Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 2 of 195
Found at i:114108 original size:20 final size:21
Alignment explanation
Indices: 114075--114114 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
114065 TCCGACCAAC
114075 TTCCGACGAAA-TTTCCAGAT
1 TTCCGACGAAATTTTCCAGAT
* *
114095 TTCCGGCGACATTTTCCAGA
1 TTCCGACGAAATTTTCCAGA
114115 ATCCGGCACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (21 bp):
TTCCGACGAAATTTTCCAGAT
Found at i:114472 original size:8 final size:8
Alignment explanation
Indices: 114440--114592 Score: 53
Period size: 8 Copynumber: 18.2 Consensus size: 8
114430 CCGCTCCAGG
114440 TTTTTTT-
1 TTTTTTTA
114447 TTTTTTT-
1 TTTTTTTA
* **
114454 TCTTTGAA
1 TTTTTTTA
114462 TTTTTTTA
1 TTTTTTTA
114470 TTTGTTTATA
1 TTT-TTT-TA
114480 TGTTTTTTTA
1 --TTTTTTTA
114490 TTTTTTTA
1 TTTTTTTA
*
114498 TTTATTATA
1 TTT-TTTTA
**
114507 TTAGGTTTA
1 TT-TTTTTA
**
114516 -TTTAATA
1 TTTTTTTA
114523 TTCTTTTTA
1 TT-TTTTTA
*
114532 TCTTAGTTTA
1 T-TT-TTTTA
*
114542 TTTTTAT-
1 TTTTTTTA
114549 TTTTTTTA
1 TTTTTTTA
*
114557 CTTTCTTTA
1 -TTTTTTTA
*
114566 TTTTTATA
1 TTTTTTTA
* *
114574 TTATTATA
1 TTTTTTTA
114582 TTTTTATTA
1 TTTTT-TTA
114591 TT
1 TT
114593 CTATTTTCTT
Statistics
Matches: 106, Mismatches: 26, Indels: 26
0.67 0.16 0.16
Matches are distributed among these distances:
7 19 0.18
8 40 0.38
9 31 0.29
10 10 0.09
11 3 0.03
12 3 0.03
ACGTcount: A:0.18, C:0.03, G:0.04, T:0.75
Consensus pattern (8 bp):
TTTTTTTA
Found at i:114555 original size:25 final size:25
Alignment explanation
Indices: 114486--114572 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 25
114476 TATATGTTTT
* *
114486 TTTATTTTT-TTATTTATTATATTAGG
1 TTTATTTTTATT-TTTTTTATCTTA-G
* *
114512 TTTATTTAATATTCTTTTTATCTTAG
1 TTTATTT-TTATTTTTTTTATCTTAG
**
114538 TTTATTTTTATTTTTTTTA-CTTTC
1 TTTATTTTTATTTTTTTTATCTTAG
114562 TTTATTTTTAT
1 TTTATTTTTAT
114573 ATTATTATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
24 14 0.27
25 10 0.20
26 15 0.29
27 10 0.20
28 2 0.04
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (25 bp):
TTTATTTTTATTTTTTTTATCTTAG
Found at i:114730 original size:29 final size:30
Alignment explanation
Indices: 114698--114788 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 30
114688 GAGATTTTTG
114698 AGAAAAGTTGAAAGTATCAATTTTCCTT-A
1 AGAAAAGTTGAAAGTATCAATTTTCCTTGA
**
114727 AGAATAAAGTTTCGAAA--AAAAATATTT--TTGA
1 AG-A-AAAG-TT-GAAAGTATCAAT-TTTCCTTGA
*
114758 GGAAAAGTTGAAAGTATCAATTTTCCTTGA
1 AGAAAAGTTGAAAGTATCAATTTTCCTTGA
114788 A
1 A
114789 AATCAAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 19
0.65 0.08 0.27
Matches are distributed among these distances:
27 4 0.09
28 5 0.11
29 10 0.22
30 8 0.17
31 10 0.22
32 5 0.11
33 4 0.09
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (30 bp):
AGAAAAGTTGAAAGTATCAATTTTCCTTGA
Found at i:114746 original size:117 final size:117
Alignment explanation
Indices: 114607--114900 Score: 400
Period size: 117 Copynumber: 2.5 Consensus size: 117
114597 TTTCTTCAAA
*
114607 TAAAAATCAAATTTCAAAAAAAAATATTTTTAGGGAAAAAGTTGAAAGTATCAATTTTTCTT-AG
1 TAAAAAT-AAATTTC-AAAAAAAATATTTTT-GGG-AAAAGTTGAAAGTATCAATTTTCCTTGA-
* * *
114671 AAAT-ACATTTTC-AAAAAGAGATTTTTGA-GAAAAGTTGAAAGTATCAATTTTCCT
61 AAATCAAAATTTCAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
*
114725 TAAGAATAAAGTTTCGAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAA
1 TAAAAATAAA-TTTC-AAAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTGAAA
*
114790 ATCAAAATTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
63 ATCAAAATTTCAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* *
114845 TAAAAATAAATTTC-CAAAAAATATTTTTGGGGAAAAGTTAAAAGTATCAATTTTCC
1 TAAAAATAAATTTCAAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCC
114901 CTACACAAGA
Statistics
Matches: 159, Mismatches: 10, Indels: 15
0.86 0.05 0.08
Matches are distributed among these distances:
117 71 0.45
118 35 0.22
119 18 0.11
120 35 0.22
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (117 bp):
TAAAAATAAATTTCAAAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC
AAAATTTCAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
Found at i:114775 original size:60 final size:58
Alignment explanation
Indices: 114615--114900 Score: 368
Period size: 60 Copynumber: 4.9 Consensus size: 58
114605 AATAAAAATC
*
114615 AAATTTCAAAAAAAAATATTTTT-AGGGAAAAAGTTGAAAGTATCAATTTTTCTT-AGAAAT
1 AAATTTC-AAAAAAAATATTTTTGA-GG-AAAAGTTGAAAGTATCAATTTTCCTTAAG-AAT
* * *
114675 ACATTTTC-AAAAAGAGATTTTTGA-GAAAAGTTGAAAGTATCAATTTTCCTTAAGAAT
1 A-AATTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAAT
114732 AAAGTTTCGAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAA-AAT
1 AAA-TTTC-AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAGAAT
*
114792 CAAAATTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
1 --AAATTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAAT
* * *
114852 AAATTTC-CAAAAAATATTTTTGGGGAAAAGTTAAAAGTATCAATTTTCC
1 AAATTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
114901 CTACACAAGA
Statistics
Matches: 205, Mismatches: 10, Indels: 25
0.85 0.04 0.10
Matches are distributed among these distances:
56 1 0.00
57 72 0.35
58 10 0.05
59 28 0.14
60 80 0.39
61 11 0.05
62 3 0.01
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (58 bp):
AAATTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAAT
Found at i:120118 original size:80 final size:79
Alignment explanation
Indices: 120012--120457 Score: 623
Period size: 80 Copynumber: 5.5 Consensus size: 79
120002 GTCTAGGAGT
120012 ATTTACCTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTC-AAGTTCGT-TGCC
1 ATTTA-CTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TCGTGTGCC
*
120075 TCTGTTTAAAGGAGCA
64 TCTGTTTAGAGGAGCA
120091 ATTTACTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTTCAAAGTCGTGGT
1 ATTTACTTTCC-AAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTAC-TTTTCAAAGTCGT-GT
120155 GCCTCTGTTTAGAGGAGCA
61 GCCTCTGTTTAGAGGAGCA
* * *
120174 ATTTACTTTTCAAGTTCGTTGCCTCTGTTTAGAAGAGCAATTTACTTTCCAAAGTTCCGT-TGCC
1 ATTTACTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-T-CGTGTGCC
120238 TCTGTTTAGAGGAGCA
64 TCTGTTTAGAGGAGCA
*
120254 ATTTACTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCT
1 ATTTACTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT-GTGCCT
*
120319 TTGTTTAGAGGAGCA
65 CTGTTTAGAGGAGCA
*
120334 ATTTACTTTCCAAAGTTTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTTGTGC
1 ATTTACTTTCC-AAG-TTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCG-TGTGC
120399 CTCTGTTTAGAGGAGCA
63 CTCTGTTTAGAGGAGCA
*
120416 ATTTATGTTTCTCAAAG-TCGTTGAGCCTCTGTTTAGAGGAGC
1 ATTTA-CTTTC-C-AAGTTCGTT--GCCTCTGTTTAGAGGAGC
120458 TTTGGTCAAA
Statistics
Matches: 337, Mismatches: 11, Indels: 33
0.88 0.03 0.09
Matches are distributed among these distances:
78 13 0.04
79 9 0.03
80 136 0.40
81 38 0.11
82 80 0.24
83 38 0.11
84 23 0.07
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (79 bp):
ATTTACTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGTGCCTC
TGTTTAGAGGAGCA
Found at i:120129 original size:41 final size:40
Alignment explanation
Indices: 120012--120457 Score: 604
Period size: 41 Copynumber: 11.0 Consensus size: 40
120002 GTCTAGGAGT
120012 ATTTACCTTTCC-AAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTA-CTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
* *
120052 ATTTACTTTTC-AAGTTCGTTGCCTCTGTTTAAAGGAGCA
1 ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
120091 ATTTACTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
*
120132 ATTTACTTTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTAC-TTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
* *
120174 ATTTACTTTTC-AAGTTCGTTGCCTCTGTTTAGAAGAGCA
1 ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
120213 ATTTACTTTCCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTT-CGTTGCCTCTGTTTAGAGGAGCA
120254 ATTTACTTTCC-AAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
*
120293 ATTTACTTTCCAAAG-TCGTGGTGCCTTTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
120334 ATTTACTTTCCAAAGTTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAG-TTCGTTGCCTCTGTTTAGAGGAGCA
* *
120375 ATTTATTTTTCAAAG-TCGTTGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTTCG-T-TGCCTCTGTTTAGAGGAGCA
*
120416 ATTTATGTTTCTCAAAG-TCGTTGAGCCTCTGTTTAGAGGAGC
1 ATTTA-CTTTC-CAAAGTTCGTT--GCCTCTGTTTAGAGGAGC
120458 TTTGGTCAAA
Statistics
Matches: 374, Mismatches: 14, Indels: 33
0.89 0.03 0.08
Matches are distributed among these distances:
39 116 0.31
40 25 0.07
41 159 0.43
42 44 0.12
43 30 0.08
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (40 bp):
ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
Found at i:120249 original size:122 final size:120
Alignment explanation
Indices: 120019--120457 Score: 599
Period size: 122 Copynumber: 3.6 Consensus size: 120
120009 AGTATTTACC
*
120019 TTTCCAAGTTCGT-TGCCTCTGTTTAGAGGAGCAATTTACTTTTC-AAGTTCGTTGCCTCTGTTT
1 TTTCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TCGTTGCCTCTGTTT
120082 A-AAGGAGCAATTTACTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTT
64 AGAA-GAGCAATTTACTTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTT
120140 TTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTC-AAGTTCGTTGCCTCTGTTT
1 TTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TCGTTGCCTCTGTTT
120204 AGAAGAGCAATTTACTTTCCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTAC--
64 AGAAGAGCAATTTACTTTCCAAAGTT-CGTTGCCTCTGTTTAGAGGAGCAATTTACTT
* * *
120260 TTTCCAAGTTCGT-TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTTTGTT
1 TTTCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT--TGCCTCTGTT
*
120324 TAGAGGAGCAATTTACTTTCCAAAGTTTCGTTGCCTCTGTTTAGAGGAGCAATTTA-TT
63 TAGAAGAGCAATTTACTTTCCAAAG-TTCGTTGCCTCTGTTTAGAGGAGCAATTTACTT
*
120382 TTTCAAAGTCGTTGTGCCTCTGTTTAGAGGAGCAATTTATGTTTCTCAAAGTCGTTGAGCCTCTG
1 TTTCAAAGTCG-TGTGCCTCTGTTTAGAGGAGCAATTTA-CTTT-TCAAAGTCGTT--GCCTCTG
*
120447 TTTAGAGGAGC
61 TTTAGAAGAGC
120458 TTTGGTCAAA
Statistics
Matches: 291, Mismatches: 9, Indels: 32
0.88 0.03 0.10
Matches are distributed among these distances:
119 34 0.12
120 14 0.05
121 75 0.26
122 107 0.37
123 29 0.10
124 6 0.02
125 26 0.09
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (120 bp):
TTTCAAAGTCGTGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCTCTGTTTAG
AAGAGCAATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTT
Found at i:120508 original size:18 final size:18
Alignment explanation
Indices: 120465--120501 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
120455 AGCTTTGGTC
120465 AAAAACAAAAAAATAAAA
1 AAAAACAAAAAAATAAAA
120483 AAAAACAAAAAAATAAAA
1 AAAAACAAAAAAATAAAA
120501 A
1 A
120502 GTGACAACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.89, C:0.05, G:0.00, T:0.05
Consensus pattern (18 bp):
AAAAACAAAAAAATAAAA
Found at i:120712 original size:16 final size:16
Alignment explanation
Indices: 120693--120833 Score: 65
Period size: 16 Copynumber: 9.1 Consensus size: 16
120683 TCTTTTGTAT
120693 TTTATGTATT-TTATTA
1 TTTAT-TATTATTATTA
120709 TTTATTATTATTATTA
1 TTTATTATTATTATTA
* *
120725 TATATTAATA-TATGTA
1 TTTATTATTATTAT-TA
120741 --TATCT-TTATTTATTTA
1 TTTAT-TATTA-TTA-TTA
* *
120757 TTTATTTTCTATTAATA
1 TTTATTAT-TATTATTA
*
120774 TTTA-TATGTATT-GTA
1 TTTATTAT-TATTATTA
120789 TTTA-TA-TAGTTA-TA
1 TTTATTATTA-TTATTA
*
120803 TATATTATTA-TATT-
1 TTTATTATTATTATTA
120817 TTTATTATT-TTATTA
1 TTTATTATTATTATTA
120832 TT
1 TT
120834 AATTTTTTTT
Statistics
Matches: 99, Mismatches: 9, Indels: 35
0.69 0.06 0.24
Matches are distributed among these distances:
13 2 0.02
14 26 0.26
15 21 0.21
16 33 0.33
17 8 0.08
18 7 0.07
19 2 0.02
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:120763 original size:52 final size:51
Alignment explanation
Indices: 120693--120836 Score: 134
Period size: 52 Copynumber: 2.8 Consensus size: 51
120683 TCTTTTGTAT
* *
120693 TTTATGTATTTTA-TTATTTATTATTATTATTATATATTAATATATGTATATC
1 TTTATATA-TTTATTTATTT-TTATTATTATTATATATTAATATATGTATATA
* * * * *
120745 TTTATTTATTTATTTATTTTCTATTAATATT-TATATGTATTGTATTTATATA
1 TTTATATATTTATTTATTTT-TATTATTATTATATAT-TAATATATGTATATA
*
120797 GTTATATATATTATTATATTTTTATTATT-TTAT-TATTAAT
1 TTTATATAT-TTATT-TATTTTTATTATTATTATATATTAAT
120837 TTTTTTTTCT
Statistics
Matches: 76, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
51 13 0.17
52 45 0.59
53 12 0.16
54 6 0.08
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (51 bp):
TTTATATATTTATTTATTTTTATTATTATTATATATTAATATATGTATATA
Found at i:120816 original size:8 final size:8
Alignment explanation
Indices: 120703--120834 Score: 56
Period size: 8 Copynumber: 16.8 Consensus size: 8
120693 TTTATGTATT
120703 TTATTAT-
1 TTATTATA
120710 TTATTATTA
1 TTATTA-TA
120719 TTATTATA
1 TTATTATA
120727 -TATTA-A
1 TTATTATA
120733 TATATGTATA
1 T-TAT-TATA
120743 TCT-TTAT-
1 T-TATTATA
120750 TTATT-TA
1 TTATTATA
120757 TTTATT-T-
1 -TTATTATA
120764 TCTATTA-A
1 T-TATTATA
120772 -TATTTATA
1 TTA-TTATA
*
120780 TGTATTGTA
1 T-TATTATA
120789 TT-TATATA
1 TTAT-TATA
120797 GTTATATATA
1 -TTAT-TATA
120807 TTATTATA
1 TTATTATA
120815 TT-TT-TA
1 TTATTATA
*
120821 TTATTTTA
1 TTATTATA
120829 TTATTA
1 TTATTA
120835 ATTTTTTTTT
Statistics
Matches: 100, Mismatches: 4, Indels: 41
0.69 0.03 0.28
Matches are distributed among these distances:
6 10 0.10
7 26 0.26
8 33 0.33
9 20 0.20
10 11 0.11
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (8 bp):
TTATTATA
Found at i:121806 original size:21 final size:21
Alignment explanation
Indices: 121761--121814 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
121751 GCCGCTCCAG
*
121761 GTTTTTTTTTTTTCTTTGAAT
1 GTTTTTTTTATTTCTTTGAAT
*
121782 -TTTTTTTTATTTGTTT-ATAT
1 GTTTTTTTTATTTCTTTGA-AT
121802 GTTTTTTTTATTT
1 GTTTTTTTTATTT
121815 TTTTTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 16 0.55
21 12 0.41
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (21 bp):
GTTTTTTTTATTTCTTTGAAT
Found at i:121869 original size:17 final size:16
Alignment explanation
Indices: 121810--121874 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 16
121800 ATGTTTTTTT
*
121810 TATTTTTTTTATTTATTA
1 TATTATTTTTATTTA--A
**
121828 TATTAGGTTTATTTAA
1 TATTATTTTTATTTAA
* *
121844 TATTCTTTTTATCTTAG
1 TATTATTTTTAT-TTAA
121861 TATTATTTTTATTT
1 TATTATTTTTATTT
121875 TTGTTTTACT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
16 12 0.32
17 14 0.37
18 12 0.32
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (16 bp):
TATTATTTTTATTTAA
Found at i:121909 original size:27 final size:27
Alignment explanation
Indices: 121866--121920 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
121856 CTTAGTATTA
*
121866 TTTTTATTTTTGTTTTACT-TTTTTTAT
1 TTTTTATTTTTGATTTA-TATTTTTTAT
121893 TTTTTATTATTT-ATTTATATTTTTTAT
1 TTTTTATT-TTTGATTTATATTTTTTAT
121920 T
1 T
121921 ATTCTGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 1 0.04
27 21 0.84
28 3 0.12
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (27 bp):
TTTTTATTTTTGATTTATATTTTTTAT
Found at i:121913 original size:20 final size:20
Alignment explanation
Indices: 121780--121923 Score: 87
Period size: 20 Copynumber: 6.7 Consensus size: 20
121770 TTTTCTTTGA
* *
121780 ATTTTTTTTTATTTGTTTAT
1 ATTTTTTATTATTTATTTAT
* *
121800 ATGTTTTTTTTATTT-TTTTT
1 AT-TTTTTATTATTTATTTAT
121820 ATTTATTATATTAGGTTTATTTAAT
1 ATTT-TT-TATTA--TTTATTT-AT
*
121845 ATTCTTTTTATCTTAGTATTATTTTT
1 A-T-TTTTTA--TTA-T-TTATTTAT
*
121871 ATTTTTGTTTTACTTT-TTT-T
1 ATTTTT-TATTA-TTTATTTAT
121891 ATTTTTTATTATTTATTTAT
1 ATTTTTTATTATTTATTTAT
121911 ATTTTTTATTATT
1 ATTTTTTATTATT
121924 CTGTTTTCTT
Statistics
Matches: 102, Mismatches: 7, Indels: 30
0.73 0.05 0.22
Matches are distributed among these distances:
18 3 0.03
19 9 0.09
20 31 0.30
21 19 0.19
22 2 0.02
23 7 0.07
24 7 0.07
25 6 0.06
26 7 0.07
27 11 0.11
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.74
Consensus pattern (20 bp):
ATTTTTTATTATTTATTTAT
Found at i:122043 original size:59 final size:58
Alignment explanation
Indices: 121957--122173 Score: 314
Period size: 59 Copynumber: 3.7 Consensus size: 58
121947 AATTTTCCAA
*
121957 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATACATTTTC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-AAATAAATTTTC
* * *
122016 AAAAAAGAGATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAAGTTTC
1 AAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAA-AATAAATTTTC
*
122075 GAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
1 -AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAATAAATTTTC
*
122135 --AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTT
122174 TCCTACACAA
Statistics
Matches: 144, Mismatches: 9, Indels: 12
0.87 0.05 0.07
Matches are distributed among these distances:
57 38 0.26
58 2 0.01
59 51 0.35
60 50 0.35
61 3 0.02
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (58 bp):
AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAATTTTC
Found at i:122083 original size:119 final size:117
Alignment explanation
Indices: 121957--122173 Score: 371
Period size: 119 Copynumber: 1.8 Consensus size: 117
121947 AATTTTCCAA
* *
121957 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATACATTTTCAAAAAA
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC-AAAAA
122022 GAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAAGTTTCG
65 -AGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAAGTTTCG
*
122076 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAA
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAA
* *
122141 TATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
66 GATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
122174 TCCTACACAA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
117 32 0.34
118 5 0.05
119 56 0.60
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (117 bp):
AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAA
GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAAGTTTCG
Found at i:122109 original size:60 final size:59
Alignment explanation
Indices: 121957--122173 Score: 316
Period size: 60 Copynumber: 3.7 Consensus size: 59
121947 AATTTTCCAA
*
121957 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAATACATTTTC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAG-AATAAATTTTC
* * *
122016 AAAAAAGAGATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAAGTTTC
1 AAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTC
* *
122075 GAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
1 -AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTC
*
122135 --AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTT
122174 TCCTACACAA
Statistics
Matches: 144, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
57 38 0.26
58 1 0.01
59 50 0.35
60 54 0.38
61 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (59 bp):
AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTC
Found at i:122868 original size:100 final size:101
Alignment explanation
Indices: 122754--122997 Score: 271
Period size: 100 Copynumber: 2.4 Consensus size: 101
122744 ATTTGATAAA
*
122754 AAAAAAAGTAATCAATTAAGGTGTTCACTTTGA-A-AAACACCTTAATTGACATGAGCAAAT-AA
1 AAAAAAAGTAATCAATTAAGGTGTTCA-TAT-ACACAAACACCTTAATTGACATGAGCAAATAAA
* * * * * *
122816 GGTGTTCATCATTAGAAATGCCTTAATTGATTATGTGTT
64 GCT-TTCACCATTAGAAACGCCTTAATTGAGTATATATT
* * *
122855 AAAAAAA-TGATCAATTAAGGTGTTCATATACACAAACATCTTAATTGACTTGAGCAAATAAAGC
1 AAAAAAAGTAATCAATTAAGGTGTTCATATACACAAACACCTTAATTGACATGAGCAAATAAAGC
122919 TTTCACCATTAGAAACGCCTTAATTGAGTATATATT
66 TTTCACCATTAGAAACGCCTTAATTGAGTATATATT
** *
122955 AAAAACTAAAAAACGATCAATTAAGGCGTTCATATACACAAAC
1 -AAAA--AAAGTA--ATCAATTAAGGTGTTCATATACACAAAC
122998 TCTTTATTTG
Statistics
Matches: 121, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
98 1 0.01
99 3 0.02
100 72 0.60
101 15 0.12
103 3 0.02
106 27 0.22
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (101 bp):
AAAAAAAGTAATCAATTAAGGTGTTCATATACACAAACACCTTAATTGACATGAGCAAATAAAGC
TTTCACCATTAGAAACGCCTTAATTGAGTATATATT
Found at i:123103 original size:63 final size:63
Alignment explanation
Indices: 122957--123104 Score: 144
Period size: 63 Copynumber: 2.3 Consensus size: 63
122947 TATATATTAA
* * * *
122957 AAACT-AAAAAACGATCAATTAAGGCGTTCATATACACAAACTCTTTATTTGATGATGTTTTAT
1 AAACTAAAAAAAAG-TCAATTAAGGCGATCATATACACAAACTCTTTAATTGATAATGTTTTAT
* * * *
123020 AAATTATAAAACTAA-T-AATTAAGGTGATCATATTA-ACAAA-TGTTTTAATTGATAATGTTTT
1 AAACTA-AAAA-AAAGTCAATTAAGGCGATCATA-TACACAAACT-CTTTAATTGATAATGTTTT
123081 AT
62 AT
123083 AAACTAAAAAAAAGTCAATTAA
1 AAACTAAAAAAAAGTCAATTAA
123105 AATATTTATT
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
61 2 0.03
62 6 0.09
63 52 0.76
64 3 0.04
65 4 0.06
66 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.35
Consensus pattern (63 bp):
AAACTAAAAAAAAGTCAATTAAGGCGATCATATACACAAACTCTTTAATTGATAATGTTTTAT
Found at i:123747 original size:16 final size:16
Alignment explanation
Indices: 123728--123778 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
123718 AAACAATTAT
*
123728 AAATACTAACATTTAA
1 AAATACTAACATTTTA
* *
123744 AAATAAT-GCATTTTA
1 AAATACTAACATTTTA
*
123759 AAATACTAAAATTTTA
1 AAATACTAACATTTTA
123775 AAAT
1 AAAT
123779 GATGCATTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (16 bp):
AAATACTAACATTTTA
Found at i:123766 original size:31 final size:31
Alignment explanation
Indices: 123728--123786 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
123718 AAACAATTAT
*
123728 AAATACTAACATTTAAAAATAATGCATTTTA
1 AAATACTAAAATTTAAAAATAATGCATTTTA
* *
123759 AAATACTAAAATTTTAAAATGATGCATT
1 AAATACTAAAATTTAAAAATAATGCATT
123787 CTAACAAGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (31 bp):
AAATACTAAAATTTAAAAATAATGCATTTTA
Found at i:126173 original size:19 final size:20
Alignment explanation
Indices: 126129--126177 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
126119 ATATTTTCAA
126129 TAAAATTATATTTTTTATTT
1 TAAAATTATATTTTTTATTT
*
126149 TAAAATTGTATTTTTT-TTGT
1 TAAAATTATATTTTTTATT-T
126169 T-AAATTATA
1 TAAAATTATA
126178 AAATTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (20 bp):
TAAAATTATATTTTTTATTT
Found at i:126244 original size:91 final size:88
Alignment explanation
Indices: 126117--126372 Score: 245
Period size: 91 Copynumber: 2.8 Consensus size: 88
126107 AATTTTTATA
*
126117 ATATATTTTCAATAAAATTATATTTTTTATTTTAAAATTGTATTTTTTTTGTTAAATTATAAAAT
1 ATATATTTTCAAT-AAATTATTTTTTTTA-TTTAAAA-TGTATTTTTTTTGTTAAATTATAAAAT
*
126182 TTAAAAAAATCATT-TTTTTAAA-ATT
63 TTAAAAAAAT-ATTATTTTAAAATATT
* * *
126207 ATATATTTTCTAGATAAATTATTTTTTTTACTTTAAAAAATGTAATTCTTATTG--AAACTATAA
1 ATATATTTTC-A-ATAAATTATTTTTTTTA-TTT--AAAATGT-ATTTTTTTTGTTAAATTATAA
*
126270 AATTTTAAAAAATATTATTTTAAAATATT
60 AATTTAAAAAAATATTATTTTAAAATATT
* * * * * *
126299 ATATATTTTCAATAAACTTA-TATTTTTATCTAAAA-ATATATTATTTGTTAGAATTATAGAATT
1 ATATATTTTCAATAAA-TTATTTTTTTTATTTAAAATGTATTTTTTTTGTTA-AATTATAAAATT
126362 TCAAAAAAATA
64 T-AAAAAAATA
126373 AAATTTAATA
Statistics
Matches: 137, Mismatches: 17, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
85 6 0.04
86 1 0.01
87 5 0.04
88 11 0.08
89 10 0.07
90 25 0.18
91 49 0.36
92 18 0.13
93 12 0.09
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (88 bp):
ATATATTTTCAATAAATTATTTTTTTTATTTAAAATGTATTTTTTTTGTTAAATTATAAAATTTA
AAAAAATATTATTTTAAAATATT
Found at i:133701 original size:2 final size:2
Alignment explanation
Indices: 133694--133731 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
133684 CTTGTTATGT
133694 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
133732 AACGTGAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:134872 original size:15 final size:16
Alignment explanation
Indices: 134841--134873 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
134831 ATTAATAAAA
*
134841 TTTTCATTTTTACCTT
1 TTTTCATCTTTACCTT
134857 TTTTCATCTTTA-CTT
1 TTTTCATCTTTACCTT
134872 TT
1 TT
134874 GATTGCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTCATCTTTACCTT
Found at i:135656 original size:18 final size:18
Alignment explanation
Indices: 135633--135674 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
135623 AATTTCCATT
*
135633 TCTCACGCTCACGCTCAC
1 TCTCACGCTCACCCTCAC
* *
135651 TCTCACTCTCACCCTTAC
1 TCTCACGCTCACCCTCAC
135669 TCTCAC
1 TCTCAC
135675 ACACACACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.50, G:0.05, T:0.29
Consensus pattern (18 bp):
TCTCACGCTCACCCTCAC
Found at i:149419 original size:2 final size:2
Alignment explanation
Indices: 149412--149447 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
149402 TTCCTTCATA
149412 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
149448 CATCACATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:151061 original size:11 final size:11
Alignment explanation
Indices: 151045--151109 Score: 69
Period size: 11 Copynumber: 5.8 Consensus size: 11
151035 CGCCCCCGAC
151045 CAGCCACCCTA
1 CAGCCACCCTA
* *
151056 CAGCCACCGTT
1 CAGCCACCCTA
* *
151067 CAACTACCCTA
1 CAGCCACCCTA
151078 CCAGCC-CACCTA
1 -CAGCCAC-CCTA
151090 CAGCCACCCTA
1 CAGCCACCCTA
151101 CAGCCACCC
1 CAGCCACCC
151110 AGATTCCCCT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
11 35 0.81
12 8 0.19
ACGTcount: A:0.26, C:0.54, G:0.09, T:0.11
Consensus pattern (11 bp):
CAGCCACCCTA
Found at i:152442 original size:15 final size:15
Alignment explanation
Indices: 152408--152538 Score: 69
Period size: 15 Copynumber: 8.7 Consensus size: 15
152398 CCAAAAGCCC
* *
152408 TAAAATCCAAA-CCC
1 TAAAATCTAAATCCT
152422 TAAAATCTAAATCCT
1 TAAAATCTAAATCCT
*
152437 TAAAATCCGAAA-CCT
1 TAAAAT-CTAAATCCT
152452 CTAAAATCTAAA-CCT
1 -TAAAATCTAAATCCT
* * *
152467 CAAAATCCAAATCCC
1 TAAAATCTAAATCCT
*
152482 TAAAATTTAAAACTCC-
1 TAAAATCT-AAA-TCCT
152498 TAAAAT-TCAAAT-CT
1 TAAAATCT-AAATCCT
* *
152512 CAAAATCCAAAATTCC-
1 TAAAAT-CTAAA-TCCT
152528 TAAAATCTAAA
1 TAAAATCTAAA
152539 CCCAAACCTC
Statistics
Matches: 91, Mismatches: 15, Indels: 21
0.72 0.12 0.17
Matches are distributed among these distances:
13 1 0.01
14 25 0.27
15 36 0.40
16 25 0.27
17 4 0.04
ACGTcount: A:0.50, C:0.25, G:0.01, T:0.24
Consensus pattern (15 bp):
TAAAATCTAAATCCT
Found at i:152501 original size:45 final size:44
Alignment explanation
Indices: 152400--152538 Score: 138
Period size: 45 Copynumber: 3.1 Consensus size: 44
152390 TTAGGTTTCC
* * * *
152400 AAAAGCCCTAAAATCCAAACC-CTAAAATCTAAATCCTTAAAATCC
1 AAAA-CCCTAAAATCTAAACCTC-AAAATCCAAATCCCTAAAATCT
* *
152445 GAAACCTCTAAAATCTAAACCTCAAAATCCAAATCCCTAAAATTT
1 AAAACC-CTAAAATCTAAACCTCAAAATCCAAATCCCTAAAATCT
* *
152490 AAAACTCCTAAAAT-TCAAATCTCAAAATCCAAAATTCCTAAAATCT
1 AAAAC-CCTAAAATCT-AAACCTCAAAATCC-AAATCCCTAAAATCT
152536 AAA
1 AAA
152539 CCCAAACCTC
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
44 3 0.04
45 58 0.73
46 18 0.23
ACGTcount: A:0.50, C:0.26, G:0.01, T:0.23
Consensus pattern (44 bp):
AAAACCCTAAAATCTAAACCTCAAAATCCAAATCCCTAAAATCT
Found at i:152658 original size:31 final size:30
Alignment explanation
Indices: 152606--152663 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
152596 TCTTTCATAT
* *
152606 CTTAAAATTCAAGCTTTAAAACACTCTAAAC
1 CTTAAAATTCAACCTTCAAAAC-CTCTAAAC
152637 CTTAAAA-TCAAACCTTCAAAACCTCTA
1 CTTAAAATTC-AACCTTCAAAACCTCTA
152664 CTCAAGCCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.28
Consensus pattern (30 bp):
CTTAAAATTCAACCTTCAAAACCTCTAAAC
Found at i:154261 original size:63 final size:61
Alignment explanation
Indices: 154193--154394 Score: 167
Period size: 65 Copynumber: 3.2 Consensus size: 61
154183 CAAAAACGCT
*
154193 TTTAATAATCTCTGAAAAAATTTGTAAAGAATTATTAAAGACGTTTTTGACAAAAAAAACATC
1 TTTAATAATCTCTCAAAAAATTTGTAAAGAATTATTAAAGACGTTTTTGAC--AAAAAACATC
* * * *
154256 TTTAATATTCTCCTCAATAAAATATAG-AAAGAATTATTGAAAG-TGTTTTT-AGCCAAAAACAT
1 TTTAATAATCT-CTCAA-AAAAT-TTGTAAAGAATTATT-AAAGACGTTTTTGA-CAAAAAACAT
*
154318 T
61 C
* * * * * *
154319 TTTCAATAATCTCTCATAAAAATTTATTGAATGAATTATTTAAGACGTTTTTGACCAGAAATATC
1 TTT-AATAATCTCTCA-AAAAATTT-GT-AAAGAATTATTAAAGACGTTTTTGACAAAAAACATC
*
154384 TTGAATAATCT
1 TTTAATAATCT
154395 TATTGAATTT
Statistics
Matches: 111, Mismatches: 16, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
62 1 0.01
63 30 0.27
64 24 0.22
65 49 0.44
66 7 0.06
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (61 bp):
TTTAATAATCTCTCAAAAAATTTGTAAAGAATTATTAAAGACGTTTTTGACAAAAAACATC
Found at i:159366 original size:28 final size:29
Alignment explanation
Indices: 159287--159367 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 29
159277 ATTAGTATTT
*
159287 AAAATGATTTTT--TATTGAAATAATACA
1 AAAATAATTTTTAATATTGAAATAATACA
** * *
159314 AATTTAATTTTTTTAATAATAAAATAATA-A
1 AAAATAA--TTTTTAATATTGAAATAATACA
159344 AAAATAATTTTTAATATTGAAATA
1 AAAATAATTTTTAATATTGAAATA
159368 GTGTGATCAA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
27 4 0.10
28 15 0.37
29 5 0.12
30 6 0.15
31 11 0.27
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (29 bp):
AAAATAATTTTTAATATTGAAATAATACA
Found at i:163426 original size:2 final size:2
Alignment explanation
Indices: 163419--163444 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
163409 TGTAGGTTTA
163419 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
163445 CAAGTTCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:167115 original size:104 final size:104
Alignment explanation
Indices: 166935--167140 Score: 385
Period size: 104 Copynumber: 2.0 Consensus size: 104
166925 AGTATTTTTC
*
166935 CACGTAACTTGTCTTACCTTCATAATCAGGCTTCATTTTCAACGACCAGTTAGTTGGGACGAAAG
1 CACGTAACTTGTCTTACCTTCATAATCAGACTTCATTTTCAACGACCAGTTAGTTGGGACGAAAG
167000 AGCACGCAAAATATTTTATCAAATTTGACTATGACTTTG
66 AGCACGCAAAATATTTTATCAAATTTGACTATGACTTTG
167039 CACGTAACTTGTCTTACCTTCATAATCAGACTTCATTTTCAACGACCAGTTAGTTGGGACGAAAG
1 CACGTAACTTGTCTTACCTTCATAATCAGACTTCATTTTCAACGACCAGTTAGTTGGGACGAAAG
* *
167104 AGCACGTAAAATATTTTATCGAATTTGACTATGACTT
66 AGCACGCAAAATATTTTATCAAATTTGACTATGACTT
167141 GGCTTTCGAT
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 99 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (104 bp):
CACGTAACTTGTCTTACCTTCATAATCAGACTTCATTTTCAACGACCAGTTAGTTGGGACGAAAG
AGCACGCAAAATATTTTATCAAATTTGACTATGACTTTG
Found at i:171243 original size:20 final size:20
Alignment explanation
Indices: 171220--171257 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
171210 CTTAGACCAG
*
171220 AAATGTGTTCCTTAGGTCAA
1 AAATGTGTTACTTAGGTCAA
171240 AAATGTGTTACTTAGGTC
1 AAATGTGTTACTTAGGTC
171258 TAAGTCACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (20 bp):
AAATGTGTTACTTAGGTCAA
Found at i:174901 original size:22 final size:22
Alignment explanation
Indices: 174871--174919 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
174861 CATCTTCACA
*
174871 AACAGGCCCTTGATGGAACTTC
1 AACATGCCCTTGATGGAACTTC
174893 AACATGCCCTTGATGGAACTTC
1 AACATGCCCTTGATGGAACTTC
174915 AACAT
1 AACAT
174920 CATAGTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (22 bp):
AACATGCCCTTGATGGAACTTC
Found at i:177646 original size:29 final size:29
Alignment explanation
Indices: 177596--177655 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
177586 TCTATTTTTT
* *
177596 TATTATTATATAATGTATTAATAAATAAA
1 TATTATTATATAATGAACTAATAAATAAA
177625 TATTATTATATAA-GAAACTAATAAATAAA
1 TATTATTATATAATG-AACTAATAAATAAA
177654 TA
1 TA
177656 AAATTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (29 bp):
TATTATTATATAATGAACTAATAAATAAA
Found at i:186388 original size:31 final size:31
Alignment explanation
Indices: 186353--186413 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
186343 ACTGTTCATT
186353 ATTAACTTATTTTTTTCTTTTATTTTTTGAG
1 ATTAACTTATTTTTTTCTTTTATTTTTTGAG
*
186384 ATTAACTTTTTTTTTTCTTTTATTTTTTGA
1 ATTAACTTATTTTTTTCTTTTATTTTTTGA
186414 ATTTCTGGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (31 bp):
ATTAACTTATTTTTTTCTTTTATTTTTTGAG
Found at i:186626 original size:20 final size:20
Alignment explanation
Indices: 186588--186625 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
186578 TAGTATTGTT
186588 TTTTGTTTTCAAAAATTTTG
1 TTTTGTTTTCAAAAATTTTG
186608 TTTTGTTTT-AAAAATTTT
1 TTTTGTTTTCAAAAATTTT
186626 TTAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.63
Consensus pattern (20 bp):
TTTTGTTTTCAAAAATTTTG
Found at i:187498 original size:13 final size:13
Alignment explanation
Indices: 187463--187492 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
187453 AATTAAATTA
*
187463 TATTAAATAATAT
1 TATTGAATAATAT
187476 TATTGAATAATAT
1 TATTGAATAATAT
187489 TATT
1 TATT
187493 TCATAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
TATTGAATAATAT
Found at i:187507 original size:21 final size:22
Alignment explanation
Indices: 187481--187529 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
187471 AATATTATTG
187481 AATAATATT-ATT-TCATAAAAT
1 AATAATATTAATTAT-ATAAAAT
*
187502 AATAAT-TTAATTATATTAAAT
1 AATAATATTAATTATATAAAAT
187523 AATAATA
1 AATAATA
187530 CTTGATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 21 0.88
22 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AATAATATTAATTATATAAAAT
Found at i:187580 original size:20 final size:20
Alignment explanation
Indices: 187557--187626 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 20
187547 TTAATACCAT
*
187557 ATTAAAATTATATAATTTAA
1 ATTAATATTATATAATTTAA
*
187577 ATT-ATA-TGTAT-ATTTAA
1 ATTAATATTATATAATTTAA
187594 A-TAATATTATATCAATTTGAA
1 ATTAATATTATAT-AATTT-AA
187615 ATT-ATATTATAT
1 ATTAATATTATAT
187627 TATAGTGTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
16 1 0.02
17 10 0.24
18 8 0.20
19 2 0.05
20 7 0.17
21 12 0.29
22 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (20 bp):
ATTAATATTATATAATTTAA
Found at i:192587 original size:25 final size:25
Alignment explanation
Indices: 192559--192608 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
192549 TTGTTGTCTT
*
192559 GTCATACAAGAATTTCGTGATCTAC
1 GTCATACAAGAATTTCGTGACCTAC
192584 GTCATACAAGAATTTCGTGACCTAC
1 GTCATACAAGAATTTCGTGACCTAC
192609 ATTTACTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (25 bp):
GTCATACAAGAATTTCGTGACCTAC
Found at i:193796 original size:60 final size:61
Alignment explanation
Indices: 193656--193814 Score: 182
Period size: 61 Copynumber: 2.6 Consensus size: 61
193646 AAAATTGGGA
* *** * *
193656 ATTATTCAAGGCGTTTTT-GCCAAAAACGCCTTGAATAATCACCTCATAAAATTTGAAGTGG
1 ATTATTCAAGGCGTTTTTGGCC-AAAACGCCTTGAATAACCACAAAAAAAAATATGAAGTGG
*
193717 ATTATTGAAGGCGTTTTTGGCCATAAACGCCTTGAATAACCA-AAAAAAAAATGAT-AAG-GG
1 ATTATTCAAGGCGTTTTTGGCCA-AAACGCCTTGAATAACCACAAAAAAAAAT-ATGAAGTGG
* *
193777 ATTATTCAAGGTGTTTTTGGCCAAAATGCCTTGAATAA
1 ATTATTCAAGGCGTTTTTGGCCAAAACGCCTTGAATAA
193815 TCCCTCATAA
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
59 14 0.16
60 23 0.27
61 27 0.32
62 21 0.25
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (61 bp):
ATTATTCAAGGCGTTTTTGGCCAAAACGCCTTGAATAACCACAAAAAAAAATATGAAGTGG
Found at i:193827 original size:60 final size:61
Alignment explanation
Indices: 193656--193827 Score: 201
Period size: 60 Copynumber: 2.8 Consensus size: 61
193646 AAAATTGGGA
*
193656 ATTATTCAAGGCGTTTTT-GCCAAAAACGCCTTGAATAATCACCTCAT-AAAATTTGAAGTGG
1 ATTATTCAAGGCGTTTTTGGCC-AAAACGCCTTGAATAATC-CCTCATAAAAATATGAAGTGG
* *** *
193717 ATTATTGAAGGCGTTTTTGGCCATAAACGCCTTGAATAA-CCAAAAAAAAAATGAT-AAG-GG
1 ATTATTCAAGGCGTTTTTGGCCA-AAACGCCTTGAATAATCCCTCATAAAAAT-ATGAAGTGG
* *
193777 ATTATTCAAGGTGTTTTTGGCCAAAATGCCTTGAATAATCCCTCATAAAAA
1 ATTATTCAAGGCGTTTTTGGCCAAAACGCCTTGAATAATCCCTCATAAAAA
193828 ATTTTTTAGA
Statistics
Matches: 93, Mismatches: 13, Indels: 11
0.79 0.11 0.09
Matches are distributed among these distances:
59 14 0.15
60 33 0.35
61 27 0.29
62 19 0.20
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (61 bp):
ATTATTCAAGGCGTTTTTGGCCAAAACGCCTTGAATAATCCCTCATAAAAATATGAAGTGG
Found at i:193840 original size:60 final size:60
Alignment explanation
Indices: 193656--193877 Score: 186
Period size: 60 Copynumber: 3.7 Consensus size: 60
193646 AAAATTGGGA
* *
193656 ATTATTCAAGGCGTTTTT-GCCAAAAACGCCTTGAATAATCACCTCAT--AAAATTTGAAGTGG
1 ATTATTCAAGGCGTTTTTGGCC-AAAACGCCTTGAATAATC-CCTCATAAAAAATTT--ATTAG
* * * * * *
193717 ATTATTGAAGGCGTTTTTGGCCATAAACGCCTTGAATAA--CC-AAAAAAAAAATGATAAGGG
1 ATTATTCAAGGCGTTTTTGGCCA-AAACGCCTTGAATAATCCCTCATAAAAAATTTATTA--G
* * *
193777 ATTATTCAAGGTGTTTTTGGCCAAAATGCCTTGAATAATCCCTCATAAAAAATTTTTTAG
1 ATTATTCAAGGCGTTTTTGGCCAAAACGCCTTGAATAATCCCTCATAAAAAATTTATTAG
*** * *
193837 ATTATTCAAGATATTTTTGGCCAAAAACACCTTGGATAATC
1 ATTATTCAAGGCGTTTTTGGCC-AAAACGCCTTGAATAATC
193878 TCATGCAATT
Statistics
Matches: 129, Mismatches: 22, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
58 2 0.02
59 16 0.12
60 48 0.37
61 35 0.27
62 28 0.22
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (60 bp):
ATTATTCAAGGCGTTTTTGGCCAAAACGCCTTGAATAATCCCTCATAAAAAATTTATTAG
Found at i:193870 original size:120 final size:120
Alignment explanation
Indices: 193656--193875 Score: 275
Period size: 120 Copynumber: 1.8 Consensus size: 120
193646 AAAATTGGGA
*
193656 ATTATTCAAGGCGTTTTTGCCAAAAACGCCTTGAATAATCACCTCATAAAATTTGAAGTGGATTA
1 ATTATTCAAGGCGTTTTTGCCAAAAACGCCTTGAATAATCACCTCATAAAATTT-AAGTAGATTA
* * * * *
193721 TTGAAGGCGTTTTTGGCCATAAACGCCTTGAATAACCAAAAAAAAAATGATAAGGG
65 TTCAAGACATTTTTGGCCAAAAACACCTTGAATAACCAAAAAAAAAATGATAAGGG
* * **
193777 ATTATTCAAGGTGTTTTTGGCC-AAAATGCCTTGAATAATC-CCTCATAAAAAATTT-TTTAGAT
1 ATTATTCAAGGCGTTTTT-GCCAAAAACGCCTTGAATAATCACCTCAT--AAAATTTAAGTAGAT
* *
193839 TATTCAAGATATTTTTGGCCAAAAACACCTTGGATAA
63 TATTCAAGACATTTTTGGCCAAAAACACCTTGAATAA
193876 TCTCATGCAA
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
120 40 0.48
121 34 0.40
122 10 0.12
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (120 bp):
ATTATTCAAGGCGTTTTTGCCAAAAACGCCTTGAATAATCACCTCATAAAATTTAAGTAGATTAT
TCAAGACATTTTTGGCCAAAAACACCTTGAATAACCAAAAAAAAAATGATAAGGG
Found at i:196071 original size:12 final size:12
Alignment explanation
Indices: 196054--196078 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
196044 ATTTCCTTTT
196054 AGTTTTATTGCA
1 AGTTTTATTGCA
196066 AGTTTTATTGCA
1 AGTTTTATTGCA
196078 A
1 A
196079 AGCCCTGACC
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:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (12 bp):
AGTTTTATTGCA
Found at i:196967 original size:3 final size:3
Alignment explanation
Indices: 196959--196991 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
196949 CTATATTTTC
196959 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
196992 GTTCTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:202122 original size:12 final size:12
Alignment explanation
Indices: 202105--202129 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
202095 GATTTGGCCT
202105 AATAAATTTCTA
1 AATAAATTTCTA
202117 AATAAATTTCTA
1 AATAAATTTCTA
202129 A
1 A
202130 GCTTGTTGGT
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
AATAAATTTCTA
Found at i:208059 original size:4 final size:4
Alignment explanation
Indices: 208050--208075 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
208040 AACAATTGAC
208050 AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
208076 TCTAAGATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:218694 original size:18 final size:17
Alignment explanation
Indices: 218668--218714 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
218658 GACTAATTGT
**
218668 TTAATATATTTATTTTA
1 TTAATATATTTATCATA
218685 TTATATATATTTA-CATA
1 TTA-ATATATTTATCATA
218702 TTAATATATTTAT
1 TTAATATATTTAT
218715 AATTATAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 9 0.35
17 8 0.31
18 9 0.35
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TTAATATATTTATCATA
Found at i:220574 original size:20 final size:21
Alignment explanation
Indices: 220533--220578 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
220523 TCTGAAATTA
220533 ATAAAATATTATTTTTAAAAT
1 ATAAAATATTATTTTTAAAAT
*
220554 ATAAAATATTATTTTT-TAAT
1 ATAAAATATTATTTTTAAAAT
220574 ATAAA
1 ATAAA
220579 TATAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:220581 original size:19 final size:19
Alignment explanation
Indices: 220530--220581 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 19
220520 ATTTCTGAAA
220530 TTAATA-AAATATTATTTT
1 TTAATATAAATATTATTTT
*
220548 TAAAATATAAAATATTATTTT
1 T-TAATAT-AAATATTATTTT
220569 TTAATATAAATAT
1 TTAATATAAATAT
220582 AAAATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 1 0.03
19 10 0.34
20 5 0.17
21 13 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAATATAAATATTATTTT
Found at i:220600 original size:17 final size:16
Alignment explanation
Indices: 220572--220616 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
220562 TTATTTTTTA
220572 ATATAAATATAAA-ATT
1 ATATAAATATAAATA-T
220588 ATATAATATATAAATAT
1 ATATAA-ATATAAATAT
220605 ATATAAAT-TAAA
1 ATATAAATATAAA
220617 AATTAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.15
16 8 0.30
17 14 0.52
18 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAATATAAATAT
Found at i:223946 original size:19 final size:19
Alignment explanation
Indices: 223919--223957 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
223909 TTTTATTCTA
223919 TGATATGATATATAAT-TAT
1 TGATATGAT-TATAATATAT
*
223938 TGATTTGATTATAATATAT
1 TGATATGATTATAATATAT
223957 T
1 T
223958 TTTTAATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (19 bp):
TGATATGATTATAATATAT
Found at i:224246 original size:8 final size:8
Alignment explanation
Indices: 224233--224280 Score: 60
Period size: 8 Copynumber: 6.0 Consensus size: 8
224223 GATCACTCCT
224233 CATACACA
1 CATACACA
*
224241 CATACATA
1 CATACACA
*
224249 CATACATA
1 CATACACA
224257 CATACACA
1 CATACACA
*
224265 CACACACA
1 CATACACA
*
224273 CACACACA
1 CATACACA
224281 TATATATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (8 bp):
CATACACA
Found at i:224249 original size:4 final size:4
Alignment explanation
Indices: 224233--224262 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
224223 GATCACTCCT
*
224233 CATA CACA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CA
224263 CACACACACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (4 bp):
CATA
Found at i:224250 original size:12 final size:12
Alignment explanation
Indices: 224233--224278 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
224223 GATCACTCCT
224233 CATACACACATA
1 CATACACACATA
*
224245 CATACATACATA
1 CATACACACATA
*
224257 CATACACACACA
1 CATACACACATA
*
224269 CACACACACA
1 CATACACACA
224279 CATATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.50, C:0.37, G:0.00, T:0.13
Consensus pattern (12 bp):
CATACACACATA
Found at i:225780 original size:3 final size:3
Alignment explanation
Indices: 225774--225800 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
225764 ATCCTCCTTA
225774 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
225801 GAATTTCGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:230095 original size:13 final size:13
Alignment explanation
Indices: 230077--230101 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
230067 AATATTTCCC
230077 AATTTTTTTATTT
1 AATTTTTTTATTT
230090 AATTTTTTTATT
1 AATTTTTTTATT
230102 CTAAGAAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
AATTTTTTTATTT
Found at i:230669 original size:2 final size:2
Alignment explanation
Indices: 230662--230702 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
230652 GGGATGGTCT
230662 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
230703 TGATAAAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:234108 original size:25 final size:24
Alignment explanation
Indices: 234071--234118 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
234061 CTTTGGCAGA
*
234071 TAAGTGGAATATATTGTAAACCCTG
1 TAAGCGGAATATATTGT-AACCCTG
*
234096 TAAGCGGAGTATATTGTAACCCT
1 TAAGCGGAATATATTGTAACCCT
234119 CGTATGTCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (24 bp):
TAAGCGGAATATATTGTAACCCTG
Found at i:236903 original size:5 final size:5
Alignment explanation
Indices: 236893--236922 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
236883 GAGAATGCAA
236893 AATTT AATTT AATTT AATTT AATTT -ATTT A
1 AATTT AATTT AATTT AATTT AATTT AATTT A
236923 TACAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:239670 original size:4 final size:4
Alignment explanation
Indices: 239663--239688 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
239653 TCTCTCTCTT
239663 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
239689 ATATGAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:246352 original size:10 final size:10
Alignment explanation
Indices: 246337--246363 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
246327 GAAGGTAGTT
246337 TTTTATGCTC
1 TTTTATGCTC
246347 TTTTATGCTC
1 TTTTATGCTC
246357 TTTTATG
1 TTTTATG
246364 TTAGTATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.15, G:0.11, T:0.63
Consensus pattern (10 bp):
TTTTATGCTC
Found at i:247592 original size:2 final size:2
Alignment explanation
Indices: 247585--247616 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
247575 ATGGGTTCTG
247585 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
247617 GTGATCCAAA
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:252144 original size:197 final size:197
Alignment explanation
Indices: 251809--252204 Score: 765
Period size: 197 Copynumber: 2.0 Consensus size: 197
251799 TGCCAGCATT
251809 CAGCACATATGACTTAGCATTAACACTTGGTGGGATTTGCAGATTCAGAAACCCTCTTTCTCCAT
1 CAGCACATATGACTTAGCATTAACACTTGGTGGGATTTGCAGATTCAGAAACCCTCTTTCTCCAT
251874 ATCAAGGCCTCATAAGTTTACTTGTATAAATTGTCATAATTAGTAACATCAGTTGTGTCTTAACT
66 ATCAAGGCCTCATAAGTTTACTTGTATAAATTGTCATAATTAGTAACATCAGTTGTGTCTTAACT
251939 AATGCTTATATCTAGGCTATTCCATGTCTACAAGTCCAACATGAAGCAGATTGTCATGTAATGTC
131 AATGCTTATATCTAGGCTATTCCATGTCTACAAGTCCAACATGAAGCAGATTGTCATGTAATGTC
252004 AA
196 AA
252006 CAGCACATATGACTTAGCATTAACACTTGGTGGGATTTGCAGATTCAGAAACCCTCTTTCTCCAT
1 CAGCACATATGACTTAGCATTAACACTTGGTGGGATTTGCAGATTCAGAAACCCTCTTTCTCCAT
*
252071 ATCAAGGCCTCATAAGTTTACTTGTATAAATTGTCATAATTAGTCACATCAGTTGTGTCTTAACT
66 ATCAAGGCCTCATAAGTTTACTTGTATAAATTGTCATAATTAGTAACATCAGTTGTGTCTTAACT
* *
252136 AATGCTTATATCTAGGCTATTCCATTTCTACAAGTCCAACATTAAGCAGATTGTCATGTAATGTC
131 AATGCTTATATCTAGGCTATTCCATGTCTACAAGTCCAACATGAAGCAGATTGTCATGTAATGTC
252201 AA
196 AA
252203 CA
1 CA
252205 AACAGAAGAT
Statistics
Matches: 196, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
197 196 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (197 bp):
CAGCACATATGACTTAGCATTAACACTTGGTGGGATTTGCAGATTCAGAAACCCTCTTTCTCCAT
ATCAAGGCCTCATAAGTTTACTTGTATAAATTGTCATAATTAGTAACATCAGTTGTGTCTTAACT
AATGCTTATATCTAGGCTATTCCATGTCTACAAGTCCAACATGAAGCAGATTGTCATGTAATGTC
AA
Found at i:255589 original size:2 final size:2
Alignment explanation
Indices: 255584--255616 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
255574 TGTGTGCACA
255584 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
255617 CTAGATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:258268 original size:38 final size:38
Alignment explanation
Indices: 258219--258291 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
258209 TTCAGGTAAT
258219 TTAGTTAAGCTACCTGCAAAAGCCGATTCGGCTATAAG
1 TTAGTTAAGCTACCTGCAAAAGCCGATTCGGCTATAAG
* *
258257 TTAGTTAAGCTATCTGTAAAAGCCGATTCGGCTAT
1 TTAGTTAAGCTACCTGCAAAAGCCGATTCGGCTAT
258292 GTTATTGACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (38 bp):
TTAGTTAAGCTACCTGCAAAAGCCGATTCGGCTATAAG
Found at i:260118 original size:16 final size:16
Alignment explanation
Indices: 260097--260129 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
260087 GTACAATATC
260097 TTTCTAAAAGTTTATT
1 TTTCTAAAAGTTTATT
260113 TTTCTAAAAGTTTATT
1 TTTCTAAAAGTTTATT
260129 T
1 T
260130 ATGGTAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTCTAAAAGTTTATT
Found at i:267055 original size:2 final size:2
Alignment explanation
Indices: 267048--267096 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
267038 TTAAATATGA
* *
267048 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
267090 AT AT AT A
1 AT AT AT A
267097 AAGGAAGTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:284428 original size:2 final size:2
Alignment explanation
Indices: 284421--284456 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
284411 TGAATTAATC
284421 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
284457 TAAGAGCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:286765 original size:19 final size:19
Alignment explanation
Indices: 286743--286781 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
286733 ATTGGATCTA
286743 TGATTAAATATAAAGTAAT
1 TGATTAAATATAAAGTAAT
** *
286762 TGATTTGATTTAAAGTAAT
1 TGATTAAATATAAAGTAAT
286781 T
1 T
286782 TTAATAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (19 bp):
TGATTAAATATAAAGTAAT
Found at i:294576 original size:2 final size:2
Alignment explanation
Indices: 294571--294603 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
294561 ACACACACAC
*
294571 AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
294604 ATTGGAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:295546 original size:2 final size:2
Alignment explanation
Indices: 295539--295569 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
295529 AATGAATTAA
295539 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
295570 TACAGACTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:304137 original size:12 final size:12
Alignment explanation
Indices: 304107--304131 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
304097 TATTAGTAAA
304107 GCATAAAAGATC
1 GCATAAAAGATC
304119 GCATAAAAGATC
1 GCATAAAAGATC
304131 G
1 G
304132 TCTAAAGTTA
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:0.16, G:0.20, T:0.16
Consensus pattern (12 bp):
GCATAAAAGATC
Found at i:310649 original size:17 final size:17
Alignment explanation
Indices: 310627--310661 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
310617 TCCACTCACA
310627 AACAAACATACATACCC
1 AACAAACATACATACCC
310644 AACAAACATACATACCC
1 AACAAACATACATACCC
310661 A
1 A
310662 TAAGACGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.34, G:0.00, T:0.11
Consensus pattern (17 bp):
AACAAACATACATACCC
Found at i:310935 original size:11 final size:11
Alignment explanation
Indices: 310906--310936 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
310896 GCAATATCTG
*
310906 ACAAATCCCAA
1 ACAAATCTCAA
310917 ACAAATCTCAA
1 ACAAATCTCAA
310928 ACAAATCTC
1 ACAAATCTC
310937 TTATGAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:311273 original size:25 final size:26
Alignment explanation
Indices: 311214--311279 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
311204 TTCCTATGTC
*
311214 TCGAACCTTCGGCTCTTTTCACATCT
1 TCGAACCTTCAGCTCTTTTCACATCT
* * *
311240 T-GAATCTTCAACTCTTTTCACGT-T
1 TCGAACCTTCAGCTCTTTTCACATCT
311264 TCGAACCTTCAGCTCT
1 TCGAACCTTCAGCTCT
311280 GAGATCACTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
24 2 0.06
25 30 0.91
26 1 0.03
ACGTcount: A:0.18, C:0.32, G:0.11, T:0.39
Consensus pattern (26 bp):
TCGAACCTTCAGCTCTTTTCACATCT
Found at i:311869 original size:52 final size:51
Alignment explanation
Indices: 311812--311965 Score: 168
Period size: 52 Copynumber: 3.0 Consensus size: 51
311802 ATAACCATAC
* * *
311812 AAATTTG-CTCATTAAAAATCTCTCTCATCTTAAAATTCTTCTCTTATAAGTA
1 AAATTTGCCT-ATTAAGAATCTCTTTC-TCTTAAAATTCTTCTCTTGTAAGTA
* * * *
311864 AAATTTGCCTATTAAGAATCTCTTTCTTTTTAGAATT-TTCTCTTGCAAGTC
1 AAATTTGCCTATTAAGAATCTCTTTC-TCTTAAAATTCTTCTCTTGTAAGTA
* * *
311915 AAACTTACCTATTAAGAATCTTCTTTCTCTTAAAATTCTTCTTTTGTAAGT
1 AAATTTGCCTATTAAGAATC-TCTTTCTCTTAAAATTCTTCTCTTGTAAGT
311966 CTTTTTGTCT
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
51 37 0.44
52 46 0.54
53 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (51 bp):
AAATTTGCCTATTAAGAATCTCTTTCTCTTAAAATTCTTCTCTTGTAAGTA
Found at i:312016 original size:22 final size:22
Alignment explanation
Indices: 311991--312033 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
311981 GCAATATCTG
*
311991 ACAAATCCCAAATAAATCTCTA
1 ACAAATCCCAAACAAATCTCTA
*
312013 ACAAATCTCAAACAAATCTCT
1 ACAAATCCCAAACAAATCTCT
312034 TATGAGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (22 bp):
ACAAATCCCAAACAAATCTCTA
Found at i:312018 original size:11 final size:11
Alignment explanation
Indices: 312004--312033 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
311994 AATCCCAAAT
312004 AAATCTCTAAC
1 AAATCTCTAAC
*
312015 AAATCTCAAAC
1 AAATCTCTAAC
312026 AAATCTCT
1 AAATCTCT
312034 TATGAGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATCTCTAAC
Found at i:312993 original size:52 final size:52
Alignment explanation
Indices: 312931--313045 Score: 158
Period size: 52 Copynumber: 2.2 Consensus size: 52
312921 AAATTTGCTC
*
312931 ATTAAGAATCTCTCTCCTCTTAAAATTCTTATCTTATAAGTAAAACTTACCT
1 ATTAAGAATCTCTCTCCTCTTAAAATTCTTATCTTACAAGTAAAACTTACCT
* * * * * * *
312983 ATTAAAAATCTCTTTCCTTTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
1 ATTAAGAATCTCTCTCCTCTTAAAATTCTTATCTTACAAGTAAAACTTACCT
313035 ATTAAGAATCT
1 ATTAAGAATCT
313046 TTTTTTCTTG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (52 bp):
ATTAAGAATCTCTCTCCTCTTAAAATTCTTATCTTACAAGTAAAACTTACCT
Found at i:313980 original size:15 final size:17
Alignment explanation
Indices: 313949--313982 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
313939 TCCCTTCTCC
313949 TTTTT-CTTTCTGTTTT
1 TTTTTACTTTCTGTTTT
313965 TTTTTACTTT-TGTTTT
1 TTTTTACTTTCTGTTTT
313981 TT
1 TT
313983 ATACTTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.03, C:0.09, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTTACTTTCTGTTTT
Found at i:318673 original size:14 final size:15
Alignment explanation
Indices: 318651--318691 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
318641 CTAACTCTCC
318651 CTTTTCTTTTTTCT-
1 CTTTTCTTTTTTCTG
* *
318665 CTTTGCTTTTTTTTG
1 CTTTTCTTTTTTCTG
318680 CTTTTCTTTTTT
1 CTTTTCTTTTTT
318692 TTTACTTGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (15 bp):
CTTTTCTTTTTTCTG
Found at i:318676 original size:16 final size:15
Alignment explanation
Indices: 318651--318693 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
318641 CTAACTCTCC
*
318651 CTTTTCTTTTTTCT-
1 CTTTTCTTTTTTTTG
*
318665 CTTTGCTTTTTTTTG
1 CTTTTCTTTTTTTTG
318680 CTTTTCTTTTTTTT
1 CTTTTCTTTTTTTT
318694 TACTTGGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (15 bp):
CTTTTCTTTTTTTTG
Found at i:319317 original size:17 final size:18
Alignment explanation
Indices: 319284--319329 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
319274 GAGGGAATTT
*
319284 TGTATTTTTCTCTTTTTA
1 TGTATTTTTTTCTTTTTA
319302 TGTATTTTTTTC-TTTTA
1 TGTATTTTTTTCTTTTTA
*
319319 TCTATTTTTTT
1 TGTATTTTTTT
319330 ATGGGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.76
Consensus pattern (18 bp):
TGTATTTTTTTCTTTTTA
Found at i:329945 original size:2 final size:2
Alignment explanation
Indices: 329938--329965 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
329928 AATTGTCAAC
329938 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
329966 CGCTTGCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:334535 original size:2 final size:2
Alignment explanation
Indices: 334528--334561 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
334518 AACCCTCTAA
334528 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
334562 TTTAATCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:349885 original size:33 final size:32
Alignment explanation
Indices: 349826--349915 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 32
349816 GAAATTTTCT
* * *
349826 AATTAA-AATTTTTATTTTTTATTATTAAAATTAA
1 AATTAATAATTTATA-TATTTA-TATT-AAATAAA
**
349860 AATTAATAATTTATATATTTATATTATGTAAA
1 AATTAATAATTTATATATTTATATTAAATAAA
349892 ATATTAATAATTTATATATTTATA
1 A-ATTAATAATTTATATATTTATA
349916 GTATGTGTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
32 5 0.10
33 26 0.53
34 11 0.22
35 7 0.14
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (32 bp):
AATTAATAATTTATATATTTATATTAAATAAA
Found at i:350026 original size:11 final size:11
Alignment explanation
Indices: 350006--350045 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
349996 TTACATAATT
350006 TTTTTCATATTA
1 TTTTT-ATATTA
350018 TTTTTATATTA
1 TTTTTATATTA
350029 TATTATTATATTA
1 T-TT-TTATATTA
350042 TTTT
1 TTTT
350046 AAATTACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 8 0.31
12 9 0.35
13 9 0.35
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTATATTA
Found at i:350728 original size:19 final size:19
Alignment explanation
Indices: 350704--350748 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
350694 ATTTGTTTTT
350704 TATTATAAAGTA-AATAAAA
1 TATTATAAA-TATAATAAAA
*
350723 TATTATAAATATATTAAAA
1 TATTATAAATATAATAAAA
350742 T-TTATAA
1 TATTATAA
350749 CTATTACACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
TATTATAAATATAATAAAA
Found at i:355011 original size:14 final size:14
Alignment explanation
Indices: 354992--355020 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
354982 AAACATATGC
354992 TGTACATATATATA
1 TGTACATATATATA
355006 TGTACATATATATA
1 TGTACATATATATA
355020 T
1 T
355021 ATATATCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TGTACATATATATA
Found at i:357883 original size:57 final size:60
Alignment explanation
Indices: 357810--357970 Score: 197
Period size: 61 Copynumber: 2.7 Consensus size: 60
357800 TTTTTACATA
*
357810 AATTATTTAAGATG-TTTTTCTAATTAAAACACCTTAAAAGA-TTT-GAAAAAAAAAA-TC
1 AATTATTTAAGATGTTTTTTC-AATTAAAACACCTTAAAAGACTTTAAAAAAAAAAAACTC
* ***
357867 AATTATTTAAGGTGTTTTTTCAATTAAAATGTCTTAAAA-ACTTTTAAAAAAAAAAAAACTC
1 AATTATTTAAGATGTTTTTTCAATTAAAACACCTTAAAAGAC-TTT-AAAAAAAAAAAACTC
* *
357928 AATTATTTAAAATATTTTTTCAATTAAAACACCTTAAAAGACT
1 AATTATTTAAGATGTTTTTTCAATTAAAACACCTTAAAAGACT
357971 AATTTCTCTG
Statistics
Matches: 86, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
56 1 0.01
57 28 0.33
58 9 0.10
60 10 0.12
61 36 0.42
62 2 0.02
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (60 bp):
AATTATTTAAGATGTTTTTTCAATTAAAACACCTTAAAAGACTTTAAAAAAAAAAAACTC
Found at i:363965 original size:64 final size:64
Alignment explanation
Indices: 363636--363968 Score: 214
Period size: 64 Copynumber: 5.2 Consensus size: 64
363626 AACCAAAGAT
* * * * *
363636 CTTAATTGACTTATTTTTTAATTTATAAAACATCATCAATTAAGGC-ATGTGTTATTATG-ATCG
1 CTTAATTGA-TAATTTTTTTATTTATAAAACATCATTAATTAAGGCTATTTTTTATTATGAAT-G
363699 C
64 C
* * * * *** * * **
363700 CTTAATT-ATAAGTTTTATAATTTATAAAACATCATCAAATAAAAATGTTTGTTAACATGAATGC
1 CTTAATTGATAA-TTTTTTTATTTATAAAACATCATTAATTAAGGCTATTTTTTATTATGAATGC
* * * * *
363764 CTTAATTGACAATTTTATATT-TTT-TAAAATATCATTAGTTAAGG-TATTTTTTACTATAAATG
1 CTTAATTGATAATTTT-T-TTATTTATAAAACATCATTAATTAAGGCTATTTTTTATTATGAATG
363826 C
64 C
* * ** * * *
363827 TTTAATTGATACATTTCTTATATGAATTGAATACATCATTAATTAAGTC-ATTTTGTT-TAGATG
1 CTTAATTGATA-ATTT-TTTTATTTA-T-AAAACATCATTAATTAAGGCTATTTT-TTAT-TATG
363890 AATGC
60 AATGC
* * * **
363895 TTTAATTGATAATTTTTTTATTTATAAAACATGATTAATTAAGGCTTTTTTTTATTATGAACAC
1 CTTAATTGATAATTTTTTTATTTATAAAACATCATTAATTAAGGCTATTTTTTATTATGAATGC
363959 CTTAATTGAT
1 CTTAATTGAT
363969 GTATTAAATT
Statistics
Matches: 205, Mismatches: 47, Indels: 34
0.72 0.16 0.12
Matches are distributed among these distances:
62 2 0.01
63 53 0.26
64 83 0.40
65 15 0.07
66 8 0.04
67 24 0.12
68 20 0.10
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (64 bp):
CTTAATTGATAATTTTTTTATTTATAAAACATCATTAATTAAGGCTATTTTTTATTATGAATGC
Found at i:367034 original size:16 final size:16
Alignment explanation
Indices: 366973--367045 Score: 58
Period size: 16 Copynumber: 4.6 Consensus size: 16
366963 TAAAGTGATA
* *
366973 AAATTTAATTTGATCT
1 AAATTTAAATTAATCT
* *
366989 AAATTTGAATTGATTCT
1 AAATTTAAATT-AATCT
* * *
367006 -AATCTAAACTAATTT
1 AAATTTAAATTAATCT
*
367021 AAATTTAAATTAATCC
1 AAATTTAAATTAATCT
367037 AAATTTAAA
1 AAATTTAAA
367046 ATATTTTGAA
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
15 3 0.07
16 36 0.86
17 3 0.07
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.42
Consensus pattern (16 bp):
AAATTTAAATTAATCT
Found at i:379879 original size:22 final size:21
Alignment explanation
Indices: 379846--379890 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
379836 AGTTGATTTC
*
379846 AATATATTTAATATTAAAATT
1 AATACATTTAATATTAAAATT
* *
379867 AATACATTATAATTTTAATATT
1 AATACATT-TAATATTAAAATT
379889 AA
1 AA
379891 AAAATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
AATACATTTAATATTAAAATT
Found at i:379903 original size:28 final size:28
Alignment explanation
Indices: 379852--379906 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
379842 TTTCAATATA
* *
379852 TTTAATATTAAAATTAATACATTATAAT
1 TTTAATATTAAAAATAATAAATTATAAT
379880 TTTAATATTAAAAAATAA-AAATTATAA
1 TTTAATATT-AAAAATAATAAATTATAA
379907 AAAATTGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
TTTAATATTAAAAATAATAAATTATAAT
Found at i:383961 original size:126 final size:127
Alignment explanation
Indices: 383720--383963 Score: 341
Period size: 126 Copynumber: 1.9 Consensus size: 127
383710 CACACAGATC
*
383720 TCATTGTTGTGCTAAAGGGATCTTAAATAGTTTAACACAAGAATAAATTGCTAATAAGTTATCCA
1 TCATTGTTGTGCTAAAGGGATCCTAAATAG-TTAACACAAGAATAAATTGCTAATAAGTTATCCA
* *
383785 AAAACAGAATAAATTGCTAATAATTATATTGCTTAATCAGTATTTCTATTTTACCGTGCAGTG
65 AAAACAAAATAAATTGCTAATAATTATATTGCTTAATCAGCATTTCTATTTTACCGTGCAGTG
* ** * *
383848 TCATTGTTGTGCTAAAGGGATCCTAAATTA-TTCA-ATTAGAATACATTGCTAATAGGTTATCCA
1 TCATTGTTGTGCTAAAGGGATCCTAAA-TAGTTAACACAAGAATAAATTGCTAATAAGTTATCCA
** *
383911 AAAACAAAATAAATTGCTAATAATTATATTAG-TTAATTGGCATTTTTATTTTA
65 AAAACAAAATAAATTGCTAATAATTATATT-GCTTAATCAGCATTTCTATTTTA
383964 TGTGCATTTT
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
126 71 0.69
127 4 0.04
128 26 0.25
129 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (127 bp):
TCATTGTTGTGCTAAAGGGATCCTAAATAGTTAACACAAGAATAAATTGCTAATAAGTTATCCAA
AAACAAAATAAATTGCTAATAATTATATTGCTTAATCAGCATTTCTATTTTACCGTGCAGTG
Found at i:400537 original size:12 final size:11
Alignment explanation
Indices: 400515--400544 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
400505 CGTTGGAACT
400515 GGCTGGGCTGA
1 GGCTGGGCTGA
400526 GGCTGAGGCTGA
1 GGCTG-GGCTGA
400538 GGCTGGG
1 GGCTGGG
400545 TCGAAAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.10, C:0.17, G:0.57, T:0.17
Consensus pattern (11 bp):
GGCTGGGCTGA
Found at i:401539 original size:2 final size:2
Alignment explanation
Indices: 401532--401564 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
401522 GATGAAAGTT
401532 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
401565 TTGTTGAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:404437 original size:29 final size:29
Alignment explanation
Indices: 404405--404509 Score: 117
Period size: 30 Copynumber: 3.6 Consensus size: 29
404395 TTTTATTTAG
404405 ATAAATCTTTATACTTTTA-TTGCATCTAA
1 ATAAATCTTTA-ACTTTTATTTGCATCTAA
*
404434 ATAAA-CTCTTAACCTTTTATTTGCAACTAA
1 ATAAATCT-TTAA-CTTTTATTTGCATCTAA
*
404464 ATAAATCTTTAA-TGTTTAATTTGTATCTAA
1 ATAAATCTTTAACT-TTT-ATTTGCATCTAA
*
404494 ATAAGTCTTTAACTTT
1 ATAAATCTTTAACTTT
404510 AAATTTATAC
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
28 4 0.06
29 17 0.26
30 41 0.63
31 3 0.05
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.47
Consensus pattern (29 bp):
ATAAATCTTTAACTTTTATTTGCATCTAA
Found at i:404464 original size:30 final size:28
Alignment explanation
Indices: 404405--404472 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 28
404395 TTTTATTTAG
*
404405 ATAAATCTTTATA-CTTTTATTGCATCTAA
1 ATAAATC-TTA-ACCTTTTATTGCAACTAA
404434 ATAAACTCTTAACCTTTTATTTGCAACTAA
1 ATAAA-TCTTAACCTTTTA-TTGCAACTAA
404464 ATAAATCTT
1 ATAAATCTT
404473 TAATGTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
28 1 0.03
29 18 0.51
30 16 0.46
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.44
Consensus pattern (28 bp):
ATAAATCTTAACCTTTTATTGCAACTAA
Found at i:409390 original size:12 final size:12
Alignment explanation
Indices: 409373--409414 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
409363 TTTTTTAATA
409373 TAAATATAAAAT
1 TAAATATAAAAT
*
409385 TAAATA-AATAT
1 TAAATATAAAAT
409396 ATAAATATAAAAT
1 -TAAATATAAAAT
409409 TAAATA
1 TAAATA
409415 ATTAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 4 0.15
12 18 0.69
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAATATAAAAT
Found at i:409397 original size:18 final size:20
Alignment explanation
Indices: 409373--409414 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 20
409363 TTTTTTAATA
409373 TAAATATA-AAAT-T-AAA-
1 TAAATATATAAATATAAAAT
409389 TAAATATATAAATATAAAAT
1 TAAATATATAAATATAAAAT
409409 TAAATA
1 TAAATA
409415 ATTAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.36
17 4 0.18
18 1 0.05
19 3 0.14
20 6 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAATATATAAATATAAAAT
Found at i:409424 original size:24 final size:25
Alignment explanation
Indices: 409367--409424 Score: 93
Period size: 24 Copynumber: 2.4 Consensus size: 25
409357 AAAATATTTT
409367 TTAATATAAATATAAAATTAAATAA
1 TTAATATAAATATAAAATTAAATAA
*
409392 AT-ATATAAATATAAAATTAAATAA
1 TTAATATAAATATAAAATTAAATAA
409416 TTAAT-TAAA
1 TTAATATAAA
409425 AAATAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 27 0.90
25 3 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
TTAATATAAATATAAAATTAAATAA
Found at i:410303 original size:16 final size:17
Alignment explanation
Indices: 410272--410304 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
410262 CGGTCCATAA
410272 ATTTTGAATTAAAATTT
1 ATTTTGAATTAAAATTT
*
410289 ATTTT-AATTATAATTT
1 ATTTTGAATTAAAATTT
410305 TAAAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTTGAATTAAAATTT
Found at i:424849 original size:15 final size:15
Alignment explanation
Indices: 424829--424862 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
424819 AAGTAGGTCG
* *
424829 AATTTGTCCATATAA
1 AATTTGCCCAAATAA
424844 AATTTGCCCAAATAA
1 AATTTGCCCAAATAA
424859 AATT
1 AATT
424863 AGAATGGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (15 bp):
AATTTGCCCAAATAA
Found at i:441885 original size:2 final size:2
Alignment explanation
Indices: 441878--441905 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
441868 ATTTTCTATC
441878 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
441906 ATTTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:452513 original size:112 final size:112
Alignment explanation
Indices: 452316--452540 Score: 432
Period size: 112 Copynumber: 2.0 Consensus size: 112
452306 AGTGCAGAAG
*
452316 CTTATGTAGGCGTGGTGAGGGTAGGCACTACCTTTTAAAAGTTTAATGAGAACCAAGCTACTAGC
1 CTTATGCAGGCGTGGTGAGGGTAGGCACTACCTTTTAAAAGTTTAATGAGAACCAAGCTACTAGC
452381 ATTCACAGCGGGCAGCAAAAGTGGCCCTAAAATGAGAGTAGGACAAA
66 ATTCACAGCGGGCAGCAAAAGTGGCCCTAAAATGAGAGTAGGACAAA
452428 CTTATGCAGGCGTGGTGAGGGTAGGCACTACCTTTTAAAAGTTTAATGAGAACCAAGCTACTAGC
1 CTTATGCAGGCGTGGTGAGGGTAGGCACTACCTTTTAAAAGTTTAATGAGAACCAAGCTACTAGC
*
452493 ATTCACAGCGGGCTGCAAAAGTGGCCCTAAAATGAGAGTAGGACAAA
66 ATTCACAGCGGGCAGCAAAAGTGGCCCTAAAATGAGAGTAGGACAAA
452540 C
1 C
452541 AGTAATAACA
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 111 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (112 bp):
CTTATGCAGGCGTGGTGAGGGTAGGCACTACCTTTTAAAAGTTTAATGAGAACCAAGCTACTAGC
ATTCACAGCGGGCAGCAAAAGTGGCCCTAAAATGAGAGTAGGACAAA
Found at i:468178 original size:2 final size:2
Alignment explanation
Indices: 468165--468201 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
468155 AATGGTCATC
*
468165 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
468202 TTACATTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:475660 original size:12 final size:14
Alignment explanation
Indices: 475631--475663 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
475621 AAATAAACAA
475631 AAAATAAGTAAGAT
1 AAAATAAGTAAGAT
475645 AAAATAAGT-A-AT
1 AAAATAAGTAAGAT
475657 AAAATAA
1 AAAATAA
475664 AATAAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
13 1 0.05
14 9 0.47
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (14 bp):
AAAATAAGTAAGAT
Found at i:482005 original size:15 final size:15
Alignment explanation
Indices: 481985--482021 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
481975 TTGTAGCTTC
481985 AAAAAAAAAAGAAAA
1 AAAAAAAAAAGAAAA
*
482000 AAAAAAAAAAGGAAA
1 AAAAAAAAAAGAAAA
*
482015 AGAAAAA
1 AAAAAAA
482022 CCAGAGACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGAAAA
Found at i:482006 original size:16 final size:17
Alignment explanation
Indices: 481985--482021 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
481975 TTGTAGCTTC
481985 AAAAAAAAAAGAAAA-A
1 AAAAAAAAAAGAAAAGA
*
482001 AAAAAAAAAGGAAAAGA
1 AAAAAAAAAAGAAAAGA
482018 AAAA
1 AAAA
482022 CCAGAGACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAGA
Found at i:494074 original size:676 final size:676
Alignment explanation
Indices: 492783--494136 Score: 2708
Period size: 676 Copynumber: 2.0 Consensus size: 676
492773 CCAATCACAG
492783 TCCAAAACAACAAAAACAGCCAATTCTTGAATGTCAAAGCAAAATATAAAAAGCAATAACTGTCT
1 TCCAAAACAACAAAAACAGCCAATTCTTGAATGTCAAAGCAAAATATAAAAAGCAATAACTGTCT
492848 CCAAGAAAAAGAAAATAATAAACAGAAAAGGTGGCAAGCGGGAACCTGAGTGACAGAAAGGGTAG
66 CCAAGAAAAAGAAAATAATAAACAGAAAAGGTGGCAAGCGGGAACCTGAGTGACAGAAAGGGTAG
492913 AAGTTTGAGAGAACGTCAAGTCGTTGGCCTAGCCTTGCCGCCTTTGGTTTTGGTTTTTACATTTT
131 AAGTTTGAGAGAACGTCAAGTCGTTGGCCTAGCCTTGCCGCCTTTGGTTTTGGTTTTTACATTTT
492978 AGCAAGGCGACGTGTAGAATGGAAATGGGAACCACCTGTTTGACATGACTGGCGTTTGGGCAACG
196 AGCAAGGCGACGTGTAGAATGGAAATGGGAACCACCTGTTTGACATGACTGGCGTTTGGGCAACG
493043 CTGGTTAAGAATAATTGGTTGATGCTGACAGGTGCCACCCAACTTCCAAAAAATAGACTTCAACT
261 CTGGTTAAGAATAATTGGTTGATGCTGACAGGTGCCACCCAACTTCCAAAAAATAGACTTCAACT
493108 TCGATCCCGGGTTGCAAATTATTTGCTCAAATTAATTAACTAGTCGATGGCATGGCAAACTGTGA
326 TCGATCCCGGGTTGCAAATTATTTGCTCAAATTAATTAACTAGTCGATGGCATGGCAAACTGTGA
493173 TGAAATAGATAGTGATGAACGAAAGAATAGAGTACGAGACTAAAAAAGAAAGAAAAGTTTGAGAA
391 TGAAATAGATAGTGATGAACGAAAGAATAGAGTACGAGACTAAAAAAGAAAGAAAAGTTTGAGAA
493238 TATAAAACCGGATAATTTTTATTCATAATCTTGAAATAATCTATTTATATATTTATAACTGATTT
456 TATAAAACCGGATAATTTTTATTCATAATCTTGAAATAATCTATTTATATATTTATAACTGATTT
493303 TTTAAATTACTCGTAATACTATCTTATTATTATGCATAATTATAGTTTATTTTTTAAATTACTCA
521 TTTAAATTACTCGTAATACTATCTTATTATTATGCATAATTATAGTTTATTTTTTAAATTACTCA
493368 CACCACTATCGCACTATTACCTTAATTCATTCCCTAAATTATTTGTACTACTATCCCACCATTAA
586 CACCACTATCGCACTATTACCTTAATTCATTCCCTAAATTATTTGTACTACTATCCCACCATTAA
493433 TTATAGCTAAATTACTCACACCACTA
651 TTATAGCTAAATTACTCACACCACTA
493459 TCCAAAACAACAAAAACAGCCAATTCTTGAATGTCAAAGCAAAATATAAAAAGCAATAACTGTCT
1 TCCAAAACAACAAAAACAGCCAATTCTTGAATGTCAAAGCAAAATATAAAAAGCAATAACTGTCT
493524 CCAAGAAAAAGAAAATAATAAACAGAAAAGGTGGCAAGCGGGAACCTGAGTGACAGAAAGGGTAG
66 CCAAGAAAAAGAAAATAATAAACAGAAAAGGTGGCAAGCGGGAACCTGAGTGACAGAAAGGGTAG
493589 AAGTTTGAGAGAACGTCAAGTCGTTGGCCTAGCCTTGCCGCCTTTGGTTTTGGTTTTTACATTTT
131 AAGTTTGAGAGAACGTCAAGTCGTTGGCCTAGCCTTGCCGCCTTTGGTTTTGGTTTTTACATTTT
493654 AGCAAGGCGACGTGTAGAATGGAAATGGGAACCACCTGTTTGACATGACTGGCGTTTGGGCAACG
196 AGCAAGGCGACGTGTAGAATGGAAATGGGAACCACCTGTTTGACATGACTGGCGTTTGGGCAACG
493719 CTGGTTAAGAATAATTGGTTGATGCTGACAGGTGCCACCCAACTTCCAAAAAATAGACTTCAACT
261 CTGGTTAAGAATAATTGGTTGATGCTGACAGGTGCCACCCAACTTCCAAAAAATAGACTTCAACT
493784 TCGATCCCGGGTTGCAAATTATTTGCTCAAATTAATTAACTAGTCGATGGCATGGCAAACTGTGA
326 TCGATCCCGGGTTGCAAATTATTTGCTCAAATTAATTAACTAGTCGATGGCATGGCAAACTGTGA
493849 TGAAATAGATAGTGATGAACGAAAGAATAGAGTACGAGACTAAAAAAGAAAGAAAAGTTTGAGAA
391 TGAAATAGATAGTGATGAACGAAAGAATAGAGTACGAGACTAAAAAAGAAAGAAAAGTTTGAGAA
493914 TATAAAACCGGATAATTTTTATTCATAATCTTGAAATAATCTATTTATATATTTATAACTGATTT
456 TATAAAACCGGATAATTTTTATTCATAATCTTGAAATAATCTATTTATATATTTATAACTGATTT
493979 TTTAAATTACTCGTAATACTATCTTATTATTATGCATAATTATAGTTTATTTTTTAAATTACTCA
521 TTTAAATTACTCGTAATACTATCTTATTATTATGCATAATTATAGTTTATTTTTTAAATTACTCA
494044 CACCACTATCGCACTATTACCTTAATTCATTCCCTAAATTATTTGTACTACTATCCCACCATTAA
586 CACCACTATCGCACTATTACCTTAATTCATTCCCTAAATTATTTGTACTACTATCCCACCATTAA
494109 TTATAGCTAAATTACTCACACCACTA
651 TTATAGCTAAATTACTCACACCACTA
494135 TC
1 TC
494137 GTAAACTTAC
Statistics
Matches: 678, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
676 678 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (676 bp):
TCCAAAACAACAAAAACAGCCAATTCTTGAATGTCAAAGCAAAATATAAAAAGCAATAACTGTCT
CCAAGAAAAAGAAAATAATAAACAGAAAAGGTGGCAAGCGGGAACCTGAGTGACAGAAAGGGTAG
AAGTTTGAGAGAACGTCAAGTCGTTGGCCTAGCCTTGCCGCCTTTGGTTTTGGTTTTTACATTTT
AGCAAGGCGACGTGTAGAATGGAAATGGGAACCACCTGTTTGACATGACTGGCGTTTGGGCAACG
CTGGTTAAGAATAATTGGTTGATGCTGACAGGTGCCACCCAACTTCCAAAAAATAGACTTCAACT
TCGATCCCGGGTTGCAAATTATTTGCTCAAATTAATTAACTAGTCGATGGCATGGCAAACTGTGA
TGAAATAGATAGTGATGAACGAAAGAATAGAGTACGAGACTAAAAAAGAAAGAAAAGTTTGAGAA
TATAAAACCGGATAATTTTTATTCATAATCTTGAAATAATCTATTTATATATTTATAACTGATTT
TTTAAATTACTCGTAATACTATCTTATTATTATGCATAATTATAGTTTATTTTTTAAATTACTCA
CACCACTATCGCACTATTACCTTAATTCATTCCCTAAATTATTTGTACTACTATCCCACCATTAA
TTATAGCTAAATTACTCACACCACTA
Done.