Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005397.1 Hibiscus syriacus cultivar Beakdansim tig00012370_pilon, 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: 1218879
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:6033 original size:14 final size:14
Alignment explanation
Indices: 6007--6057 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
5997 ATGCCCTCGC
*
6007 ATAG-CTCGCTCGG
1 ATAGCCTCGGTCGG
6020 ATAGCCTCGGTCGG
1 ATAGCCTCGGTCGG
6034 AT-GCTCTCGGTCGG
1 ATAGC-CTCGGTCGG
*
6048 ATGGCCTCGG
1 ATAGCCTCGG
6058 ATGCCTAGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
13 6 0.18
14 26 0.76
15 2 0.06
ACGTcount: A:0.12, C:0.29, G:0.35, T:0.24
Consensus pattern (14 bp):
ATAGCCTCGGTCGG
Found at i:9580 original size:28 final size:28
Alignment explanation
Indices: 9542--9597 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
9532 GATCGTTATC
* * *
9542 GTGTTACCGTGACAGTTCACGGTGTTAA
1 GTGTTAACGTGACAGTCCACAGTGTTAA
*
9570 GTGTTAACGTGACGGTCCACAGTGTTAA
1 GTGTTAACGTGACAGTCCACAGTGTTAA
9598 CGTAGAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (28 bp):
GTGTTAACGTGACAGTCCACAGTGTTAA
Found at i:14476 original size:24 final size:24
Alignment explanation
Indices: 14448--14496 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
14438 AACATAAAAT
* *
14448 AATTGGATGAAACAAAAAAAATGA
1 AATTGAATAAAACAAAAAAAATGA
* *
14472 AATTGAATAAAATAAAATAAATGA
1 AATTGAATAAAACAAAAAAAATGA
14496 A
1 A
14497 GATAAAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.20
Consensus pattern (24 bp):
AATTGAATAAAACAAAAAAAATGA
Found at i:14600 original size:10 final size:11
Alignment explanation
Indices: 14578--14724 Score: 53
Period size: 11 Copynumber: 13.2 Consensus size: 11
14568 GCAAAGAAAC
14578 TAAAAATATAA
1 TAAAAATATAA
14589 TAAAAATA-AA
1 TAAAAATATAA
*
14599 TAAATAGTATACA
1 TAAA-AATATA-A
14612 T--AAA-ATAA
1 TAAAAATATAA
14620 TAAAAATATATA
1 TAAAAATATA-A
14632 TTTATAAAA-AT-A
1 --TA-AAAATATAA
14644 TAAAAATAT-A
1 TAAAAATATAA
* *
14654 TGTATAATATAA
1 T-AAAAATATAA
14666 T-AAAATACTAAA
1 TAAAAATA-T-AA
**
14678 TAGTAATAATAA
1 TAAAAAT-ATAA
14690 TAATAAATA-AA
1 TAA-AAATATAA
14701 TGAAAAATA-AA
1 T-AAAAATATAA
* *
14712 TATACATATAA
1 TAAAAATATAA
14723 TA
1 TA
14725 TTAACTAAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 40
0.67 0.07 0.26
Matches are distributed among these distances:
8 2 0.02
9 7 0.07
10 26 0.25
11 37 0.35
12 15 0.14
13 9 0.09
14 5 0.05
15 4 0.04
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (11 bp):
TAAAAATATAA
Found at i:14631 original size:22 final size:22
Alignment explanation
Indices: 14578--14698 Score: 90
Period size: 22 Copynumber: 5.4 Consensus size: 22
14568 GCAAAGAAAC
14578 TAAAAATATA-ATA-AAAATAA
1 TAAAAATATATATATAAAATAA
* *
14598 -ATAAATAGTATACATAAAATAA
1 TAAAAATA-TATATATAAAATAA
14620 TAAAAATATATATTTATAAAA-ATA
1 TAAAAATATATA--TATAAAATA-A
* *
14644 TAAAAATATATGTATAATATAA
1 TAAAAATATATATATAAAATAA
*
14666 T-AAAATACTAAATAGTAATAATAA
1 TAAAAATA-TATATA-TAA-AATAA
14690 TAATAAATA
1 TAA-AAATA
14699 AATGAAAAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
19 6 0.08
20 2 0.03
21 8 0.10
22 23 0.29
23 11 0.14
24 23 0.29
25 1 0.01
26 5 0.06
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAAATATATATATAAAATAA
Found at i:14782 original size:2 final size:2
Alignment explanation
Indices: 14775--14799 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14765 TGAAGTAAGA
14775 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
14800 ACATTGGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20353 original size:35 final size:36
Alignment explanation
Indices: 20313--20393 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 36
20303 AAATTTTTTC
* * * * *
20313 ATTATTTTTA-ATAATATTTAAATTATTTATTTACT
1 ATTATTTTTATAAAAAAATTAAATTATTCATATACT
20348 ATTATTTTTTATAAAAAAATTAAATTATTCATATACT
1 ATTA-TTTTTATAAAAAAATTAAATTATTCATATACT
*
20385 ATTGTTTTT
1 ATTATTTTT
20394 TTAGTACAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
35 4 0.11
36 11 0.29
37 23 0.61
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (36 bp):
ATTATTTTTATAAAAAAATTAAATTATTCATATACT
Found at i:25260 original size:21 final size:22
Alignment explanation
Indices: 25225--25266 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
25215 GATTTGAGCT
*
25225 TAATATATTTATTTAATATATA
1 TAATATATATATTTAATATATA
25247 TAATATA-ATATTTAATATAT
1 TAATATATATATTTAATATAT
25267 TTTGCTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATATATATATTTAATATATA
Found at i:25757 original size:43 final size:43
Alignment explanation
Indices: 25677--25758 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
25667 GATCCTGTTG
* *
25677 TAACCTAACAAGAATTATGGAGGTCCGTCATAGAGTGATATGA
1 TAACCTAACAAGAATTATGGAGGTCCATCATACAGTGATATGA
* *
25720 TAACCTAACAATAATTAT-GAGTGTCCATTATACAGTGAT
1 TAACCTAACAAGAATTATGGAG-GTCCATCATACAGTGAT
25759 GGGCTGAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 3 0.09
43 31 0.91
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (43 bp):
TAACCTAACAAGAATTATGGAGGTCCATCATACAGTGATATGA
Found at i:27748 original size:7 final size:7
Alignment explanation
Indices: 27736--27768 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
27726 GTCAAAGAAA
27736 GTCAACG
1 GTCAACG
27743 GTCAACG
1 GTCAACG
27750 GTC-ACG
1 GTCAACG
27756 GTCAACG
1 GTCAACG
27763 GTCAAC
1 GTCAAC
27769 AGTCGGGTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:27758 original size:13 final size:13
Alignment explanation
Indices: 27740--27766 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27730 AAGAAAGTCA
27740 ACGGTCAACGGTC
1 ACGGTCAACGGTC
27753 ACGGTCAACGGTC
1 ACGGTCAACGGTC
27766 A
1 A
27767 ACAGTCGGGT
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:0.26, C:0.30, G:0.30, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:27803 original size:19 final size:19
Alignment explanation
Indices: 27779--27849 Score: 74
Period size: 19 Copynumber: 3.6 Consensus size: 19
27769 AGTCGGGTCG
27779 GGTCAACCCGGTTCAG-ACC
1 GGTCAA-CCGGTTCAGAACC
27798 GGTCAAACCGGTTC-GAACC
1 GGTC-AACCGGTTCAGAACC
* *
27817 GGTCTAACCGGTTCAAAACT
1 GGTC-AACCGGTTCAGAACC
27837 GGTCAAACCGGTT
1 GGTC-AACCGGTT
27850 TTCCAGCAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
18 1 0.02
19 27 0.60
20 17 0.38
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.20
Consensus pattern (19 bp):
GGTCAACCGGTTCAGAACC
Found at i:27809 original size:9 final size:9
Alignment explanation
Indices: 27779--27848 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
27769 AGTCGGGTCG
*
27779 GGTCAACCC
1 GGTCAAACC
*
27788 GGTTCAGACC
1 GG-TCAAACC
27798 GGTCAAACC
1 GGTCAAACC
*
27807 GGTTCGAACC
1 GG-TCAAACC
*
27817 GGTCTAACC
1 GGTCAAACC
*
27826 GGTTCAAAACT
1 GG-TC-AAACC
27837 GGTCAAACC
1 GGTCAAACC
27846 GGT
1 GGT
27849 TTTCCAGCAG
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
9 25 0.51
10 19 0.39
11 5 0.10
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.19
Consensus pattern (9 bp):
GGTCAAACC
Found at i:35020 original size:7 final size:7
Alignment explanation
Indices: 35008--35046 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
34998 GTCAAAGAAA
35008 GTCAACG
1 GTCAACG
35015 GTCAACG
1 GTCAACG
35022 GTC-ACG
1 GTCAACG
35028 GTCAACG
1 GTCAACG
35035 GTC-ACG
1 GTCAACG
35041 GTCAAC
1 GTCAAC
35047 AGTCGGGTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.26, C:0.31, G:0.28, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:35030 original size:13 final size:13
Alignment explanation
Indices: 35012--35046 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
35002 AAGAAAGTCA
35012 ACGGTCAACGGTC
1 ACGGTCAACGGTC
35025 ACGGTCAACGGTC
1 ACGGTCAACGGTC
35038 ACGGTCAAC
1 ACGGTCAAC
35047 AGTCGGGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.26, C:0.31, G:0.29, T:0.14
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:35111 original size:10 final size:10
Alignment explanation
Indices: 35059--35127 Score: 63
Period size: 9 Copynumber: 7.1 Consensus size: 10
35049 TCGGGTCGGG
*
35059 TCAACCCGGT
1 TCAAACCGGT
*
35069 TCAGACCGG-
1 TCAAACCGGT
35078 TCAAACCGGT
1 TCAAACCGGT
*
35088 TCGAACCGG-
1 TCAAACCGGT
*
35097 TCAAACTGGT
1 TCAAACCGGT
*
35107 TCAAAACTGG-
1 TC-AAACCGGT
35117 TCAAACCGGT
1 TCAAACCGGT
35127 T
1 T
35128 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 21 0.44
10 20 0.42
11 7 0.15
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:35120 original size:20 final size:19
Alignment explanation
Indices: 35057--35127 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
35047 AGTCGGGTCG
* *
35057 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
*
35076 GGTCAAACCGGTTCGAACC
1 GGTCAAACCGGTTCAAACC
* *
35095 GGTCAAACTGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
35115 GGTCAAACCGGTT
1 GGTCAAACCGGTT
35128 TTCCAGCAGC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 29 0.66
20 15 0.34
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:36140 original size:25 final size:26
Alignment explanation
Indices: 36110--36188 Score: 88
Period size: 25 Copynumber: 3.0 Consensus size: 26
36100 ATATTTAAAG
36110 TATTTTTTGTCAAAATAAGTACCTAA
1 TATTTTTTGTCAAAATAAGTACCTAA
* * *
36136 T-TTTTTTGTCACAATAAATACTTAAAA
1 TATTTTTTGTCAAAATAAGTACCT--AA
* *
36163 TATTTTTTGTTAAAATAAGTATCTAA
1 TATTTTTTGTCAAAATAAGTACCTAA
36189 AGTATTCATT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
25 19 0.45
26 3 0.07
27 3 0.07
28 17 0.40
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (26 bp):
TATTTTTTGTCAAAATAAGTACCTAA
Found at i:36189 original size:28 final size:27
Alignment explanation
Indices: 36105--36194 Score: 87
Period size: 28 Copynumber: 3.3 Consensus size: 27
36095 TTTAAATATT
*
36105 TAAAGTATTTTTTGTCAAAATAAGTACC
1 TAAAATATTTTTTGTCAAAATAAGTA-C
* *
36133 T--AAT-TTTTTTGTCACAATAAATAC
1 TAAAATATTTTTTGTCAAAATAAGTAC
*
36157 TTAAAATATTTTTTGTTAAAATAAGTATC
1 -TAAAATATTTTTTGTCAAAATAAGTA-C
*
36186 TAAAGTATT
1 TAAAATATT
36195 CATTTTTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
24 1 0.02
25 18 0.36
26 2 0.04
27 3 0.06
28 25 0.50
29 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (27 bp):
TAAAATATTTTTTGTCAAAATAAGTAC
Found at i:37693 original size:21 final size:21
Alignment explanation
Indices: 37661--37712 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
37651 TTTTTATTAA
37661 AAATATTTTTA-CATTTTAAAC
1 AAATA-TTTTACCATTTTAAAC
37682 AGAATATTTTACCATTTTAAAC
1 A-AATATTTTACCATTTTAAAC
37704 AAA-ATTTTA
1 AAATATTTTA
37713 GATCAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.21
21 8 0.28
22 15 0.52
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (21 bp):
AAATATTTTACCATTTTAAAC
Found at i:38816 original size:18 final size:19
Alignment explanation
Indices: 38780--38817 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
38770 ATCTTATTAA
*
38780 AGTATATTTTATTATATTT
1 AGTATATTTTAGTATATTT
*
38799 AGTATTTTTTAGTA-ATTT
1 AGTATATTTTAGTATATTT
38817 A
1 A
38818 TTTAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (19 bp):
AGTATATTTTAGTATATTT
Found at i:38832 original size:13 final size:14
Alignment explanation
Indices: 38814--38843 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
38804 TTTTTAGTAA
38814 TTTATTTAATT-AT
1 TTTATTTAATTAAT
38827 TTTATTTAATTAAT
1 TTTATTTAATTAAT
38841 TTT
1 TTT
38844 TTTTGCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATTTAATTAAT
Found at i:38846 original size:17 final size:17
Alignment explanation
Indices: 38813--38845 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38803 TTTTTTAGTA
*
38813 ATTTATTTAATTATTTT
1 ATTTAATTAATTATTTT
38830 ATTTAATTAATT-TTTT
1 ATTTAATTAATTATTTT
38846 TTGCAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTAATTAATTATTTT
Found at i:46925 original size:83 final size:85
Alignment explanation
Indices: 46782--46947 Score: 246
Period size: 83 Copynumber: 2.0 Consensus size: 85
46772 TGGTTCCGCA
* * *
46782 ACTCCTTGACAGATGCCAAAGTGAAGTTCCAGTAGGAAACAGCCTTTGAAGATTAGATTAGAATA
1 ACTCCTTGACAAATGCCAAAGTGAAGTTCCAGTAGG-AACAGCCTTTAAAGATTAAATTAGAATA
*
46847 GAGTTGATTGTTCTCTTTACG
65 GAGTAGATTGTTCTCTTTACG
* * *
46868 ACTCCTTGACAAATGGC-ACGTGAAGTTCGAGTAGG-ACAGCCTTTAAAGATTAAATTAGAATAG
1 ACTCCTTGACAAATGCCAAAGTGAAGTTCCAGTAGGAACAGCCTTTAAAGATTAAATTAGAATAG
46931 AGTAGATTGTTCTCTTT
66 AGTAGATTGTTCTCTTT
46948 CGCGTCACTA
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
83 42 0.58
85 16 0.22
86 15 0.21
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (85 bp):
ACTCCTTGACAAATGCCAAAGTGAAGTTCCAGTAGGAACAGCCTTTAAAGATTAAATTAGAATAG
AGTAGATTGTTCTCTTTACG
Found at i:51876 original size:2 final size:2
Alignment explanation
Indices: 51869--51925 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
51859 TAATTTACTA
51869 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51911 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
51926 CTTCAACATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52496 original size:60 final size:60
Alignment explanation
Indices: 52417--52611 Score: 257
Period size: 60 Copynumber: 3.2 Consensus size: 60
52407 TAATAATAAA
* * *
52417 TAAACGAACACGAATAACTTCAAAAATAAATAAATAAATATGGACATGATATTAAAAATT
1 TAAACGAACACGAACAACTTCAAAAATAAATAAATGAATATGAACATGATATTAAAAATT
* * * ** * *
52477 TAAACGACCACAAACAACTTCAAAAATAAATATATGAATATGAAGGTGATTTTTAAAATT
1 TAAACGAACACGAACAACTTCAAAAATAAATAAATGAATATGAACATGATATTAAAAATT
*
52537 TAAACGAACACGAAC-ACTTTCAAAAATAAATAATTGAATATGAACATGATATTAAAAATT
1 TAAACGAACACGAACAAC-TTCAAAAATAAATAAATGAATATGAACATGATATTAAAAATT
* *
52597 TCAACAAACACGAAC
1 TAAACGAACACGAAC
52612 TTAACATGAA
Statistics
Matches: 114, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
59 2 0.02
60 112 0.98
ACGTcount: A:0.53, C:0.13, G:0.09, T:0.25
Consensus pattern (60 bp):
TAAACGAACACGAACAACTTCAAAAATAAATAAATGAATATGAACATGATATTAAAAATT
Found at i:53954 original size:24 final size:24
Alignment explanation
Indices: 53923--53979 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
53913 GTCATTATGG
53923 AAGAAACTGCCCCACTGAAAGTGA
1 AAGAAACTGCCCCACTGAAAGTGA
53947 AAGAAACTGCCCCACTGAAAGTGA
1 AAGAAACTGCCCCACTGAAAGTGA
53971 AAGAAACTG
1 AAGAAACTG
53980 ATTTGAGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (24 bp):
AAGAAACTGCCCCACTGAAAGTGA
Found at i:65812 original size:7 final size:7
Alignment explanation
Indices: 65800--65844 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
65790 CTTTTTAGGA
65800 TTAGGGT
1 TTAGGGT
65807 TTAGGGT
1 TTAGGGT
* *
65814 TTAAGAT
1 TTAGGGT
*
65821 TTAGGAT
1 TTAGGGT
65828 TTAGGGT
1 TTAGGGT
65835 TTAGGGT
1 TTAGGGT
65842 TTA
1 TTA
65845 TGCTTTATGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (7 bp):
TTAGGGT
Found at i:67070 original size:19 final size:19
Alignment explanation
Indices: 67046--67090 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
67036 AGAGTCTTTT
67046 TTTAATAATAAAATTATAA
1 TTTAATAATAAAATTATAA
**
67065 TTTAATCTTAAAATTATAA
1 TTTAATAATAAAATTATAA
*
67084 ATTAATA
1 TTTAATA
67091 TAATAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTAATAATAAAATTATAA
Found at i:73197 original size:13 final size:12
Alignment explanation
Indices: 73166--73190 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
73156 ATTTAGATGA
73166 TATTAAATATTT
1 TATTAAATATTT
73178 TATTAAATATTT
1 TATTAAATATTT
73190 T
1 T
73191 TTTTAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTAAATATTT
Found at i:77490 original size:17 final size:17
Alignment explanation
Indices: 77465--77497 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
77455 GAAATATTAT
*
77465 TATAGTAAAAGATATAA
1 TATAATAAAAGATATAA
77482 TATAATAAAAGATATA
1 TATAATAAAAGATATA
77498 TAGTAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (17 bp):
TATAATAAAAGATATAA
Found at i:77500 original size:31 final size:31
Alignment explanation
Indices: 77465--77523 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
77455 GAAATATTAT
* * *
77465 TATAGTAAAAGATATAATATAATAAAAGATA
1 TATAGTAAAAGATACAATACAAGAAAAGATA
77496 TATAGTAAAAGATACAATACAAGAAAAG
1 TATAGTAAAAGATACAATACAAGAAAAG
77524 GAACGGTACA
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:0.61, C:0.03, G:0.12, T:0.24
Consensus pattern (31 bp):
TATAGTAAAAGATACAATACAAGAAAAGATA
Found at i:77504 original size:14 final size:14
Alignment explanation
Indices: 77465--77509 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
77455 GAAATATTAT
77465 TATAGTAAAAGATATAA
1 TATAGTAAAAG--AT-A
*
77482 TATAATAAAAGATA
1 TATAGTAAAAGATA
77496 TATAGTAAAAGATA
1 TATAGTAAAAGATA
77510 CAATACAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 14 0.54
15 2 0.08
17 10 0.38
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (14 bp):
TATAGTAAAAGATA
Found at i:102235 original size:23 final size:23
Alignment explanation
Indices: 102209--102278 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 23
102199 TACTTGATAT
102209 ATTTGATTTATTTCAAATTTTAA
1 ATTTGATTTATTTCAAATTTTAA
* * *
102232 ATTTG----A-GTCAAATTTAAT
1 ATTTGATTTATTTCAAATTTTAA
102250 ATTTGATTTATTTCAAATTTTAA
1 ATTTGATTTATTTCAAATTTTAA
102273 ATTTGA
1 ATTTGA
102279 GTCAAATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
18 14 0.39
19 1 0.03
22 1 0.03
23 20 0.56
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (23 bp):
ATTTGATTTATTTCAAATTTTAA
Found at i:102252 original size:41 final size:41
Alignment explanation
Indices: 102207--102289 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
102197 TTTACTTGAT
102207 ATATTTGATTTATTTCAAATTTTAAATTTGAGTCAAATTTA
1 ATATTTGATTTATTTCAAATTTTAAATTTGAGTCAAATTTA
102248 ATATTTGATTTATTTCAAATTTTAAATTTGAGTCAAATTTA
1 ATATTTGATTTATTTCAAATTTTAAATTTGAGTCAAATTTA
102289 A
1 A
102290 ATATGTAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (41 bp):
ATATTTGATTTATTTCAAATTTTAAATTTGAGTCAAATTTA
Found at i:105690 original size:2 final size:2
Alignment explanation
Indices: 105595--105671 Score: 131
Period size: 2 Copynumber: 39.5 Consensus size: 2
105585 TTAAATAATT
*
105595 TA TA TA TA -A AA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
105635 TA TA 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 TA TA T
105672 GAGTTTTATT
Statistics
Matches: 72, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
1 2 0.03
2 70 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:111930 original size:23 final size:24
Alignment explanation
Indices: 111897--111942 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
111887 ATCATACCAT
* *
111897 TCAATATAAAGTA-AAATAAATTA
1 TCAATAAAAAGTATAAAAAAATTA
111920 TCAATAAAAAGTATAAAAAAATT
1 TCAATAAAAAGTATAAAAAAATT
111943 TATAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (24 bp):
TCAATAAAAAGTATAAAAAAATTA
Found at i:114386 original size:7 final size:7
Alignment explanation
Indices: 114354--114385 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
114344 GTCACCTTCT
114354 CCTTTTG
1 CCTTTTG
114361 CCTTTTG
1 CCTTTTG
114368 CCTTTTG
1 CCTTTTG
114375 -CTTTTG
1 CCTTTTG
114381 -CTTTT
1 CCTTTT
114386 TTTTTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 11 0.44
7 14 0.56
ACGTcount: A:0.00, C:0.25, G:0.12, T:0.62
Consensus pattern (7 bp):
CCTTTTG
Found at i:128438 original size:18 final size:21
Alignment explanation
Indices: 128415--128457 Score: 65
Period size: 18 Copynumber: 2.2 Consensus size: 21
128405 ATATTATATT
128415 AATAAAAAA-TT-AAA-TTAA
1 AATAAAAAATTTAAAATTTAA
128433 AATAAAAAATTTAAAATTTAA
1 AATAAAAAATTTAAAATTTAA
128454 AATA
1 AATA
128458 TGAAACTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 3 0.14
21 8 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AATAAAAAATTTAAAATTTAA
Found at i:128467 original size:21 final size:21
Alignment explanation
Indices: 128415--128468 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
128405 ATATTATATT
128415 AATAAAAAA-TT-AAA-TTAA
1 AATAAAAAACTTAAAATTTAA
*
128433 AATAAAAAATTTAAAATTTAA
1 AATAAAAAACTTAAAATTTAA
**
128454 AATATGAAACTTAAA
1 AATAAAAAACTTAAA
128469 TCCTAAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.30
19 2 0.07
20 3 0.10
21 16 0.53
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AATAAAAAACTTAAAATTTAA
Found at i:128999 original size:13 final size:13
Alignment explanation
Indices: 128983--129025 Score: 65
Period size: 11 Copynumber: 3.5 Consensus size: 13
128973 CGTTCCGATT
128983 ACCCGATTACCCG
1 ACCCGATTACCCG
128996 ACCCGATTA-CC-
1 ACCCGATTACCCG
129007 ACCCGATT-CCCG
1 ACCCGATTACCCG
129019 ACCCGAT
1 ACCCGAT
129026 AAATATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.36
12 9 0.32
13 9 0.32
ACGTcount: A:0.23, C:0.47, G:0.14, T:0.16
Consensus pattern (13 bp):
ACCCGATTACCCG
Found at i:135286 original size:20 final size:20
Alignment explanation
Indices: 135261--135300 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
135251 TCTTAATGAG
135261 AAAGACAGAAAGAATTCCAT
1 AAAGACAGAAAGAATTCCAT
135281 AAAGACAGAAAGAATTCCAT
1 AAAGACAGAAAGAATTCCAT
135301 CTACTCTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.15, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAGACAGAAAGAATTCCAT
Found at i:138590 original size:52 final size:52
Alignment explanation
Indices: 138491--138591 Score: 159
Period size: 52 Copynumber: 1.9 Consensus size: 52
138481 TACCCCAAAT
*
138491 TTTGGTTAGTGACTAAAACATAAATTTTGAAAGTTTAGTGGCCAAAGTACAA
1 TTTGGTTAGTGACTAAAACATAAATTTTGAAAGTTTAATGGCCAAAGTACAA
* *
138543 TTTGGTTTGTGACTAAAACATAAATTTTGAAAG-TTACATGGCTAAAGTA
1 TTTGGTTAGTGACTAAAACATAAATTTTGAAAGTTTA-ATGGCCAAAGTA
138592 TAAAGTTGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 3 0.07
52 42 0.93
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.35
Consensus pattern (52 bp):
TTTGGTTAGTGACTAAAACATAAATTTTGAAAGTTTAATGGCCAAAGTACAA
Found at i:151568 original size:23 final size:23
Alignment explanation
Indices: 151542--151594 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
151532 GGAATAATTA
*
151542 TGTCTTTATGACATATTTATCTC
1 TGTCTTTATGACACATTTATCTC
151565 TGTCTTTATGACACATTTATCTC
1 TGTCTTTATGACACATTTATCTC
151588 TGTCTTT
1 TGTCTTT
151595 GACATTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.09, T:0.53
Consensus pattern (23 bp):
TGTCTTTATGACACATTTATCTC
Found at i:152866 original size:20 final size:21
Alignment explanation
Indices: 152838--152882 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
152828 TATTGTCAAT
152838 TTATAATGCATTAT-AAACTA
1 TTATAATGCATTATGAAACTA
* *
152858 TTATGATGCATTATGTAACTA
1 TTATAATGCATTATGAAACTA
152879 TTAT
1 TTAT
152883 TAGTTGCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (21 bp):
TTATAATGCATTATGAAACTA
Found at i:156956 original size:76 final size:76
Alignment explanation
Indices: 156830--156982 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
156820 ATTACAAAAA
156830 TTCAATTAAAAAGTTTATCAAACTAATTCATGCATCATGTCATCCACTCATTCGATCGGTTGTCA
1 TTCAATTAAAAAGTTTATCAAACTAATTCATGCATCATGTCATCCACTCATTCGATCGGTTGTCA
156895 TTATATTACTT
66 TTATATTACTT
156906 TTCAATTAAAAAGTTTATCAAACTAATTCATGCATCATGTCATCCACTCATTCGATCGGTTGTCA
1 TTCAATTAAAAAGTTTATCAAACTAATTCATGCATCATGTCATCCACTCATTCGATCGGTTGTCA
156971 TTATATTACTT
66 TTATATTACTT
156982 T
1 T
156983 GATTTATGCA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (76 bp):
TTCAATTAAAAAGTTTATCAAACTAATTCATGCATCATGTCATCCACTCATTCGATCGGTTGTCA
TTATATTACTT
Found at i:160781 original size:14 final size:14
Alignment explanation
Indices: 160762--160789 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
160752 AAGTGAAAAA
160762 ATAGTTATATAATT
1 ATAGTTATATAATT
160776 ATAGTTATATAATT
1 ATAGTTATATAATT
160790 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:166167 original size:54 final size:53
Alignment explanation
Indices: 166092--166201 Score: 184
Period size: 54 Copynumber: 2.1 Consensus size: 53
166082 AACGTTTTAA
* *
166092 ATTTAAACCAAAGATCAATGACATTTAGGATAGTTTACCCTATATTCTAAATG
1 ATTTAAACCAAAGATCAATGACATTTAGGATAGTGTACCCTATAATCTAAATG
*
166145 ATTTCAAACCAAAGATCAATGACATTTGGGATAGTGTACCCTATAATCTAAATG
1 ATTT-AAACCAAAGATCAATGACATTTAGGATAGTGTACCCTATAATCTAAATG
166199 ATT
1 ATT
166202 CCTTACTATG
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
53 4 0.08
54 49 0.92
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (53 bp):
ATTTAAACCAAAGATCAATGACATTTAGGATAGTGTACCCTATAATCTAAATG
Found at i:171516 original size:3 final size:3
Alignment explanation
Indices: 171508--171533 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
171498 TTACTCCACA
171508 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
171534 AGACTAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:180899 original size:21 final size:20
Alignment explanation
Indices: 180875--180938 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
180865 CCAGATTCGA
180875 AACGCGATAGTCCAAAATCGC
1 AACGCGATA-TCCAAAATCGC
** *
180896 AACGCGAT-TTTAAGATTCGC
1 AACGCGATATCCAA-AATCGC
180916 AACGCGATACTCCAAAATCGC
1 AACGCGATA-TCCAAAATCGC
180937 AA
1 AA
180939 TGCATTTGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 3 0.09
20 13 0.38
21 15 0.44
22 3 0.09
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.19
Consensus pattern (20 bp):
AACGCGATATCCAAAATCGC
Found at i:182572 original size:14 final size:15
Alignment explanation
Indices: 182553--182582 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
182543 AAAAATACTC
182553 AAATTAAATT-ATAA
1 AAATTAAATTAATAA
182567 AAATTAAATTAATAA
1 AAATTAAATTAATAA
182582 A
1 A
182583 TTTCATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTAAATTAATAA
Found at i:186042 original size:200 final size:200
Alignment explanation
Indices: 185699--186069 Score: 593
Period size: 200 Copynumber: 1.9 Consensus size: 200
185689 ATGGATATGA
* * *
185699 CCCTCCAAAGACATGGAAAAACTTGGGAAAATTTTATCATATTCGTGTCAATCACATACTCATAT
1 CCCTCCAAAGACATGGAAAAACGTGGGAAAAATTTATCATATTCGTGTCAATAACATACTCATAT
* * *
185764 TCAAGACTCACAACCAAGTTTGAGTAACATTTTCTGCAACAATAAATGCATACATTATCGTGATT
66 TAAAGACTCACAACCAAGTTTGAGTAACATTTGCTGCAACAATAAATACATACATTATCGTGATT
185829 ATTGGATTTTAGATTTAGTTTCGTAATTCAAAATCGGGACTATTGGCACATATTTACTCCGTTGC
131 ATTGGATTTTAGATTTAGTTTCGTAATTCAAAATCGGGACTATTGGCACATATTTACTCCGTTGC
185894 AAGCG
196 AAGCG
* * *
185899 CCCTCCAAAGACGA-GGAAGAACGTGGGAAAAATTTATCATATTCGTGTTAATAACCTACTCATA
1 CCCTCCAAAGAC-ATGGAAAAACGTGGGAAAAATTTATCATATTCGTGTCAATAACATACTCATA
* *
185963 TTAAATACTCACAACCAAGTTTGAGTAACATTTGCTGCAACAATAAATACGA-ACATTATTGTGA
65 TTAAAGACTCACAACCAAGTTTGAGTAACATTTGCTGCAACAATAAATAC-ATACATTATCGTGA
* *
186027 TTATTGGATTTTAGATTTAGTTTTGTAATTCAGAATCGGGACT
129 TTATTGGATTTTAGATTTAGTTTCGTAATTCAAAATCGGGACT
186070 CTTGCTACAT
Statistics
Matches: 156, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
200 154 0.99
201 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (200 bp):
CCCTCCAAAGACATGGAAAAACGTGGGAAAAATTTATCATATTCGTGTCAATAACATACTCATAT
TAAAGACTCACAACCAAGTTTGAGTAACATTTGCTGCAACAATAAATACATACATTATCGTGATT
ATTGGATTTTAGATTTAGTTTCGTAATTCAAAATCGGGACTATTGGCACATATTTACTCCGTTGC
AAGCG
Found at i:187826 original size:25 final size:25
Alignment explanation
Indices: 187798--187846 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
187788 TGCGATATTA
187798 TTCTATCGGGTTTTATGAACACTTC
1 TTCTATCGGGTTTTATGAACACTTC
187823 TTCTATCGGGTTTTATGAACACTT
1 TTCTATCGGGTTTTATGAACACTT
187847 GCATAATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.45
Consensus pattern (25 bp):
TTCTATCGGGTTTTATGAACACTTC
Found at i:189452 original size:5 final size:5
Alignment explanation
Indices: 189442--189471 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
189432 AAGGAAAATT
*
189442 AAGAA AAGAA AAGAA AAGAA AAGAA TAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
189472 CCCAAAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (5 bp):
AAGAA
Found at i:193455 original size:19 final size:19
Alignment explanation
Indices: 193431--193469 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
193421 TTTTAAGATC
193431 CGACCCGAGTTTGAGGGAT
1 CGACCCGAGTTTGAGGGAT
193450 CGACCCGAGTTTGAGGGAT
1 CGACCCGAGTTTGAGGGAT
193469 C
1 C
193470 AATCATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.23, G:0.36, T:0.21
Consensus pattern (19 bp):
CGACCCGAGTTTGAGGGAT
Found at i:196111 original size:30 final size:30
Alignment explanation
Indices: 196083--196141 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
196073 AATTAGAGAT
*
196083 AGGGATAGAGAAAAGGAAAAGGAAAGAGACA
1 AGGGAAAG-GAAAAGGAAAAGGAAAGAGACA
* *
196114 AGGGAAAGGAAAGGGAAAAGGAGAGAGA
1 AGGGAAAGGAAAAGGAAAAGGAAAGAGA
196142 GAAAATTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.56, C:0.02, G:0.41, T:0.02
Consensus pattern (30 bp):
AGGGAAAGGAAAAGGAAAAGGAAAGAGACA
Found at i:196116 original size:18 final size:18
Alignment explanation
Indices: 196089--196135 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
196079 AGATAGGGAT
196089 AGAGAAAAGGAAAAGGAA
1 AGAGAAAAGGAAAAGGAA
* *
196107 AGAGACAAGGGAAAGGAA
1 AGAGAAAAGGAAAAGGAA
*
196125 AGGGAAAAGGA
1 AGAGAAAAGGA
196136 GAGAGAGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.60, C:0.02, G:0.38, T:0.00
Consensus pattern (18 bp):
AGAGAAAAGGAAAAGGAA
Found at i:196197 original size:18 final size:18
Alignment explanation
Indices: 196152--196200 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
196142 GAAAATTAAG
*
196152 GATCGAGAGAAGGAGAGG
1 GATCGAGAGAAGGAGAGA
** * *
196170 GAAGGTGAGAAGGATAGA
1 GATCGAGAGAAGGAGAGA
196188 GATCGAGAGAAGG
1 GATCGAGAGAAGG
196201 GAAAGGAGAG
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.04, G:0.47, T:0.08
Consensus pattern (18 bp):
GATCGAGAGAAGGAGAGA
Found at i:206168 original size:23 final size:23
Alignment explanation
Indices: 206137--206228 Score: 130
Period size: 23 Copynumber: 4.0 Consensus size: 23
206127 CACCACAGCT
* *
206137 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGTAGTGCCA
* * *
206160 AGTAGAATTACACCGTAGTGCCG
1 CGTAGAATTGCACCGTAGTGCCA
*
206183 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAATTGCACCGTAGTGCCA
206206 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGTAGTGCCA
206229 TATAATAATG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGTAGTGCCA
Found at i:209147 original size:13 final size:13
Alignment explanation
Indices: 209119--209157 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
209109 TGGGCAAGGT
*
209119 TTTGAAAA-ACTA
1 TTTGAAAATAATA
209131 TTTGAAAATAATA
1 TTTGAAAATAATA
*
209144 TTTGTAAATAATA
1 TTTGAAAATAATA
209157 T
1 T
209158 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:215591 original size:45 final size:46
Alignment explanation
Indices: 215503--215593 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
215493 TTGAAAAAGC
* * *
215503 CTGAGTGCATTGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
*
215549 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGTATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
215594 TTCGATGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:218676 original size:17 final size:17
Alignment explanation
Indices: 218650--218683 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
218640 ATCATCCTCC
218650 TTCTAAACGATTTTTTA
1 TTCTAAACGATTTTTTA
*
218667 TTCTACACGATTTTTTA
1 TTCTAAACGATTTTTTA
218684 CCACTATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (17 bp):
TTCTAAACGATTTTTTA
Found at i:220116 original size:19 final size:19
Alignment explanation
Indices: 220075--220118 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
220065 TTTCTAATTG
*
220075 TATTTTTACCTGCATAACG
1 TATTTTTACCTGCATAACA
*
220094 TATTTTTACCTAG-GTAACA
1 TATTTTTACCT-GCATAACA
220113 TATTTT
1 TATTTT
220119 CACTATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (19 bp):
TATTTTTACCTGCATAACA
Found at i:220450 original size:37 final size:39
Alignment explanation
Indices: 220408--220494 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 39
220398 AACTTAACAT
*
220408 TAAATTTTAAACGGT-G-TATTAAAATGAAAC-AAAAAC
1 TAAATTTTAAACGGTGGTTACTAAAATGAAACAAAAAAC
220444 TAAAATTTTAAACGGTGGGGTTACTAAAATGAAACAAAAAAC
1 T-AAATTTTAAACGGT--GGTTACTAAAATGAAACAAAAAAC
220486 TAAATTTTA
1 TAAATTTTA
220495 GGTGTATATT
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
36 1 0.02
37 14 0.32
40 1 0.02
41 21 0.48
42 7 0.16
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.29
Consensus pattern (39 bp):
TAAATTTTAAACGGTGGTTACTAAAATGAAACAAAAAAC
Found at i:220845 original size:6 final size:6
Alignment explanation
Indices: 220834--220858 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
220824 ATCACAGGCG
220834 CAGTCA CAGTCA CAGTCA CAGTCA C
1 CAGTCA CAGTCA CAGTCA CAGTCA C
220859 CTTGCGCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (6 bp):
CAGTCA
Found at i:224655 original size:29 final size:29
Alignment explanation
Indices: 224612--224694 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
224602 CTCACCTAAC
224612 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
224642 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
224671 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
224695 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:229416 original size:29 final size:29
Alignment explanation
Indices: 229373--229455 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
229363 CTCACCTAAC
229373 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
229403 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
229432 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
229456 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:230692 original size:41 final size:42
Alignment explanation
Indices: 230634--230716 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 42
230624 AGCTGCTGCT
230634 TTTGCCAATAAGAAAAAACAGCCATACAAAGAACCATACCAG
1 TTTGCCAATAAGAAAAAACAGCCATACAAAGAACCATACCAG
*
230676 TTTGCCAATAAG-AAAAACAGCCATACCAAGAACCATACCAG
1 TTTGCCAATAAGAAAAAACAGCCATACAAAGAACCATACCAG
230717 CCTACTCAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 28 0.70
42 12 0.30
ACGTcount: A:0.48, C:0.25, G:0.12, T:0.14
Consensus pattern (42 bp):
TTTGCCAATAAGAAAAAACAGCCATACAAAGAACCATACCAG
Found at i:232592 original size:2 final size:2
Alignment explanation
Indices: 232585--232615 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
232575 TCCTTAGGCC
232585 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 T
232616 GTGCGAGGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:233118 original size:32 final size:32
Alignment explanation
Indices: 233077--233137 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
233067 GAAAAGTCTG
*
233077 TTTTAGGTGTATGTGTATGTTTTTATTTACTA
1 TTTTAGGTGTATGTGTATGATTTTATTTACTA
233109 TTTTAGGTGTATGTGTATGATTTTATTTA
1 TTTTAGGTGTATGTGTATGATTTTATTTA
233138 TTGTTTAGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.20, C:0.02, G:0.20, T:0.59
Consensus pattern (32 bp):
TTTTAGGTGTATGTGTATGATTTTATTTACTA
Found at i:234288 original size:64 final size:64
Alignment explanation
Indices: 234218--234340 Score: 178
Period size: 65 Copynumber: 1.9 Consensus size: 64
234208 TTGGACTCTC
* *
234218 AGTGCATCGGTGCACT-A-AGAGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAAGCCT
1 AGTGCATCGATGCA-TGATAGAGTGCATCGATGCATAAAATGCATTCGATG-TTTGAAAAAGCCT
234281 A
64 A
**
234282 AGTGCATCGATGCATGATATTGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAAA
1 AGTGCATCGATGCATGATAGAGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAAA
234341 ATAATTGGTG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
63 1 0.02
64 23 0.43
65 29 0.55
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (64 bp):
AGTGCATCGATGCATGATAGAGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAAAGCCTA
Found at i:234352 original size:65 final size:64
Alignment explanation
Indices: 234238--234381 Score: 177
Period size: 65 Copynumber: 2.2 Consensus size: 64
234228 TGCACTAAGA
* *
234238 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAAGCCTAAGTGCATCGATGCAT-GATAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAA-CATAAGTGCATCGATGCATGGAT-T
*
234302 T
64 G
*
234303 GTGCATCGATGCATAAAATGCATTCGATG-TTTGAAAAA-ATAATTGGTGCATTGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAACATAA---GTGCATCGATGCATGGAT
234366 TG
63 TG
*
234368 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
234382 CACTTTGAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
62 3 0.04
64 9 0.13
65 55 0.79
66 3 0.04
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAACATAAGTGCATCGATGCATGGATTG
Found at i:234380 original size:20 final size:20
Alignment explanation
Indices: 234344--234381 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
234334 TGAAAAAATA
*
234344 ATTGGTGCATTGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
234364 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
234382 CACTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.34, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:236742 original size:82 final size:83
Alignment explanation
Indices: 236610--236809 Score: 276
Period size: 82 Copynumber: 2.4 Consensus size: 83
236600 TAGTGTTTTC
* *
236610 TATTATTTAGAAAATCTCTGTCATGTCATAGTGTTCCATCCCATCCGAAATGAAAGGCGTGTTCC
1 TATTATTTAGAGAATCTCTGTCATGTCATAGTGTTCCATCCCATACGAAATGAAAGGCGTGTTCC
* *
236675 AG-GGGAACGTTTTCCAT
66 AGAGGAAACATTTTCCAT
** * * * *
236692 TATTATTTAGAGAATCTCTGTCATGTCATAGTGTTCTGTCCCATATGAAATGAGAGGTGTGTTCG
1 TATTATTTAGAGAATCTCTGTCATGTCATAGTGTTCCATCCCATACGAAATGAAAGGCGTGTTCC
*
236757 AGAGGAAACATTTTCTAT
66 AGAGGAAACATTTTCCAT
* *
236775 TATTATTTAGAGAATCTCTTTCATGTCATAATGTT
1 TATTATTTAGAGAATCTCTGTCATGTCATAGTGTT
236810 TTATTTAGAG
Statistics
Matches: 104, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
82 59 0.57
83 45 0.43
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (83 bp):
TATTATTTAGAGAATCTCTGTCATGTCATAGTGTTCCATCCCATACGAAATGAAAGGCGTGTTCC
AGAGGAAACATTTTCCAT
Found at i:236905 original size:116 final size:116
Alignment explanation
Indices: 236694--236926 Score: 276
Period size: 116 Copynumber: 2.0 Consensus size: 116
236684 TTTTCCATTA
* ** * *
236694 TTATTTAGAGAATCTCTGTCATGTCATAGTGTTCTGTCCCATATGAAATGAGAGGTGTGTTCGAG
1 TTATTTAGAGAATCTCTATCATGTCATAGTGTTCCATCCCATATGAAATGAGACGCGTGTTCGAG
*
236759 AGGAAACATTTTCTATTATTATTTAGAGAATCTCT-TTCATGTCATAATGTT
66 AGGAAACATTTTCTATTATTATTAAGAGAATCTCTGTT-ATGTCATAATGTT
* * *
236810 TTATTTAGAGAATCTCTATTATGTCATGGTGTTCCATCCCATCTGAAATGAAAGACGCGT-TTC-
1 TTATTTAGAGAATCTCTATCATGTCATAGTGTTCCATCCCATATGAAATG--AGACGCGTGTTCG
* *** *
236873 AGGGGAAGTGTTTTAC-ATTATTATTAATAGAATCTCTGTTATGTCATAATGTT
64 AGAGGAAACATTTT-CTATTATTATTAAGAGAATCTCTGTTATGTCATAATGTT
236926 T
1 T
236927 CATCCCATCC
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
116 87 0.88
117 6 0.06
118 6 0.06
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (116 bp):
TTATTTAGAGAATCTCTATCATGTCATAGTGTTCCATCCCATATGAAATGAGACGCGTGTTCGAG
AGGAAACATTTTCTATTATTATTAAGAGAATCTCTGTTATGTCATAATGTT
Found at i:245165 original size:2 final size:2
Alignment explanation
Indices: 245154--245217 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
245144 TAGTTTACCG
245154 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
245195 TA TA TG TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
245218 TCATATTATT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:245290 original size:22 final size:20
Alignment explanation
Indices: 245265--245304 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
245255 TCATATAAAA
245265 GTAGTATATATTAATATTATTT
1 GTAGTATAT-TT-ATATTATTT
245287 GTAGTATATTTATATTAT
1 GTAGTATATTTATATTAT
245305 ATATTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (20 bp):
GTAGTATATTTATATTATTT
Found at i:250371 original size:24 final size:24
Alignment explanation
Indices: 250344--250395 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
250334 AACGGATATA
*
250344 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
250368 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
250392 TCAA
1 TCAA
250396 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:250396 original size:24 final size:24
Alignment explanation
Indices: 250360--250485 Score: 150
Period size: 24 Copynumber: 5.2 Consensus size: 24
250350 ATCAAAACAT
*
250360 AAATCAGGTCAAGTATCATATCAG
1 AAATCAGGTCAAGTATCAGATCAG
*
250384 AAATCAGGTCAAGTAACAGATCAG
1 AAATCAGGTCAAGTATCAGATCAG
* *
250408 AATTCAAGTCAAGTATCAGATCAG
1 AAATCAGGTCAAGTATCAGATCAG
*
250432 -AATCCATGTC-AGATATCAGATCAG
1 AAAT-CAGGTCAAG-TATCAGATCAG
*
250456 -AATCCATGTCAAGTATCAGATCAG
1 AAAT-CAGGTCAAGTATCAGATCAG
250480 AAATCA
1 AAATCA
250486 AATCGAAAAT
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
23 4 0.04
24 82 0.90
25 5 0.05
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (24 bp):
AAATCAGGTCAAGTATCAGATCAG
Found at i:252955 original size:15 final size:15
Alignment explanation
Indices: 252935--252984 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
252925 GGTCAACTCC
252935 GGTCAACGGTCAACA
1 GGTCAACGGTCAACA
252950 GGTCAACGGTCAACA
1 GGTCAACGGTCAACA
*
252965 GGTCAACGGGTCAACG
1 GGTCAAC-GGTCAACA
252981 GGTC
1 GGTC
252985 GGGTCAACGG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 22 0.67
16 11 0.33
ACGTcount: A:0.28, C:0.26, G:0.32, T:0.14
Consensus pattern (15 bp):
GGTCAACGGTCAACA
Found at i:252976 original size:23 final size:23
Alignment explanation
Indices: 252935--252984 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
252925 GGTCAACTCC
252935 GGTCAAC-GGTCAACAGGTCAAC-
1 GGTCAACAGGTCAAC-GGTCAACA
*
252957 GGTCAACAGGTCAACGGGTCAACG
1 GGTCAACAGGTCAAC-GGTCAACA
252981 GGTC
1 GGTC
252985 GGGTCAACGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 7 0.28
23 14 0.56
24 4 0.16
ACGTcount: A:0.28, C:0.26, G:0.32, T:0.14
Consensus pattern (23 bp):
GGTCAACAGGTCAACGGTCAACA
Found at i:253002 original size:18 final size:18
Alignment explanation
Indices: 252965--253055 Score: 102
Period size: 18 Copynumber: 5.2 Consensus size: 18
252955 ACGGTCAACA
252965 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
252986 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
253004 GGTCAA-----CGGGTCG
1 GGTCAACGGGTCGGGTCG
* *
253017 AGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
253035 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
253053 GGT
1 GGT
253056 TGTGACCGGT
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
13 11 0.18
18 39 0.64
21 11 0.18
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.16
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:253006 original size:31 final size:31
Alignment explanation
Indices: 252971--253051 Score: 144
Period size: 31 Copynumber: 2.6 Consensus size: 31
252961 AACAGGTCAA
252971 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
* *
253002 CGGGTCAACGGGTCGAGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
253033 CGGGTCAACGGGTCGGGTC
1 CGGGTCAACGGGTCGGGTC
253052 GGGTTGTGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.15, C:0.22, G:0.47, T:0.16
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
Found at i:253015 original size:8 final size:8
Alignment explanation
Indices: 252935--252997 Score: 73
Period size: 8 Copynumber: 8.5 Consensus size: 8
252925 GGTCAACTCC
252935 GGTCAAC-
1 GGTCAACG
*
252942 GGTCAACA
1 GGTCAACG
252950 GGTCAAC-
1 GGTCAACG
*
252957 GGTCAACA
1 GGTCAACG
252965 GGTCAACG
1 GGTCAACG
252973 GGTCAACG
1 GGTCAACG
252981 GGT---CG
1 GGTCAACG
252986 GGTCAACG
1 GGTCAACG
252994 GGTC
1 GGTC
252998 GGGTCGGGTC
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
5 5 0.10
7 14 0.28
8 31 0.62
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.14
Consensus pattern (8 bp):
GGTCAACG
Found at i:253051 original size:13 final size:13
Alignment explanation
Indices: 252971--253002 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
252961 AACAGGTCAA
252971 CGGGTCAACGGGT
1 CGGGTCAACGGGT
252984 CGGGTCAACGGGT
1 CGGGTCAACGGGT
252997 CGGGTC
1 CGGGTC
253003 GGGTCAACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:257616 original size:5 final size:5
Alignment explanation
Indices: 257606--257631 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
257596 TGACTTAGAA
257606 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
257632 AATAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:262743 original size:90 final size:90
Alignment explanation
Indices: 262580--262757 Score: 275
Period size: 90 Copynumber: 2.0 Consensus size: 90
262570 TAATCCTGAA
* * * * *
262580 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTCAAATAATAAAATCCCTAGTATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTCAAATAAAAAAAACCCTAATATGAT
262645 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
* * *
262670 TATTAAATTCCAATTAATTAAATATATATTTAATTAATTTGAATTAAAAAAAACCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTCAAATAAAAAAAACCCTAATATGAT
*
262735 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
262758 GTGTGTTAGG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTCAAATAAAAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:268575 original size:17 final size:16
Alignment explanation
Indices: 268553--268586 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
268543 TTAAAGGCTA
*
268553 TTTGTACTATTTCTCTC
1 TTTGTAATATTTC-CTC
268570 TTTGTAATATTTCCTC
1 TTTGTAATATTTCCTC
268586 T
1 T
268587 ACTAGTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.15, C:0.21, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTGTAATATTTCCTC
Found at i:275113 original size:40 final size:40
Alignment explanation
Indices: 275056--275140 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
275046 AGTATAGCGT
275056 TTTTTACTTGTAATCTGCCTAAATGTAAATGATTTGGTTA
1 TTTTTACTTGTAATCTGCCTAAATGTAAATGATTTGGTTA
* *
275096 TTTTTACTTTTATTCTGCCTAAATGTAAATGATTTGGTTA
1 TTTTTACTTGTAATCTGCCTAAATGTAAATGATTTGGTTA
275136 TTTTT
1 TTTTT
275141 CACATGAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.25, C:0.09, G:0.13, T:0.53
Consensus pattern (40 bp):
TTTTTACTTGTAATCTGCCTAAATGTAAATGATTTGGTTA
Found at i:282505 original size:35 final size:34
Alignment explanation
Indices: 282444--282552 Score: 148
Period size: 35 Copynumber: 3.1 Consensus size: 34
282434 GTATTGTTAA
282444 AAAATGGTTTTCAAATTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAATTTGGTAAATGTTTCTTTG
282478 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAA-TTTGGTAAATGTTTCTTTG
* * *
282513 AAAAATAGTTTCTCAAAATTTGGTAGATGTTT-GTTG
1 -AAAATGGTTT-TC-AAATTTGGTAAATGTTTCTTTG
282549 AAAA
1 AAAA
282553 ATGATAATGG
Statistics
Matches: 68, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
34 15 0.22
35 23 0.34
36 12 0.18
37 15 0.22
38 3 0.04
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (34 bp):
AAAATGGTTTTCAAATTTGGTAAATGTTTCTTTG
Found at i:284888 original size:11 final size:11
Alignment explanation
Indices: 284872--284897 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
284862 TGGTCCTCAA
284872 CTTTTATGAAT
1 CTTTTATGAAT
284883 CTTTTATGAAT
1 CTTTTATGAAT
284894 CTTT
1 CTTT
284898 GAAAAGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.58
Consensus pattern (11 bp):
CTTTTATGAAT
Found at i:288840 original size:23 final size:23
Alignment explanation
Indices: 288791--288840 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
288781 AAAGACAAAA
*
288791 GAAAGCATGACACAAAGGAATAT
1 GAAAGCATGACACAAAGGAATAC
* * * *
288814 GAAAGCGTGCCACAAATGCATAC
1 GAAAGCATGACACAAAGGAATAC
288837 GAAA
1 GAAA
288841 ATGTGATATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (23 bp):
GAAAGCATGACACAAAGGAATAC
Found at i:293642 original size:60 final size:61
Alignment explanation
Indices: 293572--293734 Score: 186
Period size: 60 Copynumber: 2.7 Consensus size: 61
293562 AATTGGAAGA
* *
293572 TTCAAAAGTTTAGGGACCAATTTAAAATAATAGTCATAATTTGGAAATAAAATTAGAAT-G
1 TTCAAAAGTTTAAGGACCAATTTAAAATAAGAGTCATAATTTGGAAATAAAATTAGAATAG
* * * * * * * * *
293632 TTCAAAAGTTTAAGGACTAATCTAAAGTAAGAGTTATAGTTTGGAGATGAAATTGGAATAT
1 TTCAAAAGTTTAAGGACCAATTTAAAATAAGAGTCATAATTTGGAAATAAAATTAGAATAG
* * *
293693 TTCAAAA-TTTAAGGATCAATTTAAAATGAGACTCATAATTTG
1 TTCAAAAGTTTAAGGACCAATTTAAAATAAGAGTCATAATTTG
293735 AGAACATATA
Statistics
Matches: 83, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
60 76 0.92
61 7 0.08
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.33
Consensus pattern (61 bp):
TTCAAAAGTTTAAGGACCAATTTAAAATAAGAGTCATAATTTGGAAATAAAATTAGAATAG
Found at i:297526 original size:2 final size:2
Alignment explanation
Indices: 297519--297553 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
297509 CTTAATGGTG
297519 TA 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 TA T
297554 TCTTTGTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:300575 original size:2 final size:2
Alignment explanation
Indices: 300568--300609 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
300558 AACAATCTCG
300568 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
300610 GGATAAAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:307775 original size:43 final size:43
Alignment explanation
Indices: 307720--307853 Score: 259
Period size: 43 Copynumber: 3.1 Consensus size: 43
307710 ATCATAGACA
*
307720 CATAATTGATCATTTGATCCTCCAAACTAATGGAGATATAGAG
1 CATAGTTGATCATTTGATCCTCCAAACTAATGGAGATATAGAG
307763 CATAGTTGATCATTTGATCCTCCAAACTAATGGAGATATAGAG
1 CATAGTTGATCATTTGATCCTCCAAACTAATGGAGATATAGAG
307806 CATAGTTGATCATTTGATCCTCCAAACTAATGGAGATATAGAG
1 CATAGTTGATCATTTGATCCTCCAAACTAATGGAGATATAGAG
307849 CATAG
1 CATAG
307854 GTCATTCAAC
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 90 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (43 bp):
CATAGTTGATCATTTGATCCTCCAAACTAATGGAGATATAGAG
Found at i:308368 original size:27 final size:27
Alignment explanation
Indices: 308338--308397 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
308328 GCCTTGCTAA
*
308338 CAACATAGACATCATTATAATCAATTC
1 CAACATAGACATCATTATAATCAATCC
308365 CAACATAGACATCATTATAATCAATCC
1 CAACATAGACATCATTATAATCAATCC
308392 CAACAT
1 CAACAT
308398 TAATTCCAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.45, C:0.25, G:0.03, T:0.27
Consensus pattern (27 bp):
CAACATAGACATCATTATAATCAATCC
Found at i:308414 original size:39 final size:39
Alignment explanation
Indices: 308360--308442 Score: 157
Period size: 39 Copynumber: 2.1 Consensus size: 39
308350 CATTATAATC
*
308360 AATTCCAACATAGACATCATTATAATCAATCCCAACATT
1 AATTCCAACATAGACATCATTATAATCAATCCCAAAATT
308399 AATTCCAACATAGACATCATTATAATCAATCCCAAAATT
1 AATTCCAACATAGACATCATTATAATCAATCCCAAAATT
308438 AATTC
1 AATTC
308443 TAAACTAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (39 bp):
AATTCCAACATAGACATCATTATAATCAATCCCAAAATT
Found at i:310251 original size:29 final size:29
Alignment explanation
Indices: 310209--310265 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
310199 GACCGTTGAC
*
310209 ATGTGTTATTTTAGTAATTAATTCAAAAT
1 ATGTGCTATTTTAGTAATTAATTCAAAAT
*
310238 ATGTGCTATTTTAGTAATTAATTTAAAA
1 ATGTGCTATTTTAGTAATTAATTCAAAA
310266 AGGGTGCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.47
Consensus pattern (29 bp):
ATGTGCTATTTTAGTAATTAATTCAAAAT
Found at i:310283 original size:29 final size:29
Alignment explanation
Indices: 310215--310277 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
310205 TGACATGTGT
*
310215 TATTTTAGTAATTAATTCAAAATATGTGC
1 TATTTTAGTAATTAATTCAAAATAGGTGC
*
310244 TATTTTAGTAATTAATTTAAAA-AGGGTGC
1 TATTTTAGTAATTAATTCAAAATA-GGTGC
310273 TATTT
1 TATTT
310278 CTGTAAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.46
Consensus pattern (29 bp):
TATTTTAGTAATTAATTCAAAATAGGTGC
Found at i:313967 original size:29 final size:29
Alignment explanation
Indices: 313930--314010 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 29
313920 AACACCCTTT
* *
313930 TTTTAAATTAATTACTAAAATAGCACCTA
1 TTTTGAATTAATTACTAAAATAGCAACTA
313959 TTTTGAATTAATTACTAAAATAGCAACTA
1 TTTTGAATTAATTACTAAAATAGCAACTA
*
313988 TTTCGAATTAATTACTAAAATAG
1 TTTTGAATTAATTACTAAAATAG
314011 TACCGGTCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.38
Consensus pattern (29 bp):
TTTTGAATTAATTACTAAAATAGCAACTA
Found at i:315415 original size:34 final size:34
Alignment explanation
Indices: 315368--315439 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
315358 CTTTCCTCAG
315368 TTAT-TTATAACTTTACTTAGATTAATGGGTAAA
1 TTATATTATAACTTTACTTAGATTAATGGGTAAA
*
315401 TTATATTATAACTTTACTTTGATTAATGGGTAAA
1 TTATATTATAACTTTACTTAGATTAATGGGTAAA
315435 TTATA
1 TTATA
315440 CTATTCCTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 4 0.11
34 33 0.89
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (34 bp):
TTATATTATAACTTTACTTAGATTAATGGGTAAA
Found at i:317445 original size:14 final size:14
Alignment explanation
Indices: 317423--317488 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
317413 AAATTTTAAG
* *
317423 TTAGAGTTTAGGGT
1 TTAGGGTTTAGGAT
*
317437 TTAGGGTTTAGAAGT
1 TTAGGGTTTAGGA-T
* *
317452 TATAGAG-TTATGAT
1 T-TAGGGTTTAGGAT
317466 TTAGGGTTTAGGAT
1 TTAGGGTTTAGGAT
317480 TTAGAGGTT
1 TTAG-GGTT
317489 ATGGAGTTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
13 4 0.10
14 22 0.55
15 10 0.25
16 4 0.10
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (14 bp):
TTAGGGTTTAGGAT
Found at i:317521 original size:36 final size:36
Alignment explanation
Indices: 317421--317521 Score: 141
Period size: 36 Copynumber: 2.8 Consensus size: 36
317411 ATAAATTTTA
* *
317421 AGTTA-GAGTTTAGGGTTTAGGGTTTAGAAGTTATAG
1 AGTTATGA-TTTAGGGTTTAGGATTTAGAGGTTATAG
*
317457 AGTTATGATTTAGGGTTTAGGATTTAGAGGTTATGG
1 AGTTATGATTTAGGGTTTAGGATTTAGAGGTTATAG
**
317493 AGTTATGATTTAGGGTTTATAATTTAGAG
1 AGTTATGATTTAGGGTTTAGGATTTAGAG
317522 TTTTAAGTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 57 0.97
37 2 0.03
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.42
Consensus pattern (36 bp):
AGTTATGATTTAGGGTTTAGGATTTAGAGGTTATAG
Found at i:317729 original size:7 final size:7
Alignment explanation
Indices: 317717--317741 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
317707 TTTATCTTGA
317717 GGTTTAG
1 GGTTTAG
317724 GGTTTAG
1 GGTTTAG
317731 GGTTTAG
1 GGTTTAG
317738 GGTT
1 GGTT
317742 GAAGAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:320027 original size:19 final size:19
Alignment explanation
Indices: 320003--320048 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
319993 AGAGCCAGGA
320003 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
320022 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
320041 GTGCATCG
1 GTGCATCG
320049 GTTCATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:321692 original size:23 final size:23
Alignment explanation
Indices: 321637--321694 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
321627 AAATAATTGA
*
321637 AAAACATGCCA-AAAAGCATAAG
1 AAAACATGTCATAAAAGCATAAG
***
321659 AAAATGGGTCATAAAAGCATAAG
1 AAAACATGTCATAAAAGCATAAG
321682 AAAACATGTCATA
1 AAAACATGTCATA
321695 CCGATAAACT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.55, C:0.14, G:0.16, T:0.16
Consensus pattern (23 bp):
AAAACATGTCATAAAAGCATAAG
Found at i:326617 original size:90 final size:90
Alignment explanation
Indices: 326383--326597 Score: 403
Period size: 90 Copynumber: 2.4 Consensus size: 90
326373 CAGCTTAGGT
326383 AAATTTCTAAACCATAGGTTAATACTAACCATTTCTATCAAGGAAGATAGAACACTCACCTAATA
1 AAATTTCTAAACCATAGGTTAATACTAACCATTTCTATCAAGGAAGATAGAACACTCACCTAATA
326448 CATGAACAGAAAAATCAGTTTAGAA
66 CATGAACAGAAAAATCAGTTTAGAA
* * *
326473 AAAATTCTAAACCATAAGTTAATACTAACCATTTCTATCAACGAAGATAGAACACTCACCTAATA
1 AAATTTCTAAACCATAGGTTAATACTAACCATTTCTATCAAGGAAGATAGAACACTCACCTAATA
326538 CATGAACAGAAAAATCAGTTTAGAA
66 CATGAACAGAAAAATCAGTTTAGAA
326563 AAATTTCTAAACCATAGGTTAATACTAACCATTTC
1 AAATTTCTAAACCATAGGTTAATACTAACCATTTC
326598 AGCTTAGGAT
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 120 1.00
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.27
Consensus pattern (90 bp):
AAATTTCTAAACCATAGGTTAATACTAACCATTTCTATCAAGGAAGATAGAACACTCACCTAATA
CATGAACAGAAAAATCAGTTTAGAA
Found at i:329536 original size:32 final size:32
Alignment explanation
Indices: 329500--329561 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
329490 TGCATCCCAA
* * * *
329500 AAAGGTGCATCCTATGTGGCACGCCTCCCCTC
1 AAAGGCGCATCCGACGTGGCACACCTCCCCTC
*
329532 AAAGGCGCGTCCGACGTGGCACACCTCCCC
1 AAAGGCGCATCCGACGTGGCACACCTCCCC
329562 CGGGTTCCCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.19, C:0.40, G:0.24, T:0.16
Consensus pattern (32 bp):
AAAGGCGCATCCGACGTGGCACACCTCCCCTC
Found at i:329743 original size:24 final size:24
Alignment explanation
Indices: 329703--329761 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
329693 TTTTGTTATC
329703 TTTTTATTTAATAAATTTAT-TATTA
1 TTTTTA-TTAATAAATTT-TGTATTA
329728 TTTTTATTACAT-AATTTTGTATTA
1 TTTTTATTA-ATAAATTTTGTATTA
329752 -TTTTATTAAT
1 TTTTTATTAAT
329762 TGATTATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 2 0.06
23 9 0.28
24 13 0.41
25 8 0.25
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTTTATTAATAAATTTTGTATTA
Found at i:334029 original size:14 final size:14
Alignment explanation
Indices: 334010--334042 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
334000 GGTTCGTATT
334010 GAAACGTATTTATG
1 GAAACGTATTTATG
334024 GAAACGTATTTATG
1 GAAACGTATTTATG
334038 GAAAC
1 GAAAC
334043 TTTATCCGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (14 bp):
GAAACGTATTTATG
Found at i:334362 original size:60 final size:59
Alignment explanation
Indices: 334269--334439 Score: 182
Period size: 60 Copynumber: 2.8 Consensus size: 59
334259 GTTTTGTATC
* * * *
334269 GAAGGCATCTCTATACTGAGGTCAAAAAAGCTGGCAGATGAGTGTCTCCCTCT-AAAGCTG
1 GAAGGCATATCTATATTGAGGTCAAAGAAGCTGGCA-ATGAATGTCTCCCTCTGAAA-CTG
* * *
334329 GAAGGCATATCTATATTGAGGTCGAAGAAGCTGGCAAGTGAATGTCTCCCCCTGGAACTG
1 GAAGGCATATCTATATTGAGGTCAAAGAAGCTGGCAA-TGAATGTCTCCCTCTGAAACTG
* * * * * *
334389 GAAGGCGTATCCATGTTGACGTCAAAGAAGTTGACAAATGAATGTCTCCCT
1 GAAGGCATATCTATATTGAGGTCAAAGAAGCTGGC-AATGAATGTCTCCCT
334440 ATTGAACTTG
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
59 1 0.01
60 88 0.95
61 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (59 bp):
GAAGGCATATCTATATTGAGGTCAAAGAAGCTGGCAATGAATGTCTCCCTCTGAAACTG
Found at i:334935 original size:8 final size:8
Alignment explanation
Indices: 334918--334985 Score: 73
Period size: 8 Copynumber: 8.2 Consensus size: 8
334908 ATTTTTAGAA
*
334918 TTTGAAAG
1 TTTGAGAG
334926 TTTGAGAG
1 TTTGAGAG
*
334934 TTTGATAG
1 TTTGAGAG
*
334942 TTTCAGAG
1 TTTGAGAG
*
334950 TTAGAGAG
1 TTTGAGAG
*
334958 TTTGAGAA
1 TTTGAGAG
334966 TTTAAGAGAG
1 TTT--GAGAG
334976 TTTGAGAG
1 TTTGAGAG
334984 TT
1 TT
334986 CGAGCAATTA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
8 42 0.86
10 7 0.14
ACGTcount: A:0.31, C:0.01, G:0.29, T:0.38
Consensus pattern (8 bp):
TTTGAGAG
Found at i:342950 original size:2 final size:2
Alignment explanation
Indices: 342943--342978 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
342933 GACATTGCTT
342943 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
342979 GGCACACACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:347601 original size:28 final size:28
Alignment explanation
Indices: 347569--347636 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
347559 CAAAGGTTGG
* *
347569 CCTCCCTTATATTTTTCAACCTCAGCAT
1 CCTCCCTTATATTTATCAACCTCAACAT
347597 CCTCCCTTATATTTATCAACCTCAACAT
1 CCTCCCTTATATTTATCAACCTCAACAT
347625 CCTCCCTTATAT
1 CCTCCCTTATAT
347637 CTCTCTCATC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.24, C:0.37, G:0.01, T:0.38
Consensus pattern (28 bp):
CCTCCCTTATATTTATCAACCTCAACAT
Found at i:354189 original size:13 final size:13
Alignment explanation
Indices: 354171--354198 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
354161 CCGAGTCAAC
354171 CCGTTGACTTTGA
1 CCGTTGACTTTGA
354184 CCGTTGACTTTGA
1 CCGTTGACTTTGA
354197 CC
1 CC
354199 AAAAAATTTA
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:0.14, C:0.29, G:0.21, T:0.36
Consensus pattern (13 bp):
CCGTTGACTTTGA
Found at i:355653 original size:44 final size:44
Alignment explanation
Indices: 355590--355677 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
355580 TATATGTATT
*
355590 TCAGTTTTGAAAATTTGACAAACAATTAAAATGCAAATTAATTA
1 TCAGTTTTGAAAAATTGACAAACAATTAAAATGCAAATTAATTA
*
355634 TCAGTTTTGAAAAATTGACAAACAATTAAAATGCAAGTTAATTA
1 TCAGTTTTGAAAAATTGACAAACAATTAAAATGCAAATTAATTA
355678 GCATTTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33
Consensus pattern (44 bp):
TCAGTTTTGAAAAATTGACAAACAATTAAAATGCAAATTAATTA
Found at i:355747 original size:12 final size:12
Alignment explanation
Indices: 355730--355761 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
355720 CCAAGTCACG
355730 AAATCATTTATT
1 AAATCATTTATT
*
355742 AAATCAATTATT
1 AAATCATTTATT
355754 AAATCATT
1 AAATCATT
355762 GAATCACTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATCATTTATT
Found at i:357431 original size:3 final size:3
Alignment explanation
Indices: 357423--357550 Score: 220
Period size: 3 Copynumber: 42.7 Consensus size: 3
357413 TTTTTATCCA
* * *
357423 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
357471 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
357519 TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
357551 AATATATTAA
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 117 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:357592 original size:20 final size:19
Alignment explanation
Indices: 357550--357593 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
357540 TATTATTATT
* * *
357550 AAATATATTAAATACATAT
1 AAATATATTAAAAACAAAC
357569 AAATATTATTAAAAACAAAC
1 AAATA-TATTAAAAACAAAC
357589 AAATA
1 AAATA
357594 ATAAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATATATTAAAAACAAAC
Done.