Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, 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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 10 of 100
Found at i:2623163 original size:41 final size:41
Alignment explanation
Indices: 2623106--2623189 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 41
2623096 AGCATGATGC
*
2623106 CTTTGAAACCAAAAAGAAAAACGATGAAAGCAATTAAAGGA
1 CTTTGAAACCAAAAAGAAAAACGATGAAAGCAATCAAAGGA
* *
2623147 CTTTG-AACCTAAAAAGAAAAATGATGAAAGGAATCAAAGGA
1 CTTTGAAACC-AAAAAGAAAAACGATGAAAGCAATCAAAGGA
2623188 CT
1 CT
2623190 AGGAAAAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
40 4 0.10
41 35 0.90
ACGTcount: A:0.54, C:0.12, G:0.18, T:0.17
Consensus pattern (41 bp):
CTTTGAAACCAAAAAGAAAAACGATGAAAGCAATCAAAGGA
Found at i:2625089 original size:32 final size:32
Alignment explanation
Indices: 2625053--2625118 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
2625043 ACAATATCGC
* *
2625053 CATACTTCTCATTCT-TTTTCAACTCCACAAAA
1 CATACTTCTCATTCTCTTCT-AACTCAACAAAA
2625085 CATACTTCTCATTCTCTTCTAACTCAACAAAA
1 CATACTTCTCATTCTCTTCTAACTCAACAAAA
2625117 CA
1 CA
2625119 ACTCATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 28 0.90
33 3 0.10
ACGTcount: A:0.33, C:0.32, G:0.00, T:0.35
Consensus pattern (32 bp):
CATACTTCTCATTCTCTTCTAACTCAACAAAA
Found at i:2627495 original size:22 final size:22
Alignment explanation
Indices: 2627465--2627511 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2627455 AATTTTGAAT
2627465 TTTAAGATTTTGGAGTTTAGAG
1 TTTAAGATTTTGGAGTTTAGAG
* * *
2627487 TTTAGGATTTTGGATTTTAGGG
1 TTTAAGATTTTGGAGTTTAGAG
2627509 TTT
1 TTT
2627512 TGATTTCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (22 bp):
TTTAAGATTTTGGAGTTTAGAG
Found at i:2627605 original size:29 final size:27
Alignment explanation
Indices: 2627502--2627613 Score: 100
Period size: 30 Copynumber: 3.9 Consensus size: 27
2627492 GATTTTGGAT
* *
2627502 TTTAGGGTTTTGATTTCGAGGTTTGAGG
1 TTTAGGGTTTAG-TTTCAAGGTTTGAGG
* * *
2627530 TGT-GGGTTTTAGTTTTATGGTTTTGAGAG
1 TTTAGGG-TTTAGTTTCAAGG-TTTGAG-G
*
2627559 TTTAGGGTTTCAATTTCAAGGTTTAGAGG
1 TTTAGGGTTT-AGTTTCAAGGTTT-GAGG
2627588 TTTTAGGGTTTAGTTTCAAGGTTTGA
1 -TTTAGGGTTTAGTTTCAAGGTTTGA
2627614 AAGATTTAAG
Statistics
Matches: 67, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
27 8 0.12
28 14 0.21
29 22 0.33
30 23 0.34
ACGTcount: A:0.18, C:0.04, G:0.31, T:0.47
Consensus pattern (27 bp):
TTTAGGGTTTAGTTTCAAGGTTTGAGG
Found at i:2627621 original size:29 final size:28
Alignment explanation
Indices: 2627502--2627627 Score: 78
Period size: 29 Copynumber: 4.4 Consensus size: 28
2627492 GATTTTGGAT
* * *
2627502 TTTAGGGTTTTGATTTCGAGGTTTG-AGG
1 TTTAGGGTTTAG-TTTCAAGGTTTGAAAG
* * * *
2627530 TGT-GGGTTTTAGTTTTATGGTTTTGAGAG
1 TTTAGGG-TTTAGTTTCAAGG-TTTGAAAG
* *
2627559 TTTAGGGTTTCAATTTCAAGGTTT-AGAGG
1 TTTAGGGTTT-AGTTTCAAGGTTTGA-AAG
2627588 TTTTAGGGTTTAGTTTCAAGGTTTGAAAG
1 -TTTAGGGTTTAGTTTCAAGGTTTGAAAG
*
2627617 ATTTAAGGTTT
1 -TTTAGGGTTT
2627628 CGATTTTAGG
Statistics
Matches: 73, Mismatches: 17, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
27 8 0.11
28 11 0.15
29 33 0.45
30 21 0.29
ACGTcount: A:0.20, C:0.03, G:0.30, T:0.47
Consensus pattern (28 bp):
TTTAGGGTTTAGTTTCAAGGTTTGAAAG
Found at i:2627627 original size:59 final size:58
Alignment explanation
Indices: 2627537--2627655 Score: 132
Period size: 59 Copynumber: 2.0 Consensus size: 58
2627527 AGGTGTGGGT
* * * * * *
2627537 TTTAGTTTTATGGTTTTGAGAGTTTAGGGTTTCAATTTCAAGGTTTAGAGGTTTTAGGG
1 TTTAGTTTCAAGGTTTTGAAAGTTTAAGGTTTCAATTTCAAGGTTT-GAGATTTTAAGG
* * *
2627596 TTTAGTTTCAAGG-TTTGAAAGATTTAAGGTTTCGATTTTAGGGTTTGAGATTTTAAGG
1 TTTAGTTTCAAGGTTTTGAAAG-TTTAAGGTTTCAATTTCAAGGTTTGAGATTTTAAGG
2627654 TT
1 TT
2627656 AGATTTTGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
58 19 0.38
59 31 0.62
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.47
Consensus pattern (58 bp):
TTTAGTTTCAAGGTTTTGAAAGTTTAAGGTTTCAATTTCAAGGTTTGAGATTTTAAGG
Found at i:2627640 original size:14 final size:15
Alignment explanation
Indices: 2627551--2627655 Score: 67
Period size: 14 Copynumber: 7.1 Consensus size: 15
2627541 GTTTTATGGT
* *
2627551 TTTGAGAGTTTAGGG
1 TTTGAGATTTTAAGG
* *
2627566 TTTCA-ATTTCAAGG
1 TTTGAGATTTTAAGG
* *
2627580 TTTAGAGGTTTTAGGG
1 TTT-GAGATTTTAAGG
*
2627596 TTT-AG-TTTCAAGG
1 TTTGAGATTTTAAGG
2627609 TTTGAAAGA-TTTAAGG
1 TTTG--AGATTTTAAGG
* *
2627625 TTT-CGATTTTAGGG
1 TTTGAGATTTTAAGG
2627639 TTTGAGATTTTAAGG
1 TTTGAGATTTTAAGG
2627654 TT
1 TT
2627656 AGATTTTGAT
Statistics
Matches: 67, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
13 11 0.16
14 20 0.30
15 16 0.24
16 20 0.30
ACGTcount: A:0.24, C:0.04, G:0.28, T:0.45
Consensus pattern (15 bp):
TTTGAGATTTTAAGG
Found at i:2627650 original size:29 final size:29
Alignment explanation
Indices: 2627551--2627655 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 29
2627541 GTTTTATGGT
* * *
2627551 TTTGAGAGTTTAGGGTTTCAATTTCAAGG
1 TTTGAGATTTTAAGGTTTCGATTTCAAGG
* * *
2627580 TTTAGAGGTTTTAGGGTTTAG-TTTCAAGG
1 TTT-GAGATTTTAAGGTTTCGATTTCAAGG
* *
2627609 TTTGAAAGA-TTTAAGGTTTCGATTTTAGGG
1 TTTG--AGATTTTAAGGTTTCGATTTCAAGG
2627639 TTTGAGATTTTAAGGTT
1 TTTGAGATTTTAAGGTT
2627656 AGATTTTGAT
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
28 4 0.06
29 33 0.53
30 25 0.40
ACGTcount: A:0.24, C:0.04, G:0.28, T:0.45
Consensus pattern (29 bp):
TTTGAGATTTTAAGGTTTCGATTTCAAGG
Found at i:2627661 original size:13 final size:14
Alignment explanation
Indices: 2627571--2627662 Score: 64
Period size: 16 Copynumber: 6.4 Consensus size: 14
2627561 TAGGGTTTCA
*
2627571 ATTTCAAGGTTTAG
1 ATTTTAAGGTTTAG
*
2627585 AGGTTTTAGGGTTTAG
1 A--TTTTAAGGTTTAG
*
2627601 -TTTCAAGGTTTGAAAG
1 ATTTTAAGGTTT---AG
*
2627617 A-TTTAAGGTTTCG
1 ATTTTAAGGTTTAG
*
2627630 ATTTTAGGGTTTGAG
1 ATTTTAAGGTTT-AG
2627645 ATTTTAAGG-TTAG
1 ATTTTAAGGTTTAG
2627658 ATTTT
1 ATTTT
2627663 GATTTTTGGA
Statistics
Matches: 61, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
13 18 0.30
14 12 0.20
15 9 0.15
16 22 0.36
ACGTcount: A:0.25, C:0.03, G:0.26, T:0.46
Consensus pattern (14 bp):
ATTTTAAGGTTTAG
Found at i:2627731 original size:15 final size:15
Alignment explanation
Indices: 2627711--2627793 Score: 52
Period size: 15 Copynumber: 5.7 Consensus size: 15
2627701 GGTTTTATGG
2627711 TTTGGATTTTAAGGT
1 TTTGGATTTTAAGGT
* *
2627726 TTTGGA-TTCAAGGG
1 TTTGGATTTTAAGGT
*
2627740 TTTGGAAGTTTTGA-GT
1 TTTGG-A-TTTTAAGGT
*
2627756 TTT-GATTTT-AGGA
1 TTTGGATTTTAAGGT
*
2627769 TTTGG-GTTTATAGGT
1 TTTGGATTTTA-AGGT
2627784 TTT-GATTTTA
1 TTTGGATTTTA
2627794 GAGTTAGGAT
Statistics
Matches: 51, Mismatches: 9, Indels: 16
0.67 0.12 0.21
Matches are distributed among these distances:
12 1 0.02
13 11 0.22
14 14 0.27
15 18 0.35
16 4 0.08
17 3 0.06
ACGTcount: A:0.19, C:0.01, G:0.28, T:0.52
Consensus pattern (15 bp):
TTTGGATTTTAAGGT
Found at i:2627813 original size:28 final size:28
Alignment explanation
Indices: 2627748--2627813 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
2627738 GGTTTGGAAG
* *
2627748 TTTTGAGTTTTGATTTTAGGATTTGGGT
1 TTTTGAGTTTTGATTTTAGGATTAGGAT
*
2627776 TTAT-AGGTTTTGATTTTA-GAGTTAGGAT
1 TTTTGA-GTTTTGATTTTAGGA-TTAGGAT
2627804 TTTTGAGTTT
1 TTTTGAGTTT
2627814 AGACTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
27 3 0.10
28 27 0.87
29 1 0.03
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.56
Consensus pattern (28 bp):
TTTTGAGTTTTGATTTTAGGATTAGGAT
Found at i:2630048 original size:37 final size:37
Alignment explanation
Indices: 2629994--2631507 Score: 372
Period size: 37 Copynumber: 40.8 Consensus size: 37
2629984 CACGAGTCAA
* * *
2629994 AAAG-TAAAAAATTGATCGAGACAATACCGCGAGTCG
1 AAAGATAAAGAATCGATCGAGACAACACCGCGAGTCG
* * ***
2630030 AAAGATAAAGAATCGATCGAAAAAACACTATGAGTCG
1 AAAGATAAAGAATCGATCGAGACAACACCGCGAGTCG
* * * * *
2630067 AAAGGTAAAGAATCGATTGGGACAACACCACAAGTCG
1 AAAGATAAAGAATCGATCGAGACAACACCGCGAGTCG
* * ***
2630104 AATA-ATAAAGAAAAT-GATTGGGACAACACCAAAAGTCG
1 AA-AGATAAAG--AATCGATCGAGACAACACCGCGAGTCG
* * * * *
2630142 AGA-ATAAAAAAAT-GATC-AGGATAACATCGCAAGTCG
1 AAAGAT-AAAGAATCGATCGA-GACAACACCGCGAGTCG
* * *
2630178 AGAAG-TGAAGAATCGATCGAGACAATACCGCGAGTCT
1 A-AAGATAAAGAATCGATCGAGACAACACCGCGAGTCG
* * *
2630215 AAA-AGTAAAGAATCGATTGGGACAACATCC-CGAGTTG
1 AAAGA-TAAAGAATCGATCGAGACAACA-CCGCGAGTCG
* * * *
2630252 AAAGGTAAAGAATCGATCGAGACAAAATCGCTAGTCG
1 AAAGATAAAGAATCGATCGAGACAACACCGCGAGTCG
* * * ** *
2630289 AAAGGTAAAGAATCGATC-AGGATAACATCGTAAGTTG
1 AAAGATAAAGAATCGATCGA-GACAACACCGCGAGTCG
* * * *
2630326 AAAGGTAAAAAATCGA-CTGAGACAACACCGCAAGTTG
1 AAAGATAAAGAATCGATC-GAGACAACACCGCGAGTCG
* * * * *
2630363 AAAGGTAAAGAATCGATCGAGACAGCACCTCAAGTTG
1 AAAGATAAAGAATCGATCGAGACAACACCGCGAGTCG
* * *** *
2630400 AATA-ATAAAGAAAAT-GATTG-GAATAACACCAAAAGTTG
1 AA-AGATAAAG--AATCGATCGAG-ACAACACCGCGAGTCG
* * * *
2630438 AGAACA-AAAAAAT-GATCGAGACAACACCGTGAGTTG
1 A-AAGATAAAGAATCGATCGAGACAACACCGCGAGTCG
* * * *
2630474 AAA-AGTAAAGAATCGACCGGGACAACACTGTGAGTC-
1 AAAGA-TAAAGAATCGATCGAGACAACACCGCGAGTCG
* * * **
2630510 -AAGAAATAAGAAAACGA-CTGGGACAACACTACGAGTC-
1 AAAGATA-AAG-AATCGATC-GAGACAACACCGCGAGTCG
* * * * *
2630547 AAGAAATAAGAAAAT-GATTGGGACAACACTGCGAGTC-
1 AA-AGATAA-AGAATCGATCGAGACAACACCGCGAGTCG
* * * * ** *
2630584 AAAAAGT-AAGTAATCGATCGGGACAATAACTTGAGACG
1 AAAGA-TAAAG-AATCGATCGAGACAACACCGCGAGTCG
* * *
2630622 AAAGGTAAAGAATCGA-CCAGGACAACACCACGAGTCG
1 AAAGATAAAGAATCGATCGA-GACAACACCGCGAGTCG
* * * * * *
2630659 AAAGGTAAAAAATCGATCGGGATAACACCTCAAGTC-
1 AAAGATAAAGAATCGATCGAGACAACACCGCGAGTCG
* * * * * * **
2630695 AAACAATGAAGAATAGATCGAGATAATACTGCGAGTTA
1 AAA-GATAAAGAATCGATCGAGACAACACCGCGAGTCG
* * * ***
2630733 AAAAAGTAAAAAAAT-GATCGAGATAACATTACGAGTCG
1 AAAGA-T-AAAGAATCGATCGAGACAACACCGCGAGTCG
* *
2630771 AGAAG-TAAAGAATCGATCGGGACAACACTGCGAGTCG
1 A-AAGATAAAGAATCGATCGAGACAACACCGCGAGTCG
* * **
2630808 AGAA-ATAAGAAAAT-GATCGGGACAACACCGTAAGTCG
1 A-AAGATAA-AGAATCGATCGAGACAACACCGCGAGTCG
* * * *
2630845 AAAAATGAAGAATCGATCGAGACAACACTGCGAGTCA
1 AAAGATAAAGAATCGATCGAGACAACACCGCGAGTCG
* * * ** * *
2630882 AAAAAT-AAGTAATCGA-CTGGGATAACACTACGAATCA
1 AAAGATAAAG-AATCGATC-GAGACAACACCGCGAGTCG
* * *
2630919 AAAGGTAAAGAATCGATCGCGACAACACCACGAGTCG
1 AAAGATAAAGAATCGATCGAGACAACACCGCGAGTCG
* *** *
2630956 AAAGGTAAAGAATCGATCGAGACAACACCATAAGT-A
1 AAAGATAAAGAATCGATCGAGACAACACCGCGAGTCG
* * * * * *
2630992 AAACAGTAAAAAATCAATCG-GAATAACACTGCGAGTCA
1 AAAGA-TAAAGAATCGATCGAG-ACAACACCGCGAGTCG
* * * * *
2631030 AAAAAGTAAGAAAAT-GA-CTGGGATAACACCACGAGTC-
1 AAAGA-TAA-AGAATCGATC-GAGACAACACCGCGAGTCG
* * * ** *
2631067 AGA-ATTAAGAATACGA-CTGGGACAACACCATGAGTTG
1 AAAGATAAAGAAT-CGATC-GAGACAACACCGCGAGTCG
* * **
2631104 AGAAG-TAAAGAATTGATCGAAACAACATTGCGAGTCG
1 A-AAGATAAAGAATCGATCGAGACAACACCGCGAGTCG
* *
2631141 AGAA-ATAAGAAAAT-GA-CTGAGACAACACTGCGAGTC-
1 A-AAGATAA-AGAATCGATC-GAGACAACACCGCGAGTCG
* * **
2631177 AAAAAGTGAAGAATCGA-CTGAGACAACATAGCGAGTC-
1 AAAGA-TAAAGAATCGATC-GAGACAACACCGCGAGTCG
* * * * * *
2631214 AAAAAGT-AAGTAATTGATCAAGACAACACCTCAAGTTG
1 AAAGA-TAAAG-AATCGATCGAGACAACACCGCGAGTCG
* *
2631252 AAA-AGTAAAGAATCGA-CTGAGACAACATCGCAAGTCG
1 AAAGA-TAAAGAATCGATC-GAGACAACACCGCGAGTCG
* * *
2631289 AAAAGTAAGTAAAAAAAATC-AACTGAAACAACACCGCGAGTCG
1 -AAAG--A-T--AAAGAATCGATC-GAGACAACACCGCGAGTCG
* ** **
2631332 AAA-AGTAAAAAATCGATCGAGACAACACCGTAAGTAA
1 AAAGA-TAAAGAATCGATCGAGACAACACCGCGAGTCG
* * * * * *
2631369 AAAAAAAAAGAATCCATTGAGACAACACTG-AATGTCG
1 AAAGATAAAGAATCGATCGAGACAACACCGCGA-GTCG
* * * * * *
2631406 AGAATAAAAAAAAT-GATCGGGATAACACTGCGAGTCG
1 A-AAGATAAAGAATCGATCGAGACAACACCGCGAGTCG
* * * **
2631443 AGAAG-TAAGAAAAT-GATCGGGATAACACCGTAAGTC-
1 A-AAGATAA-AGAATCGATCGAGACAACACCGCGAGTCG
* *
2631479 AAA-ATTAAGAATC-ATCGGGACAACACCGC
1 AAAGATAAAGAATCGATCGAGACAACACCGC
2631508 AAGTTAAAAA
Statistics
Matches: 1142, Mismatches: 240, Indels: 194
0.72 0.15 0.12
Matches are distributed among these distances:
34 23 0.02
35 14 0.01
36 132 0.12
37 756 0.66
38 157 0.14
39 28 0.02
41 3 0.00
42 4 0.00
43 25 0.02
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (37 bp):
AAAGATAAAGAATCGATCGAGACAACACCGCGAGTCG
Found at i:2630132 original size:38 final size:36
Alignment explanation
Indices: 2630081--2630157 Score: 118
Period size: 38 Copynumber: 2.1 Consensus size: 36
2630071 GTAAAGAATC
* *
2630081 GATTGGGACAACACCACAAGTCGAATAATAAAGAAAAT
1 GATTGGGACAACACCAAAAGTCG-AGAATAAA-AAAAT
2630119 GATTGGGACAACACCAAAAGTCGAGAATAAAAAAAT
1 GATTGGGACAACACCAAAAGTCGAGAATAAAAAAAT
2630155 GAT
1 GAT
2630158 CAGGATAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 8 0.22
37 7 0.19
38 22 0.59
ACGTcount: A:0.51, C:0.14, G:0.19, T:0.16
Consensus pattern (36 bp):
GATTGGGACAACACCAAAAGTCGAGAATAAAAAAAT
Found at i:2631406 original size:117 final size:111
Alignment explanation
Indices: 2631188--2631482 Score: 256
Period size: 117 Copynumber: 2.6 Consensus size: 111
2631178 AAAAGTGAAG
* * * * * * **
2631188 AATCGACTGAGACAACATAGCGAGTCAAAAAGTAAGTAATTGATCAAGACAACACC-TCAAGTTG
1 AATCAACTGAGACAACACAGCGAGTCGAAAAGTAA-AAAATGATCGAGACAACACCGT-AAGTAA
** *
2631252 AAAAGTAAAGAATCGACTGAGACAACATCGCAAGTCGAAAAGTAAGTAAAAAA
64 AAAAAAAAAGAATCCACTGAGACAACATCGCAAGTCG---AG-AA-TAAAAAA
* *
2631305 AATCAACTGAAACAACACCGCGAGTCGAAAAGTAAAAAATCGATCGAGACAACACCGTAAGTAAA
1 AATCAACTGAGACAACACAGCGAGTCGAAAAGTAAAAAAT-GATCGAGACAACACCGTAAGTAAA
*
2631370 AAAAAAAAGAATCCATTGAGACAACA-CTG-AATGTCGAGAATAAAAAA
65 AAAAAAAAGAATCCACTGAGACAACATC-GCAA-GTCGAGAATAAAAAA
* * * * * * * * *
2631417 AATGATC-GGGATAACACTGCGAGTCGAGAAGTAAGAAAATGATCGGGATAACACCGTAAGTCAA
1 AATCAACTGAGACAACACAGCGAGTCGAAAAGTAA-AAAATGATCGAGACAACACCGTAAGTAAA
2631481 AA
65 AA
2631483 TTAAGAATCA
Statistics
Matches: 149, Mismatches: 24, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
111 45 0.30
112 17 0.11
113 2 0.01
114 2 0.01
116 6 0.04
117 76 0.51
118 1 0.01
ACGTcount: A:0.49, C:0.17, G:0.19, T:0.15
Consensus pattern (111 bp):
AATCAACTGAGACAACACAGCGAGTCGAAAAGTAAAAAATGATCGAGACAACACCGTAAGTAAAA
AAAAAAAGAATCCACTGAGACAACATCGCAAGTCGAGAATAAAAAA
Found at i:2632310 original size:66 final size:65
Alignment explanation
Indices: 2632232--2632381 Score: 187
Period size: 66 Copynumber: 2.3 Consensus size: 65
2632222 TGAGGCTAGA
* *
2632232 TAAACTGGGCTTAAAACTTCGTTAATGACTAGGTAAATTGGACTTAAGATTTTC-TT-AGGAGCC
1 TAAACTGGGCTTAAAACTTCATTAATGACTAGATAAATTGGACTTAA-A-TTTCATTAAGG-GCC
2632295 AGC
63 AGC
* * * * *
2632298 TAAACTGAGCTTAAAACTTCATTGATGGCTAGATAAATTGGGCTTAAATTTCATTAAGGGCTAGC
1 TAAACTGGGCTTAAAACTTCATTAATGACTAGATAAATTGGACTTAAATTTCATTAAGGGCCAGC
*
2632363 TAAATTGGGCTTAAAACTT
1 TAAACTGGGCTTAAAACTT
2632382 TATTGGTGCC
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
64 4 0.05
65 25 0.34
66 44 0.60
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (65 bp):
TAAACTGGGCTTAAAACTTCATTAATGACTAGATAAATTGGACTTAAATTTCATTAAGGGCCAGC
Found at i:2632343 original size:33 final size:33
Alignment explanation
Indices: 2632164--2632566 Score: 191
Period size: 32 Copynumber: 12.5 Consensus size: 33
2632154 TTTTGGAACT
* * * * *
2632164 AGATAAACTGGG-TTTAAATTTAATTGAGGGTC
1 AGATAAACTGGGCTTAAAACTTCATTGATGGCC
* * *
2632196 AGTTAAACTGGGCTTAAAACCTCATTTGA-GGCT
1 AGATAAACTGGGCTTAAAACTTCA-TTGATGGCC
* * * *
2632229 AGATAAACTGGGCTTAAAACTTCGTTAATGACT
1 AGATAAACTGGGCTTAAAACTTCATTGATGGCC
* * * ** *
2632262 AGGTAAATTGGACTTAAGATTTTC-TT-AGGAGCC
1 AGATAAACTGGGCTTAA-AACTTCATTGATG-GCC
* * *
2632295 AGCTAAACTGAGCTTAAAACTTCATTGATGGCT
1 AGATAAACTGGGCTTAAAACTTCATTGATGGCC
* * * * *
2632328 AGATAAATTGGGCTT-AAATTTCATTAAGGGCT
1 AGATAAACTGGGCTTAAAACTTCATTGATGGCC
* * * *
2632360 AGCTAAATTGGGCTTAAAACTTTATTGGT-GCC
1 AGATAAACTGGGCTTAAAACTTCATTGATGGCC
* * ** * *
2632392 AGATAATCTGAGCTTATGACTTTATTGGT-GCC
1 AGATAAACTGGGCTTAAAACTTCATTGATGGCC
* *
2632424 CGTTAAACTGGGCTTAAAACTTCATTGAT-GCC
1 AGATAAACTGGGCTTAAAACTTCATTGATGGCC
* * * ** *
2632456 AGATAATCCGAGCTTATGACTTTATT-A-GTGCC
1 AGATAAACTGGGCTTAAAACTTCATTGATG-GCC
* ** * *
2632488 AGCTAAACTGGATTTAAAACTTTATTGAT-GTC
1 AGATAAACTGGGCTTAAAACTTCATTGATGGCC
* ** * *
2632520 AGATCATTTAGGCTTAAGACTTCATTGAT-GCC
1 AGATAAACTGGGCTTAAAACTTCATTGATGGCC
*
2632552 AGCTAAACTGGGCTT
1 AGATAAACTGGGCTT
2632567 GAATTTTTTT
Statistics
Matches: 272, Mismatches: 87, Indels: 24
0.71 0.23 0.06
Matches are distributed among these distances:
31 1 0.00
32 173 0.64
33 88 0.32
34 10 0.04
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (33 bp):
AGATAAACTGGGCTTAAAACTTCATTGATGGCC
Found at i:2632436 original size:64 final size:64
Alignment explanation
Indices: 2632292--2632566 Score: 272
Period size: 64 Copynumber: 4.3 Consensus size: 64
2632282 TTTCTTAGGA
* * * * *
2632292 GCCAGCTAAACTGAGCTTAAAACTTCATTGATGGCTAGATAAAT-TGGGCTTA--AATTTCATTA
1 GCCAGCTAAACTGGGCTTAAAACTTTATTGAT-GCCAGAT-AATCTGAGCTTATGACTTT-ATT-
2632354 AGG-
62 -GGT
* * *
2632357 GCTAGCTAAATTGGGCTTAAAACTTTATTGGTGCCAGATAATCTGAGCTTATGACTTTATTGGT
1 GCCAGCTAAACTGGGCTTAAAACTTTATTGATGCCAGATAATCTGAGCTTATGACTTTATTGGT
* * * * *
2632421 GCCCGTTAAACTGGGCTTAAAACTTCATTGATGCCAGATAATCCGAGCTTATGACTTTATTAGT
1 GCCAGCTAAACTGGGCTTAAAACTTTATTGATGCCAGATAATCTGAGCTTATGACTTTATTGGT
** * * * * * *
2632485 GCCAGCTAAACTGGATTTAAAACTTTATTGATGTCAGATCAT-TTAGGCTTAAGACTTCATTGAT
1 GCCAGCTAAACTGGGCTTAAAACTTTATTGATGCCAGATAATCTGA-GCTTATGACTTTATTGGT
2632549 GCCAGCTAAACTGGGCTT
1 GCCAGCTAAACTGGGCTT
2632567 GAATTTTTTT
Statistics
Matches: 174, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
63 6 0.03
64 134 0.77
65 30 0.17
66 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (64 bp):
GCCAGCTAAACTGGGCTTAAAACTTTATTGATGCCAGATAATCTGAGCTTATGACTTTATTGGT
Found at i:2633987 original size:13 final size:13
Alignment explanation
Indices: 2633955--2633989 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2633945 GTGTTATAAC
2633955 TATTTTTTTTCTT
1 TATTTTTTTTCTT
*
2633968 TACTTTTTTTCTT
1 TATTTTTTTTCTT
2633981 T-TTTTTTTT
1 TATTTTTTTT
2633990 GACTTGCCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.86
Consensus pattern (13 bp):
TATTTTTTTTCTT
Found at i:2636315 original size:4 final size:4
Alignment explanation
Indices: 2636289--2636335 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
2636279 TGTATTATAT
* * *
2636289 TGAA TGAA T-ACA TAAA TGGA TGAA TGAA TGAA TGAA TGAA CGAA TGA
1 TGAA TGAA TGA-A TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGA
2636336 GAGAATGCAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
3 1 0.03
4 34 0.94
5 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.23, T:0.23
Consensus pattern (4 bp):
TGAA
Found at i:2639756 original size:22 final size:22
Alignment explanation
Indices: 2639731--2639777 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2639721 AATTTTCAAT
2639731 TTTAAGATTTTGGATTTTAGAG
1 TTTAAGATTTTGGATTTTAGAG
* *
2639753 TTTAGGATTTTGGATTTTAGGG
1 TTTAAGATTTTGGATTTTAGAG
2639775 TTT
1 TTT
2639778 CGATTTCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (22 bp):
TTTAAGATTTTGGATTTTAGAG
Found at i:2639855 original size:29 final size:29
Alignment explanation
Indices: 2639768--2639898 Score: 90
Period size: 29 Copynumber: 4.6 Consensus size: 29
2639758 GATTTTGGAT
* *
2639768 TTTAGGGTTTCGATTTCAAGG-TTCAAGG
1 TTTAGGGTTTCAATTTCAAGGTTTAAAGG
* * * **
2639796 TTT-GGGTTTTAGTTT-ATGGTTTTGAGAG
1 TTTAGGGTTTCAATTTCAAGGTTTAAAG-G
*
2639824 TTTAGGGTTTCAATTTCGAGGTTTAAAGG
1 TTTAGGGTTTCAATTTCAAGGTTTAAAGG
* * * *
2639853 TTTTTGGGTTT-ATTTTTAAGGTTTGAAAGA
1 -TTTAGGGTTTCAATTTCAAGGTTT-AAAGG
*
2639883 TTTAAGGTTTCAATTT
1 TTTAGGGTTTCAATTT
2639899 TAGGGTTTGA
Statistics
Matches: 76, Mismatches: 20, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
26 3 0.04
27 13 0.17
28 7 0.09
29 29 0.38
30 24 0.32
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.48
Consensus pattern (29 bp):
TTTAGGGTTTCAATTTCAAGGTTTAAAGG
Found at i:2639905 original size:14 final size:15
Alignment explanation
Indices: 2639883--2639920 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2639873 GTTTGAAAGA
2639883 TTTAAGGTTTCA-AT
1 TTTAAGGTTTCAGAT
* *
2639897 TTTAGGGTTTGAGAT
1 TTTAAGGTTTCAGAT
2639912 TTTAAGGTT
1 TTTAAGGTT
2639921 AGATTTTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.50
Consensus pattern (15 bp):
TTTAAGGTTTCAGAT
Found at i:2639993 original size:22 final size:23
Alignment explanation
Indices: 2639950--2639995 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
2639940 TTCAAACTTT
*
2639950 GGGTTTAGGTTTTGAAGGTTTTG
1 GGGTTTAGGTTTTGAAGATTTTG
2639973 GGGTTT-GGATTTT-AAGATTTTG
1 GGGTTTAGG-TTTTGAAGATTTTG
2639995 G
1 G
2639996 ATTCAAGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (23 bp):
GGGTTTAGGTTTTGAAGATTTTG
Found at i:2640038 original size:14 final size:14
Alignment explanation
Indices: 2640019--2640078 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
2640009 GAAGTTTTGA
2640019 GTTTTGATTTTAGG
1 GTTTTGATTTTAGG
* *
2640033 GTTTTG-GTTTACAG
1 GTTTTGATTTTA-GG
*
2640047 GTTTTGATTTTAGA
1 GTTTTGATTTTAGG
** *
2640061 GTTAGGGTTTTAGG
1 GTTTTGATTTTAGG
2640075 GTTT
1 GTTT
2640079 AGACTTTTTA
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
13 4 0.12
14 26 0.76
15 4 0.12
ACGTcount: A:0.15, C:0.02, G:0.30, T:0.53
Consensus pattern (14 bp):
GTTTTGATTTTAGG
Found at i:2640378 original size:21 final size:21
Alignment explanation
Indices: 2640352--2640393 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2640342 AAAATATTTT
2640352 ATTATTACTATTAATT-TTTAA
1 ATTATTACTATT-ATTATTTAA
*
2640373 ATTATTATTATTATTATTTAA
1 ATTATTACTATTATTATTTAA
2640394 GCATTTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTATTACTATTATTATTTAA
Found at i:2642354 original size:58 final size:58
Alignment explanation
Indices: 2642279--2642393 Score: 176
Period size: 58 Copynumber: 2.0 Consensus size: 58
2642269 TCTTCCCAGG
* * * *
2642279 AATCTGGCTTTAATACTACTTATTAAGGATCATCACAGCTCTGATATCATTTGTTAGA
1 AATCTCGCTCTAATACTACTTATTAAGGATCACCACAGCTCTGATATCACTTGTTAGA
* *
2642337 AATCTCGCTCTAATACTACTTGTTAGGGATCACCACAGCTCTGATATCACTTGTTAG
1 AATCTCGCTCTAATACTACTTATTAAGGATCACCACAGCTCTGATATCACTTGTTAG
2642394 GAGATCGACA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.36
Consensus pattern (58 bp):
AATCTCGCTCTAATACTACTTATTAAGGATCACCACAGCTCTGATATCACTTGTTAGA
Found at i:2642389 original size:31 final size:31
Alignment explanation
Indices: 2642296--2642399 Score: 92
Period size: 31 Copynumber: 3.5 Consensus size: 31
2642286 CTTTAATACT
* *
2642296 ACTTATTAAGGATCATCACAGCTCTGATATC
1 ACTTGTTAGGGATCATCACAGCTCTGATATC
* * * *
2642327 ATTTGTTA--GA-AATCTC-GCTCTAATA-C
1 ACTTGTTAGGGATCATCACAGCTCTGATATC
*
2642353 TACTTGTTAGGGATCACCACAGCTCTGATATC
1 -ACTTGTTAGGGATCATCACAGCTCTGATATC
2642385 ACTTGTTAGGAGATC
1 ACTTGTTAGG-GATC
2642400 GACACACACA
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
26 1 0.02
27 15 0.27
28 4 0.07
29 4 0.07
30 3 0.05
31 24 0.43
32 5 0.09
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (31 bp):
ACTTGTTAGGGATCATCACAGCTCTGATATC
Found at i:2647446 original size:52 final size:52
Alignment explanation
Indices: 2647351--2647507 Score: 174
Period size: 52 Copynumber: 3.0 Consensus size: 52
2647341 TATAACCATA
* * * * * * *
2647351 CAAACTTGCCCATTAAGAATCCCTATCCTCTTAAAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTCTTTTTAGAATTCTTCTCCTGCAAGT
* *
2647403 CAAACTTGCCTATTAAGAATCTCTTTCTTTTTAGAATTTTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTCTTTTTAGAATTCTTCTCCTGCAAGT
* **
2647455 CAAACTTACCTATTAAGAATCT-TTT-TTCTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTCTT-T-TTAGAATTCTTCTCCTGCAAGT
2647507 C
1 C
2647508 TTTTTGTCCA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
50 2 0.02
51 4 0.04
52 85 0.93
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCTCTTTCTTTTTAGAATTCTTCTCCTGCAAGT
Found at i:2647859 original size:25 final size:25
Alignment explanation
Indices: 2647811--2647898 Score: 81
Period size: 25 Copynumber: 3.6 Consensus size: 25
2647801 CCCAAACCTC
* * *
2647811 GAACTTTCAATTC-TTTCACGTCTT
1 GAACCTTCAACTCTTTTCACATCTT
*
2647835 GAACCTTCGACTCTTTTCACATCTT
1 GAACCTTCAACTCTTTTCACATCTT
* *
2647860 GAATCTTCAACTCTTCTCACAT-TT
1 GAACCTTCAACTCTTTTCACATCTT
* *
2647884 CAAACCTTCAGCTCT
1 -GAACCTTCAACTCT
2647899 GATACCACTT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
24 12 0.23
25 40 0.77
ACGTcount: A:0.23, C:0.31, G:0.07, T:0.40
Consensus pattern (25 bp):
GAACCTTCAACTCTTTTCACATCTT
Found at i:2647935 original size:31 final size:31
Alignment explanation
Indices: 2647892--2647975 Score: 143
Period size: 30 Copynumber: 2.7 Consensus size: 31
2647882 TTCAAACCTT
*
2647892 CAGCTCTGATACCACTTGTTGGGGAACACCA
1 CAGCTCTGATACCATTTGTTGGGGAACACCA
*
2647923 CAGCTCTAATACCATTTGTT-GGGAACACCA
1 CAGCTCTGATACCATTTGTTGGGGAACACCA
2647953 CAGCTCTGATACCATTTGTTGGG
1 CAGCTCTGATACCATTTGTTGGG
2647976 CTAAAAGCCT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
30 29 0.59
31 20 0.41
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.27
Consensus pattern (31 bp):
CAGCTCTGATACCATTTGTTGGGGAACACCA
Found at i:2648550 original size:52 final size:52
Alignment explanation
Indices: 2648460--2648616 Score: 199
Period size: 52 Copynumber: 3.0 Consensus size: 52
2648450 TATAACCATA
* * * * *
2648460 CAAACTTGCCCATTAAGAATCCCTATCCTCTTAAAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* *
2648512 CAAACTTGCCTATTAAGAATCTCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* * **
2648564 CAAACTTACCTATTAAGAATCAT-TTTTCTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATC-TCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
2648616 C
1 C
2648617 TTCTTGTCCA
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
52 92 0.99
53 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.40
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:2650523 original size:29 final size:29
Alignment explanation
Indices: 2650485--2650573 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 29
2650475 TTTGTAAAAA
2650485 ATAAATATGATTAAGTAAAATATATAAAT
1 ATAAATATGATTAAGTAAAATATATAAAT
* * * *
2650514 ATAAATATGA--ATGT-CAATACATCACAT
1 ATAAATATGATTAAGTAAAATATAT-AAAT
*
2650541 ATAAATATGATTAAGTAAAATATAGAAAT
1 ATAAATATGATTAAGTAAAATATATAAAT
2650570 ATAA
1 ATAA
2650574 TATAATATTA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
26 6 0.13
27 16 0.34
29 20 0.43
30 5 0.11
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.31
Consensus pattern (29 bp):
ATAAATATGATTAAGTAAAATATATAAAT
Found at i:2650963 original size:22 final size:22
Alignment explanation
Indices: 2650903--2650964 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
2650893 ATCATGAAAG
*
2650903 AATATATAAAAAAATAATTTTAA
1 AATATA-AAAAAAAGAATTTTAA
*
2650926 AATATAAAAAGTAAGAATTTT-A
1 AATATAAAAA-AAAGAATTTTAA
*
2650948 AATGTTAAAAAAAAGAA
1 AAT-ATAAAAAAAAGAA
2650965 ATAGGACATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (22 bp):
AATATAAAAAAAAGAATTTTAA
Found at i:2658869 original size:332 final size:333
Alignment explanation
Indices: 2658052--2659357 Score: 1533
Period size: 332 Copynumber: 4.0 Consensus size: 333
2658042 AACTTTGCCA
* * * * **
2658052 CCTTCGGTAGTGTGTGATGTTTCACGACTTCTATGAGCATACTGACTGGGAGCCCTAGTCAGGGA
1 CCTTTGGTAATGTTTGATGTTTCACGACTTCCATGAGCATACCAACTGGGAGCCCTAGTCAGGGA
* * * * ** * *
2658117 TATGAACGAGCTGTTTCTTTCTTTTTAGGGCGTTTGAGTTGACATGCAACCCTTCTTCACTCTCT
66 CATGAACAAGCTGCTTCTTTCTCTTCGGGGCGTTTAAGTTGACATGCAACCCTTTTTCACTCTCT
* *
2658182 TTGAAAGGCTTCAAACTAAATTAAATTACAGTTCGAAGCCTTTTAAAGAGAGTGGAGAAAAGTTG
131 TTGAAAGGCTTCAAACTAAATTAAACTACAGTTCGAAGCCTTTAAAAGAGAGTGGAGAAAAGTTG
* * * * * *
2658247 TCATGATTTTATCCAGTCTCGTGGCGGGAACACATATATCTACTACCTCCTCCTTTCTTAATGTT
196 TCATGACTTTATCCAGTTTCGCGACGGGAACACATATATCTACTACCTCCTGCTTTCTTATTGTT
* * * *
2658312 TTTTAGGTTTTATTTTGAACACTTTCAGTGAT--A---G----AT-T--T-GAAGAAAAGTAGGT
261 TTTCAGGTTTTATTTTGAACGCTTTCAGTGATAAATCTGAAAAATATCATCGAAGAAAAGCATGT
2658364 TGGCTTTT
326 TGGCTTTT
* ** * *** * *
2658372 CCTTTGGTAATGTTTGATGTTTCACGGCTTCCATGAGCATACCGGCTAGGAGTTTTAGTCAAGAA
1 CCTTTGGTAATGTTTGATGTTTCACGACTTCCATGAGCATACCAACTGGGAGCCCTAGTCAGGGA
* * * * *
2658437 CATGAACAAGTTTCTTCTTTC-CATCGGGGCATTTGAGTTGACATGCAACCCTTTTTCACTCTCT
66 CATGAACAAGCTGCTTCTTTCTCTTCGGGGCGTTTAAGTTGACATGCAACCCTTTTTCACTCTCT
*
2658501 TTGAAAGGCTTCAAACTAAATTAAATTACAGTTCGAAGCCTTTAAAAGAGAGTGGAGAAAAGTTG
131 TTGAAAGGCTTCAAACTAAATTAAACTACAGTTCGAAGCCTTTAAAAGAGAGTGGAGAAAAGTTG
* * * * * *
2658566 TGATGACTTTATCCAGTTTCGTGGCGGG-ACGACATATATCTACTACCTCCGGCTTTCTTACTCT
196 TCATGACTTTATCCAGTTTCGCGACGGGAAC-ACATATATCTACTACCTCCTGCTTTCTTATTGT
* * * *
2658630 TTTTTAGGTTTTATTTTGAACGCTATCACTGATAAATCTGAAAAATAACATCGAAGAAAAGCATG
260 TTTTCAGGTTTTATTTTGAACGCTTTCAGTGATAAATCTGAAAAATATCATCGAAGAAAAGCATG
2658695 TTGGCTTTT
325 TTGGCTTTT
*
2658704 CCTTT-GTAATGTTTGATGTTTCACGGCTTCCATGAGCATACCAACTGGGAGCCCTAGTCAGGGA
1 CCTTTGGTAATGTTTGATGTTTCACGACTTCCATGAGCATACCAACTGGGAGCCCTAGTCAGGGA
* * *
2658768 CATGAACAAGCTACTTATTTCTCTTCGGGGCGTTTAAGTTAACATGCAACCCTTTTTCACTCTCT
66 CATGAACAAGCTGCTTCTTTCTCTTCGGGGCGTTTAAGTTGACATGCAACCCTTTTTCACTCTCT
* *
2658833 TTGAAAGGCTTCAAACTAAATTAAACTACAGTTCGAAGCCTTTAAAAGAGAGCGAAGAAAAGTTG
131 TTGAAAGGCTTCAAACTAAATTAAACTACAGTTCGAAGCCTTTAAAAGAGAGTGGAGAAAAGTTG
* *
2658898 TCATG---------AGTTTCGCGACGAGAACACATATATCTACTACCTTCTGCTTTCTTATTGTT
196 TCATGACTTTATCCAGTTTCGCGACGGGAACACATATATCTACTACCTCCTGCTTTCTTATTGTT
* * * *
2658954 TTTCAGGTTTTATTTTGAAGGCTTTTAGTGATATATCTGAAAAATATCATTGAAGAAAAAGCATG
261 TTTCAGGTTTTATTTTGAACGCTTTCAGTGATAAATCTGAAAAATATCATCGAAG-AAAAGCATG
2659019 TTGGCTTTT
325 TTGGCTTTT
* * * * **
2659028 CCTTTGGTAGTGTTTGATGTTTCA-GACTTCTATGAGCATACTAGCTGGGAGCCCTAACCAGGGA
1 CCTTTGGTAATGTTTGATGTTTCACGACTTCCATGAGCATACCAACTGGGAGCCCTAGTCAGGGA
* * *
2659092 AATGAACGAGCTGCTTCTTTCT-TTACGAGGCG-TTAGAGTTGACATGCAACCCTTTTTCACTCT
66 CATGAACAAGCTGCTTCTTTCTCTT-CGGGGCGTTTA-AGTTGACATGCAACCCTTTTTCACTCT
* * *
2659155 CTTTGAAAGGCTTCAATCTAAATTAAACTACAGTTC-ATAGCC-TTCAAAGAGAG-CGA-AAATA
129 CTTTGAAAGGCTTCAAACTAAATTAAACTACAGTTCGA-AGCCTTTAAAAGAGAGTGGAGAAA-A
* * * * * * *
2659216 TGTTATCATGATTTTATCCAGCTTCGCGATGGGAACACATGTATCTATTACCTCCTACTTTCTTA
192 -GTTGTCATGACTTTATCCAGTTTCGCGACGGGAACACATATATCTACTACCTCCTGCTTTCTTA
* * * * * *
2659281 TTGTTTTTCAGGTATAATTTTGAAGGCCTTCAGTGATAAATCTGAAAACTATCATCAAAGAAAAG
256 TTGTTTTTCAGGTTTTATTTTGAACGCTTTCAGTGATAAATCTGAAAAATATCATCGAAGAAAAG
2659346 CATGTTGGCTTT
321 CATGTTGGCTTT
2659358 CGGAAGACAC
Statistics
Matches: 849, Mismatches: 105, Indels: 53
0.84 0.10 0.05
Matches are distributed among these distances:
318 2 0.00
319 185 0.22
320 68 0.08
321 4 0.00
322 2 0.00
323 112 0.13
324 149 0.18
325 17 0.02
328 2 0.00
331 87 0.10
332 221 0.26
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (333 bp):
CCTTTGGTAATGTTTGATGTTTCACGACTTCCATGAGCATACCAACTGGGAGCCCTAGTCAGGGA
CATGAACAAGCTGCTTCTTTCTCTTCGGGGCGTTTAAGTTGACATGCAACCCTTTTTCACTCTCT
TTGAAAGGCTTCAAACTAAATTAAACTACAGTTCGAAGCCTTTAAAAGAGAGTGGAGAAAAGTTG
TCATGACTTTATCCAGTTTCGCGACGGGAACACATATATCTACTACCTCCTGCTTTCTTATTGTT
TTTCAGGTTTTATTTTGAACGCTTTCAGTGATAAATCTGAAAAATATCATCGAAGAAAAGCATGT
TGGCTTTT
Found at i:2660786 original size:13 final size:13
Alignment explanation
Indices: 2660768--2660792 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2660758 TTTCAGTAAG
2660768 AGATTTTATTAAA
1 AGATTTTATTAAA
2660781 AGATTTTATTAA
1 AGATTTTATTAA
2660793 TTAAGTAGTA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
AGATTTTATTAAA
Found at i:2661669 original size:9 final size:10
Alignment explanation
Indices: 2661617--2661669 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
2661607 CATCTAGGAG
2661617 TTTTTTTGGA
1 TTTTTTTGGA
* *
2661627 TTTTTCTAGA
1 TTTTTTTGGA
* **
2661637 ATTTTTTCAA
1 TTTTTTTGGA
2661647 TTTTTTTGGA
1 TTTTTTTGGA
2661657 TTTTTTTGG-
1 TTTTTTTGGA
2661666 TTTT
1 TTTT
2661670 GGTTGAATTT
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
9 4 0.12
10 30 0.88
ACGTcount: A:0.13, C:0.04, G:0.13, T:0.70
Consensus pattern (10 bp):
TTTTTTTGGA
Found at i:2662100 original size:13 final size:15
Alignment explanation
Indices: 2662081--2662115 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
2662071 TTTCTAACCC
2662081 ATTTTTTA-TTTATT
1 ATTTTTTATTTTATT
2662095 -TTTTTTATTTTATT
1 ATTTTTTATTTTATT
2662109 ATTTTTT
1 ATTTTTT
2662116 GGTTTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.37
14 6 0.32
15 6 0.32
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
ATTTTTTATTTTATT
Found at i:2671148 original size:23 final size:23
Alignment explanation
Indices: 2671122--2671167 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2671112 GAGAAAGATA
2671122 GCCATCCTTAGTATCATGATATT
1 GCCATCCTTAGTATCATGATATT
*
2671145 GCCATCCTTAGTATTATGATATT
1 GCCATCCTTAGTATCATGATATT
2671168 ATGCGATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (23 bp):
GCCATCCTTAGTATCATGATATT
Found at i:2673800 original size:118 final size:117
Alignment explanation
Indices: 2673520--2674071 Score: 512
Period size: 118 Copynumber: 4.7 Consensus size: 117
2673510 TTTATCTATT
* * * ** * *
2673520 TGATCTTGGCTCAGTCCATATCATTTTTTATGATTTAT-AGTTTCATCCCGATCATTT-TTTTTT
1 TGATCTTGGCTTAGTCCAAATCATTTCTTATGATTCGTGA-TTTCAT-TCGATCATTTATTTTTG
* * * * *
2673583 ACCTCAAC-TCGATCATGGTCGTCTCATTTGACTCATGATTTTATCCCGGTCGCT
64 ACCTCAACTTAG-TCCTGGTCGTCTCATTTGACTTATGATTTTATCCCGATCGCA
* * * * *
2673637 TG-TCTTGGCTCAGTCCAGATCATTTCTTATGATTCGTGATTTCGTCTTGACCATTTATTTTTGA
1 TGATCTTGGCTTAGTCCAAATCATTTCTTATGATTCGTGATTTCAT-TCGATCATTTATTTTTGA
* **
2673701 CCTCAACTTAGTCCTGGTCGTCTCATTTGACTTATGGTTTTATTTCGATCGCA
65 CCTCAACTTAGTCCTGGTCGTCTCATTTGACTTATGATTTTATCCCGATCGCA
* * * *
2673754 TGATCTTGGTTTAGTTCAAATCATTTCTTATGATTCATGATTTCGTCTCGATCATTTATTTTTGA
1 TGATCTTGGCTTAGTCCAAATCATTTCTTATGATTCGTGATTTCAT-TCGATCATTTATTTTTGA
* * * * * * * *
2673819 CCTCGACTCAATCTTGATTGTCTCATTT-A---ATGATTTTATCCCGATCTCT
65 CCTCAACTTAGTCCTGGTCGTCTCATTTGACTTATGATTTTATCCCGATCGCA
2673868 TGATCTTAGG-TTAGTCCAAATCATTTCTTATGATTCGTGATTTCAATTCGATCATTTATTTTTG
1 TGATCTT-GGCTTAGTCCAAATCATTTCTTATGATTCGTGATTTC-ATTCGATCATTTATTTTTG
* * * * * * *
2673932 ACCTCGACTT-GATCCTAGTCGCCTCATTTGACTTGTGATTTTGTCCCAATTGCA
64 ACCTCAACTTAG-TCCTGGTCGTCTCATTTGACTTATGATTTTATCCCGATCGCA
* * * * * *
2673986 TGATCTTAGCTTAGTCTAGATCATTTTTTATGATTCGTTATTTTATTTCGATCATTTATTTTTGA
1 TGATCTTGGCTTAGTCCAAATCATTTCTTATGATTCGTGATTTCA-TTCGATCATTTATTTTTGA
* ** *
2674051 TCTCAACGCAGTCCTAGTCGT
65 CCTCAACTTAGTCCTGGTCGT
2674072 TTTTATTTTG
Statistics
Matches: 359, Mismatches: 62, Indels: 27
0.80 0.14 0.06
Matches are distributed among these distances:
114 92 0.26
115 4 0.01
116 44 0.12
117 56 0.16
118 162 0.45
119 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.45
Consensus pattern (117 bp):
TGATCTTGGCTTAGTCCAAATCATTTCTTATGATTCGTGATTTCATTCGATCATTTATTTTTGAC
CTCAACTTAGTCCTGGTCGTCTCATTTGACTTATGATTTTATCCCGATCGCA
Found at i:2673909 original size:114 final size:116
Alignment explanation
Indices: 2673519--2674173 Score: 491
Period size: 118 Copynumber: 5.6 Consensus size: 116
2673509 ATTTATCTAT
* * * *
2673519 TTGATCTTGGCTCAGTCCATATCATTTTTTATGATTTAT-AGTTTCATCCCGATCATTT-TTTTT
1 TTGATCTTGGCTCAGTCCAAATCATTTCTTATGATTCATGA-TTTCATCTCGATCATTTATTTTT
* * *
2673582 TACCTCAACTCGATCATGGTCGTCTCATTTGACTCATGATTTTATCCCGGTCGC
65 GACCTCAACTCAATCATGGTCGTCTCATTTGA--CATGATTTTATCCCGATCGC
* * * * *
2673636 TTG-TCTTGGCTCAGTCCAGATCATTTCTTATGATTCGTGATTTCGTCTTGACCATTTATTTTTG
1 TTGATCTTGGCTCAGTCCAAATCATTTCTTATGATTCATGATTTCATCTCGATCATTTATTTTTG
* * * * **
2673700 ACCTCAACTTAGTCCTGGTCGTCTCATTTGACTTATGGTTTTATTTCGATCGC
66 ACCTCAACTCAATCATGGTCGTCTCATTTGAC--ATGATTTTATCCCGATCGC
* * * * *
2673753 ATGATCTTGGTTTAGTTCAAATCATTTCTTATGATTCATGATTTCGTCTCGATCATTTATTTTTG
1 TTGATCTTGGCTCAGTCCAAATCATTTCTTATGATTCATGATTTCATCTCGATCATTTATTTTTG
* * * * *
2673818 ACCTCGACTCAATCTTGATTGTCTCATTT-A-ATGATTTTATCCCGATCTC
66 ACCTCAACTCAATCATGGTCGTCTCATTTGACATGATTTTATCCCGATCGC
* *
2673867 TTGATCTTAGG-TTAGTCCAAATCATTTCTTATGATTCGTGATTTCAAT-TCGATCATTTATTTT
1 TTGATCTT-GGCTCAGTCCAAATCATTTCTTATGATTCATGATTTC-ATCTCGATCATTTATTTT
* ** * * * * * * *
2673930 TGACCTCGACTTGATCCTAGTCGCCTCATTTGACTTGTGATTTTGTCCCAATTGC
64 TGACCTCAACTCAATCATGGTCGTCTCATTTGAC--ATGATTTTATCCCGATCGC
* * * * * * * * * *
2673985 ATGATCTTAGCTTAGTCTAGATCATTTTTTATGATTCGTTATTTTATTTCGATCATTTATTTTTG
1 TTGATCTTGGCTCAGTCCAAATCATTTCTTATGATTCATGATTTCATCTCGATCATTTATTTTTG
* * * * * * * * * * * * *
2674050 ATCTCAACGCAGTCCTAGTCGTTTTTATTTTGGCTTGTGGTTTTATCACGGTCAC
66 ACCTCAACTCAATCATGGTCG-TCTCA-TTTGAC--ATGATTTTATCCCGATCGC
* * * * * *
2674105 TTGATCTTAGCTCAGTCTAGATCATCTC-TATTGATTCAT-AGTTTCGTCCCGATCATTTATTTT
1 TTGATCTTGGCTCAGTCCAAATCATTTCTTA-TGATTCATGA-TTTCATCTCGATCATTTATTTT
2674168 TGACCT
64 TGACCT
2674174 TGATGCAGTC
Statistics
Matches: 436, Mismatches: 85, Indels: 31
0.79 0.15 0.06
Matches are distributed among these distances:
114 93 0.21
115 5 0.01
116 44 0.10
117 57 0.13
118 159 0.36
119 5 0.01
120 73 0.17
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.46
Consensus pattern (116 bp):
TTGATCTTGGCTCAGTCCAAATCATTTCTTATGATTCATGATTTCATCTCGATCATTTATTTTTG
ACCTCAACTCAATCATGGTCGTCTCATTTGACATGATTTTATCCCGATCGC
Found at i:2673928 original size:232 final size:232
Alignment explanation
Indices: 2673520--2674057 Score: 604
Period size: 232 Copynumber: 2.3 Consensus size: 232
2673510 TTTATCTATT
* * * * * *
2673520 TGATCTTGGCTCAGTCCATATCATTTTTTATGATTTATAGTTTCATCCCGATCATTT-TTTTTTA
1 TGATCTTGGCTTAGTTCAAATCATTTTTTATGATTCATA-TTTCATCTCGATCATTTATTTTTGA
* * *
2673584 CCTCAACTCGATCATGGTCGTCTCATTTGACTCATGATTTTATCCCGGTCGCTTGTCTTGGCTCA
65 CCTCAACTCAATCATGATCGTCTCATTTGA--CATGATTTTATCCCGATCGCTTGTCTTGGCTCA
* * *
2673649 GTCCAGATCATTTCTTATGATTCGTGATTTCGTCTTGACCATTTATTTTTGACCTCAACTT-AGT
128 GTCCAAATCATTTCTTATGATTCGTGATTTCATCTCGACCATTTATTTTTGACCTCAACTTGA-T
* * * ** *
2673713 CCTGGTCGTCTCATTTGACTTATGGTTTTATTTCGATCGCA
192 CCTAGTCGCCTCATTTGACTTATGATTTTATCCCAATCGCA
* * *
2673754 TGATCTTGGTTTAGTTCAAATCATTTCTTATGATTCATGATTTCGTCTCGATCATTTATTTTTGA
1 TGATCTTGGCTTAGTTCAAATCATTTTTTATGATTCAT-ATTTCATCTCGATCATTTATTTTTGA
* * * * *
2673819 CCTCGACTCAATCTTGATTGTCTCATTT-A-ATGATTTTATCCCGATCTCTTGATCTTAGG-TTA
65 CCTCAACTCAATCATGATCGTCTCATTTGACATGATTTTATCCCGATCGCTTG-TCTT-GGCTCA
* *
2673881 GTCCAAATCATTTCTTATGATTCGTGATTTCAAT-TCGATCATTTATTTTTGACCTCGACTTGAT
128 GTCCAAATCATTTCTTATGATTCGTGATTTC-ATCTCGACCATTTATTTTTGACCTCAACTTGAT
* * *
2673945 CCTAGTCGCCTCATTTGACTTGTGATTTTGTCCCAATTGCA
192 CCTAGTCGCCTCATTTGACTTATGATTTTATCCCAATCGCA
* * * * *
2673986 TGATCTTAGCTTAG-TCTAGATCATTTTTTATGATTCGTTATTTTATTTCGATCATTTATTTTTG
1 TGATCTTGGCTTAGTTC-AAATCATTTTTTATGATTC-ATATTTCATCTCGATCATTTATTTTTG
*
2674050 ATCTCAAC
64 ACCTCAAC
2674058 GCAGTCCTAG
Statistics
Matches: 255, Mismatches: 41, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
231 22 0.09
232 150 0.59
233 5 0.02
234 48 0.19
235 30 0.12
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (232 bp):
TGATCTTGGCTTAGTTCAAATCATTTTTTATGATTCATATTTCATCTCGATCATTTATTTTTGAC
CTCAACTCAATCATGATCGTCTCATTTGACATGATTTTATCCCGATCGCTTGTCTTGGCTCAGTC
CAAATCATTTCTTATGATTCGTGATTTCATCTCGACCATTTATTTTTGACCTCAACTTGATCCTA
GTCGCCTCATTTGACTTATGATTTTATCCCAATCGCA
Found at i:2674514 original size:3 final size:3
Alignment explanation
Indices: 2674506--2674546 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
2674496 TAGATACTTT
*
2674506 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2674547 TTTTTTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2674922 original size:21 final size:20
Alignment explanation
Indices: 2674880--2674922 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
2674870 GGTTCTGAGA
* * *
2674880 GTGAATTCAGGTTTTCGGAG
1 GTGAATTCAGGTTGTAGAAG
2674900 GTGAATTCAGGGTTGTAGAAG
1 GTGAATTCA-GGTTGTAGAAG
2674921 GT
1 GT
2674923 TCAGGGAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.23, C:0.07, G:0.37, T:0.33
Consensus pattern (20 bp):
GTGAATTCAGGTTGTAGAAG
Found at i:2675022 original size:19 final size:19
Alignment explanation
Indices: 2675000--2675036 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2674990 TAGGTTTGGT
*
2675000 TGAATTTTTTGATGAAGTA
1 TGAATTTTTCGATGAAGTA
2675019 TGAATTTTTCGATGAAGT
1 TGAATTTTTCGATGAAGT
2675037 TTCTGGCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.46
Consensus pattern (19 bp):
TGAATTTTTCGATGAAGTA
Found at i:2677934 original size:40 final size:39
Alignment explanation
Indices: 2677864--2677941 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 39
2677854 AAATCAAATT
2677864 TTAAAATTTTAAAAATAACTCCTTACCATCAAATAACACA
1 TTAAAATTTTAAAAATAACTCCTTA-CATCAAATAACACA
* *
2677904 TTAAAATTTTAAAAGTAACTCTCATT-CATCATATAACA
1 TTAAAATTTTAAAAATAACTC-C-TTACATCAAATAACA
2677942 TTTAATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 31 0.91
41 1 0.03
42 2 0.06
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.33
Consensus pattern (39 bp):
TTAAAATTTTAAAAATAACTCCTTACATCAAATAACACA
Found at i:2681357 original size:19 final size:19
Alignment explanation
Indices: 2681342--2681379 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2681332 TAAGATATAT
2681342 ACGAATAGACATGATAAAC
1 ACGAATAGACATGATAAAC
*
2681361 ACGAATATACATGAATAAA
1 ACGAATAGACATG-ATAAA
2681380 TATGATTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.18
Consensus pattern (19 bp):
ACGAATAGACATGATAAAC
Found at i:2681368 original size:29 final size:29
Alignment explanation
Indices: 2681336--2681401 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
2681326 AATAACTAAG
* *
2681336 ATATATACGAATAGACATGATAAACACGA
1 ATATATACGAATAAACATGATAAACACAA
* * * *
2681365 ATATACATGAATAAATATGATTAACACAA
1 ATATATACGAATAAACATGATAAACACAA
2681394 ATATATAC
1 ATATATAC
2681402 AAAACATGAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (29 bp):
ATATATACGAATAAACATGATAAACACAA
Found at i:2682873 original size:16 final size:16
Alignment explanation
Indices: 2682854--2682885 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2682844 ATTTTTAAAA
*
2682854 TTTTAAATTATATTAT
1 TTTTAAATCATATTAT
2682870 TTTTAAATCATATTAT
1 TTTTAAATCATATTAT
2682886 GTATCATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTAAATCATATTAT
Found at i:2696668 original size:22 final size:22
Alignment explanation
Indices: 2696626--2696668 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2696616 AAATTAAATG
* *
2696626 ATATTATTTTATTAATGAATAA
1 ATATTATTTTATAAATAAATAA
2696648 ATATTAATTTTA-AAATAAATA
1 ATATT-ATTTTATAAATAAATA
2696669 TATAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATATTATTTTATAAATAAATAA
Found at i:2696715 original size:26 final size:26
Alignment explanation
Indices: 2696683--2696762 Score: 90
Period size: 31 Copynumber: 2.9 Consensus size: 26
2696673 AATATTTTTA
2696683 TATTTATTTATTAATAAAATA-ATAT
1 TATTTATTTATTAATAAAATATATAT
*
2696708 TATCTTATTTACATAATTAATAATATTATAT
1 TAT-TTATTTA-TTAA-TAA-AATA-TATAT
2696739 TATTTAATTTATTAATAAAATATA
1 TATTT-ATTTATTAATAAAATATA
2696763 AAATTTATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
25 3 0.07
26 7 0.15
27 5 0.11
28 7 0.15
29 7 0.15
30 5 0.11
31 12 0.26
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (26 bp):
TATTTATTTATTAATAAAATATATAT
Found at i:2704892 original size:16 final size:17
Alignment explanation
Indices: 2704857--2704898 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2704847 TTATTTTTTG
*
2704857 ATATATTATTTTTATTAA
1 ATAT-TTATTTTTATAAA
2704875 ATATTTATTTTTA-AAA
1 ATATTTATTTTTATAAA
*
2704891 ATAATTAT
1 ATATTTAT
2704899 ATAAATCACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 9 0.41
17 9 0.41
18 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATTTATTTTTATAAA
Found at i:2709417 original size:12 final size:13
Alignment explanation
Indices: 2709402--2709434 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2709392 TACTATATAT
2709402 AAAAAGAGAAAA-
1 AAAAAGAGAAAAG
*
2709414 AAAAAGAAAAAAG
1 AAAAAGAGAAAAG
2709427 AAAAAGAG
1 AAAAAGAG
2709435 CAGTGCATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAAGAGAAAAG
Found at i:2717331 original size:3 final size:3
Alignment explanation
Indices: 2717323--2717363 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
2717313 GATTTGTGGT
*
2717323 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG TTG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
2717364 TTAGCTTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.37
Consensus pattern (3 bp):
ATG
Found at i:2720668 original size:27 final size:27
Alignment explanation
Indices: 2720638--2720725 Score: 149
Period size: 27 Copynumber: 3.3 Consensus size: 27
2720628 TTTCAATGCC
2720638 ACTATCATACTTGCACGTTCATAATCT
1 ACTATCATACTTGCACGTTCATAATCT
2720665 ACTATCATACTTGCACGTTCATAATCT
1 ACTATCATACTTGCACGTTCATAATCT
* *
2720692 ACTATCATACTTGCATGTTCATTATCT
1 ACTATCATACTTGCACGTTCATAATCT
*
2720719 GCTATCA
1 ACTATCA
2720726 AGAACAAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.39
Consensus pattern (27 bp):
ACTATCATACTTGCACGTTCATAATCT
Found at i:2723201 original size:11 final size:11
Alignment explanation
Indices: 2723181--2723211 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2723171 ATTCATAAAT
2723181 AAATTCATTTA
1 AAATTCATTTA
*
2723192 AAATTTATTTA
1 AAATTCATTTA
2723203 AAATTCATT
1 AAATTCATT
2723212 CCTTTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATTCATTTA
Found at i:2723359 original size:14 final size:15
Alignment explanation
Indices: 2723333--2723361 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2723323 AGTTTATTTA
2723333 AATTTATTTTATTAT
1 AATTTATTTTATTAT
2723348 AATTTA-TTTATTAT
1 AATTTATTTTATTAT
2723362 TTGTAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AATTTATTTTATTAT
Found at i:2731202 original size:133 final size:134
Alignment explanation
Indices: 2730956--2731468 Score: 750
Period size: 134 Copynumber: 3.8 Consensus size: 134
2730946 AAATTCAAGT
* * *
2730956 TTCAAGTCGGTAG-TTGCGCAATTGAAATCC-A-CGCACTGGAATCCGGATTAAAACCCTAAAAA
1 TTCAAGTCGGT-GTTTGCGCAATTGAAAACCAAGCGCACCGGAATCCCGATTAAAACCCTAAAAA
* * *
2731018 TCTCCCGATCGATTCAATGAAACAAAAAAAGAAGGAAGCTACAATATTTTAACGTAATTTGTTGC
65 TCTCCCGATCGATTCAATGAAAC-AAAAAAGAAGGAAGCTATAAAATTTTAACGTAATTGGTTGC
2731083 CCCAAA
129 CCCAAA
*
2731089 TTCAAGTCGGTGTTTGCGCAATTGAAAACCAAGCGCACC-GAATCCCAATTAAAACCCTAAAAAT
1 TTCAAGTCGGTGTTTGCGCAATTGAAAACCAAGCGCACCGGAATCCCGATTAAAACCCTAAAAAT
* *
2731153 CTCCCGTTCGATTTAATGAAACAAAAAAGAAGGAAGCTATAAAATTTTAACGTAATTGGTTGCCC
66 CTCCCGATCGATTCAATGAAACAAAAAAGAAGGAAGCTATAAAATTTTAACGTAATTGGTTGCCC
2731218 CAAA
131 CAAA
*
2731222 TTCAAGTCGGTGTTTGCGCAATTGAAAACCAAGCGCACCGGAATCCCGATTAAAACCCTAAAAAA
1 TTCAAGTCGGTGTTTGCGCAATTGAAAACCAAGCGCACCGGAATCCCGATTAAAACCCTAAAAAT
* *
2731287 CTCCCGATCGATGCAATGATACAAAAAAGAAGGAAGCTATAAAATTTTAACGTAATTGGTTGCCC
66 CTCCCGATCGATTCAATGAAACAAAAAAGAAGGAAGCTATAAAATTTTAACGTAATTGGTTGCCC
2731352 CAAA
131 CAAA
* * * *
2731356 TTCAAGTCGGTGGTTGTGCAATTGAAAACCACGCCCACCGGAATCCCGATTAAAACCCTAAAAA-
1 TTCAAGTCGGTGTTTGCGCAATTGAAAACCAAGCGCACCGGAATCCCGATTAAAACCCTAAAAAT
* * * *
2731420 CTCCCAATCGATGCAATGCACCAA-AAATAAAGAAGGGATCTATAAAATT
66 CTCCCGATCGATTCAATG-A--AACAAA-AAAGAAGGAAGCTATAAAATT
2731469 AGCACGTTTC
Statistics
Matches: 349, Mismatches: 23, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
132 1 0.00
133 127 0.36
134 193 0.55
135 8 0.02
136 20 0.06
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.23
Consensus pattern (134 bp):
TTCAAGTCGGTGTTTGCGCAATTGAAAACCAAGCGCACCGGAATCCCGATTAAAACCCTAAAAAT
CTCCCGATCGATTCAATGAAACAAAAAAGAAGGAAGCTATAAAATTTTAACGTAATTGGTTGCCC
CAAA
Found at i:2732635 original size:23 final size:24
Alignment explanation
Indices: 2732591--2732635 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2732581 ATTAGGATTA
*
2732591 AATTTTTATTTAGTTTATATAATT
1 AATTTTAATTTAGTTTATATAATT
*
2732615 AATTTTAATTTATTTTA-ATAA
1 AATTTTAATTTAGTTTATATAA
2732636 AAATGCAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
AATTTTAATTTAGTTTATATAATT
Found at i:2734559 original size:28 final size:28
Alignment explanation
Indices: 2734502--2734561 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
2734492 TTATAAAAAA
* * * **
2734502 CATAGAAGCATAACGACGTCGTTTTGAG
1 CATAGAACCAAAACGACATCGTTTCAAG
2734530 CATAGAACCAAAACGACATCGTTTCAAG
1 CATAGAACCAAAACGACATCGTTTCAAG
2734558 CATA
1 CATA
2734562 AGAGGATCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (28 bp):
CATAGAACCAAAACGACATCGTTTCAAG
Found at i:2735535 original size:271 final size:270
Alignment explanation
Indices: 2735030--2735544 Score: 834
Period size: 271 Copynumber: 1.9 Consensus size: 270
2735020 GATGTTGAAA
*
2735030 AATTATTATTAATAAATTTTAAAAAAATAAAATATATAATAAATTTTTTATTAATTTTCAAAAAT
1 AATTATTATTAATAAATTTTAAAAAAATAAAATATATAAGAAATTTTTTATTAATTTTCAAAAAT
* * *
2735095 TGTAGAAATTAAACTTACTCCGAAAGTCCGCCTAGATGATGGAAATTTTTAGAGATGTTCACGTT
66 TATAGAAATTAAACTTACTCCGAAAGTCCGCCTAGATGATAGAAATTTTTAAAGATGTTCACGTT
* * *
2735160 TTAATTAAACCCCAAACTTAAATCCTAAACCTTTATCCTAAATCTATTTCAAAACCTTAAGGATA
131 TTAATTAAACCCCAAACTTAAACCCTAAACCTTTACCCTAAATCTATTTCAAAACCTTAAAGATA
*
2735225 CGTGTAAAAATCTCACATAAAATGATTTGTTCCCGAATGCTGCCTAAATAATGTAATTCCGCCTA
196 CGTGCAAAAATCTCACATAAAATGATTTGTTCCCGAATGCTGCCTAAATAATGTAATTCCGCCTA
2735290 AATATTAGGG
261 AATATTAGGG
*
2735300 AATTATTATTAATAAATTTTTAAAAAAATTAAATATATAAGAAATTTTTTATTAATTTTCAAAAA
1 AATTATTATTAATAAA-TTTTAAAAAAATAAAATATATAAGAAATTTTTTATTAATTTTCAAAAA
* * * * *
2735365 TTATAGAAATTAAACTTTCTCCGAAAGTTCGCTTAGATGATAGAGATTTTTAAAGATGTTCGCGT
65 TTATAGAAATTAAACTTACTCCGAAAGTCCGCCTAGATGATAGAAATTTTTAAAGATGTTCACGT
* *
2735430 TTTAATTAAACCCCAAACTTAAACCCT-AACCTTTTACCCTAAATCTATTTCTAAATCTTAAAGA
130 TTTAATTAAACCCCAAACTTAAACCCTAAACC-TTTACCCTAAATCTATTTCAAAACCTTAAAGA
* * *
2735494 TACGTGCAAAAATCTCACATGAAATGATTTGTTCTCGAATGCTGCTTAAAT
194 TACGTGCAAAAATCTCACATAAAATGATTTGTTCCCGAATGCTGCCTAAAT
2735545 GATAGGGTAT
Statistics
Matches: 224, Mismatches: 19, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
270 20 0.09
271 204 0.91
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (270 bp):
AATTATTATTAATAAATTTTAAAAAAATAAAATATATAAGAAATTTTTTATTAATTTTCAAAAAT
TATAGAAATTAAACTTACTCCGAAAGTCCGCCTAGATGATAGAAATTTTTAAAGATGTTCACGTT
TTAATTAAACCCCAAACTTAAACCCTAAACCTTTACCCTAAATCTATTTCAAAACCTTAAAGATA
CGTGCAAAAATCTCACATAAAATGATTTGTTCCCGAATGCTGCCTAAATAATGTAATTCCGCCTA
AATATTAGGG
Found at i:2738673 original size:25 final size:25
Alignment explanation
Indices: 2738642--2738722 Score: 114
Period size: 25 Copynumber: 3.3 Consensus size: 25
2738632 TAACTTTTAT
2738642 TTTTATTAGTTTAATATTATAATTA
1 TTTTATTAGTTTAATATTATAATTA
*
2738667 TTTTATTTGTTTAATA-TA-AA-TA
1 TTTTATTAGTTTAATATTATAATTA
*
2738689 TTTTTATTAGTTTAATATAATAATTA
1 -TTTTATTAGTTTAATATTATAATTA
2738715 TTTTATTA
1 TTTTATTA
2738723 AATTTTAACA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
22 2 0.04
23 17 0.35
24 3 0.06
25 25 0.51
26 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (25 bp):
TTTTATTAGTTTAATATTATAATTA
Found at i:2738701 original size:23 final size:23
Alignment explanation
Indices: 2738639--2738708 Score: 97
Period size: 23 Copynumber: 3.0 Consensus size: 23
2738629 CACTAACTTT
2738639 TATTTTTATTAGTTTAATATTATAA
1 TATTTTTATTAGTTTAATA-TA-AA
*
2738664 T-TATTTTATTTGTTTAATATAAA
1 TAT-TTTTATTAGTTTAATATAAA
2738687 TATTTTTATTAGTTTAATATAA
1 TATTTTTATTAGTTTAATATAA
2738709 TAATTATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 21 0.51
24 4 0.10
25 16 0.39
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TATTTTTATTAGTTTAATATAAA
Found at i:2738705 original size:17 final size:17
Alignment explanation
Indices: 2738639--2738706 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 17
2738629 CACTAACTTT
2738639 TATTTTTATTAGTTTAA
1 TATTTTTATTAGTTTAA
* *
2738656 TATTATAATTA-TTT--
1 TATTTTTATTAGTTTAA
* * *
2738670 TATTTGT-TTAATATAAA
1 TATTTTTATTAGT-TTAA
2738687 TATTTTTATTAGTTTAA
1 TATTTTTATTAGTTTAA
2738704 TAT
1 TAT
2738707 AATAATTATT
Statistics
Matches: 37, Mismatches: 9, Indels: 10
0.66 0.16 0.18
Matches are distributed among these distances:
13 3 0.08
14 5 0.14
15 1 0.03
16 3 0.08
17 21 0.57
18 4 0.11
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (17 bp):
TATTTTTATTAGTTTAA
Found at i:2738820 original size:26 final size:27
Alignment explanation
Indices: 2738784--2738837 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
2738774 TATTTAAAAA
*
2738784 TAATTTAATAAAT-TTTAATAAATTAT
1 TAATTTAATAAATATTAAATAAATTAT
* *
2738810 TAATTTTATAAATATTAAATAATTTAT
1 TAATTTAATAAATATTAAATAAATTAT
2738837 T
1 T
2738838 TTTTGTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TAATTTAATAAATATTAAATAAATTAT
Found at i:2738822 original size:16 final size:16
Alignment explanation
Indices: 2738794--2738827 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
2738784 TAATTTAATA
2738794 AATTTTAATAAATTATT
1 AATTTTAATAAA-TATT
2738811 AATTTT-ATAAATATT
1 AATTTTAATAAATATT
2738826 AA
1 AA
2738828 ATAATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 5 0.29
17 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTTAATAAATATT
Found at i:2739250 original size:27 final size:28
Alignment explanation
Indices: 2739220--2739277 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
2739210 TTTTTTATTG
* *
2739220 ATATTTTTTAATTACAATTATTATAA-A
1 ATATTTTTTAACTACAATTATAATAATA
*
2739247 ATATTTTTTAACTATAATTATAATAATA
1 ATATTTTTTAACTACAATTATAATAATA
2739275 ATA
1 ATA
2739278 ATTATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (28 bp):
ATATTTTTTAACTACAATTATAATAATA
Found at i:2745308 original size:7 final size:7
Alignment explanation
Indices: 2745296--2745320 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2745286 ATGGCTGTAA
2745296 TATATTT
1 TATATTT
2745303 TATATTT
1 TATATTT
2745310 TATATTT
1 TATATTT
2745317 TATA
1 TATA
2745321 GTTGAGGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TATATTT
Found at i:2745822 original size:28 final size:28
Alignment explanation
Indices: 2745782--2745839 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
2745772 AAAAAGAGAG
2745782 TTGCCTTTGAAATGTTAAGGCATAATAA
1 TTGCCTTTGAAATGTTAAGGCATAATAA
2745810 TTGCCTTTGAAATGTTAAGGCATAATAA
1 TTGCCTTTGAAATGTTAAGGCATAATAA
2745838 TT
1 TT
2745840 CATTTACTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (28 bp):
TTGCCTTTGAAATGTTAAGGCATAATAA
Found at i:2748959 original size:22 final size:22
Alignment explanation
Indices: 2748924--2748965 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2748914 TGAGGGATCA
* *
2748924 TAATTTTAGGGATACAAATACT
1 TAATTCTAGAGATACAAATACT
2748946 TAATTCTAGAGATACAAATA
1 TAATTCTAGAGATACAAATA
2748966 TAAATATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (22 bp):
TAATTCTAGAGATACAAATACT
Found at i:2749646 original size:13 final size:13
Alignment explanation
Indices: 2749628--2749663 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2749618 CACAACATAT
2749628 GCTATATATCAGC
1 GCTATATATCAGC
2749641 GCTATATATCAGC
1 GCTATATATCAGC
*
2749654 TCTAGTATAT
1 GCTA-TATAT
2749664 GAGAGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (13 bp):
GCTATATATCAGC
Found at i:2750949 original size:179 final size:179
Alignment explanation
Indices: 2750649--2751009 Score: 713
Period size: 179 Copynumber: 2.0 Consensus size: 179
2750639 TTCCTTTCCT
2750649 AATGGCAATAGGCAGATCATAATCACTAGTTATAGTTTTAGGATATTCATGCTCATTTTGAGAAA
1 AATGGCAATAGGCAGATCATAATCACTAGTTATAGTTTTAGGATATTCATGCTCATTTTGAGAAA
2750714 CAGAGTCAAAAACTGTAGTTACCTCATTTCTAGAGTTAGGATCAGGTTCTTGGACTGGCACTGGT
66 CAGAGTCAAAAACTGTAGTTACCTCATTTCTAGAGTTAGGATCAGGTTCTTGGACTGGCACTGGT
*
2750779 TCAGGATCTGGAACTTTCTTTCTTGAGTACACCTGTAATTCCTTTATAG
131 TCAGGATCTGAAACTTTCTTTCTTGAGTACACCTGTAATTCCTTTATAG
2750828 AATGGCAATAGGCAGATCATAATCACTAGTTATAGTTTTAGGATATTCATGCTCATTTTGAGAAA
1 AATGGCAATAGGCAGATCATAATCACTAGTTATAGTTTTAGGATATTCATGCTCATTTTGAGAAA
2750893 CAGAGTCAAAAACTGTAGTTACCTCATTTCTAGAGTTAGGATCAGGTTCTTGGACTGGCACTGGT
66 CAGAGTCAAAAACTGTAGTTACCTCATTTCTAGAGTTAGGATCAGGTTCTTGGACTGGCACTGGT
2750958 TCAGGATCTGAAACTTTCTTTCTTGAGTACACCTGTAATTCCTTTATAG
131 TCAGGATCTGAAACTTTCTTTCTTGAGTACACCTGTAATTCCTTTATAG
2751007 AAT
1 AAT
2751010 CAAGAACAAT
Statistics
Matches: 181, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
179 181 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (179 bp):
AATGGCAATAGGCAGATCATAATCACTAGTTATAGTTTTAGGATATTCATGCTCATTTTGAGAAA
CAGAGTCAAAAACTGTAGTTACCTCATTTCTAGAGTTAGGATCAGGTTCTTGGACTGGCACTGGT
TCAGGATCTGAAACTTTCTTTCTTGAGTACACCTGTAATTCCTTTATAG
Found at i:2753041 original size:22 final size:22
Alignment explanation
Indices: 2753016--2753057 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2753006 TTGTCTATCC
* *
2753016 TAATTTTAGGGATACAAATACT
1 TAATTCTAGAGATACAAATACT
2753038 TAATTCTAGAGATACAAATA
1 TAATTCTAGAGATACAAATA
2753058 TAAATATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (22 bp):
TAATTCTAGAGATACAAATACT
Found at i:2754897 original size:23 final size:23
Alignment explanation
Indices: 2754854--2754907 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2754844 ATCCATGCCT
* *
2754854 TTGCTTATGGAACCATCTTTAAA
1 TTGCTTATGGAAACATATTTAAA
* *
2754877 TTGCTTATGGAAAGATATTTATA
1 TTGCTTATGGAAACATATTTAAA
2754900 TCTGCTTA
1 T-TGCTTA
2754908 ACCAAAAACG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (23 bp):
TTGCTTATGGAAACATATTTAAA
Found at i:2757555 original size:291 final size:291
Alignment explanation
Indices: 2757031--2757614 Score: 1123
Period size: 291 Copynumber: 2.0 Consensus size: 291
2757021 TTCGTACAAG
2757031 GAAGTAGCGTTGGCCCCTCCAGGTAGTATTTTCAAACTGCATTTCAGGCCTGAAACTGATTGTTC
1 GAAGTAGCGTTGGCCCCTCCAGGTAGTATTTTCAAACTGCATTTCAGGCCTGAAACTGATTGTTC
2757096 TGATAACCCAAACTTCAACACTGAAAAATGTCGAGAGGAAATGAACGAAATGAAAGACAATTTTG
66 TGATAACCCAAACTTCAACACTGAAAAATGTCGAGAGGAAATGAACGAAATGAAAGACAATTTTG
* *
2757161 ATCCGTTGACTACGGGGATAACAAACATATTTGAAAAGAAGAGTGAGAACACCATATTGGATTCA
131 ATCCGTTGACTACGGGGATAACAAACATATTTGAAAAGAAGAGTGAAAACACCATATTGGATCCA
2757226 ACAGACAGCTCGAAAGAGGAAATTGGTATAGTTGAAAACAAAGAAGGAACTAGGCCAACTGCTGT
196 ACAGACAGCTCGAAAGAGGAAATTGGTATAGTTGAAAACAAAGAAGGAACTAGGCCAACTGCTGT
* *
2757291 GATGGAAGATCACTCTCCTTTGGTGGTGTCT
261 GATGGAAGATAACTCTCCTTTGGTGATGTCT
2757322 GAAGTAGCGTTGGCCCCTCCAGGTAGTATTTTCAAACTGCATTTCAGGCCTGAAACTGATTGTTC
1 GAAGTAGCGTTGGCCCCTCCAGGTAGTATTTTCAAACTGCATTTCAGGCCTGAAACTGATTGTTC
*
2757387 TGATAACCCAAACTTCAACACTGAAAAATGTCGAGAGGAAATGAATGAAATGAAAGACAATTTTG
66 TGATAACCCAAACTTCAACACTGAAAAATGTCGAGAGGAAATGAACGAAATGAAAGACAATTTTG
2757452 ATCCGTTGACTACGGGGATAACAAACATATTTGAAAAGAAGAGTGAAAACACCATATTGGATCCA
131 ATCCGTTGACTACGGGGATAACAAACATATTTGAAAAGAAGAGTGAAAACACCATATTGGATCCA
2757517 ACAGACAGCTCGAAAGAGGAAATTGGTATAGTTGAAAACAAAGAAGGAACTAGGCCAACTGCTGT
196 ACAGACAGCTCGAAAGAGGAAATTGGTATAGTTGAAAACAAAGAAGGAACTAGGCCAACTGCTGT
2757582 GATGGAAGATAACTCTCCTTTGGTGATGTCT
261 GATGGAAGATAACTCTCCTTTGGTGATGTCT
2757613 GA
1 GA
2757615 GGGAGTGGAG
Statistics
Matches: 288, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
291 288 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (291 bp):
GAAGTAGCGTTGGCCCCTCCAGGTAGTATTTTCAAACTGCATTTCAGGCCTGAAACTGATTGTTC
TGATAACCCAAACTTCAACACTGAAAAATGTCGAGAGGAAATGAACGAAATGAAAGACAATTTTG
ATCCGTTGACTACGGGGATAACAAACATATTTGAAAAGAAGAGTGAAAACACCATATTGGATCCA
ACAGACAGCTCGAAAGAGGAAATTGGTATAGTTGAAAACAAAGAAGGAACTAGGCCAACTGCTGT
GATGGAAGATAACTCTCCTTTGGTGATGTCT
Found at i:2763935 original size:2 final size:2
Alignment explanation
Indices: 2763930--2763972 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
2763920 TTTTATATTC
* * *
2763930 AT AT AT AT AT AT AT GT AT AT GT AT AT CT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2763971 AT
1 AT
2763973 TAATAAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2763992 original size:8 final size:8
Alignment explanation
Indices: 2763979--2764008 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2763969 ATATTAATAA
2763979 ATTTATCT
1 ATTTATCT
2763987 ATTTATCT
1 ATTTATCT
*
2763995 ATCTATCT
1 ATTTATCT
2764003 ATTTAT
1 ATTTAT
2764009 ATTTTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTATCT
Found at i:2764079 original size:14 final size:15
Alignment explanation
Indices: 2764060--2764097 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
2764050 ATCACTTTTA
2764060 TTTTTTTCTA-TTTC
1 TTTTTTTCTACTTTC
*
2764074 TTTTTTTTTACTTTC
1 TTTTTTTCTACTTTC
2764089 TTTATTTTC
1 TTT-TTTTC
2764098 CTTTCTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 9 0.45
15 7 0.35
16 4 0.20
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTCTACTTTC
Found at i:2764080 original size:15 final size:16
Alignment explanation
Indices: 2764060--2764097 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
2764050 ATCACTTTTA
2764060 TTTTTTTCTA-TTTCT
1 TTTTTTTCTACTTTCT
2764075 TTTTTTT-TACTTTCT
1 TTTTTTTCTACTTTCT
*
2764090 TTATTTTC
1 TTTTTTTC
2764098 CTTTCTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTTCTACTTTCT
Found at i:2769220 original size:2 final size:2
Alignment explanation
Indices: 2769213--2769238 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2769203 TTAAATGGGA
2769213 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
2769239 GAAATAAAAT
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:2775980 original size:22 final size:22
Alignment explanation
Indices: 2775932--2775985 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
2775922 ATAAATAACG
* *
2775932 CTTTAA-TT-AATTTTTTTATT
1 CTTTAATTTAAATATTTATATT
2775952 -TTT-ATTTAAATATTTATATT
1 CTTTAATTTAAATATTTATATT
2775972 CTTTAATTTAAATA
1 CTTTAATTTAAATA
2775986 AAAATAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 1 0.04
19 5 0.18
20 10 0.36
21 3 0.11
22 9 0.32
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (22 bp):
CTTTAATTTAAATATTTATATT
Found at i:2776016 original size:17 final size:19
Alignment explanation
Indices: 2775984--2776023 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
2775974 TTAATTTAAA
*
2775984 TAAAAATAATAATATTTTT
1 TAAAAATAATAATATTTAT
2776003 TAAAAAT-A-AATATTTAT
1 TAAAAATAATAATATTTAT
2776020 TAAA
1 TAAA
2776024 GGTCTATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
18 1 0.05
19 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAAATAATAATATTTAT
Found at i:2783353 original size:29 final size:29
Alignment explanation
Indices: 2783315--2783370 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
2783305 CTGTAGAGAA
*
2783315 TGCTGGTTCATAGTTGATAGTTATGTAGT
1 TGCTGATTCATAGTTGATAGTTATGTAGT
*
2783344 TGCTGATTCATAGTTGATAGTTGTGTA
1 TGCTGATTCATAGTTGATAGTTATGTA
2783371 ACTCGTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.07, G:0.27, T:0.45
Consensus pattern (29 bp):
TGCTGATTCATAGTTGATAGTTATGTAGT
Found at i:2788109 original size:5 final size:5
Alignment explanation
Indices: 2788095--2788129 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
2788085 CATTGGCTCC
2788095 AGAG- AGAGA AGAGA AGAGA AGAGA AGAGA GAGAGA
1 AGAGA AGAGA AGAGA AGAGA AGAGA AGAGA -AGAGA
2788130 GTGCGTCACC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.14
5 20 0.69
6 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (5 bp):
AGAGA
Found at i:2788688 original size:13 final size:13
Alignment explanation
Indices: 2788672--2788697 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2788662 TTTTTTATTA
2788672 AAAAATTTTAAAT
1 AAAAATTTTAAAT
2788685 AAAAATTTTAAAT
1 AAAAATTTTAAAT
2788698 TAATTAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAAATTTTAAAT
Found at i:2788880 original size:26 final size:27
Alignment explanation
Indices: 2788851--2788914 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
2788841 ATTTTTAATA
* *
2788851 ATTATTTTTACATATTATTAA-TTTTT
1 ATTATTTTTAAAAATTATTAATTTTTT
* **
2788877 ATTAATTAAAAAAATTATTAATTTTTT
1 ATTATTTTTAAAAATTATTAATTTTTT
2788904 ATTGATTTTTA
1 ATT-ATTTTTA
2788915 TTAATTTATA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
26 16 0.57
27 8 0.29
28 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (27 bp):
ATTATTTTTAAAAATTATTAATTTTTT
Found at i:2794729 original size:20 final size:20
Alignment explanation
Indices: 2794704--2794741 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2794694 CAAATTTTGT
2794704 TACATCCACCATATTAACGA
1 TACATCCACCATATTAACGA
*
2794724 TACATCCACCGTATTAAC
1 TACATCCACCATATTAAC
2794742 ATGTGCCAAG
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:0.37, C:0.32, G:0.05, T:0.26
Consensus pattern (20 bp):
TACATCCACCATATTAACGA
Found at i:2803080 original size:29 final size:29
Alignment explanation
Indices: 2802990--2803082 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 29
2802980 TAGTAAAATA
*
2802990 TTTAACGTGATATCTTAACTTTTTAAAATTT
1 TTTAATGTGATATCTTAAC--TTTAAAATTT
* ** *
2803021 TTTAATATGATA-C-CCACTTCTAAAA-TA
1 TTTAATGTGATATCTTAACTT-TAAAATTT
2803048 TTTAATGTGATATCTTAACTTTAAAATTT
1 TTTAATGTGATATCTTAACTTTAAAATTT
2803077 TTTAAT
1 TTTAAT
2803083 ATAATATATG
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
27 14 0.29
28 11 0.22
29 13 0.27
30 1 0.02
31 10 0.20
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.48
Consensus pattern (29 bp):
TTTAATGTGATATCTTAACTTTAAAATTT
Found at i:2803089 original size:29 final size:29
Alignment explanation
Indices: 2802997--2803089 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
2802987 ATATTTAACG
2802997 TGATATCTTAACTTTTTAAAATTTTTTAATA
1 TGATATCTTAAC--TTTAAAATTTTTTAATA
** * *
2803028 TGATA-C-CCACTTCTAAAA-TATTTAATG
1 TGATATCTTAACTT-TAAAATTTTTTAATA
2803055 TGATATCTTAACTTTAAAATTTTTTAATA
1 TGATATCTTAACTTTAAAATTTTTTAATA
*
2803084 TAATAT
1 TGATAT
2803090 ATGATCTATG
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
27 14 0.29
28 11 0.22
29 18 0.37
30 1 0.02
31 5 0.10
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (29 bp):
TGATATCTTAACTTTAAAATTTTTTAATA
Found at i:2805095 original size:4 final size:4
Alignment explanation
Indices: 2805086--2805111 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2805076 GGCAAAGAGT
2805086 CACG CACG CACG CACG CACG CACG CA
1 CACG CACG CACG CACG CACG CACG CA
2805112 GGGTTCAAAA
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:0.27, C:0.50, G:0.23, T:0.00
Consensus pattern (4 bp):
CACG
Found at i:2805430 original size:18 final size:18
Alignment explanation
Indices: 2805383--2805444 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
2805373 TAATTAAATG
*
2805383 ATAAATACTTATTTTAATA
1 ATAAATAATTATTTT-ATA
*
2805402 TATTAATTAATTATTTTATA
1 -A-TAAATAATTATTTTATA
*
2805422 ATAAATAATTAATTTTTTA
1 ATAAATAATT-ATTTTATA
2805441 ATAA
1 ATAA
2805445 TGATTATGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 8 0.22
19 12 0.33
20 4 0.11
21 12 0.33
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
ATAAATAATTATTTTATA
Found at i:2806675 original size:33 final size:33
Alignment explanation
Indices: 2806628--2806694 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
2806618 ACTCCTTTAT
*
2806628 TATTTTACGAATCGAATTGTTATTTTGAATATC
1 TATTTTACGAATCGAATTGTCATTTTGAATATC
* *
2806661 TATTTTACCG-ATCGAATTGTCGTTTTGAGTATC
1 TATTTTA-CGAATCGAATTGTCATTTTGAATATC
2806694 T
1 T
2806695 GCCCTCCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (33 bp):
TATTTTACGAATCGAATTGTCATTTTGAATATC
Found at i:2808448 original size:12 final size:12
Alignment explanation
Indices: 2808423--2808455 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2808413 TTTTTTAATT
2808423 TTTATATT-ATA
1 TTTATATTCATA
*
2808434 TTTATCTTCATA
1 TTTATATTCATA
2808446 TTTATATTCA
1 TTTATATTCA
2808456 ATAAATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTATATTCATA
Found at i:2810561 original size:87 final size:87
Alignment explanation
Indices: 2810415--2810589 Score: 350
Period size: 87 Copynumber: 2.0 Consensus size: 87
2810405 AAAAAAAATA
2810415 GAAAACACATGTACCACATGAATGATGTCAACTGCTCTTTGATTGGCTTGAAACACCTTCACAAG
1 GAAAACACATGTACCACATGAATGATGTCAACTGCTCTTTGATTGGCTTGAAACACCTTCACAAG
2810480 GTGGAACACCGGGGACACCATT
66 GTGGAACACCGGGGACACCATT
2810502 GAAAACACATGTACCACATGAATGATGTCAACTGCTCTTTGATTGGCTTGAAACACCTTCACAAG
1 GAAAACACATGTACCACATGAATGATGTCAACTGCTCTTTGATTGGCTTGAAACACCTTCACAAG
2810567 GTGGAACACCGGGGACACCATT
66 GTGGAACACCGGGGACACCATT
2810589 G
1 G
2810590 GACCACTTCA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (87 bp):
GAAAACACATGTACCACATGAATGATGTCAACTGCTCTTTGATTGGCTTGAAACACCTTCACAAG
GTGGAACACCGGGGACACCATT
Found at i:2815592 original size:23 final size:23
Alignment explanation
Indices: 2815561--2815605 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2815551 ATTCGATTAT
*
2815561 TTTTTAAATATAATATT-TAATAA
1 TTTTAAAATATAA-ATTCTAATAA
*
2815584 TTTTAAAATTTAAATTCTAATA
1 TTTTAAAATATAAATTCTAATA
2815606 TAGCAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTTAAAATATAAATTCTAATAA
Found at i:2819440 original size:23 final size:23
Alignment explanation
Indices: 2819414--2819461 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2819404 ACTAGTACTT
2819414 TTTTCCCATGCTTTTTAACCTCA
1 TTTTCCCATGCTTTTTAACCTCA
2819437 TTTTCCCATGCTTTTTAACCTCA
1 TTTTCCCATGCTTTTTAACCTCA
2819460 TT
1 TT
2819462 CATTTTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.17, C:0.29, G:0.04, T:0.50
Consensus pattern (23 bp):
TTTTCCCATGCTTTTTAACCTCA
Found at i:2822913 original size:17 final size:19
Alignment explanation
Indices: 2822893--2822927 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2822883 AGCTCATGCA
2822893 ATTTTTT-ATAT-TAAATT
1 ATTTTTTAATATATAAATT
2822910 ATTTTTTAATATATAAAT
1 ATTTTTTAATATATAAAT
2822928 ATCGCTGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTTTAATATATAAATT
Found at i:2831862 original size:18 final size:18
Alignment explanation
Indices: 2831839--2831873 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2831829 ATTTAGTTGA
2831839 TAAATTGAAAAAA-AAAAC
1 TAAATT-AAAAAATAAAAC
2831857 TAAATTAAAAAATAAAA
1 TAAATTAAAAAATAAAA
2831874 AATGCACTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (18 bp):
TAAATTAAAAAATAAAAC
Found at i:2837535 original size:18 final size:19
Alignment explanation
Indices: 2837499--2837537 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
2837489 TTATATTTTT
2837499 TTATTTTAGATCAAAATTA
1 TTATTTTAGATCAAAATTA
2837518 TTATTTT-GATTC-AAATTA
1 TTATTTTAGA-TCAAAATTA
2837536 TT
1 TT
2837538 TAAAAGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (19 bp):
TTATTTTAGATCAAAATTA
Found at i:2839370 original size:15 final size:16
Alignment explanation
Indices: 2839345--2839374 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2839335 AATTATAATA
2839345 TAATATTTTTAATTTT
1 TAATATTTTTAATTTT
2839361 TAAT-TTTTTAATTT
1 TAATATTTTTAATTT
2839375 GATACTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TAATATTTTTAATTTT
Found at i:2839535 original size:28 final size:31
Alignment explanation
Indices: 2839504--2839563 Score: 99
Period size: 28 Copynumber: 2.0 Consensus size: 31
2839494 TTTATAATTG
2839504 ATATCATATTAAA-ATTTT-TTA-AATTTAA
1 ATATCATATTAAATATTTTATTACAATTTAA
2839532 ATATCATATTAAATATTTTATTACAATTTAA
1 ATATCATATTAAATATTTTATTACAATTTAA
2839563 A
1 A
2839564 AATTATTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 13 0.45
29 5 0.17
30 3 0.10
31 8 0.28
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (31 bp):
ATATCATATTAAATATTTTATTACAATTTAA
Found at i:2840786 original size:41 final size:41
Alignment explanation
Indices: 2840698--2840777 Score: 142
Period size: 41 Copynumber: 1.9 Consensus size: 41
2840688 CCATCAATAG
*
2840698 AGATTTTATTGTAATGTTCCATCAAATATTATGTAAATCAA
1 AGATTTTATTGTAATGTTCCATCAAATATTATATAAATCAA
2840739 AGATTTTATTGTAATGTTCCATCAAATATTATCATAAAT
1 AGATTTTATTGTAATGTTCCATCAAATATTAT-ATAAAT
2840778 TTCTATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 32 0.86
42 5 0.14
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (41 bp):
AGATTTTATTGTAATGTTCCATCAAATATTATATAAATCAA
Found at i:2843230 original size:28 final size:26
Alignment explanation
Indices: 2843170--2843230 Score: 61
Period size: 28 Copynumber: 2.2 Consensus size: 26
2843160 AGTGAAATAT
* *
2843170 ATTTTTAATATTTTATTTTTATACAT
1 ATTTTTAATATTTAATTTTTATACAC
2843196 ATATTTTAAATATTTCAATTATTTATA-AC
1 AT-TTTT-AATATTT-AATT-TTTATACAC
2843225 ATTTTT
1 ATTTTT
2843231 CATAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 2 0.07
27 4 0.14
28 11 0.38
29 6 0.21
30 6 0.21
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTTTTAATATTTAATTTTTATACAC
Found at i:2848005 original size:16 final size:16
Alignment explanation
Indices: 2847984--2848014 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2847974 TCAATAATTT
2847984 AAATTAATTTAAACTC
1 AAATTAATTTAAACTC
*
2848000 AAATTATTTTAAACT
1 AAATTAATTTAAACT
2848015 AAAAATAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATTAATTTAAACTC
Found at i:2849619 original size:15 final size:15
Alignment explanation
Indices: 2849599--2849646 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
2849589 CCCCCCCCCC
*
2849599 CAAAAAAAAAAAAAA
1 CAAAAAAAAAGAAAA
2849614 C-AAAAAAAAGAAAA
1 CAAAAAAAAAGAAAA
* *
2849628 GAAAAGAAAAGAAAA
1 CAAAAAAAAAGAAAA
2849643 CAAA
1 CAAA
2849647 GCGGTATTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAAGAAAA
Found at i:2855817 original size:3 final size:3
Alignment explanation
Indices: 2855809--2855851 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2855799 TATCAAGAGT
2855809 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2855852 AAATTAATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2865993 original size:51 final size:51
Alignment explanation
Indices: 2865929--2866036 Score: 137
Period size: 51 Copynumber: 2.1 Consensus size: 51
2865919 AAAAATGGAA
* * * * *
2865929 ATATTTAAAATTTTAGTTAAAATTAAATATGAATTTTA-AAAAATAAAATAT
1 ATATTTAAAATTTTA-ATAAAATCAAATATAAATTTAATAAAAATAAAAAAT
* *
2865980 ATATTTAATATTTTAATAAAATCATATATAAATTTAATAAAAATAAAAAAT
1 ATATTTAAAATTTTAATAAAATCAAATATAAATTTAATAAAAATAAAAAAT
2866031 ATATTT
1 ATATTT
2866037 CATGTTAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
50 17 0.35
51 32 0.65
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (51 bp):
ATATTTAAAATTTTAATAAAATCAAATATAAATTTAATAAAAATAAAAAAT
Found at i:2866008 original size:29 final size:28
Alignment explanation
Indices: 2865961--2866018 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
2865951 TTAAATATGA
*
2865961 ATTTTAAAAAATAAAATATATATTTAAT
1 ATTTTAAAAAATAAAATATAAATTTAAT
* *
2865989 ATTTTAATAAAATCATATATAAATTTAAT
1 ATTTTAA-AAAATAAAATATAAATTTAAT
2866018 A
1 A
2866019 AAAATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTTTAAAAAATAAAATATAAATTTAAT
Found at i:2866036 original size:22 final size:21
Alignment explanation
Indices: 2865986--2866036 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
2865976 ATATATATTT
* *
2865986 AATAT-TTTAATAAAATCATA
1 AATATATTTAATAAAATAAAA
* *
2866006 TATAAATTTAATAAAAATAAAA
1 AATATATTTAAT-AAAATAAAA
2866028 AATATATTT
1 AATATATTT
2866037 CATGTTAATT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 6 0.26
22 14 0.61
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
AATATATTTAATAAAATAAAA
Found at i:2873812 original size:27 final size:27
Alignment explanation
Indices: 2873774--2873828 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
2873764 TGAATCAGAT
2873774 AGAATTTATTTGTTAAGTACTCTTCAC
1 AGAATTTATTTGTTAAGTACTCTTCAC
*
2873801 AGAATTTATTTGTTAATTACTCTTCAC
1 AGAATTTATTTGTTAAGTACTCTTCAC
2873828 A
1 A
2873829 TATGAACACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (27 bp):
AGAATTTATTTGTTAAGTACTCTTCAC
Found at i:2878095 original size:22 final size:22
Alignment explanation
Indices: 2878069--2878112 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2878059 TGTATATTTA
*
2878069 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
*
2878091 TATTTGTATCCCTATAATTAAG
1 TATTTGTATCCCTAGAATTAAG
2878113 GAAGATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:2878280 original size:23 final size:23
Alignment explanation
Indices: 2878260--2878344 Score: 107
Period size: 23 Copynumber: 3.6 Consensus size: 23
2878250 AAAATTTTCA
*
2878260 GCCTTCATTGCTGACTTTTTTAG
1 GCCTTCATTGCCGACTTTTTTAG
2878283 GCCTTCATTGCCGACTTTTTTAG
1 GCCTTCATTGCCGACTTTTTTAG
* * *
2878306 GCCTTCATTGTCGAATCCTGTTTAG
1 GCCTTCATTGCCG-A-CTTTTTTAG
*
2878331 GCCTTTATTGCCGA
1 GCCTTCATTGCCGA
2878345 ACCCTTTCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
23 34 0.63
24 2 0.04
25 18 0.33
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (23 bp):
GCCTTCATTGCCGACTTTTTTAG
Found at i:2882017 original size:22 final size:22
Alignment explanation
Indices: 2881991--2882034 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2881981 TGTATATTTA
*
2881991 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
2882013 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
2882035 GAAGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:2889448 original size:5 final size:5
Alignment explanation
Indices: 2889438--2889501 Score: 66
Period size: 5 Copynumber: 13.6 Consensus size: 5
2889428 TAGGTGTTTG
* *
2889438 TTATT TTATT TTATT TTATT CTTATT TT-TT AT-TT TTATT TT-TA TTA-T
1 TTATT TTATT TTATT TTATT -TTATT TTATT TTATT TTATT TTATT TTATT
2889485 TTA-T TTATT TTATT TTA
1 TTATT TTATT TTATT TTA
2889502 AGATATTAGC
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
4 16 0.31
5 30 0.59
6 5 0.10
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:2889472 original size:6 final size:6
Alignment explanation
Indices: 2889441--2889490 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
2889431 GTGTTTGTTA
*
2889441 TTTTA- TTTTA- TTTTAT TCTTATT TTTTAT TTTTAT TTTTAT TATTTAT
1 TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT TTTTAT TTTTAT T-TTTAT
2889489 TT
1 TT
2889491 ATTTTATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 10 0.25
6 19 0.47
7 11 0.28
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:2889475 original size:19 final size:19
Alignment explanation
Indices: 2889446--2889490 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
2889436 TGTTATTTTA
2889446 TTTTA-TTTTATTCTTATT
1 TTTTATTTTTATTCTTATT
*
2889464 TTTTATTTTTATTTTTATT
1 TTTTATTTTTATTCTTATT
*
2889483 ATTTATTT
1 TTTTATTT
2889491 ATTTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTATTTTTATTCTTATT
Found at i:2889484 original size:22 final size:21
Alignment explanation
Indices: 2889441--2889500 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 21
2889431 GTGTTTGTTA
*
2889441 TTTTATTTTATTTTATTCTTATT
1 TTTTATTTTA-TTT-TTATTATT
2889464 TTTTATTTTTATTTTTATTATT
1 TTTTA-TTTTATTTTTATTATT
2889486 TATTTATTTTATTTT
1 T-TTTATTTTATTTT
2889501 AAGATATTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
22 17 0.50
23 12 0.35
24 5 0.15
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTATTTTATTTTTATTATT
Found at i:2889487 original size:13 final size:13
Alignment explanation
Indices: 2889463--2889499 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2889453 TTATTCTTAT
2889463 TTTTTATT-TTTA
1 TTTTTATTATTTA
2889475 TTTTTATTATTTA
1 TTTTTATTATTTA
2889488 TTTATT-TTATTT
1 TTT-TTATTATTT
2889500 TAAGATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 13 0.57
14 2 0.09
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTATTATTTA
Found at i:2889495 original size:28 final size:25
Alignment explanation
Indices: 2889438--2889500 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 25
2889428 TAGGTGTTTG
2889438 TTATTTTA-TTTTATTTTATTCTTA
1 TTATTTTATTTTTATTTTATTCTTA
*
2889462 TT-TTTTATTTTTATTTTTATTATTTA
1 TTATTTTATTTTTA-TTTTATT-CTTA
2889488 TTTATTTTATTTT
1 -TTATTTTATTTT
2889501 AAGATATTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 5 0.15
24 7 0.21
25 7 0.21
26 3 0.09
27 2 0.06
28 9 0.27
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (25 bp):
TTATTTTATTTTTATTTTATTCTTA
Found at i:2890367 original size:21 final size:21
Alignment explanation
Indices: 2890346--2890385 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2890336 TTTTTTGTAT
2890346 TTTATAT-TTTATTTATTTTA
1 TTTATATGTTTATTTATTTTA
* *
2890366 TTTATGTGTTTGTTTATTTT
1 TTTATATGTTTATTTATTTT
2890386 TAAGAGTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.75
Consensus pattern (21 bp):
TTTATATGTTTATTTATTTTA
Found at i:2890498 original size:59 final size:57
Alignment explanation
Indices: 2890433--2890797 Score: 270
Period size: 58 Copynumber: 6.0 Consensus size: 57
2890423 AAAAAAATAT
* *
2890433 AAAATAAATTCATTAAAAAAACATTTTTTAGGAAAAGTTGAAAGTACCAATTTTTCTTG
1 AAAATAAATT--TTAAAAAAATATTTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTTG
* * ** * * **
2890492 AAAATAAAATTTTTAAAAATATATTTTTGAAAAAAAATTGAAAGTATCAATTTATCTCA
1 AAAAT-AAA-TTTTAAAAAAATATTTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTTG
*
2890551 AAAATAAAATTTTTAAAAAATATTTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTTG
1 AAAAT-AAATTTTAAAAAAATATTTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTTG
* ** *
2890609 ACAACAAAAATTTTTTAAAAATA-TTTTTAGGAAAAGTTGAAAGTATCAA-TTTTCTTT
1 A-AA-ATAAATTTTAAAAAAATATTTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTTG
* * * *
2890666 AAAAGTAAAAATTTTAAAATAAAAATTTCTAAAAGCATTTTGAGAAAAAGTTTG-AATTACCAAT
1 AAAA-T--AAATTTT--AA-AAAAATAT-T-------TTTT-AGGAAAAG-TTGAAAGTATCAAT
*
2890730 TTTTCTTA
50 TTTTCTTG
*
2890738 AAAATAAAAATTATTAAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAA-TTTTCTTG
1 AAAAT--AAATT-TT-AAAAAAATATTTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTTG
2890798 TATAAAAGCA
Statistics
Matches: 246, Mismatches: 36, Indels: 47
0.75 0.11 0.14
Matches are distributed among these distances:
55 1 0.00
56 2 0.01
57 8 0.03
58 74 0.30
59 68 0.28
60 14 0.06
61 22 0.09
62 3 0.01
63 1 0.00
69 1 0.00
70 11 0.04
71 25 0.10
72 16 0.07
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.38
Consensus pattern (57 bp):
AAAATAAATTTTAAAAAAATATTTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTTG
Done.