Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009724.1 Kokia drynarioides strain JFW-HI SEQ_124443, 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: 40055
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:459 original size:15 final size:16
Alignment explanation
Indices: 439--468 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
429 AAAGTATAAA
439 TAAATAT-TAAAAATG
1 TAAATATATAAAAATG
454 TAAATATATAAAAAT
1 TAAATATATAAAAAT
469 AAATAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
TAAATATATAAAAATG
Found at i:1435 original size:31 final size:31
Alignment explanation
Indices: 1400--1458 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1390 TTAGTCCTTA
* *
1400 AACTTGACAATTGTTCCCACATTAAGGCTTG
1 AACTTGACAATTGCTCCCAAATTAAGGCTTG
*
1431 AACTTGACAATTGCTCCCAAATTGAGGC
1 AACTTGACAATTGCTCCCAAATTAAGGC
1459 CTAAGCTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (31 bp):
AACTTGACAATTGCTCCCAAATTAAGGCTTG
Found at i:1779 original size:3 final size:3
Alignment explanation
Indices: 1773--1818 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
1763 TAATATTTGA
*
1773 AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1819 GTAGTAGTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11647 original size:6 final size:6
Alignment explanation
Indices: 11631--11708 Score: 59
Period size: 6 Copynumber: 12.8 Consensus size: 6
11621 AAGCTTTGAT
* * ** **
11631 TTTAAA ATTAAG TTTAAA TTTATT TTTAAA TTTAAA TTTATCTT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA
**
11681 TTTAAA TTT-GC TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
11709 TCAAATTTGA
Statistics
Matches: 53, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
5 3 0.06
6 46 0.87
8 4 0.08
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:11807 original size:15 final size:14
Alignment explanation
Indices: 11771--11807 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
11761 AGATTAAATT
11771 AAAGTCC-AATTAC
1 AAAGTCCAAATTAC
11784 AAAGTCCAAATTAC
1 AAAGTCCAAATTAC
11798 AAAGGTCCAA
1 AAA-GTCCAA
11808 GTTGGCCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 7 0.32
14 9 0.41
15 6 0.27
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.19
Consensus pattern (14 bp):
AAAGTCCAAATTAC
Found at i:12516 original size:3 final size:3
Alignment explanation
Indices: 12492--12534 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
12482 ATATTTATTA
* *
12492 AAT AATT AAT AAT ATT ATT AAT AATT AAT AAT AAT AAT AAT AA
1 AAT AA-T AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AA
12535 AGCCGAAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:12516 original size:19 final size:19
Alignment explanation
Indices: 12479--12534 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
12469 TTTATTAAAG
12479 ATAATATTTATTAAATAATTA
1 ATAATA-TTATT-AATAATTA
12500 ATAATATTATTAATAATTA
1 ATAATATTATTAATAATTA
* *
12519 ATAATAATAATAATAA
1 ATAATATTATTAATAA
12535 AGCCGAAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 22 0.67
20 5 0.15
21 6 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAATATTATTAATAATTA
Found at i:13714 original size:29 final size:29
Alignment explanation
Indices: 13667--13988 Score: 346
Period size: 29 Copynumber: 11.0 Consensus size: 29
13657 GAAGGTCCCG
13667 AAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCT
* * * * *
13696 GAACTCCCAAAAATCCCATTTTCGA-CTCT
1 AAACTTCCAAAAATTCCATTTT-TACCCCT
*
13725 GAAACTTCCAAAAA-TCTCATTTTTACCCCC
1 -AAACTTCCAAAAATTC-CATTTTTACCCCT
* *
13755 AAACTTCCAAAAATTCCATTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCT
* *
13784 AAAATTCCAAAAATTTCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCT
* * *
13813 AAACTTCCAAAAAATCCATTTTTAACCTCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCT
13843 AAACTTCCAAAAATTCCATTTTTA-CCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCT
* * *
13871 CGAACTTCCAAAAACTCCATTTTTTACCCCA
1 -AAACTTCCAAAAATTCCA-TTTTTACCCCT
* * *
13902 AAACTTCCAAATATTCAATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCT
*
13931 AAACTTCCAAAAATTCCATTTTTGACCTCT
1 AAACTTCCAAAAATTCCATTTTT-ACCCCT
* *
13961 AAACTTTCAAAAGTTACCA-TTTTACCCC
1 AAACTTCCAAAAATT-CCATTTTTACCCC
13989 CGAATGTCCA
Statistics
Matches: 242, Mismatches: 40, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
28 2 0.01
29 145 0.60
30 89 0.37
31 6 0.02
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCT
Found at i:13765 original size:59 final size:58
Alignment explanation
Indices: 13667--14002 Score: 335
Period size: 59 Copynumber: 5.7 Consensus size: 58
13657 GAAGGTCCCG
** * * * *
13667 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTCCCAAAAATCCCATTTTCGACTCTG
1 AAACTTCCAAAAATT-CATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCTA
* *
13726 AAACTTCCAAAAATCTCATTTTTACCCCCAAACTTCCAAAAATTCCA-TTTTGACCCCA
1 AAACTTCCAAAAAT-TCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCTA
* * *
13784 AAAATTCCAAAAATTTCATTTTTACCCCTAAACTTCCAAAAAAT-CCATTTTT-AACCTCA
1 AAACTTCCAAAAA-TTCATTTTTACCCCCAAACTTCC-AAAAATCCCATTTTTGACCCT-A
* * * *
13843 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAA-CTCCATTTTTTACCCCA
1 AAACTTCCAAAAATT-CATTTTTACCCCCAAACTTCCAAAAATC-CCATTTTTGACCCTA
* *
13902 AAACTTCCAAATATTCAATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCT-
1 AAACTTCCAAAAATTC-ATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACC-CTA
* * *
13961 AAACTTTCAAAAGTTACCA-TTTTACCCCCGAA-TGTCCAAAAA
1 AAACTTCCAAAAATT--CATTTTTACCCCCAAACT-TCCAAAAA
14003 AGTCCATTTT
Statistics
Matches: 234, Mismatches: 28, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
58 55 0.24
59 172 0.74
60 6 0.03
61 1 0.00
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.32
Consensus pattern (58 bp):
AAACTTCCAAAAATTCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCTA
Found at i:13826 original size:88 final size:86
Alignment explanation
Indices: 13667--13988 Score: 346
Period size: 88 Copynumber: 3.7 Consensus size: 86
13657 GAAGGTCCCG
* * * * *
13667 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTCCCAAAAATCCCATTTTCGA-CTCTGAAACT
1 AAACTTCCAAAAATTCCATTTTGACCCC-GAACTTCCAAAAATTCCATTTT-TACCCCT-AAACT
13731 TCCAAAAATCTCATTTTTACCCCC
63 TCCAAAAATCTCATTTTTACCCCC
* * *
13755 AAACTTCCAAAAATTCCATTTTGACCCCAAAAATTCCAAAAATTTCATTTTTACCCCTAAACTTC
1 AAACTTCCAAAAATTCCATTTTGACCCC-GAACTTCCAAAAATTCCATTTTTACCCCTAAACTTC
* *
13820 CAAAAAATC-CATTTTTAACCTCA
65 C-AAAAATCTCATTTTT-ACCCCC
* * *
13843 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAACTCCATTTTTTACCCCAAAACTT
1 AAACTTCCAAAAATTCCATTTTGACCC-CGAACTTCCAAAAATTCCA-TTTTTACCCCTAAACTT
*
13908 CCAAATAT-TCAATTTTTACCCCC
64 CCAAAAATCTC-ATTTTTACCCCC
** * *
13931 AAACTTCCAAAAATTCCATTTTTGACCTCTAAACTTTCAAAAGTTACCA-TTTTACCCC
1 AAACTTCCAAAAATTCCA-TTTTGACC-CCGAACTTCCAAAAATT-CCATTTTTACCCC
13989 CGAATGTCCA
Statistics
Matches: 198, Mismatches: 26, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
87 16 0.08
88 135 0.68
89 43 0.22
90 4 0.02
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.32
Consensus pattern (86 bp):
AAACTTCCAAAAATTCCATTTTGACCCCGAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCC
AAAAATCTCATTTTTACCCCC
Found at i:14037 original size:59 final size:59
Alignment explanation
Indices: 13665--14070 Score: 244
Period size: 59 Copynumber: 6.9 Consensus size: 59
13655 CTGAAGGTCC
* * ** *
13665 CGAAACTTCCAAAAATT-CCATTTTTACCCCTGAACTCCCAAAAA-TCCCATTTTCGA-CT
1 CGAAACTTTCAAAAGTTACCA-TTTTACCCCCAAACTTCCAAAAAGT-CCATTTTCGACCT
* * * *
13723 CTGAAACTTCCAAAA-AT-CTCATTTTTACCCCCAAACTTCCAAAAATTCCATTTT-GACCC
1 C-GAAACTTTCAAAAGTTAC-CA-TTTTACCCCCAAACTTCCAAAAAGTCCATTTTCGACCT
* * * * * * * **
13782 CAAAAATTCCAAAAATT-TCATTTTTACCCCTAAACTTCCAAAAAATCCATTTTTAACCT
1 CGAAACTTTCAAAAGTTACCA-TTTTACCCCCAAACTTCCAAAAAGTCCATTTTCGACCT
* * * * * * ** *
13841 CAAAACTTCCAAAAATT-CCATTTTTACCCTCGAACTTCCAAAAACTCCATTTTTTACCC
1 CGAAACTTTCAAAAGTTACCA-TTTTACCCCCAAACTTCCAAAAAGTCCATTTTCGACCT
* * * * *
13900 CAAAACTTCCAAATA-TT-CAATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCT
1 CGAAACTTTCAAA-AGTTACCA-TTTTACCCCCAAACTTCCAAAAAGTCCATTTTCGACCT
* *
13959 CTAAACTTTCAAAAGTTACCATTTTACCCCCGAA-TGTCCAAAAAAGTCCATTTTCGACCT
1 CGAAACTTTCAAAAGTTACCATTTTACCCCCAAACT-TCC-AAAAAGTCCATTTTCGACCT
* * * * * * *
14019 CGAAACTCTT-GAAA-TTACCCTTTTACCCTCTAACGTCTAAAAATTCCATTTT
1 CGAAACT-TTCAAAAGTTACCATTTTACCCCCAAACTTCCAAAAAGTCCATTTT
14071 AACCCCAAAT
Statistics
Matches: 294, Mismatches: 41, Indels: 26
0.81 0.11 0.07
Matches are distributed among these distances:
58 64 0.22
59 197 0.67
60 31 0.11
61 2 0.01
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (59 bp):
CGAAACTTTCAAAAGTTACCATTTTACCCCCAAACTTCCAAAAAGTCCATTTTCGACCT
Found at i:14120 original size:28 final size:28
Alignment explanation
Indices: 14086--14146 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
14076 CAAATTTTCT
*
14086 CAAAATTACCATTTTGCCCTCGAGAATC
1 CAAAATTACCATTTTGCCCCCGAGAATC
* * *
14114 CAAAATTACCATTTTTCCCCCGGGTATC
1 CAAAATTACCATTTTGCCCCCGAGAATC
14142 CAAAA
1 CAAAA
14147 GGTCTCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.30, G:0.10, T:0.28
Consensus pattern (28 bp):
CAAAATTACCATTTTGCCCCCGAGAATC
Found at i:14479 original size:96 final size:96
Alignment explanation
Indices: 14362--14546 Score: 232
Period size: 96 Copynumber: 1.9 Consensus size: 96
14352 AAAACTTTAA
* *
14362 AATCGAGGTAATATTCTCTTAT-TTTGAGTT-TCGAAAATTTGCGCCTTAACTTACTAGGTACAA
1 AATCGAGGCAATATTCTCTTATCTTCGA-TTCT-GAAAATTTGCGCCTTAACTTACTAGGTACAA
** *
14425 TTTTTCTTCAAATCGAAATAATCGAATACCTTT
64 CCTTTCCTCAAATCGAAATAATCGAATACCTTT
* * *
14458 AATCGAGGCAATGTT-TCCTTATCTTCGATTCTGAAAATTTGCGCCTTAACTTATTAGGTGCAAC
1 AATCGAGGCAATATTCT-CTTATCTTCGATTCTGAAAATTTGCGCCTTAACTTACTAGGTACAAC
* *
14522 CTTTCCTCAAATTGAGATAATCGAA
65 CTTTCCTCAAATCGAAATAATCGAA
14547 CATCCTTTTC
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
95 1 0.01
96 70 0.92
97 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATATTCTCTTATCTTCGATTCTGAAAATTTGCGCCTTAACTTACTAGGTACAACC
TTTCCTCAAATCGAAATAATCGAATACCTTT
Found at i:20397 original size:16 final size:16
Alignment explanation
Indices: 20378--20430 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
20368 AGTCCTACTC
*
20378 CATTATAGCTCTATTA
1 CATTATAACTCTATTA
* *
20394 CATTACAACTCTATTC
1 CATTATAACTCTATTA
*
20410 CATTATAACTCTATTT
1 CATTATAACTCTATTA
20426 CATTA
1 CATTA
20431 CAACGAACCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.43
Consensus pattern (16 bp):
CATTATAACTCTATTA
Found at i:20669 original size:4 final size:4
Alignment explanation
Indices: 20654--20696 Score: 59
Period size: 4 Copynumber: 10.2 Consensus size: 4
20644 TATAAATAGG
*
20654 TGTA TATA TGTA TGTA TGTA TGTA TGTA TGCATA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG--TA TGTA TGTA T
20697 ATTTATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 31 0.89
6 4 0.11
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (4 bp):
TGTA
Found at i:20946 original size:15 final size:15
Alignment explanation
Indices: 20926--20955 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20916 GTGGCAGCTT
20926 TCGGTGGTACTGGTG
1 TCGGTGGTACTGGTG
20941 TCGGTGGTACTGGTG
1 TCGGTGGTACTGGTG
20956 GTGGTCAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.13, G:0.47, T:0.33
Consensus pattern (15 bp):
TCGGTGGTACTGGTG
Found at i:25988 original size:43 final size:44
Alignment explanation
Indices: 25921--26011 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 44
25911 AATATCTAAA
* *
25921 TTAGTCTTTAAACTTGATAA-TTATTACATTAGGGCATGAACAT
1 TTAGTCCTTAAACTTGACAATTTATTACATTAGGGCATGAACAT
* *
25964 TTAGTCCTTAAACTTGACAGTTATTATTACATTAGGGTATGAACAT
1 TTAGTCCTTAAACTTGACA-AT-TTATTACATTAGGGCATGAACAT
26010 TT
1 TT
26012 TTTTGTCCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
43 17 0.41
46 24 0.59
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (44 bp):
TTAGTCCTTAAACTTGACAATTTATTACATTAGGGCATGAACAT
Found at i:26803 original size:13 final size:13
Alignment explanation
Indices: 26785--26840 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
26775 ATTATTTATG
26785 AAAAGTACTTTTA
1 AAAAGTACTTTTA
**
26798 AAAAGTAC-GATA
1 AAAAGTACTTTTA
*
26810 GAAAAGTATTTTTA
1 -AAAAGTACTTTTA
*
26824 AGAAGTACTTTTGA
1 AAAAGTACTTTT-A
26838 AAA
1 AAA
26841 TTTTAATTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
12 2 0.06
13 25 0.78
14 5 0.16
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.32
Consensus pattern (13 bp):
AAAAGTACTTTTA
Found at i:26839 original size:26 final size:26
Alignment explanation
Indices: 26783--26840 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
26773 GTATTATTTA
26783 TGAAAAGTACTTTTAAAAAGTACGAT
1 TGAAAAGTACTTTTAAAAAGTACGAT
* * * **
26809 AGAAAAGTATTTTTAAGAAGTACTTT
1 TGAAAAGTACTTTTAAAAAGTACGAT
26835 TGAAAA
1 TGAAAA
26841 TTTTAATTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.33
Consensus pattern (26 bp):
TGAAAAGTACTTTTAAAAAGTACGAT
Found at i:28268 original size:29 final size:28
Alignment explanation
Indices: 28236--28332 Score: 95
Period size: 29 Copynumber: 3.4 Consensus size: 28
28226 AAAATCACAT
* *
28236 TTTGACCTCTAAACTTTTCAAAATTTGTA
1 TTTGACC-CCAAACTTTTCAAAATTTGAA
**
28265 TTTGACCCCAAACTTCCCAAAAATTTGAA
1 TTTGACCCCAAACTTTTC-AAAATTTGAA
* * * *
28294 TTTAGCCCCCAAACTTTTTAAAATTTCAT
1 TTT-GACCCCAAACTTTTCAAAATTTGAA
28323 TTTGACCCCA
1 TTTGACCCCA
28333 TTTTTCCTTA
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
28 14 0.25
29 30 0.55
30 11 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (28 bp):
TTTGACCCCAAACTTTTCAAAATTTGAA
Found at i:30271 original size:22 final size:21
Alignment explanation
Indices: 30223--30274 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
30213 ATTATATTAT
**
30223 TGTTTTGGTGTTGTTTTTTGC
1 TGTTTTGGTGTTGTTTTTTAA
*
30244 TATTTTGGTGTTGTTTTTTTAA
1 TGTTTTGGTGTTG-TTTTTTAA
30266 TGTTTTGGT
1 TGTTTTGGT
30275 TTTTTTACTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.06, C:0.02, G:0.25, T:0.67
Consensus pattern (21 bp):
TGTTTTGGTGTTGTTTTTTAA
Found at i:30279 original size:16 final size:17
Alignment explanation
Indices: 30256--30292 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
30246 TTTTGGTGTT
30256 GTTTTTTTAATGTTTTG
1 GTTTTTTTAATGTTTTG
*
30273 GTTTTTTTACTGTTTTG
1 GTTTTTTTAATGTTTTG
30290 GTT
1 GTT
30293 ACTGTTGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.08, C:0.03, G:0.19, T:0.70
Consensus pattern (17 bp):
GTTTTTTTAATGTTTTG
Found at i:30366 original size:36 final size:36
Alignment explanation
Indices: 30326--30410 Score: 145
Period size: 36 Copynumber: 2.4 Consensus size: 36
30316 GTTTTGATGC
30326 TGTTATTTTTGTTACTATTTTTGTTGCTATTTTTGT
1 TGTTATTTTTGTTACTATTTTTGTTGCTATTTTTGT
*
30362 TGTTATTTTTGTTACTGTTTTTGTTGCTATTTTTGT
1 TGTTATTTTTGTTACTATTTTTGTTGCTATTTTTGT
30398 TGTT-TTTGTTGTT
1 TGTTATTT-TTGTT
30411 GTTTTGCTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
35 3 0.06
36 44 0.94
ACGTcount: A:0.08, C:0.05, G:0.16, T:0.71
Consensus pattern (36 bp):
TGTTATTTTTGTTACTATTTTTGTTGCTATTTTTGT
Found at i:30439 original size:12 final size:12
Alignment explanation
Indices: 30326--30446 Score: 106
Period size: 12 Copynumber: 10.3 Consensus size: 12
30316 GTTTTGATGC
30326 TGTTATTTTTGT
1 TGTTATTTTTGT
**
30338 TACTATTTTTGT
1 TGTTATTTTTGT
*
30350 TGCTATTTTTGT
1 TGTTATTTTTGT
30362 TGTTATTTTTGT
1 TGTTATTTTTGT
** *
30374 TACTGTTTTTGT
1 TGTTATTTTTGT
*
30386 TGCTATTTTTGT
1 TGTTATTTTTGT
30398 TG---TTTTTGT
1 TGTTATTTTTGT
* *
30407 TGTT-GTTTTGC
1 TGTTATTTTTGT
*
30418 TATTATTTTTTGT
1 TGTTA-TTTTTGT
*
30431 TGTTATTTTGGT
1 TGTTATTTTTGT
30443 TGTT
1 TGTT
30447 TGAATGTTAT
Statistics
Matches: 89, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
9 9 0.10
11 8 0.09
12 63 0.71
13 9 0.10
ACGTcount: A:0.08, C:0.04, G:0.17, T:0.70
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:30610 original size:27 final size:26
Alignment explanation
Indices: 30576--30627 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 26
30566 TATAAAGAAT
30576 TTTTAATG-TATTTTAAATTTGTTTATA
1 TTTTAATGTTATTTT-AATTT-TTTATA
30603 TTTTAATGTTTATTTTAATTTTTTA
1 TTTTAATG-TTATTTTAATTTTTTA
30628 AGTTTATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
27 12 0.52
28 5 0.22
29 6 0.26
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (26 bp):
TTTTAATGTTATTTTAATTTTTTATA
Found at i:31280 original size:17 final size:17
Alignment explanation
Indices: 31258--31337 Score: 97
Period size: 17 Copynumber: 4.7 Consensus size: 17
31248 GGCCTAACAG
*
31258 AATTTAAATGTATTTTA
1 AATTTAAATTTATTTTA
**
31275 AATTTAAAAATATTTTA
1 AATTTAAATTTATTTTA
* *
31292 AGTTTAAATTTATTTGA
1 AATTTAAATTTATTTTA
*
31309 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
*
31326 AATTTAAGTTTA
1 AATTTAAATTTA
31338 AATTTATTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 53 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:31303 original size:40 final size:39
Alignment explanation
Indices: 31258--31343 Score: 93
Period size: 40 Copynumber: 2.2 Consensus size: 39
31248 GGCCTAACAG
* *
31258 AATTTAAATGTATTTTAAATTTA-AAAATATTTTAAGTTTA
1 AATTTAAATGAAATTTAAATTTATAAAA-A-TTTAAGTTTA
** *
31298 AATTTATTTGAAATTTAAATTTATTATAAATTTAAGTTTA
1 AATTTAAATGAAATTTAAATTTA-TAAAAATTTAAGTTTA
31338 AATTTA
1 AATTTA
31344 TTTAAATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
40 35 0.90
41 1 0.03
42 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (39 bp):
AATTTAAATGAAATTTAAATTTATAAAAATTTAAGTTTA
Found at i:31327 original size:11 final size:10
Alignment explanation
Indices: 31294--31351 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
31284 ATATTTTAAG
31294 TTTAAATTTA
1 TTTAAATTTA
*
31304 TTTGAA---A
1 TTTAAATTTA
31311 TTTAAATTTA
1 TTTAAATTTA
31321 TTATAAATTTAA
1 TT-TAAATTT-A
31333 GTTTAAATTTA
1 -TTTAAATTTA
31344 TTTAAATT
1 TTTAAATT
31352 AATAATGTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 6 0.15
10 16 0.40
11 8 0.20
12 8 0.20
13 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (10 bp):
TTTAAATTTA
Found at i:34132 original size:124 final size:123
Alignment explanation
Indices: 33901--34175 Score: 417
Period size: 124 Copynumber: 2.2 Consensus size: 123
33891 AGTGTTGCGG
* *
33901 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACTAGGCTCAAAGTGAGCAAA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAAAGCTCAAAGTGAGCAAA
33966 TCTTCGAACCCCAGCTTCTTGATAAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGA
66 TCTTCGAACCCCAGCTTCTTGATAAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGA
* * * *
34024 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCCAAAGCTCGATGTGAGCGA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAA-ACAAAGCTCAAAGTGAGCAA
* * *
34089 ATCTTCGAACCCCAGCTTCTTGATGAA-ATATTGAGAAGCAGGTCGAAGCAATAAAGTGG
65 ATCTTCGAACCCCAGCTTCTTGAT-AAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGA
* * *
34148 TTACCTTCCTGATGAGATACAGAGAAGT
1 TCATCTTCCTGATGAGATACTGAGAAGT
34176 GGGCCAGATC
Statistics
Matches: 138, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
123 44 0.32
124 92 0.67
125 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (123 bp):
TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAAAGCTCAAAGTGAGCAAA
TCTTCGAACCCCAGCTTCTTGATAAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGA
Found at i:34297 original size:333 final size:333
Alignment explanation
Indices: 33691--34382 Score: 1064
Period size: 333 Copynumber: 2.1 Consensus size: 333
33681 AATGAGGCGG
* * * *
33691 TCATCTTCCTAATGAGATACAGAGAAGTATACAAACTCGATGAAATAAAGCTCAAATGTGAGCGA
1 TCATCTTCCTGATGAGATACAGAGAAGTAGACAAACTCAATGAAACAAAGCTCAAATGTGAGCGA
* *
33756 AACTTCGAACCCCTGCTTCCTGATGAGATATTGAGAAGCAGATCAAAGCAATAAAGCGGTTACCT
66 AACTTCGAACCCCAGCTTCCTGATGAAATATTGAGAAGCAGATCAAAGCAATAAAGCGGTTACCT
* * * *
33821 TCCTGATGAGATATAAAGAAGTGGGTCAGATCCGTCTTCTTGATGAGACATAGAAAAGTGGATCA
131 TCCTGATGAGATACAAAGAAGTGGGCCAGATCCGTCTTCCTGATGAGACACAGAAAAGTGGATCA
* * * * *
33886 AAATAAGTGTTGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACTAGG
196 AAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAAACCAAATCAATGAAACCAGG
*
33951 CTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCTTGATAAGATACTGAGAAGCAGGTCGAAGCAA
261 CTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCTTGATAAGATACTGAGAAGCAAGTCGAAGCAA
34016 TAAAGCGA
326 TAAAGCGA
* * *
34024 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAA-TCAATGAAGCCAAAGCTC-GATGTGAGC
1 TCATCTTCCTGATGAGATACAGAGAAGTAGA-CAAACTCAATGAA-ACAAAGCTCAAATGTGAGC
* * * * *
34087 GAATCTTCGAACCCCAGCTTCTTGATGAAATATTGAGAAGCAGGTCGAAGCAATAAAGTGGTTAC
64 GAAACTTCGAACCCCAGCTTCCTGATGAAATATTGAGAAGCAGATCAAAGCAATAAAGCGGTTAC
* *
34152 CTTCCTGATGAGATACAGAGAAGTGGGCCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGAT
129 CTTCCTGATGAGATACAAAGAAGTGGGCCAGATCCGTCTTCCTGATGAGACACAGAAAAGTGGAT
34217 CAAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAAACCAAATCAATGAAACCA
194 CAAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAAACCAAATCAATGAAACCA
* * *
34282 GGCTCAAAGTGAGCAAATCTTCGAACCCCGGCTTCTTGATGAGATACTGAGAAGTAAGTCGAAGC
259 GGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCTTGATAAGATACTGAGAAGCAAGTCGAAGC
*
34347 AATAAAGCGG
324 AATAAAGCGA
* *
34357 TTACCTTCCTGATGAGATACAGAGAA
1 TCATCTTCCTGATGAGATACAGAGAA
34383 ATGAACGGGA
Statistics
Matches: 324, Mismatches: 33, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
333 313 0.97
334 11 0.03
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (333 bp):
TCATCTTCCTGATGAGATACAGAGAAGTAGACAAACTCAATGAAACAAAGCTCAAATGTGAGCGA
AACTTCGAACCCCAGCTTCCTGATGAAATATTGAGAAGCAGATCAAAGCAATAAAGCGGTTACCT
TCCTGATGAGATACAAAGAAGTGGGCCAGATCCGTCTTCCTGATGAGACACAGAAAAGTGGATCA
AAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAAACCAAATCAATGAAACCAGG
CTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCTTGATAAGATACTGAGAAGCAAGTCGAAGCAA
TAAAGCGA
Found at i:34397 original size:209 final size:209
Alignment explanation
Indices: 34024--34698 Score: 962
Period size: 208 Copynumber: 3.2 Consensus size: 209
34014 AATAAAGCGA
* * *
34024 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCCAAAGCTCGATGTGAGCGA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACC-AAGCTCAATGTGAGCAA
* *
34089 ATCTTCGAACCCCAGCTTCTTGATGAAATATTGAGAAGCAGGTCGAAGCAATAAAGTGGTTACCT
65 ATCTTCGAACCCCAGCTTCTTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCT
** *
34154 TCCTGATGAGATACAGAGAAGTGGGCCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCA
130 TCCTGATGAGATACAGAGAAGTGAACCGGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCA
*
34219 AAACAAGTGATACGG
195 AAACAAGAGATACGG
* * *
34234 TCATCTTCCTGATGAGATACTGAGAAGTAAACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAATGTGAGCAAA
* * * *
34299 TCTTCGAACCCCGGCTTCTTGATGAGATACTGAGAAGTAAGTCGAAGCAATAAAGCGGTTACCTT
66 TCTTCGAACCCCAGCTTCTTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCTT
* * * *
34364 CCTGATGAGATACAGAGAAATGAACGGGATCCGTCTTCCTGATGAGATA-TGAAGAAGTGGATCA
131 CCTGATGAGATACAGAGAAGTGAACCGGATCCGTCTTCCTGATGAGACACAG-AGAAGTGGATCA
*
34428 AAAC-AGAGATACGA
195 AAACAAGAGATACGG
* **
34442 TCATCTTCCTGATGAGATACTGAGAAGTACACCAAATCAAT-AATATAAAGCTCAATGTGAGCGA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAA-ACCAAGCTCAATGTGAGC-A
*
34506 AA-CTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACC
64 AATCTTCGAACCCCAGCTTCTTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACC
* ** * *
34570 TTCCTAATGAGATACAGAGAAGTGAATTGGATCCGTCTTCCTGATGAAACACAAAGAAGTGGATC
129 TTCCTGATGAGATACAGAGAAGTGAACCGGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATC
* * *
34635 AAAACAAGCGATGCAG
194 AAAACAAGAGATACGG
* * *
34651 TCATCTTCTTGATGAGATACTAAGAAGTAGACCAAATCAATAAAACCA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
34699 GACATAAAGA
Statistics
Matches: 411, Mismatches: 48, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
207 2 0.00
208 181 0.44
209 181 0.44
210 47 0.11
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (209 bp):
TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAATGTGAGCAAA
TCTTCGAACCCCAGCTTCTTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCTT
CCTGATGAGATACAGAGAAGTGAACCGGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCAA
AACAAGAGATACGG
Found at i:35057 original size:17 final size:17
Alignment explanation
Indices: 35012--35057 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
35002 GGCCCAACAG
* *
35012 AATTTAAATGTATTTTA
1 AATTTAAATTTATTATA
35029 AATTTAAATTTATTATA
1 AATTTAAATTTATTATA
*
35046 AATTTAAGTTTA
1 AATTTAAATTTA
35058 AATTTATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Found at i:37011 original size:30 final size:30
Alignment explanation
Indices: 36966--37042 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
36956 TAGAAGATCC
* *
36966 CTAAACTATCCAAAAATCATATGTTGA-CA
1 CTAAACTTTCTAAAAATCATATGTTGACCA
* *
36995 CTTAAACTTTCTAAAAATTATATTTTGACCA
1 C-TAAACTTTCTAAAAATCATATGTTGACCA
37026 CTAAACTTTCTAAAAAT
1 CTAAACTTTCTAAAAAT
37043 TACATTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 1 0.02
30 38 0.90
31 3 0.07
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.35
Consensus pattern (30 bp):
CTAAACTTTCTAAAAATCATATGTTGACCA
Found at i:37043 original size:30 final size:30
Alignment explanation
Indices: 36989--37193 Score: 190
Period size: 30 Copynumber: 6.8 Consensus size: 30
36979 AAATCATATG
* * *
36989 TTGACACTTAAACTTTCTAAAAATTATATT
1 TTGACCCTCAAACTTTCTAAAAATTACATT
37019 TTGACCACT-AAACTTTCTAAAAATTACATT
1 TTGACC-CTCAAACTTTCTAAAAATTACATT
*
37049 TTTACCCTCAAAC-TTCATAAAAATTACATTT
1 TTGACCCTCAAACTTTC-TAAAAATTACA-TT
* *
37080 TTG-CCCTCGAAC-TTCATAAAAAATACATT
1 TTGACCCTCAAACTTTC-TAAAAATTACATT
* *
37109 TTGACCCCTCAAACTTTCAAAAAATTCCATTT
1 TTGA-CCCTCAAACTTTCTAAAAATTACA-TT
* * *
37141 TTGACCC-CAAATTTTCCAATAATTACCATT
1 TTGACCCTCAAACTTTCTAAAAATTA-CATT
*
37171 TT-ACCCTCAAA-TTTCTCAAAATT
1 TTGACCCTCAAACTTTCTAAAAATT
37194 CTATTTTTAA
Statistics
Matches: 148, Mismatches: 17, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
29 23 0.16
30 89 0.60
31 27 0.18
32 9 0.06
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
TTGACCCTCAAACTTTCTAAAAATTACATT
Found at i:37063 original size:60 final size:59
Alignment explanation
Indices: 36998--37236 Score: 186
Period size: 59 Copynumber: 4.0 Consensus size: 59
36988 GTTGACACTT
36998 AAACTTTCTAAAAATTATATTTTGACCACTAAACTTTCTAAAAATTACATTTTTACCCTC
1 AAACTTTCTAAAAATTATATTTTGACC-CTAAACTTTCTAAAAATTACATTTTTACCCTC
* * * *
37058 AAAC-TTCATAAAAATTACATTTTTG-CCCTCGAAC-TTCATAAAAAATACATTTTGACCCCTC
1 AAACTTTC-TAAAAATTATA-TTTTGACCCT-AAACTTTC-TAAAAATTACATTTTTA-CCCTC
* * * * *
37119 AAACTTTCAAAAAATTCCAT-TTTTGACCCCAAATTTTCCAATAATTACCA-TTTTACCCTC
1 AAACTTTCTAAAAATT--ATATTTTGACCCTAAACTTTCTAAAAATTA-CATTTTTACCCTC
* * * * ** *
37179 AAA-TTTCTCAAAATTCTATTTTTAACCCAAAAAATTCTAAAATTTACCA-TTTTACCCT
1 AAACTTTCTAAAAATTATA-TTTTGACCCTAAACTTTCTAAAAATTA-CATTTTTACCCT
37237 TGAATTTTCA
Statistics
Matches: 143, Mismatches: 23, Indels: 27
0.74 0.12 0.14
Matches are distributed among these distances:
57 1 0.01
59 50 0.35
60 42 0.29
61 38 0.27
62 11 0.08
63 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (59 bp):
AAACTTTCTAAAAATTATATTTTGACCCTAAACTTTCTAAAAATTACATTTTTACCCTC
Found at i:37226 original size:59 final size:59
Alignment explanation
Indices: 37105--37265 Score: 173
Period size: 59 Copynumber: 2.7 Consensus size: 59
37095 ATAAAAAATA
** * * **
37105 CATTTTGACCCCTCAAACTTTCAAAAAATTCCATTTTTGACCCCAAATTTTCCAATAATTAC
1 CATTTT-A-CCCTCAAA-TTTCTCAAAATTCCATTTTTAACCCAAAAAATTCCAATAATTAC
* *
37167 CATTTTACCCTCAAATTTCTCAAAATTCTATTTTTAACCCAAAAAATTCTAA-AATTTAC
1 CATTTTACCCTCAAATTTCTCAAAATTCCATTTTTAACCCAAAAAATTCCAATAA-TTAC
**
37226 CATTTTACCCTTGAATTT-TCAAAAATTCCATTTTTAACCC
1 CATTTTACCCTCAAATTTCTC-AAAATTCCATTTTTAACCC
37266 CGAACTTTCC
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
58 4 0.05
59 67 0.78
60 8 0.09
61 1 0.01
62 6 0.07
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.39
Consensus pattern (59 bp):
CATTTTACCCTCAAATTTCTCAAAATTCCATTTTTAACCCAAAAAATTCCAATAATTAC
Found at i:37279 original size:30 final size:30
Alignment explanation
Indices: 37029--37339 Score: 148
Period size: 30 Copynumber: 10.5 Consensus size: 30
37019 TTGACCACTA
* * *
37029 AACTTTCTAAAAATTACATTTTTACCCTCA
1 AACTTTCCAAAAATTCCATTTTTACCCTCG
* * *
37059 AAC-TTCATAAAAATTACATTTTTGCCCTCG
1 AACTTTC-CAAAAATTCCATTTTTACCCTCG
* * * * *
37089 AAC-TTCATAAAAAATACATTTTGACCCCTCA
1 AACTTTC-CAAAAATTCCATTTTTA-CCCTCG
* *
37120 AACTTTCAAAAAATTCCATTTTTGACCC-CA
1 AACTTTCCAAAAATTCCATTTTT-ACCCTCG
* *
37150 AATTTTCCAATAATTACCA-TTTTACCCTC-
1 AACTTTCCAAAAATT-CCATTTTTACCCTCG
* * **
37179 AAATTTCTC-AAAATTCTATTTTTAACCC-AA
1 AACTTTC-CAAAAATTCCATTTTT-ACCCTCG
** * * *
37209 AAAATTCTAAAATTTACCA-TTTTACCCTTG
1 AACTTTCCAAAAATT-CCATTTTTACCCTCG
*
37239 AA-TTTTCAAAAATTCCATTTTTAACCC-CG
1 AACTTTCCAAAAATTCCATTTTT-ACCCTCG
* *
37268 AACTTTCCAAAAATTCCCA--TTTATCCTAG
1 AACTTTCCAAAAATT-CCATTTTTACCCTCG
* *
37297 AA-TTTCCAAAAACTCCATTTTTGCCC-CTG
1 AACTTTCCAAAAATTCCATTTTTACCCTC-G
*
37326 AA-TTTCTAAAAATT
1 AACTTTCCAAAAATT
37340 ATCGTTTTAC
Statistics
Matches: 223, Mismatches: 37, Indels: 43
0.74 0.12 0.14
Matches are distributed among these distances:
27 3 0.01
28 19 0.09
29 65 0.29
30 101 0.45
31 31 0.14
32 4 0.02
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (30 bp):
AACTTTCCAAAAATTCCATTTTTACCCTCG
Found at i:37288 original size:59 final size:58
Alignment explanation
Indices: 37123--37351 Score: 205
Period size: 59 Copynumber: 3.9 Consensus size: 58
37113 CCCCTCAAAC
* *
37123 TTTCAAAAAATTCCATTTTTGACCCCAAATTTTCCAATAATTACCATTTTACCCTCA-AAT
1 TTTC-AAAAATTCCATTTTTAACCCCAAA-TTTCCAAAAATTACCATTTTACCCT-AGAAT
* * * * * *
37183 TTCTC-AAAATTCTATTTTTAACCCAAAAAATTCTAAAATTTACCATTTTACCCTTGAAT
1 TT-TCAAAAATTCCATTTTTAACCC-CAAATTTCCAAAAATTACCATTTTACCCTAGAAT
* * *
37242 TTTCAAAAATTCCATTTTTAACCCCGAACTTTCCAAAAATTCCCA-TTTATCCTAGAAT
1 TTTCAAAAATTCCATTTTTAACCCC-AAATTTCCAAAAATTACCATTTTACCCTAGAAT
* * * * * * *
37300 TTCCAAAAACTCCATTTTT-GCCCCTGAATTTCTAAAAATTATCGTTTTACCC
1 TTTCAAAAATTCCATTTTTAACCCC-AAATTTCCAAAAATTACCATTTTACCC
37352 CCAAACGTAA
Statistics
Matches: 135, Mismatches: 28, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
57 17 0.13
58 36 0.27
59 75 0.56
60 5 0.04
61 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.38
Consensus pattern (58 bp):
TTTCAAAAATTCCATTTTTAACCCCAAATTTCCAAAAATTACCATTTTACCCTAGAAT
Found at i:39549 original size:24 final size:24
Alignment explanation
Indices: 39505--39556 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
39495 TTTCTAAAAG
*
39505 ATTTAGTATTTATTAATATAATAT
1 ATTTAGTATTTATTAACATAATAT
* * *
39529 ATTTTGTATTTATTAGCATAATTT
1 ATTTAGTATTTATTAACATAATAT
39553 ATTT
1 ATTT
39557 GACTTACGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (24 bp):
ATTTAGTATTTATTAACATAATAT
Done.