Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015997.1 Corchorus olitorius cultivar O-4 contig16030, 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: 87566
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:944 original size:13 final size:13
Alignment explanation
Indices: 913--950 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
903 AAATGAAAAC
913 TAATATA-ATATA
1 TAATATATATATA
*
925 -AAGATATATATA
1 TAATATATATATA
937 TAATATATATATA
1 TAATATATATATA
950 T
1 T
951 CTTTATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 5 0.23
12 5 0.23
13 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (13 bp):
TAATATATATATA
Found at i:950 original size:19 final size:19
Alignment explanation
Indices: 915--966 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
905 ATGAAAACTA
* *
915 ATATAATATAAAGATATAT
1 ATATAATATATATATATAT
*
934 ATATAATATATATATATCT
1 ATATAATATATATATATAT
* *
953 TTATATTATATATA
1 ATATAATATATATA
967 AAGAAATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
ATATAATATATATATATAT
Found at i:1509 original size:43 final size:42
Alignment explanation
Indices: 1448--1546 Score: 164
Period size: 43 Copynumber: 2.3 Consensus size: 42
1438 TATGGGCTTC
*
1448 AGAACTAATACTTCAGATTTAATTGTTTGTAGCAATT-GAGTCT
1 AGAACTAATACTTCAGATTTAATTGTTTGTAGCAATTGGAG--G
1491 AGAACTAATACTTCAGATTTAATTGTTTGTAGCAATTGGAGG
1 AGAACTAATACTTCAGATTTAATTGTTTGTAGCAATTGGAGG
1533 AGAACTAATACTTC
1 AGAACTAATACTTC
1547 CTTCCAAGAG
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
42 14 0.26
43 37 0.69
44 3 0.06
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.36
Consensus pattern (42 bp):
AGAACTAATACTTCAGATTTAATTGTTTGTAGCAATTGGAGG
Found at i:3547 original size:7 final size:7
Alignment explanation
Indices: 3535--3576 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
3525 GTTAGTTAGG
3535 AAAAGAA
1 AAAAGAA
3542 AAAAGAA
1 AAAAGAA
3549 AAAAG-A
1 AAAAGAA
3555 AAAAGAA
1 AAAAGAA
3562 AAAA-AA
1 AAAAGAA
3568 AAGAAGAA
1 AA-AAGAA
3576 A
1 A
3577 TGAGATAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 10 0.31
7 19 0.59
8 3 0.09
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:3550 original size:6 final size:6
Alignment explanation
Indices: 3535--3572 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
3525 GTTAGTTAGG
3535 AAAAGAA AAAAGAA AAAAGA AAAAGA AAAA-A AAAAGA A
1 AAAAG-A AAAAG-A AAAAGA AAAAGA AAAAGA AAAAGA A
3573 GAAATGAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.17
6 13 0.43
7 12 0.40
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:3554 original size:14 final size:14
Alignment explanation
Indices: 3535--3576 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
3525 GTTAGTTAGG
3535 AAAAGAAAAAAGAA
1 AAAAGAAAAAAGAA
3549 AAAAG-AAAAAGAA
1 AAAAGAAAAAAGAA
3562 AAAA-AAAAGAAGAA
1 AAAAGAAAA-AAGAA
3576 A
1 A
3577 TGAGATAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAGAA
Found at i:3560 original size:20 final size:20
Alignment explanation
Indices: 3535--3576 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3525 GTTAGTTAGG
3535 AAAAGAAAAAAGAAAA-AAGA
1 AAAAGAAAAAA-AAAAGAAGA
3555 AAAAGAAAAAAAAAAGAAGA
1 AAAAGAAAAAAAAAAGAAGA
3575 AA
1 AA
3577 TGAGATAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAAAAAAGAAGA
Found at i:12715 original size:8 final size:8
Alignment explanation
Indices: 12700--12739 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
12690 GAAAAAAATG
12700 AATGAAAA
1 AATGAAAA
*
12708 ATTGAAAA
1 AATGAAAA
12716 AATGAAAA
1 AATGAAAA
12724 AATG--AA
1 AATGAAAA
12730 AATGAAAA
1 AATGAAAA
12738 AA
1 AA
12740 AGGAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 6 0.21
8 22 0.79
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.15
Consensus pattern (8 bp):
AATGAAAA
Found at i:12721 original size:16 final size:16
Alignment explanation
Indices: 12700--12739 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
12690 GAAAAAAATG
*
12700 AATGAAAAATTGAAAA
1 AATGAAAAAATGAAAA
12716 AATGAAAAAATG--AA
1 AATGAAAAAATGAAAA
12730 AATGAAAAAA
1 AATGAAAAAA
12740 AGGAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.52
16 11 0.48
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.15
Consensus pattern (16 bp):
AATGAAAAAATGAAAA
Found at i:12734 original size:30 final size:30
Alignment explanation
Indices: 12682--12738 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
12672 TCCCAATAAT
12682 AAAAGAATGAAAAAAATGAATGAAAAATTG
1 AAAAGAATGAAAAAAATGAATGAAAAATTG
12712 AAAA-AATG-AAAAAATGAAAATGAAAAA
1 AAAAGAATGAAAAAAATG--AATGAAAAA
12739 AAGGAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 8 0.32
29 4 0.16
30 13 0.52
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (30 bp):
AAAAGAATGAAAAAAATGAATGAAAAATTG
Found at i:12740 original size:9 final size:9
Alignment explanation
Indices: 12682--12731 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
12672 TCCCAATAAT
*
12682 AAAAGAATG
1 AAAAAAATG
12691 AAAAAAATG
1 AAAAAAATG
12700 AATGAAAAATTG
1 AA--AAAAA-TG
12712 -AAAAAATG
1 AAAAAAATG
12720 -AAAAAATG
1 AAAAAAATG
12728 AAAA
1 AAAA
12732 TGAAAAAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
8 10 0.28
9 18 0.50
11 6 0.17
12 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (9 bp):
AAAAAAATG
Found at i:13164 original size:24 final size:24
Alignment explanation
Indices: 13129--13174 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
13119 AAATTTAAAA
*
13129 AAAAAAAACAAATCAAAGTCAATC
1 AAAAAAAACAAATCAAAATCAATC
*
13153 AAAAAAATCAAATCAAAATCAA
1 AAAAAAAACAAATCAAAATCAA
13175 AAATCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.70, C:0.15, G:0.02, T:0.13
Consensus pattern (24 bp):
AAAAAAAACAAATCAAAATCAATC
Found at i:13176 original size:19 final size:20
Alignment explanation
Indices: 13149--13189 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
13139 AATCAAAGTC
13149 AATCAAAAAAATC-AAATCAA
1 AATC-AAAAAATCAAAATCAA
13169 AATC-AAAAATCAAAATCAA
1 AATCAAAAAATCAAAATCAA
13188 AA
1 AA
13190 GAGAATTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 9 0.45
20 4 0.20
ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15
Consensus pattern (20 bp):
AATCAAAAAATCAAAATCAA
Found at i:13178 original size:13 final size:13
Alignment explanation
Indices: 13162--13189 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
13152 CAAAAAAATC
13162 AAATCAAAATCAA
1 AAATCAAAATCAA
13175 AAATCAAAATCAA
1 AAATCAAAATCAA
13188 AA
1 AA
13190 GAGAATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (13 bp):
AAATCAAAATCAA
Found at i:13179 original size:7 final size:6
Alignment explanation
Indices: 13156--13189 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
13146 GTCAATCAAA
13156 AAAATC -AAATC AAAATC AAAAATC AAAATC AAAA
1 AAAATC AAAATC AAAATC -AAAATC AAAATC AAAA
13190 GAGAATTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 15 0.58
7 6 0.23
ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:14585 original size:50 final size:50
Alignment explanation
Indices: 14510--14847 Score: 532
Period size: 50 Copynumber: 6.8 Consensus size: 50
14500 CGAATGCTTT
* * *
14510 GGCTTTTCCATAAGCCAAACTCGTTTCAATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
*
14560 GGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* ** *
14610 GGCTTTTCCATAAGTTAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
*
14660 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTAAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* ** *
14710 GGCTCTTCCACAAGCCAAACTCGTTTCTTTACGAGTCAAATATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* *
14760 GGCCTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
*
14810 GGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
14848 TTTCAAACCT
Statistics
Matches: 261, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 261 1.00
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
Found at i:15039 original size:50 final size:50
Alignment explanation
Indices: 14904--15087 Score: 255
Period size: 50 Copynumber: 3.6 Consensus size: 50
14894 CATTACCTTT
*
14904 TTTTAAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACTGTCC
1 TTTT-AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
14955 TTTTATAGAATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTA-AG-ATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
15007 TTTTGAGATTGAATTGGTAGACAGTTCAAAGGATAAACCGG-AGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGAT-AAGCGGAAGACGGTCC
* * *
15057 TTTTAATATT-AGATTGGAAGACAATTCAAAG
1 TTTTAAGATTGA-ATTGGTAGACAGTTCAAAG
15088 AAGTTGATCG
Statistics
Matches: 122, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
49 1 0.01
50 62 0.51
51 13 0.11
52 46 0.38
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.28
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:16437 original size:7 final size:7
Alignment explanation
Indices: 16425--16460 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
16415 GTTAGTTAGG
16425 AAAAGAA
1 AAAAGAA
16432 AAAAGAA
1 AAAAGAA
16439 AAAAG-A
1 AAAAGAA
16445 AAAAG-A
1 AAAAGAA
16451 AAAAGAA
1 AAAAGAA
16458 AAA
1 AAA
16461 GAAGAAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.43
7 16 0.57
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:16440 original size:6 final size:6
Alignment explanation
Indices: 16425--16463 Score: 60
Period size: 6 Copynumber: 6.2 Consensus size: 6
16415 GTTAGTTAGG
16425 AAAAGAA AAAAGAA AAAAGA AAAAGA AAAAGA AAAAGA A
1 AAAAG-A AAAAG-A AAAAGA AAAAGA AAAAGA AAAAGA A
16464 GAAATGAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 20 0.62
7 12 0.38
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:17694 original size:17 final size:17
Alignment explanation
Indices: 17668--17702 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
17658 AGAAGGTTCG
17668 GGTAAAGAAGAAGAAGA
1 GGTAAAGAAGAAGAAGA
*
17685 GGTAAGGAAGAAGAAGA
1 GGTAAAGAAGAAGAAGA
17702 G
1 G
17703 AAGAGTCGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.40, T:0.06
Consensus pattern (17 bp):
GGTAAAGAAGAAGAAGA
Found at i:18903 original size:2 final size:2
Alignment explanation
Indices: 18896--18928 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18886 TATTTACTAG
18896 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18929 TGATTGATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23646 original size:20 final size:20
Alignment explanation
Indices: 23621--23663 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
23611 GAGTACACAA
**
23621 GAGGAAGGATTTTGGTGGCG
1 GAGGAAGGAGGTTGGTGGCG
*
23641 GAGGAAGGAGGTTGGTGGTG
1 GAGGAAGGAGGTTGGTGGCG
23661 GAG
1 GAG
23664 TTTATGGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.02, G:0.56, T:0.21
Consensus pattern (20 bp):
GAGGAAGGAGGTTGGTGGCG
Found at i:24239 original size:27 final size:27
Alignment explanation
Indices: 24209--24262 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
24199 TTTCAGTTTT
24209 ATTTTCCTGATATGGAATTTTTATCAA
1 ATTTTCCTGATATGGAATTTTTATCAA
*
24236 ATTTTCCTGGTATGGAATTTTTATCAA
1 ATTTTCCTGATATGGAATTTTTATCAA
24263 CTTTCATCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (27 bp):
ATTTTCCTGATATGGAATTTTTATCAA
Found at i:29769 original size:25 final size:25
Alignment explanation
Indices: 29741--29789 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
29731 AAAAGCAAAT
29741 GCAAAATAAACC-CTAATAATGCTCA
1 GCAAAATAAACCTC-AATAATGCTCA
* *
29766 GCAAAGTAAACTTCAATAATGCTC
1 GCAAAATAAACCTCAATAATGCTC
29790 GGAAAGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.22
Consensus pattern (25 bp):
GCAAAATAAACCTCAATAATGCTCA
Found at i:29808 original size:25 final size:25
Alignment explanation
Indices: 29755--29808 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
29745 AATAAACCCT
* *
29755 AATAATGCTCAGCAAAGTAAACTTC
1 AATAATGCTCAGCAAAGTAAAATTA
*
29780 AATAATGCTC-GGAAAGTCAAAATTA
1 AATAATGCTCAGCAAAGT-AAAATTA
29805 AATA
1 AATA
29809 CTGAACTCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (25 bp):
AATAATGCTCAGCAAAGTAAAATTA
Found at i:30818 original size:2 final size:2
Alignment explanation
Indices: 30811--30852 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
30801 TTGGCATTGT
30811 TC TC TC TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
30852 T
1 T
30853 ATATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:41402 original size:2 final size:2
Alignment explanation
Indices: 41397--41423 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41387 TATATATATA
41397 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
41424 AAATTAGTAC
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:46031 original size:38 final size:38
Alignment explanation
Indices: 45989--46064 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
45979 ATGCGTCCCA
45989 ATATTTACACTACTCTATGAGACTGAGGCTGTTATTGT
1 ATATTTACACTACTCTATGAGACTGAGGCTGTTATTGT
46027 ATATTTACACTACTCTATGAGACTGAGGCTGTTATTGT
1 ATATTTACACTACTCTATGAGACTGAGGCTGTTATTGT
46065 TTGACTCTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (38 bp):
ATATTTACACTACTCTATGAGACTGAGGCTGTTATTGT
Found at i:57737 original size:250 final size:252
Alignment explanation
Indices: 57295--57822 Score: 952
Period size: 250 Copynumber: 2.1 Consensus size: 252
57285 GGGAAAGGAC
*
57295 GGTAAAAGTACCTGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCATGTACTTTTTTT
1 GGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCATGTACTTTTTTT
* **
57360 TCTACAAATTCGTCCCTCTACTATCATAACCTATCACCTGAGGTCCCTCACGTTAGTGTGCCGTG
66 TCTACAAATTCGTCCCTCTACTATCATAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGTG
57425 ACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGACA
131 ACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGACA
57490 CGTGGAATAAAAATTAAATA-TTTTTTAATATACTTTATTTTATTAAAATTTATTTT
196 CGTGGAATAAAAATTAAATATTTTTTTAATATACTTTATTTTATTAAAATTTATTTT
* *
57546 GGTAAAAGTACCCGAGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTG-ACTTTTTTT
1 GGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCATGTACTTTTTTT
57610 TCTACAAATTCGTCCCTCTACTATCATAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGTG
66 TCTACAAATTCGTCCCTCTACTATCATAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGTG
* *
57675 ACAGACCCGTCAAATATGCTGATGTGGCACTAACATCGTCTTTTTTGCTGACGTGGCAGGTGACA
131 ACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGACA
* *
57740 CGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATTTTATTGAAATTTATTTT
196 CGTGGAATAAAAATTAAATATTTTTTTAATATACTTTATTTTATTAAAATTTATTTT
57797 GGTAAAAGTACCCGGGAGGTCCCTGT
1 GGTAAAAGTACCCGGGAGGTCCCTGT
57823 CTAACTTTTA
Statistics
Matches: 265, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
250 154 0.58
251 111 0.42
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (252 bp):
GGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCATGTACTTTTTTT
TCTACAAATTCGTCCCTCTACTATCATAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGTG
ACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGACA
CGTGGAATAAAAATTAAATATTTTTTTAATATACTTTATTTTATTAAAATTTATTTT
Found at i:65435 original size:85 final size:85
Alignment explanation
Indices: 65208--65420 Score: 365
Period size: 85 Copynumber: 2.5 Consensus size: 85
65198 CTTAGAATTT
*
65208 TGTCTCTCTT-TCCTGCTTTTTATTCTCAATTTCATGCTATTTTTGTCTTCAAACTGATATTGCT
1 TGTCTCTCTTAT-CTGCTTTTTATTCTCAATTTCATGCTATTTTTGTCTTCAAACTGATACTGCT
*
65272 GTTATAATGTTGAGAGATTAG
65 GTTATAATGATGAGAGATTAG
*
65293 TGTCTCTCTTATCTGCTTTTTATTCTCAATTTCATGTTATTTTTGTCTTCAAACTGATACTGCTG
1 TGTCTCTCTTATCTGCTTTTTATTCTCAATTTCATGCTATTTTTGTCTTCAAACTGATACTGCTG
*
65358 TTTTAATGATGAGAGATTAG
66 TTATAATGATGAGAGATTAG
*
65378 TGTCTCTCTTATCTGCTTTTTATTCTCAAGTTCATGCTATTTT
1 TGTCTCTCTTATCTGCTTTTTATTCTCAATTTCATGCTATTTT
65421 GGTTATCGAA
Statistics
Matches: 121, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
85 120 0.99
86 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.51
Consensus pattern (85 bp):
TGTCTCTCTTATCTGCTTTTTATTCTCAATTTCATGCTATTTTTGTCTTCAAACTGATACTGCTG
TTATAATGATGAGAGATTAG
Found at i:65936 original size:141 final size:137
Alignment explanation
Indices: 65685--65948 Score: 395
Period size: 141 Copynumber: 1.9 Consensus size: 137
65675 TTTTTAATTC
* *
65685 CTTTGCCTTTTGCAGGTCCTTGATGTCACTCTCGCCTTCGCTGTTTGTTGAGGTGAGCCTCTGAA
1 CTTTGCCTTTTGCAGGTCCTTGATGTCACTCTCGCATTCGCTGTTTGTTGAGGTCAGCCTCTGAA
* * *
65750 AATTTTAATGCTCTTTTTGGGTTTTTTGCCTTAAGCGGCTGATAAGCAACTTTTTTGTAGTTATC
66 AATTTTAATGCTCTTTTTGGGTTTTTTGCCTGAAGCAGCTGATAAGCAACTCTTTTGTAGTTATC
65815 TTGATTT
131 TTGATTT
* *
65822 CTTTGCCTTTTGCAGGTCTCCTTGATGTCACTCTCGCATTGGCTGTTTGTTGAGGTCCGCCCATC
1 CTTTGCCTTTTGCAGG--TCCTTGATGTCACTCTCGCATTCGCTGTTTGTTGAGGTCAG-CC-TC
* *
65887 TGAAAATTTTTATGCTCTTTTT-GGTTGTTTTGCCTGAAGCAGCTTATAAGCAACTCTTTTGT
62 TGAAAATTTTAATGCTCTTTTTGGGTT-TTTTGCCTGAAGCAGCTGATAAGCAACTCTTTTGT
65949 TGTTCTCTCT
Statistics
Matches: 113, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
137 16 0.14
139 37 0.33
140 6 0.05
141 54 0.48
ACGTcount: A:0.15, C:0.20, G:0.21, T:0.44
Consensus pattern (137 bp):
CTTTGCCTTTTGCAGGTCCTTGATGTCACTCTCGCATTCGCTGTTTGTTGAGGTCAGCCTCTGAA
AATTTTAATGCTCTTTTTGGGTTTTTTGCCTGAAGCAGCTGATAAGCAACTCTTTTGTAGTTATC
TTGATTT
Found at i:73778 original size:35 final size:35
Alignment explanation
Indices: 73732--73805 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
73722 GGTTCAAATG
73732 CATCAATCTAACCATAAGAACAAAAGGAGAACCGA
1 CATCAATCTAACCATAAGAACAAAAGGAGAACCGA
73767 CATCAATCTAACCATAAGAACAAAAGGAGAACCGA
1 CATCAATCTAACCATAAGAACAAAAGGAGAACCGA
73802 CATC
1 CATC
73806 TGTTTCGACC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.50, C:0.24, G:0.14, T:0.12
Consensus pattern (35 bp):
CATCAATCTAACCATAAGAACAAAAGGAGAACCGA
Found at i:76303 original size:101 final size:101
Alignment explanation
Indices: 76145--76539 Score: 632
Period size: 101 Copynumber: 3.9 Consensus size: 101
76135 CTTCCCTTGG
*
76145 ATCATTCTCTGCAATAATTCCCCCACTGGGGGGCAATCAGGCCGAGCGCCACCTTTCTCGGCCGT
1 ATCATTCTCTGCAATAATTCCCCCACTGGGGGGCAATCAGGCCGAGCGCCATCTTTCTCGGCCGT
*
76210 AAGACCCCATGACGGGCCGTAAGATCGACAGACACT
66 AAGACCCCATGACGGGCCGTAAGATCGGCAGACACT
* * * *
76246 ATCATTCTCTACAATAATCCCCCCACTGGGGGGCAATCAGGCCGAACGCCATCTTTCTCTGCCGT
1 ATCATTCTCTGCAATAATTCCCCCACTGGGGGGCAATCAGGCCGAGCGCCATCTTTCTCGGCCGT
76311 AAGACCCCATGACGGGCCGTAAGATCGGCAGACACT
66 AAGACCCCATGACGGGCCGTAAGATCGGCAGACACT
*
76347 ATCATTCTCTGCAATAATTCCCCCACTGGGGGGCAACCAGGCCGAGCGCCATCTTTCTCGGCCGT
1 ATCATTCTCTGCAATAATTCCCCCACTGGGGGGCAATCAGGCCGAGCGCCATCTTTCTCGGCCGT
* * * * *
76412 AAGACCCCATGACGGGCTGTAAGACCGGCGGACGCC
66 AAGACCCCATGACGGGCCGTAAGATCGGCAGACACT
* *
76448 A-CATTCTCTGCAATAATTTCCCCACT-GGGGGCAATCAGGCCGAGCGCCATCTTTCTCGGCTGT
1 ATCATTCTCTGCAATAATTCCCCCACTGGGGGGCAATCAGGCCGAGCGCCATCTTTCTCGGCCGT
* *
76511 AAGACCCCATGACGGGCTGTAAGACCGGC
66 AAGACCCCATGACGGGCCGTAAGATCGGC
76540 GGACGCCCTC
Statistics
Matches: 275, Mismatches: 19, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
99 64 0.23
100 24 0.09
101 187 0.68
ACGTcount: A:0.23, C:0.33, G:0.24, T:0.19
Consensus pattern (101 bp):
ATCATTCTCTGCAATAATTCCCCCACTGGGGGGCAATCAGGCCGAGCGCCATCTTTCTCGGCCGT
AAGACCCCATGACGGGCCGTAAGATCGGCAGACACT
Found at i:76448 original size:51 final size:51
Alignment explanation
Indices: 76393--76569 Score: 150
Period size: 51 Copynumber: 3.5 Consensus size: 51
76383 CCAGGCCGAG
* *
76393 CGCCATCTTTCTCGGCCGTAAGACCCCATGACGGGCTGTAAGACCGGCGGA
1 CGCCATCATTCTCGGCAGTAAGACCCCATGACGGGCTGTAAGACCGGCGGA
* * ** * * * *
76444 CGCCA-CATTCTCTGCAATAATTTCCCCACTG--GGG--GCAA-TCAGGCCGA
1 CGCCATCATTCTCGGCAGTAA-GACCCCA-TGACGGGCTGTAAGACCGGCGGA
* *
76491 GCGCCATCTTTCTCGGCTGTAAGACCCCATGACGGGCTGTAAGACCGGCGGA
1 -CGCCATCATTCTCGGCAGTAAGACCCCATGACGGGCTGTAAGACCGGCGGA
* * *
76543 CGCCCTCATTCTAGGCAGTAAGTCCCC
1 CGCCATCATTCTCGGCAGTAAGACCCC
76570 TTGTTGGGCA
Statistics
Matches: 92, Mismatches: 25, Indels: 18
0.68 0.19 0.13
Matches are distributed among these distances:
47 8 0.09
48 13 0.14
49 14 0.15
50 14 0.15
51 35 0.38
52 8 0.09
ACGTcount: A:0.20, C:0.34, G:0.26, T:0.20
Consensus pattern (51 bp):
CGCCATCATTCTCGGCAGTAAGACCCCATGACGGGCTGTAAGACCGGCGGA
Found at i:76519 original size:48 final size:48
Alignment explanation
Indices: 76367--76519 Score: 114
Period size: 49 Copynumber: 3.1 Consensus size: 48
76357 GCAATAATTC
* *
76367 CCCCACTGGGGGGCAACCAGGCCGAGCGCCATCTTTCTCGGCCGTAAGA
1 CCCCACT-GGGGGCAAACAGGCCGAGCGCCATCTTTCTCGGCAGTAAGA
* * * * * * **
76416 CCCCA-TGACGGGCTGTAAGACCGGCGGA-CGCCA-CATTCTCTGCAATAATTT
1 CCCCACTG--GGG--GCAA-ACAGGCCGAGCGCCATCTTTCTCGGCAGTAA-GA
* *
76467 CCCCACTGGGGGCAATCAGGCCGAGCGCCATCTTTCTCGGCTGTAAGA
1 CCCCACTGGGGGCAAACAGGCCGAGCGCCATCTTTCTCGGCAGTAAGA
76515 CCCCA
1 CCCCA
76520 TGACGGGCTG
Statistics
Matches: 75, Mismatches: 20, Indels: 19
0.66 0.18 0.17
Matches are distributed among these distances:
47 7 0.09
48 14 0.19
49 19 0.25
50 14 0.19
51 13 0.17
52 8 0.11
ACGTcount: A:0.20, C:0.35, G:0.27, T:0.18
Consensus pattern (48 bp):
CCCCACTGGGGGCAAACAGGCCGAGCGCCATCTTTCTCGGCAGTAAGA
Found at i:76899 original size:26 final size:27
Alignment explanation
Indices: 76870--76924 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
76860 AAAGAAGCCA
76870 TGCGACACT-CCCAGGTGGCAGAACTC
1 TGCGACACTCCCCAGGTGGCAGAACTC
* * *
76896 TGCGGCACTCCCCATGTGGCAGAATTC
1 TGCGACACTCCCCAGGTGGCAGAACTC
76923 TG
1 TG
76925 AAAGAATTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.20, C:0.33, G:0.27, T:0.20
Consensus pattern (27 bp):
TGCGACACTCCCCAGGTGGCAGAACTC
Found at i:76996 original size:56 final size:56
Alignment explanation
Indices: 76901--77056 Score: 217
Period size: 56 Copynumber: 2.8 Consensus size: 56
76891 AACTCTGCGG
*
76901 CACTCCCCATGTGGCAGAATTCTGAAAGAATTAGCGCGCCCAAACG-CATCACGCGA
1 CACTCCCCATGTGGCAGAATTCTGAAAGAAGTAGCGCGCCCAAACGTC-TCACGCGA
* * *
76957 CACTCCCCATGTGGCAGAATTCTGAAAGAAGTAGTGCGCCCGAACGTCTCACGCGG
1 CACTCCCCATGTGGCAGAATTCTGAAAGAAGTAGCGCGCCCAAACGTCTCACGCGA
* *
77013 CACTCCCCATGTTGCAGAACTCT-AAGAGAAGTAGCGCGCACCAA
1 CACTCCCCATGTGGCAGAATTCTGAA-AGAAGTAGCGCGC-CCAA
77057 CGCCCTAACT
Statistics
Matches: 89, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
55 2 0.02
56 83 0.93
57 4 0.04
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (56 bp):
CACTCCCCATGTGGCAGAATTCTGAAAGAAGTAGCGCGCCCAAACGTCTCACGCGA
Found at i:77541 original size:36 final size:37
Alignment explanation
Indices: 77501--77572 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 37
77491 TCGGCAATAT
* *
77501 CAGTCGTGCGCCCTAAGACCATATTGG-CAACCACGA
1 CAGTCGTGCACCCTAAGACCACATTGGTCAACCACGA
* *
77537 CAGTCGTGCACCGTAAGACCACATTGGTCAGCCACG
1 CAGTCGTGCACCCTAAGACCACATTGGTCAACCACG
77573 GCCCCCGAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 24 0.77
37 7 0.23
ACGTcount: A:0.26, C:0.33, G:0.24, T:0.17
Consensus pattern (37 bp):
CAGTCGTGCACCCTAAGACCACATTGGTCAACCACGA
Found at i:77629 original size:117 final size:115
Alignment explanation
Indices: 77387--77637 Score: 376
Period size: 115 Copynumber: 2.2 Consensus size: 115
77377 GACGAAGCCA
* * *
77387 AGTCGTGCGCCGTAAGACCACATTGGCAGCCACGACGGCCGTCCGCCGTAAAACCACATTGGCAG
1 AGTCGTGCGCCGTAAGACCACATTGGCAACCACGACAGCCGTCCACCGTAAAACCACATTGGCAG
* *
77452 CCACGCCCCCCCCGCTCTGTAAGTCCCCAGCGGCATCCCTCGGCAATATC
66 CCACGCCCCCCCAGCGCTGTAAGTCCCCAGCGGCATCCCTCGGCAATATC
* * * * *
77502 AGTCGTGCGCCCTAAGACCATATTGGCAACCACGACAGTCGTGCACCGTAAGACCACATTGGTCA
1 AGTCGTGCGCCGTAAGACCACATTGGCAACCACGACAGCCGTCCACCGTAAAACCACATTGG-CA
* *
77567 GCCACGGCCCCCGAGCGCTGTAAGTCCCCCAGCGGCATCCCTCGGCAATATC
65 GCCACGCCCCCCCAGCGCTGTAAGT-CCCCAGCGGCATCCCTCGGCAATATC
77619 AGTCGTGCGCCGTAAGACC
1 AGTCGTGCGCCGTAAGACC
77638 CCCAGTGGTT
Statistics
Matches: 121, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
115 54 0.45
116 23 0.19
117 44 0.36
ACGTcount: A:0.22, C:0.38, G:0.24, T:0.16
Consensus pattern (115 bp):
AGTCGTGCGCCGTAAGACCACATTGGCAACCACGACAGCCGTCCACCGTAAAACCACATTGGCAG
CCACGCCCCCCCAGCGCTGTAAGTCCCCAGCGGCATCCCTCGGCAATATC
Found at i:77736 original size:65 final size:66
Alignment explanation
Indices: 77616--77864 Score: 360
Period size: 66 Copynumber: 3.8 Consensus size: 66
77606 CCTCGGCAAT
*
77616 ATCA-GTCGTGCGCCGTAAGACCCCCAGTGGTTGGCCCCCCTGCAATCTCCCCGGCGGGACGTTC
1 ATCAGGTCGTGCGCCGTAAGACCCCCAGTGGTTGGCCCCCCTGCAGTCTCCCCGGCGGGACGTTC
77680 A
66 A
* * *
77681 ATCAGGTCGTGTGCCGTAAGACCCCCAGTGGTTGG-CCCCCTACTGTCTCCCCGGCGGGACGTTC
1 ATCAGGTCGTGCGCCGTAAGACCCCCAGTGGTTGGCCCCCCTGCAGTCTCCCCGGCGGGACGTTC
77745 A
66 A
* * * * *
77746 ATCAGGTGGTGCGCCTTAAGACCCTCAGTGGTTGGCCCCCCTGCAGTCTCCCCAGCGGAACGTT-
1 ATCAGGTCGTGCGCCGTAAGACCCCCAGTGGTTGGCCCCCCTGCAGTCTCCCCGGCGGGACGTTC
77810 A
66 A
* * *
77811 AGTCAGGTCGTGTGCCGTAAGACCCCAAGTGGTTGGCCCCCCTGCAGTTTCCCC
1 A-TCAGGTCGTGCGCCGTAAGACCCCCAGTGGTTGGCCCCCCTGCAGTCTCCCC
77865 AACAGAATAA
Statistics
Matches: 163, Mismatches: 18, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
65 64 0.39
66 99 0.61
ACGTcount: A:0.15, C:0.36, G:0.28, T:0.21
Consensus pattern (66 bp):
ATCAGGTCGTGCGCCGTAAGACCCCCAGTGGTTGGCCCCCCTGCAGTCTCCCCGGCGGGACGTTC
A
Found at i:80326 original size:125 final size:126
Alignment explanation
Indices: 80104--80333 Score: 340
Period size: 126 Copynumber: 1.8 Consensus size: 126
80094 GCGACGTGGT
* * * **
80104 GAAAATTACTTGTTCCTGCTCTATAGAGAAAGGAAGGTGAGAGATATGTGGACAATAAATTAGGT
1 GAAAACTACTTGTTCCTGCTCAATAGAGAAAGCAAGGTGAGAGATAAATGGACAATAAATTAGGT
80169 TATTTTGGGGATGATTTCTTCATGATTCAAAGA-GGAAAATCTTTTGATGATTTAAAAAGG
66 TATTTTGGGGATGATTTCTTCATGATTCAAAGAGGGAAAATCTTTTGATGATTTAAAAAGG
* *
80229 GAAAACTACTTAGTTCTTGCTCAATAGAGAGAGCAAGGTGAGAGATAAATGGACAATAAATT-GG
1 GAAAACTACTT-GTTCCTGCTCAATAGAGAAAGCAAGGTGAGAGATAAATGGACAATAAATTAGG
* *
80293 ATT-TTTTGGGGTTGATTTCTTGATGATTCAAAGAGGGAAAA
65 -TTATTTTGGGGATGATTTCTTCATGATTCAAAGAGGGAAAA
80334 CTACTTGGTT
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
125 41 0.44
126 52 0.56
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (126 bp):
GAAAACTACTTGTTCCTGCTCAATAGAGAAAGCAAGGTGAGAGATAAATGGACAATAAATTAGGT
TATTTTGGGGATGATTTCTTCATGATTCAAAGAGGGAAAATCTTTTGATGATTTAAAAAGG
Found at i:80398 original size:107 final size:108
Alignment explanation
Indices: 80241--80440 Score: 312
Period size: 107 Copynumber: 1.9 Consensus size: 108
80231 AAACTACTTA
* * * * *
80241 GTTCTTGCTCAATAGAGAGAGCAAGGTGAGAGATAAATGGACAATAAATTGGATT-TTTTGGGGT
1 GTTCTTACTCAATAGAGAGAGCAAGCTAAGAGATAAATGGACAACAAATTGGATTCTTTTGGGAT
80305 TGATTTCTTGATGATTCAAAGAGGGAAAACTACTTGGTTCTTG
66 TGATTTCTTGATGATTCAAAGAGGGAAAACTACTTGGTTCTTG
* * * *
80348 GTTCTTACTCCATAGAGAGAGCAAGCTAAGAGATAAGTGGATAACGAATTGGATTCTTTTGGGAT
1 GTTCTTACTCAATAGAGAGAGCAAGCTAAGAGATAAATGGACAACAAATTGGATTCTTTTGGGAT
80413 TGATTTCTTGATGATTCAAAGAGGGAAA
66 TGATTTCTTGATGATTCAAAGAGGGAAA
80441 TCTTTGTATT
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
107 47 0.57
108 36 0.43
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.32
Consensus pattern (108 bp):
GTTCTTACTCAATAGAGAGAGCAAGCTAAGAGATAAATGGACAACAAATTGGATTCTTTTGGGAT
TGATTTCTTGATGATTCAAAGAGGGAAAACTACTTGGTTCTTG
Found at i:80802 original size:49 final size:48
Alignment explanation
Indices: 80726--80822 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 48
80716 TTGAGCTCAT
* *
80726 GCTAAAAATGTGCAAATTCGATTTTTTTAAAAAT-ATTTAATCAAGCTTA
1 GCTAAAAATGTGCAAATTCGATATTTTT--AAATGATATAATCAAGCTTA
80775 GCTAAAAATGTGCAAATTCGATATTTTTAAATGATATAATCAAGCTTA
1 GCTAAAAATGTGCAAATTCGATATTTTTAAATGATATAATCAAGCTTA
80823 TCGGTCGAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
47 4 0.09
48 14 0.31
49 27 0.60
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.37
Consensus pattern (48 bp):
GCTAAAAATGTGCAAATTCGATATTTTTAAATGATATAATCAAGCTTA
Found at i:84217 original size:13 final size:13
Alignment explanation
Indices: 84199--84225 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
84189 ATAATTGCGC
84199 TCCATCAAAGACA
1 TCCATCAAAGACA
84212 TCCATCAAAGACA
1 TCCATCAAAGACA
84225 T
1 T
84226 TATAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.30, G:0.07, T:0.19
Consensus pattern (13 bp):
TCCATCAAAGACA
Found at i:86598 original size:22 final size:22
Alignment explanation
Indices: 86567--86627 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
86557 AAAATGGCAT
*
86567 GGCACGGCACGACCCACT-TGCC
1 GGCACAGCACGACCCA-TGTGCC
86589 GGCACAGCACGACCCATGTGCC
1 GGCACAGCACGACCCATGTGCC
* *
86611 GACGCAGCACGACCCAT
1 GGCACAGCACGACCCAT
86628 TTTTAATGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.23, C:0.43, G:0.26, T:0.08
Consensus pattern (22 bp):
GGCACAGCACGACCCATGTGCC
Done.