Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004876.1 Kokia drynarioides strain JFW-HI SEQ_118552, 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: 49817
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:345 original size:198 final size:198
Alignment explanation
Indices: 1--1970 Score: 3080
Period size: 198 Copynumber: 10.0 Consensus size: 198
* *
1 GTACCACAGAAGCATGAAAGGGAAAGATTTAAGTCGTAACGCCGAATCTAGTACCACGAAGATAT
1 GTACCTCAGAAGCATGAAAGGGAAAGATTTAAGTCGTAACGGCGAATCTAGTACCACGAAGATAT
66 GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTAA
66 GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTAA
* * * *
131 GCCACAACGGCGAATCCAGTACCACAAAGACAAAAGAGGGAAAGGTTTAAGTCGCAATGGCGAAC
131 GCCACAATGGCGAATCCAGTACCACGAAGACACAAGAGGGAAAGGTTTAAGTCGCAACGGCGAAC
196 CTT
196 CTT
* ** *
199 GTACCTCAGAAGCTTGAAAGGGAAAGATTTAAGTCGTAATAGTGAATCTAGTACCACGAAGATAT
1 GTACCTCAGAAGCATGAAAGGGAAAGATTTAAGTCGTAACGGCGAATCTAGTACCACGAAGATAT
*
264 GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACTTTAGAGACATGAAGGGAAAGATTTAA
66 GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTAA
* * * * *
329 GCCACAATGGCGAATCCAGTACCATGAAGACACAAGAGGAAAAGATTTAAGTCGCAATGACGAAC
131 GCCACAATGGCGAATCCAGTACCACGAAGACACAAGAGGGAAAGGTTTAAGTCGCAACGGCGAAC
394 CTT
196 CTT
* * *
397 GTACCACAGAAGCATAAAAGGGAAAGATTTAAGTTGTAACGGCGAATCTAGTACCACGAAGATAT
1 GTACCTCAGAAGCATGAAAGGGAAAGATTTAAGTCGTAACGGCGAATCTAGTACCACGAAGATAT
* * *
462 GAAGGGAAAGGTTTAAGTCGCAATGTCGAACCTTATGCCTTCGAGACATGAAGGGAAAGATTTAA
66 GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTAA
* * * *
527 GCCACAACGGCGAATCCAGTACAACGAAGACACAAGAGGGAAAGGTTGAAGTCGTAACGGCGAAC
131 GCCACAATGGCGAATCCAGTACCACGAAGACACAAGAGGGAAAGGTTTAAGTCGCAACGGCGAAC
592 CTT
196 CTT
* **
595 GTACCTCAGAAGCATGAAAGGGAAAGATTTAAGTCGCAATAGCGAATCTAGTACCACGAAGATAT
1 GTACCTCAGAAGCATGAAAGGGAAAGATTTAAGTCGTAACGGCGAATCTAGTACCACGAAGATAT
*
660 GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGTAAAGATTTAA
66 GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTAA
* * * * *
725 GCCACAATGGCGAATTCAGTACCACGAAGACACAAGAGGAAAAGATTTAAGTCACAACGACGAAC
131 GCCACAATGGCGAATCCAGTACCACGAAGACACAAGAGGGAAAGGTTTAAGTCGCAACGGCGAAC
790 CTT
196 CTT
* * *
793 GTACCACAAAAGCATGAAAGGGAAAGATTTAAGTCGTAACGGTGAATCTAGTACCACGAAGATAT
1 GTACCTCAGAAGCATGAAAGGGAAAGATTTAAGTCGTAACGGCGAATCTAGTACCACGAAGATAT
*
858 GAAGGGAAAGGTTTAAGTCGTAATGGCGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTAA
66 GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTAA
* * *
923 GCCACAATGGCGAATCCAGTACCACAAAGACACAAGAGGGAAAGGTTTAAGTCGTAATGGCGAAC
131 GCCACAATGGCGAATCCAGTACCACGAAGACACAAGAGGGAAAGGTTTAAGTCGCAACGGCGAAC
988 CTT
196 CTT
* * * *
991 GTACCTCAGAAGCATGAAAGGGAAAGATTTAAGCCGTAATGGTGAATCTATTACCACGAAGATAT
1 GTACCTCAGAAGCATGAAAGGGAAAGATTTAAGTCGTAACGGCGAATCTAGTACCACGAAGATAT
* * *
1056 GAAGGGAGAGGTTTAAGTCGCAATAGTGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTAA
66 GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTAA
* * * ***
1121 GCCACAATGGCGAATTCAGTACCACGAAGACACAAGAGGAAAAGATTTAAGTCGCAACAATGAAC
131 GCCACAATGGCGAATCCAGTACCACGAAGACACAAGAGGGAAAGGTTTAAGTCGCAACGGCGAAC
1186 CTT
196 CTT
* * *
1189 GTACCACAGAAGAATGAAAGGGAAAGATTTAAGTCATAACGGCGAATCTAGTACCACGAAGATAT
1 GTACCTCAGAAGCATGAAAGGGAAAGATTTAAGTCGTAACGGCGAATCTAGTACCACGAAGATAT
* * * *
1254 GAAGTGAAAGGTTTAAGTCACAATGGCGAACCTTATGCCTTCGAGACATGAAGGGAAAGATTTAA
66 GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTAA
* * * * *
1319 GCCACAATGGAGAATCCAGTACAACGAAGACACAAGAGGGAAAGGTTGAAGTCGTAACAGCGAAC
131 GCCACAATGGCGAATCCAGTACCACGAAGACACAAGAGGGAAAGGTTTAAGTCGCAACGGCGAAC
1384 CTT
196 CTT
* ** *
1387 GTACCTCAGAAGCATGAAAGGGAAAGATTTAAGTCGCAATAGCGAATCTAGTACCATGAAGATAT
1 GTACCTCAGAAGCATGAAAGGGAAAGATTTAAGTCGTAACGGCGAATCTAGTACCACGAAGATAT
*
1452 GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGTAAAGATTTAA
66 GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTAA
* * * * *
1517 GCCACAATGGCGGATCCATTACCACAAAGACATAAGAGGGAAAGGTTTAAGTCGCAATGGCGAAC
131 GCCACAATGGCGAATCCAGTACCACGAAGACACAAGAGGGAAAGGTTTAAGTCGCAACGGCGAAC
1582 CTT
196 CTT
*
1585 GTACCTCAGAAGCATGAAAGGGAAAGATTTAAGCCGTAACGGCGAATCTAGTACCACGAAGATAT
1 GTACCTCAGAAGCATGAAAGGGAAAGATTTAAGTCGTAACGGCGAATCTAGTACCACGAAGATAT
* *
1650 GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAGAGACATGAAGGGAAAGTTTTAA
66 GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTAA
* * * *
1715 GCCACAACGGCAAATCCAGTACCACGAAGACACAAGAGGGAAAGGTTTAAGTCGCAACAGTGAAC
131 GCCACAATGGCGAATCCAGTACCACGAAGACACAAGAGGGAAAGGTTTAAGTCGCAACGGCGAAC
1780 CTT
196 CTT
* * *
1783 GTACATCAGAAGCATGAAAGGGAAAGATTTAAGAT-GGAACGGCGAATCTAGTACCACAAAGATA
1 GTACCTCAGAAGCATGAAAGGGAAAGATTTAAG-TCGTAACGGCGAATCTAGTACCACGAAGATA
* * *
1847 TGAAGGGAAAGGTATAA-TCGCAATGGCGAACCTTATGCCTTCGAGACATGAAGGGAAAGATTTA
65 TGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTA
** *
1911 AGCCACAGCGGCGAATCCAGTACCACGAAGACACAAGAGGGAAAGGTTTAAGTCGTAACG
130 AGCCACAATGGCGAATCCAGTACCACGAAGACACAAGAGGGAAAGGTTTAAGTCGCAACG
1971 AAGAACCTGA
Statistics
Matches: 1609, Mismatches: 162, Indels: 3
0.91 0.09 0.00
Matches are distributed among these distances:
197 99 0.06
198 1510 0.94
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (198 bp):
GTACCTCAGAAGCATGAAAGGGAAAGATTTAAGTCGTAACGGCGAATCTAGTACCACGAAGATAT
GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTAA
GCCACAATGGCGAATCCAGTACCACGAAGACACAAGAGGGAAAGGTTTAAGTCGCAACGGCGAAC
CTT
Found at i:2656 original size:35 final size:35
Alignment explanation
Indices: 2617--2698 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 35
2607 CTCAACTCAT
2617 TTTAAATTTATTTTAAGATTAAATTTAT-TTTAAAA
1 TTTAAATTTATTTTAAGATTAAATTTATATTT-AAA
* *
2652 TTTAAATTTAATTTAAGTTTAAATTTATATTTAAA
1 TTTAAATTTATTTTAAGATTAAATTTATATTTAAA
*
2687 TTTAAAATTATT
1 TTTAAATTTATT
2699 CTAAATTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 39 0.93
36 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (35 bp):
TTTAAATTTATTTTAAGATTAAATTTATATTTAAA
Found at i:2660 original size:6 final size:6
Alignment explanation
Indices: 2617--2710 Score: 74
Period size: 6 Copynumber: 16.2 Consensus size: 6
2607 CTCAACTCAT
* *
2617 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* * *
2663 TTTAAG TTTAAA TTTATA TTTAAA TTTAAA ATT--A TTCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA
2710 T
1 T
2711 AAATAGAAGT
Statistics
Matches: 69, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
4 2 0.03
5 15 0.22
6 45 0.65
7 7 0.10
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:2705 original size:17 final size:17
Alignment explanation
Indices: 2617--2710 Score: 118
Period size: 17 Copynumber: 5.4 Consensus size: 17
2607 CTCAACTCAT
2617 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
2635 -TTAAATTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* *
2652 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
2669 TTTAAATTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
* *
2687 TTTAAAATTATTCTAAA
1 TTTAAATTTATTTTAAA
2704 TTTAAAT
1 TTTAAAT
2711 AAATAGAAGT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
17 37 0.56
18 29 0.44
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:2708 original size:35 final size:34
Alignment explanation
Indices: 2617--2710 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 34
2607 CTCAACTCAT
2617 TTTAAATTTATTTTAAGA-TTAAATTTATTTTAAAA
1 TTTAAATTTA-TTTAA-ATTTAAATTTATTTTAAAA
*
2652 TTTAAATTTAATTTAAGTTTAAATTTATATTT-AAA
1 TTTAAATTT-ATTTAAATTTAAATTTAT-TTTAAAA
*
2687 TTTAAAATTATTCTAAATTTAAAT
1 TTTAAATTTATT-TAAATTTAAAT
2711 AAATAGAAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
34 3 0.06
35 45 0.87
36 4 0.08
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTTAAATTTAAATTTATTTTAAAA
Found at i:3300 original size:23 final size:22
Alignment explanation
Indices: 3264--3311 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
3254 GTTTCAAAGC
*
3264 ATTTATATATATTAATATATTT
1 ATTTATATACATTAATATATTT
3286 ATTTATTATACATTAATATATTT
1 ATTTA-TATACATTAATATATTT
3309 ATT
1 ATT
3312 AACTAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTATATACATTAATATATTT
Found at i:4406 original size:29 final size:28
Alignment explanation
Indices: 4374--4581 Score: 150
Period size: 29 Copynumber: 7.1 Consensus size: 28
4364 TCATATTTCG
*
4374 ACCCCAAACTTTCCAAGAATTACATTTTT
1 ACCCCGAACTTTCCAA-AATTACATTTTT
* * * *
4403 ACCCTTGAACTTTTACAAAATTACCTTTTG
1 ACCC-CGAAC-TTTCCAAAATTACATTTTT
** * *
4433 ACCTTGAATTTTCCAAAATTCCATTTTTT
1 ACCCCGAACTTTCCAAAATTACA-TTTTT
* *
4462 ACCTCGAATTTTCCAAAATT-CTATTTTT
1 ACCCCGAACTTTCCAAAATTAC-ATTTTT
* * *
4490 AACCCCAAATTTTCTAAAAATTACATTTTT
1 -ACCCCGAACTTTC-CAAAATTACATTTTT
* * *
4520 AAACTCGAACTTTCCAAAATTCCATTTTT
1 -ACCCCGAACTTTCCAAAATTACATTTTT
*
4549 GACCTCGAA-TTTCCAAAATTTACATTTTT
1 -ACCCCGAACTTTCCAAAA-TTACATTTTT
4578 ACCC
1 ACCC
4582 TTAAACTTTC
Statistics
Matches: 146, Mismatches: 25, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
28 29 0.20
29 72 0.49
30 38 0.26
31 7 0.05
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (28 bp):
ACCCCGAACTTTCCAAAATTACATTTTT
Found at i:4648 original size:30 final size:30
Alignment explanation
Indices: 4595--4768 Score: 162
Period size: 30 Copynumber: 5.9 Consensus size: 30
4585 AACTTTCCAA
*
4595 CCTAAATTTTAC-AAAATTCCATTTTTGAC
1 CCTAAATTTTCCAAAAATTCCATTTTTGAC
*
4624 CCTAAATTTTCCAAAAATTACATTTTT-AC
1 CCTAAATTTTCCAAAAATTCCATTTTTGAC
* * *
4653 TCCCAAACTTTCC-ATAATTCCATTTTTGA-
1 -CCTAAATTTTCCAAAAATTCCATTTTTGAC
* *
4682 CCTCGAATTTTCCAAAAATTACATTTTT-AC
1 CCT-AAATTTTCCAAAAATTCCATTTTTGAC
* * * *
4712 CCTCGAACTTT-CTAAAATTCCATTCTTGAC
1 CCT-AAATTTTCCAAAAATTCCATTTTTGAC
* *
4742 CCTAGATTTTCCAAAAATTTCATTTTT
1 CCTAAATTTTCCAAAAATTCCATTTTT
4769 TACTCCAAAC
Statistics
Matches: 116, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.02
29 50 0.43
30 64 0.55
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
CCTAAATTTTCCAAAAATTCCATTTTTGAC
Found at i:4680 original size:59 final size:59
Alignment explanation
Indices: 4606--4798 Score: 239
Period size: 59 Copynumber: 3.2 Consensus size: 59
4596 CTAAATTTTA
4606 CAAAATTCCATTTTTGACCCTAAATTTTCCAAAAATTACATTTTTACTCCCAAACTTTC
1 CAAAATTCCATTTTTGACCCTAAATTTTCCAAAAATTACATTTTTACTCCCAAACTTTC
* * *
4665 CATAATTCCATTTTTGA-CCTCGAATTTTCCAAAAATTACATTTTTAC-CCTCGAACTTTC
1 CAAAATTCCATTTTTGACCCT-AAATTTTCCAAAAATTACATTTTTACTCC-CAAACTTTC
* * * * *
4724 TAAAATTCCATTCTTGACCCTAGATTTTCCAAAAATTTCATTTTTTACT-CCAAACCTCTC
1 CAAAATTCCATTTTTGACCCTAAATTTTCCAAAAATTACA-TTTTTACTCCCAAA-CTTTC
*
4784 AAAAATTACCATTTT
1 CAAAATT-CCATTTT
4799 ACCCCCAAAT
Statistics
Matches: 114, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
58 5 0.04
59 82 0.72
60 21 0.18
61 6 0.05
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.40
Consensus pattern (59 bp):
CAAAATTCCATTTTTGACCCTAAATTTTCCAAAAATTACATTTTTACTCCCAAACTTTC
Found at i:4807 original size:30 final size:30
Alignment explanation
Indices: 4773--4862 Score: 78
Period size: 30 Copynumber: 3.0 Consensus size: 30
4763 ATTTTTTACT
4773 CCAAACCTCTCAAAAATTACCATTTTACCC
1 CCAAACCTCTCAAAAATTACCATTTTACCC
** * *
4803 CCAAATGTCT-AAAAA-CACCATTTTTGACGC
1 CCAAACCTCTCAAAAATTACCA-TTTT-ACCC
* * *
4833 CGAATCTTC-CAAAAATTACCATTTTACCC
1 CCAAACCTCTCAAAAATTACCATTTTACCC
4862 C
1 C
4863 TGAATGTCTA
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
28 4 0.09
29 13 0.28
30 25 0.54
31 4 0.09
ACGTcount: A:0.36, C:0.32, G:0.04, T:0.28
Consensus pattern (30 bp):
CCAAACCTCTCAAAAATTACCATTTTACCC
Found at i:4816 original size:29 final size:29
Alignment explanation
Indices: 4784--4878 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 29
4774 CAAACCTCTC
*
4784 AAAAATTACCATTTTACCCCCAAATGTCT
1 AAAAATTACCATTTTACCCCCGAATGTCT
* * * *
4813 AAAAA-CACCATTTTTGA-CGCCGAATCTTCC
1 AAAAATTACCA-TTTT-ACCCCCGAAT-GTCT
*
4843 AAAAATTACCATTTTACCCCTGAATGTCT
1 AAAAATTACCATTTTACCCCCGAATGTCT
4872 AAAAATT
1 AAAAATT
4879 TCATTTTTAA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
28 4 0.08
29 25 0.49
30 18 0.35
31 4 0.08
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCCGAATGTCT
Found at i:4817 original size:59 final size:57
Alignment explanation
Indices: 4754--4916 Score: 182
Period size: 59 Copynumber: 2.8 Consensus size: 57
4744 TAGATTTTCC
* *
4754 AAAAATTTCATTTTTTACTCCAAACCTCTCAAAAATTACCATTTTACCCCCAAATGTCT
1 AAAAATTTCATTTTTAAC-CCGAACCT-TCAAAAATTACCATTTTACCCCCAAATGTCT
*** * * **
4813 AAAAACACCATTTTTGACGCCGAATCTTCCAAAAATTACCATTTTACCCCTGAATGTCT
1 AAAAATTTCATTTTTAAC-CCGAACCTT-CAAAAATTACCATTTTACCCCCAAATGTCT
*
4872 AAAAATTTCATTTTTAACCTCGAACCTTTCGAAAATTACCATTTT
1 AAAAATTTCATTTTTAACC-CGAACC-TTCAAAAATTACCATTTT
4917 GTTCTCGGAG
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
58 2 0.02
59 82 0.95
60 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (57 bp):
AAAAATTTCATTTTTAACCCGAACCTTCAAAAATTACCATTTTACCCCCAAATGTCT
Found at i:4817 original size:118 final size:119
Alignment explanation
Indices: 4607--4917 Score: 291
Period size: 118 Copynumber: 2.6 Consensus size: 119
4597 TAAATTTTAC
* * * *
4607 AAAATTCCATTTTTGACCCTAAATTTTCCAAAAATTACA-TTTTTACTCCCAAA-CTTTCCATAA
1 AAAATTCCA-TTTTGACCCTAGATTTTCCAAAAATTTCATTTTTTACT-CCAAACCTTTCAAAAA
* * * * * * *
4670 TT-CCATTTTTGACCTCGAATTTTCCAAAAATTA-CATTTTT-ACCCTCGAA-CTTTCT
64 TTACCA-TTTTGACCCCCAAATGTCCAAAAA-CACCATTTTTGACCC-CGAATCTTCCA
*
4725 AAAATTCCATTCTTGACCCTAGATTTTCCAAAAATTTCATTTTTTACTCCAAACCTCTCAAAAAT
1 AAAATTCCATT-TTGACCCTAGATTTTCCAAAAATTTCATTTTTTACTCCAAACCTTTCAAAAAT
* *
4790 TACCATTTT-ACCCCCAAATGTCTAAAAACACCATTTTTGACGCCGAATCTTCCA
65 TACCATTTTGACCCCCAAATGTCCAAAAACACCATTTTTGACCCCGAATCTTCCA
* * * * * *
4844 AAAATTACCATTTT-ACCCCT-GAATGTCTAAAAATTTCATTTTTAAC-CTCGAACCTTTCGAAA
1 AAAATT-CCATTTTGA-CCCTAGATTTTCCAAAAATTTCATTTTTTACTC-CAAACCTTTCAAAA
4906 ATTACCATTTTG
63 ATTACCATTTTG
4918 TTCTCGGAGT
Statistics
Matches: 161, Mismatches: 21, Indels: 21
0.79 0.10 0.10
Matches are distributed among these distances:
117 4 0.02
118 109 0.68
119 40 0.25
120 8 0.05
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (119 bp):
AAAATTCCATTTTGACCCTAGATTTTCCAAAAATTTCATTTTTTACTCCAAACCTTTCAAAAATT
ACCATTTTGACCCCCAAATGTCCAAAAACACCATTTTTGACCCCGAATCTTCCA
Found at i:12319 original size:35 final size:35
Alignment explanation
Indices: 12280--12361 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 35
12270 CTCAACTCAT
12280 TTTAAATTTATTTTAAGATTAAATTTAT-TTTAAAA
1 TTTAAATTTATTTTAAGATTAAATTTATATTT-AAA
* *
12315 TTTAAATTTAATTTAAGTTTAAATTTATATTTAAA
1 TTTAAATTTATTTTAAGATTAAATTTATATTTAAA
*
12350 TTTAAAATTATT
1 TTTAAATTTATT
12362 CTAAATTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 39 0.93
36 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (35 bp):
TTTAAATTTATTTTAAGATTAAATTTATATTTAAA
Found at i:12323 original size:6 final size:6
Alignment explanation
Indices: 12280--12373 Score: 74
Period size: 6 Copynumber: 16.2 Consensus size: 6
12270 CTCAACTCAT
* *
12280 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* * *
12326 TTTAAG TTTAAA TTTATA TTTAAA TTTAAA ATT--A TTCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA
12373 T
1 T
12374 AAATAGAAGT
Statistics
Matches: 69, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
4 2 0.03
5 15 0.22
6 45 0.65
7 7 0.10
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:12368 original size:17 final size:17
Alignment explanation
Indices: 12280--12373 Score: 118
Period size: 17 Copynumber: 5.4 Consensus size: 17
12270 CTCAACTCAT
12280 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
12298 -TTAAATTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* *
12315 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
12332 TTTAAATTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
* *
12350 TTTAAAATTATTCTAAA
1 TTTAAATTTATTTTAAA
12367 TTTAAAT
1 TTTAAAT
12374 AAATAGAAGT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
17 37 0.56
18 29 0.44
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:12371 original size:35 final size:34
Alignment explanation
Indices: 12280--12373 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 34
12270 CTCAACTCAT
12280 TTTAAATTTATTTTAAGA-TTAAATTTATTTTAAAA
1 TTTAAATTTA-TTTAA-ATTTAAATTTATTTTAAAA
*
12315 TTTAAATTTAATTTAAGTTTAAATTTATATTT-AAA
1 TTTAAATTT-ATTTAAATTTAAATTTAT-TTTAAAA
*
12350 TTTAAAATTATTCTAAATTTAAAT
1 TTTAAATTTATT-TAAATTTAAAT
12374 AAATAGAAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
34 3 0.06
35 45 0.87
36 4 0.08
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTTAAATTTAAATTTATTTTAAAA
Found at i:12963 original size:23 final size:22
Alignment explanation
Indices: 12927--12974 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
12917 GTTTCAAAGC
*
12927 ATTTATATATATTAATATATTT
1 ATTTATATACATTAATATATTT
12949 ATTTATTATACATTAATATATTT
1 ATTTA-TATACATTAATATATTT
12972 ATT
1 ATT
12975 AACTAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTATATACATTAATATATTT
Found at i:14069 original size:29 final size:28
Alignment explanation
Indices: 14037--14244 Score: 150
Period size: 29 Copynumber: 7.1 Consensus size: 28
14027 TCATATTTCG
*
14037 ACCCCAAACTTTCCAAGAATTACATTTTT
1 ACCCCGAACTTTCCAA-AATTACATTTTT
* * * *
14066 ACCCTTGAACTTTTACAAAATTACCTTTTG
1 ACCC-CGAAC-TTTCCAAAATTACATTTTT
** * *
14096 ACCTTGAATTTTCCAAAATTCCATTTTTT
1 ACCCCGAACTTTCCAAAATTACA-TTTTT
* *
14125 ACCTCGAATTTTCCAAAATT-CTATTTTT
1 ACCCCGAACTTTCCAAAATTAC-ATTTTT
* * *
14153 AACCCCAAATTTTCTAAAAATTACATTTTT
1 -ACCCCGAACTTTC-CAAAATTACATTTTT
* * *
14183 AAACTCGAACTTTCCAAAATTCCATTTTT
1 -ACCCCGAACTTTCCAAAATTACATTTTT
*
14212 GACCTCGAA-TTTCCAAAATTTACATTTTT
1 -ACCCCGAACTTTCCAAAA-TTACATTTTT
14241 ACCC
1 ACCC
14245 TTAAACTTTC
Statistics
Matches: 146, Mismatches: 25, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
28 29 0.20
29 72 0.49
30 38 0.26
31 7 0.05
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (28 bp):
ACCCCGAACTTTCCAAAATTACATTTTT
Found at i:14311 original size:30 final size:30
Alignment explanation
Indices: 14258--14431 Score: 162
Period size: 30 Copynumber: 5.9 Consensus size: 30
14248 AACTTTCCAA
*
14258 CCTAAATTTTAC-AAAATTCCATTTTTGAC
1 CCTAAATTTTCCAAAAATTCCATTTTTGAC
*
14287 CCTAAATTTTCCAAAAATTACATTTTT-AC
1 CCTAAATTTTCCAAAAATTCCATTTTTGAC
* * *
14316 TCCCAAACTTTCC-ATAATTCCATTTTTGA-
1 -CCTAAATTTTCCAAAAATTCCATTTTTGAC
* *
14345 CCTCGAATTTTCCAAAAATTACATTTTT-AC
1 CCT-AAATTTTCCAAAAATTCCATTTTTGAC
* * * *
14375 CCTCGAACTTT-CTAAAATTCCATTCTTGAC
1 CCT-AAATTTTCCAAAAATTCCATTTTTGAC
* *
14405 CCTAGATTTTCCAAAAATTTCATTTTT
1 CCTAAATTTTCCAAAAATTCCATTTTT
14432 TACTCCAAAC
Statistics
Matches: 116, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.02
29 50 0.43
30 64 0.55
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
CCTAAATTTTCCAAAAATTCCATTTTTGAC
Found at i:14343 original size:59 final size:59
Alignment explanation
Indices: 14269--14461 Score: 239
Period size: 59 Copynumber: 3.2 Consensus size: 59
14259 CTAAATTTTA
14269 CAAAATTCCATTTTTGACCCTAAATTTTCCAAAAATTACATTTTTACTCCCAAACTTTC
1 CAAAATTCCATTTTTGACCCTAAATTTTCCAAAAATTACATTTTTACTCCCAAACTTTC
* * *
14328 CATAATTCCATTTTTGA-CCTCGAATTTTCCAAAAATTACATTTTTAC-CCTCGAACTTTC
1 CAAAATTCCATTTTTGACCCT-AAATTTTCCAAAAATTACATTTTTACTCC-CAAACTTTC
* * * * *
14387 TAAAATTCCATTCTTGACCCTAGATTTTCCAAAAATTTCATTTTTTACT-CCAAACCTCTC
1 CAAAATTCCATTTTTGACCCTAAATTTTCCAAAAATTACA-TTTTTACTCCCAAA-CTTTC
*
14447 AAAAATTACCATTTT
1 CAAAATT-CCATTTT
14462 ACCCCCAAAT
Statistics
Matches: 114, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
58 5 0.04
59 82 0.72
60 21 0.18
61 6 0.05
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.40
Consensus pattern (59 bp):
CAAAATTCCATTTTTGACCCTAAATTTTCCAAAAATTACATTTTTACTCCCAAACTTTC
Found at i:14470 original size:30 final size:30
Alignment explanation
Indices: 14436--14525 Score: 78
Period size: 30 Copynumber: 3.0 Consensus size: 30
14426 ATTTTTTACT
14436 CCAAACCTCTCAAAAATTACCATTTTACCC
1 CCAAACCTCTCAAAAATTACCATTTTACCC
** * *
14466 CCAAATGTCT-AAAAA-CACCATTTTTGACGC
1 CCAAACCTCTCAAAAATTACCA-TTTT-ACCC
* * *
14496 CGAATCTTC-CAAAAATTACCATTTTACCC
1 CCAAACCTCTCAAAAATTACCATTTTACCC
14525 C
1 C
14526 TGAATGTCTA
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
28 4 0.09
29 13 0.28
30 25 0.54
31 4 0.09
ACGTcount: A:0.36, C:0.32, G:0.04, T:0.28
Consensus pattern (30 bp):
CCAAACCTCTCAAAAATTACCATTTTACCC
Found at i:14479 original size:29 final size:29
Alignment explanation
Indices: 14447--14541 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 29
14437 CAAACCTCTC
*
14447 AAAAATTACCATTTTACCCCCAAATGTCT
1 AAAAATTACCATTTTACCCCCGAATGTCT
* * * *
14476 AAAAA-CACCATTTTTGA-CGCCGAATCTTCC
1 AAAAATTACCA-TTTT-ACCCCCGAAT-GTCT
*
14506 AAAAATTACCATTTTACCCCTGAATGTCT
1 AAAAATTACCATTTTACCCCCGAATGTCT
14535 AAAAATT
1 AAAAATT
14542 TCATTTTTAA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
28 4 0.08
29 25 0.49
30 18 0.35
31 4 0.08
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCCGAATGTCT
Found at i:14480 original size:59 final size:57
Alignment explanation
Indices: 14417--14579 Score: 182
Period size: 59 Copynumber: 2.8 Consensus size: 57
14407 TAGATTTTCC
* *
14417 AAAAATTTCATTTTTTACTCCAAACCTCTCAAAAATTACCATTTTACCCCCAAATGTCT
1 AAAAATTTCATTTTTAAC-CCGAACCT-TCAAAAATTACCATTTTACCCCCAAATGTCT
*** * * **
14476 AAAAACACCATTTTTGACGCCGAATCTTCCAAAAATTACCATTTTACCCCTGAATGTCT
1 AAAAATTTCATTTTTAAC-CCGAACCTT-CAAAAATTACCATTTTACCCCCAAATGTCT
*
14535 AAAAATTTCATTTTTAACCTCGAACCTTTCGAAAATTACCATTTT
1 AAAAATTTCATTTTTAACC-CGAACC-TTCAAAAATTACCATTTT
14580 GTTCTCGGAG
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
58 2 0.02
59 82 0.95
60 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (57 bp):
AAAAATTTCATTTTTAACCCGAACCTTCAAAAATTACCATTTTACCCCCAAATGTCT
Found at i:14480 original size:118 final size:119
Alignment explanation
Indices: 14270--14580 Score: 291
Period size: 118 Copynumber: 2.6 Consensus size: 119
14260 TAAATTTTAC
* * * *
14270 AAAATTCCATTTTTGACCCTAAATTTTCCAAAAATTACA-TTTTTACTCCCAAA-CTTTCCATAA
1 AAAATTCCA-TTTTGACCCTAGATTTTCCAAAAATTTCATTTTTTACT-CCAAACCTTTCAAAAA
* * * * * * *
14333 TT-CCATTTTTGACCTCGAATTTTCCAAAAATTA-CATTTTT-ACCCTCGAA-CTTTCT
64 TTACCA-TTTTGACCCCCAAATGTCCAAAAA-CACCATTTTTGACCC-CGAATCTTCCA
*
14388 AAAATTCCATTCTTGACCCTAGATTTTCCAAAAATTTCATTTTTTACTCCAAACCTCTCAAAAAT
1 AAAATTCCATT-TTGACCCTAGATTTTCCAAAAATTTCATTTTTTACTCCAAACCTTTCAAAAAT
* *
14453 TACCATTTT-ACCCCCAAATGTCTAAAAACACCATTTTTGACGCCGAATCTTCCA
65 TACCATTTTGACCCCCAAATGTCCAAAAACACCATTTTTGACCCCGAATCTTCCA
* * * * * *
14507 AAAATTACCATTTT-ACCCCT-GAATGTCTAAAAATTTCATTTTTAAC-CTCGAACCTTTCGAAA
1 AAAATT-CCATTTTGA-CCCTAGATTTTCCAAAAATTTCATTTTTTACTC-CAAACCTTTCAAAA
14569 ATTACCATTTTG
63 ATTACCATTTTG
14581 TTCTCGGAGT
Statistics
Matches: 161, Mismatches: 21, Indels: 21
0.79 0.10 0.10
Matches are distributed among these distances:
117 4 0.02
118 109 0.68
119 40 0.25
120 8 0.05
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (119 bp):
AAAATTCCATTTTGACCCTAGATTTTCCAAAAATTTCATTTTTTACTCCAAACCTTTCAAAAATT
ACCATTTTGACCCCCAAATGTCCAAAAACACCATTTTTGACCCCGAATCTTCCA
Found at i:22438 original size:23 final size:24
Alignment explanation
Indices: 22412--22458 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
22402 TTTTATATTA
22412 TTTTATATAT-TTTTTAAAAATAT
1 TTTTATATATATTTTTAAAAATAT
*
22435 TTTTATATATATTTTTAAATATAT
1 TTTTATATATATTTTTAAAAATAT
22459 ATAATACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTATATATATTTTTAAAAATAT
Found at i:22450 original size:12 final size:12
Alignment explanation
Indices: 22401--22458 Score: 68
Period size: 12 Copynumber: 5.1 Consensus size: 12
22391 GTGTTAAAAT
22401 TTTTTATAT-TA
1 TTTTTATATATA
22412 -TTTTATATAT-
1 TTTTTATATATA
* *
22422 TTTTTAAAAATA
1 TTTTTATATATA
22434 TTTTTATATATA
1 TTTTTATATATA
*
22446 TTTTTAAATATA
1 TTTTTATATATA
22458 T
1 T
22459 ATAATACATT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
10 8 0.21
11 9 0.23
12 22 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTTTATATATA
Found at i:24246 original size:27 final size:26
Alignment explanation
Indices: 24216--24277 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
24206 ATTTCGTGTT
*
24216 CAAATTTGCAAATTACAAAAAATAAAC
1 CAAATTTGCAAATTA-AAAAAAAAAAC
*
24243 CAAAATTTG-AAATTAAAAAAAAAAAT
1 C-AAATTTGCAAATTAAAAAAAAAAAC
24269 CAAATTTGC
1 CAAATTTGC
24278 CCCTTAAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 7 0.23
26 10 0.32
27 7 0.23
28 7 0.23
ACGTcount: A:0.60, C:0.11, G:0.05, T:0.24
Consensus pattern (26 bp):
CAAATTTGCAAATTAAAAAAAAAAAC
Found at i:33547 original size:16 final size:16
Alignment explanation
Indices: 33522--33564 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
33512 CACTTATACC
33522 AAAT-AAATAATGGAT
1 AAATAAAATAATGGAT
33537 AAATAAAATAATGGAT
1 AAATAAAATAATGGAT
33553 AAATAAAA-AATG
1 AAATAAAATAATG
33565 AATTTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.30
16 19 0.70
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (16 bp):
AAATAAAATAATGGAT
Found at i:42204 original size:144 final size:145
Alignment explanation
Indices: 41964--42245 Score: 494
Period size: 144 Copynumber: 2.0 Consensus size: 145
41954 CTGAAAGCCC
*
41964 ATTGGAAGATAGATCCAATTCAACCAAATTCGTTAGTCTCCCAATATCTTCTGGAATGGAGCCAC
1 ATTGGAAGATAGATCCAATGCAACCAAATTCGTTAGTCTCCCAATATCTTCTGGAATGGAGCCAC
* *
42029 TAAGTTGGTTGCTTTGAAGGAGCAACGAGGCAAGATTGG-TTAAGTTGCTGACAGAAGATGGGAT
66 TAAGTTGGTTGCTTTGAAGAAACAACGAGGCAAGATTGGTTTAAGTTGCTGACAGAAGATGGGAT
42093 TGGACCAACAAGACT
131 TGGACCAACAAGACT
* * * *
42108 ATTGGAGGATAGATTCAATGCAACCAAATTCGTTAGTCTCCCAATATCTTCTGGAATGGATCCAT
1 ATTGGAAGATAGATCCAATGCAACCAAATTCGTTAGTCTCCCAATATCTTCTGGAATGGAGCCAC
42173 TAAGTTGGTTGCTTTGAAGAAACAACGAGGCAAGATTGGTTTAAGTTGCTGACAGAAGATGGGAT
66 TAAGTTGGTTGCTTTGAAGAAACAACGAGGCAAGATTGGTTTAAGTTGCTGACAGAAGATGGGAT
42238 TGGACCAA
131 TGGACCAA
42246 AAAACCAGTT
Statistics
Matches: 130, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
144 97 0.75
145 33 0.25
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (145 bp):
ATTGGAAGATAGATCCAATGCAACCAAATTCGTTAGTCTCCCAATATCTTCTGGAATGGAGCCAC
TAAGTTGGTTGCTTTGAAGAAACAACGAGGCAAGATTGGTTTAAGTTGCTGACAGAAGATGGGAT
TGGACCAACAAGACT
Found at i:42311 original size:145 final size:144
Alignment explanation
Indices: 41962--42299 Score: 396
Period size: 144 Copynumber: 2.3 Consensus size: 144
41952 ACCTGAAAGC
* * * * * ** *
41962 CCATTGGAAGATAGATCCAATTCAACCAAATTCGTTAGTCTCCCAATATCTTCTGGAATGGAGCC
1 CCATTGGAGGAGAGATTCAATGCAACCAAAGTCCCTAGTCTCCCAACATCTTCTGGAATGGAGCC
* *
42027 ACTAAGTTGGTTGCTTTGAAGGAGCAACGAGGCAAGATTGGTTAAGTTGCTGACAGAAGATGGGA
66 ACTAAGTTGGTTGCTTTGAAGAAACAACGAGGCAAGATTGGTTAAGTTGCTGACAGAAGATGGGA
*
42092 TTGGACCAACAAGA
131 TTGGACCAACAAAA
* * * ** * *
42106 CTATTGGAGGATAGATTCAATGCAACCAAATTCGTTAGTCTCCCAATATCTTCTGGAATGGATCC
1 CCATTGGAGGAGAGATTCAATGCAACCAAAGTCCCTAGTCTCCCAACATCTTCTGGAATGGAGCC
*
42171 ATTAAGTTGGTTGCTTTGAAGAAACAACGAGGCAAGATTGGTTTAAGTTGCTGACAGAAGATGGG
66 ACTAAGTTGGTTGCTTTGAAGAAACAACGAGGCAAGATTGG-TTAAGTTGCTGACAGAAGATGGG
42236 ATTGGACCAA-AAAA
130 ATTGGACCAACAAAA
*** *
42250 CCAGTTGTTTGAGAGA-TCAA-GATCAACCATAGTCCCTAG-CTCTCCAACAT
1 CCA-TTGGAGGAGAGATTCAATG--CAACCAAAGTCCCTAGTCTC-CCAACAT
42300 TTGGTGGAAT
Statistics
Matches: 170, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
143 1 0.01
144 110 0.65
145 59 0.35
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (144 bp):
CCATTGGAGGAGAGATTCAATGCAACCAAAGTCCCTAGTCTCCCAACATCTTCTGGAATGGAGCC
ACTAAGTTGGTTGCTTTGAAGAAACAACGAGGCAAGATTGGTTAAGTTGCTGACAGAAGATGGGA
TTGGACCAACAAAA
Found at i:42842 original size:22 final size:23
Alignment explanation
Indices: 42817--42860 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
42807 CTTCAATTAA
42817 ATTTTAAATATTTT-AAATTTAT
1 ATTTTAAATATTTTAAAATTTAT
42839 ATTTTAAATATTTTAAAATTTA
1 ATTTTAAATATTTTAAAATTTA
42861 AAAGTAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTTTAAATATTTTAAAATTTAT
Found at i:47197 original size:29 final size:29
Alignment explanation
Indices: 47135--47221 Score: 84
Period size: 31 Copynumber: 2.9 Consensus size: 29
47125 AATTTACAAT
* * * *
47135 AATTAGATCAAATCAAAATTTCATATATAA
1 AATTACATAAAATC-AAAGTTCATGTATAA
*
47165 AATTACATAAAATCAAAGTTCATGTATAC
1 AATTACATAAAATCAAAGTTCATGTATAA
* *
47194 AATTGCACATTAAATCATAGTTCATGTA
1 AATT--ACATAAAATCAAAGTTCATGTA
47222 GAGTTTTGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 16 0.33
30 12 0.25
31 20 0.42
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (29 bp):
AATTACATAAAATCAAAGTTCATGTATAA
Found at i:49022 original size:25 final size:23
Alignment explanation
Indices: 48994--49044 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
48984 CACCTAATAA
48994 TTAGAAACTAAAGATTGTGAATGTG
1 TTAG-AAC-AAAGATTGTGAATGTG
* * *
49019 TTAGTACCATGATTGTGAATGTG
1 TTAGAACAAAGATTGTGAATGTG
49042 TTA
1 TTA
49045 TGATGCTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 17 0.74
24 2 0.09
25 4 0.17
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (23 bp):
TTAGAACAAAGATTGTGAATGTG
Done.