Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000511.1 Kokia drynarioides strain JFW-HI SEQ_111394, 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: 255935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:2508 original size:14 final size:16
Alignment explanation
Indices: 2479--2510 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2469 AGTACATATG
2479 CTCTGTTTTTCTTTTT
1 CTCTGTTTTTCTTTTT
2495 CTCT-TTTTTCTTTTT
1 CTCTGTTTTTCTTTTT
2510 C
1 C
2511 ATTTTAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.75
Consensus pattern (16 bp):
CTCTGTTTTTCTTTTT
Found at i:22290 original size:16 final size:16
Alignment explanation
Indices: 22269--22300 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
22259 TCAAATCCAC
22269 TAAATTTGAACCTTTA
1 TAAATTTGAACCTTTA
22285 TAAATTTGAACCTTTA
1 TAAATTTGAACCTTTA
22301 AGGACAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (16 bp):
TAAATTTGAACCTTTA
Found at i:23211 original size:27 final size:27
Alignment explanation
Indices: 23158--23211 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
23148 CAAAAACTTG
**
23158 TTAAAATTTAATTTATTTCAAGGTTTT
1 TTAAAATTTAATTTATTTCAACCTTTT
*
23185 TTAAAAGTTTATTTTA-TTCAACCTTTT
1 TTAAAA-TTTAATTTATTTCAACCTTTT
23212 GAAAATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.31, C:0.07, G:0.06, T:0.56
Consensus pattern (27 bp):
TTAAAATTTAATTTATTTCAACCTTTT
Found at i:42247 original size:50 final size:51
Alignment explanation
Indices: 42084--42253 Score: 180
Period size: 51 Copynumber: 3.3 Consensus size: 51
42074 CAAAGACATA
** * * * *
42084 TAGTCATCGGACCTCTTGTTCCATATAGGAATTCATATACTCACGAAGACACT
1 TAGTCATCGGACCT-TTAATCTATA-AAGAATTCATTTACTCACGATGACACT
* * * ** *
42137 GAGTCATCGGACCTTTAATCTATCATGAATTCATTTACTCGTGATAACACT
1 TAGTCATCGGACCTTTAATCTATAAAGAATTCATTTACTCACGATGACACT
* *
42188 TAGTCATCGGACCTTTAATCTGTAAAGGATT-ATTTACTCACGATGACACT
1 TAGTCATCGGACCTTTAATCTATAAAGAATTCATTTACTCACGATGACACT
*
42238 TAGTTATCGGACCTTT
1 TAGTCATCGGACCTTT
42254 TCGTTTATAG
Statistics
Matches: 97, Mismatches: 20, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
50 31 0.32
51 47 0.48
52 6 0.06
53 13 0.13
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (51 bp):
TAGTCATCGGACCTTTAATCTATAAAGAATTCATTTACTCACGATGACACT
Found at i:42579 original size:51 final size:51
Alignment explanation
Indices: 42503--42604 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
42493 TTCAATTTAT
*
42503 CATATTAAATCACACAATCAATTATTTAACATAGTCAAACACCTTTTGGTA
1 CATATTAAATCACACAATCAATTATTTAACATAATCAAACACCTTTTGGTA
42554 CATATTAAATCACACAATCAATTATTTAACATAATCAAACACCTTTTGGTA
1 CATATTAAATCACACAATCAATTATTTAACATAATCAAACACCTTTTGGTA
42605 AAATTATGAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (51 bp):
CATATTAAATCACACAATCAATTATTTAACATAATCAAACACCTTTTGGTA
Found at i:55235 original size:45 final size:46
Alignment explanation
Indices: 55184--55274 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 46
55174 AATTCAAAAT
* *
55184 AATTTTCAAAAATTC-AAAATATTT-ATAAAAATTCCAAAATTTATA
1 AATTTTCAAAAATTCTAAAA-ATTTCAAAAAAATTCCAAAAATTATA
*
55229 AATTTTCAAAAATTCTAAAAATTTCAAAAAAATTCTAAAAATTATA
1 AATTTTCAAAAATTCTAAAAATTTCAAAAAAATTCCAAAAATTATA
55275 TAAAGAAGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
45 19 0.46
46 22 0.54
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (46 bp):
AATTTTCAAAAATTCTAAAAATTTCAAAAAAATTCCAAAAATTATA
Found at i:55249 original size:10 final size:10
Alignment explanation
Indices: 55236--55269 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
55226 ATAAATTTTC
55236 AAAAATTCTA
1 AAAAATTCTA
* *
55246 AAAATTTCAA
1 AAAAATTCTA
55256 AAAAATTCTA
1 AAAAATTCTA
55266 AAAA
1 AAAA
55270 TTATATAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAATTCTA
Found at i:55250 original size:9 final size:9
Alignment explanation
Indices: 55191--55271 Score: 51
Period size: 9 Copynumber: 8.8 Consensus size: 9
55181 AATAATTTTC
55191 AAAAATTC-
1 AAAAATTCT
*
55199 AAAATATTTAT
1 AAAA-A-TTCT
55210 AAAAATTC-
1 AAAAATTCT
*
55218 CAAAATT-T
1 AAAAATTCT
* *
55226 ATAAATTTT
1 AAAAATTCT
55235 CAAAAATTCT
1 -AAAAATTCT
*
55245 AAAAATTTCAA
1 AAAAA-TTC-T
55256 AAAAATTCT
1 AAAAATTCT
55265 AAAAATT
1 AAAAATT
55272 ATATAAAGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
8 15 0.27
9 16 0.29
10 16 0.29
11 9 0.16
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAAATTCT
Found at i:55258 original size:18 final size:17
Alignment explanation
Indices: 55191--55258 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 17
55181 AATAATTTTC
55191 AAAAA-TTCAAAATATTT
1 AAAAATTTCAAAA-ATTT
* *
55208 ATAAAAATTCCAAAATTT
1 A-AAAATTTCAAAAATTT
*
55226 ATAAATTTTCAAAAATTCT
1 A-AAAATTTCAAAAATT-T
55245 AAAAATTTCAAAAA
1 AAAAATTTCAAAAA
55259 AATTCTAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
17 1 0.02
18 34 0.79
19 8 0.19
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAAATTTCAAAAATTT
Found at i:55295 original size:9 final size:9
Alignment explanation
Indices: 55159--55297 Score: 50
Period size: 9 Copynumber: 14.4 Consensus size: 9
55149 GATCTTTCTA
*
55159 AAAAAATTAC
1 AAAAAATT-T
*
55169 AAAATAATTC
1 AAAA-AATTT
55179 AAAATAATTTT
1 AAAA-AA-TTT
* *
55190 CAAAAATTC
1 AAAAAATTT
*
55199 AAAATATTT
1 AAAAAATTT
55208 ATAAAAA-TT
1 A-AAAAATTT
**
55217 CCAAAATTT
1 AAAAAATTT
* *
55226 ATAAATTTT
1 AAAAAATTT
*
55235 CAAAAATTCT
1 AAAAAATT-T
55245 -AAAAATTT
1 AAAAAATTT
55253 CAAAAAAATTCT
1 --AAAAAATT-T
55265 -AAAAATTAT
1 AAAAAATT-T
*
55274 ATAAAGAAGTT
1 A-AAA-AATTT
55285 AAAAAATTT
1 AAAAAATTT
55294 AAAA
1 AAAA
55298 GTTTCTAGAA
Statistics
Matches: 99, Mismatches: 18, Indels: 25
0.70 0.13 0.18
Matches are distributed among these distances:
8 5 0.05
9 47 0.47
10 22 0.22
11 21 0.21
12 4 0.04
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.32
Consensus pattern (9 bp):
AAAAAATTT
Found at i:55639 original size:52 final size:52
Alignment explanation
Indices: 55582--55686 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
55572 ATGATAAAAA
55582 AGAATTCATCAACTAGAATTTTTTTACTCAATTCGACTTGATTCAATCAAAC
1 AGAATTCATCAACTAGAATTTTTTTACTCAATTCGACTTGATTCAATCAAAC
55634 AGAATTCATCAACTAGAATTTTTTTACTCAATTCGACTTGATTCAATCAAAC
1 AGAATTCATCAACTAGAATTTTTTTACTCAATTCGACTTGATTCAATCAAAC
55686 A
1 A
55687 CTCATCTCTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (52 bp):
AGAATTCATCAACTAGAATTTTTTTACTCAATTCGACTTGATTCAATCAAAC
Found at i:59725 original size:19 final size:19
Alignment explanation
Indices: 59671--59724 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
59661 ATGTTAAAAT
*
59671 CAAGTTAAAATATTTTATA
1 CAAGTCAAAATATTTTATA
59690 CAAGTCAAAATCATTTTA-A
1 CAAGTCAAAAT-ATTTTATA
*
59709 CAATTCAAAATATTTT
1 CAAGTCAAAATATTTT
59725 TCAAACAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.66
20 6 0.19
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (19 bp):
CAAGTCAAAATATTTTATA
Found at i:80891 original size:83 final size:83
Alignment explanation
Indices: 80752--80917 Score: 332
Period size: 83 Copynumber: 2.0 Consensus size: 83
80742 ACAAGTATAC
80752 GGGTCAGGTTGTAATATAGTTTGTACAACAAAACACTTGGTAGTTGACCGCCACCGAACATACTC
1 GGGTCAGGTTGTAATATAGTTTGTACAACAAAACACTTGGTAGTTGACCGCCACCGAACATACTC
80817 CCGTTTGGGATGTGTTTT
66 CCGTTTGGGATGTGTTTT
80835 GGGTCAGGTTGTAATATAGTTTGTACAACAAAACACTTGGTAGTTGACCGCCACCGAACATACTC
1 GGGTCAGGTTGTAATATAGTTTGTACAACAAAACACTTGGTAGTTGACCGCCACCGAACATACTC
80900 CCGTTTGGGATGTGTTTT
66 CCGTTTGGGATGTGTTTT
80918 CGACTTCCGT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (83 bp):
GGGTCAGGTTGTAATATAGTTTGTACAACAAAACACTTGGTAGTTGACCGCCACCGAACATACTC
CCGTTTGGGATGTGTTTT
Found at i:81559 original size:26 final size:26
Alignment explanation
Indices: 81510--81564 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
81500 TATTGCGCCT
* *
81510 AGAATTGTCGCTGTAGGAACCTGTTC
1 AGAATTATCGCTGTAGGAACCTGTCC
*
81536 AGAATTATCGCTGT-GTGAATCTGTCC
1 AGAATTATCGCTGTAG-GAACCTGTCC
81562 AGA
1 AGA
81565 GTTGTCGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (26 bp):
AGAATTATCGCTGTAGGAACCTGTCC
Found at i:89667 original size:24 final size:24
Alignment explanation
Indices: 89640--89694 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
89630 ACAGAAGTGG
*
89640 AAGAAGTGGAAGAAGAA-GAAGGAA
1 AAGAAGTAGAA-AAGAAGGAAGGAA
* *
89664 AAGAAGAAGAAAGGAAGGAAGGAA
1 AAGAAGTAGAAAAGAAGGAAGGAA
89688 AAGAAGT
1 AAGAAGT
89695 CGAGGCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.60, C:0.00, G:0.36, T:0.04
Consensus pattern (24 bp):
AAGAAGTAGAAAAGAAGGAAGGAA
Found at i:97115 original size:36 final size:36
Alignment explanation
Indices: 97068--97140 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
97058 TTGATGAAGG
*
97068 GTAAGGGAAAATTGTCCTTCCTAGTTGCCTTGTTAA
1 GTAAGGGAAAATGGTCCTTCCTAGTTGCCTTGTTAA
97104 GTAAGGGAAAATGGTCCTTCCTAGTTGCCTTGTTAA
1 GTAAGGGAAAATGGTCCTTCCTAGTTGCCTTGTTAA
97140 G
1 G
97141 CATTTGGTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (36 bp):
GTAAGGGAAAATGGTCCTTCCTAGTTGCCTTGTTAA
Found at i:101634 original size:115 final size:115
Alignment explanation
Indices: 101432--101659 Score: 429
Period size: 115 Copynumber: 2.0 Consensus size: 115
101422 CATTGTGTAC
101432 CTGAAAAAGAAATGATGTCAATCCTGCGACACTGCCATGATGCCCCTTATGGAGGTCATTTTGGT
1 CTGAAAAAGAAATGATGTCAATCCTGCGACACTGCCATGATGCCCCTTATGGAGGTCATTTTGGT
*
101497 GGAACAAGGACTACTGCAAAGGCCCTACAATCAAGATTTTATTAGCCCTA
66 GGAACAAGCACTACTGCAAAGGCCCTACAATCAAGATTTTATTAGCCCTA
101547 CTGAAAAAGAAATGATGTCAATCCTGCGACACTGCCATGATGCCCCTTATGGAGGTCATTTTGGT
1 CTGAAAAAGAAATGATGTCAATCCTGCGACACTGCCATGATGCCCCTTATGGAGGTCATTTTGGT
* *
101612 GGAACAAGCACTATTGCAAAGGCCCTACAATCAGGATTTTATTAGCCC
66 GGAACAAGCACTACTGCAAAGGCCCTACAATCAAGATTTTATTAGCCC
101660 AACTTGTTTC
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
115 110 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (115 bp):
CTGAAAAAGAAATGATGTCAATCCTGCGACACTGCCATGATGCCCCTTATGGAGGTCATTTTGGT
GGAACAAGCACTACTGCAAAGGCCCTACAATCAAGATTTTATTAGCCCTA
Found at i:110721 original size:35 final size:35
Alignment explanation
Indices: 110675--110770 Score: 104
Period size: 35 Copynumber: 2.7 Consensus size: 35
110665 ATAAACACAT
* *
110675 TAATAATAAAATAAAATAACAAT-GTTACAATCAAA
1 TAATAATAAAATAAAATAACAATAGTAACAAAC-AA
* * *
110710 TAATAACAAAATAAAAAAATAATAGTAACAAACAA
1 TAATAATAAAATAAAATAACAATAGTAACAAACAA
*
110745 TAATAATAATAATAATAATAATAATA
1 TAATAATAA-AATAA-AATAACAATA
110771 ATAATAAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
35 30 0.59
36 12 0.24
37 9 0.18
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (35 bp):
TAATAATAAAATAAAATAACAATAGTAACAAACAA
Found at i:110733 original size:3 final size:3
Alignment explanation
Indices: 110708--110777 Score: 72
Period size: 3 Copynumber: 23.7 Consensus size: 3
110698 GTTACAATCA
* * * * *
110708 AAT AAT AAC AA- AAT AA- AAA AAT AAT AGT AACA AAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
110752 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
110778 ATTGTTACTA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
2 4 0.07
3 51 0.89
4 2 0.04
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:111025 original size:4 final size:4
Alignment explanation
Indices: 111016--111070 Score: 55
Period size: 4 Copynumber: 14.8 Consensus size: 4
111006 GAAATGCTAG
* * *
111016 AAAT AAAT AAAT AAAT AAAT -AAT AAA- CAAT AAAT AAA- AAA- GAAC
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
111060 AAAT AAAT AAA
1 AAAT AAAT AAA
111071 ATTAAGAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
3 10 0.23
4 33 0.77
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:111048 original size:18 final size:18
Alignment explanation
Indices: 111024--111071 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
111014 AGAAATAAAT
111024 AAATAAATAAATAATA-AAC
1 AAATAAATAAA-AA-AGAAC
111043 -AATAAATAAAAAAGAAC
1 AAATAAATAAAAAAGAAC
111060 AAATAAATAAAA
1 AAATAAATAAAA
111072 TTAAGAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 1 0.04
17 5 0.19
18 21 0.78
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (18 bp):
AAATAAATAAAAAAGAAC
Found at i:116630 original size:22 final size:21
Alignment explanation
Indices: 116597--116637 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
116587 AAAACTTAAA
*
116597 TAACATATAACCAAAAGCATT
1 TAACATAAAACCAAAAGCATT
*
116618 TAACAATAAAACCTAAAGCA
1 TAAC-ATAAAACCAAAAGCA
116638 AGAAACATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.20
Consensus pattern (21 bp):
TAACATAAAACCAAAAGCATT
Found at i:118652 original size:20 final size:20
Alignment explanation
Indices: 118621--118682 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
118611 TTTTGAAGTG
*
118621 TTAAAATGATTTTGACTTGA
1 TTAAAATCATTTTGACTTGA
* *
118641 TTGAAATCATTTTGACTTGT
1 TTAAAATCATTTTGACTTGA
*
118661 TTAAAATCATTTTAACTTGA
1 TTAAAATCATTTTGACTTGA
118681 TT
1 TT
118683 TTAAAATTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.48
Consensus pattern (20 bp):
TTAAAATCATTTTGACTTGA
Found at i:119196 original size:37 final size:37
Alignment explanation
Indices: 119155--119229 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
119145 AAAACATCAT
* *
119155 TTGTATATAAAAATATCAATAAA-ACATTCAAGTTCAA
1 TTGTATATAAAAATACCAATAAAGAAATT-AAGTTCAA
* *
119192 TTGTATTTATAAATACCAATAAAGAAATTAAGTTCAA
1 TTGTATATAAAAATACCAATAAAGAAATTAAGTTCAA
119229 T
1 T
119230 CAAAATAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 29 0.88
38 4 0.12
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (37 bp):
TTGTATATAAAAATACCAATAAAGAAATTAAGTTCAA
Found at i:121840 original size:20 final size:20
Alignment explanation
Indices: 121808--121846 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
121798 CTGTCAATAT
121808 TTTTATAAAAGTATCGATAA
1 TTTTATAAAAGTATCGATAA
121828 TTTTA-AAACAGTATCGATA
1 TTTTATAAA-AGTATCGATA
121847 TCAAATTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (20 bp):
TTTTATAAAAGTATCGATAA
Found at i:127382 original size:19 final size:20
Alignment explanation
Indices: 127335--127382 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
127325 TTGATAATTC
127335 TTAA-TATTA-AATTATAAA
1 TTAATTATTATAATTATAAA
*
127353 TTAAATT-TTATAATT-TATA
1 TT-AATTATTATAATTATAAA
127372 TTAATTATTAT
1 TTAATTATTAT
127383 CAAAAGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTATTATAATTATAAA
Found at i:128002 original size:18 final size:19
Alignment explanation
Indices: 127962--128003 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
127952 CTTAATTTAT
*
127962 TTAATTTATTATTAACTTT
1 TTAATTTATTATTAACTTG
127981 TTAATTTA-TATTTAA-TTG
1 TTAATTTATTA-TTAACTTG
127999 TTAAT
1 TTAAT
128004 ATTTTATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TTAATTTATTATTAACTTG
Found at i:128905 original size:12 final size:12
Alignment explanation
Indices: 128888--128921 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
128878 TGAAGAAGAA
*
128888 GAAGAATATCCT
1 GAAGAAGATCCT
128900 GAAGAAGATCCT
1 GAAGAAGATCCT
*
128912 GAGGAAGATC
1 GAAGAAGATC
128922 TTGTGGAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (12 bp):
GAAGAAGATCCT
Found at i:133069 original size:12 final size:12
Alignment explanation
Indices: 133052--133077 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
133042 GAATGAATAA
133052 GATACTAAAGGG
1 GATACTAAAGGG
133064 GATACTAAAGGG
1 GATACTAAAGGG
133076 GA
1 GA
133078 AGCATAGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.35, T:0.15
Consensus pattern (12 bp):
GATACTAAAGGG
Found at i:133967 original size:40 final size:39
Alignment explanation
Indices: 133866--133973 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 39
133856 GTCATGACAT
* *
133866 AACATGTCTATGTTGCAATAAACCCCCTATGTCACAACAT
1 AACATGTCTATGTTGCAACAAA-CCCCTATGTCACAACAC
* * * *
133906 AGA-ATGTCAATGTCGCGACAAACCGCCTATGTCACTACAC
1 A-ACATGTCTATGTTGCAACAAACC-CCTATGTCACAACAC
*
133946 AACATGTTTATGTTGCAACAAACCCCTA
1 AACATGTCTATGTTGCAACAAACCCCTA
133974 AACATGGCTA
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
39 7 0.13
40 47 0.85
41 1 0.02
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (39 bp):
AACATGTCTATGTTGCAACAAACCCCTATGTCACAACAC
Found at i:137770 original size:26 final size:26
Alignment explanation
Indices: 137739--137830 Score: 98
Period size: 26 Copynumber: 3.5 Consensus size: 26
137729 GCTGGATAAG
137739 TATGTCCAGAATTGTCACTGCA-GAA
1 TATGTCCAGAATTGTCACTGCATGAA
* *
137764 -ACTTGTCCAGAATTATCGCTGCATGAA
1 TA--TGTCCAGAATTGTCACTGCATGAA
* * *
137791 TATGTCCAGAGTTGTCACTGTATGAG
1 TATGTCCAGAATTGTCACTGCATGAA
*
137817 CATGTCCAGAATTG
1 TATGTCCAGAATTG
137831 CGCCCAGAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
24 1 0.02
26 49 0.91
27 3 0.06
28 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (26 bp):
TATGTCCAGAATTGTCACTGCATGAA
Found at i:144843 original size:35 final size:35
Alignment explanation
Indices: 144797--144868 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
144787 TATCAGAGAG
*
144797 TATGAGCCCTCAATTGAGGAGGCTAACTTAGGGGA
1 TATGAGCCCTCAATTGAGGACGCTAACTTAGGGGA
* * *
144832 TATGAGTCCTCAATTGAGGACGTTGACTTAGGGGA
1 TATGAGCCCTCAATTGAGGACGCTAACTTAGGGGA
144867 TA
1 TA
144869 AAGACCAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (35 bp):
TATGAGCCCTCAATTGAGGACGCTAACTTAGGGGA
Found at i:149036 original size:71 final size:67
Alignment explanation
Indices: 148952--149087 Score: 166
Period size: 67 Copynumber: 2.0 Consensus size: 67
148942 TGATTAAATT
* *
148952 TAATCACTTTAATATTAAATCTTATTAAAATAATA-AAATAGATAAATATTAAATTAAATTTAAT
1 TAATCACTTTAATA--AAA-ATTAATAAAATAATATAAA-A-ATAAATATTAAATTAAATTTAAT
149016 ATTAAGA
61 ATTAAGA
* * * *
149023 TAATCACTTTAATAAAAATTAATAAAATACTATTAAAATAAGTATTAAATTTAATTTAATATTAA
1 TAATCACTTTAATAAAAATTAATAAAATAATATAAAAATAAATATTAAATTAAATTTAATATTAA
149088 ACTATTAATG
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
67 26 0.45
68 13 0.22
69 5 0.09
71 14 0.24
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (67 bp):
TAATCACTTTAATAAAAATTAATAAAATAATATAAAAATAAATATTAAATTAAATTTAATATTAA
GA
Found at i:157619 original size:18 final size:18
Alignment explanation
Indices: 157576--157620 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
157566 TTTTTCAAGA
157576 TTTATTTTCATGGTTATC
1 TTTATTTTCATGGTTATC
* *
157594 TTGT-TTTTCATTGTTATG
1 TT-TATTTTCATGGTTATC
157612 TTTATTTTC
1 TTTATTTTC
157621 TTCACTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 1 0.04
18 21 0.91
19 1 0.04
ACGTcount: A:0.13, C:0.09, G:0.11, T:0.67
Consensus pattern (18 bp):
TTTATTTTCATGGTTATC
Found at i:167116 original size:21 final size:21
Alignment explanation
Indices: 167083--167126 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
167073 TGACATGAAT
167083 AATTTTTTCAAAAATTAATTA
1 AATTTTTTCAAAAATTAATTA
*
167104 AATTATTTT-AAAAATTGATTA
1 AATT-TTTTCAAAAATTAATTA
167125 AA
1 AA
167127 ACTTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
AATTTTTTCAAAAATTAATTA
Found at i:167196 original size:29 final size:28
Alignment explanation
Indices: 167151--167223 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
167141 AAAAATATAG
* *
167151 AAAATTATTAAATTTATTTAAAAAG-TTC
1 AAAATTATAAAAATTATTT-AAAAGTTTC
*
167179 AAAATATATAAAAATTATTTAAAAGTTTG
1 AAAAT-TATAAAAATTATTTAAAAGTTTC
167208 AAAATTATAGAAAATT
1 AAAATTATA-AAAATT
167224 GTAAAAGGCA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 14 0.36
29 25 0.64
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.38
Consensus pattern (28 bp):
AAAATTATAAAAATTATTTAAAAGTTTC
Found at i:173071 original size:21 final size:22
Alignment explanation
Indices: 173046--173120 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 22
173036 AGAGTGAACC
173046 CTAAATTGCACTCTGGTGCCCT
1 CTAAATTGCACTCTGGTGCCCT
*
173068 -TAAATTGCACTCTGATG-CCT
1 CTAAATTGCACTCTGGTGCCCT
*
173088 CGAAATTGCACT-TCGGTGCCC-
1 CTAAATTGCACTCT-GGTGCCCT
173109 CTATAA-TGCACT
1 CTA-AATTGCACT
173121 TCAGTGCCCC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
20 4 0.09
21 37 0.82
22 4 0.09
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (22 bp):
CTAAATTGCACTCTGGTGCCCT
Found at i:176086 original size:38 final size:38
Alignment explanation
Indices: 176035--176118 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
176025 TGAGTCTATT
* * *
176035 CAAAATTACGCCCAAAATTGTCACTACATGACGATGTC
1 CAAAATTGCGCCCAAAATTATCACTACATGACGATGTA
*
176073 CAAAATTGCGCCCAAAATTATCACTGCATGACGATGTA
1 CAAAATTGCGCCCAAAATTATCACTACATGACGATGTA
176111 CAAAATTG
1 CAAAATTG
176119 TCACTGTATG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (38 bp):
CAAAATTGCGCCCAAAATTATCACTACATGACGATGTA
Found at i:180550 original size:42 final size:42
Alignment explanation
Indices: 180418--180602 Score: 169
Period size: 43 Copynumber: 4.4 Consensus size: 42
180408 TGTATAAATA
* * * *
180418 GAAGACTCATGTCTCG-GATTGAGCACGAGAATTTGTATGAATG
1 GAAGACTCATGTCTCGAGA-TGAGCATGAGAATATG-ATTAAAG
* * * * *
180461 GAAGACTCGTGACTCGAAATGAGCATGTGGATAT-ATTAAAG
1 GAAGACTCATGTCTCGAGATGAGCATGAGAATATGATTAAAG
* *
180502 GAAGACTCATGTCTTGAGATGAGAATGAGAATATGATTAAAG
1 GAAGACTCATGTCTCGAGATGAGCATGAGAATATGATTAAAG
* * *
180544 GAAGACTCATGGCTC-AGAATGAGCATGAGATTATGTTTAAAAG
1 GAAGACTCATGTCTCGAG-ATGAGCATGAGAATATGATT-AAAG
* *
180587 GAAGACTTATGACTCG
1 GAAGACTCATGTCTCG
180603 GTAAAGCATA
Statistics
Matches: 114, Mismatches: 23, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
41 34 0.30
42 37 0.32
43 42 0.37
44 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (42 bp):
GAAGACTCATGTCTCGAGATGAGCATGAGAATATGATTAAAG
Found at i:180611 original size:42 final size:41
Alignment explanation
Indices: 180460--180628 Score: 116
Period size: 42 Copynumber: 4.1 Consensus size: 41
180450 TTGTATGAAT
* * *
180460 GGAAGACTCGTGACTC-GAAATGAGCATGTGGATAT-ATT-AAA
1 GGAAGACTCATGACTCAG-AA-GAGCATG-AGATATGTTTAAAA
* * * * *
180501 GGAAGACTCATGTCTTGAGATGAGAATGAGAATATGATT-AAA
1 GGAAGACTCATGAC-TCAGAAGAGCATGAG-ATATGTTTAAAA
*
180543 GGAAGACTCATGGCTCAGAATGAGCATGAGATTATGTTTAAAA
1 GGAAGACTCATGACTCAGAA-GAGCATGAGA-TATGTTTAAAA
* * *
180586 GGAAGACTTATGACTCGGTAA-AGCATAAGAT-TGTTTAAAA
1 GGAAGACTCATGACTCAG-AAGAGCATGAGATATGTTTAAAA
180626 GGA
1 GGA
180629 TTACTAGTGA
Statistics
Matches: 105, Mismatches: 15, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
40 13 0.12
41 28 0.27
42 43 0.41
43 19 0.18
44 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.25
Consensus pattern (41 bp):
GGAAGACTCATGACTCAGAAGAGCATGAGATATGTTTAAAA
Found at i:180653 original size:27 final size:27
Alignment explanation
Indices: 180612--180666 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
180602 GGTAAAGCAT
180612 AAGATTGTTTAAAAGGATTACTAGTGA
1 AAGATTGTTTAAAAGGATTACTAGTGA
*
180639 AAGATTGTTTTAAAGGATTACTAGTGA
1 AAGATTGTTTAAAAGGATTACTAGTGA
180666 A
1 A
180667 TATGGGAAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.35
Consensus pattern (27 bp):
AAGATTGTTTAAAAGGATTACTAGTGA
Found at i:184592 original size:21 final size:21
Alignment explanation
Indices: 184562--184661 Score: 164
Period size: 21 Copynumber: 4.8 Consensus size: 21
184552 TAGCGTAGAC
*
184562 TTCTATCGATACAAGTGACAG
1 TTCTACCGATACAAGTGACAG
184583 TTCTACCGATACAAGTGACAG
1 TTCTACCGATACAAGTGACAG
184604 TTCTACCGATACAAGTGACAG
1 TTCTACCGATACAAGTGACAG
**
184625 TTCTACCGATACAAGTGACTC
1 TTCTACCGATACAAGTGACAG
*
184646 TTCTACCGAAACAAGT
1 TTCTACCGATACAAGT
184662 ATTACTTTTA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 75 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (21 bp):
TTCTACCGATACAAGTGACAG
Found at i:184674 original size:42 final size:42
Alignment explanation
Indices: 184560--184678 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
184550 AATAGCGTAG
* * *
184560 ACTTCTATCGATACAAGTGACAGTTCTACCGATACAAGTGAC
1 ACTTCTACCGAAACAAGTGACACTTCTACCGATACAAGTGAC
* * *
184602 AGTTCTACCGATACAAGTGACAGTTCTACCGATACAAGTGAC
1 ACTTCTACCGAAACAAGTGACACTTCTACCGATACAAGTGAC
* * *
184644 TCTTCTACCGAAACAAGT-ATTACTTTTACCGATAC
1 ACTTCTACCGAAACAAGTGA-CACTTCTACCGATAC
184679 TAAAAACTCC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 1 0.01
42 67 0.99
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (42 bp):
ACTTCTACCGAAACAAGTGACACTTCTACCGATACAAGTGAC
Found at i:185449 original size:52 final size:52
Alignment explanation
Indices: 185393--185581 Score: 175
Period size: 52 Copynumber: 3.6 Consensus size: 52
185383 GTATTGGGAA
** *
185393 TCATATACTCATGACGACATGTAGTCATCGGACCTCAAAATCCGTAAAGGAT
1 TCATATACTCATGACGACACATAATCATCGGACCTCAAAATCCGTAAAGGAT
* * * *
185445 TCATATACTCATGATGACACATAATCATCGGACCTCATAATCTGTATAGGAT
1 TCATATACTCATGACGACACATAATCATCGGACCTCAAAATCCGTAAAGGAT
* * * * * * **
185497 TCATATACTCACGATGGCACAGAGTCATCAGACCT-TTAATCCG-AAATGGGAT
1 TCATATACTCATGACGACACATAATCATCGGACCTCAAAATCCGTAAA--GGAT
* * *
185549 TCATATAACTCATGATGACACAGAGTCATCGGA
1 TCATAT-ACTCATGACGACACATAATCATCGGA
185582 TCTTTTTGCA
Statistics
Matches: 116, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
50 2 0.02
51 6 0.05
52 85 0.73
53 23 0.20
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (52 bp):
TCATATACTCATGACGACACATAATCATCGGACCTCAAAATCCGTAAAGGAT
Found at i:185502 original size:104 final size:104
Alignment explanation
Indices: 185393--185581 Score: 242
Period size: 104 Copynumber: 1.8 Consensus size: 104
185383 GTATTGGGAA
* *
185393 TCATATACTCATGA-CG-ACATGTAGTCATCGGACCTCAAAATCCGTAAA-GGATTCATAT-ACT
1 TCATATACTCACGATCGCACA-G-AGTCATCAGACCT-AAAATCCG-AAAGGGATTCATATAACT
*
185454 CATGATGACACATAATCATCGGACCTCATAATCTGTATAGGAT
62 CATGATGACACAGAATCATCGGACCTCATAATCTGTATAGGAT
* **
185497 TCATATACTCACGATGGCACAGAGTCATCAGACCTTTAATCCGAAATGGGATTCATATAACTCAT
1 TCATATACTCACGATCGCACAGAGTCATCAGACCTAAAATCCGAAA-GGGATTCATATAACTCAT
*
185562 GATGACACAGAGTCATCGGA
65 GATGACACAGAATCATCGGA
185582 TCTTTTTGCA
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
102 3 0.04
103 6 0.08
104 35 0.48
105 26 0.36
106 3 0.04
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (104 bp):
TCATATACTCACGATCGCACAGAGTCATCAGACCTAAAATCCGAAAGGGATTCATATAACTCATG
ATGACACAGAATCATCGGACCTCATAATCTGTATAGGAT
Found at i:191859 original size:21 final size:21
Alignment explanation
Indices: 191834--191889 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
191824 AATAGTGCAG
191834 ACTTCTACCGATACAAGTGACT
1 ACTTCTACCGATACAAGT-ACT
* * *
191856 -CTTCTACCAAAACAAGTATT
1 ACTTCTACCGATACAAGTACT
191876 ACTTCTACCGATAC
1 ACTTCTACCGATAC
191890 TAAAAACTCC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.34, C:0.29, G:0.09, T:0.29
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTACT
Found at i:192082 original size:21 final size:21
Alignment explanation
Indices: 192044--192083 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
192034 TACCCTGTAC
* *
192044 TTCTACCGATACATGTATGAG
1 TTCTACCGAAACAAGTATGAG
*
192065 TTCTACTGAAACAAGTATG
1 TTCTACCGAAACAAGTATG
192084 CAGAATCATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (21 bp):
TTCTACCGAAACAAGTATGAG
Found at i:192668 original size:52 final size:52
Alignment explanation
Indices: 192607--192795 Score: 200
Period size: 52 Copynumber: 3.6 Consensus size: 52
192597 GTATTGGGAA
* * *
192607 TCATTTACTCACGACGACATATAGTCATCGGACCTCATAATCCGAAAAGGAT
1 TCATATACTCACGATGACATAGAGTCATCGGACCTCATAATCCGAAAAGGAT
* * * * * * * *
192659 TGATATACTCACAATGACAGATAATCATCGGACCTCATAATTCGTATAGGAT
1 TCATATACTCACGATGACATAGAGTCATCGGACCTCATAATCCGAAAAGGAT
* * * *
192711 TCATATACTCACGATGACATAGAGTCTTTGAACCT-TTAATCCGAAATAGGAT
1 TCATATACTCACGATGACATAGAGTCATCGGACCTCATAATCCGAAA-AGGAT
* *
192763 TCATATAACTCACGATGGCACAGAGTCATCGGA
1 TCATAT-ACTCACGATGACATAGAGTCATCGGA
192796 TCTTTTTGCG
Statistics
Matches: 109, Mismatches: 26, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
51 7 0.06
52 81 0.74
53 21 0.19
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (52 bp):
TCATATACTCACGATGACATAGAGTCATCGGACCTCATAATCCGAAAAGGAT
Found at i:192762 original size:104 final size:102
Alignment explanation
Indices: 192560--192795 Score: 244
Period size: 104 Copynumber: 2.3 Consensus size: 102
192550 TACATTTTTT
* * *
192560 TATACTCACAATGACACAGTCATCGGACCATTAATCCGTATTGGGAATCATTTACTCACGACGAC
1 TATACTCACAATGACACAATCATCGGACCATTAATCCGTATTAGGAATCATATACTCACGACGAC
* * *
192625 ATATAGTCATCGGACCTCATAATCCGAAAAGGATTGA
66 ATAGAGTCATCGAACCTCATAATCCGAAAAGGATTCA
* * *
192662 TATACTCACAATGACAGATAATCATCGGACC-TCATAATTCGTA-TAGGATTCATATACTCACGA
1 TATACTCACAATGAC--ACAATCATCGGACCAT--TAATCCGTATTAGGAATCATATACTCACGA
* * * *
192725 TGACATAGAGTCTTTGAACCT-TTAATCCGAAATAGGATTCA
62 CGACATAGAGTCATCGAACCTCATAATCCGAAA-AGGATTCA
* *
192766 TATAACTCACGATGGCACAGAGTCATCGGA
1 TAT-ACTCACAATGACACA-A-TCATCGGA
192796 TCTTTTTGCG
Statistics
Matches: 110, Mismatches: 16, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
102 15 0.14
103 13 0.12
104 56 0.51
105 26 0.24
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (102 bp):
TATACTCACAATGACACAATCATCGGACCATTAATCCGTATTAGGAATCATATACTCACGACGAC
ATAGAGTCATCGAACCTCATAATCCGAAAAGGATTCA
Found at i:210172 original size:10 final size:11
Alignment explanation
Indices: 210145--210171 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
210135 TGAAAGAAGT
210145 GAAAAACAAGC
1 GAAAAACAAGC
210156 GAAAAACAAGC
1 GAAAAACAAGC
210167 GAAAA
1 GAAAA
210172 CCGTACAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.15, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAAACAAGC
Found at i:217920 original size:17 final size:17
Alignment explanation
Indices: 217900--217976 Score: 84
Period size: 17 Copynumber: 4.6 Consensus size: 17
217890 ATGGAACCTA
*
217900 ATTTTAAATTTTAATTT
1 ATTTTAAATTTGAATTT
*
217917 A-TTTAAGTTTGAATTT
1 ATTTTAAATTTGAATTT
* * *
217933 ATTTCAAATTTAAACTT
1 ATTTTAAATTTGAATTT
* *
217950 ATTTTGAGTTTGAATTT
1 ATTTTAAATTTGAATTT
217967 ATTTTAAATT
1 ATTTTAAATT
217977 AAATGTAAAT
Statistics
Matches: 46, Mismatches: 13, Indels: 2
0.75 0.21 0.03
Matches are distributed among these distances:
16 14 0.30
17 32 0.70
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTGAATTT
Found at i:217979 original size:33 final size:33
Alignment explanation
Indices: 217900--217976 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 33
217890 ATGGAACCTA
* *
217900 ATTTTAAATTTTAATTTATTTAAGTTTGAATTT
1 ATTTTAAATTTAAACTTATTTAAGTTTGAATTT
* *
217933 ATTTCAAATTTAAACTTATTTTGAGTTTGAATTT
1 ATTTTAAATTTAAACTTA-TTTAAGTTTGAATTT
217967 ATTTTAAATT
1 ATTTTAAATT
217977 AAATGTAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
33 15 0.39
34 23 0.61
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (33 bp):
ATTTTAAATTTAAACTTATTTAAGTTTGAATTT
Found at i:218629 original size:18 final size:19
Alignment explanation
Indices: 218608--218643 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
218598 AAAACATTTT
218608 ATAATAA-ATAAATAAAAA
1 ATAATAATATAAATAAAAA
*
218626 ATAATAATATTAATAAAA
1 ATAATAATATAAATAAAA
218644 TAAAAAGAAA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
ATAATAATATAAATAAAAA
Found at i:219717 original size:30 final size:30
Alignment explanation
Indices: 219674--219777 Score: 109
Period size: 30 Copynumber: 3.5 Consensus size: 30
219664 ACCCTCAAGC
* *
219674 TTTTTCTAGAATTATATTTTAACCCCAAAA
1 TTTTTCTAAAATTATATTTTAACCCCTAAA
* **
219704 TTTTTCCAAAATTATATTTTAACCTTTAAA
1 TTTTTCTAAAATTATATTTTAACCCCTAAA
* * * *
219734 CTTTTCTAAAATTACATTTTAGCCCCTGAA
1 TTTTTCTAAAATTATATTTTAACCCCTAAA
* *
219764 TTTCTCAAAAATTA
1 TTTTTCTAAAATTA
219778 CACTTTTTCC
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.36, C:0.17, G:0.03, T:0.44
Consensus pattern (30 bp):
TTTTTCTAAAATTATATTTTAACCCCTAAA
Found at i:219793 original size:60 final size:58
Alignment explanation
Indices: 219675--219956 Score: 188
Period size: 57 Copynumber: 4.8 Consensus size: 58
219665 CCCTCAAGCT
* * ** * * * * *
219675 TTTTCTAGAATTATATTTTAACCCCAAAATTTTTCCAAAATTATATTTTAACCTTTAAAC
1 TTTTCTAAAATTACATTTT-ACCCCTGAATTTCTCAAAAATTACATTTT-TCCCTTAAAC
219735 TTTTCTAAAATTACATTTTAGCCCCTGAATTTCTCAAAAATTACACTTTTTCCCTTAAAC
1 TTTTCTAAAATTACATTTTA-CCCCTGAATTTCTCAAAAATTACA-TTTTTCCCTTAAAC
* * **
219795 --TTCTAAAAATTACATTTTTACCCCTGAACTTCT-AAAAATTACAATTTTCCCTCGAAC
1 TTTTCT-AAAATTACA-TTTTACCCCTGAATTTCTCAAAAATTACATTTTTCCCTTAAAC
* * * *
219852 --TTCTGAAAATTATATTTTTACCCTTG-ATCTTC-CAAAAATTACATTTTAACCC-CAAAC
1 TTTTCT-AAAATTACA-TTTTACCCCTGAAT-TTCTCAAAAATTACATTTT-TCCCTTAAAC
* * * * * *
219909 -TTCCAAAAATCACATTTTTACCTC-GAACTTCTCAAAAATCACATTTTT
1 TTTTCTAAAATTACA-TTTTACCCCTGAATTTCTCAAAAATTACATTTTT
219957 ATCCCGAACC
Statistics
Matches: 183, Mismatches: 29, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
56 5 0.03
57 84 0.46
58 19 0.10
59 22 0.12
60 49 0.27
61 4 0.02
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (58 bp):
TTTTCTAAAATTACATTTTACCCCTGAATTTCTCAAAAATTACATTTTTCCCTTAAAC
Found at i:219862 original size:57 final size:58
Alignment explanation
Indices: 219737--219956 Score: 238
Period size: 57 Copynumber: 3.8 Consensus size: 58
219727 CTTTAAACTT
* * *
219737 TTCT-AAAATTACA-TTTTAGCCCCTGAATTTCTCAAAAATTACACTTTTTCCCTTAAAC
1 TTCTAAAAATTACATTTTTA-CCCCTGAACTTCTCAAAAATTACA-ATTTTCCCTCAAAC
*
219795 TTCTAAAAATTACATTTTTACCCCTGAACTTCT-AAAAATTACAATTTTCCCTCGAAC
1 TTCTAAAAATTACATTTTTACCCCTGAACTTCTCAAAAATTACAATTTTCCCTCAAAC
* * * *
219852 TTCTGAAAATTATATTTTTACCCTTGATCTTC-CAAAAATTAC-ATTTTAACCC-CAAAC
1 TTCTAAAAATTACATTTTTACCCCTGAACTTCTCAAAAATTACAATTTT--CCCTCAAAC
* * * * *
219909 TTCCAAAAATCACATTTTTACCTC-GAACTTCTCAAAAATCACATTTTT
1 TTCTAAAAATTACATTTTTACCCCTGAACTTCTCAAAAATTACAATTTT
219957 ATCCCGAACC
Statistics
Matches: 137, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
56 11 0.08
57 79 0.58
58 21 0.15
59 21 0.15
60 5 0.04
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (58 bp):
TTCTAAAAATTACATTTTTACCCCTGAACTTCTCAAAAATTACAATTTTCCCTCAAAC
Found at i:219957 original size:29 final size:29
Alignment explanation
Indices: 219732--219988 Score: 197
Period size: 29 Copynumber: 8.9 Consensus size: 29
219722 TTAACCTTTA
* * *
219732 AACTTTTCTAAAATTACA-TTTTAGCCCCTG
1 AACTTCTCAAAAATTACATTTTTA-CCTC-G
* * **
219762 AATTTCTCAAAAATTACACTTTTTCCCTTA
1 AACTTCTCAAAAATTACA-TTTTTACCTCG
*
219792 AACTTCT-AAAAATTACATTTTTACCCCTG
1 AACTTCTCAAAAATTACATTTTTACCTC-G
* *
219821 AACTTCT-AAAAATTACAATTTTCCCTCG
1 AACTTCTCAAAAATTACATTTTTACCTCG
* * *
219849 AACTTCT-GAAAATTATATTTTTACCCTTG
1 AACTTCTCAAAAATTACATTTTTA-CCTCG
* * * *
219878 ATCTTC-CAAAAATTACATTTTAACCCCA
1 AACTTCTCAAAAATTACATTTTTACCTCG
*
219906 AACTTC-CAAAAATCACATTTTTACCTCG
1 AACTTCTCAAAAATTACATTTTTACCTCG
*
219934 AACTTCTCAAAAATCACATTTTTATCC-CG
1 AACTTCTCAAAAATTACATTTTTA-CCTCG
* **
219963 AAC-CCTCCTAAATTGACATTTTTACC
1 AACTTCTCAAAAATT-ACATTTTTACC
219989 CTTAAAACTT
Statistics
Matches: 183, Mismatches: 36, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
28 67 0.37
29 87 0.48
30 23 0.13
31 2 0.01
32 4 0.02
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (29 bp):
AACTTCTCAAAAATTACATTTTTACCTCG
Found at i:220390 original size:97 final size:97
Alignment explanation
Indices: 220283--220476 Score: 334
Period size: 97 Copynumber: 2.0 Consensus size: 97
220273 AAAATATTTA
* *
220283 AAATCGAGGCAATATTCTTTTATTTCAGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAT
1 AAATCGAGGCAATATTCTTTTATCTCAGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACAAT
220348 TTTTCTTCAAACCCGGATAATCGAATACCCTT
66 TTTTCTTCAAACCCGGATAATCGAATACCCTT
*
220380 AAATCGAGGCAATATTCTTTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACAAT
1 AAATCGAGGCAATATTCTTTTATCTCAGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACAAT
* * *
220445 TTTTCTTCAAATCGGGATAATTGAATACCCTT
66 TTTTCTTCAAACCCGGATAATCGAATACCCTT
220477 TTTAAGGGTT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 91 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (97 bp):
AAATCGAGGCAATATTCTTTTATCTCAGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACAAT
TTTTCTTCAAACCCGGATAATCGAATACCCTT
Found at i:231837 original size:78 final size:79
Alignment explanation
Indices: 231739--232122 Score: 519
Period size: 78 Copynumber: 4.9 Consensus size: 79
231729 GTTGAAGATT
** * * *
231739 TGATCTTTTACCCCGAGCTTGGGATAGATCACCATCAACCAATCTCTTACCTCGAACCTGGGGCA
1 TGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCTCGAGCCTAGGGCA
231804 GATTGCAGCCATTC
66 GATTGCAGCCATTC
* * *
231818 T-ATCTTTTACCCTGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCTCGAGCCTAGGGTA
1 TGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCTCGAGCCTAGGGCA
* * *
231882 GATTACAGTC-GTC
66 GATTGCAGCCATTC
*
231895 TGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCT-GAGGC
1 TGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCTCGAGCCTAG-GGC
* *
231959 AGATTGTAACCATT-
65 AGATTGCAGCCATTC
* *
231973 TGATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCTAATCTCTTACCTCGAGCCTAGGGCA
1 TGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCTCGAGCCTAGGGCA
*
232038 TATTGCAGCCGA-TC
66 GATTGCAGCC-ATTC
* * * *
232052 -GATCTTTTACCCCGAGCTTGAGGCAAATCACCATCAGCCAATCTCTTACCCCGAGCCTCGGGCA
1 TGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCTCGAGCCTAGGGCA
232116 GATTGCA
66 GATTGCA
232123 ATCATTTGAA
Statistics
Matches: 266, Mismatches: 33, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
77 4 0.02
78 258 0.97
79 4 0.02
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (79 bp):
TGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCTCGAGCCTAGGGCA
GATTGCAGCCATTC
Found at i:231867 original size:39 final size:39
Alignment explanation
Indices: 231741--232118 Score: 248
Period size: 39 Copynumber: 9.7 Consensus size: 39
231731 TGAAGATTTG
* * ** **
231741 ATCTTTTACCCCGAGCTTGGGATAGATCACCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* * *
231780 ATCTCTTACCTCGAACCTGGGGCAGATTGCAGCCAT---TCT
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATCAGTCA
* * *
231819 ATCTTTTACCCTGAGCTTGGGGCAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* * * * *
231858 ATCTCTTACCTCGAGCCTAGGGTAGATTA-CAGTC-GTCTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TCAGTC-A
* * *
231897 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* **** * * **
231936 ATCTCTTACCCCGAGCCTGAGGCAGATTGTAACCATTTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
*
231975 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAG-CTA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTC-A
* * * ** * * *
232014 ATCTCTTACCTCGAGCCTAGGGCATAT-TGCAGCCGATCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAG-TCA
* * * * *
232053 ATCTTTTACCCCGAGCTTGAGGCAAATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
*
232092 ATCTCTTACCCCGAGCCTCGGGCAGAT
1 ATCTCTTACCCCGAGCCTGGGGCAGAT
232119 TGCAATCATT
Statistics
Matches: 247, Mismatches: 78, Indels: 28
0.70 0.22 0.08
Matches are distributed among these distances:
36 4 0.02
37 2 0.01
38 10 0.04
39 215 0.87
40 10 0.04
41 2 0.01
42 4 0.02
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
Found at i:232548 original size:7 final size:7
Alignment explanation
Indices: 232536--232560 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
232526 AATGGAACTC
232536 AATTTTA
1 AATTTTA
232543 AATTTTA
1 AATTTTA
232550 AATTTTA
1 AATTTTA
232557 AATT
1 AATT
232561 ATTCAAGTTT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:232582 original size:33 final size:35
Alignment explanation
Indices: 232544--232620 Score: 106
Period size: 34 Copynumber: 2.3 Consensus size: 35
232534 TCAATTTTAA
232544 ATTTTAAATTTTAAA-TTA-TTCAAGTTTGAACTT
1 ATTTTAAATTTTAAACTTATTTCAAGTTTGAACTT
** *
232577 ATTTTAAA-TTTAAACTTATTTTGAGTTTGAATTT
1 ATTTTAAATTTTAAACTTATTTCAAGTTTGAACTT
232611 ATTTTAAATT
1 ATTTTAAATT
232621 AAATTTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 6 0.16
33 11 0.29
34 20 0.53
35 1 0.03
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (35 bp):
ATTTTAAATTTTAAACTTATTTCAAGTTTGAACTT
Found at i:232594 original size:17 final size:17
Alignment explanation
Indices: 232544--232620 Score: 68
Period size: 17 Copynumber: 4.6 Consensus size: 17
232534 TCAATTTTAA
232544 ATTTTAAATTTTAAA-TT
1 ATTTTAAA-TTTAAACTT
* * *
232561 A-TTCAAGTTTGAACTT
1 ATTTTAAATTTAAACTT
232577 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAACTT
* * * *
232594 ATTTTGAGTTTGAATTT
1 ATTTTAAATTTAAACTT
232611 ATTTTAAATT
1 ATTTTAAATT
232621 AAATTTAAAT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
15 5 0.11
16 7 0.15
17 34 0.74
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTAAACTT
Found at i:233575 original size:16 final size:16
Alignment explanation
Indices: 233556--233586 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
233546 ACCGTTTAAA
233556 AAAAAGAATAAAAAGG
1 AAAAAGAATAAAAAGG
*
233572 AAAAAGAATCAAAAG
1 AAAAAGAATAAAAAG
233587 ATCCGATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.16, T:0.06
Consensus pattern (16 bp):
AAAAAGAATAAAAAGG
Found at i:234374 original size:30 final size:30
Alignment explanation
Indices: 234320--234493 Score: 103
Period size: 30 Copynumber: 5.9 Consensus size: 30
234310 TCAAAAGGTA
*
234320 CCTAAAC--TTTTAGAAATCACATTTTGACC
1 CCTAAACTTTTTTA-AAATTACATTTTGACC
234349 CCTAAACTTTTTTAAAATTACATTTTGACC
1 CCTAAACTTTTTTAAAATTACATTTTGACC
* *
234379 CC-AAA-TTTTTTCCAAAATTATATTTT-AGC
1 CCTAAACTTTTTT--AAAATTACATTTTGACC
* ** * * *
234408 TCTCAAACTTTTCCAAATTTTCATTTTAGTCC
1 CCT-AAACTTTTTTAAAATTACATTTT-GACC
* * * *
234440 CC-GAACTTCTTAAAAATTACACTTTT-CCC
1 CCTAAACTTTTTTAAAATTACA-TTTTGACC
* *
234469 CCTAAA-TTTCTAAAAATTACATTTT
1 CCTAAACTTTTTTAAAATTACATTTT
234494 TCCCTCGAAC
Statistics
Matches: 112, Mismatches: 22, Indels: 23
0.71 0.14 0.15
Matches are distributed among these distances:
28 10 0.09
29 30 0.27
30 54 0.48
31 12 0.11
32 6 0.05
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.41
Consensus pattern (30 bp):
CCTAAACTTTTTTAAAATTACATTTTGACC
Found at i:234469 original size:28 final size:29
Alignment explanation
Indices: 234437--234521 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
234427 TTCATTTTAG
234437 TCCCCGAACTTCT-TAAAAATTACACTTT
1 TCCCCGAACTTCTCTAAAAATTACACTTT
* * *
234465 TCCCCCTAAATT-TCTAAAAATTACATTTT
1 T-CCCCGAACTTCTCTAAAAATTACACTTT
*
234494 TCCCTCGAACTTC-C--AAAATTACATTTT
1 TCCC-CGAACTTCTCTAAAAATTACACTTT
234521 T
1 T
234522 GCCCTTGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
27 14 0.29
28 5 0.10
29 29 0.60
ACGTcount: A:0.32, C:0.27, G:0.02, T:0.39
Consensus pattern (29 bp):
TCCCCGAACTTCTCTAAAAATTACACTTT
Found at i:234526 original size:28 final size:27
Alignment explanation
Indices: 234481--234666 Score: 156
Period size: 29 Copynumber: 6.5 Consensus size: 27
234471 TAAATTTCTA
234481 AAAATTACATTTTTCCCTCGAACTTCC
1 AAAATTACATTTTTCCCTCGAACTTCC
* *
234508 AAAATTACATTTTTGCCCTTGAAATTCC
1 AAAATTACATTTTT-CCCTCGAACTTCC
* *
234536 AAAGATCACATTTTTACCCTCGATCTTCC
1 AAA-ATTACATTTTT-CCCTCGAACTTCC
*
234565 GAAAATTACATTTTGCCCTCGAACTTCTC
1 -AAAATTACATTTTTCCCTCGAACTTC-C
* * *
234594 AAAAATCACATTTTTACCTCTAACTCTCCC
1 -AAAATTACATTTTTCCCTCGAACT-T-CC
* * * **
234624 AAAATAATATTTTTATCTCTAAAACTTTCC
1 AAAATTACA-TTTT-TCCCTCGAAC-TTCC
234654 AAAATTACATTTT
1 AAAATTACATTTT
234667 AACCCCAAAC
Statistics
Matches: 127, Mismatches: 23, Indels: 16
0.77 0.14 0.10
Matches are distributed among these distances:
27 14 0.11
28 25 0.20
29 61 0.48
30 18 0.14
31 8 0.06
32 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (27 bp):
AAAATTACATTTTTCCCTCGAACTTCC
Found at i:234628 original size:58 final size:58
Alignment explanation
Indices: 234452--234637 Score: 193
Period size: 57 Copynumber: 3.2 Consensus size: 58
234442 GAACTTCTTA
* * * * *
234452 AAAATTACACTTTT-CCCCCTAAATT-TCTAAAAATTACATTTTTCCCTCGAACTT-CC
1 AAAATTACATTTTTGCCCTCGAAATTCTC-AAAAATCACATTTTTACCTCGAACTTCCC
* * * *
234508 AAAATTACATTTTTGCCCTTGAAATTC-CAAAGATCACATTTTTACCCTCGATCTTCCG
1 AAAATTACATTTTTGCCCTCGAAATTCTCAAAAATCACATTTTTA-CCTCGAACTTCCC
* *
234566 AAAATTACA-TTTTGCCCTCGAACTTCTCAAAAATCACATTTTTACCTCTAACTCTCCC
1 AAAATTACATTTTTGCCCTCGAAATTCTCAAAAATCACATTTTTACCTCGAACT-TCCC
* *
234624 AAAATAATATTTTT
1 AAAATTACATTTTT
234638 ATCTCTAAAA
Statistics
Matches: 106, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
56 26 0.25
57 40 0.38
58 36 0.34
59 4 0.04
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.37
Consensus pattern (58 bp):
AAAATTACATTTTTGCCCTCGAAATTCTCAAAAATCACATTTTTACCTCGAACTTCCC
Found at i:235121 original size:97 final size:97
Alignment explanation
Indices: 234947--235132 Score: 275
Period size: 97 Copynumber: 1.9 Consensus size: 97
234937 TAAAATCGAG
* * * * * *
234947 GCAATATTCTTTTATTTCTGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCATAATTTTTCTTC
1 GCAATAATCCTTTATCTCGGGTTTTGAAAATTTGTCCCTTAACTTACTAGGCACAATTTTTCTTC
235012 AAACCGAAATAATCGAATACCCTTAAATAGAA
66 AAACCGAAATAATCGAATACCCTTAAATAGAA
* *
235044 GCAATAATCCTTTATCTCGGGTTTTGAAAATTTGTCCCTTAACTTACTAGGCGCGATTTTTCTTC
1 GCAATAATCCTTTATCTCGGGTTTTGAAAATTTGTCCCTTAACTTACTAGGCACAATTTTTCTTC
*
235109 AAATC-AATATAATCGAATACCCTT
66 AAACCGAA-ATAATCGAATACCCTT
235133 TTTCAAGGTT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
96 2 0.03
97 77 0.97
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (97 bp):
GCAATAATCCTTTATCTCGGGTTTTGAAAATTTGTCCCTTAACTTACTAGGCACAATTTTTCTTC
AAACCGAAATAATCGAATACCCTTAAATAGAA
Found at i:241011 original size:26 final size:26
Alignment explanation
Indices: 240981--241030 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
240971 CTTAGTCCCG
*
240981 ACGATGCGACGGTCCTTCATGTCCTA
1 ACGATCCGACGGTCCTTCATGTCCTA
241007 ACGATCCGACGGTCCTTCATGTCC
1 ACGATCCGACGGTCCTTCATGTCC
241031 CGACAACACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.18, C:0.34, G:0.22, T:0.26
Consensus pattern (26 bp):
ACGATCCGACGGTCCTTCATGTCCTA
Found at i:243681 original size:13 final size:12
Alignment explanation
Indices: 243665--243713 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
243655 TTAAACTAAG
*
243665 CTTTTAAAAAGTA
1 CTTTTTAAAA-TA
243678 CTTTTTAAAATCA
1 CTTTTTAAAAT-A
*
243691 CTTTTCCAAAATA
1 CTTTT-TAAAATA
243704 CTTTTTAAAA
1 CTTTTTAAAA
243714 GCACTTCTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 5 0.16
13 21 0.68
14 5 0.16
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (12 bp):
CTTTTTAAAATA
Found at i:243694 original size:26 final size:26
Alignment explanation
Indices: 243665--243719 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
243655 TTAAACTAAG
*
243665 CTTTT-AAAAAGTACTTTTTAAAATCA
1 CTTTTCAAAAA-TACTTTTTAAAAGCA
*
243691 CTTTTCCAAAATACTTTTTAAAAGCA
1 CTTTTCAAAAATACTTTTTAAAAGCA
243717 CTT
1 CTT
243720 CTGAAAAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (26 bp):
CTTTTCAAAAATACTTTTTAAAAGCA
Found at i:243719 original size:13 final size:13
Alignment explanation
Indices: 243665--243729 Score: 51
Period size: 13 Copynumber: 5.0 Consensus size: 13
243655 TTAAACTAAG
* *
243665 CTTTTAAAAAGTA
1 CTTTTTAAAAGCA
*
243678 CTTTTTAAAATCA
1 CTTTTTAAAAGCA
* *
243691 CTTTTCCAAAA-TA
1 CTTTT-TAAAAGCA
243704 CTTTTTAAAAGCA
1 CTTTTTAAAAGCA
* *
243717 CTTCTGAAAAGCA
1 CTTTTTAAAAGCA
243730 ATGTTAAACT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
12 4 0.10
13 33 0.80
14 4 0.10
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (13 bp):
CTTTTTAAAAGCA
Found at i:244103 original size:60 final size:60
Alignment explanation
Indices: 244003--244134 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 60
243993 TAATAAATTT
* **
244003 AAGTACCAAATTGAATCTAAAAAAAGCTTAAGTGCCAAATTTA-GAAAAAATGACAAGTTC
1 AAGTACCAAATTGAATCCAAAAAAAGCTTAAGAACCAAA-TTAGGAAAAAATGACAAGTTC
* * * * * *
244063 -AGATACCAAATTGGATCCAAAAAAAGTTTATGAACTAAATTAGGAAAAAGTGTCAAGTTC
1 AAG-TACCAAATTGAATCCAAAAAAAGCTTAAGAACCAAATTAGGAAAAAATGACAAGTTC
244123 AAGTACCAAATT
1 AAGTACCAAATT
244135 AGATAATAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
59 5 0.08
60 53 0.88
61 2 0.03
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.24
Consensus pattern (60 bp):
AAGTACCAAATTGAATCCAAAAAAAGCTTAAGAACCAAATTAGGAAAAAATGACAAGTTC
Found at i:250887 original size:18 final size:17
Alignment explanation
Indices: 250864--250910 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
250854 CATTCGGCCC
250864 AAACAAAACAAAATAAA
1 AAACAAAACAAAATAAA
250881 TAAAC-AAACAAACATAAA
1 -AAACAAAACAAA-ATAAA
*
250899 ATACAAAA-AAAA
1 AAACAAAACAAAA
250911 AACTTTCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 1 0.04
17 13 0.50
18 12 0.46
ACGTcount: A:0.79, C:0.13, G:0.00, T:0.09
Consensus pattern (17 bp):
AAACAAAACAAAATAAA
Found at i:250905 original size:17 final size:17
Alignment explanation
Indices: 250864--250898 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
250854 CATTCGGCCC
250864 AAACAAAACAAAATAAAT
1 AAAC-AAACAAAATAAAT
250882 AAACAAACAAACATAAA
1 AAACAAACAAA-ATAAA
250899 ATACAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.77, C:0.14, G:0.00, T:0.09
Consensus pattern (17 bp):
AAACAAACAAAATAAAT
Found at i:250978 original size:28 final size:27
Alignment explanation
Indices: 250931--250985 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
250921 GAAAAGGTCC
250931 ATTAAACCCAATAGTCCAAATTACAAAA
1 ATTAAACCCAATAG-CCAAATTACAAAA
250959 ATTAAACCCAAGTA-CACAAATTACAAA
1 ATTAAACCCAA-TAGC-CAAATTACAAA
250986 TGACCCAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 1 0.04
28 22 0.88
29 2 0.08
ACGTcount: A:0.55, C:0.22, G:0.04, T:0.20
Consensus pattern (27 bp):
ATTAAACCCAATAGCCAAATTACAAAA
Found at i:254695 original size:2 final size:2
Alignment explanation
Indices: 254688--254712 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
254678 AATTAAATTG
254688 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
254713 AATAGTTATG
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:255775 original size:99 final size:99
Alignment explanation
Indices: 255604--255823 Score: 368
Period size: 99 Copynumber: 2.2 Consensus size: 99
255594 GACCACAAGT
*
255604 CGATGAGGCACTGGGTGCCAAATTACTTTGATTTAACCGATGAAACACTGGGTGTCACTTACATT
1 CGATGAGGCACTGGGTGCCAAATTACTTCGATTTAACCGATGAAACACTGGGTGTCACTTACATT
*
255669 ATAGCGCTGGGCACGACTATTACTTCGGTTTATC
66 ATAGCGCTGGGCACGACTATTACTTCGGTTTAGC
* * *
255703 CGATGAGGCACTGGGTGCCAAATTACTTCGGTTTAACCGATGAGACACTGGGTGTCACTTGCATT
1 CGATGAGGCACTGGGTGCCAAATTACTTCGATTTAACCGATGAAACACTGGGTGTCACTTACATT
*
255768 ATAGCGCTGGGCGCGACTATTACTTCGGTTTAGC
66 ATAGCGCTGGGCACGACTATTACTTCGGTTTAGC
* *
255802 TGATGAGGCACTAGGTGCCAAA
1 CGATGAGGCACTGGGTGCCAAA
255824 CTGGTGTGTT
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 113 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (99 bp):
CGATGAGGCACTGGGTGCCAAATTACTTCGATTTAACCGATGAAACACTGGGTGTCACTTACATT
ATAGCGCTGGGCACGACTATTACTTCGGTTTAGC
Done.