA---ATTT
1 AAATAATTAAAAAACCTATTT
9329 -AATAATTAAAAAACCTATTT
1 AAATAATTAAAAAACCTATTT
9349 AAA
1 AAA
9352 ATTTAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
15 5 0.17
16 4 0.14
17 4 0.14
19 4 0.14
20 4 0.14
21 8 0.28
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATAATTAAAAAACCTATTT
Found at i:11912 original size:21 final size:20
Alignment explanation
Indices: 11880--11938 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 20
11870 TACATATATT
11880 TTTATATTTCGAAATATTTG
1 TTTATATTTCGAAATATTTG
*
11900 TTTATATTTTCGAAATATTTT
1 TTTATA-TTTCGAAATATTTG
* *
11921 TTTACAATT-GAAATATTT
1 TTTATATTTCGAAATATTT
11939 TTGAATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.26
20 8 0.23
21 18 0.51
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (20 bp):
TTTATATTTCGAAATATTTG
Found at i:12960 original size:30 final size:30
Alignment explanation
Indices: 12926--13017 Score: 148
Period size: 30 Copynumber: 3.1 Consensus size: 30
12916 ATTTTGATTT
* *
12926 TTTCGTTTATTTTTTAAATTTAATTTGTAA
1 TTTCGTTTATATTTTAAATTTAATTTATAA
* *
12956 TTTCGTTTATATTTTAAATTTAATTTCTCA
1 TTTCGTTTATATTTTAAATTTAATTTATAA
12986 TTTCGTTTATATTTTAAATTTAATTTATAA
1 TTTCGTTTATATTTTAAATTTAATTTATAA
13016 TT
1 TT
13018 ATTATTTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.62
Consensus pattern (30 bp):
TTTCGTTTATATTTTAAATTTAATTTATAA
Found at i:12969 original size:23 final size:23
Alignment explanation
Indices: 12938--12982 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12928 TCGTTTATTT
*
12938 TTTAAA-TTTAATTTGTAATTTCG
1 TTTAAATTTTAAATT-TAATTTCG
*
12961 TTTATATTTTAAATTTAATTTC
1 TTTAAATTTTAAATTTAATTTC
12983 TCATTTCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTAAATTTTAAATTTAATTTCG
Found at i:13971 original size:18 final size:18
Alignment explanation
Indices: 13943--13993 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
13933 CATGAAAGAA
13943 ATTAA-TTTTTTATTCAT
1 ATTAATTTTTTTATTCAT
13960 ATTAATTTTTTTATTCAT
1 ATTAATTTTTTTATTCAT
* *
13978 ATCAATTATTTTATTC
1 ATTAATTTTTTTATTC
13994 GACCATAGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 5 0.16
18 26 0.84
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTAATTTTTTTATTCAT
Found at i:14108 original size:54 final size:55
Alignment explanation
Indices: 13992--14141 Score: 196
Period size: 54 Copynumber: 2.7 Consensus size: 55
13982 ATTATTTTAT
* * *
13992 TCGACCATAGCTTGGTAGACA-CTTAAAAAATATATTTTTATCTGATAAAGGCGGTG
1 TCGACCATGGCTTGATAGACATC-CAAAAAATAT-TTTTTATCTGATAAAGGCGGTG
* *
14048 TCGACCATGGCTTGATAGAC-TCCCAAAAATATTTTTTATCTGATAAAGGGGGTG
1 TCGACCATGGCTTGATAGACATCCAAAAAATATTTTTTATCTGATAAAGGCGGTG
* * *
14102 TTGACCATGGCTTGGTTGACATCCAAAAAATATTTTTTAT
1 TCGACCATGGCTTGATAGACATCCAAAAAATATTTTTTAT
14142 TCGTATTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
54 38 0.46
55 26 0.31
56 19 0.23
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (55 bp):
TCGACCATGGCTTGATAGACATCCAAAAAATATTTTTTATCTGATAAAGGCGGTG
Found at i:15006 original size:2 final size:2
Alignment explanation
Indices: 14999--15030 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
14989 ATTAAAGTTC
14999 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
15031 GTGTGTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17492 original size:73 final size:72
Alignment explanation
Indices: 17291--17545 Score: 345
Period size: 72 Copynumber: 3.6 Consensus size: 72
17281 AACAAATTTT
* * * * * *
17291 ATATCC-AAAATCAAATATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAAAACAT
1 ATATCCAAAAACCAAACATAAATAACTATTGATAAAACTAGATTGCACATAAATAAGTAGAACAT
17355 AAATTCA
66 AAATTCA
*
17362 ATATCCAAAAACCAAACATAAATAATTATTGATAAAACTAGATTGCACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAATAACTATTGATAAAACTAGATTGCACATAAATAAGTAGAACAT
17427 AAATTCA
66 AAATTCA
* * * * *
17434 ACATCCAAAAACCATAC-TCATCATAACTATTGATAAAGCTAGATTGCATATAAATAAGTAGAAC
1 ATATCCAAAAACCAAACAT-A-AATAACTATTGATAAAACTAGATTGCACATAAATAAGTAGAAC
*
17498 AT-AATTTA
64 ATAAATTCA
*
17506 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTA
1 ATATCCAAAAACCAAACATAAATAACTATTGATAAAACTA
17546 ATTTAACATT
Statistics
Matches: 161, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
71 24 0.15
72 95 0.59
73 42 0.26
ACGTcount: A:0.54, C:0.16, G:0.05, T:0.25
Consensus pattern (72 bp):
ATATCCAAAAACCAAACATAAATAACTATTGATAAAACTAGATTGCACATAAATAAGTAGAACAT
AAATTCA
Found at i:18025 original size:18 final size:18
Alignment explanation
Indices: 17977--18046 Score: 97
Period size: 18 Copynumber: 3.9 Consensus size: 18
17967 CGTTTCCATC
17977 AATGTTAACATCATTTGA
1 AATGTTAACATCATTTGA
*
17995 AAT-TTGAATATCATTTGA
1 AATGTT-AACATCATTTGA
* *
18013 AGTGTTAACATCATTTAA
1 AATGTTAACATCATTTGA
18031 AATGTTAACATCATTT
1 AATGTTAACATCATTT
18047 CTTGCATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
17 2 0.04
18 41 0.91
19 2 0.04
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (18 bp):
AATGTTAACATCATTTGA
Found at i:27411 original size:22 final size:20
Alignment explanation
Indices: 27384--27423 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
27374 TGTTAGTTTT
27384 TATTTTATTTTATTAGTATTAA
1 TATTTTATTTT-TTA-TATTAA
27406 TATTTTATTTTTTATATT
1 TATTTTATTTTTTATATT
27424 TTGATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 3 0.17
22 11 0.61
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (20 bp):
TATTTTATTTTTTATATTAA
Found at i:29565 original size:18 final size:20
Alignment explanation
Indices: 29528--29565 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
29518 AACATTGGAC
*
29528 TCATAGAGTCGAATCATATA
1 TCATAGAGTCGAAACATATA
29548 TCATA-AGT-GAAACATATA
1 TCATAGAGTCGAAACATATA
29566 GCTAACACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (20 bp):
TCATAGAGTCGAAACATATA
Found at i:29968 original size:23 final size:23
Alignment explanation
Indices: 29940--30177 Score: 314
Period size: 23 Copynumber: 10.3 Consensus size: 23
29930 ATCTTAATTC
* *
29940 TTTAAGGACAAATCACAATAATA
1 TTTAAGCACAAATCACATTAATA
29963 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
29986 TTTAACCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
** * *
30009 TTTAATTATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
30032 TTTAAGCACAAATCAAATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
30055 TTTAAGTATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
30078 CTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
30101 CTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * **
30124 TTTAATCATAAATCATTTTAATA
1 TTTAAGCACAAATCACATTAATA
30147 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
30170 TTTAAGCA
1 TTTAAGCA
30178 TAGATATAAG
Statistics
Matches: 189, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 189 1.00
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.34
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:31287 original size:17 final size:17
Alignment explanation
Indices: 31265--31352 Score: 95
Period size: 17 Copynumber: 5.1 Consensus size: 17
31255 CAACATTTAA
*
31265 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
* *
31282 ATTTTAAGTTTAAAATT
1 ATTTTAAATTTAAATTT
31299 ATTTTAAATTTAAACTTAT
1 ATTTTAAATTTAAA-TT-T
* * *
31318 TTTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
31335 ATTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
31352 A
1 A
31353 AAATTTAAAG
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
17 44 0.75
18 3 0.05
19 12 0.20
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:31310 original size:6 final size:6
Alignment explanation
Indices: 31259--31361 Score: 50
Period size: 6 Copynumber: 17.2 Consensus size: 6
31249 CAGGCCCAAC
* * * * *
31259 ATTTAA ATTTTAA ATTTTA ATTT-A TTTTAA GTTTAA AATT-A TTTTAA
1 ATTTAA A-TTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * * * * *
31306 ATTTAA ACTTATT TTTTGA GTTTAA ATTT-A TTTTGA ATTTAA ATTTAAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
31355 ATTTAA A
1 ATTTAA A
31362 GTCCAAAATT
Statistics
Matches: 71, Mismatches: 20, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
5 11 0.15
6 46 0.65
7 14 0.20
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (6 bp):
ATTTAA
Found at i:31337 original size:36 final size:34
Alignment explanation
Indices: 31265--31352 Score: 113
Period size: 36 Copynumber: 2.5 Consensus size: 34
31255 CAACATTTAA
*
31265 ATTTTAAATTTTAATTTATTTTAAGTTTAAAATT
1 ATTTTAAATTTAAATTTATTTTAAGTTTAAAATT
* * *
31299 ATTTTAAATTTAAACTTATTTTTTGAGTTTAAATTT
1 ATTTTAAATTTAAA-TT-TATTTTAAGTTTAAAATT
*
31335 ATTTTGAATTTAAATTTA
1 ATTTTAAATTTAAATTTA
31353 AAATTTAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 14 0.30
35 4 0.09
36 28 0.61
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (34 bp):
ATTTTAAATTTAAATTTATTTTAAGTTTAAAATT
Found at i:32034 original size:3 final size:3
Alignment explanation
Indices: 32026--32105 Score: 90
Period size: 3 Copynumber: 26.0 Consensus size: 3
32016 TAAATAACAT
*
32026 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -ATA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
** *
32071 TAA TAA TGT TAA TAA TAAA TAAA TAA TAA GAA TAA
1 TAA TAA TAA TAA TAA T-AA T-AA TAA TAA TAA TAA
32106 AAAAGGAAAG
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
2 1 0.02
3 57 0.86
4 8 0.12
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:33561 original size:29 final size:29
Alignment explanation
Indices: 33527--33743 Score: 211
Period size: 30 Copynumber: 7.3 Consensus size: 29
33517 AGAAATCACG
* *
33527 TTTTTACCCTCAAACTTCTCAAAAATTACA
1 TTTTGACCCTTAAACTT-TCAAAAATTACA
* ** * *
33557 TTTTAACCCTTATATTTTTTAAAAATTACG
1 TTTTGACCCTTA-AACTTTCAAAAATTACA
* *
33587 TTTTGACCCTTAAACTTTCCAAAATTATA
1 TTTTGACCCTTAAACTTTCAAAAATTACA
*
33616 TTTCGACCCTTAAACTTTCTAAAAATTACA
1 TTTTGACCCTTAAACTTTC-AAAAATTACA
* *
33646 TTTTGACCCTTAAACTTTCTAAAATTATA
1 TTTTGACCCTTAAACTTTCAAAAATTACA
* *
33675 TTTTGACCCTTGAACTTTCTAAGAATTACA
1 TTTTGACCCTTAAACTTTC-AAAAATTACA
* ** * *
33705 TTTTGAGCCTCGAACTTCCAAAAATCACCA
1 TTTTGACCCTTAAACTTTCAAAAATTA-CA
33735 TTTT-ACCCT
1 TTTTGACCCT
33744 CGAGTATCCA
Statistics
Matches: 154, Mismatches: 29, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
29 65 0.42
30 86 0.56
31 3 0.02
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (29 bp):
TTTTGACCCTTAAACTTTCAAAAATTACA
Found at i:33640 original size:59 final size:59
Alignment explanation
Indices: 33512--33727 Score: 245
Period size: 59 Copynumber: 3.7 Consensus size: 59
33502 GTCCCAAAAT
* * * * * * * * *
33512 TTTCTAGAAATCACGTTTTTACCCTCAAACTTCTCAAAAATTACATTTTAACCCTTATAT
1 TTTCTAAAAATTACATTTTGACCCTCAAACTT-TCCAAAATTATATTTTGACCCTTAAAC
* * * *
33572 TTTTTAAAAATTACGTTTTGACCCTTAAACTTTCCAAAATTATATTTCGACCCTTAAAC
1 TTTCTAAAAATTACATTTTGACCCTCAAACTTTCCAAAATTATATTTTGACCCTTAAAC
* * *
33631 TTTCTAAAAATTACATTTTGACCCTTAAACTTTCTAAAATTATATTTTGACCCTTGAAC
1 TTTCTAAAAATTACATTTTGACCCTCAAACTTTCCAAAATTATATTTTGACCCTTAAAC
* * *
33690 TTTCTAAGAATTACATTTTGAGCCTCGAAC-TTCCAAAA
1 TTTCTAAAAATTACATTTTGACCCTCAAACTTTCCAAAA
33728 ATCACCATTT
Statistics
Matches: 135, Mismatches: 21, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
58 7 0.05
59 101 0.75
60 27 0.20
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.40
Consensus pattern (59 bp):
TTTCTAAAAATTACATTTTGACCCTCAAACTTTCCAAAATTATATTTTGACCCTTAAAC
Found at i:37961 original size:23 final size:23
Alignment explanation
Indices: 37101--37958 Score: 1090
Period size: 23 Copynumber: 37.3 Consensus size: 23
37091 ATCTTAATTC
37101 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
37124 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
37147 TTTAACCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
***
37170 TTTAAGTGTAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
37193 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
37216 TTTAAGCAAAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
37239 TTTGAGAACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
37262 TTTCAGAACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
37285 TTTAAGAACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
37308 TTTAAGCACAAATAACATTAATA
1 TTTAAGCACAAATCACATTAATA
37331 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
37354 TTTGAGAACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
37377 TTTCAA-AACAAATCATATTAATA
1 TTT-AAGCACAAATCACATTAATA
*
37400 TTTAAGAACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
37423 TTTAAGCACAAAT-ACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
37445 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
37468 TTTAAGCACAAATTACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
37491 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
37514 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
** *
37537 TTTTTGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
37560 TTTAAGCATAAATCACATTACTA
1 TTTAAGCACAAATCACATTAATA
* * *
37583 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
37606 TTTAAGCATAAATCACTTTAATA
1 TTTAAGCACAAATCACATTAATA
*
37629 TTTAAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
37652 TTTAAGCAAAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
37675 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
37698 TTTGAGCACAAACCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
37721 TCTGAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * * *
37744 TTTAAGCATAAATAATATTAACA
1 TTTAAGCACAAATCACATTAATA
* * *
37767 CTTAAGCATAAATCACAATAATA
1 TTTAAGCACAAATCACATTAATA
* * *
37790 TTTAAGCATAAATCATATTATTA
1 TTTAAGCACAAATCACATTAATA
* *
37813 TTTAAGCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
37836 TTTAAGCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* **
37859 TTTGAGCACAAATCTTATTAATA
1 TTTAAGCACAAATCACATTAATA
37882 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * * *
37905 TTTAAACATAAATCATATTAACA
1 TTTAAGCACAAATCACATTAATA
* *
37928 TTTAAGCATAAATCACAATAATA
1 TTTAAGCACAAATCACATTAATA
37951 TTTAAGCA
1 TTTAAGCA
37959 TAAGTGTAAG
Statistics
Matches: 737, Mismatches: 95, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
22 23 0.03
23 713 0.97
24 1 0.00
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:38791 original size:19 final size:19
Alignment explanation
Indices: 38763--38800 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
38753 GGGATGGCAA
*
38763 ACACAGATACTTGAGATTT
1 ACACAAATACTTGAGATTT
38782 ACACAAATACTTGAGATTT
1 ACACAAATACTTGAGATTT
38801 TTTTTACCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (19 bp):
ACACAAATACTTGAGATTT
Found at i:41453 original size:21 final size:20
Alignment explanation
Indices: 41411--41449 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41401 ATTTAGTCAT
*
41411 TTTTTATTTTTATTTTAATA
1 TTTTTATTTTTAATTTAATA
*
41431 TTTTTGTTTTTAATTTAAT
1 TTTTTATTTTTAATTTAAT
41450 TATTACATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTTATTTTTAATTTAATA
Found at i:42060 original size:22 final size:21
Alignment explanation
Indices: 42035--42093 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
42025 TAGGTTTATG
42035 TTTTATTTATTTTTATATTTTA
1 TTTTATTTATTTTTAT-TTTTA
* * * *
42057 TTTTAATTGTTGGTTGTTTTTA
1 TTTTATTTATT-TTTATTTTTA
42079 TTTTATTTTATTTTT
1 TTTTA-TTTATTTTT
42094 TACGCACTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
22 21 0.75
23 7 0.25
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (21 bp):
TTTTATTTATTTTTATTTTTA
Found at i:53243 original size:20 final size:20
Alignment explanation
Indices: 53218--53262 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
53208 ATTTGGTATT
*
53218 GATACTATTT-TAAAATTATC
1 GATACT-TTTATAAAAATATC
53238 GATACTTTTATAAAAATATC
1 GATACTTTTATAAAAATATC
53258 GATAC
1 GATAC
53263 CATGGGGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (20 bp):
GATACTTTTATAAAAATATC
Found at i:53814 original size:13 final size:13
Alignment explanation
Indices: 53796--53826 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
53786 TAATGAATGT
53796 TATCAAGATTCTC
1 TATCAAGATTCTC
53809 TATCAAGATTCTC
1 TATCAAGATTCTC
*
53822 AATCA
1 TATCA
53827 CTCTATCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.35
Consensus pattern (13 bp):
TATCAAGATTCTC
Found at i:56906 original size:19 final size:19
Alignment explanation
Indices: 56884--57103 Score: 237
Period size: 19 Copynumber: 11.7 Consensus size: 19
56874 TCAGTAATTT
* *
56884 GCTCTTACGATCCAGTATT
1 GCTCTTACGAGCCAGTATC
*
56903 GCTCTTACGAGCCAGTATT
1 GCTCTTACGAGCCAGTATC
*
56922 GCTCTTACGAGCCAATATC
1 GCTCTTACGAGCCAGTATC
* *
56941 GCTCTTATGAGACAGTATC
1 GCTCTTACGAGCCAGTATC
*
56960 GCTCTTATGAGCCAGTATC
1 GCTCTTACGAGCCAGTATC
56979 GCTCTTACGAGCCAGTATC
1 GCTCTTACGAGCCAGTATC
*
56998 ACTCTTACGAGCCAGTATC
1 GCTCTTACGAGCCAGTATC
**********
57017 -NNNNNNNNNNCCAGTATC
1 GCTCTTACGAGCCAGTATC
57035 GCTCTTACGAGCCAGTATC
1 GCTCTTACGAGCCAGTATC
*
57054 ACTCTTACGAGCCAGTATC
1 GCTCTTACGAGCCAGTATC
*
57073 ACTCTTA-GAGCCAGTATC
1 GCTCTTACGAGCCAGTATC
*
57091 GCACTTACGAGCC
1 GCTCTTACGAGCC
57104 CTCTTACGAG
Statistics
Matches: 167, Mismatches: 32, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
18 24 0.14
19 143 0.86
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.27
Consensus pattern (19 bp):
GCTCTTACGAGCCAGTATC
Found at i:57087 original size:56 final size:57
Alignment explanation
Indices: 56885--57103 Score: 244
Period size: 56 Copynumber: 3.9 Consensus size: 57
56875 CAGTAATTTG
* * * * *
56885 CTCTTACGATCCAGTATTGCTCTTACGAGCCAGTATTGCTCTTACGAGCCAATATCG
1 CTCTTACGAGCCAGTATCGCTCTTACGAGCCAGTATCGCTCTTACGAGCCAGTATCA
* * *
56942 CTCTTATGAGACAGTATCGCTCTTATGAGCCAGTATCGCTCTTACGAGCCAGTATCA
1 CTCTTACGAGCCAGTATCGCTCTTACGAGCCAGTATCGCTCTTACGAGCCAGTATCA
**********
56999 CTCTTACGAGCCAGTATC-NNNNNNNNNNCCAGTATCGCTCTTACGAGCCAGTATCA
1 CTCTTACGAGCCAGTATCGCTCTTACGAGCCAGTATCGCTCTTACGAGCCAGTATCA
* *
57055 CTCTTACGAGCCAGTATCACTCTTA-GAGCCAGTATCGCACTTACGAGCC
1 CTCTTACGAGCCAGTATCGCTCTTACGAGCCAGTATCGCTCTTACGAGCC
57104 CTCTTACGAG
Statistics
Matches: 131, Mismatches: 30, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
56 66 0.50
57 65 0.50
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.27
Consensus pattern (57 bp):
CTCTTACGAGCCAGTATCGCTCTTACGAGCCAGTATCGCTCTTACGAGCCAGTATCA
Found at i:57139 original size:18 final size:18
Alignment explanation
Indices: 57109--57173 Score: 103
Period size: 18 Copynumber: 3.6 Consensus size: 18
57099 GAGCCCTCTT
57109 ACGAGCCAATATGCTCAA
1 ACGAGCCAATATGCTCAA
* * *
57127 ACGAGTCAGTATGCTCTA
1 ACGAGCCAATATGCTCAA
57145 ACGAGCCAATATGCTCAA
1 ACGAGCCAATATGCTCAA
57163 ACGAGCCAATA
1 ACGAGCCAATA
57174 CAGTACTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (18 bp):
ACGAGCCAATATGCTCAA
Found at i:83220 original size:17 final size:17
Alignment explanation
Indices: 83200--83256 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
83190 GCTGTCATCA
83200 CATTTCATTTGTCATTG
1 CATTTCATTTGTCATTG
* *
83217 CATTT-TTCTTGTCAATG
1 CATTTCAT-TTGTCATTG
83234 CATCTTCA-TTGTCATTG
1 CAT-TTCATTTGTCATTG
83251 CATTTC
1 CATTTC
83257 CATATATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 4 0.12
17 27 0.82
18 2 0.06
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.51
Consensus pattern (17 bp):
CATTTCATTTGTCATTG
Found at i:83995 original size:51 final size:51
Alignment explanation
Indices: 83919--84020 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
83909 GCTAGCATTA
83919 ATGAAGTTGCAATTTTAAGTATTCATACTTATGAATTGTTGGTGCAATATT
1 ATGAAGTTGCAATTTTAAGTATTCATACTTATGAATTGTTGGTGCAATATT
83970 ATGAAGTTGCAATTTTAAGTATTCATACTTATGAATTGTTGGTGCAATATT
1 ATGAAGTTGCAATTTTAAGTATTCATACTTATGAATTGTTGGTGCAATATT
84021 CTATTATTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (51 bp):
ATGAAGTTGCAATTTTAAGTATTCATACTTATGAATTGTTGGTGCAATATT
Found at i:86143 original size:15 final size:15
Alignment explanation
Indices: 86119--86148 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
86109 TTGCGTTTGT
*
86119 CGGAGTACTTTTGAC
1 CGGAGCACTTTTGAC
86134 CGGAGCACTTTTGAC
1 CGGAGCACTTTTGAC
86149 TGAAGCTCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (15 bp):
CGGAGCACTTTTGAC
Found at i:89574 original size:12 final size:12
Alignment explanation
Indices: 89557--89591 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
89547 TTTTGGGAGC
89557 ATAAAATAAAAG
1 ATAAAATAAAAG
*
89569 ATAAAATAAAAT
1 ATAAAATAAAAG
*
89581 ACAAAATAAAA
1 ATAAAATAAAA
89592 AAAAAAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:89579 original size:17 final size:17
Alignment explanation
Indices: 89557--89595 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
89547 TTTTGGGAGC
89557 ATAAAATA-AAAGATAAA
1 ATAAAATACAAA-ATAAA
89574 ATAAAATACAAAATAAA
1 ATAAAATACAAAATAAA
89591 A-AAAA
1 ATAAAA
89596 AAGTTAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.19
17 14 0.67
18 3 0.14
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (17 bp):
ATAAAATACAAAATAAA
Found at i:93713 original size:13 final size:12
Alignment explanation
Indices: 93663--93711 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
93653 GGTCAAATAA
*
93663 AATATTTAATTT
1 AATATTGAATTT
*
93675 AATATTTAATTT
1 AATATTGAATTT
93687 AATATTGAATTTT
1 AATATTGAA-TTT
93700 AATATTGAATTT
1 AATATTGAATTT
93712 TATTATTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
12 23 0.66
13 12 0.34
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
AATATTGAATTT
Found at i:93718 original size:13 final size:13
Alignment explanation
Indices: 93663--93718 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
93653 GGTCAAATAA
*
93663 AATATTTAA-TTT
1 AATATTGAATTTT
*
93675 AATATTTAA-TTT
1 AATATTGAATTTT
93687 AATATTGAATTTT
1 AATATTGAATTTT
93700 AATATTGAATTTT
1 AATATTGAATTTT
*
93713 ATTATT
1 AATATT
93719 ATTCTAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
12 20 0.49
13 21 0.51
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (13 bp):
AATATTGAATTTT
Done.