Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 47 of 55
Found at i:9462387 original size:21 final size:23
Alignment explanation
Indices: 9462361--9462418 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 23
9462351 ACCAAAAAAG
*
9462361 GTAGTATCGGTACCAC-CACTAA
1 GTAGTATCGATACCACACACTAA
*
9462383 G-AGTATCGATACTACTACACTAA
1 GTAGTATCGATACCAC-ACACTAA
9462406 GTAGTATCGATAC
1 GTAGTATCGATAC
9462419 TATATATAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 12 0.39
22 1 0.03
23 7 0.23
24 11 0.35
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (23 bp):
GTAGTATCGATACCACACACTAA
Found at i:9462429 original size:21 final size:24
Alignment explanation
Indices: 9462361--9462420 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
9462351 ACCAAAAAAG
* *
9462361 GTAGTATCGGTACCAC--CACTAA
1 GTAGTATCGATACTACTACACTAA
9462383 G-AGTATCGATACTACTACACTAA
1 GTAGTATCGATACTACTACACTAA
9462406 GTAGTATCGATACTA
1 GTAGTATCGATACTA
9462421 TATATAGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.36
22 1 0.03
23 7 0.21
24 13 0.39
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (24 bp):
GTAGTATCGATACTACTACACTAA
Found at i:9462898 original size:15 final size:16
Alignment explanation
Indices: 9462878--9462918 Score: 61
Period size: 14 Copynumber: 2.8 Consensus size: 16
9462868 GAAGTTGCGA
9462878 TAATAATTGAAGGG-G
1 TAATAATTGAAGGGAG
9462893 TAATAATTG-AGGGAG
1 TAATAATTGAAGGGAG
9462908 -AATAATTGAAG
1 TAATAATTGAAG
9462919 AAGAGCTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.27
Consensus pattern (16 bp):
TAATAATTGAAGGGAG
Found at i:9463587 original size:3 final size:3
Alignment explanation
Indices: 9463581--9463611 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
9463571 AATAAAGATT
9463581 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
9463612 AAATAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9463856 original size:2 final size:2
Alignment explanation
Indices: 9463849--9463881 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9463839 CACGTATTGT
9463849 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9463882 TTGATTATCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9464193 original size:25 final size:25
Alignment explanation
Indices: 9464145--9464203 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
9464135 AATATTAATT
*
9464145 ATTATATTAAATAAATATCATAAAATA
1 ATTAT-TTAAATAAAAATCATAAAA-A
**
9464172 ATT-TTTAAATAAAAATTTTAAAAA
1 ATTATTTAAATAAAAATCATAAAAA
9464196 ATTATTTA
1 ATTATTTA
9464204 GCTGTACATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 4 0.14
25 20 0.71
26 1 0.04
27 3 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTATTTAAATAAAAATCATAAAAA
Found at i:9467540 original size:138 final size:138
Alignment explanation
Indices: 9467292--9467787 Score: 776
Period size: 138 Copynumber: 3.6 Consensus size: 138
9467282 GTACTATTCA
* ** * * *
9467292 GGTGAAGGCGTGTTCCCAAGGACGCACTTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
1 GGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
* *
9467357 TATTATGTCACTCATGTCCCCCGAAGAACTATTCATGTCATTACCTATTATTTCTGAGGAGACTT
66 TATTATGTCACTCATGTCCCCCGAAGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTT
9467422 GGCAAAGT
131 GGCAAAGT
* *
9467430 GGTGAAGGCGCATTCCCGGGGGCGCTCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
1 GGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
* * * * *
9467495 TATTATGTCACTCATGTCTCTCGGAGAACTATTTATATCAGTACCTATTATTTCTGAGGGGACTT
66 TATTATGTCACTCATGTCCCCCGAAGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTT
9467560 GGCAAAGT
131 GGCAAAGT
*
9467568 GGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCAATTATTTTGTCAGAGAATATGTTATCATTGCCC
1 GGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
* ** *
9467633 TATTATATCACTCATGTCCCCCGAAGAACTATTCATGTCAGTTTCTATTATTTTTGAGGGGACTT
66 TATTATGTCACTCATGTCCCCCGAAGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTT
9467698 GGCAAAGT
131 GGCAAAGT
* * * *
9467706 GGTGAAGGCGCGTTCCCGGGGGCGCGCATTCTATTATTTTGTCAGATAATATGTTATCATTGCCT
1 GGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
9467771 TATTATGTCACTCATGT
66 TATTATGTCACTCATGT
9467788 GAAATTGGAT
Statistics
Matches: 327, Mismatches: 31, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
138 327 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (138 bp):
GGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
TATTATGTCACTCATGTCCCCCGAAGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTT
GGCAAAGT
Found at i:9467858 original size:23 final size:23
Alignment explanation
Indices: 9467832--9467894 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
9467822 ATGTGAAGTT
9467832 TGAATAAATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
9467855 TGAATAAATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
* *
9467878 TGGATAAATTGAATAAA
1 TGAATAAATTGGATAAA
9467895 TGTGAAGTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAATAAATTGGATAAAATGTTA
Found at i:9468702 original size:22 final size:21
Alignment explanation
Indices: 9468653--9468722 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
9468643 GGTGTCATAA
* * * *
9468653 AACCCTGCGGACTAGGCATAT
1 AACCCTGAGGGCTAGGAATGT
*
9468674 AA-CCTGACGGGCTATGAATGT
1 AACCCTGA-GGGCTAGGAATGT
9468695 AACCCTGAGGGCTAGGAATGT
1 AACCCTGAGGGCTAGGAATGT
9468716 AACCCTG
1 AACCCTG
9468723 CGGAGATGGC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 4 0.10
21 32 0.78
22 5 0.12
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (21 bp):
AACCCTGAGGGCTAGGAATGT
Found at i:9472617 original size:29 final size:29
Alignment explanation
Indices: 9472575--9472634 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
9472565 ATTCTACAGT
9472575 GATCTCGTAGGACGCCATGCAATCCAGGC
1 GATCTCGTAGGACGCCATGCAATCCAGGC
*
9472604 GATCTTGTAGGACGCCATGCAATCCAGGC
1 GATCTCGTAGGACGCCATGCAATCCAGGC
9472633 GA
1 GA
9472635 CATACGGGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.18
Consensus pattern (29 bp):
GATCTCGTAGGACGCCATGCAATCCAGGC
Found at i:9472769 original size:32 final size:32
Alignment explanation
Indices: 9472728--9472806 Score: 149
Period size: 32 Copynumber: 2.5 Consensus size: 32
9472718 TATACGAGGT
9472728 GAGGTCGCCATGCAGACGAGCCAGCCAATGGA
1 GAGGTCGCCATGCAGACGAGCCAGCCAATGGA
*
9472760 GAGGTCGCCATGCAAACGAGCCAGCCAATGGA
1 GAGGTCGCCATGCAGACGAGCCAGCCAATGGA
9472792 GAGGTCGCCATGCAG
1 GAGGTCGCCATGCAG
9472807 TCTGGGCGAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.28, C:0.28, G:0.34, T:0.10
Consensus pattern (32 bp):
GAGGTCGCCATGCAGACGAGCCAGCCAATGGA
Found at i:9472837 original size:29 final size:29
Alignment explanation
Indices: 9472793--9472887 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
9472783 GCCAATGGAG
* **
9472793 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
9472822 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
9472851 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
9472880 AGGTCGCC
1 AGGTCGCC
9472888 CCGGCGTCAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:9472987 original size:48 final size:48
Alignment explanation
Indices: 9472922--9473016 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
9472912 CATGCATGCA
9472922 CATGCAGCCAAGATAACTTCACGTGCTCCTGCTCCC-CTGCATGCCTG
1 CATGCAGCCAAGATAACTTCACGTGCTCCTGCTCCCGCTGCATGCCTG
9472969 CATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCGCTGCATGCCT
1 CATGCA-GCCAAGATAACTTCACGTGCTCCTGCTCCCGCTGCATGCCT
9473017 ACAGCTATTG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 6 0.13
48 30 0.65
49 10 0.22
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.24
Consensus pattern (48 bp):
CATGCAGCCAAGATAACTTCACGTGCTCCTGCTCCCGCTGCATGCCTG
Found at i:9477667 original size:17 final size:18
Alignment explanation
Indices: 9477647--9477688 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
9477637 TTTTTGCCTT
9477647 TTTTTTTG-CCTTTTTTG
1 TTTTTTTGTCCTTTTTTG
**
9477664 -TTTTTTGTTTTTTTTTG
1 TTTTTTTGTCCTTTTTTG
9477681 TTTTTTTG
1 TTTTTTTG
9477689 GAAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 7 0.33
17 7 0.33
18 7 0.33
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.83
Consensus pattern (18 bp):
TTTTTTTGTCCTTTTTTG
Found at i:9477674 original size:12 final size:11
Alignment explanation
Indices: 9477624--9477687 Score: 65
Period size: 12 Copynumber: 5.4 Consensus size: 11
9477614 TTTTTGGCTC
9477624 TTTTTTTGTTT
1 TTTTTTTGTTT
*
9477635 TTTTTTTGCCTT
1 TTTTTTTG-TTT
9477647 TTTTTTTGCCTTT
1 TTTTTTTG--TTT
*
9477660 TTTGTTTTTTGTT
1 TTT-TTTTGT-TT
9477673 TTTTTTTGTTT
1 TTTTTTTGTTT
9477684 TTTT
1 TTTT
9477688 GGAAAAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
11 14 0.31
12 16 0.36
13 11 0.24
14 4 0.09
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.84
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:9478981 original size:16 final size:18
Alignment explanation
Indices: 9478960--9478998 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
9478950 GGAGATAAGG
*
9478960 TAAATTTGTTTA-TATT-
1 TAAATTAGTTTATTATTA
9478976 TAAATTAGTTTATTATTA
1 TAAATTAGTTTATTATTA
9478994 TAAAT
1 TAAAT
9478999 GTTAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAAATTAGTTTATTATTA
Found at i:9479269 original size:32 final size:33
Alignment explanation
Indices: 9479233--9479309 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 33
9479223 TTAGTTAGTA
*
9479233 AGTTTATTAGTAG-TATA-TTATAATGAAAAAAT
1 AGTTTATTAGTAGTTATAGTTAT-ATAAAAAAAT
*
9479265 AGTTTATTAGTTAGTTTTAGTTATATAAAAAAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAAAAT
*
9479299 ATTTTATTAGT
1 AGTTTATTAGT
9479310 GTTTAAGGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 10 0.26
33 4 0.10
34 21 0.54
35 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAAAAT
Found at i:9479365 original size:8 final size:8
Alignment explanation
Indices: 9479352--9479384 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
9479342 TTTAAAAAGT
*
9479352 TTAGTTTG
1 TTAGTTTA
9479360 TTAGTTTA
1 TTAGTTTA
9479368 TTAGTTTA
1 TTAGTTTA
9479376 TTAGTTTA
1 TTAGTTTA
9479384 T
1 T
9479385 ATATTATAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (8 bp):
TTAGTTTA
Found at i:9479396 original size:15 final size:16
Alignment explanation
Indices: 9479362--9479412 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
9479352 TTAGTTTGTT
*
9479362 AGTTTATTAGT-TTATT
1 AGTTTATTA-TATTATA
9479378 AGTTTA-TATATTATA
1 AGTTTATTATATTATA
9479393 AG-TTATTATATTA-A
1 AGTTTATTATATTATA
9479407 AGTTTA
1 AGTTTA
9479413 GTGTTGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 7 0.23
15 18 0.58
16 6 0.19
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (16 bp):
AGTTTATTATATTATA
Found at i:9481565 original size:17 final size:17
Alignment explanation
Indices: 9481543--9481575 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9481533 CAATGATGTT
*
9481543 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
9481560 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
9481576 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:9481592 original size:24 final size:22
Alignment explanation
Indices: 9481560--9481627 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
9481550 AAATCATTAC
9481560 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* ** *
9481582 TAGTAAATCAACTGTTTTAATCA-T
1 TAGT--ATCAAATAATTAAAT-ATT
9481606 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
9481628 AACAATAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
21 1 0.03
22 16 0.47
24 16 0.47
25 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:9481802 original size:14 final size:14
Alignment explanation
Indices: 9481783--9481822 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
9481773 TAGTAATAAT
9481783 TATTAAATCATTAG
1 TATTAAATCATTAG
*
9481797 TATTAAATCATTAT
1 TATTAAATCATTAG
*
9481811 TA-TAAATAATTA
1 TATTAAATCATTA
9481823 CTAAATAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (14 bp):
TATTAAATCATTAG
Found at i:9481862 original size:26 final size:26
Alignment explanation
Indices: 9481832--9482004 Score: 155
Period size: 26 Copynumber: 6.9 Consensus size: 26
9481822 ACTAAATAAC
* *
9481832 ATAATAATTATTATAAAATCATTATT
1 ATAATGATTATTATCAAATCATTATT
*
9481858 ATAATGATTATTATCAAATCATTACT
1 ATAATGATTATTATCAAATCATTATT
* * * * * *
9481884 A-AATCATCA-AATC-ATTAAATATT
1 ATAATGATTATTATCAAATCATTATT
* * *
9481907 -TAA--ATCATTATTAAATTATT-TT
1 ATAATGATTATTATCAAATCATTATT
*
9481929 ATAATGATTATGA-CTAAATCATTATT
1 ATAATGATTATTATC-AAATCATTATT
*
9481955 ATAATGATTATTATCAAATCATTACT
1 ATAATGATTATTATCAAATCATTATT
9481981 ATAATGATTATTATCAAATCATTA
1 ATAATGATTATTATCAAATCATTA
9482005 CTAATCATCA
Statistics
Matches: 117, Mismatches: 21, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
21 4 0.03
22 4 0.03
23 15 0.13
24 3 0.03
25 18 0.15
26 72 0.62
27 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (26 bp):
ATAATGATTATTATCAAATCATTATT
Found at i:9481869 original size:12 final size:12
Alignment explanation
Indices: 9481765--9482117 Score: 66
Period size: 12 Copynumber: 28.9 Consensus size: 12
9481755 TTAGTATTCT
9481765 ATAATTATTAGTA
1 ATAATTATTA-TA
9481778 ATAATTATTA-A
1 ATAATTATTATA
* *
9481789 ATCATTAGTATTAA
1 ATAATTATTA-T-A
*
9481803 ATCATTATTATAA
1 ATAATTATTAT-A
*
9481816 ATAATTACTA-A
1 ATAATTATTATA
* *
9481827 ATAA-CATAATA
1 ATAATTATTATA
* *
9481838 ATTATTA-TAAA
1 ATAATTATTATA
*
9481849 ATCATTATTATA
1 ATAATTATTATA
* *
9481861 ATGATTATTATC
1 ATAATTATTATA
*
9481873 A-AATCATTACTAA
1 ATAATTATTA-T-A
* * *
9481886 ATCATCA-AATCA
1 ATAATTATTAT-A
* *
9481898 TTAAATATT-TAA
1 ATAATTATTAT-A
*
9481910 ATCATTATTA-A
1 ATAATTATTATA
*
9481921 ATTATT-TTATA
1 ATAATTATTATA
* *
9481932 ATGATTATGACTAA
1 ATAATTATTA-T-A
*
9481946 ATCATTATTATA
1 ATAATTATTATA
*
9481958 ATGATTATTATCAA
1 ATAATTATTAT--A
* *
9481972 ATCATTACTATA
1 ATAATTATTATA
* *
9481984 ATGATTATTATC
1 ATAATTATTATA
*
9481996 A-AATCATTACTA
1 ATAATTATTA-TA
* * *
9482008 ATCATCA-AATCA
1 ATAATTATTAT-A
* *
9482020 TTAAATATT-TAA
1 ATAATTATTAT-A
*
9482032 ATCATTATTA-A
1 ATAATTATTATA
* *
9482043 ATCATTTTTATA
1 ATAATTATTATA
*
9482055 ATGATTATTACTAA
1 ATAATTATTA-T-A
*
9482069 ATCATTATTATA
1 ATAATTATTATA
*
9482081 ATGATTATTATCAA
1 ATAATTATTAT--A
* *
9482095 ATCATTACTATA
1 ATAATTATTATA
*
9482107 ATGATTATTAT
1 ATAATTATTAT
9482118 CAATCATTAC
Statistics
Matches: 248, Mismatches: 65, Indels: 55
0.67 0.18 0.15
Matches are distributed among these distances:
10 5 0.02
11 61 0.25
12 98 0.40
13 31 0.12
14 53 0.21
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (12 bp):
ATAATTATTATA
Found at i:9481975 original size:123 final size:124
Alignment explanation
Indices: 9481832--9482183 Score: 631
Period size: 123 Copynumber: 2.9 Consensus size: 124
9481822 ACTAAATAAC
* * *
9481832 ATAATAATTATTATAAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
1 ATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
*
9481897 ATTAAATATTTAAATCATTATTAAATTA-TTTTATAATGATTATGACTAAATCATTATT
66 ATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATGACTAAATCATTATT
9481955 ATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACT-AATCATCAAATC
1 ATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
*
9482019 ATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATT
66 ATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATGACTAAATCATTATT
9482078 ATAATGATTATTATCAAATCATTACTATAATGATTATTATC-AATCATTACTAAATCATCAAATC
1 ATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
9482142 ATT-AATATTTAAATCATTATTAAATCATTTTTATAATGATTA
66 ATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTA
9482184 ATAAATACAT
Statistics
Matches: 222, Mismatches: 5, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
122 88 0.40
123 134 0.60
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (124 bp):
ATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
ATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATGACTAAATCATTATT
Found at i:9482005 original size:26 final size:26
Alignment explanation
Indices: 9481928--9482129 Score: 201
Period size: 26 Copynumber: 8.1 Consensus size: 26
9481918 TAAATTATTT
* *
9481928 TATAATGATTATGA-CTAAATCATTAT
1 TATAATGATTATTATC-AAATCATTAC
9481954 TATAATGATTATTATCAAATCATTAC
1 TATAATGATTATTATCAAATCATTAC
9481980 TATAATGATTATTATCAAATCATTAC
1 TATAATGATTATTATCAAATCATTAC
* * * * *
9482006 TAATCATCA-AATCATTAAAT-ATT--
1 T-ATAATGATTATTATCAAATCATTAC
* **
9482029 TA-AATCATTA-T-T-AAATCATTTT
1 TATAATGATTATTATCAAATCATTAC
*
9482051 TATAATGATTATTA-CTAAATCATTAT
1 TATAATGATTATTATC-AAATCATTAC
9482077 TATAATGATTATTATCAAATCATTAC
1 TATAATGATTATTATCAAATCATTAC
9482103 TATAATGATTATTATC-AATCATTAC
1 TATAATGATTATTATCAAATCATTAC
9482128 TA
1 TA
9482130 AATCATCAAA
Statistics
Matches: 151, Mismatches: 13, Indels: 25
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.03
20 4 0.03
21 4 0.03
22 4 0.03
23 8 0.05
24 1 0.01
25 14 0.09
26 105 0.70
27 7 0.05
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (26 bp):
TATAATGATTATTATCAAATCATTAC
Found at i:9482044 original size:97 final size:96
Alignment explanation
Indices: 9481835--9482104 Score: 304
Period size: 97 Copynumber: 2.8 Consensus size: 96
9481825 AAATAACATA
* * * * *
9481835 ATAATTATTATAAAATCATTATTATAATGATTATTATCAAATCATTACTA-AATCATCAAATCAT
1 ATAATCATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGAT--TATTAT
* *
9481899 TAAAT-ATT--TAAATCATTATTAAATTATTTT
64 CAAATCATTACTAAATCATCATTAAATTATTTT
*
9481929 ATAATGATTATGACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTA
1 ATAATCATTAT---TAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTA
9481994 TCAAATCATTACTAATCATCAAATCATTAAA-TA-TTT
63 TCAAATCATTACTAA--ATC--ATCATTAAATTATTTT
* *
9482030 A-AATCATTATTAAATCATTTTTATAATGATTATTA-CTAAATCATTATTATAATGATTATTATC
1 ATAATCATTATTAAATCATTATTATAATGATTATTATC-AAATCATTACTATAATGATTATTATC
9482093 AAATCATTACTA
65 AAATCATTACTA
9482105 TAATGATTAT
Statistics
Matches: 154, Mismatches: 10, Indels: 21
0.83 0.05 0.11
Matches are distributed among these distances:
94 10 0.06
96 9 0.06
97 102 0.66
98 5 0.03
99 3 0.02
100 8 0.05
101 7 0.05
102 2 0.01
103 8 0.05
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (96 bp):
ATAATCATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCA
AATCATTACTAAATCATCATTAAATTATTTT
Found at i:9482188 original size:23 final size:23
Alignment explanation
Indices: 9482027--9482189 Score: 80
Period size: 26 Copynumber: 6.8 Consensus size: 23
9482017 TCATTAAATA
* *
9482027 TTTA-AATCATTATTAAATCATT
1 TTTATAATGATTAATAAATCATT
9482049 TTTATAATGATTATTACTAAATCATT
1 TTTATAATGATTA--A-TAAATCATT
*
9482075 ATTATAATGATTATTATCAAATCATT
1 TTTATAATGATTA--AT-AAATCATT
** *
9482101 ACTATAATGATTATTATCAATCATT
1 TTTATAATGATTA--ATAAATCATT
** * * * * * *
9482126 ACTA-AATCATCAAATCATTAATA
1 TTTATAATGAT-TAATAAATCATT
* *
9482149 TTTA-AATCATTATTAAATCATT
1 TTTATAATGATTAATAAATCATT
9482171 TTTATAATGATTAATAAAT
1 TTTATAATGATTAATAAAT
9482190 ACATAGAATA
Statistics
Matches: 114, Mismatches: 20, Indels: 13
0.78 0.14 0.09
Matches are distributed among these distances:
22 14 0.12
23 34 0.30
24 5 0.04
25 13 0.11
26 48 0.42
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTATAATGATTAATAAATCATT
Found at i:9485078 original size:26 final size:24
Alignment explanation
Indices: 9485018--9485078 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
9485008 TACTAATATT
*
9485018 ATTAATAATGATTTAATAATTATT
1 ATTAATAATGATTTAATAATTATG
* *
9485042 ATTAATCTAATGATTTGATATTTAATG
1 ATTAA--TAATGATTTAATAATT-ATG
9485069 ATTTAATAAT
1 A-TTAATAAT
9485079 AATATGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.17
26 18 0.60
27 3 0.10
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (24 bp):
ATTAATAATGATTTAATAATTATG
Found at i:9485332 original size:17 final size:17
Alignment explanation
Indices: 9485310--9485372 Score: 72
Period size: 17 Copynumber: 3.5 Consensus size: 17
9485300 TACAATATAA
9485310 TAAACAAAATATTTTTT
1 TAAACAAAATATTTTTT
* *
9485327 TAAACAACACTAAATATTTT
1 TAAACAA-A--ATATTTTTT
*
9485347 TAAACACAATATTTTTT
1 TAAACAAAATATTTTTT
9485364 TAAACAAAA
1 TAAACAAAA
9485373 ATTATCTCGC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 22 0.59
18 1 0.03
19 1 0.03
20 13 0.35
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAACAAAATATTTTTT
Found at i:9485461 original size:14 final size:14
Alignment explanation
Indices: 9485442--9485468 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9485432 CACATACACA
9485442 ACAACAAAAAATAG
1 ACAACAAAAAATAG
9485456 ACAACAAAAAATA
1 ACAACAAAAAATA
9485469 ATAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
ACAACAAAAAATAG
Found at i:9485461 original size:17 final size:17
Alignment explanation
Indices: 9485439--9485471 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9485429 TTACACATAC
9485439 ACAACAACAAAA-AATAG
1 ACAACAA-AAAATAATAG
9485456 ACAACAAAAAATAATA
1 ACAACAAAAAATAATA
9485472 AATTACTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.15, G:0.03, T:0.09
Consensus pattern (17 bp):
ACAACAAAAAATAATAG
Found at i:9485901 original size:21 final size:21
Alignment explanation
Indices: 9485868--9485916 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
9485858 AATATAATAT
*
9485868 ATAACTTAAACTAACCAACTA
1 ATAACTTAAACTAACAAACTA
* *
9485889 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
9485910 ATTAACT
1 A-TAACT
9485917 AGATTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:9486384 original size:35 final size:35
Alignment explanation
Indices: 9486344--9486411 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
9486334 TGGATGCAAC
*
9486344 GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
1 GCATGCATGAGTGATACAGTTAAAGCTGGGTCGTT
*
9486379 GCATGCATGAGTGCTACAGTTAAAGCTGGGTCG
1 GCATGCATGAGTGATACAGTTAAAGCTGGGTCG
9486412 CGATGCAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (35 bp):
GCATGCATGAGTGATACAGTTAAAGCTGGGTCGTT
Found at i:9486468 original size:12 final size:12
Alignment explanation
Indices: 9486451--9486475 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9486441 TCCATGGCGA
9486451 CCTACCACCTAC
1 CCTACCACCTAC
9486463 CCTACCACCTAC
1 CCTACCACCTAC
9486475 C
1 C
9486476 ATGTCGTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.60, G:0.00, T:0.16
Consensus pattern (12 bp):
CCTACCACCTAC
Found at i:9486502 original size:29 final size:29
Alignment explanation
Indices: 9486469--9486539 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
9486459 CTACCCTACC
9486469 ACCTACCATGTCGTAGGGACTCCATGGCG
1 ACCTACCATGTCGTAGGGACTCCATGGCG
*
9486498 ACCTACCATGTCGTCGGGACTCCATGGCG
1 ACCTACCATGTCGTAGGGACTCCATGGCG
9486527 ACCTACCATGTCG
1 ACCTACCATGTCG
9486540 CGATGTCGCC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.20, C:0.34, G:0.25, T:0.21
Consensus pattern (29 bp):
ACCTACCATGTCGTAGGGACTCCATGGCG
Found at i:9486846 original size:29 final size:30
Alignment explanation
Indices: 9486759--9486847 Score: 155
Period size: 29 Copynumber: 3.0 Consensus size: 30
9486749 CAGCAAATCT
*
9486759 TATAGGACGCCGGGCGTGCATGGCGTCCT-
1 TATAGGACGCCGGGCGTGCATGGCGACCTA
9486788 TATAGGACGCCGGGCGTGCATGGCGACCTA
1 TATAGGACGCCGGGCGTGCATGGCGACCTA
9486818 TA-AGGACGCCGGGCGTGCATGGCGACCTA
1 TATAGGACGCCGGGCGTGCATGGCGACCTA
9486847 T
1 T
9486848 GTTGCCACTG
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 56 0.97
30 2 0.03
ACGTcount: A:0.18, C:0.27, G:0.37, T:0.18
Consensus pattern (30 bp):
TATAGGACGCCGGGCGTGCATGGCGACCTA
Found at i:9488033 original size:13 final size:13
Alignment explanation
Indices: 9488015--9488039 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9488005 ACCCTCTTGA
9488015 TGTTTCTTTTGGG
1 TGTTTCTTTTGGG
9488028 TGTTTCTTTTGG
1 TGTTTCTTTTGG
9488040 TGCCCCTCCA
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:0.00, C:0.08, G:0.28, T:0.64
Consensus pattern (13 bp):
TGTTTCTTTTGGG
Found at i:9491439 original size:17 final size:18
Alignment explanation
Indices: 9491417--9491450 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9491407 TTGGCCGGTC
9491417 CGGTTC-GAACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
9491434 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
9491451 CTAATAACGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Found at i:9491649 original size:15 final size:16
Alignment explanation
Indices: 9491629--9491667 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
9491619 TAAAGTTTAA
9491629 AATATA-TATTCAAAT
1 AATATATTATTCAAAT
9491644 AATATATTCTATTCAAAT
1 AATATA-T-TATTCAAAT
9491662 AATATA
1 AATATA
9491668 CTTAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
18 15 0.71
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATATTATTCAAAT
Found at i:9491662 original size:30 final size:30
Alignment explanation
Indices: 9491628--9491686 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
9491618 TTAAAGTTTA
9491628 AAAT-ATATA-TTCAAATAATATATTCTATTC
1 AAATAATATACTT-AAA-AATATATTCTATTC
*
9491658 AAATAATATACTTAAAAATATATTTTATT
1 AAATAATATACTTAAAAATATATTCTATT
9491687 TTAAAGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 16 0.62
31 8 0.31
32 2 0.08
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (30 bp):
AAATAATATACTTAAAAATATATTCTATTC
Found at i:9501346 original size:40 final size:36
Alignment explanation
Indices: 9501276--9501350 Score: 98
Period size: 40 Copynumber: 2.0 Consensus size: 36
9501266 GTAAGTATTA
9501276 AAACAAAACTAAAATTTTAATGTATTAAAAATAAAG
1 AAACAAAACTAAAATTTTAATGTATTAAAAATAAAG
9501312 AAACAAAA-TAAAATTGTTAAATGCTGAATTAAAAATAAA
1 AAACAAAACTAAAATT-TT-AATG-T--ATTAAAAATAAA
9501351 ATAAATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
35 7 0.21
36 10 0.29
37 4 0.12
38 1 0.03
40 12 0.35
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (36 bp):
AAACAAAACTAAAATTTTAATGTATTAAAAATAAAG
Found at i:9507823 original size:28 final size:29
Alignment explanation
Indices: 9507787--9507848 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
9507777 TTTATAGAGA
9507787 AAATCACAT-T-TGGTTTTAAAATATATAT
1 AAATCACATATAT-GTTTTAAAATATATAT
*
9507815 AAATGACATAATATGTTTTAAAATATATAT
1 AAATCACAT-ATATGTTTTAAAATATATAT
9507845 AAAT
1 AAAT
9507849 ATTTTATAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 8 0.27
30 21 0.70
31 1 0.03
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.40
Consensus pattern (29 bp):
AAATCACATATATGTTTTAAAATATATAT
Found at i:9514215 original size:26 final size:27
Alignment explanation
Indices: 9514186--9514244 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
9514176 TGTTTGATTT
* *
9514186 TATTTGATAGGAAT-GTAAGATTACAA
1 TATTTGATAGAAATAATAAGATTACAA
* *
9514212 TATTTGGTTGAAATAATAAGATTACAA
1 TATTTGATAGAAATAATAAGATTACAA
*
9514239 TGTTTG
1 TATTTG
9514245 GTTGAAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (27 bp):
TATTTGATAGAAATAATAAGATTACAA
Found at i:9516256 original size:29 final size:29
Alignment explanation
Indices: 9516217--9516285 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
9516207 TATTTGATAG
*
9516217 GAATGTAAGATTACAATATTTGGTTGAAA
1 GAATATAAGATTACAATATTTGGTTGAAA
* *
9516246 TAATATAAGATTACAATGTTTGGTTGAAA
1 GAATATAAGATTACAATATTTGGTTGAAA
9516275 GAATATAAGAT
1 GAATATAAGAT
9516286 AGAAAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (29 bp):
GAATATAAGATTACAATATTTGGTTGAAA
Found at i:9523273 original size:23 final size:22
Alignment explanation
Indices: 9523237--9523314 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
9523227 TAGAGAGAAT
9523237 CGATACCCCCTTGAAGGGGAAC
1 CGATACCCCCTTGAAGGGGAAC
*
9523259 CGATTCCCCCTTTGAAGGGGAAC
1 CGATACCCCC-TTGAAGGGGAAC
* * *
9523282 CGATTCCCCCCTGTAGGGGAAC
1 CGATACCCCCTTGAAGGGGAAC
9523304 CGATACCCCCT
1 CGATACCCCCT
9523315 GGGGTTCTGG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
22 28 0.56
23 22 0.44
ACGTcount: A:0.22, C:0.36, G:0.24, T:0.18
Consensus pattern (22 bp):
CGATACCCCCTTGAAGGGGAAC
Found at i:9525520 original size:13 final size:13
Alignment explanation
Indices: 9525502--9525529 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
9525492 CACACTTATT
9525502 TTAAAACACACAC
1 TTAAAACACACAC
9525515 TTAAAACACACAC
1 TTAAAACACACAC
9525528 TT
1 TT
9525530 CTCCCCCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (13 bp):
TTAAAACACACAC
Found at i:9527833 original size:20 final size:21
Alignment explanation
Indices: 9527779--9527841 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
9527769 GATTCCCCTG
9527779 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
9527803 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
9527823 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
9527842 TGAACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:9536946 original size:17 final size:18
Alignment explanation
Indices: 9536908--9536946 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
9536898 AATTTGAGTT
9536908 ATTTAAAATTTTATAAAA
1 ATTTAAAATTTTATAAAA
* *
9536926 ATTTAATATTTT-TAGAA
1 ATTTAAAATTTTATAAAA
9536943 ATTT
1 ATTT
9536947 TCAATTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTTAAAATTTTATAAAA
Found at i:9538028 original size:258 final size:255
Alignment explanation
Indices: 9537502--9538028 Score: 814
Period size: 257 Copynumber: 2.0 Consensus size: 255
9537492 TCGGGTCGGG
* *
9537502 TCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTTGGGTCGAGTTCGGGTTTAGGGTGAAA
1 TCGGGTCGGGTCGATTTTTTTAAGTGTGATATTCGGGTAGGGTCGAGTTCGGGTTTAGGGTGAAA
* *
9537567 AATACCGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATCATACCCC
66 AATACCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCC
** *
9537632 TCTATATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTATTATTT
131 TC-ATATATAATTTTTACCAATTAAGTCACTATTTTTATTGAATAAAAATATTTTTTTATTATTT
9537697 TGGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTT
195 TGGGTCGGGT---GTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTT
* *
9537761 T--GGTCGGGTCGATTTTTTTTAGTGTGATATTCGGGTAGGGTCGGGTTCGGGTTTAGGGTGAAA
1 TCGGGTCGGGTCGATTTTTTTAAGTGTGATATTCGGGTAGGGTCGAGTTCGGGTTTAGGGTGAAA
*
9537824 AATACCCGACCCGACCCAAAAATATATAATTTTATCTTATATATTTAGGAATAATTACAATAATA
66 AATA-CCGACCCGA---AAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATA
9537889 CCCCTC-TATAT-ATTTTTACCAATTAAGTCACTATTTTTATTGAATAAAAATAATTTTTTTATT
127 CCCCTCATATATAATTTTTACCAATTAAGTCACTATTTTTATTGAATAAAAAT-ATTTTTTTATT
*
9537952 ATTTTGGGTCGGGT-T-GGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTT
191 ATTTTGGGTCGGGTGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTT
9538015 GATCGGGTCGGGTC
1 --TCGGGTCGGGTC
9538029 TCGGATGGAG
Statistics
Matches: 248, Mismatches: 11, Indels: 19
0.89 0.04 0.07
Matches are distributed among these distances:
254 47 0.19
255 1 0.00
256 1 0.00
257 62 0.25
258 55 0.22
259 31 0.12
261 51 0.21
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (255 bp):
TCGGGTCGGGTCGATTTTTTTAAGTGTGATATTCGGGTAGGGTCGAGTTCGGGTTTAGGGTGAAA
AATACCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCC
TCATATATAATTTTTACCAATTAAGTCACTATTTTTATTGAATAAAAATATTTTTTTATTATTTT
GGGTCGGGTGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTT
Found at i:9538089 original size:254 final size:258
Alignment explanation
Indices: 9537571--9538033 Score: 645
Period size: 261 Copynumber: 1.8 Consensus size: 258
9537561 GTGAAAAATA
*
9537571 CCGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATCATACCCCTCTA
1 CCGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC-A
** *
9537636 TATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTATTATTTTGGG
65 TATATAATTTTTACCAATTAAGTCACTATTTTTATTGAATAAAAATATTTTTTTATTATTTTGGG
*
9537701 TCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTTGGTC
130 TCGGGT---GTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTTGATC
** * *** * * *** *
9537766 GGGTCGATTTTTTTTAGTGTGATATTCGGGTAGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCC
192 GGGTCGAGGTCTCGGAGTGTGAGATTCGGCTAGGGTCGGGTTCGGG-TTAGGACCAAAAAAACCC
9537831 GAC
256 GAC
*
9537834 CCGACCC-AAAA-ATATATAATTTTATCTTATATATTTAGGAATAATTACAATAATACCCCTC-T
1 CCGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCAT
9537896 ATAT-ATTTTTACCAATTAAGTCACTATTTTTATTGAATAAAAATAATTTTTTTATTATTTTGGG
66 ATATAATTTTTACCAATTAAGTCACTATTTTTATTGAATAAAAAT-ATTTTTTTATTATTTTGGG
*
9537960 TCGGGT-T-GGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTA-TTTTGATCGGG
130 TCGGGTGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTTGATCGGG
9538022 TCG-GGTCTCGGA
195 TCGAGGTCTCGGA
9538034 TGGAGGTTCC
Statistics
Matches: 186, Mismatches: 13, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
252 3 0.02
253 13 0.07
254 43 0.23
255 1 0.01
258 37 0.20
259 30 0.16
261 48 0.26
262 4 0.02
263 7 0.04
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (258 bp):
CCGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCAT
ATATAATTTTTACCAATTAAGTCACTATTTTTATTGAATAAAAATATTTTTTTATTATTTTGGGT
CGGGTGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTTGATCGGGT
CGAGGTCTCGGAGTGTGAGATTCGGCTAGGGTCGGGTTCGGGTTAGGACCAAAAAAACCCGAC
Found at i:9538433 original size:18 final size:17
Alignment explanation
Indices: 9538389--9538439 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
9538379 TATGGAATTG
*
9538389 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
**
9538406 GATTTTAATTCCTTCACA
1 GATTCCAATTCC-TCACA
9538424 GATTCCAATTTCCTCA
1 GATTCCAA-TTCCTCA
9538440 GAAACATTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 10 0.37
18 13 0.48
19 4 0.15
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.37
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:9559205 original size:20 final size:20
Alignment explanation
Indices: 9559176--9559213 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9559166 CAGAACCCCA
9559176 GGGGGAATCGATTCCCTCGT
1 GGGGGAATCGATTCCCTCGT
*
9559196 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
9559214 TGCACCAAAA
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:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCGT
Found at i:9569082 original size:52 final size:52
Alignment explanation
Indices: 9568998--9569114 Score: 155
Period size: 52 Copynumber: 2.2 Consensus size: 52
9568988 GACAATTAAT
* *
9568998 GTCTAATTTCAACATATTAAGACACTAAAACCATAAATAAA-CTAAAGCAAA
1 GTCTAATTTCAACATATTAAGACAATAAAACCATAAATAAATCGAAAGCAAA
* * * **
9569049 GTGTAATTTCAACATAGTTGAGACAATAAAACCATAATTAAATCGAAATTAAA
1 GTCTAATTTCAACATA-TTAAGACAATAAAACCATAAATAAATCGAAAGCAAA
9569102 GTCTAATTTCAAC
1 GTCTAATTTCAAC
9569115 CATAACAGAG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 15 0.27
52 22 0.39
53 19 0.34
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.27
Consensus pattern (52 bp):
GTCTAATTTCAACATATTAAGACAATAAAACCATAAATAAATCGAAAGCAAA
Found at i:9570443 original size:2 final size:2
Alignment explanation
Indices: 9570431--9570480 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
9570421 CAAATCTTTC
*
9570431 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9570473 AT AT AT AT
1 AT AT AT AT
9570481 GCATGACTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9571849 original size:3 final size:3
Alignment explanation
Indices: 9571841--9571883 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
9571831 ATTTTTTATT
9571841 TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
9571884 ATTTAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:9572301 original size:45 final size:45
Alignment explanation
Indices: 9572227--9572769 Score: 879
Period size: 45 Copynumber: 12.0 Consensus size: 45
9572217 TCAAAAAGCT
* *
9572227 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGGCTTACAGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
9572274 CCCAAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* * *
9572319 CCCAAAGGTTTTGAAAACATCATACGCTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
9572364 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATAA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
9572409 CCCGAAGGTTTTAAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* * *
9572454 CCCAAAGATTTTGAAAACATCATGCACTGAAGGGCTTATAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* * * *
9572499 CCCAAAGATTTTGAAAACATCATGCACTGAAGGGCTTATAGATAA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
9572544 CTCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
9572589 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
9572634 CCCGAAGGTTTTGAAAACATTATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
9572679 CCTGAAGGTTTTGAAAACACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTG-AAA-ACATCATGCACTGAAGGGCTTACAGATGA
*
9572726 CCAGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
9572770 TGAGAAATAG
Statistics
Matches: 468, Mismatches: 26, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
45 415 0.89
46 6 0.01
47 47 0.10
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:9573474 original size:22 final size:22
Alignment explanation
Indices: 9573427--9573526 Score: 157
Period size: 22 Copynumber: 4.6 Consensus size: 22
9573417 AATAAAGCTT
* *
9573427 TCATCTTTGAAAAGA-AATTTA
1 TCATCTTTGAAGAGAGAATCTA
9573448 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
9573470 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* *
9573492 TCATTTTTTAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
9573514 TCATCTTTGAAGA
1 TCATCTTTGAAGA
9573527 ATGTAGATAT
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
21 14 0.19
22 58 0.81
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:9574394 original size:75 final size:74
Alignment explanation
Indices: 9574255--9574427 Score: 220
Period size: 75 Copynumber: 2.3 Consensus size: 74
9574245 TATATAGGTC
* * * *
9574255 TTCAGCATGCCCTAACATTTGCTGATACAGACGTTCAAAATGCACCAACATTCCTAATTCTGATT
1 TTCAGCATGCCC-AGCATTTGCTGATACAAACGTTCAAAATGCACCAACATTCATAATTATGATT
9574320 GAAAGGGGCT
65 GAAAGGGGCT
* * ** * *
9574330 TTCAGCATGCTCCAGCATTTGCTGATACAAAGGTTTAAAATGCGTCAATATTCATGATTATGATT
1 TTCAGCATGC-CCAGCATTTGCTGATACAAACGTTCAAAATGCACCAACATTCATAATTATGATT
*
9574395 GAAATGGGCT
65 GAAAGGGGCT
9574405 TTCAGCATGCCCCAGCATTTGCT
1 TTCAGCATG-CCCAGCATTTGCT
9574428 TTTTTGATGT
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
75 82 0.96
76 3 0.04
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (74 bp):
TTCAGCATGCCCAGCATTTGCTGATACAAACGTTCAAAATGCACCAACATTCATAATTATGATTG
AAAGGGGCT
Found at i:9574453 original size:38 final size:38
Alignment explanation
Indices: 9574402--9574496 Score: 95
Period size: 40 Copynumber: 2.4 Consensus size: 38
9574392 ATTGAAATGG
** *
9574402 GCTTTCAGCATGCCCCAGCATTTGCTTTT-T-TGATGTGA
1 GCTTTCAAAATGCCCCAACATTT--TTTTATATGATGTGA
9574440 GCTTTCAAAATGCCCCAACATTTTTTTCATACTGATGTGA
1 GCTTTCAAAATGCCCCAACATTTTTTT-ATA-TGATGTGA
* *
9574480 TCCTTCAAAATGCCCCA
1 GCTTTCAAAATGCCCCA
9574497 CATGGATCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
36 4 0.08
38 21 0.44
40 23 0.48
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (38 bp):
GCTTTCAAAATGCCCCAACATTTTTTTATATGATGTGA
Found at i:9576579 original size:72 final size:72
Alignment explanation
Indices: 9576462--9576605 Score: 234
Period size: 72 Copynumber: 2.0 Consensus size: 72
9576452 GTATAATAGT
* *
9576462 ATAACAAATTAGCTGAATATTATCCATAAAGTCGGGGCGATTAACCAATTGCTTTAAGGGGATAA
1 ATAACAAATTAGCTGAATATTATCCATAAAGCCGGGACGATTAACCAATTGCTTTAAGGGGATAA
9576527 CTCAAGC
66 CTCAAGC
* * * *
9576534 ATAACAGATTAGCTGAATATTATCCATAAAGCCGTGACTATTAACCAATTGCTTTAGGGGGATAA
1 ATAACAAATTAGCTGAATATTATCCATAAAGCCGGGACGATTAACCAATTGCTTTAAGGGGATAA
9576599 CTCAAGC
66 CTCAAGC
9576606 TTTATTGTAT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (72 bp):
ATAACAAATTAGCTGAATATTATCCATAAAGCCGGGACGATTAACCAATTGCTTTAAGGGGATAA
CTCAAGC
Found at i:9579108 original size:20 final size:19
Alignment explanation
Indices: 9579085--9579126 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
9579075 CAAATTGTGC
9579085 AATAAAAAAGCAAACATAAA
1 AATAAAAAAGCAAA-ATAAA
* *
9579105 AATACAAATGCAAAATAAA
1 AATAAAAAAGCAAAATAAA
9579124 AAT
1 AAT
9579127 GCAAAGATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.71, C:0.10, G:0.05, T:0.14
Consensus pattern (19 bp):
AATAAAAAAGCAAAATAAA
Found at i:9579145 original size:7 final size:7
Alignment explanation
Indices: 9579110--9579150 Score: 50
Period size: 6 Copynumber: 6.0 Consensus size: 7
9579100 ATAAAAATAC
9579110 AAATGCA
1 AAATGCA
*
9579117 AAAT-AA
1 AAATGCA
9579123 AAATGCA
1 AAATGCA
9579130 AAGATGCA
1 AA-ATGCA
9579138 AAATGC-
1 AAATGCA
9579144 AAATGCA
1 AAATGCA
9579151 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 11 0.38
7 11 0.38
8 7 0.24
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:9579150 original size:13 final size:13
Alignment explanation
Indices: 9579103--9579146 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
9579093 AGCAAACATA
9579103 AAAATACAAATGC
1 AAAATACAAATGC
*
9579116 AAAATAAAAATGC
1 AAAATACAAATGC
*
9579129 AAAGATGCAAAATGC
1 AAA-ATAC-AAATGC
9579144 AAA
1 AAA
9579147 TGCATGTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
14 2 0.08
15 9 0.35
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.14
Consensus pattern (13 bp):
AAAATACAAATGC
Found at i:9582322 original size:2 final size:2
Alignment explanation
Indices: 9582315--9582344 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
9582305 TTTCATATGC
*
9582315 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9582345 TAGCATGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9593043 original size:22 final size:21
Alignment explanation
Indices: 9593017--9593091 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 21
9593007 GGGCCATCAG
9593017 TAAGTCTTTCGAGCATGATGA
1 TAAGTCTTTCGAGCATGATGA
* * *
9593038 TGAAGTCCTTCGGGCCATCA-G-
1 T-AAGTCTTTCGAG-CATGATGA
*
9593059 TAAGTCTTTCGAGGATGATGA
1 TAAGTCTTTCGAGCATGATGA
*
9593080 TTAAATCTTTCG
1 -TAAGTCTTTCG
9593092 GGTAATTGTA
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
19 3 0.07
20 11 0.27
21 2 0.05
22 21 0.51
23 4 0.10
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (21 bp):
TAAGTCTTTCGAGCATGATGA
Found at i:9593069 original size:20 final size:20
Alignment explanation
Indices: 9593003--9593069 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
9592993 AATTTAAATC
9593003 CTTT-GGGCCATCAGTAAGT
1 CTTTCGGGCCATCAGTAAGT
* *
9593022 CTTTCGAG-CATGATGATGAAGT
1 CTTTCGGGCCATCA-G-T-AAGT
*
9593044 CCTTCGGGCCATCAGTAAGT
1 CTTTCGGGCCATCAGTAAGT
9593064 CTTTCG
1 CTTTCG
9593070 AGGATGATGA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
19 8 0.22
20 12 0.32
21 2 0.05
22 11 0.30
23 4 0.11
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.31
Consensus pattern (20 bp):
CTTTCGGGCCATCAGTAAGT
Found at i:9593092 original size:42 final size:42
Alignment explanation
Indices: 9592996--9593664 Score: 315
Period size: 42 Copynumber: 15.5 Consensus size: 42
9592986 AGTAAACAAT
*
9592996 TTAAATCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGA
1 TTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA
* * *
9593038 TGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGGATGATGA
1 TTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA
* ** * * *
9593080 TTAAATCTTTCGGGTAAT-TGTAAGCCTTCACCGAAG-A-GTAGTGAA
1 TTAAATCCTTCGGGCCATCAGTAAGTCTT--TCG-AGCATG-A-TG-A
** * *
9593125 GCAAATCCATCAGTAAGTGACATCAGTAAGTCTTTCGAGCATGATGA
1 TTAAATCCTTC-G---G-GCCATCAGTAAGTCTTTCGAGCATGATGA
* *
9593172 TTAAATCCTTCGGGTCATCATTAAGTCTTTCGAGCATGATGA
1 TTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA
* *
9593214 TGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA
1 TTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA
** ** * *
9593256 TTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG-A-GTAGTGAA
1 TTAAATCCTTCGGGCCATCAGTAAGTCTT--TCG-AGCATG-A-TG-A
** * *
9593302 GAAAATCCGTTAGTAAGTGCCATCAGTAAGTCTTTCGAGTATGATGA
1 TTAAATCC-TTCG---G-GCCATCAGTAAGTCTTTCGAGCATGATGA
** *** * * *
9593349 TTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAG-ATTAGTGAA
1 TTAAATCCTTCGGGCCATCAGTAAGTCTT-TC-G-AGCATGA-TG-A
** * *
9593395 GCAAATCCGTAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGA
1 TTAAATCC-T--T-CGGGCCATCAGTAAGTCTTTCGAGCATGATGA
* * * * *
9593441 TGAAATCCTTTGGTCTATCAGTAAGTCTTTTGAGCATGATGA
1 TTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA
* * * * * *
9593483 TTAAATCCTTCGGG-TAACTGGTAAG-CCTTC-ACCGAAGA-GTA
1 TTAAATCCTTCGGGCCATC-AGTAAGTCTTTCGAGC-ATGATG-A
* * * **
9593524 GTGAAGCAAAT----CCATCAGTAAGTCTTTCGAGCATGATGA
1 TTAAATC-CTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA
* *
9593563 TGAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGA
1 TTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA
* * ** * * *
9593605 TTAAATCCTTCAGGTCATTTGTGAGTCTCTCGAGCAAGATGA
1 TTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA
* *
9593647 -TAAATCCTTTGGGTCATC
1 TTAAATCCTTCGGGCCATC
9593665 CATAAGACCT
Statistics
Matches: 464, Mismatches: 114, Indels: 99
0.69 0.17 0.15
Matches are distributed among these distances:
38 6 0.01
39 13 0.03
40 6 0.01
41 37 0.08
42 255 0.55
43 9 0.02
44 12 0.03
45 17 0.04
46 26 0.06
47 24 0.05
48 12 0.03
49 11 0.02
50 17 0.04
51 19 0.04
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (42 bp):
TTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA
Found at i:9593203 original size:20 final size:19
Alignment explanation
Indices: 9593180--9593250 Score: 52
Period size: 20 Copynumber: 3.5 Consensus size: 19
9593170 GATTAAATCC
9593180 TTCGGGTCATCATTAAGTCT
1 TTCGGG-CATCATTAAGTCT
* * *
9593200 TTCGAGCATGATGATGAAGTCC
1 TTCGGGCATCAT--T-AAGTCT
*
9593222 TTCGGGCCATCAGTAAGTCT
1 TTCGGG-CATCATTAAGTCT
*
9593242 TTCGAGCAT
1 TTCGGGCAT
9593251 GATGATTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
19 8 0.21
20 15 0.38
21 2 0.05
22 10 0.26
23 4 0.10
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (19 bp):
TTCGGGCATCATTAAGTCT
Found at i:9593302 original size:84 final size:84
Alignment explanation
Indices: 9593145--9593450 Score: 305
Period size: 93 Copynumber: 3.4 Consensus size: 84
9593135 CAGTAAGTGA
* * * * *
9593145 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCATTAAGTCTTTCGAGC-AT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAAT-TTTAAG-CCTTC-ACCGAA
*
9593209 GAT-GATGAAG-TCC-TTCGGGC
63 GATAG-TGAAGATCCGTTAGGGC
9593229 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTT-TAAGCCTTCACCGAAGA
9593294 GTAGTGAAGAAAATCCGTTAGTAAGTGC
65 -TAGTGAAG---ATCCGTTAG---G-GC
* *
9593322 CATCAGTAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAA-TTTTAAGCCTTCACCGAAGA
*
9593387 TTAGTGAAGCAAATCCGTAGTAAGTGC
65 -TAGTGAAG---ATCCGT--T-AGGGC
*
9593414 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
9593451 TGGTCTATCA
Statistics
Matches: 192, Mismatches: 13, Indels: 26
0.83 0.06 0.11
Matches are distributed among these distances:
82 2 0.01
83 8 0.04
84 54 0.28
85 1 0.01
88 3 0.02
89 3 0.02
92 38 0.20
93 77 0.40
94 3 0.02
95 1 0.01
96 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (84 bp):
CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTTAAGCCTTCACCGAAGAT
AGTGAAGATCCGTTAGGGC
Found at i:9593386 original size:93 final size:92
Alignment explanation
Indices: 9593227--9593450 Score: 385
Period size: 93 Copynumber: 2.4 Consensus size: 92
9593217 AGTCCTTCGG
9593227 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAA
9593292 GAGTAGTGAAGAAAATCCGTTAGTAAGT
66 GAGTAGTGAAGAAAATCCG-TAGTAAGT
* * *
9593320 GCCATCAGTAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAA
* *
9593385 GATTAGTGAAGCAAATCCGTAGTAAGT
66 GAGTAGTGAAGAAAATCCGTAGTAAGT
*
9593412 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTT
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
9593451 TGGTCTATCA
Statistics
Matches: 124, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 45 0.36
93 79 0.64
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (92 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAA
GAGTAGTGAAGAAAATCCGTAGTAAGT
Found at i:9593480 original size:134 final size:132
Alignment explanation
Indices: 9593009--9593626 Score: 569
Period size: 134 Copynumber: 4.7 Consensus size: 132
9592999 AATCCTTTGG
* * *
9593009 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGGA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCA
*
9593074 TGATGATTAAATCTTTCGGGTAA-TTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAG
66 TGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC-T-A-
9593138 TAAGT
128 TAAGT
* * *
9593143 GACATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCATTAAGTCTTTCGAGCA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCA
* * ** ** * * **
9593208 TGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTT--TCG-AGCA-T-GATG-ATTAAATCCT-T
66 TGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG-AGTAG-TGAAGCAAATCCTAT
* *
9593266 -CGG
129 AAGT
** ** * * * * *
9593269 GTAATTTGTAAGCCTTCACCGAAG-A-GTAGTGAAGAAAATCCGTTAGTAAGTGCCATCAGTAAG
1 GCCATCAGTAAGTCTT--TCG-AGCATG-A-TGATG-AAATCC-TTCG---G-GTCATCAGTAAG
* * * *
9593332 TCTTTCGAGTATGATGATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGATTAGTGAAGC
55 TCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGC
9593397 AAATCCGTAGTAAGT
120 AAATCC-TA-TAAGT
* *
9593412 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTT-TGGTCTATCAGTAAGTCTTTTGAGC
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTC-ATCAGTAAGTCTTTCGAGC
* *
9593476 ATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACCGAAGAGTAGTGAAG------C-A-A
65 ATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCTATA
9593533 A-T
130 AGT
9593535 -CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCA
* *
9593599 TGATGATTAAATCCTTCAGGTCATTTGT
66 TGATGATTAAATCCTTCGGGTAATTTGT
9593627 GAGTCTCTCG
Statistics
Matches: 389, Mismatches: 67, Indels: 68
0.74 0.13 0.13
Matches are distributed among these distances:
122 81 0.21
123 5 0.01
124 2 0.01
126 13 0.03
127 2 0.01
128 5 0.01
129 5 0.01
130 7 0.02
131 11 0.03
132 5 0.01
133 5 0.01
134 145 0.37
135 55 0.14
137 2 0.01
138 7 0.02
139 14 0.04
140 7 0.02
141 4 0.01
142 2 0.01
143 12 0.03
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (132 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCA
TGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCTATAA
GT
Found at i:9593574 original size:22 final size:21
Alignment explanation
Indices: 9593549--9593615 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
9593539 CAGTAAGTCT
9593549 TTCGAGCATGATGATGAAATCC
1 TTCGAGCATGATGAT-AAATCC
* * * *
9593571 TTCGGGTCATCA-G-TAAGTCT
1 TTCGAG-CATGATGATAAATCC
9593591 TTCGAGCATGATGATTAAATCC
1 TTCGAGCATGATGA-TAAATCC
9593613 TTC
1 TTC
9593616 AGGTCATTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
19 4 0.12
20 10 0.30
21 1 0.03
22 14 0.42
23 4 0.12
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (21 bp):
TTCGAGCATGATGATAAATCC
Found at i:9594162 original size:53 final size:53
Alignment explanation
Indices: 9594038--9594391 Score: 475
Period size: 53 Copynumber: 6.7 Consensus size: 53
9594028 AGAATCACAC
* *
9594038 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAG-G-A-CTGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
*
9594088 CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
** * * *
9594141 TGGAAGATTGTTCGAGGTCTACTCCCTGAAGTAAGAGGGAGGGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* *
9594194 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
*
9594247 CAGAAGATTGTTCGAGTTCTAC-CCCTGAAGCAAGAGGGAGCGAACCCGTAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * ***
9594299 CAGAAGATTATTCGAGTTCTACTCCTTGAAGCAATAGGGAGCGAACCCGTTTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
9594352 TAGAAGATTGTTTGAGTTCTTTAATCCCTGAA-CAAGAGGG
1 CAGAAGATTGTTCGAGTTC--TACTCCCTGAAGCAAGAGGG
9594392 GGTGAATCCG
Statistics
Matches: 268, Mismatches: 30, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
50 39 0.15
51 1 0.00
52 50 0.19
53 162 0.60
54 7 0.03
55 9 0.03
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:9594226 original size:106 final size:106
Alignment explanation
Indices: 9594038--9594391 Score: 484
Period size: 105 Copynumber: 3.4 Consensus size: 106
9594028 AGAATCACAC
* *
9594038 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGA-GG-A-CTGTAGGCAGAAGATTGTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGGGAACCCGTAGGCAGAAGATTGTT
9594100 CGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGG
66 CGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGG
** * *
9594141 TGGAAGATTGTTCGAGGTCTACTCCCTGAAGTAAGAGGGAGGGAACCCGTAGGCAGAAGATTGTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGGGAACCCGTAGGCAGAAGATTGTT
* * *
9594206 CGAGTTTTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGG
66 CGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
9594247 CAGAAGATTGTTCGAGTTCTAC-CCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAGAAGATTATT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGGGAACCCGTAGGCAGAAGATTGTT
* ***
9594311 CGAGTTCTACTCCTTGAAGCAATAGGGAGCGAACCCGTTTT
66 CGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
9594352 TAGAAGATTGTTTGAGTTCTTTAATCCCTGAA-CAAGAGGG
1 CAGAAGATTGTTCGAGTTC--TACTCCCTGAAGCAAGAGGG
9594392 GGTGAATCCG
Statistics
Matches: 219, Mismatches: 26, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
103 35 0.16
104 2 0.01
105 90 0.41
106 75 0.34
107 10 0.05
108 7 0.03
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (106 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGGGAACCCGTAGGCAGAAGATTGTT
CGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:9594329 original size:158 final size:158
Alignment explanation
Indices: 9594038--9594402 Score: 504
Period size: 158 Copynumber: 2.3 Consensus size: 158
9594028 AGAATCACAC
*
9594038 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAG-G-ACTGTAGGCAGAAGATTGTTC
1 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGTGAACCGTAGGCAGAAGATTGTTC
* * ** *
9594101 GAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGGTGGAAGATTGTTCGAGGTCTACTCC
66 GAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAGAAGATTATTCGAGGTCTACTCC
* *
9594166 CTGAAGTAAGAGGGAGGGAACCCGTAGG
131 CTGAAGCAAGAGGGAGCGAACCCGTAGG
9594194 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAGAAGATTGTT
1 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGTGAA-CCGTAGGCAGAAGATTGTT
*
9594259 CGAGTTCTAC-CCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAGAAGATTATTCGAGTTCTACTC
65 CGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAGAAGATTATTCGAGGTCTACTC
* * ***
9594323 CTTGAAGCAATAGGGAGCGAACCCGTTTT
130 CCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * *
9594352 TAGAAGATTGTTTGAGTTCTTTAATCCCTGAA-CAAGAGGGGGTGAATCCGT
1 CAGAAGATTGTTCGAG-T-TTTACTCCCTGAAGCAAGAGGGAGTGAA-CCGT
9594403 CATTTGAAGA
Statistics
Matches: 185, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
156 41 0.22
157 1 0.01
158 85 0.46
159 46 0.25
160 12 0.06
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (158 bp):
CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGTGAACCGTAGGCAGAAGATTGTTC
GAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAGAAGATTATTCGAGGTCTACTCC
CTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:9600515 original size:17 final size:17
Alignment explanation
Indices: 9600495--9600529 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
9600485 ATCATGAGAC
*
9600495 AAATCTTATCTTAAAAA
1 AAATCTTATATTAAAAA
9600512 AAATCTTATATTAAAAA
1 AAATCTTATATTAAAAA
9600529 A
1 A
9600530 CAATTGCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATCTTATATTAAAAA
Found at i:9601909 original size:28 final size:29
Alignment explanation
Indices: 9601878--9601933 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
9601868 TTAAAAGTTT
9601878 AAAATTAT-ATTGAAA-CAAAAAATATTCC
1 AAAATTATAATT-AAATCAAAAAATATTCC
*
9601906 AAAATTATAATTAAATTAAAAAATATTC
1 AAAATTATAATTAAATCAAAAAATATTC
9601934 ACTTTGCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAATTATAATTAAATCAAAAAATATTCC
Found at i:9602640 original size:51 final size:51
Alignment explanation
Indices: 9602604--9602721 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
9602594 GATTTGGCGC
*
9602604 CACGTGGGGTATAGCGCGCCCCCTGTACCGCGCTATACGCTGACATAGCTTA
1 CACGT-GGGTATAGCGCGCCCCCTGTACCGCGCTATACGCTGACATAGCTGA
* * ** *
9602656 CACGTGGGTATAGCGCGCCCCCTGTTCCGCGCTATA-GTTG-TTTATCTGA
1 CACGTGGGTATAGCGCGCCCCCTGTACCGCGCTATACGCTGACATAGCTGA
*
9602705 CACGTGGGTATAACGCG
1 CACGTGGGTATAGCGCG
9602722 GTACAGGGGG
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
49 21 0.36
50 3 0.05
51 30 0.51
52 5 0.08
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.25
Consensus pattern (51 bp):
CACGTGGGTATAGCGCGCCCCCTGTACCGCGCTATACGCTGACATAGCTGA
Found at i:9603053 original size:45 final size:48
Alignment explanation
Indices: 9602990--9603102 Score: 153
Period size: 53 Copynumber: 2.3 Consensus size: 48
9602980 CGGTAACATT
9602990 TTAAGAATT-ATTTGTAATAA-T-TTG-TTTAATGCATGATTATTAGA
1 TTAAGAATTAATTTGTAATAATTGTTGTTTTAATGCATGATTATTAGA
9603034 TTAAGAATTAATTTGTAATAATTTGTTGATTTATTTAATGCATGATTATTAGA
1 TTAAGAATTAATTTGTAATAA-TTGTTG---T-TTTAATGCATGATTATTAGA
9603087 TTAAGAATTAATTTGT
1 TTAAGAATTAATTTGT
9603103 GTTTAGTAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 9
0.87 0.00 0.13
Matches are distributed among these distances:
44 9 0.15
45 11 0.18
47 1 0.02
48 3 0.05
53 36 0.60
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (48 bp):
TTAAGAATTAATTTGTAATAATTGTTGTTTTAATGCATGATTATTAGA
Found at i:9603098 original size:26 final size:26
Alignment explanation
Indices: 9603015--9603098 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 26
9603005 AATAATTTGT
9603015 TTAATGCATGATTATTAGATTAAGAA
1 TTAATGCATGATTATTAGATTAAGAA
* * * * *
9603041 TTAATTTGTAATAATT-TGTTGATT--TAT
1 TTAA--TG-CATGATTAT-TAGATTAAGAA
9603068 TTAATGCATGATTATTAGATTAAGAA
1 TTAATGCATGATTATTAGATTAAGAA
9603094 TTAAT
1 TTAAT
9603099 TTGTGTTTAG
Statistics
Matches: 41, Mismatches: 10, Indels: 14
0.63 0.15 0.22
Matches are distributed among these distances:
24 10 0.24
25 3 0.07
26 10 0.24
27 5 0.12
28 3 0.07
29 10 0.24
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.46
Consensus pattern (26 bp):
TTAATGCATGATTATTAGATTAAGAA
Found at i:9604399 original size:18 final size:18
Alignment explanation
Indices: 9604372--9604415 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
9604362 ACAACAGCCA
*
9604372 CCGCAGCCATTTATGATT
1 CCGCAGCCATATATGATT
*
9604390 CCGCATCCATATATGATGT
1 CCGCAGCCATATATGAT-T
9604409 -CGCAGCC
1 CCGCAGCC
9604416 TTTCCATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (18 bp):
CCGCAGCCATATATGATT
Found at i:9604953 original size:26 final size:24
Alignment explanation
Indices: 9604882--9604953 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
9604872 TTATATTTGT
9604882 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
9604907 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
9604929 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
9604954 GTTGGATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:9610076 original size:35 final size:34
Alignment explanation
Indices: 9609991--9610077 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
9609981 AATATAATTT
*
9609991 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
9610025 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
9610063 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
9610078 ATTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:9612315 original size:111 final size:111
Alignment explanation
Indices: 9612188--9612405 Score: 373
Period size: 111 Copynumber: 2.0 Consensus size: 111
9612178 CAAAAATTAT
* *
9612188 TTCTTAATTTAATAATCATGTATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAATT
1 TTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAATT
* *
9612253 AAAACGTTAAAATATTACTGTATCAGCAAAGTGTCGAGATATTTAA
66 AAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATATTTAA
*
9612299 TTCTTAATCTAATAATCATGCATTAAATAAATCAATTAATTATTACTAATAATTTAAATTAAATT
1 TTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAATT
* *
9612364 AAAACGTTAAAATGTTACCGTATCAGTAAAGTGTAGAGATAT
66 AAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
9612406 ATGATTTCCA
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 100 1.00
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (111 bp):
TTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAATT
AAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATATTTAA
Found at i:9618089 original size:28 final size:28
Alignment explanation
Indices: 9618047--9618121 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
9618037 AAATTTAAAA
*
9618047 AATTATGAAATTATAAATA-TTAGGGACCCT
1 AATTAT-AAA-TATAAAAAGTT-GGGACCCT
*
9618077 AATTATAAATATAAAAAGTTGGGATCCT
1 AATTATAAATATAAAAAGTTGGGACCCT
* *
9618105 AATTGTAAATACAAAAA
1 AATTATAAATATAAAAA
9618122 AATGGGGGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
28 29 0.73
29 5 0.12
30 6 0.15
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (28 bp):
AATTATAAATATAAAAAGTTGGGACCCT
Found at i:9618127 original size:28 final size:28
Alignment explanation
Indices: 9618069--9618127 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
9618059 ATAAATATTA
* **
9618069 GGGACCCTAATTATAAATATAAAAAGTT
1 GGGACCCTAATTATAAATACAAAAAAAT
* *
9618097 GGGATCCTAATTGTAAATACAAAAAAAT
1 GGGACCCTAATTATAAATACAAAAAAAT
9618125 GGG
1 GGG
9618128 GGCCTTGAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (28 bp):
GGGACCCTAATTATAAATACAAAAAAAT
Found at i:9626806 original size:21 final size:21
Alignment explanation
Indices: 9626780--9626822 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
9626770 TCCTGATGAG
9626780 AGTGTTGGTCTAATAGCAATT
1 AGTGTTGGTCTAATAGCAATT
9626801 AGTGTTGGTCTAATAGCAATT
1 AGTGTTGGTCTAATAGCAATT
9626822 A
1 A
9626823 ATAGGGACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.37
Consensus pattern (21 bp):
AGTGTTGGTCTAATAGCAATT
Found at i:9637955 original size:19 final size:19
Alignment explanation
Indices: 9637933--9637972 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
9637923 TAAAAAAAAT
9637933 ATACATTTTTA-ATTAATAA
1 ATACATTTTTAGA-TAATAA
9637952 ATACATTTTTAGATAATAA
1 ATACATTTTTAGATAATAA
9637971 AT
1 AT
9637973 CAAAAGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (19 bp):
ATACATTTTTAGATAATAA
Found at i:9638225 original size:18 final size:18
Alignment explanation
Indices: 9638188--9638221 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9638178 AATATCTGAA
*
9638188 TTCAAACATAAAATTTAT
1 TTCAAAAATAAAATTTAT
9638206 TTCAAAAAT-AAATTTA
1 TTCAAAAATAAAATTTA
9638222 ATTTTTTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
TTCAAAAATAAAATTTAT
Found at i:9638618 original size:23 final size:23
Alignment explanation
Indices: 9638586--9638648 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
9638576 CCTCGTTAAA
* *
9638586 AAGTTAAGATGAGAATATAATTT
1 AAGTTCAGATAAGAATATAATTT
9638609 AAGTTCAGATAAGAATATAATTT
1 AAGTTCAGATAAGAATATAATTT
* *
9638632 AGGTCCAGATAAGAATA
1 AAGTTCAGATAAGAATA
9638649 AATGATATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30
Consensus pattern (23 bp):
AAGTTCAGATAAGAATATAATTT
Found at i:9638804 original size:29 final size:27
Alignment explanation
Indices: 9638599--9638879 Score: 138
Period size: 30 Copynumber: 9.7 Consensus size: 27
9638589 TTAAGATGAG
* *
9638599 AATATAATTTAAGTTCAGATAAGAAT-
1 AATATATTTTAAGTTAAGATAAGAATA
* **
9638625 -ATA-A-TTTAGGTCCAGATAAGAATA
1 AATATATTTTAAGTTAAGATAAGAATA
*
9638649 AATGATATGTTTTAAGTTAAAATAAGAATTA
1 AAT-ATA--TTTTAAGTTAAGATAAGAA-TA
* * * * *
9638680 ATTATAATTAATAATTTAAGGTAAAAATAA
1 AATAT-ATT-TTAAGTTAAGATAAGAAT-A
* * *
9638710 AATATATATAATAATTTAAGTTAAGAATA
1 AATATAT-T-TTAAGTTAAGATAAGAATA
* *
9638739 TAATTTATGTAATAAGTTAAGATAAGAATTA
1 -AATATAT-T-TTAAGTTAAGATAAGAA-TA
9638770 AATATATTTTAAGTTAAGATAAAGAATA
1 AATATATTTTAAGTTAAGAT-AAGAATA
* *
9638798 CAATATATTTTTAGATTAAGATAGGAATAA
1 -AATATATTTTAAG-TTAAGATAAGAAT-A
* * **
9638828 AATATATTTAACAAGTTAAAATATTAATAA
1 AATATATTT--TAAGTTAAGATAAGAAT-A
9638858 AATATATTTTTAATGTTAAGAT
1 AATATA-TTTTAA-GTTAAGAT
9638880 GTAACATTAA
Statistics
Matches: 203, Mismatches: 30, Indels: 40
0.74 0.11 0.15
Matches are distributed among these distances:
23 17 0.08
24 1 0.00
25 5 0.02
26 1 0.00
27 1 0.00
28 13 0.06
29 40 0.20
30 113 0.56
31 12 0.06
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (27 bp):
AATATATTTTAAGTTAAGATAAGAATA
Found at i:9638844 original size:88 final size:88
Alignment explanation
Indices: 9638638--9638879 Score: 220
Period size: 88 Copynumber: 2.7 Consensus size: 88
9638628 ATTTAGGTCC
*** * * * *
9638638 AGATAAGAAT-AAATGATATGTTTTAAGTTAAAATAAGAATTAATTATAATTAATAATTTAAGGT
1 AGATAAGAATAAAAT-ATATGTAACAAGTTAAAATAAGAATTAAATAT-ATT-TTAAGTTAAGAT
9638702 AAAAATAAAATATATATAATAATTTA
63 AAAAATAAAATATATATAATAATTTA
* * * * *
9638728 AGTTAAGAATATAATTTATGTAATAAGTTAAGATAAGAATTAAATATATTTTAAGTTAAGATAAA
1 AGATAAGAATAAAATATATGTAACAAGTTAAAATAAGAATTAAATATATTTTAAGTTAAGATAAA
* **
9638793 GAATACAATATAT-TTTTAGA-TTA
66 -AATAAAATATATATAATA-ATTTA
* * ** *
9638816 AGATAGGAATAAAATATATTTAACAAGTTAAAATATTAATAAAATATATTTTTAATGTTAAGAT
1 AGATAAGAATAAAATATATGTAACAAGTTAAAATAAGAATTAAATATA-TTTTAA-GTTAAGAT
9638880 GTAACATTAA
Statistics
Matches: 124, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
88 56 0.45
89 21 0.17
90 44 0.35
91 3 0.02
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.38
Consensus pattern (88 bp):
AGATAAGAATAAAATATATGTAACAAGTTAAAATAAGAATTAAATATATTTTAAGTTAAGATAAA
AATAAAATATATATAATAATTTA
Found at i:9640463 original size:25 final size:27
Alignment explanation
Indices: 9640402--9640466 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
9640392 CCTCAATTAA
* *
9640402 TTTAATATTAATTAAATAAATATATAT
1 TTTAATATTTATGAAATAAATATATAT
* *
9640429 TTAAATTATTTATGATATAAATA-AT-T
1 TTTAA-TATTTATGAAATAAATATATAT
9640455 TTTAATATTTAT
1 TTTAATATTTAT
9640467 TTAATTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
25 7 0.22
26 5 0.16
27 6 0.19
28 14 0.44
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
TTTAATATTTATGAAATAAATATATAT
Found at i:9643945 original size:20 final size:20
Alignment explanation
Indices: 9643903--9644139 Score: 108
Period size: 20 Copynumber: 11.8 Consensus size: 20
9643893 AGGATTCGCA
* * *
9643903 TTGCGAATTCGAAATTTGCG
1 TTGCGAATTCGAAAATCGAG
9643923 TTGCGAATTCGAAAATCGAG
1 TTGCGAATTCGAAAATCGAG
** *
9643943 TTGCGAAAAC-AAAATTCTTA-
1 TTGCGAATTCGAAAA-TC-GAG
* * *
9643963 TTGCAAAATT-GAAACTCGCG
1 TTGC-GAATTCGAAAATCGAG
*
9643983 TTGCGAATTAGAAAATCGAG
1 TTGCGAATTCGAAAATCGAG
** * *
9644003 TTGCGAAAACGAAACTCGTG
1 TTGCGAATTCGAAAATCGAG
**
9644023 TTGCGAATTTAAAAATCGAG
1 TTGCGAATTCGAAAATCGAG
*** * * *
9644043 TTGCGAAAAAGAAATTTGTG
1 TTGCGAATTCGAAAATCGAG
*
9644063 TTGCGAAAATATC-AAATTCGAG
1 TTGCG--AAT-TCGAAAATCGAG
** *
9644085 TTGCGAAATT-G-ACTTCTGTG
1 TTGCG-AATTCGAAAATC-GAG
* *
9644105 TTGCGAATTCCAAATTCGAG
1 TTGCGAATTCGAAAATCGAG
9644125 TTGCGAATTCGAAAA
1 TTGCGAATTCGAAAA
9644140 CTGTGTTGCG
Statistics
Matches: 159, Mismatches: 45, Indels: 26
0.69 0.20 0.11
Matches are distributed among these distances:
19 16 0.10
20 115 0.72
21 14 0.09
22 14 0.09
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (20 bp):
TTGCGAATTCGAAAATCGAG
Found at i:9644046 original size:60 final size:60
Alignment explanation
Indices: 9643922--9644049 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
9643912 CGAAATTTGC
* * * * * *
9643922 GTTGCGAATTCGAAAATCGAGTTGCGAAAACAAAATTCTTATTGCAAAATTGAAACTCGC
1 GTTGCGAATTAGAAAATCGAGTTGCGAAAACAAAACTCGTATTGCAAAATTAAAAATCGA
* * * *
9643982 GTTGCGAATTAGAAAATCGAGTTGCGAAAACGAAACTCGTGTTGCGAATTTAAAAATCGA
1 GTTGCGAATTAGAAAATCGAGTTGCGAAAACAAAACTCGTATTGCAAAATTAAAAATCGA
9644042 GTTGCGAA
1 GTTGCGAA
9644050 AAAGAAATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (60 bp):
GTTGCGAATTAGAAAATCGAGTTGCGAAAACAAAACTCGTATTGCAAAATTAAAAATCGA
Found at i:9644056 original size:60 final size:60
Alignment explanation
Indices: 9643933--9644071 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 60
9643923 TTGCGAATTC
* * * * * **
9643933 GAAAATCGAGTTGCGAAAACAAAATTCTTATTGCAAAATTGAAACTCGCGTTGCGAATTA
1 GAAAATCGAGTTGCGAAAACAAAACTCGTATTGCAAAATTAAAAATCGAGTTGCGAAAAA
* * * *
9643993 GAAAATCGAGTTGCGAAAACGAAACTCGTGTTGCGAATTTAAAAATCGAGTTGCGAAAAA
1 GAAAATCGAGTTGCGAAAACAAAACTCGTATTGCAAAATTAAAAATCGAGTTGCGAAAAA
* * *
9644053 GAAATTTGTGTTGCGAAAA
1 GAAAATCGAGTTGCGAAAA
9644072 TATCAAATTC
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (60 bp):
GAAAATCGAGTTGCGAAAACAAAACTCGTATTGCAAAATTAAAAATCGAGTTGCGAAAAA
Found at i:9644144 original size:40 final size:41
Alignment explanation
Indices: 9643903--9644151 Score: 151
Period size: 40 Copynumber: 6.2 Consensus size: 41
9643893 AGGATTCGCA
* * * *
9643903 TTGCGAATTCGAAATTTGCGTTGCGAATTCGAAAA-TCGAG
1 TTGCGAATTCAAAATTCGAGTTGCGAATTCGAAAACTCGTG
** * * *
9643943 TTGCGAAAACAAAATTCTTA-TTGCAAAATT-G-AAACTCGCG
1 TTGCGAATTCAAAATTC-GAGTTGC-GAATTCGAAAACTCGTG
* **
9643983 TTGCGAATT-AGAAAATCGAGTTGCGAAAACG-AAACTCGTG
1 TTGCGAATTCA-AAATTCGAGTTGCGAATTCGAAAACTCGTG
* * *** * *
9644023 TTGCGAATTTAAAAATCGAGTTGCGAAAAAG-AAATTTGTG
1 TTGCGAATTCAAAATTCGAGTTGCGAATTCGAAAACTCGTG
***
9644063 TTGCGAAAATATC-AAATTCGAGTTGCGAAATT-GACTTCT-GTG
1 TTGCG--AAT-TCAAAATTCGAGTTGCG-AATTCGAAAACTCGTG
*
9644105 TTGCGAATTCCAAATTCGAGTTGCGAATTCGAAAACT-GTG
1 TTGCGAATTCAAAATTCGAGTTGCGAATTCGAAAACTCGTG
9644145 TTGCGAA
1 TTGCGAA
9644152 ATTAGCTTTC
Statistics
Matches: 165, Mismatches: 30, Indels: 28
0.74 0.13 0.13
Matches are distributed among these distances:
39 13 0.08
40 118 0.72
41 5 0.03
42 25 0.15
43 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (41 bp):
TTGCGAATTCAAAATTCGAGTTGCGAATTCGAAAACTCGTG
Found at i:9644145 original size:82 final size:80
Alignment explanation
Indices: 9644018--9644214 Score: 209
Period size: 82 Copynumber: 2.5 Consensus size: 80
9644008 AAAACGAAAC
* * *** ** *
9644018 TCGTGTTGCGAATTTAAAAATCGAGTTGCGAAAAAGAAATTTGTGTTGCGAAAATATCAAATTCG
1 TCGTGTTGCGAATTCAAAATTCGAGTTGCGAATTCGAAAACTGTGTTGCGAAAATAGC--ATTCG
*
9644083 AGTTGCGAAATTGAC-T
64 AGTTACGAAATTGACTT
* * * *
9644099 TCTGTGTTGCGAATTCCAAATTCGAGTTGCGAATTCGAAAACTGTGTTGCGAAATTAGCTTTCGT
1 TC-GTGTTGCGAATTCAAAATTCGAGTTGCGAATTCGAAAACTGTGTTGCGAAAATAGCATTCGA
*
9644164 GTTACGAAATTGGCTT
65 GTTACGAAATTGACTT
* *
9644180 TCATGTTGCGAATTCAAAATT-GAGTTGCAAATTCG
1 TCGTGTTGCGAATTCAAAATTCGAGTTGCGAATTCG
9644215 TTGGTTATTT
Statistics
Matches: 97, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
79 13 0.13
80 33 0.34
81 5 0.05
82 46 0.47
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (80 bp):
TCGTGTTGCGAATTCAAAATTCGAGTTGCGAATTCGAAAACTGTGTTGCGAAAATAGCATTCGAG
TTACGAAATTGACTT
Found at i:9644147 original size:20 final size:19
Alignment explanation
Indices: 9644100--9644151 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
9644090 AAATTGACTT
*
9644100 CTGTGTTGCGAATTCCAAA
1 CTGTGTTGCGAATTCAAAA
* *
9644119 TTCGAGTTGCGAATTCGAAAA
1 CT-GTGTTGCGAATTC-AAAA
9644140 CTGTGTTGCGAA
1 CTGTGTTGCGAA
9644152 ATTAGCTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 1 0.04
20 21 0.81
21 4 0.15
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (19 bp):
CTGTGTTGCGAATTCAAAA
Found at i:9644165 original size:20 final size:20
Alignment explanation
Indices: 9644142--9644191 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
9644132 TTCGAAAACT
9644142 GTGTTGCGAAATTAGCTTTC
1 GTGTTGCGAAATTAGCTTTC
* *
9644162 GTGTTACGAAATTGGCTTTC
1 GTGTTGCGAAATTAGCTTTC
*
9644182 ATGTTGCGAA
1 GTGTTGCGAA
9644192 TTCAAAATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (20 bp):
GTGTTGCGAAATTAGCTTTC
Found at i:9648685 original size:64 final size:65
Alignment explanation
Indices: 9648611--9648740 Score: 217
Period size: 64 Copynumber: 2.0 Consensus size: 65
9648601 TCCCTAATTT
* **
9648611 AATATTCTTCAATTATTCCTTTTTTATACCATACTTACAATTCAATTCATTCAAATTCAA-AAGA
1 AATATTCTTCAATTATTCATTTTTTATACCATACCCACAATTCAATTCATTCAAATTCAACAAGA
*
9648675 AATATTCTTCAATTATTTATTTTTTATACCATACCCACAATTCAATTCATTCAAATTCAACAAGA
1 AATATTCTTCAATTATTCATTTTTTATACCATACCCACAATTCAATTCATTCAAATTCAACAAGA
9648740 A
1 A
9648741 TGAGAATGTT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
64 56 0.92
65 5 0.08
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.41
Consensus pattern (65 bp):
AATATTCTTCAATTATTCATTTTTTATACCATACCCACAATTCAATTCATTCAAATTCAACAAGA
Found at i:9649176 original size:20 final size:20
Alignment explanation
Indices: 9649153--9649204 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
9649143 AACGCGATCC
9649153 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
9649173 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
9649193 CCAAAATCGCAA
1 CCAGAATCGCAA
9649205 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:9649285 original size:20 final size:20
Alignment explanation
Indices: 9649260--9649453 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
9649250 GATTTTCCAT
* *
9649260 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
9649280 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
9649300 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
9649320 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
9649340 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
9649360 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
9649380 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
9649400 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
9649421 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
9649441 AATCGCAACGCGA
1 AATCGCAACGCGA
9649454 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:9649305 original size:40 final size:39
Alignment explanation
Indices: 9649256--9649453 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
9649246 TTGCGATTTT
* ** *
9649256 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
9649294 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
9649335 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
9649375 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
9649414 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
9649454 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:9649343 original size:60 final size:60
Alignment explanation
Indices: 9649260--9649452 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
9649250 GATTTTCCAT
* ** * *
9649260 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
9649320 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
9649380 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
9649441 AATCGCAACGCG
1 AATCGCAACGCG
9649453 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:9649872 original size:33 final size:33
Alignment explanation
Indices: 9649833--9649903 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
9649823 TTCACTTAGA
*
9649833 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
9649866 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
9649899 TTTCA
1 TTTCA
9649904 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:9650043 original size:14 final size:14
Alignment explanation
Indices: 9650024--9650078 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
9650014 AGAATGACTG
9650024 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
9650038 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
9650057 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
9650071 TCGCAACG
1 TCGCAACG
9650079 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:9650061 original size:33 final size:33
Alignment explanation
Indices: 9650024--9650094 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
9650014 AGAATGACTG
**
9650024 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
9650057 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
9650090 TCGCA
1 TCGCA
9650095 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:9650112 original size:19 final size:19
Alignment explanation
Indices: 9650090--9650187 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
9650080 GAAACCAAAA
*
9650090 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
9650109 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
9650123 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
9650142 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
9650156 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
9650175 TCGCGTTGCGATT
1 TCGCGTTGCGATT
9650188 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:9650131 original size:14 final size:14
Alignment explanation
Indices: 9650112--9650201 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
9650102 TTTCATTTCG
9650112 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
9650126 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
9650145 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
9650159 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
9650176 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
9650192 CGTTGCGATT
1 CGTTGCGATT
9650202 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:9650137 original size:33 final size:33
Alignment explanation
Indices: 9650095--9650209 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
9650085 CAAAATCGCA
9650095 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
9650128 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
9650161 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
9650194 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
9650210 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:9652220 original size:93 final size:93
Alignment explanation
Indices: 9651907--9652564 Score: 1293
Period size: 93 Copynumber: 7.1 Consensus size: 93
9651897 TAGATTGCTT
*
9651907 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
9651972 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
9651999 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
9652063 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
9652091 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
9652156 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
9652184 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
9652249 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
9652277 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
9652342 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
9652370 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
9652435 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
9652463 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
9652528 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
9652556 AGTAAATTT
1 AGTAAATTT
9652565 ATCCATTCAA
Statistics
Matches: 563, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
91 2 0.00
92 150 0.27
93 411 0.73
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:9652687 original size:33 final size:32
Alignment explanation
Indices: 9652644--9652736 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
9652634 TGCGAAACCA
**
9652644 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
9652676 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
9652709 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
9652737 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:9652734 original size:52 final size:52
Alignment explanation
Indices: 9652608--9652736 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
9652598 TAGTTTACTT
** *
9652608 TCGCAACACGAAACTTAAAATCGCAATGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
9652660 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
9652713 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
9652737 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 41 0.67
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:9652742 original size:19 final size:19
Alignment explanation
Indices: 9652608--9652736 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
9652598 TAGTTTACTT
* *
9652608 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
*
9652628 TCGCAATGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
9652647 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
9652666 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
9652680 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
9652699 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
9652713 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
9652732 TCGCA
1 TCGCA
9652737 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 12 0.14
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:9652754 original size:19 final size:19
Alignment explanation
Indices: 9652732--9652866 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
9652722 GAAACCAAAA
*
9652732 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
9652751 TCGCGTTGCGA--TTC--T
1 TCGCGTTGCGATTTTCATT
9652766 TC-CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
9652784 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
9652800 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
9652817 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
9652836 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
9652856 TCGTGTTGCGA
1 TCGCGTTGCGA
9652867 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
15 3 0.03
16 8 0.08
17 8 0.08
18 3 0.03
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:9652779 original size:33 final size:33
Alignment explanation
Indices: 9652737--9652829 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
9652727 CAAAATCGCA
9652737 TTGCGATTTTCATTTCGCGTTGCGATTCT-TCCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGT-CG
*
9652770 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
9652803 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
9652830 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 56 0.98
34 1 0.02
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:9654811 original size:14 final size:14
Alignment explanation
Indices: 9654792--9654827 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
9654782 ATTGTTTAAT
9654792 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
9654806 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
9654820 TGATTTGT
1 TGATTTGT
9654828 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:9654950 original size:19 final size:18
Alignment explanation
Indices: 9654934--9655014 Score: 116
Period size: 19 Copynumber: 4.6 Consensus size: 18
9654924 AAAAATGACT
9654934 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
9654953 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
9654971 ATCGCAA--CGAAA-G-A
1 ATCGCAATGCGAAATGAA
9654985 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
9655004 ATCGCAATGCG
1 ATCGCAATGCG
9655015 TTTATAATTT
Statistics
Matches: 57, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
14 8 0.14
15 1 0.02
16 10 0.18
17 1 0.02
18 9 0.16
19 28 0.49
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Done.