Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008044.1 Hibiscus syriacus cultivar Beakdansim tig00110532_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: 979496
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:8769 original size:24 final size:24
Alignment explanation
Indices: 8735--8788 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
8725 CTGAAAAATC
8735 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
8759 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
8783 ATCAAA
1 ATCAAA
8789 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:9654 original size:20 final size:20
Alignment explanation
Indices: 9629--9675 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
9619 AAATTCAGTA
* *
9629 TTGCGATGGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
9649 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
9669 TTGCGAT
1 TTGCGAT
9676 TTACGTATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:9685 original size:20 final size:20
Alignment explanation
Indices: 9662--9754 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
9652 CGATAGTCAG
*
9662 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
9682 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
9702 A-GCGCATTGCGATTTTTCAA
1 ATTCGCATTGCGA-TTTACGT
*
9722 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
9742 ATTCGCATTGCGA
1 ATTCGCATTGCGA
9755 ATTAAGAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
19 10 0.17
20 41 0.68
21 9 0.15
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:9775 original size:41 final size:40
Alignment explanation
Indices: 9684--9776 Score: 105
Period size: 41 Copynumber: 2.3 Consensus size: 40
9674 ATTTACGTAT
* ** *
9684 TCGCATTGCGATTTACGTAGCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGATTTACGTAGCGCATTGCGAATTAACAAAA
* * *
9724 TCGCGTTGCGATTTACGTATTCGCATTGCGAATTAAGAAAA
1 TCGCATTGCGATTTACGTA-GCGCATTGCGAATTAACAAAA
*
9765 TCGCAATGCGAT
1 TCGCATTGCGAT
9777 AGTCAGAATC
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 18 0.42
41 25 0.58
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (40 bp):
TCGCATTGCGATTTACGTAGCGCATTGCGAATTAACAAAA
Found at i:13165 original size:32 final size:31
Alignment explanation
Indices: 13095--13158 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
13085 AGTAAATTAT
** *
13095 CATAAAAGATGAGGGGACAAAGTGTAATTAA
1 CATAAAAGATGAGGGGACAAAGTCAAAATAA
13126 CCATAAAAGATGAAGGGGACAAAGTCAAAATAA
1 -CATAAAAGATG-AGGGGACAAAGTCAAAATAA
13159 ATTAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.52, C:0.09, G:0.23, T:0.16
Consensus pattern (31 bp):
CATAAAAGATGAGGGGACAAAGTCAAAATAA
Found at i:21081 original size:15 final size:15
Alignment explanation
Indices: 21061--21090 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21051 TTATGGGTTA
*
21061 AACAATAATTCTAAC
1 AACAATAAGTCTAAC
21076 AACAATAAGTCTAAC
1 AACAATAAGTCTAAC
21091 CATCAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.20, G:0.03, T:0.23
Consensus pattern (15 bp):
AACAATAAGTCTAAC
Found at i:27711 original size:23 final size:23
Alignment explanation
Indices: 27669--27753 Score: 136
Period size: 23 Copynumber: 3.7 Consensus size: 23
27659 ATAGGGCAGA
* *
27669 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
27691 GGGAACCGATTCCCCCTTTGAAA
1 GGGAACCGATTCCCCCTTTGAAG
27714 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
27737 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
27754 AGGGGAATCG
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
22 14 0.24
23 44 0.76
ACGTcount: A:0.24, C:0.32, G:0.25, T:0.20
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:27773 original size:20 final size:19
Alignment explanation
Indices: 27735--27777 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
27725 CCCCCTTTGA
*
27735 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATCCCCCCT
*
27754 AGGGGAATCGATACCCCCCT
1 AGGGGAACCGAT-CCCCCCT
27774 -GGGG
1 AGGGG
27778 TTCAGGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.21, C:0.33, G:0.33, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATCCCCCCT
Found at i:32390 original size:3 final size:3
Alignment explanation
Indices: 32382--32414 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
32372 ATTTGTAATG
32382 TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
32415 TTTTTGGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:34636 original size:45 final size:45
Alignment explanation
Indices: 34581--34701 Score: 152
Period size: 45 Copynumber: 2.7 Consensus size: 45
34571 ATGATACTGG
* *
34581 AGCCGATGGCAAGGAGCCTAAACCTAATACAGAAAATACCATCGA
1 AGCCAATGGCAAGGAGCCTAAACCTAATACAGAAAATACCACCGA
** * * *
34626 AGCCTTTGGCAAGGAGCCTAAACCTAATGCAGAAAATGCCGCCGA
1 AGCCAATGGCAAGGAGCCTAAACCTAATACAGAAAATACCACCGA
* * *
34671 AGCCAAAGGCAACGAGCCTAACCCTAATACA
1 AGCCAATGGCAAGGAGCCTAAACCTAATACA
34702 AAGAAGTTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 64 1.00
ACGTcount: A:0.39, C:0.27, G:0.21, T:0.13
Consensus pattern (45 bp):
AGCCAATGGCAAGGAGCCTAAACCTAATACAGAAAATACCACCGA
Found at i:36557 original size:14 final size:14
Alignment explanation
Indices: 36538--36564 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36528 ATTTACCAGT
36538 AACAAAATCATTTA
1 AACAAAATCATTTA
36552 AACAAAATCATTT
1 AACAAAATCATTT
36565 GTTTAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (14 bp):
AACAAAATCATTTA
Found at i:37131 original size:13 final size:13
Alignment explanation
Indices: 37115--37158 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
37105 ACATAAATAG
*
37115 TCAAAGTCAACCA
1 TCAAAGTCAACAA
* *
37128 TCAATGATCAACGA
1 TCAAAG-TCAACAA
37142 TCAAAGTCAACAA
1 TCAAAGTCAACAA
37155 TCAA
1 TCAA
37159 TGGTCAAGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.48, C:0.25, G:0.09, T:0.18
Consensus pattern (13 bp):
TCAAAGTCAACAA
Found at i:38359 original size:29 final size:29
Alignment explanation
Indices: 38305--38466 Score: 166
Period size: 29 Copynumber: 5.6 Consensus size: 29
38295 TATGTAGAGG
* * *
38305 ATCCCATGTAGAATCAGGATGAGGATATA
1 ATCCCATGCAGAATCAGAACGAGGATATA
* * *
38334 ATCTCATGCAAAATCAGAACGGGGATATA
1 ATCCCATGCAGAATCAGAACGAGGATATA
* *
38363 ATCCCATGCAAAATCA-ACAAGAGGATATA
1 ATCCCATGCAGAATCAGA-ACGAGGATATA
* * *
38392 ATCCCATGCAGACTCAGGACGGGGATATA
1 ATCCCATGCAGAATCAGAACGAGGATATA
* *
38421 ATCCTATGTAGAATCATG-ACGAGGATATA
1 ATCCCATGCAGAATCA-GAACGAGGATATA
*
38450 TTCCCATGCAGAATCAG
1 ATCCCATGCAGAATCAG
38467 GAATTCATCG
Statistics
Matches: 109, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
28 2 0.02
29 106 0.97
30 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (29 bp):
ATCCCATGCAGAATCAGAACGAGGATATA
Found at i:38455 original size:87 final size:87
Alignment explanation
Indices: 38305--38465 Score: 209
Period size: 87 Copynumber: 1.9 Consensus size: 87
38295 TATGTAGAGG
* * *
38305 ATCCCATGTAGAATCAGGATGAGGATATAATCTCATGCAAAATCAGAACGGGGATATAATCCCAT
1 ATCCCATGCAGAATCAGGACGAGGATATAATCTCATGCAAAATCAGAACGAGGATATAATCCCAT
38370 GCAAAATCAACAAGAGGATATA
66 GCAAAATCAACAAGAGGATATA
* * * * *
38392 ATCCCATGCAGACTCAGGACGGGGATATAATC-CTATGTAGAATCATG-ACGAGGATATATTCCC
1 ATCCCATGCAGAATCAGGACGAGGATATAATCTC-ATGCAAAATCA-GAACGAGGATATAATCCC
*
38455 ATGCAGAATCA
64 ATGCAAAATCA
38466 GGAATTCATC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
86 1 0.02
87 61 0.97
88 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (87 bp):
ATCCCATGCAGAATCAGGACGAGGATATAATCTCATGCAAAATCAGAACGAGGATATAATCCCAT
GCAAAATCAACAAGAGGATATA
Found at i:38467 original size:58 final size:58
Alignment explanation
Indices: 38305--38468 Score: 211
Period size: 58 Copynumber: 2.8 Consensus size: 58
38295 TATGTAGAGG
* * * * *
38305 ATCCCATGTAGAATCAGGATGAGGATATAATCTCATGCAAAATCAGAACGGGGATATA
1 ATCCCATGTAGAATCAAGAAGAGGATATAATCCCATGCAGAATCAGGACGGGGATATA
* * * *
38363 ATCCCATGCAAAATCAACAAGAGGATATAATCCCATGCAGACTCAGGACGGGGATATA
1 ATCCCATGTAGAATCAAGAAGAGGATATAATCCCATGCAGAATCAGGACGGGGATATA
* * * *
38421 ATCCTATGTAGAATCATGACGAGGATATATTCCCATGCAGAATCAGGA
1 ATCCCATGTAGAATCAAGAAGAGGATATAATCCCATGCAGAATCAGGA
38469 ATTCATCGGT
Statistics
Matches: 89, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 89 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (58 bp):
ATCCCATGTAGAATCAAGAAGAGGATATAATCCCATGCAGAATCAGGACGGGGATATA
Found at i:41471 original size:30 final size:30
Alignment explanation
Indices: 41437--41503 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
41427 GCTAACGTCG
* *
41437 AGTGATTATTTTGTAACAAAAGATAACATT
1 AGTGATCATTTTGAAACAAAAGATAACATT
* *
41467 AGTGAACATTTTGAAACAAATGATAACATT
1 AGTGATCATTTTGAAACAAAAGATAACATT
41497 AGTGATC
1 AGTGATC
41504 GATGTGACTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (30 bp):
AGTGATCATTTTGAAACAAAAGATAACATT
Found at i:43276 original size:66 final size:66
Alignment explanation
Indices: 43146--43285 Score: 185
Period size: 66 Copynumber: 2.1 Consensus size: 66
43136 AAAAACTGTT
* * * *
43146 AAGATTTAATAGTTAAAATTAATTAAAAATTAATTATTTTTTTATTATATATATGTATTAAATTT
1 AAGATTTAATAGTTAAAATTAATTAAAAATTAATTATTTTTTGATTAGAGATATGTAATAAATTT
43211 A
66 A
* *
43212 AAGATTTAATAGTTAAAATTAATTAAAATTTTAATTATTTTTTGATTAGAGA-A-GTTAATGAAT
1 AAGATTTAATAGTTAAAATTAATTAAAA-ATTAATTATTTTTTGATTAGAGATATG-TAATAAAT
43275 TTA
64 TTA
*
43278 AATATTTA
1 AAGATTTA
43286 GTTCAATAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
65 1 0.02
66 45 0.69
67 19 0.29
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (66 bp):
AAGATTTAATAGTTAAAATTAATTAAAAATTAATTATTTTTTGATTAGAGATATGTAATAAATTT
A
Found at i:45339 original size:13 final size:13
Alignment explanation
Indices: 45321--45347 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
45311 TAAAATAGTC
45321 TGTTATGTTTTCT
1 TGTTATGTTTTCT
45334 TGTTATGTTTTCT
1 TGTTATGTTTTCT
45347 T
1 T
45348 ATTTCATTCA
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:0.07, C:0.07, G:0.15, T:0.70
Consensus pattern (13 bp):
TGTTATGTTTTCT
Found at i:50064 original size:14 final size:14
Alignment explanation
Indices: 50045--50071 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
50035 TCTGATACCA
50045 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
50059 TGTAGAAAACAGA
1 TGTAGAAAACAGA
50072 ATAGTCTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.22, T:0.15
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:50892 original size:17 final size:16
Alignment explanation
Indices: 50870--50905 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
50860 TTATGAGGTG
*
50870 AAAATATTATTATTATA
1 AAAATATAATTATT-TA
50887 AAAATATAATTATTTA
1 AAAATATAATTATTTA
50903 AAA
1 AAA
50906 TAATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAATATAATTATTTA
Found at i:51275 original size:16 final size:17
Alignment explanation
Indices: 51233--51279 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
51223 ATGCATCAAA
51233 GTAATCTTATATTCCTC
1 GTAATCTTATATTCCTC
* * *
51250 CTAATGTTATATTCC-G
1 GTAATCTTATATTCCTC
51266 GTAATCTTAT-TTCC
1 GTAATCTTATATTCC
51280 AAATGTAATC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 4 0.16
16 8 0.32
17 13 0.52
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (17 bp):
GTAATCTTATATTCCTC
Found at i:57648 original size:14 final size:15
Alignment explanation
Indices: 57629--57698 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 15
57619 GGGTTCCTAC
57629 AAAAAAAA-TAAAAT
1 AAAAAAAATTAAAAT
57643 AAAAAAATTATTAATAAT
1 AAAAAAA--ATTAA-AAT
*
57661 AATAAATAAATTATAAT
1 AA-AAA-AAATTAAAAT
* *
57678 AATAAAAATAAAAAT
1 AAAAAAAATTAAAAT
57693 ATAAAA
1 A-AAAA
57699 CCCGGTCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
14 7 0.16
15 9 0.20
16 6 0.14
17 8 0.18
18 9 0.20
19 3 0.07
20 2 0.05
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAAAAATTAAAAT
Found at i:57662 original size:23 final size:22
Alignment explanation
Indices: 57635--57691 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
57625 CTACAAAAAA
57635 AATAAAATAAAAAAATTAT--T
1 AATAAAATAAAAAAATTATAAT
*
57655 AATAATAATAAATAAATTATAAT
1 AATAA-AATAAAAAAATTATAAT
57678 AATAAAAATAAAAA
1 AAT-AAAATAAAAA
57692 TATAAAACCC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 5 0.16
21 13 0.42
23 11 0.35
24 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
AATAAAATAAAAAAATTATAAT
Found at i:57677 original size:20 final size:21
Alignment explanation
Indices: 57635--57689 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
57625 CTACAAAAAA
*
57635 AATAA-AATAAAAAAATTATT
1 AATAATAATAAATAAATTATT
57655 AATAATAATAAATAAATTA-T
1 AATAATAATAAATAAATTATT
57675 AATAATAA-AAATAAA
1 AATAATAATAAATAAA
57690 AATATAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 7 0.21
20 14 0.42
21 12 0.36
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AATAATAATAAATAAATTATT
Found at i:57695 original size:20 final size:20
Alignment explanation
Indices: 57635--57696 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
57625 CTACAAAAAA
*
57635 AATAAAATAAAAAAATTATTAAT
1 AATAAAA-ATAAAAA-TA-TAAT
*
57658 AATAATAAAT-AAATTATAAT
1 AATAA-AAATAAAAATATAAT
57678 AATAAAAATAAAAATATAA
1 AATAAAAATAAAAATATAA
57697 AACCCGGTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 4 0.12
20 17 0.50
21 2 0.06
22 3 0.09
23 6 0.18
24 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AATAAAAATAAAAATATAAT
Found at i:62100 original size:18 final size:17
Alignment explanation
Indices: 62046--62094 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
62036 TTAGACCCTT
* *
62046 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
62064 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
62082 AGTGCATTCGATG
1 AGTGCA-TCGATG
62095 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:62135 original size:19 final size:19
Alignment explanation
Indices: 62111--62162 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
62101 AATAGCCAGA
* *
62111 GTGCATCGATGTATGGTTG
1 GTGCATCGATGCATGGCTG
62130 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
*
62149 GTGCATCAATGCAT
1 GTGCATCGATGCAT
62163 CAAATGCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTG
Found at i:62226 original size:84 final size:83
Alignment explanation
Indices: 62066--62228 Score: 211
Period size: 84 Copynumber: 2.0 Consensus size: 83
62056 TGCACTAAGA
* * * * * **
62066 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGTATGGTTGG
1 GTGCATCAATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAATGCATCGATGCATGGTAAG
62131 TGCATCGATGCATGGCTG
66 TGCATCGATGCATGGCTG
* * *
62149 GTGCATCAATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAATGCATCGGTGCATGGTA
1 GTGCATCAATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAATGCATCGATGCATGGTA
62213 AGTGCATCGATGCATG
64 AGTGCATCGATGCATG
62229 AAAAGCATTC
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
83 27 0.40
84 38 0.56
85 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (83 bp):
GTGCATCAATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAATGCATCGATGCATGGTAAG
TGCATCGATGCATGGCTG
Found at i:62283 original size:65 final size:65
Alignment explanation
Indices: 62128--62294 Score: 171
Period size: 65 Copynumber: 2.6 Consensus size: 65
62118 GATGTATGGT
* *
62128 TGGTGCATCGATGCATGGCTGGTGCATCAATGCATCAAATGCATTCGATGTTTTCATAAAATCCT
1 TGGTGCATCGATGCATGGTTGGTGCATCAATGCATCAAAAGCATTCGATG-TTTCATAAAAT-CT
62193 CA
64 CA
* * ** * * **
62195 --ATGCATCGGTGCATGGTAAGTGCATCGATGCATGAAAAGCATTCGATG-TTCAATTTAAT-TC
1 TGGTGCATCGATGCATGGTTGGTGCATCAATGCATCAAAAGCATTCGATGTTTC-ATAAAATCTC
62256 A
65 A
*
62257 TGGTGCATCGATGCATGGATTGGTGCATCAGTGCATCA
1 TGGTGCATCGATGCATGG-TTGGTGCATCAATGCATCA
62295 CTCTGAAAAA
Statistics
Matches: 79, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 19 0.24
65 54 0.68
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (65 bp):
TGGTGCATCGATGCATGGTTGGTGCATCAATGCATCAAAAGCATTCGATGTTTCATAAAATCTCA
Found at i:63291 original size:20 final size:20
Alignment explanation
Indices: 63266--63306 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
63256 ATAATTTTTT
63266 TATATTATTA-AAATTCATTA
1 TATATTATTACAAA-TCATTA
*
63286 TATATTTTTACAAATCATTA
1 TATATTATTACAAATCATTA
63306 T
1 T
63307 TTTTCTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (20 bp):
TATATTATTACAAATCATTA
Found at i:64428 original size:3 final size:3
Alignment explanation
Indices: 64422--64446 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
64412 CCTCCTCCTC
64422 CTG CTG CTG CTG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG C
64447 CGTGTACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.32, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:66987 original size:21 final size:21
Alignment explanation
Indices: 66960--67018 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
66950 TTCCGAGTTA
*
66960 CCCGCGACGGCCACAATAGCG
1 CCCGCGACGGCCGCAATAGCG
* *
66981 TCCGCGACAGCCGCAATAGCG
1 CCCGCGACGGCCGCAATAGCG
67002 CCCGCGACGGCCGCAAT
1 CCCGCGACGGCCGCAAT
67019 CACGGTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.42, G:0.29, T:0.07
Consensus pattern (21 bp):
CCCGCGACGGCCGCAATAGCG
Found at i:68136 original size:24 final size:24
Alignment explanation
Indices: 68108--68173 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
68098 TCAGCCACTA
* * * *
68108 CAGCCTCCGCAGCCGCCACAGTCT
1 CAGCCTCAGCAACAGCCACAATCT
68132 CAGCCTCAGCAACAGCCACAATCT
1 CAGCCTCAGCAACAGCCACAATCT
* * *
68156 CAGTCTCAACAGCAGCCA
1 CAGCCTCAGCAACAGCCA
68174 ACCACAAGAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.27, C:0.44, G:0.17, T:0.12
Consensus pattern (24 bp):
CAGCCTCAGCAACAGCCACAATCT
Found at i:71340 original size:2 final size:2
Alignment explanation
Indices: 71333--71373 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
71323 CGTGTTGTAA
* * *
71333 TC TC TC TC CC TC TC CC TC TC CC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
71374 ATCAACATAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (2 bp):
TC
Found at i:71371 original size:12 final size:12
Alignment explanation
Indices: 71333--71373 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
71323 CGTGTTGTAA
71333 TCTCTCTCCCTC
1 TCTCTCTCCCTC
*
71345 TCCCTCTCCCTC
1 TCTCTCTCCCTC
*
71357 TCTCTCTCTCTC
1 TCTCTCTCCCTC
71369 TCTCT
1 TCTCT
71374 ATCAACATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (12 bp):
TCTCTCTCCCTC
Found at i:78608 original size:15 final size:14
Alignment explanation
Indices: 78573--78612 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 14
78563 CAACGTTAGT
78573 TACAACTAACTTTA
1 TACAACTAACTTTA
78587 T---ACTAACGTTTA
1 TACAACTAAC-TTTA
78599 TACAACTAACTTTA
1 TACAACTAACTTTA
78613 GTTACAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
11 6 0.27
12 5 0.23
14 5 0.23
15 6 0.27
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.38
Consensus pattern (14 bp):
TACAACTAACTTTA
Found at i:83566 original size:106 final size:108
Alignment explanation
Indices: 83437--83693 Score: 288
Period size: 110 Copynumber: 2.4 Consensus size: 108
83427 AAGTATTGTT
* ** **
83437 TCGAGTCCAATATCC-TCTACTGTGAAGTTGAAATTGGTTCTG-G-AACTGGGAAATTATTTATT
1 TCGAGTCCAATATCCTTC-GCTGTGAAGTTGAAATTGACTCTGAGAAACTAAGAAATTATTTATT
*** * * *
83499 GACAGTTAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTACTGTC-
65 GACAACCAATCGCCCCTTCGTCGTGAAGTTGAACTTGTACTG-CA
* * *
83543 TCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAAGAAATTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-A-GAAACTAAGAAATTATTTAT
**
83608 TGACAACCAATCGCCCCTTCGTCGTGAAGTTGAACTTGTGTTGCA
64 TGACAACCAATCGCCCCTTCGTCGTGAAGTTGAACTTGTACTGCA
* *
83653 TTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGCCTCT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
83694 AAAAATGGGA
Statistics
Matches: 126, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
106 35 0.28
107 2 0.02
109 2 0.02
110 87 0.69
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.35
Consensus pattern (108 bp):
TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAGAAACTAAGAAATTATTTATTG
ACAACCAATCGCCCCTTCGTCGTGAAGTTGAACTTGTACTGCA
Found at i:84825 original size:7 final size:7
Alignment explanation
Indices: 84809--84860 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
84799 ACCCACCTTA
84809 TTTT-TC
1 TTTTCTC
84815 TTTTCTC
1 TTTTCTC
*
84822 TTTTCTT
1 TTTTCTC
*
84829 TTGTTCTT
1 TT-TTCTC
84837 TTTTCTC
1 TTTTCTC
84844 TTTTTCTC
1 -TTTTCTC
*
84852 TTTTTTC
1 TTTTCTC
84859 TT
1 TT
84861 CTTTCAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
6 4 0.10
7 22 0.55
8 14 0.35
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (7 bp):
TTTTCTC
Found at i:84840 original size:15 final size:15
Alignment explanation
Indices: 84817--84860 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
84807 TATTTTTCTT
*
84817 TTCTCTTTTCTTTTG
1 TTCTTTTTTCTTTTG
*
84832 TTCTTTTTTCTCTTTT
1 TTCTTTTTTCT-TTTG
84848 TCTCTTTTTTCTT
1 T-TCTTTTTTCTT
84861 CTTTCAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.40
16 5 0.20
17 10 0.40
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.77
Consensus pattern (15 bp):
TTCTTTTTTCTTTTG
Found at i:84845 original size:17 final size:18
Alignment explanation
Indices: 84824--84864 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
84814 CTTTTCTCTT
84824 TTCTTTTGT-TCTTTTTTC
1 TTCTTTT-TCTCTTTTTTC
84842 -TCTTTTTCTCTTTTTTC
1 TTCTTTTTCTCTTTTTTC
84859 TTCTTT
1 TTCTTT
84865 CAATTTAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 1 0.05
17 15 0.71
18 5 0.24
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (18 bp):
TTCTTTTTCTCTTTTTTC
Found at i:94039 original size:20 final size:20
Alignment explanation
Indices: 94014--94053 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
94004 AACAACAGAA
*
94014 TAAAACTGATTCTATCTAAT
1 TAAAACTGATCCTATCTAAT
94034 TAAAACTGATCCTATCTAAT
1 TAAAACTGATCCTATCTAAT
94054 AACTAACAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAACTGATCCTATCTAAT
Found at i:94084 original size:53 final size:53
Alignment explanation
Indices: 94003--94122 Score: 201
Period size: 53 Copynumber: 2.3 Consensus size: 53
93993 TGAATAAAAT
94003 TAAC-AACAGAAT--AAAACTGATTCTATCTAATTAAAACTGATCCTATCTAA
1 TAACTAACAGAATAAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAA
* *
94053 TAACTAACAGAATAAAAAATTGATTCTATCTAATTAAAACTGATCTTATCTAA
1 TAACTAACAGAATAAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAA
94106 TAACTAACAGAATAAAA
1 TAACTAACAGAATAAAA
94123 TATCTAGTTA
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
50 4 0.06
51 8 0.12
53 53 0.82
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (53 bp):
TAACTAACAGAATAAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAA
Found at i:96199 original size:17 final size:17
Alignment explanation
Indices: 96166--96203 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
96156 TCTCCCCCGG
96166 AAAAGAGTTTTTGTCAA
1 AAAAGAGTTTTTGTCAA
*
96183 AAAAG-GTTATTTTTCAA
1 AAAAGAGTT-TTTGTCAA
96200 AAAA
1 AAAA
96204 CGTGACATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.34
Consensus pattern (17 bp):
AAAAGAGTTTTTGTCAA
Found at i:98747 original size:53 final size:53
Alignment explanation
Indices: 98671--98786 Score: 191
Period size: 53 Copynumber: 2.2 Consensus size: 53
98661 TAAAATTAGC
* *
98671 AACAGAAT--AAAATTGATTCTATCTAATTAAAACTGATCATATCTAATAACT
1 AACAGAATAAAAAATTGATTATATCTAATTAAAACGGATCATATCTAATAACT
*
98722 AACAGAATAAAAAATTGATTATATCTAATTAAAACGGATCCTATCTAATAACT
1 AACAGAATAAAAAATTGATTATATCTAATTAAAACGGATCATATCTAATAACT
98775 AACAGAATAAAA
1 AACAGAATAAAA
98787 TATCTACTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 8 0.13
53 52 0.87
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.29
Consensus pattern (53 bp):
AACAGAATAAAAAATTGATTATATCTAATTAAAACGGATCATATCTAATAACT
Found at i:100233 original size:10 final size:10
Alignment explanation
Indices: 100220--100253 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
100210 AAAACCAAAA
100220 AAAATAATAT
1 AAAATAATAT
100230 AAAATAATAT
1 AAAATAATAT
*
100240 AATATAATAGT
1 AAAATAATA-T
100251 AAA
1 AAA
100254 GAACCAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 18 0.86
11 3 0.14
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (10 bp):
AAAATAATAT
Found at i:101667 original size:44 final size:44
Alignment explanation
Indices: 101619--101707 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
101609 GACATATTTT
*
101619 AATATTCAAATTTAAATAGATAATAATATCTTTTAGTATCTTTA
1 AATATTCAAATTTAAACAGATAATAATATCTTTTAGTATCTTTA
* *
101663 AATATTCAAATTTAAACATATAATAATATCTTTTATTATCTTTA
1 AATATTCAAATTTAAACAGATAATAATATCTTTTAGTATCTTTA
101707 A
1 A
101708 TTTTAAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (44 bp):
AATATTCAAATTTAAACAGATAATAATATCTTTTAGTATCTTTA
Found at i:102359 original size:2 final size:2
Alignment explanation
Indices: 102337--102511 Score: 152
Period size: 2 Copynumber: 95.0 Consensus size: 2
102327 AATAATACAA
*
102337 AT AT A- AT AT AT AA ACT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
102378 AT AT AT AT AT AT A- AT AA AT AT A- AC AT AT A- 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
* *
102417 AT -T GT AT A- AT AT AT A- AT AT AT AT AC A- AT AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
102453 A- AT A- AT A- AT A- AT A- AT AT AT AT AT AT AT AT A- 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
102489 A- AT AT AT AT ACT AT ACT AT AT AT
1 AT AT AT AT AT A-T AT A-T AT AT AT
102512 GCATATAAAA
Statistics
Matches: 145, Mismatches: 7, Indels: 42
0.75 0.04 0.22
Matches are distributed among these distances:
1 18 0.12
2 122 0.84
3 5 0.03
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:102363 original size:18 final size:17
Alignment explanation
Indices: 102337--102511 Score: 171
Period size: 16 Copynumber: 10.0 Consensus size: 17
102327 AATAATACAA
*
102337 ATATAATATATAAACTA-
1 ATATAATATATATA-TAT
102354 ATAT-ATATATATATAT
1 ATATAATATATATATAT
102370 ATAT-ATATATATATAT
1 ATATAATATATATATAT
* *
102386 ATATAATAAATATA-AC
1 ATATAATATATATATAT
102402 ATATAATATATATATATT
1 ATATAATATATATATA-T
*
102420 GTATAATATATAATATAT
1 ATATAATATAT-ATATAT
*
102438 ATACAATATAATAATAATAAT
1 ATATAATAT-AT-AT-AT-AT
102459 AATAATAATATATATATAT
1 -AT-ATAATATATATATAT
102478 ATATAATATATA-ATAT
1 ATATAATATATATATAT
*
102494 ATATACTATACTATATAT
1 ATATAATATA-TATATAT
102512 GCATATAAAA
Statistics
Matches: 136, Mismatches: 10, Indels: 23
0.80 0.06 0.14
Matches are distributed among these distances:
15 2 0.01
16 55 0.40
17 25 0.18
18 24 0.18
19 12 0.09
20 4 0.03
21 4 0.03
22 4 0.03
23 6 0.04
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
ATATAATATATATATAT
Found at i:110474 original size:24 final size:24
Alignment explanation
Indices: 110407--110466 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
110397 TACAAAGGCA
*
110407 TGTGCTTTTGCAGCAGACGAAACC
1 TGTGCTTTTGCAGCAGATGAAACC
* * *
110431 TATTCTTTTGCAGCAGATGAAACT
1 TGTGCTTTTGCAGCAGATGAAACC
110455 TGTGCTTTTGCA
1 TGTGCTTTTGCA
110467 ACTGATGAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (24 bp):
TGTGCTTTTGCAGCAGATGAAACC
Found at i:114316 original size:23 final size:23
Alignment explanation
Indices: 114290--114339 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
114280 TAGGCCCCCA
*
114290 TAGGATATCGGTACCTCCATAGC
1 TAGGATATCGATACCTCCATAGC
*
114313 TAGGTTATCGATACCTCCATAGC
1 TAGGATATCGATACCTCCATAGC
114336 TAGG
1 TAGG
114340 GTCCTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (23 bp):
TAGGATATCGATACCTCCATAGC
Found at i:117453 original size:19 final size:20
Alignment explanation
Indices: 117414--117455 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
117404 TTAGATTGTA
* *
117414 AAATAAGATAAATGAATATT
1 AAATAAGATAAAAGAAAATT
117434 AAATAA-ATAAAAGAAAATT
1 AAATAAGATAAAAGAAAATT
117453 AAA
1 AAA
117456 AATATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (20 bp):
AAATAAGATAAAAGAAAATT
Found at i:117483 original size:16 final size:16
Alignment explanation
Indices: 117447--117484 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
117437 TAAATAAAAG
117447 AAAATTA-AAAATATT
1 AAAATTAGAAAATATT
*
117462 -AAATTAGAAACTATT
1 AAAATTAGAAAATATT
117477 AAAATTAG
1 AAAATTAG
117485 GGGTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 6 0.30
15 7 0.35
16 7 0.35
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (16 bp):
AAAATTAGAAAATATT
Found at i:118760 original size:2 final size:2
Alignment explanation
Indices: 118755--118818 Score: 64
Period size: 2 Copynumber: 32.0 Consensus size: 2
118745 ACAGCCATTT
118755 TA TA TA TA TA TA TA TA TA -A TA TCA TA TA -A TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
118795 -A TA TA CTA TA CTA TA CTA TA TA TA
1 TA TA TA -TA TA -TA TA -TA TA TA TA
118819 CATAAAAAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
1 4 0.07
2 42 0.78
3 8 0.15
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:118791 original size:22 final size:22
Alignment explanation
Indices: 118755--118816 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 22
118745 ACAGCCATTT
118755 TATATATATATATATATAATAT-C
1 TATA-ATATA-ATATATAATATAC
118778 ATATAATATAATATATAATATAC
1 -TATAATATAATATATAATATAC
* *
118801 TATACTATACTATATA
1 TATAATATAATATATA
118817 TACATAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 25 0.71
23 6 0.17
24 4 0.11
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (22 bp):
TATAATATAATATATAATATAC
Found at i:127302 original size:26 final size:26
Alignment explanation
Indices: 127266--127318 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
127256 TTTATTCAGA
127266 ATAAAAGTTCGGAGGTGGGAAAAAGC
1 ATAAAAGTTCGGAGGTGGGAAAAAGC
*
127292 ATAAAAGTTCGGAGGTGGGAAGAAGC
1 ATAAAAGTTCGGAGGTGGGAAAAAGC
127318 A
1 A
127319 AAGGTTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.36, T:0.15
Consensus pattern (26 bp):
ATAAAAGTTCGGAGGTGGGAAAAAGC
Found at i:129340 original size:32 final size:30
Alignment explanation
Indices: 129287--129345 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
129277 GACTAAAATT
129287 AAAAAATATAATATTAATGATAATTTTATA
1 AAAAAATATAATATTAATGATAATTTTATA
129317 AAAAAATAT-ATAGTTCAATTGATAATTTT
1 AAAAAATATAATA-TT-AA-TGATAATTTT
129346 GTTTTGGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 3 0.12
30 11 0.42
31 2 0.08
32 10 0.38
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (30 bp):
AAAAAATATAATATTAATGATAATTTTATA
Found at i:130920 original size:17 final size:16
Alignment explanation
Indices: 130898--130931 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
130888 TAAAAACAGT
130898 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
130915 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
130931 A
1 A
130932 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:131450 original size:24 final size:24
Alignment explanation
Indices: 131406--131452 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
131396 ATAAAGAACC
*
131406 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
131430 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
131453 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:134637 original size:21 final size:21
Alignment explanation
Indices: 134598--134637 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
134588 CTGGGCTAGG
*
134598 GGAATCGATACCCATTCAAGA
1 GGAATCGATACCCACTCAAGA
*
134619 GGAATCGATACCCCCTCAA
1 GGAATCGATACCCACTCAA
134638 ACGACTATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.17
Consensus pattern (21 bp):
GGAATCGATACCCACTCAAGA
Found at i:135366 original size:103 final size:103
Alignment explanation
Indices: 135182--135502 Score: 572
Period size: 103 Copynumber: 3.1 Consensus size: 103
135172 GTAGAGGGTC
* *
135182 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAGGTCTGGTGAGACACATAC
*
135247 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
135285 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAGGTCTGGTGAGACACATAC
*
135350 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
135388 TATGTGGTCCTTCGAGACATATATATATTCTTTGGAACATGTGTGAA-GTCTGGTGAGACACATA
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGT-AAGGTCTGGTGAGACACATA
135452 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
65 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
135491 TATGTGGTCCTT
1 TATGTGGTCCTT
135503 ATGGACATTA
Statistics
Matches: 210, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
103 208 0.99
104 2 0.01
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:135552 original size:23 final size:23
Alignment explanation
Indices: 135519--135581 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
135509 ATTATTATAT
135519 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
135542 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
135565 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
135582 ATATGAGCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:141646 original size:18 final size:18
Alignment explanation
Indices: 141623--141659 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
141613 AGAACGCTAG
*
141623 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
*
141641 AGGGGAACCGATTCCCCC
1 AGGGGAACCGATACCCCC
141659 A
1 A
141660 TAATAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.35, G:0.27, T:0.11
Consensus pattern (18 bp):
AGGGGAACCGATACCCCC
Found at i:142403 original size:102 final size:103
Alignment explanation
Indices: 142139--142458 Score: 552
Period size: 103 Copynumber: 3.1 Consensus size: 103
142129 GTAGAGGGTC
*
142139 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACGCATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
*
142204 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATAA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
142242 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
* * *
142307 TTGATCCTTGGTATATGTATATGATTCTTAA-AAATGT
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* * *
142344 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
142409 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
142447 TATGTGGTCCTT
1 TATGTGGTCCTT
142459 ATGGACATTA
Statistics
Matches: 203, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
102 94 0.46
103 109 0.54
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:149362 original size:2 final size:2
Alignment explanation
Indices: 149355--149387 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
149345 AAAATATTAA
149355 AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
149388 CACTACTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:152208 original size:23 final size:24
Alignment explanation
Indices: 152165--152213 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
152155 AGTCTTCCTG
* *
152165 ATGATGTATAAAACATCTATGTAC
1 ATGATCTATAAAACATATATGTAC
152189 ATGATCTAT-AAACATATATGTAC
1 ATGATCTATAAAACATATATGTAC
152212 AT
1 AT
152214 TGTCATACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (24 bp):
ATGATCTATAAAACATATATGTAC
Found at i:152888 original size:45 final size:45
Alignment explanation
Indices: 152833--153191 Score: 601
Period size: 45 Copynumber: 8.0 Consensus size: 45
152823 ATTATTCATT
* *
152833 ATTTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATAC
1 ATTTT-ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
152879 AATTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
152924 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
152969 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGAACCGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
153014 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACTGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* **
153059 ATTTTATTTATGTCATCCTTTCATTTCTTTAATGCACCGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
153104 ATTTTATTTATGTCACCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
153149 ATATTATTTATGGCATCCTTTCATGCCTTTAATGAACCGTTAT
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTAT
153192 TATATTAAAT
Statistics
Matches: 295, Mismatches: 18, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
45 291 0.99
46 4 0.01
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.45
Consensus pattern (45 bp):
ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:153414 original size:23 final size:23
Alignment explanation
Indices: 153385--153432 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
153375 TATAATCTAC
153385 ACAAGCATCCATTAAAGGCACAT
1 ACAAGCATCCATTAAAGGCACAT
*
153408 ACAAGCATCCATTAAAGGCGCAT
1 ACAAGCATCCATTAAAGGCACAT
153431 AC
1 AC
153433 CATACAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.17
Consensus pattern (23 bp):
ACAAGCATCCATTAAAGGCACAT
Found at i:155153 original size:30 final size:31
Alignment explanation
Indices: 155095--155153 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
155085 AACCATGCAC
* * *
155095 AACTTTTCTAAAATTGCTAAATTAGTCCCTT
1 AACTTTTCAAAAATTACTAAAATAGTCCCTT
155126 AACTTTTCAAAAATTAC-AAAATAGTCCC
1 AACTTTTCAAAAATTACTAAAATAGTCCC
155154 CAAATTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (31 bp):
AACTTTTCAAAAATTACTAAAATAGTCCCTT
Found at i:165133 original size:21 final size:20
Alignment explanation
Indices: 165085--165137 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
165075 CCCTTCAAGG
*
165085 AGTATCGATACTCGGGGTCC
1 AGTATCGATACTCGGAGTCC
*
165105 AATATCGATACTCAGAGAG-CC
1 AGTATCGATACTC-G-GAGTCC
165126 AGTATCGATACT
1 AGTATCGATACT
165138 GACACATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.43
21 14 0.50
22 2 0.07
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (20 bp):
AGTATCGATACTCGGAGTCC
Found at i:176337 original size:14 final size:15
Alignment explanation
Indices: 176318--176354 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
176308 CCATTGTTTG
176318 TCTTCTTCCTC-TCT
1 TCTTCTTCCTCATCT
*
176332 TCTTCTTCATCATCT
1 TCTTCTTCCTCATCT
176347 TC-TCTTCC
1 TCTTCTTCC
176355 AAGTCAAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (15 bp):
TCTTCTTCCTCATCT
Found at i:205497 original size:24 final size:23
Alignment explanation
Indices: 205453--205499 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
205443 AGGGTTCTAC
* *
205453 GTGGTCTTTTGGGACATTTCATA
1 GTGGTCCTTTGGGACAATTCATA
205476 GTGGTCCTTTGGGACAAATTCATA
1 GTGGTCCTTTGGGAC-AATTCATA
205500 TGCCCCAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (23 bp):
GTGGTCCTTTGGGACAATTCATA
Found at i:213734 original size:18 final size:18
Alignment explanation
Indices: 213711--213745 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
213701 AAGATATATG
213711 ATATGAACATAAGAGATC
1 ATATGAACATAAGAGATC
*
213729 ATATGAACATGAGAGAT
1 ATATGAACATAAGAGAT
213746 GTGATTATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.09, G:0.20, T:0.23
Consensus pattern (18 bp):
ATATGAACATAAGAGATC
Found at i:218076 original size:27 final size:27
Alignment explanation
Indices: 218044--218106 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
218034 GAGATATGTG
218044 ATGATATGATAATATGTTATAAGATAT
1 ATGATATGATAATATGTTATAAGATAT
218071 ATGATATGATAATATGTTATAAGATAT
1 ATGATATGATAATATGTTATAAGATAT
218098 ATGATATGA
1 ATGATATGA
218107 ACATAAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (27 bp):
ATGATATGATAATATGTTATAAGATAT
Found at i:218124 original size:18 final size:18
Alignment explanation
Indices: 218101--218135 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
218091 AAGATATATG
218101 ATATGAACATAAGAGATC
1 ATATGAACATAAGAGATC
*
218119 ATATGAACATGAGAGAT
1 ATATGAACATAAGAGAT
218136 GTGATTATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.09, G:0.20, T:0.23
Consensus pattern (18 bp):
ATATGAACATAAGAGATC
Found at i:218372 original size:23 final size:24
Alignment explanation
Indices: 218342--218388 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
218332 AGGGTTATAC
* *
218342 GTGGTCCTTTGGGA-AATTTCATA
1 GTGGTCCTTCGGGACAAATTCATA
218365 GTGGTCCTTCGGGACAAATTCATA
1 GTGGTCCTTCGGGACAAATTCATA
218389 TGGCCCTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (24 bp):
GTGGTCCTTCGGGACAAATTCATA
Found at i:222337 original size:16 final size:18
Alignment explanation
Indices: 222316--222353 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
222306 CTTGATTTAA
222316 TTTTCCT-TTTT-CTTTT
1 TTTTCCTGTTTTCCTTTT
222332 TTTTCCTGTTTTCCTTTT
1 TTTTCCTGTTTTCCTTTT
222350 TTTT
1 TTTT
222354 TACCTAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 4 0.20
18 9 0.45
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTCCTGTTTTCCTTTT
Found at i:222656 original size:2 final size:2
Alignment explanation
Indices: 222649--222680 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
222639 ACAACAAAGG
222649 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
222681 TTAAAAGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:224351 original size:27 final size:27
Alignment explanation
Indices: 224321--224376 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
224311 GTAATTATGT
*
224321 AAAAATGAAAATGTAAATACAAACGTA
1 AAAAATGAAAATGCAAATACAAACGTA
* * *
224348 AAAAATGCAAATGCAAATGCAAATGTA
1 AAAAATGAAAATGCAAATACAAACGTA
224375 AA
1 AA
224377 TATGTTATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.61, C:0.09, G:0.12, T:0.18
Consensus pattern (27 bp):
AAAAATGAAAATGCAAATACAAACGTA
Found at i:226023 original size:28 final size:29
Alignment explanation
Indices: 225960--226025 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
225950 AATTTAATAC
*
225960 TTGAAAATAAAATAATATACATATAAATAT
1 TTGAAAAT-AAATAATATACATATAAAAAT
*
225990 TATGAAAAT-AATAAGTATATATA-AAAAAT
1 T-TGAAAATAAATAA-TATACATATAAAAAT
226019 TTGAAAA
1 TTGAAAA
226026 GAAAGAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 6 0.19
29 11 0.34
30 8 0.25
31 7 0.22
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.32
Consensus pattern (29 bp):
TTGAAAATAAATAATATACATATAAAAAT
Found at i:228241 original size:3 final size:3
Alignment explanation
Indices: 228233--228304 Score: 76
Period size: 3 Copynumber: 23.7 Consensus size: 3
228223 GGCCTGTTTG
* * *
228233 TAA TAA TAA AAA TAT TAAA TAA TAA AAA TATA TAA TAAA TAA TAA T-A
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA
228280 TAA TAA T-A TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
228305 TAAATAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 4 0.07
3 46 0.79
4 8 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:228269 original size:23 final size:23
Alignment explanation
Indices: 228238--228307 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 23
228228 GTTTGTAATA
*
228238 ATAAAAATATTAAATAATAAAAAT
1 ATAATAATA-TAAATAATAAAAAT
228262 AT-AT-A-ATAAATAAT---AAT
1 ATAATAATATAAATAATAAAAAT
*
228279 ATAATAATATAATAATAATAATAAT
1 ATAATAATAT-A-AATAATAAAAAT
228304 ATAA
1 ATAA
228308 ATAAAAATCG
Statistics
Matches: 37, Mismatches: 1, Indels: 15
0.70 0.02 0.28
Matches are distributed among these distances:
17 5 0.14
18 2 0.05
19 1 0.03
20 10 0.27
21 2 0.05
22 7 0.19
23 1 0.03
24 2 0.05
25 7 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAATAATATAAATAATAAAAAT
Found at i:228282 original size:25 final size:25
Alignment explanation
Indices: 228235--228308 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 25
228225 CCTGTTTGTA
* *
228235 ATAATAAAAATATTAAATAATAAAAAT
1 ATAATAATAATAAT-AAT-ATAAAAAT
*
228262 AT-ATAATAAATAATAATATAATAAT
1 ATAATAAT-AATAATAATATAAAAAT
228287 ATAATAATAATAATAATATAAA
1 ATAATAATAATAATAATATAAA
228309 TAAAAATCGG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 22 0.54
26 12 0.29
27 7 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (25 bp):
ATAATAATAATAATAATATAAAAAT
Found at i:228284 original size:8 final size:8
Alignment explanation
Indices: 228233--228307 Score: 78
Period size: 8 Copynumber: 10.4 Consensus size: 8
228223 GGCCTGTTTG
228233 TAATAATA
1 TAATAATA
228241 -AA-AATA
1 TAATAATA
228247 T--TAA-A
1 TAATAATA
228252 TAATAA-A
1 TAATAATA
228259 -AAT-ATA
1 TAATAATA
228265 TAATAA-A
1 TAATAATA
228272 TAATAATA
1 TAATAATA
228280 TAATAATA
1 TAATAATA
228288 TAATAATAA
1 TAATAAT-A
228297 TAATAATA
1 TAATAATA
228305 TAA
1 TAA
228308 ATAAAAATCG
Statistics
Matches: 58, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
5 3 0.05
6 10 0.17
7 16 0.28
8 21 0.36
9 8 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
TAATAATA
Found at i:228310 original size:23 final size:23
Alignment explanation
Indices: 228250--228310 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
228240 AAAAATATTA
*
228250 AATAATAAAAATATATAATAAAT
1 AATAATATAAATATATAATAAAT
228273 AATAATAT-AATAATATAATAATAAT
1 AATAATATAAAT-ATATAAT-A-AAT
228298 AATAATATAAATA
1 AATAATATAAATA
228311 AAAATCGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 3 0.09
23 14 0.42
24 1 0.03
25 12 0.36
26 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AATAATATAAATATATAATAAAT
Found at i:232248 original size:15 final size:15
Alignment explanation
Indices: 232226--232270 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
232216 TACAATATTA
232226 ATAC-TAATA-ATAT
1 ATACATAATATATAT
*
232239 ATAACTTAATATA-AT
1 AT-ACATAATATATAT
232254 ATACATAATATATAT
1 ATACATAATATATAT
232269 AT
1 AT
232271 TGTATATACG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 2 0.07
14 11 0.41
15 13 0.48
16 1 0.04
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
ATACATAATATATAT
Found at i:232316 original size:9 final size:9
Alignment explanation
Indices: 232247--232365 Score: 69
Period size: 9 Copynumber: 14.1 Consensus size: 9
232237 ATATAACTTA
232247 ATATAATAT
1 ATATAATAT
*
232256 ACATAATAT
1 ATATAATAT
* *
232265 ATATATTGT
1 ATATAATAT
***
232274 ATATACGCT
1 ATATAATAT
*
232283 ATTTAATAT
1 ATATAATAT
*
232292 A-ATACTAT
1 ATATAATAT
232300 ACTA-AATAT
1 A-TATAATAT
232309 ATATAATAT
1 ATATAATAT
232318 ATAT--TAT
1 ATATAATAT
232325 A-A-AATAT
1 ATATAATAT
232332 ATA-AATACT
1 ATATAATA-T
232341 ATAT-A-AT
1 ATATAATAT
232348 -TATAATAT
1 ATATAATAT
*
232356 ATATATTAT
1 ATATAATAT
232365 A
1 A
232366 CGTAACATTT
Statistics
Matches: 84, Mismatches: 15, Indels: 22
0.69 0.12 0.18
Matches are distributed among these distances:
6 4 0.05
7 10 0.12
8 16 0.19
9 53 0.63
10 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (9 bp):
ATATAATAT
Found at i:232331 original size:40 final size:40
Alignment explanation
Indices: 232288--232365 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
232278 ACGCTATTTA
232288 ATAT-AATACTATACTAAATATATATAATATATATTATAAAAT
1 ATATAAATACTATA-TAAATATA-AT-ATATATATTATAAAAT
*
232330 ATATAAATACTATATAATTATAATATATATATTATA
1 ATATAAATACTATATAAATATAATATATATATTATA
232366 CGTAACATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
40 12 0.35
41 2 0.06
42 11 0.32
43 9 0.26
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (40 bp):
ATATAAATACTATATAAATATAATATATATATTATAAAAT
Found at i:232958 original size:17 final size:17
Alignment explanation
Indices: 232917--232959 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
232907 TTCTACAAAT
232917 TTTTG-TTTAATCATAA
1 TTTTGTTTTAATCATAA
232933 TTTTGTTTTAATCATAA
1 TTTTGTTTTAATCATAA
232950 TTTTGTTTTA
1 TTTTGTTTTA
232960 TTAAGCTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.63
Consensus pattern (17 bp):
TTTTGTTTTAATCATAA
Found at i:241589 original size:23 final size:22
Alignment explanation
Indices: 241548--241604 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 22
241538 TAGTGCAGGA
*
241548 GGAATCGATACCCCCTTGAAGG
1 GGAATCGATTCCCCCTTGAAGG
241570 GGAATCGATTCCCCCTTTGAAGG
1 GGAATCGATTCCCCC-TTGAAGG
*
241593 GGAACCGATTCC
1 GGAATCGATTCC
241605 TTCCCAAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.21
Consensus pattern (22 bp):
GGAATCGATTCCCCCTTGAAGG
Found at i:259944 original size:11 final size:12
Alignment explanation
Indices: 259913--259937 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
259903 GCATTCAGAT
259913 GAAATGCAATGA
1 GAAATGCAATGA
259925 GAAATGCAATGA
1 GAAATGCAATGA
259937 G
1 G
259938 GATGCAACAA
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:0.48, C:0.08, G:0.28, T:0.16
Consensus pattern (12 bp):
GAAATGCAATGA
Found at i:265058 original size:11 final size:11
Alignment explanation
Indices: 265042--265074 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
265032 ATGAAATCGT
265042 GATCGATCGAC
1 GATCGATCGAC
265053 GATCGATCGAC
1 GATCGATCGAC
*
265064 GGTCGATCGAC
1 GATCGATCGAC
265075 CATCAAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.24, C:0.27, G:0.30, T:0.18
Consensus pattern (11 bp):
GATCGATCGAC
Found at i:265302 original size:18 final size:18
Alignment explanation
Indices: 265267--265301 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
265257 TTTTCAAAGT
*
265267 TTTGTGTTTATTTCAAAA
1 TTTGTGTTTATTTAAAAA
265285 TTTGTGTTT-TTTAAAAA
1 TTTGTGTTTATTTAAAAA
265302 AAATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (18 bp):
TTTGTGTTTATTTAAAAA
Found at i:265461 original size:29 final size:30
Alignment explanation
Indices: 265418--265476 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
265408 TTTGAGTTAT
* *
265418 GAAATGAAACGTTAGACACCAAATTGGAAC
1 GAAATGAAACATTAGACACCAAAATGGAAC
* *
265448 GAAAT-AAACATTAGGCACTAAAATGGAAC
1 GAAATGAAACATTAGACACCAAAATGGAAC
265477 AAAAGGCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.49, C:0.15, G:0.19, T:0.17
Consensus pattern (30 bp):
GAAATGAAACATTAGACACCAAAATGGAAC
Found at i:276636 original size:2 final size:2
Alignment explanation
Indices: 276624--276666 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
276614 ATAAAATAAA
276624 AT AT A- 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
276665 AT
1 AT
276667 TTCTTTCATA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:293031 original size:143 final size:140
Alignment explanation
Indices: 292749--293031 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
292739 AACTTGGCAT
292749 ATAACTATTGCTCTTTAATTATCTGTAAAATGATGTAGAGATGTTAATCATGTTCTTCTTCCGAT
1 ATAACTATTGCTCTTTAATTATCTGTAAAATGATGTAGAGATGTTAATCATGTTCTTCTTCCGAT
292814 TAAGATACACAAATTTCATTGATGAAGATTACCATAAAATGATCTAAATAGGGATGAAAAACTTG
66 TAAGATACACAAATTTCATTGATGAAGATTACCATAAAATGATCTAAATAGGGATGAAAAACTTG
292879 ATTCATCAAA
131 ATTCATCAAA
292889 ATAACTATTGCTCTTTAATTATCTGTAAAATGATGTAGAGATGTTAATCATGTTCTTCTTCCGAT
1 ATAACTATTGCTCTTTAATTATCTGTAAAATGATGTAGAGATGTTAATCATGTTCTTCTTCCGAT
292954 TAAGAATACACAAGAATTTCATTGATGAAGATTACCATAAAATGATCTAAATAGGGATGAAAAAC
66 TAAG-ATACAC-A-AATTTCATTGATGAAGATTACCATAAAATGATCTAAATAGGGATGAAAAAC
293019 TTGATTCATCAAA
128 TTGATTCATCAAA
293032 TCCATGAATG
Statistics
Matches: 140, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
140 69 0.49
141 6 0.04
142 1 0.01
143 64 0.46
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (140 bp):
ATAACTATTGCTCTTTAATTATCTGTAAAATGATGTAGAGATGTTAATCATGTTCTTCTTCCGAT
TAAGATACACAAATTTCATTGATGAAGATTACCATAAAATGATCTAAATAGGGATGAAAAACTTG
ATTCATCAAA
Found at i:296080 original size:14 final size:13
Alignment explanation
Indices: 296046--296080 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
296036 AAATTTTGAA
*
296046 AAAACTATGTTTG
1 AAAACAATGTTTG
296059 AAAACAATGTTTG
1 AAAACAATGTTTG
296072 AAAATCAAT
1 AAAA-CAAT
296081 ATATAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (13 bp):
AAAACAATGTTTG
Found at i:313758 original size:24 final size:26
Alignment explanation
Indices: 313717--313765 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
313707 TGGTTACTTA
313717 AAGAAGATGAATGATGGAGAAATGAAT
1 AAGAAGATGAATGATGGA-AAATGAAT
313744 AAGAAGAT-AA-G-TGGAAAATGAA
1 AAGAAGATGAATGATGGAAAATGAA
313766 ACCCACGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 7 0.32
24 4 0.18
25 1 0.05
26 2 0.09
27 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.16
Consensus pattern (26 bp):
AAGAAGATGAATGATGGAAAATGAAT
Found at i:319765 original size:21 final size:21
Alignment explanation
Indices: 319724--319766 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
319714 TTGTTTTTCA
*
319724 ATTTTGAAACATCATTTTTAT
1 ATTTTGAAACATCATTCTTAT
*
319745 ATTTTGAAA-ATAGATTCTTAT
1 ATTTTGAAACAT-CATTCTTAT
319766 A
1 A
319767 ATCCGAAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (21 bp):
ATTTTGAAACATCATTCTTAT
Found at i:320931 original size:64 final size:62
Alignment explanation
Indices: 320861--321040 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 62
320851 TGGAACACTT
* * *
320861 AGTGCATCGGTGCACTAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGA-AAAAGCCTG
1 AGTGCATCGATGCA-T-AGTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAA-CCCG
*
320925 AGTGCATCGATGCATGGTATGTGCATCGATGCATCAAATGCATTCGATGTTTTCATTAAAACCCG
1 AGTGCATCGATGCATAG--TGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-TAAAACCCG
* * * * *
320990 AGTGAATCGATGCATGGAGAGTGCATCGATGCATGAACTGCATTCCATGTT
1 AGTGCATCGATGCAT--AGTGTGCATCGATGCATCAAATGCATTCGATGTT
321041 CAATTAATTC
Statistics
Matches: 100, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 48 0.48
65 45 0.45
66 4 0.04
67 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (62 bp):
AGTGCATCGATGCATAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCG
Found at i:321032 original size:65 final size:64
Alignment explanation
Indices: 320881--321040 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 64
320871 TGCACTAAGT
* * * *
320881 GTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAAGCCCGAGTGAATCGATGCATGGTAA
320945 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATTAAAA-CCCGAGTGAATCGATGCATGG-A
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA--AAAAGCCCGAGTGAATCGATGCATGGTA
321008 GA
64 -A
* * *
321010 GTGCATCGATGCATGAACTGCATTCCATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
321041 CAATTAATTC
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 35 0.41
65 47 0.55
66 4 0.05
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAAGCCCGAGTGAATCGATGCATGGTAA
Found at i:321079 original size:65 final size:65
Alignment explanation
Indices: 320881--321082 Score: 186
Period size: 65 Copynumber: 3.1 Consensus size: 65
320871 TGCACTAAGT
* * *
320881 GTGCATCGATGCATCAAATGCATTCGATGTTT--TGAAAAAGCCTGAGTGCATCGATGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCCATGTTTCAT-TAAAA-CCCGAGTGCATCGATGCATGGAT
320943 AT-
64 -TG
* *
320945 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATTAAAACCCGAGTGAATCGATGCATGGA--
1 GTGCATCGATGCATCAAATGCATTCCATG-TTTCATTAAAACCCGAGTGCATCGATGCATGGATT
321008 G
65 G
* * ** **
321009 AGTGCATCGATGCATGAACTGCATTCCATG-TTCAATTAATTCATTG-GTGCATCGATGCATGGA
1 -GTGCATCGATGCATCAAATGCATTCCATGTTTC-ATTAAAAC-CCGAGTGCATCGATGCATGGA
321072 TTG
63 TTG
321075 GTGCATCG
1 GTGCATCG
321083 GTGTATCCCT
Statistics
Matches: 117, Mismatches: 11, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
63 3 0.03
64 51 0.44
65 57 0.49
66 5 0.04
67 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCCATGTTTCATTAAAACCCGAGTGCATCGATGCATGGATTG
Found at i:321559 original size:16 final size:16
Alignment explanation
Indices: 321538--321570 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
321528 CCCAATCAAA
*
321538 TGATGTCACGTGTCAC
1 TGATGTCACATGTCAC
321554 TGATGTCACATGTCAC
1 TGATGTCACATGTCAC
321570 T
1 T
321571 ATTTGGTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33
Consensus pattern (16 bp):
TGATGTCACATGTCAC
Found at i:321854 original size:20 final size:21
Alignment explanation
Indices: 321825--321869 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
321815 AATATTATTT
321825 ATATAGATTAATTT-TTAAAA
1 ATATAGATTAATTTATTAAAA
* *
321845 ATATATATTAATTTATTAAAT
1 ATATAGATTAATTTATTAAAA
321866 ATAT
1 ATAT
321870 TTTATTATAA
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:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATATAGATTAATTTATTAAAA
Found at i:321999 original size:30 final size:30
Alignment explanation
Indices: 321959--322102 Score: 113
Period size: 30 Copynumber: 4.9 Consensus size: 30
321949 TTAATATACG
*
321959 AATAAAATATATTTAATAATTTAAAATAAT
1 AATAAAATATATTTAATAAATTAAAATAAT
* * *
321989 AATATAATATATTTAGTAAATTAAGATAA-
1 AATAAAATATATTTAATAAATTAAAATAAT
* *
322018 AAT-ATATACT-TTTAA-AAGTTAAAATAAT
1 AATAAAATA-TATTTAATAAATTAAAATAAT
* * **
322046 AATAAAATATATTTTCAA-AACTTCAGCTAAT
1 AATAAAATATA-TTT-AATAAATTAAAATAAT
*
322077 AAT-AAATA-ATTTAATAAAATAAAATA
1 AATAAAATATATTTAATAAATTAAAATA
322103 TTTCAAAATT
Statistics
Matches: 88, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
27 12 0.14
28 20 0.23
29 9 0.10
30 33 0.38
31 14 0.16
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (30 bp):
AATAAAATATATTTAATAAATTAAAATAAT
Found at i:323684 original size:23 final size:24
Alignment explanation
Indices: 323642--323689 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
323632 ATGAAAAAAG
* *
323642 TGTCATAAAGACATAGAAAA-ATA
1 TGTCATAAAGACAAAAAAAAGATA
*
323665 TGTCATAAAGATAAAAAAAAGATA
1 TGTCATAAAGACAAAAAAAAGATA
323689 T
1 T
323690 ATCAAAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.23
Consensus pattern (24 bp):
TGTCATAAAGACAAAAAAAAGATA
Found at i:323702 original size:24 final size:23
Alignment explanation
Indices: 323658--323702 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
323648 AAAGACATAG
* * *
323658 AAAAATATGTCATAAAGATAAAA
1 AAAAATATATCAAAAACATAAAA
323681 AAAAGATATATCAAAAACATAA
1 AAAA-ATATATCAAAAACATAA
323703 TTATTAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (23 bp):
AAAAATATATCAAAAACATAAAA
Found at i:326944 original size:3 final size:3
Alignment explanation
Indices: 326936--326979 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
326926 TTACCTTTTT
326936 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
326980 TTATTATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:326989 original size:134 final size:133
Alignment explanation
Indices: 326727--326973 Score: 307
Period size: 134 Copynumber: 1.9 Consensus size: 133
326717 TTAACTATTT
* * ***
326727 GCTAATGCGATTCGCTCTTATGAAAATGTCTTCTCTTATATTTCTCTATCTAAAGACCTATTTGA
1 GCTAATGCGATTCGCTCTTATGAAAATGTCTTCACCTATATTTCTCTATCTAAAGACCTAAAAGA
* * * * * * * * * * * *
326792 TTACTTTTTTTAGTATTACTATTATTATTATTATCATTATTATATTAATTTAAAATACTATATTT
66 TTACCTTTTTTAATAATAC-ATAATAATAATAATAATAATAATAATAATATAAAATACTATATTT
326857 TTTC
130 TTTC
* *
326861 GCTAATGCTATTCGCTTTTATGAAAATGTCTTCACCTATATTTCTCTATCTAAAGACCTAAAAGA
1 GCTAATGCGATTCGCTCTTATGAAAATGTCTTCACCTATATTTCTCTATCTAAAGACCTAAAAGA
326926 TTACCTTTTTTAATAATA-ATAATAATAATAATAATAATAATAATAATA
66 TTACCTTTTTTAATAATACATAATAATAATAATAATAATAATAATAATA
326974 ATAATATTAT
Statistics
Matches: 94, Mismatches: 19, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
132 21 0.22
134 73 0.78
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (133 bp):
GCTAATGCGATTCGCTCTTATGAAAATGTCTTCACCTATATTTCTCTATCTAAAGACCTAAAAGA
TTACCTTTTTTAATAATACATAATAATAATAATAATAATAATAATAATATAAAATACTATATTTT
TTC
Found at i:327707 original size:31 final size:31
Alignment explanation
Indices: 327679--327739 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
327669 ATTAAATTGA
327679 TATTTTATCTAAATTTTA-CGGGTCAAATTAG
1 TATTTTATCTAAATTTTAGC-GGTCAAATTAG
327710 TATTTTATCTAAATTTTAGCGGTCAAATTA
1 TATTTTATCTAAATTTTAGCGGTCAAATTA
327740 AAAACCAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (31 bp):
TATTTTATCTAAATTTTAGCGGTCAAATTAG
Found at i:328601 original size:31 final size:31
Alignment explanation
Indices: 328566--328627 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
328556 ACTTATGATA
* *
328566 ATGTAGCGATTTAATCTAGATTTGATATAAT
1 ATGTAGCCATTTAATCTAGATGTGATATAAT
* *
328597 ATGTAGCCATTTCATCTAGATGTGATTTAAT
1 ATGTAGCCATTTAATCTAGATGTGATATAAT
328628 TCGATCGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (31 bp):
ATGTAGCCATTTAATCTAGATGTGATATAAT
Found at i:329411 original size:68 final size:69
Alignment explanation
Indices: 329339--329473 Score: 245
Period size: 68 Copynumber: 2.0 Consensus size: 69
329329 AAAAATTTGG
*
329339 TGAACAAAAGTTTATAAGGTTTGAATATTATAGTATAATTTTAAAGACTAAATTGATTAAAT-TT
1 TGAACAAAAGTTTATAAGGTTTGAATATTATAGTATAATTTTAAAGACTAAATTAATTAAATGTT
329403 TTAA
66 TTAA
*
329407 TGAACAAAAGTTTATAAGGTTTGAATATTATAGTATAATTTTAAAGACTAATTTAATTAAATGTT
1 TGAACAAAAGTTTATAAGGTTTGAATATTATAGTATAATTTTAAAGACTAAATTAATTAAATGTT
329472 TT
66 TT
329474 TAAAACAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
68 60 0.94
69 4 0.06
ACGTcount: A:0.43, C:0.03, G:0.12, T:0.42
Consensus pattern (69 bp):
TGAACAAAAGTTTATAAGGTTTGAATATTATAGTATAATTTTAAAGACTAAATTAATTAAATGTT
TTAA
Found at i:330132 original size:12 final size:11
Alignment explanation
Indices: 330107--330144 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
330097 ACATATATAC
330107 ATAAGTAA-AT
1 ATAAGTAATAT
330117 ATAAGTACATAT
1 ATAAGTA-ATAT
330129 ATAAGT-ATAT
1 ATAAGTAATAT
330139 ATAAGT
1 ATAAGT
330145 GTGTGCGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 17 0.65
11 1 0.04
12 8 0.31
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.34
Consensus pattern (11 bp):
ATAAGTAATAT
Found at i:330812 original size:14 final size:14
Alignment explanation
Indices: 330795--330840 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
330785 TTAATGAAAT
*
330795 TAATTTAATGATTA
1 TAATTTAAGGATTA
330809 TAA-TT-AGGATTTA
1 TAATTTAAGGA-TTA
*
330822 TAATATAAGGATTA
1 TAATTTAAGGATTA
330836 TAATT
1 TAATT
330841 ATAGTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
12 3 0.12
13 8 0.31
14 11 0.42
15 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (14 bp):
TAATTTAAGGATTA
Found at i:330843 original size:15 final size:13
Alignment explanation
Indices: 330799--330841 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
330789 TGAAATTAAT
*
330799 TTAATGATTATAA
1 TTAAGGATTATAA
330812 TT-AGGATTTATAA
1 TTAAGGA-TTATAA
330825 TATAAGGATTATAA
1 T-TAAGGATTATAA
330839 TTA
1 TTA
330842 TAGTTTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 3 0.12
13 11 0.42
14 8 0.31
15 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (13 bp):
TTAAGGATTATAA
Found at i:330848 original size:27 final size:27
Alignment explanation
Indices: 330795--330849 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
330785 TTAATGAAAT
* * *
330795 TAATTTAATGATTATAATTAGGATTTA
1 TAATATAAGGATTATAATTAAGATTTA
330822 TAATATAAGGATTATAATTATAG-TTTA
1 TAATATAAGGATTATAATTA-AGATTTA
330849 T
1 T
330850 TATAAATTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (27 bp):
TAATATAAGGATTATAATTAAGATTTA
Found at i:330999 original size:16 final size:16
Alignment explanation
Indices: 330978--331008 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
330968 TATAGGCCAG
330978 GTTTATAACAGGTCAA
1 GTTTATAACAGGTCAA
330994 GTTTATAACAGGTCA
1 GTTTATAACAGGTCA
331009 GGTAATACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (16 bp):
GTTTATAACAGGTCAA
Found at i:334059 original size:45 final size:45
Alignment explanation
Indices: 334008--334115 Score: 155
Period size: 45 Copynumber: 2.4 Consensus size: 45
333998 TATAAAATCT
* *
334008 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATACA
* * *
334053 CTTACCATTTGTTCAATAAGCTCGTAAGCTTATTTTACTAATACA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATACA
*
334098 CTTGCCA-TTATTCCATAA
1 CTTACCATTTATTCCATAA
334116 CCATATACCA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 9 0.16
45 46 0.84
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATACA
Found at i:334137 original size:20 final size:20
Alignment explanation
Indices: 334112--334154 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
334102 CCATTATTCC
* *
334112 ATAACCATATACCATAGAAA
1 ATAACCATAAACAATAGAAA
*
334132 ATAACCATAAACAATAGACA
1 ATAACCATAAACAATAGAAA
334152 ATA
1 ATA
334155 GCCCAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.58, C:0.19, G:0.05, T:0.19
Consensus pattern (20 bp):
ATAACCATAAACAATAGAAA
Found at i:334295 original size:60 final size:59
Alignment explanation
Indices: 334216--334345 Score: 161
Period size: 60 Copynumber: 2.2 Consensus size: 59
334206 CGTAGTGCAA
* * * * *
334216 TCCCGAATATGACACATAAGGTCGTGTCCACCATCTATACTAGGTATCCTTAAGTACAGT
1 TCCCGAATATGACACATAAGCTAGTGCCCACCATATACACTAGGTATCCTTAAGTACA-T
* * * **
334276 TCCCGAATATTACATATAAGCTAGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGCTAGTGCCCACCATATACACTAGGTATCCTTAAGTACAT
334335 TCCCGAATATG
1 TCCCGAATATG
334346 CAGCCTGCTG
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
59 11 0.19
60 48 0.81
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGCTAGTGCCCACCATATACACTAGGTATCCTTAAGTACAT
Found at i:341696 original size:7 final size:7
Alignment explanation
Indices: 341684--341709 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
341674 AGATTCACTA
341684 AAAATTG
1 AAAATTG
341691 AAAATTG
1 AAAATTG
341698 AAAATTG
1 AAAATTG
341705 AAAAT
1 AAAAT
341710 GACCCACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.27
Consensus pattern (7 bp):
AAAATTG
Done.