Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013497.1 Kokia drynarioides strain JFW-HI SEQ_128523, 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: 38962
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:1841 original size:108 final size:110
Alignment explanation
Indices: 1723--1988 Score: 410
Period size: 118 Copynumber: 2.4 Consensus size: 110
1713 CCAAGTCAAG
*
1723 CTTGGGTAAACATAAAATATATTAATATCATACTTAGATC-T-GACCCATGAACACCTACACGAG
1 CTTGGGTAAACATAAAATATATTAATATCATGCTTAGATCTTCGACCCATGAACACCTACACGAG
*
1786 ATGATATTGAGCAAAAAAAATATGTTAAAAAACAAAAAAAAATTA
66 ATGATATTAAGCAAAAAAAATATGTTAAAAAACAAAAAAAAATTA
1831 CTTGGGTAAACATAAAATATATTAATATCATGCTTAGATCCAACTTGATCCGACCCATGAACACC
1 CTTGGGTAAACATAAAATATATTAATATCATGCTTAGAT----C-T--T-CGACCCATGAACACC
*
1896 TACACGAGATGATATTAAGCAGAAAAAATATGTTAAAAAACAAAAAAAAATTA
58 TACACGAGATGATATTAAGCAAAAAAAATATGTTAAAAAACAAAAAAAAATTA
*
1949 CTTGGGTAAACATAAAATATTTTAATATCATGCTTAGATC
1 CTTGGGTAAACATAAAATATATTAATATCATGCTTAGATC
1989 CAACTTCATC
Statistics
Matches: 144, Mismatches: 4, Indels: 14
0.89 0.02 0.09
Matches are distributed among these distances:
108 38 0.26
112 1 0.01
114 1 0.01
116 1 0.01
118 103 0.72
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.27
Consensus pattern (110 bp):
CTTGGGTAAACATAAAATATATTAATATCATGCTTAGATCTTCGACCCATGAACACCTACACGAG
ATGATATTAAGCAAAAAAAATATGTTAAAAAACAAAAAAAAATTA
Found at i:1974 original size:118 final size:118
Alignment explanation
Indices: 1754--2018 Score: 476
Period size: 118 Copynumber: 2.2 Consensus size: 118
1744 TTAATATCAT
* *
1754 ACTTAGATCTGACCCATGAACACCTACACGAGATGATATTGAGCAAAAAAAATATGTTAAAAAAC
1 ACTT-GATCCGACCCATGAACACCTACACGAGATGATATTAAGCAAAAAAAATATGTTAAAAAAC
1819 AAAAAAAAATTACTTGGGTAAACATAAAATATATTAATATCATGCTTAGATCCA
65 AAAAAAAAATTACTTGGGTAAACATAAAATATATTAATATCATGCTTAGATCCA
*
1873 ACTTGATCCGACCCATGAACACCTACACGAGATGATATTAAGCAGAAAAAATATGTTAAAAAACA
1 ACTTGATCCGACCCATGAACACCTACACGAGATGATATTAAGCAAAAAAAATATGTTAAAAAACA
*
1938 AAAAAAAATTACTTGGGTAAACATAAAATATTTTAATATCATGCTTAGATCCA
66 AAAAAAAATTACTTGGGTAAACATAAAATATATTAATATCATGCTTAGATCCA
*
1991 ACTTCATCCGACCCATGAACACCTACAC
1 ACTTGATCCGACCCATGAACACCTACAC
2019 CAGGGGCAAA
Statistics
Matches: 141, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
118 137 0.97
119 4 0.03
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (118 bp):
ACTTGATCCGACCCATGAACACCTACACGAGATGATATTAAGCAAAAAAAATATGTTAAAAAACA
AAAAAAAATTACTTGGGTAAACATAAAATATATTAATATCATGCTTAGATCCA
Found at i:3375 original size:15 final size:14
Alignment explanation
Indices: 3357--3397 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
3347 TGGAAAATAT
3357 TTTTAATTTATTCGA
1 TTTTAATTTATT-GA
*
3372 TTTTAATTTATTTA
1 TTTTAATTTATTGA
3386 TTTTAATATTAT
1 TTTTAAT-TTAT
3398 ATTATCCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTTAATTTATTGA
Found at i:3800 original size:8 final size:8
Alignment explanation
Indices: 3787--3819 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
3777 ACCCGACCCC
3787 CCCTCTCT
1 CCCTCTCT
3795 CCCTCTCT
1 CCCTCTCT
3803 CCCTCTCT
1 CCCTCTCT
3811 CCCTCTCT
1 CCCTCTCT
3819 C
1 C
3820 TGTGTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (8 bp):
CCCTCTCT
Found at i:18403 original size:144 final size:143
Alignment explanation
Indices: 18143--18427 Score: 301
Period size: 143 Copynumber: 2.0 Consensus size: 143
18133 CTTTTACTAG
* * * *
18143 AAAAAACTAAAACTAATTCTAAAAGATGATAAATAAATAAATAAATAAAAGATCAAATCGATTTT
1 AAAAAACTAAAACTAATTCTAAAAAAAGATAAAAAAATAAATAAATAAAAGATCAAATAGATTTT
* * * * * * *
18208 CATATAAAAACTCAATTTTTCCCAATAAAAACTCAAATAATTCTTTGTAAAATCTTAGATTTTTC
66 CAAATAAAAAATCAAGTTTTCCCAATAAAAACCCAAATAATTCTCTATAAAA-CTCAGATTTTTC
18273 CC-TTTAATCAGGA
130 CCATTTAATCAGGA
* *
18286 AAAAAACTAAAATTAATGT-TAAAAAAAGA-AAAAAAATAAATGAAATAAAAAGAT-AAATAGTT
1 AAAAAACTAAAACTAAT-TCTAAAAAAAGATAAAAAAATAAAT-AAAT-AAAAGATCAAATAGAT
** * ** *
18348 TTTCCAAATAAAAAATCAAGTTTTCCCTGT-AAAACCCAAGTTTTTTCTCTATAAAACTCAGTTT
63 TTT-CAAATAAAAAATCAAGTTTTCCCAATAAAAACCCAA-ATAATTCTCTATAAAACTCAGATT
*
18412 TTTCCCATTTACTCAG
126 TTTCCCATTTAATCAG
18428 TTTTTATTTT
Statistics
Matches: 116, Mismatches: 20, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
142 11 0.09
143 57 0.49
144 48 0.41
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (143 bp):
AAAAAACTAAAACTAATTCTAAAAAAAGATAAAAAAATAAATAAATAAAAGATCAAATAGATTTT
CAAATAAAAAATCAAGTTTTCCCAATAAAAACCCAAATAATTCTCTATAAAACTCAGATTTTTCC
CATTTAATCAGGA
Found at i:18410 original size:21 final size:22
Alignment explanation
Indices: 18368--18417 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
18358 AAAAATCAAG
*
18368 TTTTCCCTGTAAAACCCAAGTT
1 TTTTCCCTATAAAACCCAAGTT
* *
18390 TTTTCTCTATAAAACTC-AGTT
1 TTTTCCCTATAAAACCCAAGTT
18411 TTTTCCC
1 TTTTCCC
18418 ATTTACTCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.24, C:0.26, G:0.06, T:0.44
Consensus pattern (22 bp):
TTTTCCCTATAAAACCCAAGTT
Found at i:19629 original size:6 final size:6
Alignment explanation
Indices: 19618--19691 Score: 50
Period size: 6 Copynumber: 12.5 Consensus size: 6
19608 CGGGGCCAAC
* * *
19618 AAATTT AAATTT -ATTTT AAAATT AAGTTT --ATTCT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATT-T AAATTT AAATTT
19664 AAAAGTTT --ATTCT AAATTT AAATTT AAA
1 -AAA-TTT AAATT-T AAATTT AAATTT AAA
19692 ATTCATTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
4 4 0.08
5 7 0.13
6 30 0.57
7 9 0.17
8 3 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:19647 original size:17 final size:17
Alignment explanation
Indices: 19622--19664 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
19612 GCCAACAAAT
*
19622 TTAAATTTATTTTAAAA
1 TTAAATTTATTCTAAAA
* *
19639 TTAAGTTTATTCTAAAT
1 TTAAATTTATTCTAAAA
19656 TTAAATTTA
1 TTAAATTTA
19665 AAAGTTTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTCTAAAA
Found at i:19675 original size:25 final size:25
Alignment explanation
Indices: 19641--19692 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
19631 TTTTAAAATT
19641 AAGTTTATTCTAAATTTAAATTTAA
1 AAGTTTATTCTAAATTTAAATTTAA
19666 AAGTTTATTCTAAATTTAAATTTAA
1 AAGTTTATTCTAAATTTAAATTTAA
19691 AA
1 AA
19693 TTCATTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (25 bp):
AAGTTTATTCTAAATTTAAATTTAA
Found at i:21628 original size:30 final size:29
Alignment explanation
Indices: 21580--21952 Score: 341
Period size: 29 Copynumber: 12.9 Consensus size: 29
21570 AAAAATTTTG
*
21580 TTTTTACCCCCGAACTTCCAAAAATCCCA
1 TTTTTACCCTCGAACTTCCAAAAATCCCA
** **
21609 TTTTTGACCCTAAAACTTCCAAAAATTTCA
1 TTTTT-ACCCTCGAACTTCCAAAAATCCCA
* *
21639 TTTTTACCCCCGCACTTCCAAAAATCCCA
1 TTTTTACCCTCGAACTTCCAAAAATCCCA
* *
21668 TTTTTAACCTCAAAACTTCCAAAAATCCCA
1 TTTTTACCCTC-GAACTTCCAAAAATCCCA
* ** *
21698 TTTTAATCCC-AAAACTTCCAAAAATTCCA
1 TTTTTA-CCCTCGAACTTCCAAAAATCCCA
* ****
21727 TTTTTACCC-CTGAACTTCC-AAATTTTTT
1 TTTTTACCCTC-GAACTTCCAAAAATCCCA
*
21755 TTTTTATCCC-CGAATTTCCAAAAATCCCA
1 TTTTTA-CCCTCGAACTTCCAAAAATCCCA
* *
21784 TTTTTGA-CCTCGAA--TACAAAAATTCCA
1 TTTTT-ACCCTCGAACTTCCAAAAATCCCA
*
21811 TTTTTACCCCCGAACTTCCAAAAATCCCA
1 TTTTTACCCTCGAACTTCCAAAAATCCCA
*
21840 TTTTTGACCCT-GAAACTTCCAAAAATTCCA
1 TTTTT-ACCCTCG-AACTTCCAAAAATCCCA
** *
21870 TTTTTACCCTCGAACTTTTAAAAATACCA
1 TTTTTACCCTCGAACTTCCAAAAATCCCA
* *
21899 TTTTTACACTCGAACTTCAAAAAATCCCA
1 TTTTTACCCTCGAACTTCCAAAAATCCCA
*
21928 TTTTGA-CCTCGAAACTTCCAAAAAT
1 TTTTTACCCTCG-AACTTCCAAAAAT
21953 TACCATTTCA
Statistics
Matches: 280, Mismatches: 49, Indels: 30
0.78 0.14 0.08
Matches are distributed among these distances:
26 1 0.00
27 22 0.08
28 27 0.10
29 156 0.56
30 72 0.26
31 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
TTTTTACCCTCGAACTTCCAAAAATCCCA
Found at i:21662 original size:59 final size:59
Alignment explanation
Indices: 21580--21952 Score: 377
Period size: 59 Copynumber: 6.4 Consensus size: 59
21570 AAAAATTTTG
*
21580 TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTTCA
1 TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTCCA
* * *
21639 TTTTTACCCCCGCACTTCCAAAAATCCCATTTTT-AACCTCAAAACTTCCAAAAATCCCA
1 TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCT-AAAACTTCCAAAAATTCCA
* * ** * * * ***
21698 TTTTAATCCCAAAACTTCCAAAAATTCCATTTTT-ACCCCT-GAACTTCC-AAATTTTTT
1 TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCTAAAACTTCCAAAAATTCCA
* * ** *
21755 TTTTTATCCCCGAATTTCCAAAAATCCCATTTTTGA-CCTCGAA--TACAAAAATTCCA
1 TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTCCA
*
21811 TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTGAAACTTCCAAAAATTCCA
1 TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTCCA
* ** * * ** * *
21870 TTTTTACCCTCGAACTTTTAAAAATACCATTTTT-ACACTCGAACTTCAAAAAATCCCA
1 TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTCCA
* *
21928 TTTTGA-CCTCGAAACTTCCAAAAAT
1 TTTTTACCCCCG-AACTTCCAAAAAT
21953 TACCATTTCA
Statistics
Matches: 261, Mismatches: 44, Indels: 19
0.81 0.14 0.06
Matches are distributed among these distances:
55 2 0.01
56 42 0.16
57 46 0.18
58 47 0.18
59 121 0.46
60 3 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (59 bp):
TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTCCA
Found at i:21920 original size:143 final size:143
Alignment explanation
Indices: 21657--21940 Score: 337
Period size: 143 Copynumber: 2.0 Consensus size: 143
21647 CCCGCACTTC
*
21657 CAAAAATCCCATTTTTAACCTCAAAACTTCCAAAAATCCCATTTTAATCCCAAAACTTCCAAAAA
1 CAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTAATCCCAAAACTTCCAAAAA
* * **** *
21722 TTCCATTTTTACCCCTGAACTTCCAAATTTTTTTTTTTATCCCCGAATTTCC-AAAAATCCCATT
66 TTCCATTTTTACCCCTGAACTTCAAAAATACCATTTTTATCCCCGAACTTCCAAAAAATCCCA-T
21786 TTTGACCTCGAATA
130 TTTGACCTCGAATA
* ** * *
21800 CAAAAATTCCATTTTT-ACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCTGAAACTTCCAAA
1 CAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCA-TTTTAATCCC-AAAACTTCCAAA
* *
21863 AATTCCATTTTTA-CCCTCGAACTTTTAAAAATACCATTTTTA-CACTCGAACTT-CAAAAAATC
64 AATTCCATTTTTACCCCT-GAAC-TTCAAAAATACCATTTTTATC-CCCGAACTTCCAAAAAATC
21925 CCATTTTGACCTCGAA
126 CCATTTTGACCTCGAA
21941 ACTTCCAAAA
Statistics
Matches: 120, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
142 28 0.23
143 63 0.52
144 29 0.24
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (143 bp):
CAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTAATCCCAAAACTTCCAAAAA
TTCCATTTTTACCCCTGAACTTCAAAAATACCATTTTTATCCCCGAACTTCCAAAAAATCCCATT
TTGACCTCGAATA
Found at i:33682 original size:205 final size:201
Alignment explanation
Indices: 32724--33877 Score: 1591
Period size: 201 Copynumber: 5.7 Consensus size: 201
32714 AGCGATGCAA
* * *
32724 TCATTTTCCTGATGAGACACTGAGACGAAAACCCAAACGAGGCTCAAAGCGAGCAAAATCTTCGA
1 TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGCGAGCAAAATCTTCGA
* *
32789 ACCCCAGCTTCTTGATGAGACATTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGA
66 ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGA
* *
32854 GATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGAATTGAAAC-AGCG
131 GATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACG
* *
32918 ATGCGA
196 ACGCGG
*
32924 TCATCTTCCTGATGAGACATTGAGAAGAAGACCCAAACGAGGCTCAAAGCGAGCAAAATCTTCGA
1 TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGCGAGCAAAATCTTCGA
* * *
32989 ACCCCAGCTT-CTAGATGAGACATTGAGAAGCAGGTCGAAGCAATAAAAGATTAGCTTCCTAATG
66 ACCCCAGCTTCCT-GATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATG
33053 AGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAAC
130 AGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAAC
*
33118 GACGCAG
195 GACGCGG
33125 TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGCGAGCAAAATCTTCGA
1 TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGCGAGCAAAATCTTCGA
* * * *
33190 ACCCCAGCTTCTTGATGAGACATTGAGAAGCAGGTTGAAGCAATAAAAGGTTAGCTTCTTGATGA
66 ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGA
* *
33255 GATACTGAGAAGTGAACCAAATTCGTTTTCTTGATGAGATACAGAGAAGCGAATTGAAACAAACG
131 GATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACG
33320 ACGCGG
196 ACGCGG
* * *
33326 TCATCTTCCCGATGAGACACTGAGAAAAAGACCCAAACGAGGCTCAAAGCGAGCAAAATATTCGA
1 TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGCGAGCAAAATCTTCGA
* *
33391 ATCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCAATAAAAGGTTAGCTTCCTGATGA
66 ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGA
* * * *
33456 GATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGAGAATTGAAACACAGG
131 GATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACG
*
33521 ATGCGG
196 ACGCGG
* * * * * * * * *
33527 TCATCTTCCCGATGAGATATTGAGAAGAAGACCAAATCAAATCCACGCTCGATGTGAAC-AAATC
1 TCATCTTCCTGATGAGACACTGAGAAGAAGACC----CAAA-CGAGGCTCAAAGCGAGCAAAATC
* * * ** *
33591 TTCGAACCACAGTTTCCTGATGAGACACTGAGAAACAGGTCGAAGTGATAAAAGGTCAGCTTCCT
61 TTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCT
* *
33656 GATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGAATTGAAAC
126 GATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAAC
33721 AAACGACGCGG
191 AAACGACGCGG
* ** * * ** * * *
33732 TCATCTTCTTGATGAGTTACTAAGAAGAAGA-TCAAATC-A-AATCCATGCTCGATGTAAATGAA
1 TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAA-CGAGGCTCAAAG--CGA-G-CAA--AA
* * * * *
33794 TCTTCGAACCACGGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAATGGTTAGTTTA
59 TCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTC
33859 CTGATGAGATACTGAGAAG
124 CTGATGAGATACTGAGAAG
33878 AAGACCAAGT
Statistics
Matches: 856, Mismatches: 83, Indels: 25
0.89 0.09 0.03
Matches are distributed among these distances:
198 5 0.01
199 2 0.00
200 188 0.22
201 411 0.48
202 1 0.00
203 1 0.00
205 237 0.28
206 11 0.01
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (201 bp):
TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGCGAGCAAAATCTTCGA
ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGA
GATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACG
ACGCGG
Found at i:34227 original size:17 final size:17
Alignment explanation
Indices: 34202--34249 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
34192 CCGGCCCCAA
*
34202 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTC
* *
34219 TAAAATTAAGTTTATTC
1 TAAATTTAAATTTATTC
34236 TAAATTTAAATTTA
1 TAAATTTAAATTTA
34250 AAATTCATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TAAATTTAAATTTATTC
Found at i:34932 original size:59 final size:58
Alignment explanation
Indices: 34844--35174 Score: 346
Period size: 59 Copynumber: 5.7 Consensus size: 58
34834 CCCTAAACGA
* * *
34844 TCCAAAAATTCCGTTTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCTAAAACT
1 TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCTCATTTTT-ACCCTAAAACT
* *
34903 TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTTCATTTTTACCCGCAAAA-T
1 TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCTCATTTTTACCC-TAAAACT
* **
34961 TCCAAAAATCCCATTTTTAACCC-CAAAACTTCCAAAAAT-TCCATTTTTACCCCCAAACT
1 TCCAAAAATTCCATTTTT-ACCCTC-AAACTTCCAAAAATCT-CATTTTTACCCTAAAACT
* *** * * * *
35020 TTCAAAAATTTTGTTTTTACCCTCGAACTTCCCAAAATCCCATTTTTGA-CCTCGAAACT
1 TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCTCATTTTT-ACCCT-AAAACT
* * * * **
35079 TCCAAAAATTCCATTTTTACCTTCGAACTTCTAAAAATCCCATTTTTACCCTCGAACT
1 TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCTCATTTTTACCCTAAAACT
* * *
35137 TCCAAAAATCCCATTTTAACCCTGAAACTTCCAAAAAT
1 TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAAT
35175 TACCATTTCA
Statistics
Matches: 230, Mismatches: 32, Indels: 21
0.81 0.11 0.07
Matches are distributed among these distances:
58 90 0.39
59 140 0.61
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCTCATTTTTACCCTAAAACT
Found at i:34993 original size:88 final size:88
Alignment explanation
Indices: 34844--35212 Score: 449
Period size: 88 Copynumber: 4.2 Consensus size: 88
34834 CCCTAAACGA
* * * * *
34844 TCCAAAAATTCCGTTTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCTAAAACTTCCAAA
1 TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAA
34909 AATTCCATTTTTACCCTCAAACT
66 AATTCCATTTTTACCCTCAAACT
* * * *
34932 TCCAAAAATTTCATTTTTACCCGCAAAATTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAA
1 TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAA
*
34997 AATTCCATTTTTACCCCCAAACT
66 AATTCCATTTTTACCCTCAAACT
* *** * * * *
35020 TTCAAAAATTTTGTTTTTACCCTCGAACTTCCCAAAATCCCATTTTTGACCTCGAAACTTCCAAA
1 TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAA
* *
35085 AATTCCATTTTTACCTTCGAACT
66 AATTCCATTTTTACCCTCAAACT
* * **
35108 TCTAAAAATCCCATTTTTACCCTCGAACTTCCAAAAATCCCA-TTTTAACCCTGAAACTTCCAAA
1 TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAA
*
35172 AATTACCA-TTTCACCCTCGAGAA--
66 AATT-CCATTTTTACCCTC-A-AACT
35195 TCCAAAAATTACCATTTT
1 TCCAAAAATT-CCATTTT
35213 GCCCCCGGGT
Statistics
Matches: 240, Mismatches: 37, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
87 39 0.16
88 199 0.83
89 2 0.01
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (88 bp):
TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAA
AATTCCATTTTTACCCTCAAACT
Found at i:35181 original size:59 final size:57
Alignment explanation
Indices: 34844--35212 Score: 338
Period size: 59 Copynumber: 6.3 Consensus size: 57
34834 CCCTAAACGA
* * *
34844 TCCAAAAATTCCGTTTTTACCCCCG-AACTTCCAAAAATCTCATTTTTGACCCTAAAACT
1 TCCAAAAATTCCATTTTTA-CCCTGAAACTTCCAAAAATC-CATTTTT-ACCCTCAAACT
* * * *
34903 TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTTCATTTTTACCCGCAAAAT
1 TCCAAAAATTCCATTTTTACCCTGAAACTTCCAAAAA-TCCATTTTTACCCTCAAACT
* ** *
34961 TCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACT
1 TCCAAAAATTCCATTTTT-ACCCTGAAACTTCCAAAAA-TCCATTTTTACCCTCAAACT
* *** *
35020 TTCAAAAATTTTGTTTTTACCCTCG-AACTTCCCAAAATCCCATTTTTGA-CCTCGAAACT
1 TCCAAAAATTCCATTTTTACCCT-GAAACTTCCAAAAAT-CCATTTTT-ACCCTC-AAACT
* * *
35079 TCCAAAAATTCCATTTTTACCTTCG-AACTTCTAAAAATCCCATTTTTACCCTCGAACT
1 TCCAAAAATTCCATTTTTACCCT-GAAACTTCCAAAAAT-CCATTTTTACCCTCAAACT
* * *
35137 TCCAAAAATCCCATTTTAACCCTGAAACTTCCAAAAATTACCA-TTTCACCCTCGAGAA--
1 TCCAAAAATTCCATTTTTACCCTGAAACTTCCAAAAA-T-CCATTTTTACCCTC-A-AACT
35195 TCCAAAAATTACCATTTT
1 TCCAAAAATT-CCATTTT
35213 GCCCCCGGGT
Statistics
Matches: 259, Mismatches: 38, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
57 2 0.01
58 108 0.42
59 146 0.56
60 3 0.01
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (57 bp):
TCCAAAAATTCCATTTTTACCCTGAAACTTCCAAAAATCCATTTTTACCCTCAAACT
Found at i:35187 original size:29 final size:29
Alignment explanation
Indices: 34844--35212 Score: 335
Period size: 29 Copynumber: 12.6 Consensus size: 29
34834 CCCTAAACGA
* *
34844 TCCAAAAATTCCGTTTTTACCCCCG-AACT
1 TCCAAAAATTCCATTTTTA-CCCTGAAACT
*
34873 TCCAAAAA-TCTCATTTTTGACCCTAAAACT
1 TCCAAAAATTC-CATTTTT-ACCCTGAAACT
*
34903 TCCAAAAATTCCATTTTTACCCTCAAACT
1 TCCAAAAATTCCATTTTTACCCTGAAACT
* *
34932 TCCAAAAATTTCATTTTTACCC-GCAAAAT
1 TCCAAAAATTCCATTTTTACCCTG-AAACT
* **
34961 TCCAAAAATCCCATTTTTAACCCCAAAACT
1 TCCAAAAATTCCATTTTT-ACCCTGAAACT
**
34991 TCCAAAAATTCCATTTTTACCCCCAAACT
1 TCCAAAAATTCCATTTTTACCCTGAAACT
* ***
35020 TTCAAAAATTTTGTTTTTACCCTCG-AACT
1 TCCAAAAATTCCATTTTTACCCT-GAAACT
* *
35049 TCCCAAAATCCCATTTTTGA-CCTCGAAACT
1 TCCAAAAATTCCATTTTT-ACCCT-GAAACT
*
35079 TCCAAAAATTCCATTTTTACCTTCG-AACT
1 TCCAAAAATTCCATTTTTACCCT-GAAACT
* *
35108 TCTAAAAATCCCATTTTTACCCTCG-AACT
1 TCCAAAAATTCCATTTTTACCCT-GAAACT
* *
35137 TCCAAAAATCCCATTTTAACCCTGAAACT
1 TCCAAAAATTCCATTTTTACCCTGAAACT
*
35166 TCCAAAAATTACCA-TTTCACCCTCGAGAA--
1 TCCAAAAATT-CCATTTTTACCCT-GA-AACT
35195 TCCAAAAATTACCATTTT
1 TCCAAAAATT-CCATTTT
35213 GCCCCCGGGT
Statistics
Matches: 289, Mismatches: 35, Indels: 31
0.81 0.10 0.09
Matches are distributed among these distances:
28 3 0.01
29 204 0.71
30 78 0.27
31 4 0.01
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTACCCTGAAACT
Found at i:38371 original size:16 final size:17
Alignment explanation
Indices: 38318--38373 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
38308 CAAATTTATT
*
38318 TTAAAATTTAAATTTAA
1 TTAAAATTTAAATTAAA
* *
38335 TTAAAATTTAAATTGAT
1 TTAAAATTTAAATTAAA
*
38352 TTAAAACTT-AATTAAA
1 TTAAAATTTAAATTAAA
38368 TTAAAA
1 TTAAAA
38374 GTCCAAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 11 0.32
17 23 0.68
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TTAAAATTTAAATTAAA
Found at i:38382 original size:34 final size:35
Alignment explanation
Indices: 38308--38382 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 35
38298 TAAATTGATT
* * * *
38308 CAAATTTATTTTAAAATTTAAATTTAATTAAAATT
1 CAAATTGATTTTAAAACTTAAATTAAATTAAAATC
*
38343 TAAATTGA-TTTAAAACTT-AATTAAATTAAAAGTC
1 CAAATTGATTTTAAAACTTAAATTAAATTAAAA-TC
38377 CAAATT
1 CAAATT
38383 ACAAATCTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
33 12 0.36
34 15 0.45
35 6 0.18
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (35 bp):
CAAATTGATTTTAAAACTTAAATTAAATTAAAATC
Done.