Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008229.1 Hibiscus syriacus cultivar Beakdansim tig00110865_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3634043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 17
Found at i:2532428 original size:21 final size:22
Alignment explanation
Indices: 2532404--2532454 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
2532394 ATTATGGCAA
2532404 TTAATTTTTATA-TTTT-ATAAT
1 TTAATTTTTA-AGTTTTAATAAT
* *
2532425 TTAATTTCTAAGTTTTAATATT
1 TTAATTTTTAAGTTTTAATAAT
2532447 TTAATTTT
1 TTAATTTT
2532455 AAATAATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.52
22 11 0.44
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TTAATTTTTAAGTTTTAATAAT
Found at i:2538515 original size:62 final size:62
Alignment explanation
Indices: 2538413--2538896 Score: 610
Period size: 62 Copynumber: 7.8 Consensus size: 62
2538403 TCTTGTGTCC
* * * *
2538413 TAGAATCAATCCTTGACTTCTTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAG
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* * *
2538475 TAGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCTCCAG
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* * * * * * *
2538537 TAGAGTTAATCTTTGATTTCCTCTTGAATAGAAGTCAACATTTATTATTTGTGACTCCCTAG
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* ** * * * * * * **
2538599 TAGAGTTAATCTTTGACTTTGTCTTAAAGATAAGTCAACCTTTATTATTTTTGACTCCTTAG
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* ** * *
2538661 TAGAGTCAATCATTGACTTCCTTATGAAGAGAAGTCAACATTTGTTATTTATGACTCCTCAG
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* * *
2538723 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTTAACATTTGTTATTTCTGACTCCTCAA
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* * *
2538785 TAGAGTCAATCTTTGACTCCCTCATGAAGAGAAGTCAACATTTGTTATTCCTGACTCCCCAG
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* *
2538847 TAGAGTCAAAT-TTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTT
1 TAGAGTC-AATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTT
2538897 TTTACTTCCT
Statistics
Matches: 370, Mismatches: 51, Indels: 2
0.87 0.12 0.00
Matches are distributed among these distances:
62 367 0.99
63 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (62 bp):
TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
Found at i:2539140 original size:36 final size:35
Alignment explanation
Indices: 2539087--2539651 Score: 708
Period size: 36 Copynumber: 15.9 Consensus size: 35
2539077 TATTTCAAAT
* *
2539087 TTAGCCTCTACGGAAGAGTAGTGAAACAAAGTCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAG-CATC
* *
2539123 TTAGCCTTCACGAAAGAGTAGTGAAGCAAAGCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAG-CATC
*
2539159 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATA
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGC-ATC
*
2539195 TTAGCCTCCACGGAAGAGTAGTGAAGTAAAGTCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAG-CATC
* *
2539231 TTAGCCTCCACGGAAGAGTAGTGAAACAAAGCAACC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGC-ATC
*
2539267 TTAGCCTCCACGGAAGAGTAGTGAAGCAAATCAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGC-ATC
* * *
2539303 TTATCCTCCACGGAAGATTAGTGAAACAAAGTCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAG-CATC
* * * * *
2539339 TTAGCCTCCATGAAAGCGTAGTGAAGAAAAGTCATT
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAG-CATC
*
2539375 TTAGCCTCCACGGAATAGTAGTGAAGCAAAGCAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGC-ATC
*
2539411 TTAGCCTTCACGGAAGAGTAGTGAAGCAAAGCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAG-CATC
* *
2539447 TTAGCCTCCACGGAAGAGTAATGAAGTAACA-CAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAA-AGC-ATC
* *
2539483 TTAGCCTTCACGGAAGAGTAGTGAAGTAAAGCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAG-CATC
2539519 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGC-ATC
* * *
2539555 TTAGCCTTCACGGAAGAGTTGTGAAGC----CACC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCATC
2539586 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAG-CATC
* *
2539622 TTAGCATTCACGGAAGAGTAGTGAAGCAAA
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAA
2539652 AACAGATCAA
Statistics
Matches: 462, Mismatches: 51, Indels: 32
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.06
32 1 0.00
35 6 0.01
36 423 0.92
37 5 0.01
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (35 bp):
TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCATC
Found at i:2539826 original size:3 final size:3
Alignment explanation
Indices: 2539818--2539872 Score: 67
Period size: 3 Copynumber: 18.0 Consensus size: 3
2539808 CGTCCTATCT
* *
2539818 TTA TTA TTA TTA TTA ATA TTG TATA TTA TTA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T-TA TTA TTA TTA TTA
2539865 -TA TTA TTA
1 TTA TTA TTA
2539873 CAAATAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 38 0.84
4 5 0.11
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2539846 original size:16 final size:15
Alignment explanation
Indices: 2539819--2539872 Score: 74
Period size: 16 Copynumber: 3.5 Consensus size: 15
2539809 GTCCTATCTT
2539819 TATTATTATTATTAA
1 TATTATTATTATTAA
*
2539834 TATTGTATATTATTATA
1 TATTAT-TATTATTA-A
2539851 TATTATTATTATT-A
1 TATTATTATTATTAA
2539865 TATTATTA
1 TATTATTA
2539873 CAAATAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 9 0.26
15 5 0.14
16 15 0.43
17 6 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
TATTATTATTATTAA
Found at i:2541070 original size:21 final size:22
Alignment explanation
Indices: 2541046--2541096 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
2541036 ATTATGGCAA
2541046 TTAATTTTTATA-TTTT-ATAAT
1 TTAATTTTTA-AGTTTTAATAAT
* *
2541067 TTAATTTCTAAGTTTTAATATT
1 TTAATTTTTAAGTTTTAATAAT
2541089 TTAATTTT
1 TTAATTTT
2541097 AAATAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.52
22 11 0.44
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TTAATTTTTAAGTTTTAATAAT
Found at i:2547895 original size:15 final size:16
Alignment explanation
Indices: 2547875--2547904 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2547865 ATTAAAAAAA
2547875 AAATTATTGT-TTTTC
1 AAATTATTGTGTTTTC
2547890 AAATTATTGTGTTTT
1 AAATTATTGTGTTTT
2547905 GATTAAATTA
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:0.27, C:0.03, G:0.10, T:0.60
Consensus pattern (16 bp):
AAATTATTGTGTTTTC
Found at i:2548198 original size:12 final size:12
Alignment explanation
Indices: 2548165--2548190 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2548155 TAGTCGTCAA
2548165 CCAAATCCTCCT
1 CCAAATCCTCCT
2548177 CCAAATCCTCCT
1 CCAAATCCTCCT
2548189 CC
1 CC
2548191 TATTCCTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.54, G:0.00, T:0.23
Consensus pattern (12 bp):
CCAAATCCTCCT
Found at i:2549180 original size:18 final size:17
Alignment explanation
Indices: 2549142--2549176 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2549132 AACAATCGAC
2549142 TCAAATGCCTCCATATT
1 TCAAATGCCTCCATATT
2549159 TCAAATGCCTCCATATT
1 TCAAATGCCTCCATATT
2549176 T
1 T
2549177 TCAATCTTTT
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:0.29, C:0.29, G:0.06, T:0.37
Consensus pattern (17 bp):
TCAAATGCCTCCATATT
Found at i:2549733 original size:18 final size:18
Alignment explanation
Indices: 2549710--2549746 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2549700 AAAAGGGGGA
2549710 GAAGTGTGTGTTTTAAGT
1 GAAGTGTGTGTTTTAAGT
2549728 GAAGTGTGTGTTTTAAGT
1 GAAGTGTGTGTTTTAAGT
2549746 G
1 G
2549747 TGTTTTAAAA
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:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (18 bp):
GAAGTGTGTGTTTTAAGT
Found at i:2558498 original size:9 final size:9
Alignment explanation
Indices: 2558484--2558511 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2558474 AAAAAACATT
2558484 AATAAAATA
1 AATAAAATA
2558493 AATAAAATA
1 AATAAAATA
2558502 AATAAAATA
1 AATAAAATA
2558511 A
1 A
2558512 TAATAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AATAAAATA
Found at i:2558526 original size:11 final size:11
Alignment explanation
Indices: 2558502--2558540 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
2558492 AAATAAAATA
* *
2558502 AATAAAATAAT
1 AATAATATACT
2558513 AATAATATACT
1 AATAATATACT
2558524 AATAATATACT
1 AATAATATACT
2558535 AATAAT
1 AATAAT
2558541 CATATAAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAATATACT
Found at i:2558540 original size:14 final size:13
Alignment explanation
Indices: 2558483--2558546 Score: 53
Period size: 14 Copynumber: 5.0 Consensus size: 13
2558473 TAAAAAACAT
*
2558483 TAATAA-AATAAA
1 TAATAATAATATA
2558495 TAA-AATAA-ATA
1 TAATAATAATATA
*
2558506 AAATAATAATAATA
1 TAATAATAAT-ATA
*
2558520 TACTAATAATATA
1 TAATAATAATATA
*
2558533 CTAATAATCATATA
1 -TAATAATAATATA
2558547 AACCATATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
11 6 0.15
12 10 0.24
13 3 0.07
14 22 0.54
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATAATAATATA
Found at i:2558597 original size:36 final size:36
Alignment explanation
Indices: 2558557--2558776 Score: 182
Period size: 36 Copynumber: 6.2 Consensus size: 36
2558547 AACCATATAA
2558557 TATATATATATATATATTTCAAAAATATTTTT-AAAC
1 TATATAT-TATATATATTTCAAAAATATTTTTAAAAC
*
2558593 TATATATTAT-T-TA----AAAAAAAGTTTTTAAAAC
1 TATATATTATATATATTTCAAAAATA-TTTTTAAAAC
*
2558624 TATATATTATATAGT-TTTCAAAAATGA-TTTTAAAAA
1 TATATATTATATA-TATTTCAAAAAT-ATTTTTAAAAC
*
2558660 TAT-TA-TATA-AGT-TTTCAAAAAATGTTTTTAAAAC
1 TATATATTATATA-TATTTC-AAAAATATTTTTAAAAC
* *
2558694 TATATATTATATAATTTTTCAAAAAATGTTTTTAAAAC
1 TATATATTATAT-ATATTTC-AAAAATATTTTTAAAAC
* *
2558732 TATATATTATATA-AGTTTTC-AAAATGTTTTAAAAAC
1 TATATATTATATATA--TTTCAAAAATATTTTTAAAAC
2558768 TATATATTA
1 TATATATTA
2558777 AATAAGTTTT
Statistics
Matches: 158, Mismatches: 7, Indels: 38
0.78 0.03 0.19
Matches are distributed among these distances:
29 6 0.04
30 5 0.03
31 14 0.09
32 1 0.01
33 9 0.06
34 23 0.15
35 7 0.04
36 46 0.29
37 7 0.04
38 40 0.25
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (36 bp):
TATATATTATATATATTTCAAAAATATTTTTAAAAC
Found at i:2558782 original size:36 final size:37
Alignment explanation
Indices: 2558556--2558792 Score: 259
Period size: 38 Copynumber: 6.6 Consensus size: 37
2558546 AAACCATATA
*
2558556 ATATATATATATATA-TATTTCAAAAATATTTTT-AAACT
1 ATATAT-TATATA-AGT-TTTCAAAAATGTTTTTAAAACT
* *
2558594 ATATATTATTTAA------AAAAAAGTTTTTAAAACT
1 ATATATTATATAAGTTTTCAAAAATGTTTTTAAAACT
*
2558625 ATATATTATAT-AGTTTTCAAAAATGATTTT-AAA--
1 ATATATTATATAAGTTTTCAAAAATGTTTTTAAAACT
2558658 A-ATATTATATAAGTTTTCAAAAAATGTTTTTAAAACT
1 ATATATTATATAAGTTTTC-AAAAATGTTTTTAAAACT
*
2558695 ATATATTATATAATTTTTCAAAAAATGTTTTTAAAACT
1 ATATATTATATAAGTTTTC-AAAAATGTTTTTAAAACT
*
2558733 ATATATTATATAAGTTTTC-AAAATGTTTTAAAAACT
1 ATATATTATATAAGTTTTCAAAAATGTTTTTAAAACT
*
2558769 ATATATTAAATAAGTTTTTCAAAA
1 ATATATTATATAAG-TTTTCAAAA
2558793 GAGAAAATAA
Statistics
Matches: 173, Mismatches: 11, Indels: 30
0.81 0.05 0.14
Matches are distributed among these distances:
30 11 0.06
31 15 0.09
32 9 0.05
33 8 0.05
34 11 0.06
35 6 0.03
36 40 0.23
37 11 0.06
38 62 0.36
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (37 bp):
ATATATTATATAAGTTTTCAAAAATGTTTTTAAAACT
Found at i:2559149 original size:22 final size:22
Alignment explanation
Indices: 2559121--2559178 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
2559111 AGTTTTAAAA
* *
2559121 TTCGCAACTTGAATTCGCTAAT
1 TTCGCAACTAGAATTCGCCAAT
2559143 TTCGCAACTAGAATTCGCCAAT
1 TTCGCAACTAGAATTCGCCAAT
2559165 TTCGCAACTA-AATT
1 TTCGCAACTAGAATT
2559179 ACCGATGTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 4 0.12
22 30 0.88
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (22 bp):
TTCGCAACTAGAATTCGCCAAT
Found at i:2559536 original size:36 final size:37
Alignment explanation
Indices: 2559486--2559555 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 37
2559476 TTATTTTCTC
* *
2559486 TTTTCAAAAATGTTTTAAAAACTATATATTATATAAA
1 TTTTCAAAAATGTTTCAAAAACTATATAATATATAAA
2559523 TTTTC-AAAATGTTTCAAAAACTATATAATATAT
1 TTTTCAAAAATGTTTCAAAAACTATATAATATAT
2559556 GTATATTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 26 0.84
37 5 0.16
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (37 bp):
TTTTCAAAAATGTTTCAAAAACTATATAATATATAAA
Found at i:2559628 original size:2 final size:2
Alignment explanation
Indices: 2559621--2559660 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2559611 ATTTGCAAAC
* *
2559621 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2559661 AATAAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2560434 original size:40 final size:37
Alignment explanation
Indices: 2560390--2560463 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 37
2560380 AGTTTTGTTT
2560390 TTTTGTTTCATTTTTAGTATCACGCTGTTAAAAATTTTAG
1 TTTTGTTTCA-TTTTAGTATCAC-C-GTTAAAAATTTTAG
* *
2560430 TTTTGTTTTATTTTAGTATCACCGTTCAAAATTT
1 TTTTGTTTCATTTTAGTATCACCGTTAAAAATTT
2560464 AACGTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 10 0.31
38 1 0.03
39 12 0.38
40 9 0.28
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.54
Consensus pattern (37 bp):
TTTTGTTTCATTTTAGTATCACCGTTAAAAATTTTAG
Found at i:2561293 original size:60 final size:60
Alignment explanation
Indices: 2561117--2561293 Score: 212
Period size: 60 Copynumber: 3.0 Consensus size: 60
2561107 ATATGTCTCT
* * * *
2561117 AAACTATGATCATCATTCTAAATTAGT-CTCTAAACTTTTAAATATTCTACTTTCATTCTC
1 AAACTATGATCCTCATTCTAAATTAGTCCTC-AAACTTTTAAATATTCCAATTTCATCCTC
* * * * * *
2561177 AAACTATGATACTCATTTTAAATTAGTCCTTAAAATTTTTAATGTTCCAATTTCATCCTC
1 AAACTATGATCCTCATTCTAAATTAGTCCTCAAACTTTTAAATATTCCAATTTCATCCTC
* * **
2561237 AAACTATGATCCTTAGTCTAAATTAGTCCTCAAACTTTTAAACCTTCCAATTTCATC
1 AAACTATGATCCTCATTCTAAATTAGTCCTCAAACTTTTAAATATTCCAATTTCATC
2561294 TCCAAATTCA
Statistics
Matches: 97, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
60 95 0.98
61 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (60 bp):
AAACTATGATCCTCATTCTAAATTAGTCCTCAAACTTTTAAATATTCCAATTTCATCCTC
Found at i:2564741 original size:34 final size:34
Alignment explanation
Indices: 2564698--2564822 Score: 129
Period size: 34 Copynumber: 3.8 Consensus size: 34
2564688 TTCGTCCTAC
2564698 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
2564732 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
2564767 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
2564796 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
2564823 CCACAAGCAC
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 39 0.53
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:2565149 original size:24 final size:22
Alignment explanation
Indices: 2565105--2565159 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
2565095 TCATGTAATA
*
2565105 TTTTTTTACATTTTATGTATTT
1 TTTTTTTACATTTTATATATTT
2565127 TCTTTTTTAC-TTTAGTATATATTT
1 T-TTTTTTACATTT--TATATATTT
2565151 TTATTTTTA
1 TT-TTTTTA
2565160 TTTTTAGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 4 0.14
23 9 0.32
24 15 0.54
ACGTcount: A:0.20, C:0.05, G:0.04, T:0.71
Consensus pattern (22 bp):
TTTTTTTACATTTTATATATTT
Found at i:2565214 original size:42 final size:38
Alignment explanation
Indices: 2565160--2565288 Score: 115
Period size: 42 Copynumber: 3.3 Consensus size: 38
2565150 TTTATTTTTA
2565160 TTTTTAGA-TTATATATATAAATATATTA-TTTTTTTATCAGT
1 TTTTTA-ATTTATATATATAAATAT-TTACTTTTTTTAT---T
*
2565201 TTTATTAATTTATATATATATATATTTACTTTTTTTATT
1 TTT-TTAATTTATATATATAAATATTTACTTTTTTTATT
* * *
2565240 TTTTTATTTTATATATAT-TATTTTTAC-TTTTTTATT
1 TTTTTAATTTATATATATAAATATTTACTTTTTTTATT
2565276 ATTATTT-ATTTAT
1 -TT-TTTAATTTAT
2565289 TTGTTTTATT
Statistics
Matches: 79, Mismatches: 4, Indels: 14
0.81 0.04 0.14
Matches are distributed among these distances:
36 9 0.11
37 15 0.19
38 17 0.22
39 4 0.05
41 7 0.09
42 27 0.34
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (38 bp):
TTTTTAATTTATATATATAAATATTTACTTTTTTTATT
Found at i:2565242 original size:9 final size:9
Alignment explanation
Indices: 2565225--2565350 Score: 60
Period size: 9 Copynumber: 13.4 Consensus size: 9
2565215 TATATATATA
*
2565225 TTTACTTTT
1 TTTATTTTT
2565234 TTTA-TTTT
1 TTTATTTTT
2565242 TTTATTTTAT
1 TTTATTTT-T
* *
2565252 ATATATTATT
1 -TTTATTTTT
2565262 TTTACTTTTT
1 TTTA-TTTTT
2565272 TATTATTATTT
1 T-TTATT-TTT
*
2565283 ATTTATTTGT
1 -TTTATTTTT
*
2565293 TTTA-TTTC
1 TTTATTTTT
*
2565301 TATATTTTT
1 TTTATTTTT
*
2565310 TCTTCTTTTCT
1 T-TTATTTT-T
* *
2565321 TCT-TTTTC
1 TTTATTTTT
2565329 TTTATTTTT
1 TTTATTTTT
* *
2565338 TATATTTAT
1 TTTATTTTT
2565347 TTTA
1 TTTA
2565351 CTTACTATTT
Statistics
Matches: 88, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
8 15 0.17
9 36 0.41
10 17 0.19
11 19 0.22
12 1 0.01
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.75
Consensus pattern (9 bp):
TTTATTTTT
Found at i:2565251 original size:38 final size:37
Alignment explanation
Indices: 2565142--2565286 Score: 134
Period size: 38 Copynumber: 3.8 Consensus size: 37
2565132 TTTACTTTAG
** *
2565142 TATATATTT-TTATTTTTATTTTTAGATTATATATATA
1 TATATATTTATT-TTTTTATTTTTTTATTTTATATATA
* *
2565179 AATATA-TTATTTTTTTATCAGTTTTATTAATTTATATATA
1 TATATATTTATTTTTTTAT---TTTT-TTATTTTATATATA
2565219 TATATATTTACTTTTTTTATTTTTTTATTTTATATATA
1 TATATATTTA-TTTTTTTATTTTTTTATTTTATATATA
* *
2565257 T-TATTTTTACTTTTTTATTATTATTTATTT
1 TATATATTTATTTTTTTATT-TT-TTTATTT
2565287 ATTTGTTTTA
Statistics
Matches: 90, Mismatches: 9, Indels: 17
0.78 0.08 0.15
Matches are distributed among these distances:
36 18 0.20
37 16 0.18
38 21 0.23
39 8 0.09
40 15 0.17
41 3 0.03
42 9 0.10
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (37 bp):
TATATATTTATTTTTTTATTTTTTTATTTTATATATA
Found at i:2565253 original size:28 final size:27
Alignment explanation
Indices: 2565221--2565308 Score: 86
Period size: 28 Copynumber: 3.0 Consensus size: 27
2565211 TATATATATA
2565221 TATATTTACTTTTTTTATTTTTTTATTT
1 TATATTTA-TTTTTTTATTTTTTTATTT
* *
2565249 TATATATATTATTTTTACTTTTTTATTAT
1 TATATTTATT-TTTTTATTTTTTTATT-T
* *
2565278 TATTTATTTATTTGTTTTATTTCTATATTT
1 TA--TATTTATTT-TTTTATTTTTTTATTT
2565308 T
1 T
2565309 TTCTTCTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
27 2 0.04
28 22 0.45
29 3 0.06
30 3 0.06
31 19 0.39
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (27 bp):
TATATTTATTTTTTTATTTTTTTATTT
Found at i:2565274 original size:14 final size:13
Alignment explanation
Indices: 2565232--2565290 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 13
2565222 ATATTTACTT
2565232 TTTTTATTTTTTTA
1 TTTTTA-TTTTTTA
* *
2565246 TTTTATATATATTA
1 TTTT-TATTTTTTA
2565260 TTTTTACTTTTTTA
1 TTTTTA-TTTTTTA
*
2565274 TTATTATTTATTTA
1 TTTTTATTT-TTTA
2565288 TTT
1 TTT
2565291 GTTTTATTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
13 5 0.14
14 29 0.81
15 2 0.06
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:2565295 original size:23 final size:23
Alignment explanation
Indices: 2565234--2565307 Score: 62
Period size: 23 Copynumber: 3.1 Consensus size: 23
2565224 ATTTACTTTT
*
2565234 TTTATTTTTTTATTTTA-TATATA
1 TTTATTTATTT-TTTTATTATATA
* *
2565257 TTATTTTTACTTTTTTATTAT-TA
1 TT-TATTTATTTTTTTATTATATA
*
2565280 TTTATTTATTTGTTTTATTTCTATA
1 TTTATTTATTT-TTTTA-TTATATA
2565305 TTT
1 TTT
2565308 TTTCTTCTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
22 7 0.17
23 16 0.40
24 12 0.30
25 5 0.12
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (23 bp):
TTTATTTATTTTTTTATTATATA
Found at i:2565333 original size:45 final size:45
Alignment explanation
Indices: 2565258--2565344 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 45
2565248 TTATATATAT
2565258 TATTTTTACTTTTTTATTATTATTTATTTATTTGTTT-TATTTCTA
1 TATTTTTACTTTTTTATTATTATTTATTTATTT-TTTATATTTCTA
* * * *
2565303 TATTTTTTCTTCTTTTCTTCTT-TTTCTTTATTTTTTATATTT
1 TATTTTTACTT-TTTTATTATTATTTATTTATTTTTTATATTT
2565345 ATTTTACTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 3 0.08
45 25 0.69
46 8 0.22
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.76
Consensus pattern (45 bp):
TATTTTTACTTTTTTATTATTATTTATTTATTTTTTATATTTCTA
Found at i:2565455 original size:15 final size:15
Alignment explanation
Indices: 2565437--2565466 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2565427 TATTTATTTC
2565437 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
2565452 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
2565467 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:2566551 original size:5 final size:5
Alignment explanation
Indices: 2566541--2566568 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2566531 TCTTTTCATC
2566541 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
2566569 CATCACTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:2568436 original size:14 final size:13
Alignment explanation
Indices: 2568417--2568452 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2568407 AAAAAGGCAA
2568417 AAAAAAGAAGAAGC
1 AAAAAAGAA-AAGC
*
2568431 AAAAAACAAAAGC
1 AAAAAAGAAAAGC
2568444 AAAAAAGAA
1 AAAAAAGAA
2568453 CAAAATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAGC
Found at i:2568454 original size:16 final size:15
Alignment explanation
Indices: 2568408--2568464 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
2568398 ATCAGAATAA
*
2568408 AAAAGGCAAAAAAAAG
1 AAAA-GCAAAAAAAAC
2568424 AAGAAGC--AAAAAAC
1 AA-AAGCAAAAAAAAC
2568438 AAAAGCAAAAAAGAAC
1 AAAAGCAAAAAA-AAC
*
2568454 AAAATCAAAAA
1 AAAAGCAAAAA
2568465 GAAAAAGGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
13 4 0.11
14 8 0.23
15 4 0.11
16 17 0.49
17 2 0.06
ACGTcount: A:0.75, C:0.11, G:0.12, T:0.02
Consensus pattern (15 bp):
AAAAGCAAAAAAAAC
Found at i:2568457 original size:22 final size:22
Alignment explanation
Indices: 2568414--2568480 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
2568404 ATAAAAAAGG
*
2568414 CAAAAA-AAAGAAGAAGCAAAAA
1 CAAAAAGAAAAAAGAA-CAAAAA
*
2568436 -ACAAAAGCAAAAAAGAACAAAAT
1 CA-AAAAG-AAAAAAGAACAAAAA
* *
2568459 CAAAAAGAAAAAGGGACAAAAA
1 CAAAAAGAAAAAAGAACAAAAA
2568481 GCACATGCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
21 1 0.03
22 16 0.44
23 10 0.28
24 9 0.25
ACGTcount: A:0.75, C:0.10, G:0.13, T:0.01
Consensus pattern (22 bp):
CAAAAAGAAAAAAGAACAAAAA
Found at i:2568462 original size:29 final size:30
Alignment explanation
Indices: 2568408--2568472 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
2568398 ATCAGAATAA
*
2568408 AAAAGGCAAAAAAAAGAAGAAGCAAAAAAC
1 AAAAGGCAAAAAAAACAAGAAGCAAAAAAC
*
2568438 AAAA-GCAAAAAAGAACAA-AATCAAAAAGA-
1 AAAAGGCAAAAAA-AACAAGAAGCAAAAA-AC
2568467 AAAAGG
1 AAAAGG
2568473 GACAAAAAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.74, C:0.09, G:0.15, T:0.02
Consensus pattern (30 bp):
AAAAGGCAAAAAAAACAAGAAGCAAAAAAC
Found at i:2569096 original size:22 final size:22
Alignment explanation
Indices: 2569068--2569112 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
2569058 AAGCTACCCC
2569068 GTCAAACC-TTTGAGCATCAAAT
1 GTCAAACCATTT-AGCATCAAAT
2569090 GTCAAACCATTTAGCATCAAAT
1 GTCAAACCATTTAGCATCAAAT
2569112 G
1 G
2569113 AACAAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (22 bp):
GTCAAACCATTTAGCATCAAAT
Found at i:2570151 original size:30 final size:30
Alignment explanation
Indices: 2570116--2570172 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2570106 CCTTTGAGAC
*
2570116 AGTTTCTATTGAAACATAAA-CTTTGAAAAT
1 AGTTTCCATTGAAACA-AAATCTTTGAAAAT
*
2570146 AGTTTCCCTTGAAACAAAATCTTTGAA
1 AGTTTCCATTGAAACAAAATCTTTGAA
2570173 TATGTTTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (30 bp):
AGTTTCCATTGAAACAAAATCTTTGAAAAT
Found at i:2570300 original size:37 final size:36
Alignment explanation
Indices: 2570186--2570300 Score: 158
Period size: 36 Copynumber: 3.1 Consensus size: 36
2570176 GTTTTACATT
*
2570186 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * * *
2570222 AAACAAATTTTGTCTATCTTAAGACATGTTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCTCTTG
*
2570259 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
2570296 AAACA
1 AAACA
2570301 TCAATCCTTG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
36 24 0.36
37 24 0.36
38 19 0.28
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:2570406 original size:33 final size:33
Alignment explanation
Indices: 2570342--2570456 Score: 162
Period size: 33 Copynumber: 3.5 Consensus size: 33
2570332 CCTTGATACA
2570342 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACAC--AAA-AAACCTTTGAAATT
*
2570378 GTTTCTCTTGAAACACAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
*
2570411 GTTTCTCTTGAAACAC--AAAACCTTTGAGATT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
*
2570442 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
2570457 AATTTTGTCT
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 27 0.36
33 29 0.39
34 3 0.04
36 16 0.21
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.32
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
Found at i:2570503 original size:67 final size:67
Alignment explanation
Indices: 2570411--2570603 Score: 251
Period size: 67 Copynumber: 2.8 Consensus size: 67
2570401 CTTTGAAAAT
*
2570411 GTTTCTCTTGAAACACAAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
2570476 CA
66 CA
* * * *
2570478 GTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCTTTAAAACAAAATTTTGTCTCCCTTGAG
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAG
* *
2570543 GCC
65 ACA
* * * * *
2570546 GTTTCTCATGAAACAACATATATCTTTAAGATCGTTTCCCTTGAAACGAATTTTGTCT
1 GTTTCTCTTGAAAC-ACA-AAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCT
2570604 TTTTTAAGAC
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
67 40 0.37
68 33 0.31
69 13 0.12
70 21 0.20
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.38
Consensus pattern (67 bp):
GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
CA
Found at i:2571521 original size:98 final size:101
Alignment explanation
Indices: 2571198--2571613 Score: 374
Period size: 105 Copynumber: 4.0 Consensus size: 101
2571188 ATATCGTGCT
* *
2571198 ACCCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTCC
1 ACCCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCC
* ** * * * ** * * *
2571263 AAT-TTCAAAGCTGATTTTCCACGACGGAGGATATCATGCT
65 AGTGAGCCAATCTCAACTT-CACAACGAAGGATAT--TG-G
* *
2571303 ACCTATGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTCCC
1 ACCCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-CC
* * * *
2571367 AGTTTCAGGGCCAATTTCAACTTCACAGCGGAGGATATTGG
65 AG--T--GAGCCAATCTCAACTTCACAACGAAGGATATTGG
* * * * **
2571408 ACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTT-C-
1 ACCCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCA
*
2571471 G-GAGCCAATCTCAACTTCACAATGAAGGATATTGG
66 GTGAGCCAATCTCAACTTCACAACGAAGGATATTGG
* *
2571506 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCC
1 ACCCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCC
* * * *
2571571 GGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AG-T---GAGCCAATCTCAACTTCACAACGAAGGATATTGG
2571612 AC
1 AC
2571614 TTGGAACAAT
Statistics
Matches: 256, Mismatches: 40, Indels: 29
0.79 0.12 0.09
Matches are distributed among these distances:
98 80 0.31
99 3 0.01
100 1 0.00
101 1 0.00
103 4 0.02
104 9 0.04
105 95 0.37
106 43 0.17
108 13 0.05
109 7 0.03
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (101 bp):
ACCCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCA
GTGAGCCAATCTCAACTTCACAACGAAGGATATTGG
Found at i:2572206 original size:34 final size:34
Alignment explanation
Indices: 2572163--2572231 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
2572153 TTCGTCCTAC
2572163 TAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATATGATAGAATTT
*
2572197 TAGGATTCAAACTCCTAAAGATATGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATATGATAGAATTT
2572231 T
1 T
2572232 GCTAGGATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATATGATAGAATTT
Found at i:2572586 original size:22 final size:21
Alignment explanation
Indices: 2572556--2572618 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 21
2572546 CTTTTCTTTT
2572556 TTTTCATGTAATATTTTTTTAC
1 TTTT-ATGTAATATTTTTTTAC
* *
2572578 ATTTTATGTATTTTCTTTTTTAC
1 -TTTTATGTAATAT-TTTTTTAC
2572601 -TTTA-GTATATATTTTTTT
1 TTTTATGTA-ATATTTTTTT
2572619 TTTTTAGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 9 0.26
21 6 0.18
22 7 0.21
23 12 0.35
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTATGTAATATTTTTTTAC
Found at i:2572596 original size:24 final size:24
Alignment explanation
Indices: 2572569--2572636 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
2572559 TCATGTAATA
*
2572569 TTTTTTTACATTT-TATGTATTTTC
1 TTTTTTTAC-TTTATATATATTTTC
*
2572593 -TTTTTTACTTTAGTATATATTTTT
1 TTTTTTTACTTTA-TATATATTTTC
**
2572617 TTTTTTTAGATTATATATAT
1 TTTTTTTACTTTATATATAT
2572637 AATATATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
22 3 0.08
23 8 0.22
24 16 0.43
25 10 0.27
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (24 bp):
TTTTTTTACTTTATATATATTTTC
Found at i:2572714 original size:33 final size:30
Alignment explanation
Indices: 2572659--2572737 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
2572649 TTATTATCAG
**
2572659 TTTTATTAATTTA-TATATATATATATTACTTT
1 TTTTATTTTTTTATTATATATATATATTA---T
2572691 TTTTATTTTTTTATTATATATATATATTAT
1 TTTTATTTTTTTATTATATATATATATTAT
*
2572721 TTTTACTTTTTTATTAT
1 TTTTATTTTTTTATTAT
2572738 TATTTTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 17 0.40
32 11 0.26
33 15 0.35
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (30 bp):
TTTTATTTTTTTATTATATATATATATTAT
Found at i:2572738 original size:33 final size:33
Alignment explanation
Indices: 2572672--2572740 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
2572662 TATTAATTTA
*
2572672 TATATATATATATTACTTTTTTTATTTTTTTAT
1 TATATATATATATTACTTTTTTTATTTTATTAT
2572705 TATATATATATATTA-TTTTTACTT-TTTTATTAT
1 TATATATATATATTACTTTTT--TTATTTTATTAT
2572738 TAT
1 TAT
2572741 TTTATTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 5 0.15
33 26 0.79
34 2 0.06
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (33 bp):
TATATATATATATTACTTTTTTTATTTTATTAT
Found at i:2572767 original size:21 final size:20
Alignment explanation
Indices: 2572727--2572802 Score: 59
Period size: 21 Copynumber: 3.8 Consensus size: 20
2572717 TTATTTTTAC
2572727 TTTTTTATTATTATTT-TAT-
1 TTTTTTATT-TTATTTCTATA
* *
2572746 TTATTTGTTTTATTTCTATA
1 TTTTTTATTTTATTTCTATA
* *
2572766 TTTTTT-TCTTCTTTTTCTTTA
1 TTTTTTAT-TT-TATTTCTATA
2572787 TTTTTTATATTTATTT
1 TTTTTTAT-TTTATTT
2572803 TACTTACTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 7 0.16
21 18 0.40
22 3 0.07
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (20 bp):
TTTTTTATTTTATTTCTATA
Found at i:2572851 original size:20 final size:21
Alignment explanation
Indices: 2572791--2572872 Score: 69
Period size: 20 Copynumber: 3.9 Consensus size: 21
2572781 TCTTTATTTT
* * *
2572791 TTATATTTATTTTACTTACTATT
1 TTATCTTTATTTTAATT--TATC
* *
2572814 TTATCTTTGTTTT-CTTTATC
1 TTATCTTTATTTTAATTTATC
*
2572834 TTATCTTT-TTTTAATTTATT
1 TTATCTTTATTTTAATTTATC
*
2572854 TTCTCTTTATTTTAATTTA
1 TTATCTTTATTTTAATTTA
2572873 ATTAATTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
19 4 0.08
20 23 0.45
21 10 0.20
22 3 0.06
23 11 0.22
ACGTcount: A:0.20, C:0.10, G:0.01, T:0.70
Consensus pattern (21 bp):
TTATCTTTATTTTAATTTATC
Found at i:2572908 original size:15 final size:15
Alignment explanation
Indices: 2572890--2572919 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2572880 TATTTATTTC
2572890 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
2572905 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
2572920 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:2574691 original size:15 final size:13
Alignment explanation
Indices: 2574661--2574710 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
2574651 ATGTATATTA
2574661 ATAATATTTTAAT
1 ATAATATTTTAAT
2574674 ATAATATTTTTCAAT
1 ATAATA-TTTT-AAT
2574689 AT-AT-TTATTAAT
1 ATAATATT-TTAAT
2574701 ATAAATATTT
1 AT-AATATTT
2574711 AAATTCAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
12 7 0.23
13 8 0.26
14 9 0.29
15 7 0.23
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (13 bp):
ATAATATTTTAAT
Found at i:2586838 original size:31 final size:32
Alignment explanation
Indices: 2586803--2586867 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 32
2586793 ATATCTAAAA
**
2586803 TAAAATGTATAATAAATAATCTTTTATT-TTT
1 TAAAATGTATAATAAATAATAATTTATTATTT
* * *
2586834 TAAAATTTTTAATAATTAATAATTTATTATTT
1 TAAAATGTATAATAAATAATAATTTATTATTT
2586866 TA
1 TA
2586868 TAGTTTGTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (32 bp):
TAAAATGTATAATAAATAATAATTTATTATTT
Found at i:2586928 original size:21 final size:21
Alignment explanation
Indices: 2586900--2586989 Score: 62
Period size: 20 Copynumber: 4.3 Consensus size: 21
2586890 TTTTTTTTAA
*
2586900 ATTT-TAATAGTATTTTTATT
1 ATTTATAATAATATTTTTATT
2586920 ATTTATAATATATATTTTTAAATT
1 ATTTATAATA-ATATTTTT--ATT
*
2586944 A-TTAGTAAT-TTATTTTTATT
1 ATTTA-TAATAATATTTTTATT
* ** *
2586964 TTTTATTTTAATATTTTGA-T
1 ATTTATAATAATATTTTTATT
2586984 ATTTAT
1 ATTTAT
2586990 TTATTTTTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
20 15 0.27
21 15 0.27
22 14 0.25
23 3 0.05
24 8 0.15
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.64
Consensus pattern (21 bp):
ATTTATAATAATATTTTTATT
Found at i:2586935 original size:22 final size:20
Alignment explanation
Indices: 2586910--2586969 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 20
2586900 ATTTTAATAG
2586910 TATTTTTATTATTTATAATAT
1 TATTTTTATTATTTATAAT-T
2586931 ATATTTTTAAATTA-TTAGTAATT
1 -TATTTTT--ATTATTTA-TAATT
*
2586954 TATTTTTATTTTTTAT
1 TATTTTTATTATTTAT
2586970 TTTAATATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
20 4 0.12
21 3 0.09
22 14 0.42
23 4 0.12
24 8 0.24
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTTTTATTATTTATAATT
Found at i:2586952 original size:24 final size:21
Alignment explanation
Indices: 2586886--2586969 Score: 54
Period size: 22 Copynumber: 4.0 Consensus size: 21
2586876 GATATGTTTT
*
2586886 TAATTTTTTTTTAA--ATTT-
1 TAATTTATTTTTAATTATTTA
*
2586904 TAATAGTATTTTT-ATTATTTA
1 TAAT-TTATTTTTAATTATTTA
2586925 TAATATATATTTTTAAATTA-TTA
1 TAAT-T-TATTTTT-AATTATTTA
*
2586948 GTAATTTATTTTT-ATTTTTTA
1 -TAATTTATTTTTAATTATTTA
2586969 T
1 T
2586970 TTTAATATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
18 5 0.09
19 6 0.11
20 8 0.15
21 8 0.15
22 14 0.26
23 4 0.08
24 8 0.15
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TAATTTATTTTTAATTATTTA
Found at i:2587005 original size:18 final size:17
Alignment explanation
Indices: 2586967--2587018 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
2586957 TTTTATTTTT
* *
2586967 TATTTTAATATTTT-GA
1 TATTTTTATATTTTAAA
2586983 TATTTATT-TATTTTTAAA
1 TATTT-TTATA-TTTTAAA
2587001 TATTTTTATATTTTAAA
1 TATTTTTATATTTTAAA
2587018 T
1 T
2587019 TTAAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 7 0.23
17 15 0.50
18 8 0.27
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TATTTTTATATTTTAAA
Found at i:2587011 original size:26 final size:27
Alignment explanation
Indices: 2586952--2587013 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
2586942 TTATTAGTAA
* * *
2586952 TTTATTTTTATTTTTTATTTTAATATT
1 TTTATATTTATTTATTATTTAAATATT
*
2586979 TTGATATTTATTTATT-TTTAAATATT
1 TTTATATTTATTTATTATTTAAATATT
2587005 TTTATATTT
1 TTTATATTT
2587014 TAAATTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 17 0.57
27 13 0.43
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.73
Consensus pattern (27 bp):
TTTATATTTATTTATTATTTAAATATT
Found at i:2590531 original size:81 final size:81
Alignment explanation
Indices: 2590395--2590636 Score: 310
Period size: 81 Copynumber: 3.0 Consensus size: 81
2590385 ACAATGTTTA
* *
2590395 ACCATTCA-TCTTTTACTCAATAGTATTTAACCGTTCTTCTAACTAACATAATTGACACCTTTCT
1 ACCATT-ATTCTTTTACTCAATGGTATTTAACCGTT-TTCTAACTAGCATAATTGACACCTTTCT
*
2590459 GCCAATTGCACAGTTAAG
64 ACCAATTGCACAGTTAAG
* * *
2590477 -CCATTATTCTTTTACTCAATGGTCTTTAACCATTTGTCTAACTAGCATAATTGACACCTTTCTT
1 ACCATTATTCTTTTACTCAATGGTATTTAACCGTTT-TCTAACTAGCATAATTGACACCTTTCTA
* *
2590541 CCAATTGCTCAATT-AG
65 CCAATTGCACAGTTAAG
* * * *
2590557 ACCATTATTCTTTTACTCAACGATATTTAACCGTTTATCTAACTGGCATAATTGATACCTTTCTA
1 ACCATTATTCTTTTACTCAATGGTATTTAACCGTTT-TCTAACTAGCATAATTGACACCTTTCTA
*
2590622 CCAAATGCACAGTTA
65 CCAATTGCACAGTTA
2590637 GGCCCCAAAG
Statistics
Matches: 138, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
80 4 0.03
81 134 0.97
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (81 bp):
ACCATTATTCTTTTACTCAATGGTATTTAACCGTTTTCTAACTAGCATAATTGACACCTTTCTAC
CAATTGCACAGTTAAG
Found at i:2590695 original size:68 final size:68
Alignment explanation
Indices: 2590593--2591049 Score: 698
Period size: 68 Copynumber: 6.7 Consensus size: 68
2590583 TTAACCGTTT
* * ** * * *
2590593 ATCTAACTGGCATAATTGATACCTTTCTACCAAATGCACAGTTAGGCCCCAAAGGCAGTTAACCT
1 ATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCT
2590658 TTC
66 TTC
* * *
2590661 ATCTAACTAGCATAAATGACACCTTTATGTCAAATGCACAGTTAGACCTCAAAGGCACTTAGCCT
1 ATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCT
2590726 TTC
66 TTC
* *
2590729 ATCTAACTGGCATAAATGACACATTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCT
1 ATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCT
2590794 TTC
66 TTC
* * * *
2590797 ATCTAACTGGCATAAATAACACCTTTCTGTCAAATGCACATTTAGGCCTCAAAGGCACTTAACCG
1 ATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCT
2590862 TTC
66 TTC
* *
2590865 ATCTAACTGGCATAAATGACACCTTTTTGTCAAATGCACAGTTAGGCCTCAAAGGCAATTAGCCT
1 ATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCT
2590930 TTC
66 TTC
* * *
2590933 ATCTAACTGGCATAAATGACACATTTCTATCAAATGCACAATTAGGCCTCAAAGGCACTTAGCCT
1 ATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCT
2590998 TTC
66 TTC
* * *
2591001 ATCTAACTAGCATAAATGACACATTTCTGTCAAATGCATAGTTAGGCCT
1 ATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCT
2591050 ATTAATCTTT
Statistics
Matches: 353, Mismatches: 36, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 353 1.00
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (68 bp):
ATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCT
TTC
Found at i:2591383 original size:55 final size:55
Alignment explanation
Indices: 2591317--2591536 Score: 332
Period size: 55 Copynumber: 4.0 Consensus size: 55
2591307 CATAGTGTGT
* * * *
2591317 ATACAAAAATTCATACACGTAGTATGAGTTTCTCAGTTTTGTACACAAAGTGCCC
1 ATACAGAAATTCATACACTTAGTATGAATTTCTCAGTTTTGCACACAAAGTGCCC
** * *
2591372 ATATGGAAATTCATATACTTAGTATGAAATTCTCAGTTTTGCACACAAAGTGCCC
1 ATACAGAAATTCATACACTTAGTATGAATTTCTCAGTTTTGCACACAAAGTGCCC
*
2591427 ATACAAAAATTCATACACTTAGTATGAATTTCTCAGTTTTGCACACAAAGTGCCC
1 ATACAGAAATTCATACACTTAGTATGAATTTCTCAGTTTTGCACACAAAGTGCCC
* **
2591482 ATACAGAAATTCATACACTTAGTATGAATTTCTCAGTTTTTCACACTCAGTGCCC
1 ATACAGAAATTCATACACTTAGTATGAATTTCTCAGTTTTGCACACAAAGTGCCC
2591537 TTTTGGTAAT
Statistics
Matches: 148, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 148 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (55 bp):
ATACAGAAATTCATACACTTAGTATGAATTTCTCAGTTTTGCACACAAAGTGCCC
Found at i:2592448 original size:5 final size:5
Alignment explanation
Indices: 2592433--2593048 Score: 1177
Period size: 5 Copynumber: 123.6 Consensus size: 5
2592423 AAAGGTTGAC
*
2592433 TCATA TTATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
2592483 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
2592533 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
2592583 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
2592633 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TC--A TCATA TCATA
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
2592681 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TC--A TCATA TCATA
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
2592729 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
2592779 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
2592829 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
2592879 TCATA TCATA TCATATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 TCATA TCATA TC--ATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
2592931 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
2592981 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
2593031 TCATA TCATA TCATA TCA
1 TCATA TCATA TCATA TCA
2593049 GTACATAATA
Statistics
Matches: 603, Mismatches: 2, Indels: 12
0.98 0.00 0.02
Matches are distributed among these distances:
3 6 0.01
5 592 0.98
7 5 0.01
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
TCATA
Found at i:2593092 original size:13 final size:13
Alignment explanation
Indices: 2593074--2593099 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2593064 GCTCACCTGG
2593074 TATGCCTTACTAT
1 TATGCCTTACTAT
2593087 TATGCCTTACTAT
1 TATGCCTTACTAT
2593100 CGAAATCCAA
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:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGCCTTACTAT
Found at i:2595522 original size:24 final size:24
Alignment explanation
Indices: 2595485--2595532 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2595475 AATTTTGCTA
2595485 AAGGAAAAGTCTTTTCTAATGATC
1 AAGGAAAAGTCTTTTCTAATGATC
*
2595509 AAGGAAAA-TACTTTTCTGATGATC
1 AAGGAAAAGT-CTTTTCTAATGATC
2595533 CCTTGAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (24 bp):
AAGGAAAAGTCTTTTCTAATGATC
Found at i:2605473 original size:19 final size:19
Alignment explanation
Indices: 2605435--2605473 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2605425 GTAAATAATA
* * *
2605435 AATTTGTTTTTTTTATTTT
1 AATTAGTTTTTATTACTTT
2605454 AATTAGTTTTTATTACTTT
1 AATTAGTTTTTATTACTTT
2605473 A
1 A
2605474 CTAACTTTTG
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:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (19 bp):
AATTAGTTTTTATTACTTT
Found at i:2606040 original size:45 final size:47
Alignment explanation
Indices: 2605955--2606042 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 47
2605945 TTTATTATTA
* * ** *
2605955 TTTTCTAAATAAATGCATGTGAACTAGAAATTATGCGGTTAGGTTAT
1 TTTTCCAAACAAATGCATGTGAACTAGAAAGCATGAGGTTAGGTTAT
2606002 TTTTCCAAACAAA-GCATGT-AACTAGAAAGCATGAGGTTAGG
1 TTTTCCAAACAAATGCATGTGAACTAGAAAGCATGAGGTTAGG
2606043 ATACAATTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 19 0.53
46 6 0.17
47 11 0.31
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.32
Consensus pattern (47 bp):
TTTTCCAAACAAATGCATGTGAACTAGAAAGCATGAGGTTAGGTTAT
Found at i:2610502 original size:16 final size:16
Alignment explanation
Indices: 2610468--2610502 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2610458 CAGCATGAAA
*
2610468 TAATGTTGGGACATTT
1 TAATGTTGGGACATGT
*
2610484 TAATGTTGGGGCATGT
1 TAATGTTGGGACATGT
2610500 TAA
1 TAA
2610503 AGGCCCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.40
Consensus pattern (16 bp):
TAATGTTGGGACATGT
Found at i:2612272 original size:88 final size:88
Alignment explanation
Indices: 2612123--2612325 Score: 262
Period size: 88 Copynumber: 2.3 Consensus size: 88
2612113 AAAATTCACC
* * * *
2612123 CTCCACAAAAGAGTAGTGGAATGGATTTTTTAGCAAAGTATGAGAACTTCACGGAAAAGTAGTGA
1 CTCCACAAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAAACATCACGGAAAAGTAGTGA
*
2612188 AGTAATCCAAGTTTCAATCTGAA
66 AGTAATCCAAGTTTCAATATGAA
* * *
2612211 CTCCACAAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAAACATCATGGAAGAGTAGTGG
1 CTCCACAAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAAACATCACGGAAAAGTAGTGA
* * *
2612276 AGTAATCTAAGTTTGAGTATGAA
66 AGTAATCCAAGTTTCAATATGAA
* *** *
2612299 CTTCATGGAAGAGTAGTGGAACAGATT
1 CTCCACAAAAGAGTAGTGGAACGGATT
2612326 CTATTCAAGT
Statistics
Matches: 99, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
88 99 1.00
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (88 bp):
CTCCACAAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAAACATCACGGAAAAGTAGTGA
AGTAATCCAAGTTTCAATATGAA
Found at i:2614098 original size:15 final size:16
Alignment explanation
Indices: 2614079--2614126 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 16
2614069 TTATCTAGTT
2614079 TTAATATTAAATATTA
1 TTAATATTAAATATTA
*
2614095 TAATAATATT-AATAATA
1 T--TAATATTAAATATTA
2614112 TTAATATTAAATATT
1 TTAATATTAAATATT
2614127 TAGTATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 7 0.26
16 6 0.22
17 7 0.26
18 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAATATTAAATATTA
Found at i:2614109 original size:9 final size:9
Alignment explanation
Indices: 2614080--2614117 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
2614070 TATCTAGTTT
2614080 TAATATTAAA
1 TAATATT-AA
*
2614090 TATTA-TAA
1 TAATATTAA
2614098 TAATATTAA
1 TAATATTAA
2614107 TAATATTAA
1 TAATATTAA
2614116 TA
1 TA
2614118 TTAAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 6 0.24
9 15 0.60
10 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATATTAA
Found at i:2614133 original size:20 final size:18
Alignment explanation
Indices: 2614079--2614143 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 18
2614069 TTATCTAGTT
2614079 TTAATATTAAATATTATA
1 TTAATATTAAATATTATA
*
2614097 ATAATATT-AATA--ATA
1 TTAATATTAAATATTATA
2614112 TTAATATTAAATATTTAGTA
1 TTAATATTAAATA-TTA-TA
*
2614132 TTTATATTAAAT
1 TTAATATTAAAT
2614144 TAAAATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 10 0.26
16 4 0.10
17 4 0.10
18 7 0.18
19 1 0.03
20 13 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TTAATATTAAATATTATA
Found at i:2614723 original size:21 final size:21
Alignment explanation
Indices: 2614688--2614772 Score: 82
Period size: 21 Copynumber: 4.0 Consensus size: 21
2614678 GAAGTAGAAG
* *
2614688 TAGATGAATTACCTTGGTAAA
1 TAGATAAAGTACCTTGGTAAA
* * *
2614709 TATATAAAGTACCTTGTTAAC
1 TAGATAAAGTACCTTGGTAAA
*
2614730 TAGATGAAGTACCTTGGTAAA
1 TAGATAAAGTACCTTGGTAAA
* *
2614751 TAGGTGAAA-TACCTTGCTAAA
1 TAGAT-AAAGTACCTTGGTAAA
2614772 T
1 T
2614773 GTCTCTGAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
21 49 0.96
22 2 0.04
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.33
Consensus pattern (21 bp):
TAGATAAAGTACCTTGGTAAA
Found at i:2618043 original size:20 final size:20
Alignment explanation
Indices: 2618018--2618058 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2618008 GTTTTTAATC
2618018 AAAAATAAAAGAAAAAAAGA
1 AAAAATAAAAGAAAAAAAGA
* *
2618038 AAAAATAAAATAAAATAAGA
1 AAAAATAAAAGAAAAAAAGA
2618058 A
1 A
2618059 GGCACAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (20 bp):
AAAAATAAAAGAAAAAAAGA
Found at i:2618953 original size:19 final size:19
Alignment explanation
Indices: 2618929--2618972 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
2618919 CTTTTTTTCT
2618929 TTTTTTCTTTTCACTTTAA
1 TTTTTTCTTTTCACTTTAA
2618948 TTTTTTCTTTTCACTTTAA
1 TTTTTTCTTTTCACTTTAA
2618967 TTTTTT
1 TTTTTT
2618973 TTCTTTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTTCTTTTCACTTTAA
Found at i:2627037 original size:31 final size:31
Alignment explanation
Indices: 2627002--2627084 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 31
2626992 ATGTTGAATG
2627002 AAAGAAAGAAGAAAAAAAAAG-TAGTTCAAAA
1 AAAGAAAGAAGAAAAAAAAAGCT-GTTCAAAA
* *
2627033 AAAGAAAAAAGAAAAAAAAAAGCTGTTCGAAA
1 AAAGAAAGAAG-AAAAAAAAAGCTGTTCAAAA
*
2627065 GAA-AAAGAGAGAAAAAAAAA
1 AAAGAAAGA-AGAAAAAAAAA
2627085 AGACATGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
31 23 0.51
32 21 0.47
33 1 0.02
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.07
Consensus pattern (31 bp):
AAAGAAAGAAGAAAAAAAAAGCTGTTCAAAA
Found at i:2627054 original size:32 final size:33
Alignment explanation
Indices: 2627002--2627086 Score: 97
Period size: 32 Copynumber: 2.7 Consensus size: 33
2626992 ATGTTGAATG
*
2627002 AAAGAAAGAAG-AAAAAAAAAG-TAGTTC-AAAA
1 AAAGAAAAAAGAAAAAAAAAAGCT-GTTCGAAAA
*
2627033 AAAGAAAAAAGAAAAAAAAAAGCTGTTCGAAAG
1 AAAGAAAAAAGAAAAAAAAAAGCTGTTCGAAAA
* *
2627066 AAA-AAGAGAGAAAAAAAAAAG
1 AAAGAAAAAAGAAAAAAAAAAG
2627087 ACATGAAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
31 10 0.21
32 30 0.64
33 7 0.15
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.07
Consensus pattern (33 bp):
AAAGAAAAAAGAAAAAAAAAAGCTGTTCGAAAA
Found at i:2627086 original size:15 final size:17
Alignment explanation
Indices: 2627066--2627102 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
2627056 TGTTCGAAAG
*
2627066 AAAAAGAGA-GAAA-AA
1 AAAAAGACATGAAAGAA
2627081 AAAAAGACATGAAAGAA
1 AAAAAGACATGAAAGAA
2627098 AAAAA
1 AAAAA
2627103 TGGAAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 4 0.21
17 7 0.37
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (17 bp):
AAAAAGACATGAAAGAA
Found at i:2628811 original size:18 final size:18
Alignment explanation
Indices: 2628783--2628825 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2628773 TCTTCTTATT
*
2628783 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATCACTTTTA
*
2628802 TTTATTTAATCGCTTTTA
1 TTTATTTAATCACTTTTA
2628820 -TTATTT
1 TTTATTT
2628826 TAATATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 12 0.55
19 4 0.18
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCACTTTTA
Found at i:2629374 original size:21 final size:21
Alignment explanation
Indices: 2629348--2629435 Score: 131
Period size: 21 Copynumber: 4.2 Consensus size: 21
2629338 TTTCAGAGAC
*
2629348 ACTTACCAAGGCACTTCACCT
1 ACTTACCAAGGTACTTCACCT
*
2629369 ATTTACCAAGGTACTTCACCT
1 ACTTACCAAGGTACTTCACCT
*
2629390 ACTTACCAAGGTACTTCATCT
1 ACTTACCAAGGTACTTCACCT
* *
2629411 ACTTACCAAGGTAATTCATCT
1 ACTTACCAAGGTACTTCACCT
2629432 ACTT
1 ACTT
2629436 CCACTTCTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (21 bp):
ACTTACCAAGGTACTTCACCT
Found at i:2629620 original size:114 final size:113
Alignment explanation
Indices: 2629414--2629642 Score: 325
Period size: 114 Copynumber: 2.0 Consensus size: 113
2629404 TTCATCTACT
* * * *
2629414 TACCAAGGTAATTCATCTACTTCCACTTCTTCTTCTACTCCACCTTTTACCACGTATACTGAATC
1 TACCAAGGTAATTAATCTACTTCCACTTCTTCTTCTACTCCACCTTCTACCAAGTATACTAAATC
* *
2629479 AGATAATGACATCGATAAATATGATGCTAGTTGCATTGTAATAGAAGA
66 AGATAATGACATCGATAAATATAATGCTAGTAGCATTGTAATAGAAGA
* *
2629527 TACCGAAGGTAATTAATCTACTTCCACTTTTTCTTTTACTCCACCTTCTACCAAAG-ATACTAAA
1 TACC-AAGGTAATTAATCTACTTCCACTTCTTCTTCTACTCCACCTTCTACC-AAGTATACTAAA
** * *
2629591 TTGGATGATGACATCGATGAATATAATGCTAGTAGCATTGTAATAGAAGA
64 TCAGATAATGACATCGATAAATATAATGCTAGTAGCATTGTAATAGAAGA
2629641 TA
1 TA
2629643 TCAATATTCC
Statistics
Matches: 102, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
113 4 0.04
114 96 0.94
115 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (113 bp):
TACCAAGGTAATTAATCTACTTCCACTTCTTCTTCTACTCCACCTTCTACCAAGTATACTAAATC
AGATAATGACATCGATAAATATAATGCTAGTAGCATTGTAATAGAAGA
Found at i:2637159 original size:26 final size:26
Alignment explanation
Indices: 2637127--2637178 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2637117 AAAGATAGTG
2637127 GTAACATGCTTATCGATTGGTGGATA
1 GTAACATGCTTATCGATTGGTGGATA
2637153 GTAACATGCTTATCGATTGGTGGATA
1 GTAACATGCTTATCGATTGGTGGATA
2637179 CTGCTCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.35
Consensus pattern (26 bp):
GTAACATGCTTATCGATTGGTGGATA
Found at i:2642246 original size:124 final size:124
Alignment explanation
Indices: 2642026--2642254 Score: 404
Period size: 124 Copynumber: 1.8 Consensus size: 124
2642016 AAACCTCCAT
*
2642026 CCATGGTTGGATTTCAATGAAGATATCATTAAGATAGGACCACTTATGATGCTCCGGTAAGCTAT
1 CCATGGTTGGATTTCAATGAAGATATCATTAAGATAGGACCACTTATGATGCTCCAGTAAGCTAT
2642091 ATAACTCTGAATCTTTGATCTCCAACAGAAAATATCTCCCATGAGCAAAAAGCCTCGAC
66 ATAACTCTGAATCTTTGATCTCCAACAGAAAATATCTCCCATGAGCAAAAAGCCTCGAC
* **
2642150 CCATGGTTGGATTTCAATGAAGATATCCTTAAGATAGGACCACTTATGATTTTCCAGTAAGCTAT
1 CCATGGTTGGATTTCAATGAAGATATCATTAAGATAGGACCACTTATGATGCTCCAGTAAGCTAT
* *
2642215 ATACCTCTGAATCTTTGATCTCCAACAGAAAATTTCTCCC
66 ATAACTCTGAATCTTTGATCTCCAACAGAAAATATCTCCC
2642255 TCCTATGAAT
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
124 99 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (124 bp):
CCATGGTTGGATTTCAATGAAGATATCATTAAGATAGGACCACTTATGATGCTCCAGTAAGCTAT
ATAACTCTGAATCTTTGATCTCCAACAGAAAATATCTCCCATGAGCAAAAAGCCTCGAC
Found at i:2643632 original size:3 final size:3
Alignment explanation
Indices: 2643626--2643658 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2643616 AAATATTTGT
2643626 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2643659 GTCTCAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2645150 original size:46 final size:46
Alignment explanation
Indices: 2645098--2645185 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
2645088 AAGTGCCGCG
* * **
2645098 TAGAAATGTCCCGAAGGATCACATATTAGTGTCCCGAAGGACAATA
1 TAGAAATGTCCCCAAGGACCACATAGAAGTGTCCCGAAGGACAATA
* *
2645144 TAGAAATGTCCCCAAGGACCACGTAGAATTGTCCCGAAGGAC
1 TAGAAATGTCCCCAAGGACCACATAGAAGTGTCCCGAAGGAC
2645186 CGCCTAGAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (46 bp):
TAGAAATGTCCCCAAGGACCACATAGAAGTGTCCCGAAGGACAATA
Found at i:2645186 original size:23 final size:23
Alignment explanation
Indices: 2645098--2645186 Score: 97
Period size: 23 Copynumber: 3.9 Consensus size: 23
2645088 AAGTGCCGCG
*
2645098 TAGAAATGTCCCGAAGGATCACA
1 TAGAAATGTCCCGAAGGACCACA
** * * *
2645121 TATTAGTGTCCCGAAGGACAATA
1 TAGAAATGTCCCGAAGGACCACA
* *
2645144 TAGAAATGTCCCCAAGGACCACG
1 TAGAAATGTCCCGAAGGACCACA
*
2645167 TAGAATTGTCCCGAAGGACC
1 TAGAAATGTCCCGAAGGACC
2645187 GCCTAGAACC
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (23 bp):
TAGAAATGTCCCGAAGGACCACA
Found at i:2645194 original size:46 final size:46
Alignment explanation
Indices: 2645093--2645194 Score: 105
Period size: 46 Copynumber: 2.2 Consensus size: 46
2645083 CACCAAAGTG
* * * **
2645093 CCGCGTAGAAATGTCCCGAAGGATCACATATTAGTGTCCCGAAGGA
1 CCGCATAGAAATGTCCCCAAGGACCACATAGAAGTGTCCCGAAGGA
*** * *
2645139 CAATATAGAAATGTCCCCAAGGACCACGTAGAATTGTCCCGAAGGA
1 CCGCATAGAAATGTCCCCAAGGACCACATAGAAGTGTCCCGAAGGA
*
2645185 CCGCCTAGAA
1 CCGCATAGAA
2645195 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (46 bp):
CCGCATAGAAATGTCCCCAAGGACCACATAGAAGTGTCCCGAAGGA
Found at i:2645804 original size:22 final size:22
Alignment explanation
Indices: 2645776--2645826 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
2645766 GGTACAGTAC
2645776 CGATACTTCCTTACTGTGGTAT
1 CGATACTTCCTTACTGTGGTAT
2645798 CGATACTTCCTTACTGTGGTAT
1 CGATACTTCCTTACTGTGGTAT
2645820 CGATACT
1 CGATACT
2645827 ATACTTCAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.39
Consensus pattern (22 bp):
CGATACTTCCTTACTGTGGTAT
Found at i:2646813 original size:20 final size:20
Alignment explanation
Indices: 2646788--2647104 Score: 223
Period size: 20 Copynumber: 15.8 Consensus size: 20
2646778 GATTTTCTAT
*
2646788 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
*
2646808 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* * *
2646828 AATCGCAACACGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
2646848 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * * *
2646868 TATCGCATCGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * *
2646889 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
2646909 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
2646930 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
2646950 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
2646970 AATCGCAACGCGCAT-CTATA
1 AATCGCAACGCGAATACGA-A
*
2646990 AATCGCAACGAC-AATACGTA
1 AATCGCAACG-CGAATACGAA
* * * *
2647010 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
2647030 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
2647050 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGAA
*
2647070 AATCGCAATGCGAATAC-ATA
1 AATCGCAACGCGAATACGA-A
*
2647090 AATCGCAATGCGAAT
1 AATCGCAACGCGAAT
2647105 CTGTAAATCA
Statistics
Matches: 245, Mismatches: 39, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.02
20 203 0.83
21 38 0.16
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:2646835 original size:40 final size:40
Alignment explanation
Indices: 2646788--2647119 Score: 278
Period size: 40 Copynumber: 8.2 Consensus size: 40
2646778 GATTTTCTAT
* ** *
2646788 AATCGCAACGCGAATATGAAAATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGAATCCGTA
* * * * *
2646828 AATCGCAACACGAACA-TATAAATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATACGA-AAATCGCAACGCGAATCCGTA
* * * * * *
2646867 CTATCGCATCGAGTATCCGTAAAATCGCAACGCGTATCCGTA
1 -AATCGCAACGCGAATACG-AAAATCGCAACGCGAATCCGTA
*
2646909 AATCGCAACGAC-AATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACG-CGAATACG-AAAATCGCAACGCGAATCCGTA
* * * **
2646950 AATCGCAACGAGAATACGTAAATCGCAACGCGCATCTATA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGAATCCGTA
* * *
2646990 AATCGCAACGAC-AATACGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACG-CGAATACGAAAATCGCAACGCGAATCCGTA
* * * *
2647030 AATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGAATCCGTA
* * *
2647070 AATCGCAATGCGAATAC-ATAAATCGCAATGCGAATCTGTA
1 AATCGCAACGCGAATACGA-AAATCGCAACGCGAATCCGTA
*
2647110 AATCACAACG
1 AATCGCAACG
2647120 AGATTCTGAC
Statistics
Matches: 243, Mismatches: 39, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
39 3 0.01
40 171 0.70
41 67 0.28
42 2 0.01
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGAATACGAAAATCGCAACGCGAATCCGTA
Found at i:2646860 original size:60 final size:60
Alignment explanation
Indices: 2646788--2647119 Score: 260
Period size: 60 Copynumber: 5.5 Consensus size: 60
2646778 GATTTTCTAT
* * * **
2646788 AATCGCAACGCGAATATGAAAATCGCAACGCGAATATGAAAATCGCAACACGAACATATA
1 AATCGCAACGCGAATATGAAAATCGCAACGCGAATACGTAAATCGCAACGCGAACACGTA
* * ** * * * * *
2646848 AATCGCAACGCGATTCTGACTATCGCATCGAGTATCCGTAAAATCGCAACGCGTATC-CGTA
1 AATCGCAACGCGAATATGAAAATCGCAACGCGAATACGT-AAATCGCAACGCG-AACACGTA
* * * * *
2646909 AATCGCAACGAC-AATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1 AATCGCAACG-CGAATATG-AAAATCGCAACGCGAATACGTAAATCGCAACGCGAACACGTA
* * * *
2646970 AATCGCAACGCGCATCT-ATAAATCGCAACGAC-AATACGTAAATCGCAATGCGTATC-CGTA
1 AATCGCAACGCGAATATGA-AAATCGCAACG-CGAATACGTAAATCGCAACGCG-AACACGTA
* * * * * * *
2647030 AATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATACATA
1 AATCGCAACGCGAATATGAAAATCGCAACGCGAATACGTAAATCGCAACGCGAACACGTA
* * * *
2647090 AATCGCAATGCGAATCTGTAAATCACAACG
1 AATCGCAACGCGAATATGAAAATCGCAACG
2647120 AGATTCTGAC
Statistics
Matches: 214, Mismatches: 46, Indels: 24
0.75 0.16 0.08
Matches are distributed among these distances:
59 3 0.01
60 134 0.63
61 57 0.27
62 20 0.09
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGAATATGAAAATCGCAACGCGAATACGTAAATCGCAACGCGAACACGTA
Found at i:2648007 original size:24 final size:24
Alignment explanation
Indices: 2647980--2648033 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2647970 GTATTCGAAA
2647980 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2648004 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2648028 TTTGAT
1 TTTGAT
2648034 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2650678 original size:33 final size:33
Alignment explanation
Indices: 2650636--2650729 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
2650626 GGAAATGACT
*
2650636 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2650669 ATCGCAATGCGAAATGGAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2650702 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2650730 CGAATTTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2650692 original size:19 final size:19
Alignment explanation
Indices: 2650614--2650733 Score: 73
Period size: 19 Copynumber: 6.8 Consensus size: 19
2650604 CGTAACGTGA
*
2650614 AAATCGCAACGCGGAAAT-G
1 AAATCGCAATGC-GAAATGG
* *
2650633 ACTATCGCAATGCGAAATGA
1 A-AATCGCAATGCGAAATGG
* *
2650653 AAATCACAA--CGAGA--G
1 AAATCGCAATGCGAAATGG
2650668 -AATCGCAATGCGAAATGG
1 AAATCGCAATGCGAAATGG
2650686 AAATCGCAA--CG--A-GG
1 AAATCGCAATGCGAAATGG
* *
2650700 GAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGG
*
2650719 AAATCGCAACGCGAA
1 AAATCGCAATGCGAA
2650734 TTTAGTTTCG
Statistics
Matches: 76, Mismatches: 13, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
14 17 0.22
15 1 0.01
16 6 0.08
17 6 0.08
18 2 0.03
19 34 0.45
20 10 0.13
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.12
Consensus pattern (19 bp):
AAATCGCAATGCGAAATGG
Found at i:2650705 original size:86 final size:85
Alignment explanation
Indices: 2650549--2650733 Score: 217
Period size: 86 Copynumber: 2.2 Consensus size: 85
2650539 CTTAATGTCT
* ** * * * * *
2650549 ATCGCAACGCGGAAATTACTATCGCAACGAGAGAATTGCAATGTGAAATGAAAATCGTAACGTGA
1 ATCGCAACGC-GAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGA
**
2650614 AAATCGCAACGCGGAAATGACT
65 AAATCGCAACGC-GAAATGAAA
* * **
2650636 ATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGGAAATCGCAACGAGGG
1 ATCGCAACGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAA
*
2650701 AATCGCAATGCGAAATGAAA
66 AATCGCAACGCGAAATGAAA
2650721 ATCGCAACGCGAA
1 ATCGCAACGCGAA
2650734 TTTAGTTTCG
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
85 19 0.23
86 54 0.66
87 9 0.11
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.15
Consensus pattern (85 bp):
ATCGCAACGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAA
AATCGCAACGCGAAATGAAA
Found at i:2650783 original size:33 final size:33
Alignment explanation
Indices: 2650729--2650818 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
2650719 AAATCGCAAC
* * * * * *
2650729 GCGAATTTAGTTTCGCGTTGCGATTTTTTCGTT
1 GCGATTTTAATTTCGCATTGCGATTCTCTCGCT
2650762 GCGATTTTAATTTCGCATTGCGATTCTCTCGCT
1 GCGATTTTAATTTCGCATTGCGATTCTCTCGCT
* *
2650795 GCGATTTTCATTTTGCATTGCGAT
1 GCGATTTTAATTTCGCATTGCGAT
2650819 AGTCATTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.46
Consensus pattern (33 bp):
GCGATTTTAATTTCGCATTGCGATTCTCTCGCT
Found at i:2650944 original size:14 final size:14
Alignment explanation
Indices: 2650925--2650961 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2650915 CATCAATTAA
2650925 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2650939 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2650953 ACAAATCAA
1 ACAAATCAA
2650962 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2652865 original size:19 final size:19
Alignment explanation
Indices: 2652849--2652964 Score: 126
Period size: 19 Copynumber: 6.6 Consensus size: 19
2652839 AAAAATGACT
2652849 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
2652868 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
2652882 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
2652901 ATCGCAACGCGAAATGAGA
1 ATCGCAACGCGAAATGAAA
*
2652920 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
2652934 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
2652953 ATCGCAACGCGA
1 ATCGCAACGCGA
2652965 TTATAGTTTC
Statistics
Matches: 82, Mismatches: 5, Indels: 20
0.77 0.05 0.19
Matches are distributed among these distances:
14 21 0.26
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 49 0.60
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:2652907 original size:52 final size:52
Alignment explanation
Indices: 2652849--2652964 Score: 214
Period size: 52 Copynumber: 2.2 Consensus size: 52
2652839 AAAAATGACT
2652849 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAA
* *
2652901 ATCGCAACGCGAAATGAGAATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAA
2652953 ATCGCAACGCGA
1 ATCGCAACGCGA
2652965 TTATAGTTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (52 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAA
Found at i:2652983 original size:19 final size:19
Alignment explanation
Indices: 2652961--2653023 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
2652951 AAATCGCAAC
*
2652961 GCGATTATAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
2652980 GCGATTTTGGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
* *
2652999 ACGATTTTCA-TTTCGAGTT
1 GCGATTTT-AGTTTCGCGTT
2653018 GCGATT
1 GCGATT
2653024 CTCTCGTTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.14, C:0.16, G:0.25, T:0.44
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:2653034 original size:14 final size:14
Alignment explanation
Indices: 2653015--2653071 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2653005 TTCATTTCGA
2653015 GTTGCGATTCTCTC
1 GTTGCGATTCTCTC
*
2653029 GTTGCGATTTTCATTTCGC
1 GTTGCGA--TTC---TCTC
2653048 GTTGCGATTCTCTC
1 GTTGCGATTCTCTC
2653062 GTTGCGATTC
1 GTTGCGATTC
2653072 ATTTCGCGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
GTTGCGATTCTCTC
Found at i:2653042 original size:33 final size:33
Alignment explanation
Indices: 2652995--2653086 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
2652985 TTTGGTTTCG
* *
2652995 CGTTACGATTTTCATTTCGAGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
2653028 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
2653061 CGTTGCGA--TTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
2653087 AGTCATTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
31 18 0.32
33 39 0.68
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:2653052 original size:19 final size:18
Alignment explanation
Indices: 2652971--2653086 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
2652961 GCGATTATAG
**
2652971 TTTCGCGTTGCGATTTTGG
1 TTTCGCGTTGCGA-TTTCA
*
2652990 TTTCGCGTTACGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
*
2653009 TTTCGAGTTGCGA-TTC-
1 TTTCGCGTTGCGATTTCA
*
2653025 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
2653042 TTTCGCGTTGCGA-TTC-
1 TTTCGCGTTGCGATTTCA
*
2653058 --TCTCGTTGCGA-TTCA
1 TTTCGCGTTGCGATTTCA
2653073 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
2653087 AGTCATTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
14 22 0.28
16 3 0.04
17 16 0.21
19 37 0.47
ACGTcount: A:0.10, C:0.22, G:0.23, T:0.45
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:2653320 original size:94 final size:94
Alignment explanation
Indices: 2653174--2653647 Score: 817
Period size: 94 Copynumber: 5.1 Consensus size: 94
2653164 ATGGATTGCA
* *
2653174 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
2653238 TTAGCAGAATTGACAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
2653267 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCATAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
2653332 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
2653361 TTACTTTTAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
2653426 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
2653455 TTACTTTCAACCAAAAGAAAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
2653520 TTAGCAGAATTGACAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
2653549 TTAC-TTCAACTAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
2653613 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
2653643 TTACT
1 TTACT
2653648 AAGCAATCTA
Statistics
Matches: 364, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
93 21 0.06
94 343 0.94
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2655363 original size:20 final size:20
Alignment explanation
Indices: 2655338--2655400 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
2655328 TTTTGGTTGA
2655338 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
2655358 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
2655377 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
2655398 AAT
1 AAT
2655401 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:2655422 original size:33 final size:33
Alignment explanation
Indices: 2655336--2655457 Score: 145
Period size: 33 Copynumber: 3.5 Consensus size: 33
2655326 TCTTTTGGTT
2655336 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
**
2655375 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2655409 GAAATTAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2655442 GAAATGAAAATTGCAA
1 GAAATGAAAATCGCAA
2655458 TGCGATTTAG
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
33 44 0.59
34 11 0.15
36 1 0.01
37 1 0.01
38 3 0.04
40 15 0.20
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2655493 original size:14 final size:14
Alignment explanation
Indices: 2655474--2655530 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2655464 TTAGGTTTCG
2655474 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
2655488 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TT-A--TCT
*
2655507 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
2655521 CGTTGCGATT
1 CGTTGCGATT
2655531 TTCATTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:2655506 original size:33 final size:34
Alignment explanation
Indices: 2655469--2655591 Score: 140
Period size: 33 Copynumber: 3.4 Consensus size: 34
2655459 GCGATTTAGG
2655469 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCAT
*
2655502 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCAT
*
2655536 TTCTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCAT
1 TT-TCGCGTTGCGAT--T-A-TCTC--GTTGCGATTTTCAT
**
2655577 TTTCATGTTGCGATT
1 TTTCGCGTTGCGATT
2655592 TTAAGTTCAG
Statistics
Matches: 77, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
33 32 0.42
34 2 0.03
35 12 0.16
37 1 0.01
38 1 0.01
39 3 0.04
40 10 0.13
41 16 0.21
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.47
Consensus pattern (34 bp):
TTTCGCGTTGCGATTATCTCGTTGCGATTTTCAT
Found at i:2655545 original size:21 final size:20
Alignment explanation
Indices: 2655488--2655593 Score: 100
Period size: 20 Copynumber: 5.6 Consensus size: 20
2655478 GCGATTATCT
2655488 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
*
2655507 CGTTGCGA--TTC----TCT
1 CGTTGCGATTTTCATTTTCG
2655521 CGTTGCGATTTTCATTTCTCG
1 CGTTGCGATTTTCATTT-TCG
**
2655542 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
* *
2655562 TGTTGCGATTTTCATTTTCA
1 CGTTGCGATTTTCATTTTCG
*
2655582 TGTTGCGATTTT
1 CGTTGCGATTTT
2655594 AAGTTCAGAA
Statistics
Matches: 72, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 8 0.11
20 31 0.43
21 17 0.24
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:2656138 original size:20 final size:20
Alignment explanation
Indices: 2656110--2656280 Score: 166
Period size: 20 Copynumber: 8.4 Consensus size: 20
2656100 TTAAAAATCA
2656110 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* * *
2656130 CGTTACGATTTTACGTAT-TG
1 CGTTGCGA-TTTACGGATACG
2656150 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTACGGATACG
** ** * *
2656171 TATTGCGATTTACATATTCT
1 CGTTGCGATTTACGGATACG
* *
2656191 CGTTGTGATTTACAGATACG
1 CGTTGCGATTTACGGATACG
* *
2656211 CGTTGCGATTTACGTATTA-T
1 CGTTGCGATTTACGGA-TACG
2656231 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
2656251 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGGATACG
2656272 CGTTGCGAT
1 CGTTGCGAT
2656281 AGTCAGAATC
Statistics
Matches: 120, Mismatches: 25, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.02
20 81 0.68
21 37 0.31
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:2656194 original size:40 final size:41
Alignment explanation
Indices: 2656110--2656280 Score: 238
Period size: 40 Copynumber: 4.2 Consensus size: 41
2656100 TTAAAAATCA
* *
2656110 CGTTGCGATTTACGGATACGCGTTACGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
** *
2656151 CGTTGCGATTTACGGATACGTATTGCGA-TTTACATATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
2656191 CGTTGTGATTTACAGATACGCGTTGCGA-TTTACGTATTAT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
2656231 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
2656272 CGTTGCGAT
1 CGTTGCGAT
2656281 AGTCAGAATC
Statistics
Matches: 113, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 70 0.62
41 43 0.38
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:2656237 original size:60 final size:60
Alignment explanation
Indices: 2656112--2656280 Score: 166
Period size: 61 Copynumber: 2.8 Consensus size: 60
2656102 AAAAATCACG
* * *
2656112 TTGCGATTTACGGATACGCGTTACGATTTTAC-G-TATTGTCGTTGCGATTTACGGATACGTA
1 TTGCGATTTACAGATACGCGTTGCGATTTTACAGATA-CG-CGTTGCGATTTACGGATACG-A
* * * * *
2656173 TTGCGATTTACATATTCTCGTTGTGA-TTTACAGATACGCGTTGCGATTTACGTATTATCG-
1 TTGCGATTTACAGATACGCGTTGCGATTTTACAGATACGCGTTGCGATTTACGGA-TA-CGA
* * *
2656233 TTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGAT
1 TTGCGATTTACAGATACGCGTTGCGATTTTACAGATACGCGTTGCGAT
2656281 AGTCAGAATC
Statistics
Matches: 88, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
60 41 0.47
61 43 0.49
62 4 0.05
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (60 bp):
TTGCGATTTACAGATACGCGTTGCGATTTTACAGATACGCGTTGCGATTTACGGATACGA
Found at i:2656247 original size:80 final size:81
Alignment explanation
Indices: 2656110--2656280 Score: 245
Period size: 81 Copynumber: 2.1 Consensus size: 81
2656100 TTAAAAATCA
* * *
2656110 CGTTGCGATTTACGGATACGCGTTACGATTTTACGTATTGTCGTTGCGATTTACGGATACGTATT
1 CGTTGCGATTTACAGATACGCGTTACGATTTTACGTATTATCGTTGCGATTTACGGATACGCATT
2656175 GCGATTTACATATTCT
66 GCGATTTACATATTCT
* * *
2656191 CGTTGTGATTTACAGATACGCGTTGCGA-TTTACGTATTATCGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTTACAGATACGCGTTACGATTTTACGTATTATCGTTGCGATTTACGGATACGCATT
** *
2656255 GCGATTTTACGGATACT
66 GCGA-TTTACATATTCT
2656272 CGTTGCGAT
1 CGTTGCGAT
2656281 AGTCAGAATC
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 37 0.47
81 42 0.53
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (81 bp):
CGTTGCGATTTACAGATACGCGTTACGATTTTACGTATTATCGTTGCGATTTACGGATACGCATT
GCGATTTACATATTCT
Found at i:2656312 original size:20 final size:20
Alignment explanation
Indices: 2656289--2656341 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
2656279 ATAGTCAGAA
*
2656289 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
2656309 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
2656329 TCGTGTTGCGATT
1 TCGCGTTGCGATT
2656342 ATGGAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:2656316 original size:81 final size:80
Alignment explanation
Indices: 2656110--2656322 Score: 216
Period size: 81 Copynumber: 2.6 Consensus size: 80
2656100 TTAAAAATCA
* * * * *
2656110 CGTTGCGATTTACGGATACGCGTTACGATTTTACGTATT-GTCGTTGCGATTTACGGATACGTAT
1 CGTTGCGATGTACAGATACGCGTTGCGA-TTTACATATTAG-CGTTGCGATTTACGGATACGCAT
* *
2656174 TGCGATTTACATATTCT
64 TGCGATTTACAGATACT
* * * * *
2656191 CGTTGTGATTTACAGATACGCGTTGCGATTTACGTATTATCGTTGCGATTTACGGATACGCGTTG
1 CGTTGCGATGTACAGATACGCGTTGCGATTTACATATTAGCGTTGCGATTTACGGATACGCATTG
*
2656256 CGATTTTACGGATACT
66 CGA-TTTACAGATACT
* * *
2656272 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGTTCGCGTTGCGATTT
1 CGTTGCGAT-GTACAGATA-CGCGTTGCGATTTACATATTAGCGTTGCGATTT
2656323 TCATATTCGT
Statistics
Matches: 112, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
80 37 0.33
81 74 0.66
82 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.38
Consensus pattern (80 bp):
CGTTGCGATGTACAGATACGCGTTGCGATTTACATATTAGCGTTGCGATTTACGGATACGCATTG
CGATTTACAGATACT
Found at i:2656337 original size:121 final size:121
Alignment explanation
Indices: 2656110--2656341 Score: 288
Period size: 121 Copynumber: 1.9 Consensus size: 121
2656100 TTAAAAATCA
* ** * * *
2656110 CGTTGCGATTTACGGATACGCGTTACGATTTTACGTATTGTCGTTGCGATTTACGGATACGTATT
1 CGTTGCGATTTACGGATACGCGTTACGATTTTACGGATACTCGTTGCGATTCACGAATACGCATT
* *
2656175 GCGATTTACATATTCTCGTTGTGATTTACAGATACGCGTTGCGATTTACGTATTAT
66 GCGATTTACATATTCGCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTAT
* *
2656231 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGTCA-GAAT-CGCG
1 CGTTGCGATTTACGGATACGCGTTACGATTTTACGGATACTCGTTGCGAT--TCACGAATACGCA
* * * * * *
2656294 TTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCGTGTTGCGATT
64 TTGCGATTTACATATTCGCGTTGCGATTTACAGATACGCGTTGCGATT
2656342 ATGGAAAATC
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
121 88 0.95
122 3 0.03
123 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (121 bp):
CGTTGCGATTTACGGATACGCGTTACGATTTTACGGATACTCGTTGCGATTCACGAATACGCATT
GCGATTTACATATTCGCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTAT
Found at i:2662013 original size:18 final size:18
Alignment explanation
Indices: 2661982--2662026 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2661972 AAAAGAAAGC
*
2661982 TTTTCACC-ACCCTTCCT
1 TTTTCACCTACCCTTCAT
2661999 TTTTCACCTACCCTTCAT
1 TTTTCACCTACCCTTCAT
2662017 TTTTCACCTA
1 TTTTCACCTA
2662027 TTCCCTTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.16, C:0.40, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTTCACCTACCCTTCAT
Found at i:2666611 original size:2 final size:2
Alignment explanation
Indices: 2666600--2666631 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2666590 AATAATGTTT
2666600 TA TA -A 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 T
2666632 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2667871 original size:23 final size:23
Alignment explanation
Indices: 2667842--2667906 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
2667832 TAAGGACATA
2667842 AAACATTCTAGCTATTAACTCCT
1 AAACATTCTAGCTATTAACTCCT
2667865 AAACATTCTAGCTATTAACTCCT
1 AAACATTCTAGCTATTAACTCCT
*
2667888 AAATATTCTAGCTATTAAC
1 AAACATTCTAGCTATTAAC
2667907 AGCCACCGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (23 bp):
AAACATTCTAGCTATTAACTCCT
Found at i:2670208 original size:41 final size:41
Alignment explanation
Indices: 2670156--2670233 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
2670146 CTCGTCCAAC
*
2670156 TATTACCAATTATAAATTTAATATTTTTATTGAAATATTTT
1 TATTACCAATTATAAATTTAATATTTTTATTAAAATATTTT
* *
2670197 TATTTCCAATTATAAGTTTAATATTTTTATTAAAATA
1 TATTACCAATTATAAATTTAATATTTTTATTAAAATA
2670234 ATATATAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (41 bp):
TATTACCAATTATAAATTTAATATTTTTATTAAAATATTTT
Found at i:2670293 original size:9 final size:9
Alignment explanation
Indices: 2670279--2670348 Score: 50
Period size: 9 Copynumber: 7.1 Consensus size: 9
2670269 ATTAATAAAC
2670279 TTTTTATTA
1 TTTTTATTA
2670288 TTTTTATTA
1 TTTTTATTA
* *
2670297 TAAATTTAATA
1 T--TTTTATTA
2670308 TTATTTCATTTA
1 TT-TTT-A-TTA
**
2670320 TTTAAATTA
1 TTTTTATTA
2670329 TTTTATATTA
1 TTTT-TATTA
2670339 TTTTTATTA
1 TTTTTATTA
2670348 T
1 T
2670349 AAATCTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 22 0.47
10 12 0.26
11 9 0.19
12 4 0.09
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTTATTA
Found at i:2670324 original size:19 final size:19
Alignment explanation
Indices: 2670300--2670341 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2670290 TTTATTATAA
2670300 ATTTAATATTATTTCAT-TT
1 ATTTAA-ATTATTTCATATT
*
2670319 ATTTAAATTATTTTATATT
1 ATTTAAATTATTTCATATT
2670338 ATTT
1 ATTT
2670342 TTATTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTAAATTATTTCATATT
Found at i:2670348 original size:28 final size:24
Alignment explanation
Indices: 2670268--2670403 Score: 68
Period size: 23 Copynumber: 5.5 Consensus size: 24
2670258 TTGGTCGTAA
*
2670268 TATTAATAAACTTTT-TATTATTTT
1 TATTATTAAA-TTTTATATTATTTT
*
2670292 TATTA-TAAATTTAATATTATTTCATT
1 TATTATTAAATTTTATATTA-TT--TT
*
2670318 TATT-TAAATTATTTTATATTATTTT
1 TATTATTAA--ATTTTATATTATTTT
* * *
2670343 TATTA-TAAATCTAAAATTATTTCCTT
1 TATTATTAAATTTTATATTA-TT--TT
*
2670369 TATT-TTAATTGTTTTATATTATTTT
1 TATTATTAA--ATTTTATATTATTTT
2670394 TATTA-TAAAT
1 TATTATTAAAT
2670404 CTAATATTTT
Statistics
Matches: 85, Mismatches: 12, Indels: 31
0.66 0.09 0.24
Matches are distributed among these distances:
22 3 0.04
23 18 0.21
24 9 0.11
25 17 0.20
26 17 0.20
27 4 0.05
28 17 0.20
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.61
Consensus pattern (24 bp):
TATTATTAAATTTTATATTATTTT
Done.