Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012407.1 Kokia drynarioides strain JFW-HI SEQ_127411, 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: 164702
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:6447 original size:53 final size:53
Alignment explanation
Indices: 6298--6568 Score: 359
Period size: 53 Copynumber: 5.1 Consensus size: 53
6288 GTAAATGCAA
* * * * * *
6298 AAAGGTTTGATAACTCTATGTCATCATGAGTTATATGACTCCTATTACGGATT
1 AAAGGTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGAATT
* * *
6351 AAAGCTCTGATGACTC--TGTCATTGTGAGTTATGTGAATCCTATTACGAATT
1 AAAGGTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGAATT
6402 AAAGGTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGAATT
1 AAAGGTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGAATT
** *
6455 AAAGGTCCAATGACTCTGTGTCATCATGAGTTATATGAAATCCTATTACGAATT
1 AAAGGTCTGATGACTCTGTGTCATCGTGAGTTATATG-AATCCTATTACGAATT
* * * *
6509 ATAGGTCCGATAACTCTGTGTCATTGTGAGTTATATGAATCCTATTAC-AGATT
1 AAAGGTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGA-ATT
6562 AAAGGTC
1 AAAGGTC
6569 CAATGACAGA
Statistics
Matches: 194, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
51 45 0.23
52 1 0.01
53 100 0.52
54 48 0.25
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (53 bp):
AAAGGTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGAATT
Found at i:6538 original size:107 final size:104
Alignment explanation
Indices: 6306--6575 Score: 371
Period size: 107 Copynumber: 2.6 Consensus size: 104
6296 AAAAAGGTTT
* * * * * **
6306 GATAACTCTATGTCATCATGAGTTATATGACTCCTATTACGGATTAAAGCTCTGATGACTCTGTC
1 GATAACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGAATTAAAGGTCCAATGACTCTGTC
** * *
6371 ATTGTGAGTTATGTGAATCCTATTACGAATTAAAGGTCT
66 ATCATGAGTTATATGAATCCTATTACGAATTAAAGGTCC
*
6410 GATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGAATTAAAGGTCCAATGACTCTGTG
1 GATAACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGAATTAAAGGTCCAATGACTC--TG
*
6475 TCATCATGAGTTATATGAAATCCTATTACGAATTATAGGTCC
64 TCATCATGAGTTATATG-AATCCTATTACGAATTAAAGGTCC
*
6517 GATAACTCTGTGTCATTGTGAGTTATATGAATCCTATTAC-AGATTAAAGGTCCAATGAC
1 GATAACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGA-ATTAAAGGTCCAATGAC
6576 AGAGCTCCTG
Statistics
Matches: 147, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
104 53 0.36
106 17 0.12
107 77 0.52
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (104 bp):
GATAACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGAATTAAAGGTCCAATGACTCTGTC
ATCATGAGTTATATGAATCCTATTACGAATTAAAGGTCC
Found at i:13810 original size:12 final size:12
Alignment explanation
Indices: 13793--13818 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13783 GGGCACACGA
13793 TCGTGTGCTAGC
1 TCGTGTGCTAGC
13805 TCGTGTGCTAGC
1 TCGTGTGCTAGC
13817 TC
1 TC
13819 ATACGTATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.27, G:0.31, T:0.35
Consensus pattern (12 bp):
TCGTGTGCTAGC
Found at i:15122 original size:72 final size:72
Alignment explanation
Indices: 15040--15193 Score: 191
Period size: 72 Copynumber: 2.1 Consensus size: 72
15030 CTTATATACA
* *
15040 TTTACGCTCGTCAACTTGCACATATTTACGCTTGTCAACTTATATACATTTACACTCGTCAACTT
1 TTTACGCTCGTCAACTTGCACACATTTACGCTTGCCAACTTATATACATTTACACTCGTCAACTT
*
15105 GCACATG
66 GCACACG
* * * * * * ** * *
15112 TTTACACTCGTTAGCTTGCACACGTTTATGCTTGCCAGCTTATATATGTTTACGCTCGTCAGCTT
1 TTTACGCTCGTCAACTTGCACACATTTACGCTTGCCAACTTATATACATTTACACTCGTCAACTT
15177 GCACACG
66 GCACACG
15184 TTTACGCTCG
1 TTTACGCTCG
15194 CAGCTTATAT
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (72 bp):
TTTACGCTCGTCAACTTGCACACATTTACGCTTGCCAACTTATATACATTTACACTCGTCAACTT
GCACACG
Found at i:15180 original size:48 final size:47
Alignment explanation
Indices: 15109--15238 Score: 179
Period size: 47 Copynumber: 2.7 Consensus size: 47
15099 CAACTTGCAC
* * * *
15109 ATGTTTACACTCGTTAGCTTGCACACGTTTATGCTTGCCAGCTTATAT
1 ATGTTTACGCTCGTCAGCTTGCACACGTTTACGCTCG-CAGCTTATAT
15157 ATGTTTACGCTCGTCAGCTTGCACACGTTTACGCTCGCAGCTTATAT
1 ATGTTTACGCTCGTCAGCTTGCACACGTTTACGCTCGCAGCTTATAT
* * * *
15204 ATGTTTATGCTAGTCAGCTTGCACATGTTTGCGCT
1 ATGTTTACGCTCGTCAGCTTGCACACGTTTACGCT
15239 TGTAATACCC
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
47 41 0.55
48 33 0.45
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (47 bp):
ATGTTTACGCTCGTCAGCTTGCACACGTTTACGCTCGCAGCTTATAT
Found at i:15222 original size:24 final size:24
Alignment explanation
Indices: 15010--15223 Score: 115
Period size: 24 Copynumber: 9.0 Consensus size: 24
15000 CATTAGCATG
* * *
15010 TATACGTTCACGCTCATCAGCTTA
1 TATATGTTTACGCTCGTCAGCTTA
** * *
15034 TATACATTTACGCTCGTCAACTTG
1 TATATGTTTACGCTCGTCAGCTTA
* * * * *
15058 CACATATTTACGCTTGTCAACTTA
1 TATATGTTTACGCTCGTCAGCTTA
** * * *
15082 TATACATTTACACTCGTCAACTTG
1 TATATGTTTACGCTCGTCAGCTTA
* * * * *
15106 CACATGTTTACACTCGTTAGCTTG
1 TATATGTTTACGCTCGTCAGCTTA
* * * * * *
15130 CACACGTTTATGCTTGCCAGCTTA
1 TATATGTTTACGCTCGTCAGCTTA
*
15154 TATATGTTTACGCTCGTCAGCTTG
1 TATATGTTTACGCTCGTCAGCTTA
* * *
15178 CACACGTTTACGCTCG-CAGCTTA
1 TATATGTTTACGCTCGTCAGCTTA
* *
15201 TATATGTTTATGCTAGTCAGCTT
1 TATATGTTTACGCTCGTCAGCTT
15224 GCACATGTTT
Statistics
Matches: 144, Mismatches: 45, Indels: 2
0.75 0.24 0.01
Matches are distributed among these distances:
23 17 0.12
24 127 0.88
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.37
Consensus pattern (24 bp):
TATATGTTTACGCTCGTCAGCTTA
Found at i:15231 original size:24 final size:24
Alignment explanation
Indices: 15040--15238 Score: 148
Period size: 24 Copynumber: 8.3 Consensus size: 24
15030 CTTATATACA
* *
15040 TTTACGCTCGTCAACTTGCACATA
1 TTTACGCTCGTCAGCTTGCACATG
* * ** * **
15064 TTTACGCTTGTCAACTTATATACA
1 TTTACGCTCGTCAGCTTGCACATG
* *
15088 TTTACACTCGTCAACTTGCACATG
1 TTTACGCTCGTCAGCTTGCACATG
* * *
15112 TTTACACTCGTTAGCTTGCACACG
1 TTTACGCTCGTCAGCTTGCACATG
* * * ** *
15136 TTTATGCTTGCCAGCTTATATATG
1 TTTACGCTCGTCAGCTTGCACATG
*
15160 TTTACGCTCGTCAGCTTGCACACG
1 TTTACGCTCGTCAGCTTGCACATG
** *
15184 TTTACGCTCG-CAGCTTATATATG
1 TTTACGCTCGTCAGCTTGCACATG
* *
15207 TTTATGCTAGTCAGCTTGCACATG
1 TTTACGCTCGTCAGCTTGCACATG
*
15231 TTTGCGCT
1 TTTACGCT
15239 TGTAATACCC
Statistics
Matches: 132, Mismatches: 42, Indels: 2
0.75 0.24 0.01
Matches are distributed among these distances:
23 17 0.13
24 115 0.87
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (24 bp):
TTTACGCTCGTCAGCTTGCACATG
Found at i:17113 original size:18 final size:18
Alignment explanation
Indices: 17087--17121 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17077 TAAATAATAA
* *
17087 AATATTATTATTTATTAT
1 AATAATATTATTAATTAT
17105 AATAATATTATTAATTA
1 AATAATATTATTAATTA
17122 ATATATCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATAATATTATTAATTAT
Found at i:17113 original size:21 final size:20
Alignment explanation
Indices: 17083--17126 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
17073 AATATAAATA
* *
17083 ATAAAATATTATTATTTATT
1 ATAAAATATTATTAATTAAT
17103 ATAATAATATTATTAATTAAT
1 ATAA-AATATTATTAATTAAT
17124 ATA
1 ATA
17127 TCATTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAAAATATTATTAATTAAT
Found at i:22114 original size:18 final size:18
Alignment explanation
Indices: 22091--22129 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
22081 AAAAATCAAG
*
22091 TTTCATTTCAATTCT-ATT
1 TTTCATATC-ATTCTCATT
22109 TTTCATATCATTCTCATT
1 TTTCATATCATTCTCATT
22127 TTT
1 TTT
22130 GGTCTCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTCATATCATTCTCATT
Found at i:24912 original size:2 final size:2
Alignment explanation
Indices: 24905--24935 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24895 TAATGATAGG
24905 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
24936 AGAAATATTT
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:28741 original size:21 final size:21
Alignment explanation
Indices: 28715--28755 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
28705 CTCTGTCTAA
28715 CAATTCTTGCAACTCAATCTT
1 CAATTCTTGCAACTCAATCTT
*
28736 CAATTCTTTCAACTCAATCT
1 CAATTCTTGCAACTCAATCT
28756 CTATACGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.02, T:0.39
Consensus pattern (21 bp):
CAATTCTTGCAACTCAATCTT
Found at i:38591 original size:29 final size:30
Alignment explanation
Indices: 38549--38606 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
38539 ATATAATATA
38549 TATAATTCAATAATCA-TAAAATAGTTTTG
1 TATAATTCAATAATCATTAAAATAGTTTTG
*
38578 TATAATTCGATAATCATTAAAATAGTTTT
1 TATAATTCAATAATCATTAAAATAGTTTT
38607 ATACCTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (30 bp):
TATAATTCAATAATCATTAAAATAGTTTTG
Found at i:41214 original size:24 final size:24
Alignment explanation
Indices: 41186--41271 Score: 91
Period size: 24 Copynumber: 3.6 Consensus size: 24
41176 TCAGCTACGC
*
41186 TTACGTTCGTCAGCTTGCACACGT
1 TTACGCTCGTCAGCTTGCACACGT
* ** * *
41210 TTACGCTCGTCAACTTATATATGT
1 TTACGCTCGTCAGCTTGCACACGT
*
41234 TTACGCTCGTCAGCTTGCACACAT
1 TTACGCTCGTCAGCTTGCACACGT
* *
41258 TTATGCTTGTCAGC
1 TTACGCTCGTCAGC
41272 ATGAATATAA
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (24 bp):
TTACGCTCGTCAGCTTGCACACGT
Found at i:42410 original size:14 final size:15
Alignment explanation
Indices: 42391--42419 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42381 CGAGAAAATG
42391 ACCAATTT-AAGCTT
1 ACCAATTTGAAGCTT
42405 ACCAATTTGAAGCTT
1 ACCAATTTGAAGCTT
42420 GAACCTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (15 bp):
ACCAATTTGAAGCTT
Found at i:44732 original size:23 final size:23
Alignment explanation
Indices: 44689--44733 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
44679 AGAACAAAAT
*
44689 AGAACACCATCCAAGTAGATAAC
1 AGAACACCATCCAAGCAGATAAC
*
44712 AGAACACCA-CCGAAGCGGATAA
1 AGAACACCATCC-AAGCAGATAA
44734 ATAGAGAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (23 bp):
AGAACACCATCCAAGCAGATAAC
Found at i:48145 original size:20 final size:20
Alignment explanation
Indices: 48109--48153 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
48099 TCATTTAGCT
*
48109 TTAATTAATCTCTTTTAATC
1 TTAATTAATCTCATTTAATC
*
48129 TTAATTAAGTCT-ATTTACTC
1 TTAATTAA-TCTCATTTAATC
48149 TTAAT
1 TTAAT
48154 ACAAATCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.31, C:0.13, G:0.02, T:0.53
Consensus pattern (20 bp):
TTAATTAATCTCATTTAATC
Found at i:49585 original size:24 final size:24
Alignment explanation
Indices: 49553--49809 Score: 217
Period size: 24 Copynumber: 10.7 Consensus size: 24
49543 GTTCATTACA
* * *
49553 TTTACGCTCGTCAGCATGTATACG
1 TTTACGCTCGTCAGCTTGCACACG
* ** * *
49577 TTTACGCTCGCCAGCTTATATATG
1 TTTACGCTCGTCAGCTTGCACACG
*
49601 TTTACGCTCGTCAACTTGCACACG
1 TTTACGCTCGTCAGCTTGCACACG
** * *
49625 TTTACGCTCGTCAGCTTATATACA
1 TTTACGCTCGTCAGCTTGCACACG
*
49649 TTTACGCTCGTCAACTTGCACACG
1 TTTACGCTCGTCAGCTTGCACACG
* ** * *
49673 TTTACGCTCGTCAACTTATATATG
1 TTTACGCTCGTCAGCTTGCACACG
* * *
49697 TTTACGCTCATTAGCTTGCACATG
1 TTTACGCTCGTCAGCTTGCACACG
* * **** *
49721 TTTACACTCGTTAGCACAAATACG
1 TTTACGCTCGTCAGCTTGCACACG
* * *
49745 TTCACGCTCATCAGCTTGCACAAG
1 TTTACGCTCGTCAGCTTGCACACG
*
49769 TTTACGCTCGTCAGCTTGCACAAG
1 TTTACGCTCGTCAGCTTGCACACG
49793 TTTACGCTCGTCAGCTT
1 TTTACGCTCGTCAGCTT
49810 ACTCGTTAGC
Statistics
Matches: 183, Mismatches: 50, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 183 1.00
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (24 bp):
TTTACGCTCGTCAGCTTGCACACG
Found at i:49626 original size:48 final size:48
Alignment explanation
Indices: 49553--49809 Score: 289
Period size: 48 Copynumber: 5.4 Consensus size: 48
49543 GTTCATTACA
* * * * *
49553 TTTACGCTCGTCAGCATGTATACGTTTACGCTCGCCAGCTTATATATG
1 TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTATATACG
* *
49601 TTTACGCTCGTCAACTTGCACACGTTTACGCTCGTCAGCTTATATACA
1 TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTATATACG
* * *
49649 TTTACGCTCGTCAACTTGCACACGTTTACGCTCGTCAACTTATATATG
1 TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTATATACG
* * * * * ** *
49697 TTTACGCTCATTAGCTTGCACATGTTTACACTCGTTAGCACAAATACG
1 TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTATATACG
* * * ** * *
49745 TTCACGCTCATCAGCTTGCACAAGTTTACGCTCGTCAGCTTGCACAAG
1 TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTATATACG
49793 TTTACGCTCGTCAGCTT
1 TTTACGCTCGTCAGCTT
49810 ACTCGTTAGC
Statistics
Matches: 175, Mismatches: 34, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 175 1.00
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (48 bp):
TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTATATACG
Found at i:49647 original size:72 final size:72
Alignment explanation
Indices: 49553--49810 Score: 246
Period size: 72 Copynumber: 3.6 Consensus size: 72
49543 GTTCATTACA
* * * * * *
49553 TTTACGCTCGTCAGCATGTATACGTTTACGCTCGCCAGCTTATATATGTTTACGCTCGTCAACTT
1 TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTAAATACGTTTACGCTCGTCAACTT
*
49618 GCACACG
66 GCACAAG
** * * * ** *
49625 TTTACGCTCGTCAGCTTATATACATTTACGCTCGTCAACTTGCACACGTTTACGCTCGTCAACTT
1 TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTAAATACGTTTACGCTCGTCAACTT
** * *
49690 ATATATG
66 GCACAAG
* * * * * ** * * *
49697 TTTACGCTCATTAGCTTGCACATGTTTACACTCGTTAGCACAAATACGTTCACGCTCATCAGCTT
1 TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTAAATACGTTTACGCTCGTCAACTT
49762 GCACAAG
66 GCACAAG
*
49769 TTTACGCTCGTCAGCTTGCACAAGTTTACGCTCGTCAGCTTA
1 TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTA
49811 CTCGTTAGCA
Statistics
Matches: 144, Mismatches: 42, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
72 144 1.00
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (72 bp):
TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTAAATACGTTTACGCTCGTCAACTT
GCACAAG
Found at i:50256 original size:17 final size:17
Alignment explanation
Indices: 50234--50278 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 17
50224 TGTCCTGACC
50234 TTCAATTATAATTTCAT
1 TTCAATTATAATTTCAT
*
50251 TTCAATTAT-A--CCAT
1 TTCAATTATAATTTCAT
50265 TTCAATTATAATTT
1 TTCAATTATAATTT
50279 TCTAGTCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 12 0.52
15 1 0.04
16 1 0.04
17 9 0.39
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (17 bp):
TTCAATTATAATTTCAT
Found at i:51193 original size:24 final size:25
Alignment explanation
Indices: 51156--51202 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
51146 TTTTCTTTTT
*
51156 CTAGTCAAATTCTGATTA-TTTATC
1 CTAGTCAAACTCTGATTAGTTTATC
* *
51180 CTAGTCGAACTCTGTTTAGTTTA
1 CTAGTCAAACTCTGATTAGTTTA
51203 GATTATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.45
Consensus pattern (25 bp):
CTAGTCAAACTCTGATTAGTTTATC
Found at i:57546 original size:15 final size:15
Alignment explanation
Indices: 57528--57557 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
57518 TTCACTATTA
*
57528 TGTCTTTCGTATTTT
1 TGTCTTTCATATTTT
57543 TGTCTTTCATATTTT
1 TGTCTTTCATATTTT
57558 GCATGAATAG
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:0.10, C:0.13, G:0.10, T:0.67
Consensus pattern (15 bp):
TGTCTTTCATATTTT
Found at i:61049 original size:13 final size:13
Alignment explanation
Indices: 61016--61056 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
61006 TTTGTTTGAA
61016 AAAGTCAACGATC
1 AAAGTCAACGATC
*
61029 AAATTCAACGATC
1 AAAGTCAACGATC
* *
61042 AAGGTCAACGGTC
1 AAAGTCAACGATC
61055 AA
1 AA
61057 CGATGTAGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (13 bp):
AAAGTCAACGATC
Found at i:61110 original size:31 final size:30
Alignment explanation
Indices: 61051--61111 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
61041 CAAGGTCAAC
61051 GGTCAACGATGTAGGTCAATCAACAGTTCG
1 GGTCAACGATGTAGGTCAATCAACAGTTCG
* * *
61081 GGTCAACGATTTAGGTTAANTTAACAGTTCG
1 GGTCAACGATGTAGGTCAA-TCAACAGTTCG
61112 ACCAACGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.28
Consensus pattern (30 bp):
GGTCAACGATGTAGGTCAATCAACAGTTCG
Found at i:65116 original size:17 final size:19
Alignment explanation
Indices: 65070--65118 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
65060 AGTATTTTAT
65070 TAATTTAATATTAAAGTGA
1 TAATTTAATATTAAAGTGA
*
65089 TTATCTTAATATTAAA-T-A
1 TAAT-TTAATATTAAAGTGA
65107 TAATTTAATATT
1 TAATTTAATATT
65119 TATCTACAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 8 0.30
18 4 0.15
19 4 0.15
20 11 0.41
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (19 bp):
TAATTTAATATTAAAGTGA
Found at i:65133 original size:29 final size:28
Alignment explanation
Indices: 65101--65171 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 28
65091 ATCTTAATAT
65101 TAAATATAATTTAATATTTATCTACAAGA
1 TAAATAT-ATTTAATATTTATCTACAAGA
65130 T-AA-ATA-TT-ATATTTATCTACAAGA
1 TAAATATATTTAATATTTATCTACAAGA
65154 TAAATATTATATTAATAT
1 TAAATA-TAT-TTAATAT
65172 AATAAGATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
24 17 0.47
25 4 0.11
26 2 0.06
27 4 0.11
28 2 0.06
29 3 0.08
30 4 0.11
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.44
Consensus pattern (28 bp):
TAAATATATTTAATATTTATCTACAAGA
Found at i:65141 original size:24 final size:24
Alignment explanation
Indices: 65114--65166 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
65104 ATATAATTTA
65114 ATATTTATCTACAAGATAAATATT
1 ATATTTATCTACAAGATAAATATT
65138 ATATTTATCTACAAGATAAATATT
1 ATATTTATCTACAAGATAAATATT
65162 ATATT
1 ATATT
65167 AATATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (24 bp):
ATATTTATCTACAAGATAAATATT
Found at i:67068 original size:31 final size:32
Alignment explanation
Indices: 67008--67069 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
66998 CAACTCAACA
*
67008 ATTTAAATAAAAAACTTTTAAATAATTCAATG
1 ATTTAAATAAAAAACTTTCAAATAATTCAATG
* * *
67040 ATTTAAAT-GAAACCTTTCAAATATTTCAAT
1 ATTTAAATAAAAAACTTTCAAATAATTCAAT
67070 AATTATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (32 bp):
ATTTAAATAAAAAACTTTCAAATAATTCAATG
Found at i:69746 original size:22 final size:23
Alignment explanation
Indices: 69711--69761 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
69701 ATTTCCTTTA
69711 TTTC-ATTTTCCCTTTATTT-AT
1 TTTCTATTTTCCCTTTATTTCAT
*
69732 GTTTCTATTTT-CCTTTGTTTCAT
1 -TTTCTATTTTCCCTTTATTTCAT
69755 TTTCTAT
1 TTTCTAT
69762 GTTCTTCGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.12, C:0.18, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTCTATTTTCCCTTTATTTCAT
Found at i:79153 original size:38 final size:38
Alignment explanation
Indices: 79101--79245 Score: 137
Period size: 38 Copynumber: 3.7 Consensus size: 38
79091 TTAATTTTTG
*
79101 TTAAAGTGAAAAGAATAAAATTCATTCAAATAATATAAC
1 TTAAA-TGAAAAGAATAAAATTCATTTAAATAATATAAC
* * * * * ***
79140 TTAAATGAAAAGAATAAATTTACATTTTTATTGATTTTTG
1 TTAAATGAAAAGAATAAAATT-CA-TTTAAATAATATAAC
* *
79180 TTAAAATGAAAAGAATAAAATTCTTTTGAATAATATAAC
1 TT-AAATGAAAAGAATAAAATTCATTTAAATAATATAAC
*
79219 TTAAATGAAAAGAATAAATTTTCATTT
1 TTAAATGAAAAGAATAAA-ATTCATTT
79246 TTATTGGTTT
Statistics
Matches: 82, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
38 31 0.38
39 23 0.28
40 10 0.12
41 18 0.22
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (38 bp):
TTAAATGAAAAGAATAAAATTCATTTAAATAATATAAC
Found at i:79213 original size:79 final size:79
Alignment explanation
Indices: 79082--79257 Score: 289
Period size: 79 Copynumber: 2.2 Consensus size: 79
79072 CATCATATGC
* *
79082 ACATTTTTATTAATTTTTGTTAAAGTGAAAAGAATAAAATTCATTCAAATAATATAACTTAAATG
1 ACATTTTTATTGATTTTTGTTAAAATGAAAAGAATAAAATTCATTCAAATAATATAACTTAAATG
79147 AAAAGAATAAATTT
66 AAAAGAATAAATTT
* **
79161 ACATTTTTATTGATTTTTGTTAAAATGAAAAGAATAAAATTCTTTTGAATAATATAACTTAAATG
1 ACATTTTTATTGATTTTTGTTAAAATGAAAAGAATAAAATTCATTCAAATAATATAACTTAAATG
79226 AAAAGAATAAATTT
66 AAAAGAATAAATTT
* *
79240 TCATTTTTATTGGTTTTT
1 ACATTTTTATTGATTTTT
79258 ATTGATTTTA
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 90 1.00
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.43
Consensus pattern (79 bp):
ACATTTTTATTGATTTTTGTTAAAATGAAAAGAATAAAATTCATTCAAATAATATAACTTAAATG
AAAAGAATAAATTT
Found at i:79258 original size:10 final size:10
Alignment explanation
Indices: 79243--79276 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
79233 TAAATTTTCA
79243 TTTTTATTGG
1 TTTTTATTGG
79253 TTTTTATT-G
1 TTTTTATTGG
*
79262 ATTTTATTGG
1 TTTTTATTGG
79272 TTTTT
1 TTTTT
79277 TTATTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.74
Consensus pattern (10 bp):
TTTTTATTGG
Found at i:79268 original size:19 final size:17
Alignment explanation
Indices: 79244--79286 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 17
79234 AAATTTTCAT
79244 TTTTATTGGTTTTTATTGA
1 TTTTATTGGTTTTT-TT-A
79263 TTTTATTGGTTTTTTTA
1 TTTTATTGGTTTTTTTA
79280 TTTTATT
1 TTTTATT
79287 TTAATAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.33
18 2 0.08
19 14 0.58
ACGTcount: A:0.14, C:0.00, G:0.12, T:0.74
Consensus pattern (17 bp):
TTTTATTGGTTTTTTTA
Found at i:86085 original size:14 final size:15
Alignment explanation
Indices: 86050--86087 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
86040 ATTAATCTTA
86050 TATGGAATTTTGAAT
1 TATGGAATTTTGAAT
86065 TGA-GGAATTTT-AAT
1 T-ATGGAATTTTGAAT
86079 TATGGAATT
1 TATGGAATT
86088 AAAAGTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 10 0.48
15 9 0.43
16 1 0.05
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (15 bp):
TATGGAATTTTGAAT
Found at i:90563 original size:24 final size:24
Alignment explanation
Indices: 90527--90594 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
90517 TCTGAAAAGT
* * * *
90527 TGACAAGCGTAAATGTATAGTGGT
1 TGACAAGCATAAACGTATAGTCGC
**
90551 TGATGAGCATAAACGTATAGTCGC
1 TGACAAGCATAAACGTATAGTCGC
90575 TGACAAGCATAAACGTATAG
1 TGACAAGCATAAACGTATAG
90595 AATATAACTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (24 bp):
TGACAAGCATAAACGTATAGTCGC
Found at i:98225 original size:13 final size:13
Alignment explanation
Indices: 98207--98231 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
98197 TTGATTTGAT
98207 TTGATTATGTAAA
1 TTGATTATGTAAA
98220 TTGATTATGTAA
1 TTGATTATGTAA
98232 TCTTGTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGATTATGTAAA
Found at i:103623 original size:26 final size:26
Alignment explanation
Indices: 103523--103682 Score: 126
Period size: 26 Copynumber: 6.2 Consensus size: 26
103513 CTAGGTTTTG
* * *
103523 GAGCGAAATATCTATTTAGCTCGCAA
1 GAGCGAAATATCTGTCTGGCTCGCAA
* * *
103549 GAGCGAAATATCTATTTGGCTTGCAA
1 GAGCGAAATATCTGTCTGGCTCGCAA
* **
103575 GAGCGAAATATTTGTCTCACTCGCAA
1 GAGCGAAATATCTGTCTGGCTCGCAA
* * *
103601 AAGTGAAATATCTGTCTGGCTCGTAA
1 GAGCGAAATATCTGTCTGGCTCGCAA
* * ** *
103627 AAGCGATAT-TCTGTCTGGCTCATAC
1 GAGCGAAATATCTGTCTGGCTCGCAA
* * *
103652 GAGTGATAT-TCTGTCTGGCTCGTAA
1 GAGCGAAATATCTGTCTGGCTCGCAA
103677 GAGCGA
1 GAGCGA
103683 GACTTTGTCT
Statistics
Matches: 111, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
25 40 0.36
26 71 0.64
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (26 bp):
GAGCGAAATATCTGTCTGGCTCGCAA
Found at i:103644 original size:25 final size:25
Alignment explanation
Indices: 103611--103731 Score: 127
Period size: 25 Copynumber: 4.8 Consensus size: 25
103601 AAGTGAAATA
*
103611 TCTGTCTGGCTCGTAAAAGCGATAT
1 TCTGTCTGGCTCGTAAGAGCGATAT
* * *
103636 TCTGTCTGGCTCATACGAGTGATAT
1 TCTGTCTGGCTCGTAAGAGCGATAT
*
103661 TCTGTCTGGCTCGTAAGAGCGAGACT
1 TCTGTCTGGCTCGTAAGAGCGATA-T
* * *
103687 T-TGTCTTGCTCGTAAGAGCAATAA
1 TCTGTCTGGCTCGTAAGAGCGATAT
* *
103711 TCTGACTGGGCTCGTATGAGC
1 TCTGTCT-GGCTCGTAAGAGC
103732 TAAATTTCTG
Statistics
Matches: 78, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
24 1 0.01
25 64 0.82
26 13 0.17
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (25 bp):
TCTGTCTGGCTCGTAAGAGCGATAT
Found at i:105621 original size:340 final size:345
Alignment explanation
Indices: 105090--105775 Score: 1004
Period size: 340 Copynumber: 2.0 Consensus size: 345
105080 GTTCATAAGA
*
105090 AACAATCAAATGGCTCCGCAGCCCCCTCCTCCTCCTGCACGACCTACTGTATGACCTGTAGTACC
1 AACAATCAAATGGCTCCGCAGCCCCCTCCTCCTCCTACACGACC-AC--T-TGA-CTGTAGTACC
* * *
105155 TCCAGTCATGCCTCCACCTCCTCCGACAATCGAGCAGAGACACCGTATTCTAACAGATAAGGTCA
61 TCCAGTCATGCCTCCACCTCCTCCAACAATCGAGCAGAGACACCATATTCTAACAAATAAGGTCA
* *
105220 AGAAGTACGGAGCAAAGGAATTTCGAGGAAGTATCGAGGATGATCCGTCAAGAGCTGAATACTGG
126 AGAAGTACGGAGCAAAGGAATTTCGAGGAAGTACCGAGGATGATCCATCAAGAGCTGAATACTGG
* * *
105285 TTAGAAAATACTCTGAGAGTTCTGAACGAGATGGCATGCCCTCATGAAGATTATTTGAGGTGTGT
191 TTAGAAAATACCCTGAGAGTTCTAAACGAGATGGCATGCCCACATGAAGATTATTTGAGGTGTGT
* * * *
105350 TGCATCATTGTTAAAAGATGAAGCTTATAGCTGGTGGACTATAATGCTGGCAGTAGTTCCTGAAA
256 CGCATCATTGTTAAAAGATGAAGCTTATAACTGGTGGACGACAATGCTGGCAGTAGTTCCTGAAA
105415 ATGAAATT-ATTAGGAATCTTCAGG
321 ATGAAATTAATTAGGAATCTTCAGG
* * * *
105439 AACAATCCAATGGCTCTGCAGCCCCCTCCTCCTCCTACACGA-C-C-TG-CTGTAGTACTTCTAG
1 AACAATCAAATGGCTCCGCAGCCCCCTCCTCCTCCTACACGACCACTTGACTGTAGTACCTCCAG
* ** * * * *
105500 TCGTGCCTCCACCTCCTTTAACAGTTGAGCAGAGACACCATATTCTGACAAATAAGGTCAGGAAG
66 TCATGCCTCCACCTCCTCCAACAATCGAGCAGAGACACCATATTCTAACAAATAAGGTCAAGAAG
* *
105565 TATGGAGCAAAGGAATTTCGAGGAAGTACCGAGGATGATTCATCAAGAGCTGAATACTGGTTAGA
131 TACGGAGCAAAGGAATTTCGAGGAAGTACCGAGGATGATCCATCAAGAGCTGAATACTGGTTAGA
*
105630 AAATACCCTGAGAGTTCTAAACGAGATGGCATGCCCACTTGAAGATTATTTGAGGTGTGTCGCAT
196 AAATACCCTGAGAGTTCTAAACGAGATGGCATGCCCACATGAAGATTATTTGAGGTGTGTCGCAT
* * * *
105695 TATTGTTAAAAGATGAAGCTTATAACTGGTGGACGACAATGTTGGTAGTAGTTCCTGAAAATTAA
261 CATTGTTAAAAGATGAAGCTTATAACTGGTGGACGACAATGCTGGCAGTAGTTCCTGAAAATGAA
*
105760 ATTAATTCGGAATCTT
326 ATTAATTAGGAATCTT
105776 TCCAGTCTGA
Statistics
Matches: 304, Mismatches: 32, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
340 250 0.82
341 11 0.04
342 2 0.01
346 1 0.00
348 1 0.00
349 39 0.13
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (345 bp):
AACAATCAAATGGCTCCGCAGCCCCCTCCTCCTCCTACACGACCACTTGACTGTAGTACCTCCAG
TCATGCCTCCACCTCCTCCAACAATCGAGCAGAGACACCATATTCTAACAAATAAGGTCAAGAAG
TACGGAGCAAAGGAATTTCGAGGAAGTACCGAGGATGATCCATCAAGAGCTGAATACTGGTTAGA
AAATACCCTGAGAGTTCTAAACGAGATGGCATGCCCACATGAAGATTATTTGAGGTGTGTCGCAT
CATTGTTAAAAGATGAAGCTTATAACTGGTGGACGACAATGCTGGCAGTAGTTCCTGAAAATGAA
ATTAATTAGGAATCTTCAGG
Found at i:107941 original size:83 final size:83
Alignment explanation
Indices: 107847--108011 Score: 213
Period size: 83 Copynumber: 2.0 Consensus size: 83
107837 GTATTCAATA
** * * * *
107847 CGTAAGTCCAGAATGTTTACGCTCATCAGCTAATGATAATCAGAATAATCGTATTAGGTTATCCT
1 CGTAAGTCCAGAACATTTACGCTCATCAACTAATCAAAATCAGAATAATCGTATCAGGTTATCCT
***
107912 TTTGGATTTAACCAATGG
66 TTCAAATTTAACCAATGG
* * * *
107930 CGTAAGTCCAGAACATTTATGCTCGTCAACTAATCAAAATCAGAATGATCGTGTCAGGTTATCCT
1 CGTAAGTCCAGAACATTTACGCTCATCAACTAATCAAAATCAGAATAATCGTATCAGGTTATCCT
107995 TTCAAATTTAACCAATG
66 TTCAAATTTAACCAATG
108012 ATCGCTCATA
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
83 69 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (83 bp):
CGTAAGTCCAGAACATTTACGCTCATCAACTAATCAAAATCAGAATAATCGTATCAGGTTATCCT
TTCAAATTTAACCAATGG
Found at i:108513 original size:20 final size:20
Alignment explanation
Indices: 108485--108524 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
108475 TTAATTCATT
108485 CATAACATA-AATCTAATTAA
1 CATAACATATAAT-TAATTAA
*
108505 CATATCATATAATTAATTAA
1 CATAACATATAATTAATTAA
108525 ATCTTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (20 bp):
CATAACATATAATTAATTAA
Found at i:129118 original size:54 final size:54
Alignment explanation
Indices: 129010--129285 Score: 361
Period size: 54 Copynumber: 5.3 Consensus size: 54
129000 TAGGAGCTCC
* *
129010 GTCATCGGACCTTTAATCTGTAATAGGA-TTCATATAAGTCACGATGACACAGA
1 GTCATCGGACCTTTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGA
* * *
129063 GTCATCGGGCCTTTTATCCGTAATAGGATTTCATATAACTCACGATGACATAGA
1 GTCATCGGACCTTTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGA
* *
129117 GTCATCGGACCTTTAATCCGTAATAGGA-TTCATATAACTCATGATGACATAGA
1 GTCATCGGACCTTTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGA
** *
129170 GTCATCAAACATTTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGA
1 GTCATCGGACCTTTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGA
* * * *
129224 GTCAT-----C-TTAATCCTTAATAGAATTTCATATAACTAAAGATGACACAGA
1 GTCATCGGACCTTTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGA
*
129272 GTCATTGGACCTTT
1 GTCATCGGACCTTT
129286 TTGCATTTAC
Statistics
Matches: 197, Mismatches: 18, Indels: 15
0.86 0.08 0.07
Matches are distributed among these distances:
48 43 0.22
53 75 0.38
54 79 0.40
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (54 bp):
GTCATCGGACCTTTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGA
Found at i:129196 original size:107 final size:107
Alignment explanation
Indices: 129010--129276 Score: 357
Period size: 107 Copynumber: 2.5 Consensus size: 107
129000 TAGGAGCTCC
* * *** *
129010 GTCATCGGACCTTTAATCTGTAATAGGATTCATATAAGTCACGATGACACAGAGTCATCGGGCCT
1 GTCATCGGACCTTTAATCCGTAATAGGATTCATATAACTCACGATGACACAGAGTCATCAAACAT
* *
129075 TTTATCCGTAATAGGATTTCATATAACTCACGATGACATAGA
66 TTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGA
* *
129117 GTCATCGGACCTTTAATCCGTAATAGGATTCATATAACTCATGATGACATAGAGTCATCAAACAT
1 GTCATCGGACCTTTAATCCGTAATAGGATTCATATAACTCACGATGACACAGAGTCATCAAACAT
129182 TTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGA
66 TTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGA
* * * *
129224 GTCAT-----C-TTAATCCTTAATAGAATTTCATATAACTAAAGATGACACAGAGTCAT
1 GTCATCGGACCTTTAATCCGTAATAGGA-TTCATATAACTCACGATGACACAGAGTCAT
129277 TGGACCTTTT
Statistics
Matches: 144, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
101 14 0.10
102 28 0.19
107 102 0.71
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (107 bp):
GTCATCGGACCTTTAATCCGTAATAGGATTCATATAACTCACGATGACACAGAGTCATCAAACAT
TTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGA
Found at i:132972 original size:17 final size:18
Alignment explanation
Indices: 132950--132983 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
132940 TTTTAGTAGT
132950 AGTTTATTT-GTATTAAA
1 AGTTTATTTAGTATTAAA
132967 AGTTTATTTAGTATTAA
1 AGTTTATTTAGTATTAA
132984 GGTATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (18 bp):
AGTTTATTTAGTATTAAA
Found at i:137263 original size:33 final size:33
Alignment explanation
Indices: 137203--137265 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
137193 GAATGTGAAT
*
137203 CCCATTTCGATATCTACACAAATAATTAAAGAA
1 CCCATTTCGATATCTACACAAACAATTAAAGAA
* * *
137236 CCCATTTCGATATCTGCATAAGCAATTAAA
1 CCCATTTCGATATCTACACAAACAATTAAA
137266 ATTTTAATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (33 bp):
CCCATTTCGATATCTACACAAACAATTAAAGAA
Found at i:137572 original size:22 final size:23
Alignment explanation
Indices: 137526--137583 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 23
137516 AACCTATCTT
*
137526 AATAAACATACACTACAAAATAA
1 AATAAACATACACTACAAAACAA
**
137549 AATAAACATACA-TACACTACAA
1 AATAAACATACACTACAAAACAA
**
137571 AATTGACATACAC
1 AATAAACATACAC
137584 AATTCTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.59, C:0.21, G:0.02, T:0.19
Consensus pattern (23 bp):
AATAAACATACACTACAAAACAA
Found at i:145472 original size:16 final size:16
Alignment explanation
Indices: 145435--145501 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
145425 TCAACTTATT
* *
145435 TAAAATTAAAAATATA
1 TAAAATTATAAATAAA
145451 TAAAATTATAAATAAA
1 TAAAATTATAAATAAA
* *
145467 TTAAATATATAATGTTGAAA
1 TAAAAT-TATAA--AT-AAA
*
145487 TAAATTTATAAATAA
1 TAAAATTATAAATAA
145502 TAATTATAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
16 21 0.52
17 6 0.15
19 6 0.15
20 7 0.17
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
TAAAATTATAAATAAA
Found at i:152869 original size:22 final size:22
Alignment explanation
Indices: 152844--152889 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
152834 GGTACGGGGA
152844 GTGAATGATTAAACACGGCATT
1 GTGAATGATTAAACACGGCATT
152866 GTGAATGATTAAACACGGCATT
1 GTGAATGATTAAACACGGCATT
152888 GT
1 GT
152890 ATAAAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (22 bp):
GTGAATGATTAAACACGGCATT
Found at i:152986 original size:13 final size:13
Alignment explanation
Indices: 152968--152997 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
152958 GATGAGTGAG
*
152968 GATAAGGATAAGA
1 GATAAGCATAAGA
152981 GATAAGCATAAGA
1 GATAAGCATAAGA
152994 GATA
1 GATA
152998 GGGCAGAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.27, T:0.17
Consensus pattern (13 bp):
GATAAGCATAAGA
Found at i:154815 original size:14 final size:15
Alignment explanation
Indices: 154796--154834 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
154786 GTTTTTTTTT
154796 ATATAAATAATAT-A
1 ATATAAATAATATAA
154810 ATATAAATAA-ATAA
1 ATATAAATAATATAA
154824 ATATAAA-AATA
1 ATATAAATAATA
154835 GGATAATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATATAAATAATATAA
Found at i:155483 original size:23 final size:23
Alignment explanation
Indices: 155457--155501 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
155447 AATTTCAAAT
**
155457 TTCGAATTATCCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
155480 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
155502 GAATTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:163655 original size:33 final size:34
Alignment explanation
Indices: 163618--163681 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
163608 GGGCAAAATA
* *
163618 AAGGACGAAACTTACTTATTAACAA-ATTAAGAG
1 AAGGAAGAAACTTACCTATTAACAATATTAAGAG
163651 AAGGAAGAAACTTACCTATTAACAATATTAA
1 AAGGAAGAAACTTACCTATTAACAATATTAA
163682 TTAAATATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 23 0.82
34 5 0.18
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (34 bp):
AAGGAAGAAACTTACCTATTAACAATATTAAGAG
Found at i:163696 original size:13 final size:14
Alignment explanation
Indices: 163680--163708 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
163670 TAACAATATT
163680 AATTAAATA-TACA
1 AATTAAATAGTACA
163693 AATTAAATAGTACA
1 AATTAAATAGTACA
163707 AA
1 AA
163709 ACCTACTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (14 bp):
AATTAAATAGTACA
Found at i:164354 original size:82 final size:83
Alignment explanation
Indices: 164252--164419 Score: 268
Period size: 84 Copynumber: 2.0 Consensus size: 83
164242 GAACAATAAC
*
164252 AATGAAAATGACGCCCTCTTTAGTGAGA-T-TATATGAACAAATGCCCGAACCTAAATATGTTAT
1 AATGAAAATGACGCCCTCTTTAGTGAGATTATATATGAACAAATACCCGAACCTAAATATGTTAT
164315 TGCTATGGGCACGTGTAAT
66 TGCTATGGGCACGTGT-AT
** *
164334 AATGAAAATGGTGCCCTCTTTAGTGAGATTATATATGAACCAATACCCGAACCTAAATATGTTAT
1 AATGAAAATGACGCCCTCTTTAGTGAGATTATATATGAACAAATACCCGAACCTAAATATGTTAT
*
164399 TGCTATGGGCGCGTGTAT
66 TGCTATGGGCACGTGTAT
164417 AAT
1 AAT
164420 TATAGGAAGG
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
82 26 0.33
83 6 0.08
84 47 0.59
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (83 bp):
AATGAAAATGACGCCCTCTTTAGTGAGATTATATATGAACAAATACCCGAACCTAAATATGTTAT
TGCTATGGGCACGTGTAT
Found at i:164570 original size:17 final size:17
Alignment explanation
Indices: 164543--164582 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
164533 ATAAATTCTA
*
164543 AATAGACTAAATATAAAT
1 AATA-ACTAAATAAAAAT
164561 AATAACTAAATAAAAAT
1 AATAACTAAATAAAAAT
164578 AATAA
1 AATAA
164583 TTTAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (17 bp):
AATAACTAAATAAAAAT
Found at i:164598 original size:11 final size:12
Alignment explanation
Indices: 164574--164602 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
164564 AACTAAATAA
164574 AAATAATAATTT
1 AAATAATAATTT
164586 AAATAAT-ATTT
1 AAATAATAATTT
164597 AAATAA
1 AAATAA
164603 AATAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATAATAATTT
Found at i:164619 original size:29 final size:29
Alignment explanation
Indices: 164552--164619 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
164542 AAATAGACTA
164552 AATATAAATAATAACTAAATAAAAATAAT
1 AATATAAATAATAACTAAATAAAAATAAT
* **
164581 AATTTAAATAATATTTAAAT-AAAATAAT
1 AATATAAATAATAACTAAATAAAAATAAT
164609 AATATATAATA
1 AATATA-AATA
164620 TAGATAGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 13 0.38
29 21 0.62
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (29 bp):
AATATAAATAATAACTAAATAAAAATAAT
Done.