Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012818.1 Kokia drynarioides strain JFW-HI SEQ_127831, 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: 241526
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 18 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--31 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1 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 A
32 AATACACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12717 original size:19 final size:19
Alignment explanation
Indices: 12693--12739 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
12683 AGGTTTGGTG
12693 AGATGAAATCTTTTGGAGA
1 AGATGAAATCTTTTGGAGA
12712 AGATGAAATCTTTTGGAGA
1 AGATGAAATCTTTTGGAGA
12731 AGATGAAAT
1 AGATGAAAT
12740 TTTCTACCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.30
Consensus pattern (19 bp):
AGATGAAATCTTTTGGAGA
Found at i:13385 original size:21 final size:21
Alignment explanation
Indices: 13348--13387 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13338 CAAAACGAAT
*
13348 TAATTTTATCTTTTAACTTAA
1 TAATTTTATCTTGTAACTTAA
13369 TAATTTTGA-CTTGTAACTT
1 TAATTTT-ATCTTGTAACTT
13388 TAAAAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.55
Consensus pattern (21 bp):
TAATTTTATCTTGTAACTTAA
Found at i:19460 original size:41 final size:42
Alignment explanation
Indices: 19415--19878 Score: 230
Period size: 40 Copynumber: 11.7 Consensus size: 42
19405 TTGATATCGA
19415 GGTAAGAGATTGGATGATAGCTTCAATCTG-CCCATGATCAG
1 GGTAAGAGATTGGATGATAGCTTCAATCTGCCCCATGATCAG
* * * *
19456 GGTAAAAGATTGGATGATATCTTCAATTTGCCCCATAATCAG
1 GGTAAGAGATTGGATGATAGCTTCAATCTGCCCCATGATCAG
* * *
19498 GGTAAGAGATTGGATGAT-GTCTTCAATCTGTCTCATGATCGG
1 GGTAAGAGATTGGATGATAG-CTTCAATCTGCCCCATGATCAG
* * * *
19540 GGTAAGAGATTGGATG--A-CTTTAACCTACCCCATGATCTG
1 GGTAAGAGATTGGATGATAGCTTCAATCTGCCCCATGATCAG
** * ***
19579 GGTAAGAGAACGG-T-AT-GTCTTCAATCTACCTTTTGATCAG
1 GGTAAGAGATTGGATGATAG-CTTCAATCTGCCCCATGATCAG
* * * * * *
19619 GGTAAAAGATT-G--GAT-GCTTCTATTTACCCCATGGTCGG
1 GGTAAGAGATTGGATGATAGCTTCAATCTGCCCCATGATCAG
* * *
19657 GGTAAGAGATTTG-TG-T-GTCTTCAATCTACCCTC-TGATTA-
1 GGTAAGAGATTGGATGATAG-CTTCAATCTGCCC-CATGATCAG
* * * * * *
19696 GGTAAAAGATT--A-GAT-GTTTCAATCTACCCTATGGTCGG
1 GGTAAGAGATTGGATGATAGCTTCAATCTGCCCCATGATCAG
* * *
19734 GGTAAGAGA-TCGAT-AT-GTCTTCAATCTGCCCTC-TAATTAG
1 GGTAAGAGATTGGATGATAG-CTTCAATCTGCCC-CATGATCAG
*
19774 GGTAAAAGATT-GA--AT-GCTTCAATCTGCCCCATGATC-G
1 GGTAAGAGATTGGATGATAGCTTCAATCTGCCCCATGATCAG
* *
19811 GAATAA-AGATTGG-TG-T-GTCTTCAATCTGCCCTC-TGATTAG
1 G-GTAAGAGATTGGATGATAG-CTTCAATCTGCCC-CATGATCAG
19851 GGTAAGAGATT-GATG-T-GTCTTCAATCTG
1 GGTAAGAGATTGGATGATAG-CTTCAATCTG
19879 TCCCTTCCAA
Statistics
Matches: 330, Mismatches: 61, Indels: 65
0.72 0.13 0.14
Matches are distributed among these distances:
37 25 0.08
38 58 0.18
39 72 0.22
40 86 0.26
41 29 0.09
42 60 0.18
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (42 bp):
GGTAAGAGATTGGATGATAGCTTCAATCTGCCCCATGATCAG
Found at i:19684 original size:78 final size:78
Alignment explanation
Indices: 19410--19862 Score: 421
Period size: 77 Copynumber: 5.7 Consensus size: 78
19400 CCCTCTTGAT
* *
19410 ATCGAGGTAAGAGATTGGATGATAG-CTTCAATCTGCCC-ATGATCAGGGTAAAAGATTGGATGA
1 ATCGGGGTAAGAGATTGG-TG-T-GTCTTCAATCTGCCCTCTGATCAGGGTAAAAGATTGGATG-
* * *
19473 TATCTTCAATTTGCCCCATA
62 ---CTTCAATCTACCCCATG
* * * *
19493 ATCAGGGTAAGAGATTGGATGATGTCTTCAATCTG-TCTCATGATCGGGGTAAGAGATTGGATGA
1 ATCGGGGTAAGAGATTGG-TG-TGTCTTCAATCTGCCCTC-TGATCAGGGTAAAAGATTGGATG-
* *
19557 CTTTAACCTACCCCATG
62 CTTCAATCTACCCCATG
* ** * * * *
19574 ATCTGGGTAAGAGAACGGTATGTCTTCAATCTACCTTTTGATCAGGGTAAAAGATTGGATGCTTC
1 ATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGATCAGGGTAAAAGATTGGATGCTTC
* *
19639 TATTTACCCCATG
66 AATCTACCCCATG
* * * * * *
19652 GTCGGGGTAAGAGATTTGTGTGTCTTCAATCTACCCTCTGATTA-GGTAAAAGATTAGATGTTTC
1 ATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGATCAGGGTAAAAGATTGGATGCTTC
*
19716 AATCTACCCTATG
66 AATCTACCCCATG
* * * * * * *
19729 GTCGGGGTAAGAGATCGATATGTCTTCAATCTGCCCTCTAATTAGGGTAAAAGATTGAATGCTTC
1 ATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGATCAGGGTAAAAGATTGGATGCTTC
*
19794 AATCTGCCCCATG
66 AATCTACCCCATG
** * *
19807 ATCGGAATAA-AGATTGGTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAGAGATTG
1 ATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGATCAGGGTAAAAGATTG
19863 ATGTGTCTTC
Statistics
Matches: 306, Mismatches: 59, Indels: 16
0.80 0.15 0.04
Matches are distributed among these distances:
77 107 0.35
78 83 0.27
79 33 0.11
80 2 0.01
81 27 0.09
82 2 0.01
83 31 0.10
84 21 0.07
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (78 bp):
ATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGATCAGGGTAAAAGATTGGATGCTTC
AATCTACCCCATG
Found at i:19753 original size:155 final size:152
Alignment explanation
Indices: 19435--19866 Score: 454
Period size: 155 Copynumber: 2.8 Consensus size: 152
19425 TGGATGATAG
* * * *
19435 CTTCAATCTGCCC-ATGATCAGGGTAAAAGATTGGATGATATCTTCAATTTGCCCCATAATCAGG
1 CTTCAATCTACCCTCTGATCAGGGTAAAAGATTGGATG----CTTCAATTTGCCCCATGATCGGG
** **
19499 GTAAGAGATTGGATGATGTCTTCAATCTGTCTCATGATCGGGGTAAGAGATTGGATGACTTTAAC
62 GTAAGAGATTGG-TG-TGTCTTCAATCTCCCTC-TGAT-TAGGTAAGAGATT-GATG--TTTAAC
* *
19564 CTACCCCATGATCTGGGTAAGAGAACGGTATGT
120 CTACCCCATGATCGGGGTAAGAGAACGATATGT
* * * * *
19597 CTTCAATCTACCTTTTGATCAGGGTAAAAGATTGGATGCTTCTATTTACCCCATGGTCGGGGTAA
1 CTTCAATCTACCCTCTGATCAGGGTAAAAGATTGGATGCTTCAATTTGCCCCATGATCGGGGTAA
* * * *
19662 GAGATTTGTGTGTCTTCAATCTACCCTCTGATTAGGTAAAAGATTAGATGTTTCAATCTACCCTA
66 GAGATTGGTGTGTCTTCAATCT-CCCTCTGATTAGGTAAGAGATT-GATGTTT-AACCTACCCCA
* *
19727 TGGTCGGGGTAAGAGATCGATATGT
128 TGATCGGGGTAAGAGAACGATATGT
* * * * * **
19752 CTTCAATCTGCCCTCTAATTAGGGTAAAAGATTGAATGCTTCAATCTGCCCCATGATCGGAATAA
1 CTTCAATCTACCCTCTGATCAGGGTAAAAGATTGGATGCTTCAATTTGCCCCATGATCGGGGTAA
19817 -AGATTGGTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAGAGATTGATGT
66 GAGATTGGTGTGTCTTCAATCT-CCCTCTGATTA-GGTAAGAGATTGATGT
19867 GTCTTCAATC
Statistics
Matches: 230, Mismatches: 36, Indels: 16
0.82 0.13 0.06
Matches are distributed among these distances:
154 39 0.17
155 93 0.40
156 14 0.06
157 16 0.07
158 5 0.02
159 29 0.13
162 11 0.05
163 23 0.10
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (152 bp):
CTTCAATCTACCCTCTGATCAGGGTAAAAGATTGGATGCTTCAATTTGCCCCATGATCGGGGTAA
GAGATTGGTGTGTCTTCAATCTCCCTCTGATTAGGTAAGAGATTGATGTTTAACCTACCCCATGA
TCGGGGTAAGAGAACGATATGT
Found at i:20278 original size:49 final size:48
Alignment explanation
Indices: 20204--20424 Score: 176
Period size: 49 Copynumber: 4.5 Consensus size: 48
20194 AAATATAAGA
** * *
20204 TTCACCGTCATGGCTTCAATCTTTCCCCTCACATCTCTAAAGTACAAGG
1 TTCACCGTTGTGGCTTCAACCTTT-CCCTCACATCTCTAAGGTACAAGG
* * * *
20253 TCCACCGTTGTGGCTTCAACCTTTCCCTCCACATCTAT-AGGTTATAAGA
1 TTCACCGTTGTGGCTTCAACCTTTCCCT-CACATCTCTAAGG-TACAAGG
*** * * * * *
20302 TTTGTCGTTGCGGTTTCAATCCTTTTCATCACATCTTTAAGGTACAAGG
1 TTCACCGTTGTGGCTTCAA-CCTTTCCCTCACATCTCTAAGGTACAAGG
* * * ** *
20351 TTCGCCATTGTGGCCTCAACCTTTCCCTCGTATCTCTAAGGTACAAAG
1 TTCACCGTTGTGGCTTCAACCTTTCCCTCACATCTCTAAGGTACAAGG
*
20399 TTCACCGTTATGGCCTT-AACCTTTCC
1 TTCACCGTTGTGG-CTTCAACCTTTCC
20425 TACCGTATCT
Statistics
Matches: 132, Mismatches: 35, Indels: 11
0.74 0.20 0.06
Matches are distributed among these distances:
48 48 0.36
49 74 0.56
50 10 0.08
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.34
Consensus pattern (48 bp):
TTCACCGTTGTGGCTTCAACCTTTCCCTCACATCTCTAAGGTACAAGG
Found at i:20395 original size:48 final size:48
Alignment explanation
Indices: 20334--20446 Score: 138
Period size: 48 Copynumber: 2.3 Consensus size: 48
20324 TTTTCATCAC
* * *
20334 ATCTTTAAGGTACAAGGTTCGCCATTGTGGCCTCAACCTTTCCCT-CGT
1 ATCTCTAAGGTACAAGGTTCACCATTATGGCCTCAACCTTT-CCTACGT
* * *
20382 ATCTCTAAGGTACAAAGTTCACCGTTATGGCCTTAACCTTTCCTACCGT
1 ATCTCTAAGGTACAAGGTTCACCATTATGGCCTCAACCTTTCCTA-CGT
*
20431 ATCTCTAGGGTACAAG
1 ATCTCTAAGGTACAAG
20447 ATTTACCGTT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
47 3 0.05
48 35 0.64
49 17 0.31
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (48 bp):
ATCTCTAAGGTACAAGGTTCACCATTATGGCCTCAACCTTTCCTACGT
Found at i:24253 original size:23 final size:23
Alignment explanation
Indices: 24227--24272 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
24217 TTCATTTAAC
*
24227 TTAATCAAACATGTTCACGAACA
1 TTAAACAAACATGTTCACGAACA
*
24250 TTAAACGAACATGTTCACGAACA
1 TTAAACAAACATGTTCACGAACA
24273 ATATTAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.22, G:0.11, T:0.24
Consensus pattern (23 bp):
TTAAACAAACATGTTCACGAACA
Found at i:24269 original size:12 final size:12
Alignment explanation
Indices: 24234--24272 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
24224 AACTTAATCA
24234 AACATGTTCACG
1 AACATGTTCACG
**
24246 AACAT-TAAACG
1 AACATGTTCACG
24257 AACATGTTCACG
1 AACATGTTCACG
24269 AACA
1 AACA
24273 ATATTAGTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.44, C:0.23, G:0.13, T:0.21
Consensus pattern (12 bp):
AACATGTTCACG
Found at i:28216 original size:28 final size:28
Alignment explanation
Indices: 28184--28243 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
28174 TCGACCCGGC
*
28184 CCGTTGACCATTAACAGTTGATCGTTGA
1 CCGTTAACCATTAACAGTTGATCGTTGA
* * *
28212 CCGTTAATCGTTAACAGTTTATCGTTGA
1 CCGTTAACCATTAACAGTTGATCGTTGA
28240 CCGT
1 CCGT
28244 CGATAATTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (28 bp):
CCGTTAACCATTAACAGTTGATCGTTGA
Found at i:28221 original size:14 final size:14
Alignment explanation
Indices: 28204--28243 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
28194 TTAACAGTTG
28204 ATCGTTGACCGTTA
1 ATCGTTGACCGTTA
* * *
28218 ATCGTTAACAGTTT
1 ATCGTTGACCGTTA
28232 ATCGTTGACCGT
1 ATCGTTGACCGT
28244 CGATAATTGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (14 bp):
ATCGTTGACCGTTA
Found at i:28256 original size:21 final size:21
Alignment explanation
Indices: 28232--28282 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
28222 TTAACAGTTT
28232 ATCGTTGACCGTCGATAATTG
1 ATCGTTGACCGTCGATAATTG
28253 ATCGTTGACCGTCGATAATTG
1 ATCGTTGACCGTCGATAATTG
28274 ATCGTTGAC
1 ATCGTTGAC
28283 TTTTTTCGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (21 bp):
ATCGTTGACCGTCGATAATTG
Found at i:28829 original size:27 final size:27
Alignment explanation
Indices: 28773--28837 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
28763 GTGTTTTGTT
28773 AATGTGATGATT-TTGTTGAGATGAGAA
1 AATGT-ATGATTGTTGTTGAGATGAGAA
* *
28800 AATGGTATGATTGTTGTTGAGTTGTG-A
1 AAT-GTATGATTGTTGTTGAGATGAGAA
28827 AATGTAT-ATTG
1 AATGTATGATTG
28838 ATAATGTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 4 0.12
26 4 0.12
27 13 0.38
28 13 0.38
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (27 bp):
AATGTATGATTGTTGTTGAGATGAGAA
Found at i:29670 original size:49 final size:49
Alignment explanation
Indices: 29617--29818 Score: 165
Period size: 49 Copynumber: 4.1 Consensus size: 49
29607 CGGGCTAAAT
* * *
29617 CTTTCCCATCACATCTTTAAGGTACAAGGTTCGCCGTTGCGGCCTTAAC
1 CTTTCCCATCACATCTCTAAGGTACAAGGTTCACCGTTGCGGCCTCAAC
* * * * * * * * * **
29666 CTTTCCCTTCATATCTCCATGGTTCTAGATTAATCGTTGCGGTTTCAATC
1 CTTTCCCATCACATCTCTAAGGTACAAGGTTCACCGTTGCGGCCTCAA-C
** * *
29716 C-TTCCCATCATGTCTCTAAGGTACAAGGTTCGCCGTTGCGGTCTCAAC
1 CTTTCCCATCACATCTCTAAGGTACAAGGTTCACCGTTGCGGCCTCAAC
** * * * *
29764 CTTT-CTTTCGCATCTCTAAGGTACAAGGTTCATCGTTACTGCCTCAAC
1 CTTTCCCATCACATCTCTAAGGTACAAGGTTCACCGTTGCGGCCTCAAC
29812 CTTTCCC
1 CTTTCCC
29819 TCCGTATCTC
Statistics
Matches: 114, Mismatches: 36, Indels: 6
0.73 0.23 0.04
Matches are distributed among these distances:
48 40 0.35
49 72 0.63
50 2 0.02
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (49 bp):
CTTTCCCATCACATCTCTAAGGTACAAGGTTCACCGTTGCGGCCTCAAC
Found at i:29784 original size:48 final size:47
Alignment explanation
Indices: 29728--29866 Score: 143
Period size: 48 Copynumber: 2.9 Consensus size: 47
29718 TCCCATCATG
* * *
29728 TCTCTAAGGTACAAGGTTCGCCGTTGCGGTCTCAACCTTTCTTTCGCA
1 TCTCTAAGGTACAAGGTTCGCCGTTAC-GACTCAACCTTTCTTCCGCA
** * * *
29776 TCTCTAAGGTACAAGGTTCATCGTTACTGCCTCAACCTTTCCCTCCGTA
1 TCTCTAAGGTACAAGGTTCGCCGTTAC-GACTCAACCTTT-CTTCCGCA
* * *
29825 TCTCTAGGGTATAAGGTTTGCCGTTACGACATCAACCTTTCT
1 TCTCTAAGGTACAAGGTTCGCCGTTACGAC-TCAACCTTTCT
29867 AGTTAATTTA
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
48 38 0.51
49 36 0.49
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (47 bp):
TCTCTAAGGTACAAGGTTCGCCGTTACGACTCAACCTTTCTTCCGCA
Found at i:29850 original size:49 final size:48
Alignment explanation
Indices: 29728--29865 Score: 143
Period size: 49 Copynumber: 2.8 Consensus size: 48
29718 TCCCATCATG
* * * *
29728 TCTCTAAGGTACAAGGTTCGCCGTTGCGGTCTCAACCTTT-CTTTCGCA
1 TCTCTAAGGTACAAGGTTCGCCGTTAC-GCCTCAACCTTTCCCTCCGCA
** *
29776 TCTCTAAGGTACAAGGTTCATCGTTACTGCCTCAACCTTTCCCTCCGTA
1 TCTCTAAGGTACAAGGTTCGCCGTTAC-GCCTCAACCTTTCCCTCCGCA
* * * *
29825 TCTCTAGGGTATAAGGTTTGCCGTTACGACATCAACCTTTC
1 TCTCTAAGGTACAAGGTTCGCCGTTACG-CCTCAACCTTTC
29866 TAGTTAATTT
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
48 36 0.49
49 38 0.51
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (48 bp):
TCTCTAAGGTACAAGGTTCGCCGTTACGCCTCAACCTTTCCCTCCGCA
Found at i:32106 original size:30 final size:29
Alignment explanation
Indices: 32037--32110 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
32027 ATATATATAT
* *
32037 TATATTTTTATTATTTTGGAAAGATTAAA
1 TATAATTTTATTATTTTGAAAAGATTAAA
32066 T-TAAGTTTTTATTATTTT-AAAGAGATTAAAA
1 TATAA--TTTTATTATTTTGAAA-AGATT-AAA
32097 TATAATTTTATTAT
1 TATAATTTTATTAT
32111 AATTAATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 2 0.05
29 3 0.08
30 26 0.68
31 4 0.11
32 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (29 bp):
TATAATTTTATTATTTTGAAAAGATTAAA
Found at i:32134 original size:20 final size:22
Alignment explanation
Indices: 32090--32142 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
32080 TTTTAAAGAG
*
32090 ATTAAAATATAATTTTATTATA
1 ATTAAAATAAAATTTTATTATA
*
32112 ATTAATATAAAATTTTA-TA-A
1 ATTAAAATAAAATTTTATTATA
32132 ATTATAAATAA
1 ATTA-AAATAA
32143 TTTAAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 7 0.26
22 15 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTAAAATAAAATTTTATTATA
Found at i:33855 original size:17 final size:17
Alignment explanation
Indices: 33824--33856 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
33814 TAACGCAAGG
33824 GACCTTTTCATGATCCC
1 GACCTTTTCATGATCCC
33841 GACCTGTTTCA-GATCC
1 GACCT-TTTCATGATCC
33857 GTCACTGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.18, C:0.33, G:0.15, T:0.33
Consensus pattern (17 bp):
GACCTTTTCATGATCCC
Found at i:39919 original size:34 final size:34
Alignment explanation
Indices: 39845--39921 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
39835 TTTCAGTTTA
* *
39845 TGTT-TGCATCTTTAAATTAATGTCTTGCATTAT
1 TGTTCTGCATCTTTAAATTAATGACTTGCAATAT
39878 T-TATCTGCATCTTTAAATT-ATGACTTGCAATAT
1 TGT-TCTGCATCTTTAAATTAATGACTTGCAATAT
39911 GTGTTCTGCAT
1 -TGTTCTGCAT
39922 TTAATTATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 1 0.03
33 14 0.37
34 22 0.58
35 1 0.03
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (34 bp):
TGTTCTGCATCTTTAAATTAATGACTTGCAATAT
Found at i:48010 original size:36 final size:36
Alignment explanation
Indices: 47970--48040 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
47960 TAGTTATGAG
47970 TTCACTTTAAAAATATATTATCATTACGAAAGCGAT
1 TTCACTTTAAAAATATATTATCATTACGAAAGCGAT
48006 TTCACTTTAAAAATATATTATCATTACGAAAGCGA
1 TTCACTTTAAAAATATATTATCATTACGAAAGCGA
48041 ATTTATTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.35
Consensus pattern (36 bp):
TTCACTTTAAAAATATATTATCATTACGAAAGCGAT
Found at i:49534 original size:21 final size:20
Alignment explanation
Indices: 49507--49551 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
49497 CGGCTTAGGG
*
49507 GAGAGGGGAAGAGAAA-AGAA
1 GAGAAGGGAAGA-AAACAGAA
49527 GAGAAGGGAAGAAAACGAGAA
1 GAGAAGGGAAGAAAAC-AGAA
49548 GAGA
1 GAGA
49552 GGAGAGGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 11 0.50
21 8 0.36
ACGTcount: A:0.56, C:0.02, G:0.42, T:0.00
Consensus pattern (20 bp):
GAGAAGGGAAGAAAACAGAA
Found at i:56788 original size:17 final size:17
Alignment explanation
Indices: 56757--56803 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
56747 CTACATTTTA
* * *
56757 ATTGTCACTGCATTTGC
1 ATTGTCATTGTATTTCC
56774 ATTGTCATTGTATTTCC
1 ATTGTCATTGTATTTCC
56791 ATTTGTCATTGTA
1 A-TTGTCATTGTA
56804 ATTTAATGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (17 bp):
ATTGTCATTGTATTTCC
Found at i:57133 original size:2 final size:2
Alignment explanation
Indices: 57126--57155 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
57116 CAACTACTTG
*
57126 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
57156 GTTATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:57917 original size:26 final size:26
Alignment explanation
Indices: 57861--57929 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
57851 AGCATTGTGC
*
57861 CCAGAATTGTCACTGCAGGAACTTGT
1 CCAGAATTTTCACTGCAGGAACTTGT
*
57887 TCAGAATTTTCACTGC-GTGAA-TATGT
1 CCAGAATTTTCACTGCAG-GAACT-TGT
* *
57913 CCAGAGTTTTCGCTGCA
1 CCAGAATTTTCACTGCA
57930 TAAGGAGGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
25 2 0.06
26 33 0.94
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (26 bp):
CCAGAATTTTCACTGCAGGAACTTGT
Found at i:70675 original size:21 final size:21
Alignment explanation
Indices: 70648--70747 Score: 109
Period size: 21 Copynumber: 4.8 Consensus size: 21
70638 TAGTGCAAAT
70648 TTCTACCGATACAAGTGATAG
1 TTCTACCGATACAAGTGATAG
*
70669 TTTTACCGATACAAGTGACT--
1 TTCTACCGATACAAGTGA-TAG
* *
70689 TATCTACCAATACAAATGATAG
1 T-TCTACCGATACAAGTGATAG
70711 TTCTACCGATACAAGTGACT--
1 TTCTACCGATACAAGTGA-TAG
70731 TATCTACCGATACAAGT
1 T-TCTACCGATACAAGT
70748 TTTACCTTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.04
21 61 0.91
22 3 0.04
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAGTGATAG
Found at i:70696 original size:42 final size:42
Alignment explanation
Indices: 70649--70747 Score: 171
Period size: 42 Copynumber: 2.4 Consensus size: 42
70639 AGTGCAAATT
*
70649 TCTACCGATACAAGTGATAGTTTTACCGATACAAGTGACTTA
1 TCTACCGATACAAGTGATAGTTCTACCGATACAAGTGACTTA
* *
70691 TCTACCAATACAAATGATAGTTCTACCGATACAAGTGACTTA
1 TCTACCGATACAAGTGATAGTTCTACCGATACAAGTGACTTA
70733 TCTACCGATACAAGT
1 TCTACCGATACAAGT
70748 TTTACCTTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (42 bp):
TCTACCGATACAAGTGATAGTTCTACCGATACAAGTGACTTA
Found at i:70760 original size:42 final size:41
Alignment explanation
Indices: 70649--70761 Score: 145
Period size: 42 Copynumber: 2.7 Consensus size: 41
70639 AGTGCAAATT
*
70649 TCTACCGATACAAGTGATAGTTTTACCGATACAAGTGACTTA
1 TCTACCGATACAAGTGATA-CTTTACCGATACAAGTGACTTA
* * *
70691 TCTACCAATACAAATGATAGTTCTACCGATACAAGTGACTTA
1 TCTACCGATACAAGTGATACTT-TACCGATACAAGTGACTTA
**
70733 TCTACCGATACAAGTTTTACCTTTACCGA
1 TCTACCGATACAAGTGATA-CTTTACCGA
70762 CACTTTAGAG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 2 0.03
42 57 0.93
43 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (41 bp):
TCTACCGATACAAGTGATACTTTACCGATACAAGTGACTTA
Found at i:82412 original size:29 final size:25
Alignment explanation
Indices: 82350--82410 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
82340 TATAAAGACT
82350 AATCATTCATTGCTGAAACAATTCC
1 AATCATTCATTGCTGAAACAATTCC
82375 AATCATTCATTGCTGAAACAATTCC
1 AATCATTCATTGCTGAAACAATTCC
82400 AATCATTCATT
1 AATCATTCATT
82411 CAAAAATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (25 bp):
AATCATTCATTGCTGAAACAATTCC
Found at i:85065 original size:15 final size:16
Alignment explanation
Indices: 85036--85065 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
85026 AACAACACGA
85036 TGAAAAGTGAAATAAT
1 TGAAAAGTGAAATAAT
85052 TGAAAAGT-AAATAA
1 TGAAAAGTGAAATAA
85066 AAAAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (16 bp):
TGAAAAGTGAAATAAT
Found at i:88685 original size:24 final size:24
Alignment explanation
Indices: 88653--88706 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
88643 GCAATTTGTT
88653 TGTGAGTACAACGCTGCACCCCTC
1 TGTGAGTACAACGCTGCACCCCTC
88677 TGTGAGTACAACGCTGCACCCCTC
1 TGTGAGTACAACGCTGCACCCCTC
88701 TGTGAG
1 TGTGAG
88707 CGCAATCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.20, C:0.33, G:0.24, T:0.22
Consensus pattern (24 bp):
TGTGAGTACAACGCTGCACCCCTC
Found at i:90994 original size:15 final size:15
Alignment explanation
Indices: 90976--91006 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
90966 ATTACTGTAT
90976 TATATTAAAGTCAAA
1 TATATTAAAGTCAAA
90991 TATATTAAAGTCAAA
1 TATATTAAAGTCAAA
91006 T
1 T
91007 CTCAGAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (15 bp):
TATATTAAAGTCAAA
Found at i:96643 original size:17 final size:17
Alignment explanation
Indices: 96604--96651 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
96594 TGATATGTGG
*
96604 AAATGCAATGACAATAT
1 AAATGCAATGACAATAA
* *
96621 AGATGCAGTGACAATAA
1 AAATGCAATGACAATAA
*
96638 AAATGCAATAACAA
1 AAATGCAATGACAA
96652 AGGAAATGTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.54, C:0.12, G:0.15, T:0.19
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:101532 original size:23 final size:23
Alignment explanation
Indices: 101506--101549 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
101496 GTCCGCATCC
101506 AACC-ACTTAATTATTTCATTTTT
1 AACCTACTTAATT-TTTCATTTTT
* *
101529 AACCTCCTTCATTTTTCATTT
1 AACCTACTTAATTTTTCATTT
101550 AATCTTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.52
Consensus pattern (23 bp):
AACCTACTTAATTTTTCATTTTT
Found at i:103988 original size:14 final size:14
Alignment explanation
Indices: 103969--103996 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
103959 TAATGAGTAA
103969 GGAAATAGTTACAT
1 GGAAATAGTTACAT
103983 GGAAATAGTTACAT
1 GGAAATAGTTACAT
103997 CTTCAAGGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (14 bp):
GGAAATAGTTACAT
Found at i:108400 original size:12 final size:12
Alignment explanation
Indices: 108383--108413 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
108373 TCTTTTGCTT
108383 TTATTTTCTATC
1 TTATTTTCTATC
*
108395 TTATTTTCTATT
1 TTATTTTCTATC
108407 TTATTTT
1 TTATTTT
108414 ATGCTCTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (12 bp):
TTATTTTCTATC
Found at i:115430 original size:15 final size:15
Alignment explanation
Indices: 115387--115424 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
115377 TGTGAAGGAT
*
115387 ATTAATCTAAAGT--
1 ATTAATCTAAACTAA
115400 ATTAATCTAAACTAA
1 ATTAATCTAAACTAA
115415 ATTAATCTAA
1 ATTAATCTAA
115425 GTTAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
15 10 0.45
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.37
Consensus pattern (15 bp):
ATTAATCTAAACTAA
Found at i:119639 original size:21 final size:22
Alignment explanation
Indices: 119613--119654 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
119603 GAGAAAATCA
119613 AAAAGAAAAATGAGT-AGAAAC
1 AAAAGAAAAATGAGTAAGAAAC
**
119634 AAAAGAATTATGAGTAAGAAA
1 AAAAGAAAAATGAGTAAGAAA
119655 ACATGTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.64, C:0.02, G:0.19, T:0.14
Consensus pattern (22 bp):
AAAAGAAAAATGAGTAAGAAAC
Found at i:142201 original size:23 final size:23
Alignment explanation
Indices: 142164--142207 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
142154 TAAATTTTGT
142164 AAATAATTAATATTAATTATTTAG
1 AAATAATTAATATTAA-TATTTAG
*
142188 AAATATTTAA-ATTAATATTT
1 AAATAATTAATATTAATATTT
142208 CATATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 5 0.26
24 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AAATAATTAATATTAATATTTAG
Found at i:143164 original size:40 final size:40
Alignment explanation
Indices: 143127--143216 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
143117 AAATTCAAGA
*
143127 TTTAAAATTTGAGTT-TAAAATTCAAGATTTAAGTTCAAAG
1 TTTAAAATTAGAGTTAT-AAATTCAAGATTTAAGTTCAAAG
* * *
143167 TTTAATATTAGAGTTATAAATTTAAGATTTAGAATTCAAAG
1 TTTAAAATTAGAGTTATAAATTCAAGATTTA-AGTTCAAAG
*
143208 TTCAAAATT
1 TTTAAAATT
143217 TAAAATTCGA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
40 26 0.62
41 16 0.38
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.41
Consensus pattern (40 bp):
TTTAAAATTAGAGTTATAAATTCAAGATTTAAGTTCAAAG
Found at i:143168 original size:27 final size:28
Alignment explanation
Indices: 143106--143171 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 28
143096 CAAATTTGAG
*
143106 ATTCAAA-TATAAAATTCAAGATTTAAA
1 ATTCAAAGTTTAAAATTCAAGATTTAAA
**
143133 ATT-TGAGTTTAAAATTCAAGATTT-AA
1 ATTCAAAGTTTAAAATTCAAGATTTAAA
*
143159 GTTCAAAGTTTAA
1 ATTCAAAGTTTAA
143172 TATTAGAGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
26 5 0.16
27 26 0.84
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (28 bp):
ATTCAAAGTTTAAAATTCAAGATTTAAA
Found at i:143217 original size:21 final size:21
Alignment explanation
Indices: 143193--143239 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
143183 TAAATTTAAG
*
143193 ATTTAGAATTCAAAGTTCAAA
1 ATTTAAAATTCAAAGTTCAAA
* * *
143214 ATTTAAAATTCGAATTTTAAA
1 ATTTAAAATTCAAAGTTCAAA
143235 ATTTA
1 ATTTA
143240 CAGTAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (21 bp):
ATTTAAAATTCAAAGTTCAAA
Found at i:149763 original size:12 final size:13
Alignment explanation
Indices: 149743--149772 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
149733 ATCTCATTTC
149743 AAATGAAAACACA
1 AAATGAAAACACA
149756 AAAT-AAAACACA
1 AAATGAAAACACA
149768 AAATG
1 AAATG
149773 GTGTGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.70, C:0.13, G:0.07, T:0.10
Consensus pattern (13 bp):
AAATGAAAACACA
Found at i:164488 original size:21 final size:21
Alignment explanation
Indices: 164464--164522 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
164454 TCAGCTCACT
* *
164464 CAGATGAATCCACAACAAAGC
1 CAGATGCATCCACAACAAAAC
* * *
164485 CAGATGCATCAACACCAAAAT
1 CAGATGCATCCACAACAAAAC
*
164506 CAGATGCAGCCACAACA
1 CAGATGCATCCACAACA
164523 CTCTTCAATG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.46, C:0.31, G:0.14, T:0.10
Consensus pattern (21 bp):
CAGATGCATCCACAACAAAAC
Found at i:165909 original size:233 final size:233
Alignment explanation
Indices: 165502--165966 Score: 885
Period size: 233 Copynumber: 2.0 Consensus size: 233
165492 TGATTTTATT
165502 ATACTTGACTATGAGGCAGACAAGGAGGTTCCCATAATCTTGGGATGACCATTTTTAGCTACTAG
1 ATACTTGACTATGAGGCAGACAAGGAGGTTCCCATAATCTTGGGATGACCATTTTTAGCTACTAG
*
165567 ATGAAGTCTTATTGATGTTTACAAAGGTGAACTGGCCATGCGACTTAATGATGAGCATGTTACCT
66 ATGAAGTCTTATTGATGTTTACAAAGGTGAACTGGCCATGCAACTTAATGATGAGCATGTTACCT
165632 TTAGTGTTTTTGAATCTATTTAATGCAAGGATAAAGAGGAATGTCATACTGTCAATGTGTTAGAG
131 TTAGTGTTTTTGAATCTATTTAATGCAAGGATAAAGAGGAATGTCATACTGTCAATGTGTTAGAG
*
165697 GATCTAACTAAAGAAGAATTTAATGATCAAAGTACACC
196 GATCTAACTAAAGAAGAATTCAATGATCAAAGTACACC
* *
165735 ATACTTGACTGTTAGGCAGACAAGGAGGTTCCCATAATCTTGGGATGACCATTTTTAGCTACTAG
1 ATACTTGACTATGAGGCAGACAAGGAGGTTCCCATAATCTTGGGATGACCATTTTTAGCTACTAG
165800 ATGAAGTCTTATTGATGTTTACAAAGGTGAACTGGCCATGCAACTTAATGATGAGCATGTTACCT
66 ATGAAGTCTTATTGATGTTTACAAAGGTGAACTGGCCATGCAACTTAATGATGAGCATGTTACCT
165865 TTAGTGTTTTTGAATCTATTTAATGCAAGGATAAAGAGGAATGTCATACTGTCAATGTGTTAGAG
131 TTAGTGTTTTTGAATCTATTTAATGCAAGGATAAAGAGGAATGTCATACTGTCAATGTGTTAGAG
*
165930 GATCTAACTGAAGAAGAATTCAATGATCAAAGTACAC
196 GATCTAACTAAAGAAGAATTCAATGATCAAAGTACAC
165967 TACTTTCTGA
Statistics
Matches: 227, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
233 227 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (233 bp):
ATACTTGACTATGAGGCAGACAAGGAGGTTCCCATAATCTTGGGATGACCATTTTTAGCTACTAG
ATGAAGTCTTATTGATGTTTACAAAGGTGAACTGGCCATGCAACTTAATGATGAGCATGTTACCT
TTAGTGTTTTTGAATCTATTTAATGCAAGGATAAAGAGGAATGTCATACTGTCAATGTGTTAGAG
GATCTAACTAAAGAAGAATTCAATGATCAAAGTACACC
Found at i:171220 original size:14 final size:15
Alignment explanation
Indices: 171201--171230 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
171191 AAAAGCACAG
171201 AAAGGAGG-AGAAGA
1 AAAGGAGGAAGAAGA
171215 AAAGGAGGAAGAAGA
1 AAAGGAGGAAGAAGA
171230 A
1 A
171231 GCATCATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (15 bp):
AAAGGAGGAAGAAGA
Found at i:179084 original size:18 final size:20
Alignment explanation
Indices: 179058--179108 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 20
179048 TTTTTGGTGT
* *
179058 TTATTTATTTA-ATTTAAA-
1 TTATATATTTATATATAAAG
179076 TTATATA-TTATATATAAAG
1 TTATATATTTATATATAAAG
*
179095 TTATATATATATAT
1 TTATATATTTATAT
179109 GTATGTATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.11
18 12 0.44
19 7 0.26
20 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTATATATTTATATATAAAG
Found at i:184434 original size:37 final size:36
Alignment explanation
Indices: 184371--184508 Score: 177
Period size: 37 Copynumber: 3.8 Consensus size: 36
184361 TTGCACAATA
*
184371 TTCAGGCAATGTGCCTAGTAAGCTTCGTGCTAGTGTT
1 TTCAGGCAATGTGCCTAGTAGGCTTCGTG-TAGTGTT
* * * *
184408 TTTAGGCTATGTTCCTAGTAGGCTTCGTGTCGATGTT
1 TTCAGGCAATGTGCCTAGTAGGCTTCGTGTAG-TGTT
* * *
184445 TTCAGGCTATGTGCCTAGTAGGCTTCATGTCGGTGTT
1 TTCAGGCAATGTGCCTAGTAGGCTTCGTGT-AGTGTT
184482 TTCAGGCAATGTGCCTAGTAGGCTTCG
1 TTCAGGCAATGTGCCTAGTAGGCTTCG
184509 AGCTGGTAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
36 2 0.02
37 85 0.97
38 1 0.01
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.37
Consensus pattern (36 bp):
TTCAGGCAATGTGCCTAGTAGGCTTCGTGTAGTGTT
Found at i:184499 original size:74 final size:74
Alignment explanation
Indices: 184371--184508 Score: 197
Period size: 74 Copynumber: 1.9 Consensus size: 74
184361 TTGCACAATA
* * * *
184371 TTCAGGCAATGTGCCTAGTAAGCTTCGTGCTAGTGTTTTTAGGCTATGTTCCTAGTAGGCTTCGT
1 TTCAGGCAATGTGCCTAGTAAGCTTCATGCTAGTGTTTTCAGGCAATGTGCCTAGTAGGCTTCGT
184436 GTCGATGTT
66 GTCGATGTT
* * *
184445 TTCAGGCTATGTGCCTAGTAGGCTTCATG-TCGGTGTTTTCAGGCAATGTGCCTAGTAGGCTTCG
1 TTCAGGCAATGTGCCTAGTAAGCTTCATGCT-AGTGTTTTCAGGCAATGTGCCTAGTAGGCTTCG
184509 AGCTGGTAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 1 0.02
74 55 0.98
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.37
Consensus pattern (74 bp):
TTCAGGCAATGTGCCTAGTAAGCTTCATGCTAGTGTTTTCAGGCAATGTGCCTAGTAGGCTTCGT
GTCGATGTT
Found at i:188812 original size:8 final size:8
Alignment explanation
Indices: 188800--188833 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
188790 CCTTTTCACT
*
188800 GTGTTGGT
1 GTGTTGGA
188808 GTGTTGGA
1 GTGTTGGA
188816 GTGTTGGA
1 GTGTTGGA
188824 GTGTTGGA
1 GTGTTGGA
188832 GT
1 GT
188834 ATGGGTGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.09, C:0.00, G:0.50, T:0.41
Consensus pattern (8 bp):
GTGTTGGA
Found at i:190789 original size:5 final size:5
Alignment explanation
Indices: 190779--190803 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
190769 TGGAGCAATG
190779 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
190804 TGTATCTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:193371 original size:38 final size:38
Alignment explanation
Indices: 193292--193371 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
193282 ATTAAATGAG
* * * * **
193292 GTTTTAATGTGTCTTAGTTTGATACATATTTAATAGTT
1 GTTTTAATGTGTCTAAGTTTGAGACAAATTAAATACAT
*
193330 GTTTTAATGTGTCTAAGTTTGAGACAAATTAAATTCAT
1 GTTTTAATGTGTCTAAGTTTGAGACAAATTAAATACAT
193368 GTTT
1 GTTT
193372 GAATTAATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (38 bp):
GTTTTAATGTGTCTAAGTTTGAGACAAATTAAATACAT
Found at i:196635 original size:13 final size:14
Alignment explanation
Indices: 196616--196654 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
196606 GCAAAGAAAG
196616 TGAAAAGAAAGAGA
1 TGAAAAGAAAGAGA
*
196630 -GAAAAGAAAAAGA
1 TGAAAAGAAAGAGA
*
196643 TGAAAAGGAAGA
1 TGAAAAGAAAGA
196655 AAAAGAGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (14 bp):
TGAAAAGAAAGAGA
Found at i:205110 original size:21 final size:22
Alignment explanation
Indices: 205062--205115 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 22
205052 AAGACACAGG
205062 CTACCGATACTTCTATAAGTAGAA
1 CTACCGATACTTCTAT-AGTA-AA
205086 CTACCGATACTTACTAT-GT-AA
1 CTACCGATACTT-CTATAGTAAA
205107 CTACCGATA
1 CTACCGATA
205116 TAGCTCAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 11 0.38
23 2 0.07
24 12 0.41
25 4 0.14
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (22 bp):
CTACCGATACTTCTATAGTAAA
Found at i:217426 original size:17 final size:18
Alignment explanation
Indices: 217406--217442 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
217396 ATTGTCATTA
*
217406 CATTTTTA-TTGTTTCTG
1 CATTTTTAGTTGTTTCAG
217423 CA-TTTTAGTTGTTTCAG
1 CATTTTTAGTTGTTTCAG
217440 CAT
1 CAT
217443 ATGCATTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 3
0.81 0.05 0.14
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.57
Consensus pattern (18 bp):
CATTTTTAGTTGTTTCAG
Found at i:221981 original size:33 final size:35
Alignment explanation
Indices: 221942--222011 Score: 108
Period size: 33 Copynumber: 2.0 Consensus size: 35
221932 CCTATGTCTT
*
221942 TCGGAAAAACAAATGCCA-T-GGACTTAGGAAAGA
1 TCGGAAAAAAAAATGCCATTAGGACTTAGGAAAGA
221975 TCGGAAAAAAAAATGCCATTAAGGACTTAGGAAAGA
1 TCGGAAAAAAAAATGCCATT-AGGACTTAGGAAAGA
222011 T
1 T
222012 TTTCATGGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 17 0.52
34 1 0.03
36 15 0.45
ACGTcount: A:0.47, C:0.13, G:0.23, T:0.17
Consensus pattern (35 bp):
TCGGAAAAAAAAATGCCATTAGGACTTAGGAAAGA
Found at i:225327 original size:2 final size:2
Alignment explanation
Indices: 225320--225347 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
225310 CCTTTGTTTA
225320 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
225348 TACATTTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.