Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015205.1 Kokia drynarioides strain JFW-HI SEQ_130249, 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: 458668
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 480 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:287017 original size:31 final size:31
Alignment explanation
Indices: 286968--287030 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
286958 ATTTTGCACT
*
286968 TGAAACTTGAATTGTGATTCA-TATGTATACA
1 TGAAACTTGAATTGTGATT-AGAATGTATACA
*
286999 TGAAACTTTG-ATTTTGATTAGAATGTATACA
1 TGAAAC-TTGAATTGTGATTAGAATGTATACA
287030 T
1 T
287031 TTAAAGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 1 0.04
31 24 0.86
32 3 0.11
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (31 bp):
TGAAACTTGAATTGTGATTAGAATGTATACA
Found at i:291876 original size:59 final size:60
Alignment explanation
Indices: 291770--291891 Score: 169
Period size: 60 Copynumber: 2.0 Consensus size: 60
291760 TAACTTATTC
* *
291770 TTTATGCAAGAAAATAAACATACTTAAAATAATAAAAAAATACCT-AAATAACATCAACT
1 TTTATGCAAGAAAATAAACATACTTAAAACAATAAAAAAATACCTAAAATAACACCAACT
* *
291829 TTTATGCAAGAAAATGAAACATACTTAAAAGCAA-CATAAAATA-CTAAAATAACACCAACT
1 TTTATGCAAGAAAAT-AAACATACTTAAAA-CAATAAAAAAATACCTAAAATAACACCAACT
291889 TTT
1 TTT
291892 CTAATGATTC
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
59 17 0.30
60 37 0.66
61 2 0.04
ACGTcount: A:0.55, C:0.15, G:0.05, T:0.25
Consensus pattern (60 bp):
TTTATGCAAGAAAATAAACATACTTAAAACAATAAAAAAATACCTAAAATAACACCAACT
Found at i:293430 original size:6 final size:6
Alignment explanation
Indices: 293380--293429 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
293370 ACCAAACCTT
* * * *
293380 ATCTTA ATCTTG ATCTTG ATCTTG ATCTTT ATCTTG ATGTTG ATGTTG
1 ATCTTG ATCTTG ATCTTG ATCTTG ATCTTG ATCTTG ATCTTG ATCTTG
293428 AT
1 AT
293430 GGACATCCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.52
Consensus pattern (6 bp):
ATCTTG
Found at i:302841 original size:23 final size:23
Alignment explanation
Indices: 302810--303079 Score: 326
Period size: 23 Copynumber: 11.8 Consensus size: 23
302800 AAGAAAGCGT
302810 ATAT-ATTTGTGCTTAAATATTA
1 ATATGATTTGTGCTTAAATATTA
*
302832 ATATGATTTGTGCTCAAATATTA
1 ATATGATTTGTGCTTAAATATTA
* * *
302855 ATGTGATTTGTTCTTAAATATTT
1 ATATGATTTGTGCTTAAATATTA
* *
302878 ATATAATTTGTGCTCAAATATTA
1 ATATGATTTGTGCTTAAATATTA
* *
302901 ATGTGATTTTTGCTTAAATATTA
1 ATATGATTTGTGCTTAAATATTA
*
302924 ATGTGATTTGTGCTTAAATATTA
1 ATATGATTTGTGCTTAAATATTA
*
302947 ATATGATTTGTGCTCAAATATTA
1 ATATGATTTGTGCTTAAATATTA
* * *
302970 ATATGATTTTTTCTCAAATATTA
1 ATATGATTTGTGCTTAAATATTA
* * * *
302993 GTGTGGTTTATGCTTAAATATTA
1 ATATGATTTGTGCTTAAATATTA
*
303016 ATGTGATTTGTGCTTAAATATTA
1 ATATGATTTGTGCTTAAATATTA
* * *
303039 ATATGATTTATGATTAATTATTA
1 ATATGATTTGTGCTTAAATATTA
* *
303062 ATGTGATTTGTGTTTAAA
1 ATATGATTTGTGCTTAAA
303080 AAATTAAGAT
Statistics
Matches: 211, Mismatches: 36, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
22 4 0.02
23 207 0.98
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (23 bp):
ATATGATTTGTGCTTAAATATTA
Found at i:302925 original size:69 final size:69
Alignment explanation
Indices: 302810--303079 Score: 371
Period size: 69 Copynumber: 3.9 Consensus size: 69
302800 AAGAAAGCGT
* * *
302810 ATAT-ATTTGTGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTGTTCTTAAAT
1 ATATGATTTGTGCTCAAATATTAATATGATTTTTGCTCAAATATTAATGTGATTTGTGCTTAAAT
*
302874 ATTT
66 ATTA
* * *
302878 ATATAATTTGTGCTCAAATATTAATGTGATTTTTGCTTAAATATTAATGTGATTTGTGCTTAAAT
1 ATATGATTTGTGCTCAAATATTAATATGATTTTTGCTCAAATATTAATGTGATTTGTGCTTAAAT
302943 ATTA
66 ATTA
* * * *
302947 ATATGATTTGTGCTCAAATATTAATATGATTTTTTCTCAAATATTAGTGTGGTTTATGCTTAAAT
1 ATATGATTTGTGCTCAAATATTAATATGATTTTTGCTCAAATATTAATGTGATTTGTGCTTAAAT
303012 ATTA
66 ATTA
* * * * * * *
303016 ATGTGATTTGTGCTTAAATATTAATATGATTTATGATTAATTATTAATGTGATTTGTGTTTAAA
1 ATATGATTTGTGCTCAAATATTAATATGATTTTTGCTCAAATATTAATGTGATTTGTGCTTAAA
303080 AAATTAAGAT
Statistics
Matches: 177, Mismatches: 24, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
68 4 0.02
69 173 0.98
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (69 bp):
ATATGATTTGTGCTCAAATATTAATATGATTTTTGCTCAAATATTAATGTGATTTGTGCTTAAAT
ATTA
Found at i:303249 original size:36 final size:34
Alignment explanation
Indices: 303158--303259 Score: 141
Period size: 34 Copynumber: 2.9 Consensus size: 34
303148 TTGTGAAAGT
*
303158 GAAAATGTGAGTATGGTCTTCATGCCATGTGATA
1 GAAAATGTGAGTATGTTCTTCATGCCATGTGATA
* *
303192 GAAAATATCAGTATGTTCTTCATGCCATGTGATA
1 GAAAATGTGAGTATGTTCTTCATGCCATGTGATA
* *
303226 GAAAGTATGTGGGTATGTTCTTCATACCATGTGA
1 GAAA--ATGTGAGTATGTTCTTCATGCCATGTGA
303260 CTAATTATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
34 35 0.59
36 24 0.41
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (34 bp):
GAAAATGTGAGTATGTTCTTCATGCCATGTGATA
Found at i:305193 original size:21 final size:21
Alignment explanation
Indices: 305169--305208 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
305159 TACCCTGTAA
* *
305169 TTCTACCGATACATGTATGGG
1 TTCTACCGAAACAAGTATGGG
305190 TTCTACCGAAACAAGTATG
1 TTCTACCGAAACAAGTATG
305209 CAGAATCACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (21 bp):
TTCTACCGAAACAAGTATGGG
Found at i:305753 original size:24 final size:24
Alignment explanation
Indices: 305726--305788 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
305716 AGCCCACACG
*
305726 AGCCCAAAATGGTTAGCTCTTACA
1 AGCCCAAAATGGTTAGATCTTACA
* * *
305750 AGCCCAGAATGATTAGATCTTACG
1 AGCCCAAAATGGTTAGATCTTACA
*
305774 AGCCCAAAATAGTTA
1 AGCCCAAAATGGTTA
305789 ACCAATATAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (24 bp):
AGCCCAAAATGGTTAGATCTTACA
Found at i:307407 original size:22 final size:21
Alignment explanation
Indices: 307382--307422 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
307372 CACTTATACT
*
307382 AAATTTTTAATTCAATAATTAA
1 AAATCTTTAATTCAA-AATTAA
307404 AAATCTTTAATTCAAAATT
1 AAATCTTTAATTCAAAATT
307423 CCATACAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATCTTTAATTCAAAATTAA
Found at i:315812 original size:2 final size:2
Alignment explanation
Indices: 315805--315829 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
315795 AACTACTCAA
315805 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
315830 AAACAAAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:317618 original size:27 final size:27
Alignment explanation
Indices: 317588--317652 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
317578 TTTAATGCAG
317588 ATAGACATAAAGGCATTCATT-CATAAC
1 ATAGACATAAAGGCA-TCATTACATAAC
* * * *
317615 ATAGATATGAAGGCATCCTTACATAAG
1 ATAGACATAAAGGCATCATTACATAAC
*
317642 ATAGCCATAAA
1 ATAGACATAAA
317653 AGTCTTCCAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.25
Consensus pattern (27 bp):
ATAGACATAAAGGCATCATTACATAAC
Found at i:317816 original size:52 final size:54
Alignment explanation
Indices: 317760--317864 Score: 151
Period size: 52 Copynumber: 2.0 Consensus size: 54
317750 GCAACAAAGA
*
317760 CTCTTTAACAGAATCAGCCACAAAGGCT-C-TTTAATAGAATTAGCCACAAATG
1 CTCTTCAACAGAATCAGCCACAAAGGCTACATTTAATAGAATTAGCCACAAATG
* * *
317812 CTCTTCAATAGAATCAGCTACAAAGGCTCACATTTAATAGAGTTAGCCACAAA
1 CTCTTCAACAGAATCAGCCACAAAGGCT-ACATTTAATAGAATTAGCCACAAA
317865 GGCTTTTTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
52 25 0.54
54 1 0.02
55 20 0.43
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (54 bp):
CTCTTCAACAGAATCAGCCACAAAGGCTACATTTAATAGAATTAGCCACAAATG
Found at i:317863 original size:29 final size:26
Alignment explanation
Indices: 317748--317868 Score: 134
Period size: 26 Copynumber: 4.5 Consensus size: 26
317738 ATAACAGAGA
* * *
317748 TAGCAACAAAGACTCTTTAACAGAAT
1 TAGCCACAAAGGCTCTTTAATAGAAT
*
317774 CAGCCACAAAGGCTCTTTAATAGAAT
1 TAGCCACAAAGGCTCTTTAATAGAAT
* *
317800 TAGCCACAAATGCTCTTCAATAGAAT
1 TAGCCACAAAGGCTCTTTAATAGAAT
* * *
317826 CAGCTACAAAGGCTCACATTTAATAGAGT
1 TAGCCACAAAGGCT--C-TTTAATAGAAT
317855 TAGCCACAAAGGCT
1 TAGCCACAAAGGCT
317869 TTTTTGGGAA
Statistics
Matches: 78, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
26 56 0.72
28 1 0.01
29 21 0.27
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (26 bp):
TAGCCACAAAGGCTCTTTAATAGAAT
Found at i:323136 original size:51 final size:50
Alignment explanation
Indices: 323047--323336 Score: 341
Period size: 51 Copynumber: 5.6 Consensus size: 50
323037 GCTATAAACA
*
323047 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCTCTTATA-GATT
1 AAAG-GTCCGATAACTAAGTGTCATCGTGAGTAAATGAATC-CTT-TACGATT
*
323099 AAAGGTCTGATAACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATAACTAAGTGTCATCGTGAGTAAATGAATCCTTTAC-GATT
*
323150 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATAACTAAGTGTCATCGTGAGTAAATGAATCCTTTAC-GATT
* * *
323201 AAAGGTCCGATAACTAAGTGTCATCGTGAGTAAATGAATCCATAATGGATT
1 AAAGGTCCGATAACTAAGTGTCATCGTGAGTAAATGAATCCTTTA-CGATT
* * * * * * **
323252 AAAGGTCCAATGACTCAGTGTCATCATGAGTATATGAATTCCTATACGGAAA
1 AAAGGTCCGATAACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTAC-GATT
*
323304 AAGAGGTCCGATAACTATA-TGTCGTCGTGAGTA
1 AA-AGGTCCGATAACTA-AGTGTCATCGTGAGTA
323337 TTAAATGAAA
Statistics
Matches: 207, Mismatches: 24, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
49 2 0.01
50 3 0.01
51 166 0.80
52 12 0.06
53 23 0.11
54 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (50 bp):
AAAGGTCCGATAACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGATT
Found at i:323228 original size:102 final size:102
Alignment explanation
Indices: 323047--323336 Score: 397
Period size: 102 Copynumber: 2.8 Consensus size: 102
323037 GCTATAAACA
*
323047 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCTCTTATA--GATTAAAGGTCTGAT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATC-CTT-TACGGATTAAAGGTCCGAT
* *
323110 AACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
63 AACTAAGTGTCATCGTGAGTAAATGAATCCATAACGGATT
323150 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATAAC
*
323215 TAAGTGTCATCGTGAGTAAATGAATCCATAATGGATT
66 TAAGTGTCATCGTGAGTAAATGAATCCATAACGGATT
* * * * * **
323252 AAAGGTCCAATGACTCAGTGTCATCATGAGTATATGAATTCCTATACGGAAAAAGAGGTCCGATA
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATTAA-AGGTCCGATA
*
323317 ACTATA-TGTCGTCGTGAGTA
64 ACTA-AGTGTCATCGTGAGTA
323337 TTAAATGAAA
Statistics
Matches: 170, Mismatches: 12, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
100 2 0.01
101 3 0.02
102 121 0.71
103 16 0.09
104 27 0.16
105 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (102 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATAAC
TAAGTGTCATCGTGAGTAAATGAATCCATAACGGATT
Found at i:324629 original size:75 final size:75
Alignment explanation
Indices: 324506--324662 Score: 251
Period size: 75 Copynumber: 2.1 Consensus size: 75
324496 AGAGGAAACT
* * * *
324506 AATGAGGTAAACAGCAATGTTCCGACTAATGATTCTAGAGCTAGCCATAGTGCATTAATATTACC
1 AATGAAGTAAACAGCAATGCTCCGACTAATGATTCTAGAGCTAGCCATAATGCATCAATATTACC
324571 GATGACAGAG
66 GATGACAGAG
* *
324581 AATGAAGTAAACAGCAATGCTCCGACTAATGATTTTGGAGCTAGCCATAATGCATCAATATTACC
1 AATGAAGTAAACAGCAATGCTCCGACTAATGATTCTAGAGCTAGCCATAATGCATCAATATTACC
*
324646 GATGATAGAG
66 GATGACAGAG
324656 AATGAAG
1 AATGAAG
324663 CAAAGAATAC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (75 bp):
AATGAAGTAAACAGCAATGCTCCGACTAATGATTCTAGAGCTAGCCATAATGCATCAATATTACC
GATGACAGAG
Found at i:330505 original size:51 final size:51
Alignment explanation
Indices: 330417--330655 Score: 304
Period size: 51 Copynumber: 4.6 Consensus size: 51
330407 GCTATAAACA
*
330417 AAAGAGTCCGATGACTAAGTGTCATCGTGACTAAATGAATCCCTTACGAATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACGAATT
* * *
330469 AAAGGTTCGAGGACTAAGTGTCATCGTGAGTAAATGAATCCTTTAC-AGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACGA-ATT
* * *
330520 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACGAATT
* * * *
330571 AAAGGTCCGATGACTCAGTGTCATCGTGAGTATATGAATTCCTATACGGAA-C
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCT-TAC-GAATT
330623 AAGAGGTCCGATGACTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
330656 TTAAATGAAA
Statistics
Matches: 164, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
50 1 0.01
51 125 0.76
52 8 0.05
53 29 0.18
54 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACGAATT
Found at i:333713 original size:13 final size:14
Alignment explanation
Indices: 333695--333723 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
333685 TAAATTCAGG
333695 ATATC-ATTTTAGT
1 ATATCAATTTTAGT
333708 ATATCAATTTTAGT
1 ATATCAATTTTAGT
333722 AT
1 AT
333724 CAAAATCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (14 bp):
ATATCAATTTTAGT
Found at i:334180 original size:3 final size:3
Alignment explanation
Indices: 334172--334200 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
334162 TGAGGAGTGT
334172 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
334201 TAAGAAGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:340359 original size:2 final size:2
Alignment explanation
Indices: 340354--340441 Score: 76
Period size: 2 Copynumber: 44.5 Consensus size: 2
340344 AAAGAACTTT
* * * *
340354 TA TA TA TA TA TA TA CTA AA TA TA -A TG TA T- TT TCA TT TA -A TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
*
340395 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA GTG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
340437 TA TA T
1 TA TA T
340442 TAGGATATAA
Statistics
Matches: 70, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
1 4 0.06
2 62 0.89
3 4 0.06
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:340450 original size:20 final size:20
Alignment explanation
Indices: 340392--340450 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
340382 TTTTCATTTA
*
340392 ATATATATATA-TA-TATAT
1 ATATATATATATTAGGATAT
340410 ATATATATATATTAGTG-TAT
1 ATATATATATATTAG-GATAT
340430 ATATATATATATTAGGATAT
1 ATATATATATATTAGGATAT
340450 A
1 A
340451 AAGCAATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 11 0.31
19 3 0.08
20 22 0.61
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
ATATATATATATTAGGATAT
Found at i:344287 original size:87 final size:86
Alignment explanation
Indices: 344128--344294 Score: 221
Period size: 87 Copynumber: 1.9 Consensus size: 86
344118 TACATGCATA
* * * *
344128 AGGTTGAGTTCTCACTCTTAATAAGTTCATATCCCAAGATCTAGATGGTCCTGTTGAGACAGACT
1 AGGTTGAGTTATCACTCTTAATAAATTCATATCCCAAGATCTAGATGGTCCTATTAAGACAGACT
344193 TGATGAATTCACCGATGTGAG
66 TGATGAATTCACCGATGTGAG
* * * *
344214 AGGTTGAGTTTATTACTCTTAATAAATTCATATCCC-AGAGTTTGGGTGGTCCTATTAAGAC-GA
1 AGGTTGAG-TTATCACTCTTAATAAATTCATATCCCAAGA-TCTAGATGGTCCTATTAAGACAG-
344277 ACTTGATGAATTCACCGA
63 ACTTGATGAATTCACCGA
344295 ACTTAAATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
86 12 0.17
87 58 0.83
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (86 bp):
AGGTTGAGTTATCACTCTTAATAAATTCATATCCCAAGATCTAGATGGTCCTATTAAGACAGACT
TGATGAATTCACCGATGTGAG
Found at i:345251 original size:6 final size:6
Alignment explanation
Indices: 345240--345264 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
345230 ATTTTTAACA
345240 TAGTGT TAGTGT TAGTGT TAGTGT T
1 TAGTGT TAGTGT TAGTGT TAGTGT T
345265 GGAGAAGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (6 bp):
TAGTGT
Found at i:358801 original size:20 final size:21
Alignment explanation
Indices: 358763--358802 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
358753 AGAAACTCAA
* *
358763 TTAGTGGGAACCCATTTTTCC
1 TTAGTGGGAAACCAGTTTTCC
358784 TTAGT-GGAAACCAGTTTTC
1 TTAGTGGGAAACCAGTTTTC
358803 AGCCCTGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (21 bp):
TTAGTGGGAAACCAGTTTTCC
Found at i:359747 original size:2 final size:2
Alignment explanation
Indices: 359742--359774 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
359732 AAAAAATTAA
*
359742 AT AT AT AT AT AT AA 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 AT A
359775 AATTAGGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:360045 original size:13 final size:15
Alignment explanation
Indices: 360009--360061 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
359999 GGGTTATTAC
360009 TTATATATTATAATA
1 TTATATATTATAATA
* *
360024 TTATTTATTA-AGT-
1 TTATATATTATAATA
360037 TTATATATTATAATA
1 TTATATATTATAATA
*
360052 TTATTTATTA
1 TTATATATTA
360062 AGTTTAGTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 9 0.29
14 4 0.13
15 18 0.58
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TTATATATTATAATA
Found at i:360047 original size:28 final size:28
Alignment explanation
Indices: 360009--360067 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
359999 GGGTTATTAC
360009 TTATATATTATAATATTATTTATTAAGT
1 TTATATATTATAATATTATTTATTAAGT
360037 TTATATATTATAATATTATTTATTAAGT
1 TTATATATTATAATATTATTTATTAAGT
360065 TTA
1 TTA
360068 GTTAATTCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (28 bp):
TTATATATTATAATATTATTTATTAAGT
Found at i:365725 original size:52 final size:53
Alignment explanation
Indices: 365643--365749 Score: 180
Period size: 52 Copynumber: 2.0 Consensus size: 53
365633 ATGCCGGTAG
*
365643 TATTAAATATAAACCTATCTTAATATATTTGCATCTTC-AAATTGAGGAAGCT
1 TATTAAATATAAACCTATCTTAATACATTTGCATCTTCAAAATTGAGGAAGCT
* *
365695 TATTAAATATAAACCTGTGTTAATACATTTGCATCTTCAAAATTGAGGAAGCT
1 TATTAAATATAAACCTATCTTAATACATTTGCATCTTCAAAATTGAGGAAGCT
365748 TA
1 TA
365750 ACATGTTACT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
52 35 0.69
53 16 0.31
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.37
Consensus pattern (53 bp):
TATTAAATATAAACCTATCTTAATACATTTGCATCTTCAAAATTGAGGAAGCT
Found at i:379296 original size:13 final size:13
Alignment explanation
Indices: 379278--379302 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
379268 ACAGCGTTAA
379278 ATGATTTAATTAT
1 ATGATTTAATTAT
379291 ATGATTTAATTA
1 ATGATTTAATTA
379303 AAGAATTTGG
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
ATGATTTAATTAT
Found at i:379638 original size:52 final size:52
Alignment explanation
Indices: 379553--379886 Score: 515
Period size: 52 Copynumber: 6.4 Consensus size: 52
379543 CGAAAAATGC
* * * *
379553 CCGATGACTATGTGTCATCGTGAGCATAAGAATCTTTTACGGAATATGAGGT
1 CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGT
* *
379605 CCGATTACTATGTGTCATCGTGATTATATGAATCCTTTACGGATTATGAGGT
1 CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGT
*
379657 CCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATGAGGT
1 CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGT
* * * *
379709 CCGATGGCTATGTGTAATCGTGAGTATATGAACCCTTTACAGATTATGAGGT
1 CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGT
* *
379761 CCGATGACTATGTGTAATCATGAGTATATGAATCCTTTACGGATTATGAGGT
1 CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGT
* * * *
379813 CCGATGACTATGTGTAATCGTGAGTATGTGAACCCTTTACAGATTATGAGGT
1 CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGT
379865 CCGATGACTATGTGTCATCGTG
1 CCGATGACTATGTGTCATCGTG
379887 TGTAACCCTT
Statistics
Matches: 259, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 259 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (52 bp):
CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGT
Found at i:379998 original size:2 final size:2
Alignment explanation
Indices: 379991--380017 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
379981 ACATATACAT
379991 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
380018 TATATATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:380360 original size:18 final size:18
Alignment explanation
Indices: 380327--380361 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
380317 ATATTAATAC
*
380327 ACATAATATAACCACAAA
1 ACATAATACAACCACAAA
*
380345 ACATAATACAATCACAA
1 ACATAATACAACCACAA
380362 GCATAATCCA
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:0.60, C:0.23, G:0.00, T:0.17
Consensus pattern (18 bp):
ACATAATACAACCACAAA
Found at i:380569 original size:6 final size:6
Alignment explanation
Indices: 380560--380594 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
380550 TAAGTTTTAA
*
380560 TCTCAA TCTCAC TCTCAC TCTCAC TCTCAC TCTCA
1 TCTCAC TCTCAC TCTCAC TCTCAC TCTCAC TCTCA
380595 AGATACTACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.20, C:0.46, G:0.00, T:0.34
Consensus pattern (6 bp):
TCTCAC
Found at i:387524 original size:18 final size:18
Alignment explanation
Indices: 387503--387537 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
387493 ATATTAATAC
*
387503 ACATAATATAATCACAAA
1 ACATAATACAATCACAAA
387521 ACATAATACAATCACAA
1 ACATAATACAATCACAA
387538 GCATAATGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (18 bp):
ACATAATACAATCACAAA
Found at i:390432 original size:18 final size:18
Alignment explanation
Indices: 390409--390443 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
390399 GGTGTTATAG
390409 GCATGATGGGAAGAGTTA
1 GCATGATGGGAAGAGTTA
*
390427 GCATGATGGGAGGAGTT
1 GCATGATGGGAAGAGTT
390444 GGTTGTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.43, T:0.23
Consensus pattern (18 bp):
GCATGATGGGAAGAGTTA
Found at i:393382 original size:12 final size:12
Alignment explanation
Indices: 393367--393409 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
393357 ACAGTCATAC
393367 AAACATAACAAT
1 AAACATAACAAT
393379 AAACATAAC-AT
1 AAACATAACAAT
*
393390 --ACATAACAGT
1 AAACATAACAAT
393400 AAACATAACA
1 AAACATAACA
393410 TACTTAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 7 0.26
10 1 0.04
11 2 0.07
12 17 0.63
ACGTcount: A:0.63, C:0.19, G:0.02, T:0.16
Consensus pattern (12 bp):
AAACATAACAAT
Found at i:393393 original size:9 final size:9
Alignment explanation
Indices: 393381--393619 Score: 70
Period size: 9 Copynumber: 25.3 Consensus size: 9
393371 ATAACAATAA
393381 ACATAACAT
1 ACATAACAT
393390 ACATAACAGT
1 ACATAACA-T
393400 AAACATAACAT
1 --ACATAACAT
*
393411 ACTTAATTATATAT
1 AC---A-TA-ACAT
393425 ACATAACAT
1 ACATAACAT
* *
393434 ACAAAATTAT
1 ACATAA-CAT
393444 ACAT-ACAT
1 ACATAACAT
393452 A-AT-ACAT
1 ACATAACAT
* ** *
393459 ATAATAGTAA
1 A-CATAACAT
393469 ACATAACAT
1 ACATAACAT
393478 ACAT-A-AT
1 ACATAACAT
393485 A-ATATACAT
1 ACATA-ACAT
*
393494 AACAT-ACGT
1 -ACATAACAT
*
393503 ACA-AATAT
1 ACATAACAT
*
393511 ACA-AACAA
1 ACATAACAT
*
393519 ACAGTAAACACA
1 ACA-T-AACA-T
393531 ACAT-ACAT
1 ACATAACAT
*
393539 A-ATAATAT
1 ACATAACAT
393547 ACATAACAT
1 ACATAACAT
393556 ACATAACAATAT
1 ACATAAC---AT
393568 GGACCATAACAT
1 --A-CATAACAT
393580 ACATAACAGT
1 ACATAACA-T
393590 ACATAACAT
1 ACATAACAT
*
393599 ACATAATTAT
1 ACATAA-CAT
393609 ACAT-ACAT
1 ACATAACAT
393617 ACA
1 ACA
393620 CAAACAGTAA
Statistics
Matches: 175, Mismatches: 23, Indels: 65
0.67 0.09 0.25
Matches are distributed among these distances:
6 2 0.01
7 12 0.07
8 29 0.17
9 65 0.37
10 27 0.15
11 9 0.05
12 17 0.10
13 2 0.01
14 6 0.03
15 6 0.03
ACGTcount: A:0.55, C:0.18, G:0.03, T:0.25
Consensus pattern (9 bp):
ACATAACAT
Found at i:393395 original size:21 final size:21
Alignment explanation
Indices: 393369--393604 Score: 146
Period size: 21 Copynumber: 11.3 Consensus size: 21
393359 AGTCATACAA
393369 ACATAACAATAAACATAACAT
1 ACATAACAATAAACATAACAT
*
393390 ACATAACAGTAAACATAACAT
1 ACATAACAATAAACATAACAT
* * *
393411 ACTTAATTATATATACATAACAT
1 ACATAA-CA-ATAAACATAACAT
* ** * *
393434 ACAAAATTATACATACATAATAC
1 ACATAACAATA-A-ACATAACAT
* * *
393457 ATATAATAGTAAACATAACAT
1 ACATAACAATAAACATAACAT
* *
393478 ACATAATAATATACATAACAT
1 ACATAACAATAAACATAACAT
* * *
393499 ACGT-AC---AAATAT-ACAA
1 ACATAACAATAAACATAACAT
* *
393515 ACA-AACAGTAAACACAACAT
1 ACATAACAATAAACATAACAT
* *
393535 ACATAATAATATACATAACAT
1 ACATAACAATAAACATAACAT
*
393556 ACATAACAATATGGACCATAACAT
1 ACATAACAATA---AACATAACAT
*
393580 ACATAACAGT--ACATAACAT
1 ACATAACAATAAACATAACAT
393599 ACATAA
1 ACATAA
393605 TTATACATAC
Statistics
Matches: 164, Mismatches: 38, Indels: 28
0.71 0.17 0.12
Matches are distributed among these distances:
16 7 0.04
17 4 0.02
19 18 0.11
20 7 0.04
21 79 0.48
22 3 0.02
23 29 0.18
24 17 0.10
ACGTcount: A:0.56, C:0.17, G:0.03, T:0.24
Consensus pattern (21 bp):
ACATAACAATAAACATAACAT
Found at i:393776 original size:34 final size:34
Alignment explanation
Indices: 393733--393797 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
393723 CAAAAACAAA
*
393733 AAATAAAAGTTAGATATAATACCAATTAAAAAAT
1 AAATAAAAGTTAGATATAATACCAAATAAAAAAT
* *
393767 AAATAAAAGTTATATATAATACGAAATAAAA
1 AAATAAAAGTTAGATATAATACCAAATAAAA
393798 TAGAGTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.63, C:0.05, G:0.06, T:0.26
Consensus pattern (34 bp):
AAATAAAAGTTAGATATAATACCAAATAAAAAAT
Found at i:393836 original size:33 final size:33
Alignment explanation
Indices: 393794--393859 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
393784 AATACGAAAT
* * *
393794 AAAATAGAGTTAAAACCCAAAAAATAACAAAAC
1 AAAACAGAGTCAAAACCCAAAAAATAAAAAAAC
*
393827 AAAACAGAGTCAAAACCCAGAAAATAAAAAAAC
1 AAAACAGAGTCAAAACCCAAAAAATAAAAAAAC
393860 CTCATCAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.67, C:0.17, G:0.08, T:0.09
Consensus pattern (33 bp):
AAAACAGAGTCAAAACCCAAAAAATAAAAAAAC
Found at i:394169 original size:54 final size:54
Alignment explanation
Indices: 394047--394160 Score: 165
Period size: 54 Copynumber: 2.1 Consensus size: 54
394037 TTTTCAGACA
* * * * *
394047 AAAGGGTGAGTAGTCAAAACAATTGAAAGGGTTTTCTGACAGGAAGAGCAATCG
1 AAAGGGTGAGTAATCGAAACAATCGAAAGGGTTTTATGACAGGAAGAACAATCG
* *
394101 AAAGGGTGAGTAATCGAAACAATCGAAATGGTTTTATGAGAGGAAGAACAATCG
1 AAAGGGTGAGTAATCGAAACAATCGAAAGGGTTTTATGACAGGAAGAACAATCG
394155 AAAGGG
1 AAAGGG
394161 CTTGTAATCT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.41, C:0.10, G:0.30, T:0.19
Consensus pattern (54 bp):
AAAGGGTGAGTAATCGAAACAATCGAAAGGGTTTTATGACAGGAAGAACAATCG
Found at i:399403 original size:30 final size:30
Alignment explanation
Indices: 399369--399429 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
399359 CAATATTTAG
399369 ATAAAATATAGTAGGGATTATTATCATATA
1 ATAAAATATAGTAGGGATTATTATCATATA
399399 ATAAAATATAGTAGGGATTATTATCATATA
1 ATAAAATATAGTAGGGATTATTATCATATA
399429 A
1 A
399430 AACCCTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.48, C:0.03, G:0.13, T:0.36
Consensus pattern (30 bp):
ATAAAATATAGTAGGGATTATTATCATATA
Found at i:414784 original size:13 final size:13
Alignment explanation
Indices: 414768--414817 Score: 59
Period size: 12 Copynumber: 3.9 Consensus size: 13
414758 TTGAGAAGTG
414768 TTTTTAAAAAATA
1 TTTTTAAAAAATA
414781 -TTTTAAAAAATGA
1 TTTTTAAAAAAT-A
*
414794 TTTTTAAAAGA-A
1 TTTTTAAAAAATA
*
414806 TTTTTGAAAAAT
1 TTTTTAAAAAAT
414818 TTAATTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 21 0.68
13 1 0.03
14 9 0.29
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (13 bp):
TTTTTAAAAAATA
Found at i:415172 original size:20 final size:20
Alignment explanation
Indices: 415147--415185 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
415137 TCATTTAAGA
415147 AAAAATGCTT-TTAAAAAATC
1 AAAAAT-CTTATTAAAAAATC
*
415167 AAAAATTTTATTAAAAAAT
1 AAAAATCTTATTAAAAAAT
415186 TATTTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAAATCTTATTAAAAAATC
Found at i:416479 original size:12 final size:12
Alignment explanation
Indices: 416462--416488 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
416452 TATACATACG
416462 TATGTACGTACA
1 TATGTACGTACA
416474 TATGTACGTACA
1 TATGTACGTACA
416486 TAT
1 TAT
416489 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (12 bp):
TATGTACGTACA
Found at i:419136 original size:50 final size:50
Alignment explanation
Indices: 419078--419174 Score: 167
Period size: 50 Copynumber: 1.9 Consensus size: 50
419068 TTAATTTTGT
*
419078 CATGTATTATGTAACTCTCATGTTAGTTAAATATGCATCTTAAATTATGA
1 CATGTATTATGTAACTCCCATGTTAGTTAAATATGCATCTTAAATTATGA
* *
419128 CATGTATTATGTAACTCCCATGTTAGTTAAGTGTGCATCTTAAATTA
1 CATGTATTATGTAACTCCCATGTTAGTTAAATATGCATCTTAAATTA
419175 AGTCTTGCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (50 bp):
CATGTATTATGTAACTCCCATGTTAGTTAAATATGCATCTTAAATTATGA
Found at i:419751 original size:79 final size:78
Alignment explanation
Indices: 419655--419888 Score: 274
Period size: 79 Copynumber: 3.0 Consensus size: 78
419645 TGATACATTA
** *
419655 TGACTATTCAAAAGACCAAGAAAAGACTCTTCAAATGCTTATTGGATTCGGTGCACTTATAA-GA
1 TGACTATTCAAAAGACCAAGGGAAGACTCTTCAAATGCTGATT-GATTCGGTGCACTTA-AATGA
**
419719 TGATTCAA-AGCAAGG
64 CAATTCAAGA-CAAGG
* *
419734 TGACTATTTAAAAGACCAAGGGAAGACTCTTCAAATACTGATTGATTCGGTGCACTTAAATGACA
1 TGACTATTCAAAAGACCAAGGGAAGACTCTTCAAATGCTGATTGATTCGGTGCACTTAAATGACA
419799 ATTCAAGACAAGG
66 ATTCAAGACAAGG
* * ** * * * *
419812 TGACTCTTCAAAAGACCAAGGGAAGACTCTTTAAATGCTGAACGGTTTTGGTGCACTTAAAGGCC
1 TGACTATTCAAAAGACCAAGGGAAGACTCTTCAAATGCTG-ATTGATTCGGTGCACTTAAATGAC
*
419877 AATTCAATACAA
65 AATTCAAGACAA
419889 CAATTAAAGG
Statistics
Matches: 134, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
77 2 0.01
78 64 0.48
79 68 0.51
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (78 bp):
TGACTATTCAAAAGACCAAGGGAAGACTCTTCAAATGCTGATTGATTCGGTGCACTTAAATGACA
ATTCAAGACAAGG
Found at i:423724 original size:31 final size:32
Alignment explanation
Indices: 423672--423734 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
423662 TTTAATTTAA
* * *
423672 TAAGTGTTTGTATATTTAATTATGTCTTGCAT
1 TAAGTGTTTGTACATTTAATTAAGTCATGCAT
*
423704 TAAGTGTTT-TACGTTTAATTAAGTCATGCAT
1 TAAGTGTTTGTACATTTAATTAAGTCATGCAT
423735 AAACGCATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (32 bp):
TAAGTGTTTGTACATTTAATTAAGTCATGCAT
Found at i:424460 original size:79 final size:79
Alignment explanation
Indices: 424323--424558 Score: 269
Period size: 79 Copynumber: 3.0 Consensus size: 79
424313 TTGATACATT
* * * * * * * *
424323 GTGACTATTCAAAAGA-TCAAGGAAAGATTGTTCAATTGCTTATTGGTTTCGATGCACTTAAAGG
1 GTGACTCTTCAAAAGACT-AAGGGAAGACTCTTCAAATGCTAATCGGTTTCGGTGCACTTAAAGG
* *
424387 ACAGTTCAAGA-TAA
65 ACAATTCAAGACAAA
* *
424401 GTTGACTCTTCAAAAGACTAAGGGAAGACTCTTCAAATGCTGATCGGTTTCGGTTCACTTAAAGG
1 G-TGACTCTTCAAAAGACTAAGGGAAGACTCTTCAAATGCTAATCGGTTTCGGTGCACTTAAAGG
*
424466 ATAATTCAAGACAAA
65 ACAATTCAAGACAAA
* * * * * *
424481 GTGACTCTTAAAAATACCAAGGGAAGACTCTTCATATGCTAATCGGTTTTGGTGCACTTAAAGGT
1 GTGACTCTTCAAAAGACTAAGGGAAGACTCTTCAAATGCTAATCGGTTTCGGTGCACTTAAAGGA
424546 CAATTCAAGACAA
66 CAATTCAAGACAA
424559 CAATTAAAGG
Statistics
Matches: 134, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
78 1 0.01
79 129 0.96
80 4 0.03
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (79 bp):
GTGACTCTTCAAAAGACTAAGGGAAGACTCTTCAAATGCTAATCGGTTTCGGTGCACTTAAAGGA
CAATTCAAGACAAA
Found at i:424646 original size:24 final size:21
Alignment explanation
Indices: 424598--424636 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
424588 GGTAATCGAT
*
424598 CATGGTAGAAGAAAGGACTTA
1 CATGGTAGAAGAAAGGAATTA
424619 -ATGGTAGAAGAAAGGAAT
1 CATGGTAGAAGAAAGGAAT
424637 GTGACCATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.31, T:0.18
Consensus pattern (21 bp):
CATGGTAGAAGAAAGGAATTA
Found at i:432751 original size:45 final size:45
Alignment explanation
Indices: 432652--432742 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
432642 ACATAAAGAA
*
432652 AATAAATATTTTAAGGGTAAACTATCAATATAGTTACTTTTGTTT
1 AATAAATATTTTAAGGGTAAACTATCAATATAGTCACTTTTGTTT
432697 AATAAATATTTTAAGGGTAAACTATCAATATAGTCACTTTTGTTT
1 AATAAATATTTTAAGGGTAAACTATCAATATAGTCACTTTTGTTT
432742 A
1 A
432743 CTCCATATTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (45 bp):
AATAAATATTTTAAGGGTAAACTATCAATATAGTCACTTTTGTTT
Found at i:433912 original size:25 final size:22
Alignment explanation
Indices: 433879--433923 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 22
433869 AGAAGATAGA
433879 AAAATAAAGGGAAAGTAAAAAAAGG
1 AAAATAAA--GAAA-TAAAAAAAGG
433904 AAAATAAAGAAATAAAAAAA
1 AAAATAAAGAAATAAAAAAA
433924 TTAAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 4 0.20
25 8 0.40
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (22 bp):
AAAATAAAGAAATAAAAAAAGG
Found at i:452206 original size:17 final size:17
Alignment explanation
Indices: 452184--452217 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
452174 AGGCTGATAC
452184 TTAAATTGAGTTTCTTT
1 TTAAATTGAGTTTCTTT
* *
452201 TTAAATTTATTTTCTTT
1 TTAAATTGAGTTTCTTT
452218 AAATTCTTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.65
Consensus pattern (17 bp):
TTAAATTGAGTTTCTTT
Found at i:456687 original size:13 final size:13
Alignment explanation
Indices: 456669--456709 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
456659 TCGAGACTAC
456669 ATGCTTGAATATG
1 ATGCTTGAATATG
*
456682 ATGCTTGGATATG
1 ATGCTTGAATATG
*
456695 ATGCTTTAATATG
1 ATGCTTGAATATG
456708 AT
1 AT
456710 AGGGGCACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.41
Consensus pattern (13 bp):
ATGCTTGAATATG
Found at i:456992 original size:21 final size:20
Alignment explanation
Indices: 456968--457010 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
456958 ATAAAAAAAA
456968 AAGAAAAAGAAAAAAAGAGAG
1 AAGAAAAAGAAAAAAAG-GAG
*
456989 AAGAAAAAGGAAAAAAGGAG
1 AAGAAAAAGAAAAAAAGGAG
457009 AA
1 AA
457011 AATGAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (20 bp):
AAGAAAAAGAAAAAAAGGAG
Found at i:456996 original size:14 final size:14
Alignment explanation
Indices: 456937--456996 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
456927 GAGTTCGAAT
* *
456937 AAAGAAGAAGAAGA
1 AAAGAAAAAGAAAA
*
456951 AAAGAACATAAAAAAA
1 AAAGAA-A-AAGAAAA
456967 AAAGAAAAAGAAAA
1 AAAGAAAAAGAAAA
*
456981 AAAGAGAGAAGAAAA
1 AAAGA-AAAAGAAAA
456996 A
1 A
456997 GGAAAAAAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
14 17 0.45
15 10 0.26
16 11 0.29
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAAGAAAA
Found at i:458647 original size:17 final size:17
Alignment explanation
Indices: 458625--458658 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
458615 AGGCTGATAC
458625 TTAAATTGAGTTTCTTT
1 TTAAATTGAGTTTCTTT
* *
458642 TTAAATTTATTTTCTTT
1 TTAAATTGAGTTTCTTT
458659 AAATTCTTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.65
Consensus pattern (17 bp):
TTAAATTGAGTTTCTTT
Done.