Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013084.1 Corchorus olitorius cultivar O-4 contig13117, 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: 65791
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1578 original size:15 final size:15
Alignment explanation
Indices: 1548--1589 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
1538 TTACTTTGCT
1548 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
1564 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
1579 TTGTTTTCTGT
1 TTGTTTTCTGT
1590 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:7714 original size:15 final size:16
Alignment explanation
Indices: 7684--7722 Score: 71
Period size: 15 Copynumber: 2.5 Consensus size: 16
7674 TTACTTTTTT
7684 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
7700 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
7715 TTGTTTTC
1 TTGTTTTC
7723 CGTCAACCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.13, C:0.08, G:0.13, T:0.67
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:9442 original size:60 final size:60
Alignment explanation
Indices: 9326--9482 Score: 185
Period size: 60 Copynumber: 2.6 Consensus size: 60
9316 TGACACGAAA
* * * *
9326 AACTAAAAAAGACCTGTCTGAGGT-TCGAAACTGAAAGAAGACCAGTCCGTGGTCTATA-TT
1 AACTAAGAATGACCTGTCTAAGGTCT-GAAATTGAAA-AAGACCAGTCCGTGGTCTATACTT
* *
9386 AAACTGAGAATGACCTGTCTAAGGTCTGAAATTGAAAAAGACCAGTCTGTGGTCTATACTT
1 -AACTAAGAATGACCTGTCTAAGGTCTGAAATTGAAAAAGACCAGTCCGTGGTCTATACTT
* * *
9447 ATCTAAGAATGCCCTGTCTTAGGTCTGAAATT-AAAA
1 AACTAAGAATGACCTGTCTAAGGTCTGAAATTGAAAA
9483 CTGAGAAAGA
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
59 4 0.05
60 48 0.57
61 31 0.37
62 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (60 bp):
AACTAAGAATGACCTGTCTAAGGTCTGAAATTGAAAAAGACCAGTCCGTGGTCTATACTT
Found at i:9497 original size:34 final size:34
Alignment explanation
Indices: 9459--9556 Score: 110
Period size: 32 Copynumber: 2.9 Consensus size: 34
9449 CTAAGAATGC
*
9459 CCTGTCTTAGGTCTGAAATTAAAACTGAGAAAGA
1 CCTGTCTAAGGTCTGAAATTAAAACTGAGAAAGA
** * * * **
9493 CCTGTCTGGGGTCTTAAACTGAAA--GTTAAAGA
1 CCTGTCTAAGGTCTGAAATTAAAACTGAGAAAGA
9525 CCTGTCTAAGGTCTGAAATTAAAACTGAGAAA
1 CCTGTCTAAGGTCTGAAATTAAAACTGAGAAA
9557 AGATGACATG
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
32 25 0.52
34 23 0.48
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (34 bp):
CCTGTCTAAGGTCTGAAATTAAAACTGAGAAAGA
Found at i:9598 original size:39 final size:38
Alignment explanation
Indices: 9555--9923 Score: 490
Period size: 39 Copynumber: 9.5 Consensus size: 38
9545 AAAACTGAGA
* * * *
9555 AAAGATGACATGTTTCCACTCAACTTTGAAAAATACTTG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTAC-TG
*
9594 AAAGATGACCTGTTTCCAGTCAACTTTAATAACTACTG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTG
* * *
9632 AAAAGATAACCTGTTTGCAGTCAACTTTGATAAATACTTG
1 -AAAGATGACCTGTTTCCAGTCAACTTTGATAACTAC-TG
9672 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTA-TG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTG
9709 AAAAGATGACCTGTTTCCAGGT-AACTTTTGATAACTACTG
1 -AAAGATGACCTGTTTCCA-GTCAAC-TTTGATAACTACTG
*
9749 AAAAGATGACCTGTTTCCAGTCAACTTTGATAACCACTTG
1 -AAAGATGACCTGTTTCCAGTCAACTTTGATAACTAC-TG
* *
9789 AAAGATGACCTGTTTCCAGTCAACTTTGGTAACTGCTG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTG
* * *
9827 AAAAGGTGACCTGTTTCGAGTCAACTTTGATAACTGCTG
1 -AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTG
* * *
9866 AAAGATGACCTATTTCCAGTCAATTTTGATAACTGCTG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTG
9904 AAAGATGACCTGTTTCCAGT
1 AAAGATGACCTGTTTCCAGT
9924 TGTCGAAACG
Statistics
Matches: 297, Mismatches: 24, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
37 2 0.01
38 78 0.26
39 189 0.64
40 28 0.09
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (38 bp):
AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTG
Found at i:14351 original size:39 final size:38
Alignment explanation
Indices: 14236--14368 Score: 187
Period size: 38 Copynumber: 3.5 Consensus size: 38
14226 GGTGTCTACA
14236 CCAGTCAACTTTGATAACTACTGAAAGATGACATGTTT
1 CCAGTCAACTTTGATAACTACTGAAAGATGACATGTTT
* * *
14274 CCAGTCAA-TCTTGATAACTGCTAAAAGATGACTTGTTT
1 CCAGTCAACT-TTGATAACTACTGAAAGATGACATGTTT
* *
14312 CCAGTCAACTTTGATAAATACTTGAAAGATGACCTGTTT
1 CCAGTCAACTTTGATAACTAC-TGAAAGATGACATGTTT
*
14351 CCAATCAACTTTGATAAC
1 CCAGTCAACTTTGATAAC
14369 CATTTGAAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
37 1 0.01
38 50 0.60
39 32 0.39
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (38 bp):
CCAGTCAACTTTGATAACTACTGAAAGATGACATGTTT
Found at i:14576 original size:53 final size:53
Alignment explanation
Indices: 14392--14769 Score: 311
Period size: 54 Copynumber: 7.2 Consensus size: 53
14382 TTGAACGATT
* * * *
14392 GCACTAGATCACTTGAAGATAAACTTAAACCACTAGAAACATTCCTGACTGACC
1 GCACTGGATCTCTTGAAGATAAACTTAAACCACTATAAAC-TTTCTGACTGACC
* * ** * *
14446 ACACTGGACCGATTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACC
1 GCACTGGATCTCTTGAAGATAAACTTAAACCACTATAAACTTTC-TGACTGACC
* * * *
14500 GCACTTGATCTCTTGAAGATAAACTTGAACCACTATAATCTTTCTGACCGACC
1 GCACTGGATCTCTTGAAGATAAACTTAAACCACTATAAACTTTCTGACTGACC
* * * * *
14553 GCACTGGATCTCTTGAAAATAAACTTAAACCATTATAAGC--T-TGATTGATC
1 GCACTGGATCTCTTGAAGATAAACTTAAACCACTATAAACTTTCTGACTGACC
* * * ** * * *
14603 ACACTGGATCCCTTTGAAGATAAACTTAAACCATTGGAAACTTTCTGGCCGACT
1 GCACTGGATCTC-TTGAAGATAAACTTAAACCACTATAAACTTTCTGACTGACC
* * * *
14657 GTACTGGATCTCTTGAAGATAAACTTAAACCACTGTAAAC--T-TGATTGATC
1 GCACTGGATCTCTTGAAGATAAACTTAAACCACTATAAACTTTCTGACTGACC
** * * * * *
14707 GCACCAGATCCCTTAAAGATAAACTTAAACCA-TTTGAAAGTTTTTGACTGACC
1 GCACTGGATCTCTTGAAGATAAACTTAAACCACTAT-AAACTTTCTGACTGACC
* *
14760 ACACAGGATC
1 GCACTGGATC
14770 ATTAAAGTAA
Statistics
Matches: 255, Mismatches: 60, Indels: 19
0.76 0.18 0.06
Matches are distributed among these distances:
49 2 0.01
50 50 0.20
51 26 0.10
52 1 0.00
53 86 0.34
54 90 0.35
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (53 bp):
GCACTGGATCTCTTGAAGATAAACTTAAACCACTATAAACTTTCTGACTGACC
Found at i:14655 original size:104 final size:103
Alignment explanation
Indices: 14392--14738 Score: 388
Period size: 104 Copynumber: 3.3 Consensus size: 103
14382 TTGAACGATT
* * * * * *
14392 GCACTAGATCACTTGAAGATAAACTTAAACCACTAGAAACATTCCTGACTGACCACACTGGACCG
1 GCACTAGATCCCTTGAAGATAAACTTAAACCACTAGAAAC-TTTCTGACCGACCGCACTGGATCT
* * * *
14457 ATTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACC
65 CTTGAAGATAAACTTAAACCATTATAAA----CTTGATTGATC
* * * * *
14500 GCACTTGATCTCTTGAAGATAAACTTGAACCACTATAATCTTTCTGACCGACCGCACTGGATCTC
1 GCACTAGATCCCTTGAAGATAAACTTAAACCACTAGAAACTTTCTGACCGACCGCACTGGATCTC
* *
14565 TTGAAAATAAACTTAAACCATTATAAGCTTGATTGATC
66 TTGAAGATAAACTTAAACCATTATAAACTTGATTGATC
* * * * * * *
14603 ACACTGGATCCCTTTGAAGATAAACTTAAACCATTGGAAACTTTCTGGCCGACTGTACTGGATCT
1 GCACTAGATCCC-TTGAAGATAAACTTAAACCACTAGAAACTTTCTGACCGACCGCACTGGATCT
* *
14668 CTTGAAGATAAACTTAAACCACTGTAAACTTGATTGATC
65 CTTGAAGATAAACTTAAACCATTATAAACTTGATTGATC
* *
14707 GCACCAGATCCCTTAAAGATAAACTTAAACCA
1 GCACTAGATCCCTTGAAGATAAACTTAAACCA
14739 TTTGAAAGTT
Statistics
Matches: 203, Mismatches: 35, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
103 38 0.19
104 88 0.43
107 42 0.21
108 35 0.17
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (103 bp):
GCACTAGATCCCTTGAAGATAAACTTAAACCACTAGAAACTTTCTGACCGACCGCACTGGATCTC
TTGAAGATAAACTTAAACCATTATAAACTTGATTGATC
Found at i:14825 original size:24 final size:24
Alignment explanation
Indices: 14798--14890 Score: 105
Period size: 24 Copynumber: 3.9 Consensus size: 24
14788 ATTTGAGAAT
*
14798 TGAAGCTTTCAATACTTGAAAAAC
1 TGAAGCTTTGAATACTTGAAAAAC
*
14822 TGAAGCTTTGAATACTTGAAAAAT
1 TGAAGCTTTGAATACTTGAAAAAC
* * * *
14846 TAAAGTTTTGAATAATTGAAGAAC
1 TGAAGCTTTGAATACTTGAAAAAC
* * *
14870 TGAAGCATTGAAGAATTGAAA
1 TGAAGCTTTGAATACTTGAAA
14891 TTGAAGCATT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (24 bp):
TGAAGCTTTGAATACTTGAAAAAC
Found at i:14873 original size:8 final size:8
Alignment explanation
Indices: 14853--14903 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
14843 AATTAAAGTT
*
14853 TTGAATAA
1 TTGAAGAA
14861 TTGAAGAA
1 TTGAAGAA
* *
14869 CTGAAGCA
1 TTGAAGAA
14877 TTGAAGAA
1 TTGAAGAA
14885 TTG-A-AA
1 TTGAAGAA
*
14891 TTGAAGCA
1 TTGAAGAA
14899 TTGAA
1 TTGAA
14904 ATCTTGAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
6 5 0.14
7 2 0.06
8 28 0.80
ACGTcount: A:0.45, C:0.06, G:0.22, T:0.27
Consensus pattern (8 bp):
TTGAAGAA
Found at i:14895 original size:14 final size:14
Alignment explanation
Indices: 14859--14905 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
14849 AGTTTTGAAT
*
14859 AATTGAAGAACTGA
1 AATTGAAGAATTGA
14873 AGCATTGAAGAATTGA
1 A--ATTGAAGAATTGA
*
14889 AATTGAAGCATTGA
1 AATTGAAGAATTGA
14903 AAT
1 AAT
14906 CTTGAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 16 0.55
16 13 0.45
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (14 bp):
AATTGAAGAATTGA
Found at i:14898 original size:22 final size:22
Alignment explanation
Indices: 14870--14917 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
14860 ATTGAAGAAC
14870 TGAAGCATTGAAGA-ATTGAAAT
1 TGAAGCATTGAA-ATATTGAAAT
*
14892 TGAAGCATTGAAATCTTGAAAT
1 TGAAGCATTGAAATATTGAAAT
14914 TGAA
1 TGAA
14918 AAAAGGCCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (22 bp):
TGAAGCATTGAAATATTGAAAT
Found at i:15050 original size:35 final size:35
Alignment explanation
Indices: 14976--15075 Score: 87
Period size: 35 Copynumber: 2.8 Consensus size: 35
14966 TGGGTCAACT
* * * *
14976 TGAAGAAAGATCGCTCTGGATCAATTGAAGTAAAT
1 TGAAGAAAGATCACCCTGGATCAATTGAACTAAAC
* *
15011 TGAAGAATGATCACCCTGGATTAATTGAAACT-AAC
1 TGAAGAAAGATCACCCTGGATCAATTG-AACTAAAC
* *
15046 TGAAGAAA-AACTACCCTGGGTCAACTTGAA
1 TGAAGAAAGATC-ACCCTGGATCAA-TTGAA
15076 GCAAGATCGC
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
34 2 0.04
35 44 0.85
36 6 0.12
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (35 bp):
TGAAGAAAGATCACCCTGGATCAATTGAACTAAAC
Found at i:15066 original size:96 final size:96
Alignment explanation
Indices: 14925--15230 Score: 434
Period size: 96 Copynumber: 3.2 Consensus size: 96
14915 GAAAAAAGGC
* * * *
14925 CACCCTTGATCATTCTGAAA-TAAATCGAAGAAAGACCACCTTGGGTCAACTTGAAGAAAGATCG
1 CACCCTGGATCAAT-TGAAACTAACT-GAAGAAAGACCACCCTGGGTCAACTTGAAGAAAGATCG
* *
14989 CTCTGGATCAATTGAAGTAAATTGAAGAATGAT
64 CTCTGGATCGATTGAAGTAAACTGAAGAATGAT
* * * *
15022 CACCCTGGATTAATTGAAACTAACTGAAGAAAAACTACCCTGGGTCAACTTGAAGCAAGATCGCT
1 CACCCTGGATCAATTGAAACTAACTGAAGAAAGACCACCCTGGGTCAACTTGAAGAAAGATCGCT
* *
15087 ATGGACCGATTGAAGTAAACTGAAGAATGAT
66 CTGGATCGATTGAAGTAAACTGAAGAATGAT
* * * * *
15118 CGCCCTGGATCAATTGAAACTAACTGAAGATAGACCGCCCTGGGTCAACTTTAAGTAAGATCGCT
1 CACCCTGGATCAATTGAAACTAACTGAAGAAAGACCACCCTGGGTCAACTTGAAGAAAGATCGCT
15183 CTGGATCGATTGAAGTAAACTGAAGAATGAT
66 CTGGATCGATTGAAGTAAACTGAAGAATGAT
15214 CACCCTGGATCAATTGA
1 CACCCTGGATCAATTGA
15231 GCTGTTTGAA
Statistics
Matches: 185, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
96 170 0.92
97 15 0.08
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (96 bp):
CACCCTGGATCAATTGAAACTAACTGAAGAAAGACCACCCTGGGTCAACTTGAAGAAAGATCGCT
CTGGATCGATTGAAGTAAACTGAAGAATGAT
Found at i:15134 original size:35 final size:34
Alignment explanation
Indices: 15095--15230 Score: 94
Period size: 35 Copynumber: 4.1 Consensus size: 34
15085 CTATGGACCG
15095 ATTGAAGTAAACTGAAGAATGATCGCCCTGGATCA
1 ATTGAAGT-AACTGAAGAATGATCGCCCTGGATCA
* * *
15130 ATTGAAACTAACTGAAG-ATAGACCGCCCTGGGTCA
1 ATTG-AAGTAACTGAAGAAT-GATCGCCCTGGATCA
* * *
15165 ACTT----TAA--G--TAA-GATCGCTCTGGATCG
1 A-TTGAAGTAACTGAAGAATGATCGCCCTGGATCA
*
15191 ATTGAAGTAAACTGAAGAATGATCACCCTGGATCA
1 ATTGAAGT-AACTGAAGAATGATCGCCCTGGATCA
15226 ATTGA
1 ATTGA
15231 GCTGTTTGAA
Statistics
Matches: 75, Mismatches: 12, Indels: 28
0.65 0.10 0.24
Matches are distributed among these distances:
25 2 0.03
26 12 0.16
28 1 0.01
29 2 0.03
30 2 0.03
31 3 0.04
32 1 0.01
34 4 0.05
35 43 0.57
36 5 0.07
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.24
Consensus pattern (34 bp):
ATTGAAGTAACTGAAGAATGATCGCCCTGGATCA
Found at i:16284 original size:6 final size:6
Alignment explanation
Indices: 16259--16305 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
16249 GAGCTTTATA
* *
16259 TTTT-T TTTTGT TTGTTCT TTTTCT TTTTCAT TTCTCT TTTTCT TTTT
1 TTTTCT TTTTCT TT-TTCT TTTTCT TTTTC-T TTTTCT TTTTCT TTTT
16306 TCTCCCTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
5 4 0.11
6 22 0.61
7 10 0.28
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:17005 original size:13 final size:14
Alignment explanation
Indices: 16983--17032 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
16973 CTCAAAAACC
16983 TTTTGAAAACTCAT
1 TTTTGAAAACTCAT
*
16997 TTTTG-AAAC-CTT
1 TTTTGAAAACTCAT
17009 TTCTTGAAAACAT-AT
1 TT-TTGAAAAC-TCAT
17024 TTTTGAAAA
1 TTTTGAAAA
17033 ACCTCTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
12 4 0.13
13 7 0.23
14 16 0.53
15 3 0.10
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (14 bp):
TTTTGAAAACTCAT
Found at i:17578 original size:48 final size:48
Alignment explanation
Indices: 17516--17608 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
17506 TCTTATCTTA
17516 TTTTTTTGTTCAAAACACAATTGTTTATTCAAAAGAATCTAGTTTATC
1 TTTTTTTGTTCAAAACACAATTGTTTATTCAAAAGAATCTAGTTTATC
* * *
17564 TTTTTTTTTTCAAAACACACTTGTTTATTCAAAAGAATCTTGTTT
1 TTTTTTTGTTCAAAACACAATTGTTTATTCAAAAGAATCTAGTTT
17609 TGCTCATTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (48 bp):
TTTTTTTGTTCAAAACACAATTGTTTATTCAAAAGAATCTAGTTTATC
Found at i:18883 original size:19 final size:18
Alignment explanation
Indices: 18859--18894 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18849 TGAAGACTTA
18859 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
18878 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
18895 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Found at i:23731 original size:22 final size:22
Alignment explanation
Indices: 23706--23751 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
23696 TAGAATTTGA
23706 TTGTTTTTGGATTAATCTTATT
1 TTGTTTTTGGATTAATCTTATT
23728 TTGTTTTTGGATTAATCTTATT
1 TTGTTTTTGGATTAATCTTATT
23750 TT
1 TT
23752 CCCAAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.04, G:0.13, T:0.65
Consensus pattern (22 bp):
TTGTTTTTGGATTAATCTTATT
Found at i:27897 original size:52 final size:52
Alignment explanation
Indices: 27832--28020 Score: 315
Period size: 52 Copynumber: 3.6 Consensus size: 52
27822 ATTGAAAACT
*
27832 AAAACCTGATGGGAACTTTCTCAATTTGAAAAAGAGCTAAATTGAATACTTTG
1 AAAA-CTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
* * *
27885 AAAACTGATGGGAACTCTCCCAATTGGAAAAAGAGCTAAATCGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
27937 AAAACTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
*
27989 AAGACTTGATGGGAACTTTCCCAATTTGAAAA
1 AAAAC-TGATGGGAACTTTCCCAATTTGAAAA
28021 CTTAAAAACT
Statistics
Matches: 127, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
52 97 0.76
53 30 0.24
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (52 bp):
AAAACTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
Found at i:28032 original size:36 final size:37
Alignment explanation
Indices: 27992--28063 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 37
27982 TACTTTGAAG
27992 ACTTGATGGGAACTTTCCCAATTTG-AAAACTTAAAA
1 ACTTGATGGGAACTTTCCCAATTTGAAAAACTTAAAA
*
28028 ACTTGGTGGGAACTTTCCCAATTTGAAAAACTTAAA
1 ACTTGATGGGAACTTTCCCAATTTGAAAAACTTAAA
28064 TTGATGAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 24 0.71
37 10 0.29
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Consensus pattern (37 bp):
ACTTGATGGGAACTTTCCCAATTTGAAAAACTTAAAA
Found at i:28099 original size:18 final size:18
Alignment explanation
Indices: 28076--28111 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
28066 GATGAAATAC
*
28076 TTTTTTTGATTTTTGAAA
1 TTTTTTGGATTTTTGAAA
28094 TTTTTTGGATTTTTGAAA
1 TTTTTTGGATTTTTGAAA
28112 ACTTTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.14, T:0.64
Consensus pattern (18 bp):
TTTTTTGGATTTTTGAAA
Found at i:28117 original size:18 final size:18
Alignment explanation
Indices: 28078--28117 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28068 TGAAATACTT
* **
28078 TTTTTGATTTTTGAAATT
1 TTTTGGATTTTTGAAAAC
28096 TTTTGGATTTTTGAAAAC
1 TTTTGGATTTTTGAAAAC
28114 TTTT
1 TTTT
28118 TTATTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.12, T:0.62
Consensus pattern (18 bp):
TTTTGGATTTTTGAAAAC
Found at i:33117 original size:56 final size:54
Alignment explanation
Indices: 33057--33162 Score: 185
Period size: 56 Copynumber: 1.9 Consensus size: 54
33047 TAAACTCAAA
*
33057 TAGACTATAATTTAAATCAACAATAATTATTAATAGATTATATACACTAAAGTGAG
1 TAGACTATAATTTAAATCAACAATAATTATTAATAG-GT-TATACACTAAAGTGAG
33113 TAGACTATAATTTAAATCAACAATAATTATTAATAGGTTATACACTAAAG
1 TAGACTATAATTTAAATCAACAATAATTATTAATAGGTTATACACTAAAG
33163 ATGCAAATCC
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
54 12 0.24
55 1 0.02
56 36 0.73
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.34
Consensus pattern (54 bp):
TAGACTATAATTTAAATCAACAATAATTATTAATAGGTTATACACTAAAGTGAG
Found at i:44219 original size:25 final size:25
Alignment explanation
Indices: 44185--44258 Score: 121
Period size: 25 Copynumber: 3.0 Consensus size: 25
44175 CAAAGCAATC
*
44185 TTGAGCACTCTCGCCCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
* *
44210 TTGAACACTCTCGATCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
44235 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
44259 CAAACCAATC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.15, C:0.32, G:0.19, T:0.34
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:50344 original size:15 final size:15
Alignment explanation
Indices: 50324--50354 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
50314 GTTAGAAAGA
*
50324 TGGAGAGTAAAATTT
1 TGGAGAGCAAAATTT
50339 TGGAGAGCAAAATTT
1 TGGAGAGCAAAATTT
50354 T
1 T
50355 ATTGTTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (15 bp):
TGGAGAGCAAAATTT
Found at i:55803 original size:23 final size:21
Alignment explanation
Indices: 55771--55818 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
55761 AATAGAAAAA
*
55771 CAAATCAAGGGATTTAATTGTAT
1 CAAATCAAGGG-TTCAATTG-AT
*
55794 CAAATTAAGGGTTCAATTGAT
1 CAAATCAAGGGTTCAATTGAT
55815 CAAA
1 CAAA
55819 GTTAGAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 7 0.30
23 10 0.43
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (21 bp):
CAAATCAAGGGTTCAATTGAT
Found at i:58302 original size:30 final size:30
Alignment explanation
Indices: 58238--58542 Score: 381
Period size: 30 Copynumber: 10.3 Consensus size: 30
58228 ATCTGATGAG
58238 GCAATGATCCTAAACCAGGATT-AAA-AAA
1 GCAATGATCCTAAACCAGGATTAAAATAAA
*
58266 -CAATGATCCTAAACCAGGATTGAAATAAA
1 GCAATGATCCTAAACCAGGATTAAAATAAA
58295 GCAATGATCCTCAAA-CAGGATTAAAATAAA
1 GCAATGATCCT-AAACCAGGATTAAAATAAA
*
58325 GCAATGATCCTCAACCAGGATTAAAATAAA
1 GCAATGATCCTAAACCAGGATTAAAATAAA
* * *
58355 GCAGTGATCCTCAACTAGGATTAAAATAAA
1 GCAATGATCCTAAACCAGGATTAAAATAAA
* * * *
58385 GTAATGATCCTCAACCAGGATTAAATTGAA
1 GCAATGATCCTAAACCAGGATTAAAATAAA
58415 GCAATGATCCTCAAA-CAGGATTAAAATAAA
1 GCAATGATCCT-AAACCAGGATTAAAATAAA
* *
58445 GCAAAGATCCTTAACCAGGATTAAAATAAA
1 GCAATGATCCTAAACCAGGATTAAAATAAA
* *
58475 GCAACGATCCTCAAA-CAGGATTAAAATAAG
1 GCAATGATCCT-AAACCAGGATTAAAATAAA
* *
58505 GCAACGATCCTCAAA-CAGGATTAAAATAAG
1 GCAATGATCCT-AAACCAGGATTAAAATAAA
*
58535 GTAATGAT
1 GCAATGAT
58543 GTAGAATAGT
Statistics
Matches: 249, Mismatches: 20, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
27 21 0.08
28 3 0.01
29 7 0.03
30 211 0.85
31 7 0.03
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (30 bp):
GCAATGATCCTAAACCAGGATTAAAATAAA
Found at i:58352 original size:60 final size:60
Alignment explanation
Indices: 58238--58542 Score: 431
Period size: 60 Copynumber: 5.1 Consensus size: 60
58228 ATCTGATGAG
* *
58238 GCAATGATCCT-AAACCAGGATT-AAA-AAA-CAATGATCCTAAACCAGGATTGAAATAAA
1 GCAATGATCCTCAAA-CAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAA
58295 GCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAA
* * * *
58355 GCAGTGATCCTC-AACTAGGATTAAAATAAAGTAATGATCCTCAACCAGGATTAAATTGAA
1 GCAATGATCCTCAAAC-AGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAA
* *
58415 GCAATGATCCTCAAACAGGATTAAAATAAAGCAAAGATCCTTAACCAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAA
* * * * *
58475 GCAACGATCCTCAAACAGGATTAAAATAAGGCAACGATCCTCAAACAGGATTAAAATAAG
1 GCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAA
*
58535 GTAATGAT
1 GCAATGAT
58543 GTAGAATAGT
Statistics
Matches: 222, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
57 18 0.08
58 6 0.03
59 6 0.03
60 189 0.85
61 3 0.01
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (60 bp):
GCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAA
Found at i:58391 original size:90 final size:90
Alignment explanation
Indices: 58238--58542 Score: 429
Period size: 90 Copynumber: 3.4 Consensus size: 90
58228 ATCTGATGAG
*
58238 GCAATGATCCT-AAACCAGGATT-AAA-AAA-CAATGATCCTAAACCAGGATTGAAATAAAGCAA
1 GCAATGATCCTCAAA-CAGGATTAAAATAAAGCAATGATCCTAAACCAGGATTAAAATAAAGCAA
58299 TGATCCTCAAACAGGATTAAAATAAA
65 TGATCCTCAAACAGGATTAAAATAAA
* * * * *
58325 GCAATGATCCTCAACCAGGATTAAAATAAAGCAGTGATCCTCAACTAGGATTAAAATAAAGTAAT
1 GCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTAAACCAGGATTAAAATAAAGCAAT
* * *
58390 GATCCTCAACCAGGATTAAATTGAA
66 GATCCTCAAACAGGATTAAAATAAA
* * *
58415 GCAATGATCCTCAAACAGGATTAAAATAAAGCAAAGATCCTTAACCAGGATTAAAATAAAGCAAC
1 GCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTAAACCAGGATTAAAATAAAGCAAT
*
58480 GATCCTCAAACAGGATTAAAATAAG
66 GATCCTCAAACAGGATTAAAATAAA
* * *
58505 GCAACGATCCTCAAACAGGATTAAAATAAGGTAATGAT
1 GCAATGATCCTCAAACAGGATTAAAATAAAGCAATGAT
58543 GTAGAATAGT
Statistics
Matches: 190, Mismatches: 24, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
87 18 0.09
88 5 0.03
89 3 0.02
90 164 0.86
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (90 bp):
GCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTAAACCAGGATTAAAATAAAGCAAT
GATCCTCAAACAGGATTAAAATAAA
Found at i:58950 original size:71 final size:70
Alignment explanation
Indices: 58789--59431 Score: 488
Period size: 71 Copynumber: 9.0 Consensus size: 70
58779 AAACTGGAGA
* * * * * * * *
58789 AAAGATCGCCCTGGATCAAAT-GAAT-ATCTTGAAGTAAGATCGCCTTGGATCAATTGAAATGAA
1 AAAGATCGCCCTGGATCAACTAAAATAAAC-TGAAGAAAGATCACCCTGGATCAACTGAAATAAA
58852 TTGAAG
65 TTGAAG
* * * * *
58858 AAAGACCGCCCTGGGTCAACTAAAATAAACTGAAGAAAGAGCACCCTGGGTCAGCT-AAATTAAA
1 AAAGATCGCCCTGGATCAACTAAAATAAACTGAAGAAAGATCACCCTGGATCAACTGAAA-TAAA
58922 TTGAAGG
65 TTGAA-G
* * * * *
58929 AAAGATCGCCATGGATCAACTAAAAT-AACTTGAAGTAAGATCGCCATGGATCAATTGAAATAAA
1 AAAGATCGCCCTGGATCAACTAAAATAAAC-TGAAGAAAGATCACCCTGGATCAACTGAAATAAA
*
58993 CTGAAGG
65 TTGAA-G
* * *
59000 AAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTTGAAATAAA
1 AAAGATCGCCCTGGATCAACTAAAATAAACTGAAGAAAGATCACCCTGGATCAAC-TGAAATAAA
59065 TTGAAG
65 TTGAAG
* * * * * *
59071 AACGGATCGCCCTGGATCAACTAAAACAAACTAAAGAACGGATCGCCCTGGATCAACTAAAATAA
1 AA-AGATCGCCCTGGATCAACTAAAATAAACTGAAGAA-AGATCACCCTGGATCAACTGAAATAA
*
59136 ACTGAAG
64 ATTGAAG
* * * * * *
59143 AAAGGATCGCCCTGGATCAAACTTGAAATAAACTGACGGGAGGATCGCCCTGGATCAA-TTAATA
1 AAA-GATCGCCCTGGATC-AAC-TAAAATAAACTGA-AGAAAGATCACCCTGGATCAACTGAA-A
*
59207 TAAACTGAAG
61 TAAATTGAAG
* * * * * * * *
59217 AAAGGATCGCCCTAGATCAACTGAAATAAACTGAA-TAGGACCATCCTGGGTCAACTGAAATGAA
1 AAA-GATCGCCCTGGATCAACTAAAATAAACTGAAGAAAGATCACCCTGGATCAACTGAAATAAA
*
59281 TTGAAT
65 TTGAAG
** * * * * * * *
59287 AGGGATCGCCCTGGATCAACTGAAGTGAATTGAAGAAAAGATCGCCCTGGACCAACTGACATAAA
1 AAAGATCGCCCTGGATCAACTAAAATAAACTGAAG-AAAGATCACCCTGGATCAACTGAAATAAA
*
59352 CTGAATG
65 TTGAA-G
* * * * * * * * *
59359 AAAAGACCACCCTGGGTAAACTTGAAATAAACTGAAGAACGGATCGCCCTGGGTCAACTGAAATG
1 -AAAGATCGCCCTGGATCAAC-TAAAATAAACTGAAGAA-AGATCACCCTGGATCAACTGAAATA
*
59424 AACTGAAG
63 AATTGAAG
59432 CGTCTGAAAT
Statistics
Matches: 460, Mismatches: 92, Indels: 40
0.78 0.16 0.07
Matches are distributed among these distances:
69 48 0.10
70 56 0.12
71 128 0.28
72 92 0.20
73 40 0.09
74 94 0.20
75 2 0.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (70 bp):
AAAGATCGCCCTGGATCAACTAAAATAAACTGAAGAAAGATCACCCTGGATCAACTGAAATAAAT
TGAAG
Found at i:58952 original size:36 final size:34
Alignment explanation
Indices: 58778--59431 Score: 468
Period size: 36 Copynumber: 18.3 Consensus size: 34
58768 CTGGGTCAAG
* * *
58778 TAAACTGGAGAAAAGATCGCCCTGGATCAAATGAA
1 TAAACTGAAG-AAAGATCGCCCTGGATCAACTAAA
* * * *
58813 T-ATCTTGAAGTAAGATCGCCTTGGATCAATTGAAA
1 TAAAC-TGAAGAAAGATCGCCCTGGATCAACT-AAA
* * * *
58848 TGAATTGAAGAAAGACCGCCCTGGGTCAACTAAAA
1 TAAACTGAAGAAAGATCGCCCTGGATCAACT-AAA
* * * *
58883 TAAACTGAAGAAAGAGCACCCTGGGTCAGCTAAA
1 TAAACTGAAGAAAGATCGCCCTGGATCAACTAAA
* *
58917 TTAAATTGAAGGAAAGATCGCCATGGATCAACTAAA
1 -TAAACTGAA-GAAAGATCGCCCTGGATCAACTAAA
* * *
58953 -ATAACTTGAAGTAAGATCGCCATGGATCAATTGAAA
1 TA-AAC-TGAAGAAAGATCGCCCTGGATCAACT-AAA
58989 TAAACTGAAGGAAAGATCGCCCTGGATCAACTGAAA
1 TAAACTGAA-GAAAGATCGCCCTGGATCAACT-AAA
* * *
59025 TAAACTGAAGAAAGACCACCCTGGGTCAACTTGAAA
1 TAAACTGAAGAAAGATCGCCCTGGATCAAC-T-AAA
* *
59061 TAAATTGAAGAACGGATCGCCCTGGATCAACTAAAA
1 TAAACTGAAGAA-AGATCGCCCTGGATCAACT-AAA
* * *
59097 CAAACTAAAGAACGGATCGCCCTGGATCAACTAAAA
1 TAAACTGAAGAA-AGATCGCCCTGGATCAACT-AAA
59133 TAAACTGAAGAAAGGATCGCCCTGGATCAAACTTGAAA
1 TAAACTGAAGAAA-GATCGCCCTGGATC-AAC-T-AAA
* * * *
59171 TAAACTGACGGGAGGATCGCCCTGGATCAATTAATA
1 TAAACTGA-AGAAAGATCGCCCTGGATCAACTAA-A
*
59207 TAAACTGAAGAAAGGATCGCCCTAGATCAACTGAAA
1 TAAACTGAAGAAA-GATCGCCCTGGATCAACT-AAA
* * * ** *
59243 TAAACTGAA-TAGGACCATCCTGGGTCAACTGAAA
1 TAAACTGAAGAAAGATCGCCCTGGATCAACT-AAA
* * * ** *
59277 TGAATTGAATAGGGATCGCCCTGGATCAACTGAAG
1 TAAACTGAAGAAAGATCGCCCTGGATCAACT-AAA
* * * *
59312 TGAATTGAAGAAAAGATCGCCCTGGACCAACTGACA
1 TAAACTGAAG-AAAGATCGCCCTGGATCAACT-AAA
* * * *
59348 TAAACTGAATGAAAAGACCACCCTGGGTAAACTTGAAA
1 TAAACTGAA-G-AAAGATCGCCCTGGATCAAC-T-AAA
* *
59386 TAAACTGAAGAACGGATCGCCCTGGGTCAACTGAAA
1 TAAACTGAAGAA-AGATCGCCCTGGATCAACT-AAA
*
59422 TGAACTGAAG
1 TAAACTGAAG
59432 CGTCTGAAAT
Statistics
Matches: 504, Mismatches: 91, Indels: 47
0.79 0.14 0.07
Matches are distributed among these distances:
34 48 0.10
35 142 0.28
36 219 0.43
37 54 0.11
38 39 0.08
39 2 0.00
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (34 bp):
TAAACTGAAGAAAGATCGCCCTGGATCAACTAAA
Found at i:59391 original size:179 final size:177
Alignment explanation
Indices: 58786--59431 Score: 621
Period size: 179 Copynumber: 3.6 Consensus size: 177
58776 AGTAAACTGG
* * * * *
58786 AGAAAAGATCGCCCTGGATCAAATG-AAT-ATCTTGAA-GTAAGATCGCCTTGGATCAA-TTGAA
1 AGAAAAGATCGCCCTGGACCAACTGAAATAAAC-TGAAGGAAAGATCGCCCTGGATCAACTTGAA
* * * * * *
58847 ATGAATTGAAGAAAGACCGCCCTGGGTCAACTAAAATAAACTGAAGAAAGAGCACCCTGGGTCAG
65 ATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAGGACCACCCTGGGTCAA
*
58912 CTAAATTAAATTGAAGGAAA-GATCGCCATGGATCAACTAAAATAACTTGA
130 CTAAA-TAAATTGAA-GAAAGGATCGCCCTGGATCAACTAAAATAA-TTGA
* * * *
58962 AG-TAAGATCGCCATGGATCAATTGAAATAAACTGAAGGAAAGATCGCCCTGGATCAAC-TGAAA
1 AGAAAAGATCGCCCTGGACCAACTGAAATAAACTGAAGGAAAGATCGCCCTGGATCAACTTGAAA
* * * * *
59025 TAAACTGAAGAAAGACCACCCTGGGTCAACTTGAAATAAATTGAAGAACGGATCGCCCTGGATCA
66 TAAACTGAAGAAAGACCGCCCTGGGTCAAC-TGAAATAAACTGAAGAA-GGACCACCCTGGGTCA
* * * * *
59090 ACTAAAACAAACTAAAGAACGGATCGCCCTGGATCAACTAAAATAAACTGA
129 ACT-AAATAAATTGAAGAAAGGATCGCCCTGGATCAACTAAAAT-AATTGA
* * * * *
59141 AGAAAGGATCGCCCTGGATCAAACTTGAAATAAACTGACGGGAGGATCGCCCTGGATCAA-TT-A
1 AGAAAAGATCGCCCTGGA-CCAAC-TGAAATAAACTGAAGGAAAGATCGCCCTGGATCAACTTGA
* * * * *
59204 ATATAAACTGAAGAAAGGATCGCCCTAGATCAACTGAAATAAACTGAA-TAGGACCATCCTGGGT
64 A-ATAAACTGAAGAAA-GACCGCCCTGGGTCAACTGAAATAAACTGAAGAAGGACCACCCTGGGT
* * * * *
59268 CAACTGAAATGAATTGAA-TAGGGATCGCCCTGGATCAACTGAAGTGAATTGA
127 CAACT-AAATAAATTGAAGAAAGGATCGCCCTGGATCAACTAAAAT-AATTGA
* * * * * *
59320 AGAAAAGATCGCCCTGGACCAACTGACATAAACTGAATGAAAAGACCACCCTGGGTAAACTTGAA
1 AGAAAAGATCGCCCTGGACCAACTGAAATAAACTGAA-GGAAAGATCGCCCTGGATCAACTTGAA
* * *
59385 ATAAACTGAAGAACGGATCGCCCTGGGTCAACTGAAATGAACTGAAG
65 ATAAACTGAAGAA-AGACCGCCCTGGGTCAACTGAAATAAACTGAAG
59432 CGTCTGAAAT
Statistics
Matches: 383, Mismatches: 67, Indels: 36
0.79 0.14 0.07
Matches are distributed among these distances:
175 19 0.05
176 9 0.02
177 64 0.17
178 36 0.09
179 135 0.35
180 42 0.11
181 5 0.01
182 60 0.16
183 13 0.03
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (177 bp):
AGAAAAGATCGCCCTGGACCAACTGAAATAAACTGAAGGAAAGATCGCCCTGGATCAACTTGAAA
TAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAGGACCACCCTGGGTCAAC
TAAATAAATTGAAGAAAGGATCGCCCTGGATCAACTAAAATAATTGA
Found at i:59392 original size:215 final size:218
Alignment explanation
Indices: 58778--59431 Score: 622
Period size: 215 Copynumber: 3.0 Consensus size: 218
58768 CTGGGTCAAG
* * * * * * * * * *
58778 TAAACTGGAGAAAAGATCGCCCTGGATCAAATG-AAT-ATCTTGAAGTAAGATCGCCTTGGATCA
1 TAAACTGAAGGAAAGATCGCCCTAGATCAACTGAAATAAAC-TGAAGAAAGACCACCCTGGGTCA
* * * * * * * *
58841 A-TTGAAATGAATTGAAGAA-AGACCGCCCTGGGTCAACTAAAATAAACTGAAG-AAAGAGCACC
65 ACTTGAAATAAATTGAAGAACGGATCGCCCTGGATCAACTAAAACAAACTAAAGAAAAGATCGCC
** * * * * * * * *
58903 CTGGGTCAGCTAAATTAAATTGAAGGAAAGATCGCCATGGATC-AAC-TAAAAT-AACTTGAAGT
130 CTGGACCAACTAAAATAAACTGAAGAAAAGACCACCCTGGATCAAACTTGAAATAAAC-TGAAG-
*
58965 AA--GATCGCCATGGATCAATTGAAA
193 AACGGATCGCCCTGGATCAATTGAAA
*
58989 TAAACTGAAGGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAA
1 TAAACTGAAGGAAAGATCGCCCTAGATCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAA
**
59054 CTTGAAATAAATTGAAGAACGGATCGCCCTGGATCAACTAAAACAAACTAAAGAACGGATCGCCC
66 CTTGAAATAAATTGAAGAACGGATCGCCCTGGATCAACTAAAACAAACTAAAGAAAAGATCGCCC
* * * * * *
59119 TGGATCAACTAAAATAAACTGAAGAAAGGATCGCCCTGGATCAAACTTGAAATAAACTGACGGGA
131 TGGACCAACTAAAATAAACTGAAGAAAAGACCACCCTGGATCAAACTTGAAATAAACTGA-AGAA
59184 -GGATCGCCCTGGATCAATT-AATA
195 CGGATCGCCCTGGATCAATTGAA-A
* * *
59207 TAAACTGAA-GAAAGGATCGCCCTAGATCAACTGAAATAAACTGAA-TAGGACCATCCTGGGTCA
1 TAAACTGAAGGAAA-GATCGCCCTAGATCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCA
* * * * *** * *
59270 AC-TGAAATGAATTGAA-TAGGGATCGCCCTGGATCAACTGAAGTGAATTGAAGAAAAGATCGCC
65 ACTTGAAATAAATTGAAGAACGGATCGCCCTGGATCAACTAAAACAAACTAAAGAAAAGATCGCC
* * *
59333 CTGGACCAACTGACATAAACTGAATGAAAAGACCACCCTGGGT-AAACTTGAAATAAACTGAAGA
130 CTGGACCAACTAAAATAAACTGAA-GAAAAGACCACCCTGGATCAAACTTGAAATAAACTGAAGA
* *
59397 ACGGATCGCCCTGGGTCAACTGAAA
194 ACGGATCGCCCTGGATCAATTGAAA
*
59422 TGAACTGAAG
1 TAAACTGAAG
59432 CGTCTGAAAT
Statistics
Matches: 370, Mismatches: 57, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
211 30 0.08
212 22 0.06
213 19 0.05
214 30 0.08
215 144 0.39
216 32 0.09
217 32 0.09
218 61 0.16
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (218 bp):
TAAACTGAAGGAAAGATCGCCCTAGATCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAA
CTTGAAATAAATTGAAGAACGGATCGCCCTGGATCAACTAAAACAAACTAAAGAAAAGATCGCCC
TGGACCAACTAAAATAAACTGAAGAAAAGACCACCCTGGATCAAACTTGAAATAAACTGAAGAAC
GGATCGCCCTGGATCAATTGAAA
Done.