Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 117 of 182
Found at i:37915750 original size:37 final size:37
Alignment explanation
Indices: 37915709--37915779 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
37915699 ACTCTTACGG
*
37915709 CGACAGTTTTGGGTGCAATCTAGAAGTGCTCATGCGA
1 CGACAGTTTTGGGCGCAATCTAGAAGTGCTCATGCGA
*
37915746 CGACAGTTTTGGGCGTAATCTAGAAGTGCTCATG
1 CGACAGTTTTGGGCGCAATCTAGAAGTGCTCATG
37915780 TAGCGAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (37 bp):
CGACAGTTTTGGGCGCAATCTAGAAGTGCTCATGCGA
Found at i:37916844 original size:17 final size:17
Alignment explanation
Indices: 37916824--37916870 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
37916814 AACAATGTAG
37916824 ATGCAGCGACAATAAAA
1 ATGCAGCGACAATAAAA
*
37916841 ATGCAGTGACAATAAAA
1 ATGCAGCGACAATAAAA
* *
37916858 ATGTAGGGACAAT
1 ATGCAGCGACAAT
37916871 TATACTACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.17
Consensus pattern (17 bp):
ATGCAGCGACAATAAAA
Found at i:37919979 original size:37 final size:37
Alignment explanation
Indices: 37919906--37920014 Score: 112
Period size: 37 Copynumber: 2.9 Consensus size: 37
37919896 ATTTATGCAG
* * * * ** *
37919906 CGACAGTCTTAGGTGCATTCTGAAAATATTCCTGCGA
1 CGACAGTTTTGGGTGCAATCTGAAAGTGCTCATGCGA
*
37919943 CGACAGTTTTGGGTGCAATCTGAAAGTGGTCATGCGA
1 CGACAGTTTTGGGTGCAATCTGAAAGTGCTCATGCGA
* *
37919980 AGACAGTTTTGGGCGCAATCT-AGAAGTGCTCATGC
1 CGACAGTTTTGGGTGCAATCTGA-AAGTGCTCATGC
37920015 AGCGACATTA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
36 1 0.02
37 60 0.98
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (37 bp):
CGACAGTTTTGGGTGCAATCTGAAAGTGCTCATGCGA
Found at i:37932403 original size:23 final size:23
Alignment explanation
Indices: 37932324--37932410 Score: 77
Period size: 23 Copynumber: 3.8 Consensus size: 23
37932314 TACGGTTCGC
*
37932324 ACATATAGGGTTCACATGAGTAA
1 ACATATAGGGTTCACATGAATAA
* * ** * *
37932347 ACAAATAGGGTGCGTATGTAT-G
1 ACATATAGGGTTCACATGAATAA
* * *
37932369 ACATGTAAGGTTCGCATGAATAA
1 ACATATAGGGTTCACATGAATAA
37932392 ACATATAGGGTTCACATGA
1 ACATATAGGGTTCACATGA
37932411 CTATACCAAG
Statistics
Matches: 46, Mismatches: 17, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
22 15 0.33
23 31 0.67
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (23 bp):
ACATATAGGGTTCACATGAATAA
Found at i:37933567 original size:17 final size:18
Alignment explanation
Indices: 37933512--37933576 Score: 96
Period size: 18 Copynumber: 3.7 Consensus size: 18
37933502 CTCTTGCGAT
37933512 CCAGTATGCTCAAACGAG
1 CCAGTATGCTCAAACGAG
* *
37933530 CCAGTATGTTCAAATGAG
1 CCAGTATGCTCAAACGAG
*
37933548 CCAGTGTGCTC-AACGAG
1 CCAGTATGCTCAAACGAG
37933565 CCAGTATGCTCA
1 CCAGTATGCTCA
37933577 TCCTTCTGCG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
17 15 0.38
18 25 0.62
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (18 bp):
CCAGTATGCTCAAACGAG
Found at i:37934778 original size:14 final size:14
Alignment explanation
Indices: 37934759--37934804 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
37934749 AGAGTTTGCC
*
37934759 TATAGGGGTTCATA
1 TATAGGGGTTCACA
37934773 TATAGGGGTTCACA
1 TATAGGGGTTCACA
* *
37934787 TATAAGGGTCCACA
1 TATAGGGGTTCACA
37934801 TATA
1 TATA
37934805 AAGTGGTCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (14 bp):
TATAGGGGTTCACA
Found at i:37939094 original size:19 final size:19
Alignment explanation
Indices: 37939063--37939105 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
37939053 TGGTAAATAG
37939063 TTAA-TTAAATTAT-TTAAT
1 TTAATTTAAATTATATT-AT
*
37939081 TTAATTTAATTTATATTAT
1 TTAATTTAAATTATATTAT
37939100 TTAATT
1 TTAATT
37939106 ATATTGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 16 0.73
20 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAATTTAAATTATATTAT
Found at i:37939101 original size:14 final size:13
Alignment explanation
Indices: 37939063--37939110 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
37939053 TGGTAAATAG
*
37939063 TTAATTAAATTAT
1 TTAATTATATTAT
37939076 TTAATT-TA--AT
1 TTAATTATATTAT
37939086 TTAATTTATATTAT
1 TTAA-TTATATTAT
37939100 TTAATTATATT
1 TTAATTATATT
37939111 GTATTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
10 6 0.20
11 2 0.07
12 3 0.10
13 13 0.43
14 6 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTAATTATATTAT
Found at i:37941394 original size:44 final size:47
Alignment explanation
Indices: 37941313--37941403 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 47
37941303 AAAATCCATC
37941313 TATAACCATTATTGAGGAGAGAGGAAACATGAGATGAAAA-TTAAAA
1 TATAACCATTATTGAGGAGAGAGGAAACATGAGATGAAAATTTAAAA
* *
37941359 TATAACTATTATTGAGGAGAGA-G-AGCATGAGATGAAAATTTAAAA
1 TATAACCATTATTGAGGAGAGAGGAAACATGAGATGAAAATTTAAAA
37941404 AAAAAAAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
44 14 0.33
45 7 0.17
46 21 0.50
ACGTcount: A:0.48, C:0.05, G:0.22, T:0.24
Consensus pattern (47 bp):
TATAACCATTATTGAGGAGAGAGGAAACATGAGATGAAAATTTAAAA
Found at i:37943125 original size:10 final size:9
Alignment explanation
Indices: 37943096--37943146 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
37943086 GACATGTGAA
37943096 AAAAATTAT
1 AAAAATTAT
37943105 AAAAA-TAT
1 AAAAATTAT
37943113 AAAAATTATT
1 AAAAATTA-T
**
37943123 AAATTTTAAT
1 AAAAATT-AT
*
37943133 AAAAAATAT
1 AAAAATTAT
37943142 AAAAA
1 AAAAA
37943147 ATTAGAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
8 8 0.24
9 14 0.41
10 11 0.32
11 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:37943165 original size:29 final size:30
Alignment explanation
Indices: 37943105--37943176 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
37943095 AAAAAATTAT
* ** *
37943105 AAAAATAT-AAAAATTATTAAATTTTAATA
1 AAAAATATAAAAAATTATGAAATTAGAAAA
37943134 AAAAATATAAAAAATTA-GAAATTAGAAAA
1 AAAAATATAAAAAATTATGAAATTAGAAAA
37943163 AAAAAGTTATAAAA
1 AAAAA--TATAAAA
37943177 TGCATAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 21 0.58
30 8 0.22
31 7 0.19
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (30 bp):
AAAAATATAAAAAATTATGAAATTAGAAAA
Found at i:37943454 original size:29 final size:29
Alignment explanation
Indices: 37943400--37943478 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
37943390 TCTTTATATT
* * * *
37943400 TTTTATAATTTTCTTACGACTTTATA-AAA
1 TTTTATAATTTT-TTTCTAATTTCTATAAA
*
37943429 TTTTAT-A-TTTTTTCTATATTTCTATATA
1 TTTTATAATTTTTTTCTA-ATTTCTATAAA
37943457 TTTTATAATTTTTTTCTAATTT
1 TTTTATAATTTTTTTCTAATTT
37943479 TAGATATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
26 4 0.10
27 8 0.20
28 9 0.22
29 11 0.27
30 9 0.22
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.63
Consensus pattern (29 bp):
TTTTATAATTTTTTTCTAATTTCTATAAA
Found at i:37943467 original size:8 final size:9
Alignment explanation
Indices: 37943428--37943497 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
37943418 ACTTTATAAA
37943428 ATTTTATAT
1 ATTTTATAT
* *
37943437 TTTTTCTAT
1 ATTTTATAT
37943446 ATTTCTATAT
1 ATTT-TATAT
37943456 ATTTTATA-
1 ATTTTATAT
* *
37943464 ATTTTTTTCT
1 A-TTTTATAT
*
37943474 AATTTTAGAT
1 -ATTTTATAT
*
37943484 ATTTTTTAT
1 ATTTTATAT
37943493 ATTTT
1 ATTTT
37943498 TATTAAAATT
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
8 1 0.02
9 31 0.67
10 13 0.28
11 1 0.02
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (9 bp):
ATTTTATAT
Found at i:37943470 original size:30 final size:28
Alignment explanation
Indices: 37943428--37943498 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
37943418 ACTTTATAAA
*
37943428 ATTTTAT-A-TTTTTTCTATATTTCTATAT
1 ATTTTATAATTTTTTTCTA-ATTT-TAGAT
37943456 ATTTTATAATTTTTTTCTAATTTTAGAT
1 ATTTTATAATTTTTTTCTAATTTTAGAT
*
37943484 ATTTTTTATATTTTT
1 ATTTTATA-ATTTTT
37943499 ATTAAAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
28 18 0.47
29 11 0.29
30 9 0.24
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.69
Consensus pattern (28 bp):
ATTTTATAATTTTTTTCTAATTTTAGAT
Found at i:37943498 original size:19 final size:18
Alignment explanation
Indices: 37943429--37943499 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 18
37943419 CTTTATAAAA
*
37943429 TTTTATATTTTTTCTATATT
1 TTTTATA-TTTTT-AATATT
*
37943449 TCTATATATTTTATAAT-TT
1 T-TTTATATTTT-TAATATT
* *
37943468 TTTTCTAATTTTAGATATT
1 TTTTATATTTTTA-ATATT
37943487 TTTTATATTTTTA
1 TTTTATATTTTTA
37943500 TTAAAATTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
17 2 0.05
18 9 0.22
19 16 0.40
20 7 0.17
21 6 0.15
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.69
Consensus pattern (18 bp):
TTTTATATTTTTAATATT
Found at i:37943508 original size:30 final size:29
Alignment explanation
Indices: 37943452--37943530 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
37943442 CTATATTTCT
* * *
37943452 ATATATTTTATAATTTTT-TTCTAATTTTA
1 ATATTTTTTATAATTTTTATT-AAAATTTA
37943481 GATATTTTTTAT-ATTTTTATTAAAATTTA
1 -ATATTTTTTATAATTTTTATTAAAATTTA
* *
37943510 ATAGTTTTTATAAATTTTATT
1 ATATTTTTTATAATTTTTATT
37943531 GATTTTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
28 10 0.24
29 20 0.48
30 12 0.29
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (29 bp):
ATATTTTTTATAATTTTTATTAAAATTTA
Found at i:37947847 original size:23 final size:22
Alignment explanation
Indices: 37947821--37947864 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
37947811 AAAATATTTC
*
37947821 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
37947844 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
37947865 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:37951907 original size:14 final size:16
Alignment explanation
Indices: 37951888--37951919 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
37951878 GAAGTGAATA
37951888 TTGCAAA-TA-ATTTT
1 TTGCAAATTATATTTT
37951902 TTGCAAATTATATTTT
1 TTGCAAATTATATTTT
37951918 TT
1 TT
37951920 TATTGAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (16 bp):
TTGCAAATTATATTTT
Found at i:37953904 original size:18 final size:18
Alignment explanation
Indices: 37953880--37953936 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
37953870 AATTTATATG
*
37953880 AAAATCCCTAAAGGATTT
1 AAAATCCCAAAAGGATTT
* *
37953898 TAAAT-CCAAGAAAGATTT
1 AAAATCCCAA-AAGGATTT
*
37953916 AAAATCCCAAAAGGATAT
1 AAAATCCCAAAAGGATTT
37953934 AAA
1 AAA
37953937 GTTTCTCGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
17 3 0.10
18 24 0.77
19 4 0.13
ACGTcount: A:0.53, C:0.14, G:0.11, T:0.23
Consensus pattern (18 bp):
AAAATCCCAAAAGGATTT
Found at i:37956671 original size:19 final size:18
Alignment explanation
Indices: 37956647--37956684 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
37956637 GGGTAGTTGA
*
37956647 AGTTTAGTTATATTTATTT
1 AGTTTAGTTAGATTT-TTT
37956666 AGTTTAGTTAGATTTTTT
1 AGTTTAGTTAGATTTTTT
37956684 A
1 A
37956685 CACAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (18 bp):
AGTTTAGTTAGATTTTTT
Found at i:37962234 original size:98 final size:98
Alignment explanation
Indices: 37962129--37962326 Score: 378
Period size: 98 Copynumber: 2.0 Consensus size: 98
37962119 ACTGGCCAAG
* *
37962129 TTTTTTTTTCCTCCCTCAAGATTACCCTACCTCTGTTGCTTATATCTGAATCAGAGAGAGATAGA
1 TTTTTTTTGCCTCCCTCAAGATTACCCTACCTCTGTTGCTTATATCCGAATCAGAGAGAGATAGA
37962194 TTCAAATTCCTTTCTTCACTCGAAACAACTTTC
66 TTCAAATTCCTTTCTTCACTCGAAACAACTTTC
37962227 TTTTTTTTGCCTCCCTCAAGATTACCCTACCTCTGTTGCTTATATCCGAATCAGAGAGAGATAGA
1 TTTTTTTTGCCTCCCTCAAGATTACCCTACCTCTGTTGCTTATATCCGAATCAGAGAGAGATAGA
37962292 TTCAAATTCCTTTCTTCACTCGAAACAACTTTC
66 TTCAAATTCCTTTCTTCACTCGAAACAACTTTC
37962325 TT
1 TT
37962327 CCCTCTTTCC
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (98 bp):
TTTTTTTTGCCTCCCTCAAGATTACCCTACCTCTGTTGCTTATATCCGAATCAGAGAGAGATAGA
TTCAAATTCCTTTCTTCACTCGAAACAACTTTC
Found at i:37963754 original size:80 final size:80
Alignment explanation
Indices: 37963621--37963780 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 80
37963611 TCTCTCCTTT
*
37963621 AAATCTAGTCATTTTCACCTCGATTCTATTCCTCATTAAGTAGAAGCCATTTAATGTCTCTATCA
1 AAATCTAGTCATTTTCACCTCGATTATATTCCTCATTAAGTAGAAGCCATTTAATGTCTCTATCA
37963686 CCCTTTATGCATCCC
66 CCCTTTATGCATCCC
37963701 AAATCTAGTCATTTTCACCTCGATTATATTCCTCATTAAGTAGAAGCCATTTAATGTCTCTATCA
1 AAATCTAGTCATTTTCACCTCGATTATATTCCTCATTAAGTAGAAGCCATTTAATGTCTCTATCA
37963766 CCCTTTATGCATCCC
66 CCCTTTATGCATCCC
37963781 TTCCGTTTGA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.38
Consensus pattern (80 bp):
AAATCTAGTCATTTTCACCTCGATTATATTCCTCATTAAGTAGAAGCCATTTAATGTCTCTATCA
CCCTTTATGCATCCC
Found at i:37964014 original size:9 final size:9
Alignment explanation
Indices: 37963990--37964026 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
37963980 GTGTGAATCC
37963990 AAATTAA-T
1 AAATTAATT
37963998 AAATTAATT
1 AAATTAATT
*
37964007 AAACTAATT
1 AAATTAATT
37964016 AAATTAATT
1 AAATTAATT
37964025 AA
1 AA
37964027 CCCAGCTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (9 bp):
AAATTAATT
Found at i:37964730 original size:16 final size:16
Alignment explanation
Indices: 37964709--37964739 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37964699 ATAATGTGAA
*
37964709 AATAAAGTTAAAATGT
1 AATAAAGGTAAAATGT
37964725 AATAAAGGTAAAATG
1 AATAAAGGTAAAATG
37964740 GGATCCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (16 bp):
AATAAAGGTAAAATGT
Found at i:37968764 original size:17 final size:17
Alignment explanation
Indices: 37968738--37968779 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
37968728 TGTTGGACAT
*
37968738 TTCGGAGCTGGAAGAAA
1 TTCGGTGCTGGAAGAAA
37968755 TTCGGTGCTGGAAGAAA
1 TTCGGTGCTGGAAGAAA
37968772 TTCGGTGC
1 TTCGGTGC
37968780 AATGCTTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.26, C:0.14, G:0.36, T:0.24
Consensus pattern (17 bp):
TTCGGTGCTGGAAGAAA
Found at i:37975423 original size:17 final size:17
Alignment explanation
Indices: 37975386--37975425 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
37975376 TAGATGTACC
* *
37975386 GACAATAAAATTGCAGT
1 GACAATAAAAATGCAGG
*
37975403 GACAATAAAAATGTAGG
1 GACAATAAAAATGCAGG
37975420 GACAAT
1 GACAAT
37975426 TATACTACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.20, T:0.20
Consensus pattern (17 bp):
GACAATAAAAATGCAGG
Found at i:37977723 original size:16 final size:16
Alignment explanation
Indices: 37977702--37977732 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37977692 ATAATGTGAA
37977702 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
37977718 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
37977733 GGATCTACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:37980147 original size:33 final size:34
Alignment explanation
Indices: 37980105--37980169 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 34
37980095 ATTATCCTAG
37980105 TGAACTTATCT-TCATTCTAT-CTTACTGTCCTTA
1 TGAACTTATCTCT-ATTCTATGCTTACTGTCCTTA
*
37980138 TGAACTTATCTCTATTCTATGTTTACTGTCCT
1 TGAACTTATCTCTATTCTATGCTTACTGTCCT
37980170 AACGTAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 18 0.62
34 11 0.38
ACGTcount: A:0.20, C:0.23, G:0.08, T:0.49
Consensus pattern (34 bp):
TGAACTTATCTCTATTCTATGCTTACTGTCCTTA
Found at i:37986370 original size:26 final size:26
Alignment explanation
Indices: 37986318--37986371 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
37986308 GTATTAATAC
*
37986318 AATTTTTGGAGATTACAAAAATAAAG
1 AATTTTTGGAGATTACAAAAACAAAG
* *
37986344 AATTTTTGGAGATTACAAAGACGAAG
1 AATTTTTGGAGATTACAAAAACAAAG
37986370 AA
1 AA
37986372 AATGTGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.28
Consensus pattern (26 bp):
AATTTTTGGAGATTACAAAAACAAAG
Found at i:37989758 original size:31 final size:31
Alignment explanation
Indices: 37989722--37989786 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
37989712 CTACTTACTT
37989722 CATTCATTTCTCAATTTTCCCAAATAATTAA
1 CATTCATTTCTCAATTTTCCCAAATAATTAA
*
37989753 CATTCATTTCTCAATTTTCCCAAATCATTAA
1 CATTCATTTCTCAATTTTCCCAAATAATTAA
37989784 CAT
1 CAT
37989787 ACTTTAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.25, G:0.00, T:0.42
Consensus pattern (31 bp):
CATTCATTTCTCAATTTTCCCAAATAATTAA
Found at i:37991574 original size:18 final size:18
Alignment explanation
Indices: 37991551--37991633 Score: 96
Period size: 18 Copynumber: 4.7 Consensus size: 18
37991541 CTCTTGCTAT
*
37991551 CCAGTATCCTCAAACGAG
1 CCAGTATGCTCAAACGAG
* *
37991569 CCAGTATGTTCAAATGAG
1 CCAGTATGCTCAAACGAG
* *
37991587 CCAGTGTGCTCAAATGAG
1 CCAGTATGCTCAAACGAG
*
37991605 CCAATATGCTC-AACGAG
1 CCAGTATGCTCAAACGAG
*
37991622 CCAGCATGCTCA
1 CCAGTATGCTCA
37991634 TCCTTTTGTG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
17 14 0.26
18 40 0.74
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (18 bp):
CCAGTATGCTCAAACGAG
Found at i:37992837 original size:28 final size:28
Alignment explanation
Indices: 37992763--37992869 Score: 101
Period size: 28 Copynumber: 3.8 Consensus size: 28
37992753 ACAATTCGCA
* *
37992763 TATAGGGGATCACATAC-AGGTGTTTGCC
1 TATAAGGGTTCACATACAAGG-GTTTGCC
* *
37992791 TATAAGGGGTTCGCATACAAGGGTTTTCC
1 TATAA-GGGTTCACATACAAGGGTTTGCC
* * *
37992820 TATAAGGGTTCATATACATA-GGTTCGCA
1 TATAAGGGTTCACATACA-AGGGTTTGCC
*
37992848 TATAAGGGTTCACATATAAGGG
1 TATAAGGGTTCACATACAAGGG
37992870 GTCGTACACG
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
27 1 0.02
28 38 0.59
29 22 0.34
30 3 0.05
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (28 bp):
TATAAGGGTTCACATACAAGGGTTTGCC
Found at i:37992857 original size:14 final size:14
Alignment explanation
Indices: 37992791--37992869 Score: 63
Period size: 14 Copynumber: 5.6 Consensus size: 14
37992781 GGTGTTTGCC
37992791 TATAAGGGGTTCGCA
1 TATAA-GGGTTCGCA
* ** *
37992806 TACAAGGGTTTTCC
1 TATAAGGGTTCGCA
37992820 TATAAGGGTT--CA
1 TATAAGGGTTCGCA
*
37992832 TATACATAGGTTCGCA
1 TATA-A-GGGTTCGCA
*
37992848 TATAAGGGTTCACA
1 TATAAGGGTTCGCA
37992862 TATAAGGG
1 TATAAGGG
37992870 GTCGTACACG
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
12 5 0.10
13 1 0.02
14 34 0.67
15 5 0.10
16 6 0.12
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (14 bp):
TATAAGGGTTCGCA
Found at i:37999727 original size:5 final size:5
Alignment explanation
Indices: 37999719--37999755 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
37999709 TAATTAAATT
37999719 ATTTA ATTTA ATTTA ATTTA ATTT- ATATT- ATTTA ATT
1 ATTTA ATTTA ATTTA ATTTA ATTTA AT-TTA ATTTA ATT
37999756 ATATTGTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTTA
Found at i:37999739 original size:15 final size:14
Alignment explanation
Indices: 37999716--37999760 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
37999706 AGTTAATTAA
37999716 ATTATTTAATTTA-
1 ATTATTTAATTTAT
37999729 ATTTAATTTAATTTAT
1 A-TT-ATTTAATTTAT
37999745 ATTATTTAA-TTAT
1 ATTATTTAATTTAT
37999758 ATT
1 ATT
37999761 GTGCATTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.28
14 8 0.28
15 12 0.41
16 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTTAATTTAT
Found at i:38002992 original size:37 final size:36
Alignment explanation
Indices: 38002908--38003002 Score: 97
Period size: 37 Copynumber: 2.6 Consensus size: 36
38002898 CGACATGTGA
* *
38002908 AAAAAATAT-AAAAATATAAAAATTATTAAATTATT
1 AAAAAATATAAAAAATATAAAAAATATGAAATTATT
***
38002943 AAATTTTAATAAAAAATATAAAAAATATGAAATT-TT
1 AAAAAAT-ATAAAAAATATAAAAAATATGAAATTATT
38002979 ACTAAAAATATAAAAAAT-TAAAAA
1 A--AAAAATATAAAAAATATAAAAA
38003003 TTACAAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
35 4 0.08
36 11 0.23
37 30 0.62
38 3 0.06
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (36 bp):
AAAAAATATAAAAAATATAAAAAATATGAAATTATT
Found at i:38003004 original size:28 final size:29
Alignment explanation
Indices: 38002943--38003001 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
38002933 TTAAATTATT
*
38002943 AAATTTTAATAAAAAATATAAAAAATATG
1 AAATTTTAATAAAAAATATAAAAAATATA
*
38002972 AAATTTTACT-AAAAATATAAAAAAT-TA
1 AAATTTTAATAAAAAATATAAAAAATATA
38002999 AAA
1 AAA
38003002 ATTACAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 4 0.14
28 15 0.54
29 9 0.32
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (29 bp):
AAATTTTAATAAAAAATATAAAAAATATA
Found at i:38003032 original size:20 final size:19
Alignment explanation
Indices: 38002988--38003035 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
38002978 TACTAAAAAT
38002988 ATAAAAAATTAAAAATTAC
1 ATAAAAAATTAAAAATTAC
* *
38003007 AAAAAAAAGTTATAAAA-TGC
1 ATAAAAAA-TTA-AAAATTAC
38003027 ATAAAAAAT
1 ATAAAAAAT
38003036 ACATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 8 0.33
20 12 0.50
21 4 0.17
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (19 bp):
ATAAAAAATTAAAAATTAC
Found at i:38003231 original size:19 final size:20
Alignment explanation
Indices: 38003208--38003279 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 20
38003198 AGCACGATAA
38003208 TTTTTATAATTTTTTACGA-
1 TTTTTATAATTTTTTACGAC
* * * *
38003227 TTTTTGTAATTCTTTA-TAT
1 TTTTTATAATTTTTTACGAC
38003246 TTTTTATAATTTTCTTACGAC
1 TTTTTATAATTTT-TTACGAC
* *
38003267 TTTATAAAATTTT
1 TTTTTATAATTTT
38003280 ATATTTTTCT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
18 1 0.02
19 25 0.61
20 3 0.07
21 12 0.29
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTTTATAATTTTTTACGAC
Found at i:38003281 original size:38 final size:38
Alignment explanation
Indices: 38003208--38003297 Score: 105
Period size: 38 Copynumber: 2.4 Consensus size: 38
38003198 AGCACGATAA
* * *
38003208 TTTTTATAATTTTTTACGATTTTTGTAATTCTTTATAT
1 TTTTTATAATTTTTTACGATTTATGAAAATCTTTATAT
38003246 TTTTTATAATTTTCTTACGACTTTAT-AAAAT-TTTATAT
1 TTTTTATAATTTT-TTACGA-TTTATGAAAATCTTTATAT
38003284 TTTTCTAT-ATTTTT
1 TTTT-TATAATTTTT
38003298 ATAATTTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
37 1 0.02
38 29 0.63
39 12 0.26
40 4 0.09
ACGTcount: A:0.26, C:0.07, G:0.03, T:0.64
Consensus pattern (38 bp):
TTTTTATAATTTTTTACGATTTATGAAAATCTTTATAT
Found at i:38003307 original size:28 final size:28
Alignment explanation
Indices: 38003207--38003307 Score: 82
Period size: 28 Copynumber: 3.6 Consensus size: 28
38003197 TAGCACGATA
* *
38003207 ATTTTTATAATTTTTTACGATTTTTGTA-
1 ATTTTTATAATTTTTTA-TATTTTTCTAT
*
38003235 ATTCTTTAT-ATTTTTTATAATTTTCT-T
1 ATT-TTTATAATTTTTTATATTTTTCTAT
** **
38003262 ACGACTTTATAAAATTTTATATTTTTCTAT
1 A--TTTTTATAATTTTTTATATTTTTCTAT
38003292 ATTTTTATAATTTTTT
1 ATTTTTATAATTTTTT
38003308 TTCTAATTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
27 7 0.13
28 27 0.49
29 19 0.35
30 2 0.04
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (28 bp):
ATTTTTATAATTTTTTATATTTTTCTAT
Found at i:38003346 original size:30 final size:30
Alignment explanation
Indices: 38003290--38003368 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
38003280 ATATTTTTCT
* **
38003290 ATATTTTTATAATTTTTTTTCTAATTTTAG
1 ATATTTTTATAATTTTTATTAAAATTTTAG
38003320 ATATTTTCTAT-ATTTTTATTAAAA-TTTA-
1 ATATTTT-TATAATTTTTATTAAAATTTTAG
*
38003348 ATAGTTTTTATAAATTTTATT
1 ATA-TTTTTATAATTTTTATT
38003369 GATTTTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
28 6 0.14
29 16 0.38
30 17 0.40
31 3 0.07
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (30 bp):
ATATTTTTATAATTTTTATTAAAATTTTAG
Found at i:38004435 original size:209 final size:210
Alignment explanation
Indices: 38003824--38004453 Score: 1208
Period size: 210 Copynumber: 3.0 Consensus size: 210
38003814 TTCTTTTCAA
38003824 AAGTTTTGATGCTTGTAGGTATGATATCATTAATTTTCATTTTTAATTATTTTGTTTTTTCCAAT
1 AAGTTTTGATGCTTGTAGGTATGATATCATTAATTTTCATTTTTAATTATTTTGTTTTTTCCAAT
*
38003889 TAGTTTCATAATAATAAAGTAAACAGGATTTGTTATAAAATAATAATAATGATGTAAAGAATACA
66 TAGTTTCATAATAATAAAGTAAACAGGATTTGTTATAAAATAATAATAATGATGTAAAGAACACA
*
38003954 ATAATAATAGGTGAGAATAAGGAGAGAATTTGTATTGTATTCTATATATTTCATACCATTTACAA
131 AGAATAATAGGTGAGAATAAGGAGAGAATTTGTATTGTATTCTATATATTTCATACCATTTACAA
38004019 GTAGCATACTCCACT
196 GTAGCATACTCCACT
*
38004034 AAGTTTTGAGGCTTGTAGGTATGATATCATTAATTTTCATTTTTAATTATTTTGTTTTTTCCAAT
1 AAGTTTTGATGCTTGTAGGTATGATATCATTAATTTTCATTTTTAATTATTTTGTTTTTTCCAAT
38004099 TAGTTTCATAATAATAAAGTAAACAGGATTTGTTATAAAATAATAATAATGATGTAAAGAACACA
66 TAGTTTCATAATAATAAAGTAAACAGGATTTGTTATAAAATAATAATAATGATGTAAAGAACACA
*
38004164 AGAATAATAGGTGAGAATAAGGAGAGAATTTGTATTGTATTCTATATATTTCATATCATTTACAA
131 AGAATAATAGGTGAGAATAAGGAGAGAATTTGTATTGTATTCTATATATTTCATACCATTTACAA
38004229 GTAGCATACTCCACT
196 GTAGCATACTCCACT
38004244 AAGTTTTGATGCTTGTAGGTATGATATCATTAATTTTCATTTTTAATTATTTTG-TTTTTCCAAT
1 AAGTTTTGATGCTTGTAGGTATGATATCATTAATTTTCATTTTTAATTATTTTGTTTTTTCCAAT
38004308 TAGTTTCATAATAATAAAGTAAACAGGATTTGTTATAAAATAATAATAATGATGTAAAGAACACA
66 TAGTTTCATAATAATAAAGTAAACAGGATTTGTTATAAAATAATAATAATGATGTAAAGAACACA
*
38004373 AGAATAATAGGTGAGAATAAGGAGAGAATTTGTATTGCATTCTATATATTTCATACCATTTACAA
131 AGAATAATAGGTGAGAATAAGGAGAGAATTTGTATTGTATTCTATATATTTCATACCATTTACAA
38004438 GTAGCATACTCCACT
196 GTAGCATACTCCACT
38004453 A
1 A
38004454 TATATATAGG
Statistics
Matches: 413, Mismatches: 7, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
209 154 0.37
210 259 0.63
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.40
Consensus pattern (210 bp):
AAGTTTTGATGCTTGTAGGTATGATATCATTAATTTTCATTTTTAATTATTTTGTTTTTTCCAAT
TAGTTTCATAATAATAAAGTAAACAGGATTTGTTATAAAATAATAATAATGATGTAAAGAACACA
AGAATAATAGGTGAGAATAAGGAGAGAATTTGTATTGTATTCTATATATTTCATACCATTTACAA
GTAGCATACTCCACT
Found at i:38004578 original size:17 final size:17
Alignment explanation
Indices: 38004526--38004581 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
38004516 AATATGAAAA
*
38004526 GTTAAGGAAGATGGAAG
1 GTTAAAGAAGATGGAAG
*** * *
38004543 GTTAAAGGTCAAGGGAG
1 GTTAAAGAAGATGGAAG
38004560 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGGAAG
38004577 GTTAA
1 GTTAA
38004582 GAGTCAATAG
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.41, C:0.02, G:0.38, T:0.20
Consensus pattern (17 bp):
GTTAAAGAAGATGGAAG
Found at i:38004767 original size:2 final size:2
Alignment explanation
Indices: 38004760--38004787 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38004750 TCACAACCAA
38004760 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
38004788 GTAGTGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38011619 original size:44 final size:46
Alignment explanation
Indices: 38011538--38011627 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
38011528 AAAATCCATC
* *
38011538 TATAATCATTATTGAGGAGAGAGGAAATATGAGATGAAAATTAAAA
1 TATAACCATTATTGAGGAGAGAGGAAACATGAGATGAAAATTAAAA
38011584 TATAACCATTATTGAGGAGAGA-G-AACATGAGATGAAAATTAAAA
1 TATAACCATTATTGAGGAGAGAGGAAACATGAGATGAAAATTAAAA
38011628 AGAGAGAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 20 0.48
45 1 0.02
46 21 0.50
ACGTcount: A:0.50, C:0.04, G:0.21, T:0.24
Consensus pattern (46 bp):
TATAACCATTATTGAGGAGAGAGGAAACATGAGATGAAAATTAAAA
Found at i:38012210 original size:88 final size:89
Alignment explanation
Indices: 38012085--38012339 Score: 214
Period size: 88 Copynumber: 2.9 Consensus size: 89
38012075 AATTCTCAAT
* * * * * * * *
38012085 TTTTTAAAAAAAAGTAATTAAGTCACTATTTTTTTTTGCACGCATTTCGATGCTTGAATTTTTAA
1 TTTTTCAAAAAAAGTAATTAAGTCACTACTTTATTTTGCAAGCAATTAGATACTTGAATTTTCAA
*
38012150 AATAT-ATCAAAAAG-TTCATCAAAC
66 AAT-TCATCAAAAAGACTC-TCAAAC
* * * * * *
38012174 TTTTTCAAAAAAA-TAATTAAGTCTCTGCTTTATTTTGTAATCAATTAGGTATTTGAATTTTCAA
1 TTTTTCAAAAAAAGTAATTAAGTCACTACTTTATTTTGCAAGCAATTAGATACTTGAATTTTCAA
38012238 AATTCATCAAAAAGACTCTCAAAC
66 AATTCATCAAAAAGACTCTCAAAC
** * * * ** * * *
38012262 TTTTTCAAAAAAAACAATTAAATTCCCAACTTT-TTTTGCACTCAATTATATACTTGAACTGTC-
1 TTTTTCAAAAAAAGTAATT-AAGTCACTACTTTATTTTGCAAGCAATTAGATACTTGAATTTTCA
*
38012325 AAATACATCAAAAAG
65 AAATTCATCAAAAAG
38012340 GTCCTTTGAC
Statistics
Matches: 134, Mismatches: 28, Indels: 9
0.78 0.16 0.05
Matches are distributed among these distances:
87 1 0.01
88 83 0.62
89 41 0.31
90 9 0.07
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (89 bp):
TTTTTCAAAAAAAGTAATTAAGTCACTACTTTATTTTGCAAGCAATTAGATACTTGAATTTTCAA
AATTCATCAAAAAGACTCTCAAAC
Found at i:38012466 original size:19 final size:19
Alignment explanation
Indices: 38012442--38012523 Score: 60
Period size: 19 Copynumber: 4.2 Consensus size: 19
38012432 TAACATGTAG
38012442 AAAAATTATAAAAAAGTAT
1 AAAAATTATAAAAAAGTAT
* ***
38012461 AAAAATTATTAAATTTTAAT
1 AAAAATTATAAAAAAGT-AT
*
38012481 AAAAA-TATAAAAAA-AATT
1 AAAAATTATAAAAAAGTA-T
*
38012499 AAAAATTAGAAAAAAAGTTAT
1 AAAAATTA-TAAAAAAG-TAT
38012520 AAAA
1 AAAA
38012524 TGCATAAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
17 1 0.02
18 6 0.13
19 21 0.45
20 13 0.28
21 5 0.11
22 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (19 bp):
AAAAATTATAAAAAAGTAT
Found at i:38012512 original size:28 final size:28
Alignment explanation
Indices: 38012442--38012523 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 28
38012432 TAACATGTAG
**
38012442 AAAAATTATAAAAAAGTATAAAAATTATT
1 AAAAATTA-AAAAAAGTATAAAAAAAATT
**
38012471 AAATTTTAATAAAAA-TATAAAAAAAATT
1 AAAAATTAA-AAAAAGTATAAAAAAAATT
38012499 AAAAATTAGAAAAAAAGTTATAAAA
1 AAAAATT--AAAAAAAG-TATAAAA
38012524 TGCATAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
28 17 0.40
29 16 0.38
30 2 0.05
31 7 0.17
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (28 bp):
AAAAATTAAAAAAAGTATAAAAAAAATT
Found at i:38012804 original size:21 final size:21
Alignment explanation
Indices: 38012766--38012833 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
38012756 TTTTTACGAC
*
38012766 TTTATAAAATTTTATAT-TTT
1 TTTATATAATTTTATATATTT
*
38012786 TCTATAT-ATTTTATATATTT
1 TTTATATAATTTTATATATTT
* * *
38012806 TTTTTCTAATTTTAGATATTT
1 TTTATATAATTTTATATATTT
38012827 TTTATAT
1 TTTATAT
38012834 TTTATTAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 9 0.24
20 12 0.32
21 17 0.45
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (21 bp):
TTTATATAATTTTATATATTT
Found at i:38013561 original size:70 final size:67
Alignment explanation
Indices: 38013487--38013620 Score: 169
Period size: 70 Copynumber: 2.0 Consensus size: 67
38013477 TCCGAATAAG
* * * *
38013487 AAAAGGCAAAACTACATCGTTTTGATAAATGTTTACCCTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAGGCAAAACTACATCATTTCGATAAATGTTTA-CCTAT-T-AAGTTAAAAGGCAAAACCATT
38013552 ATGTT
63 ATGTT
* * **
38013557 AAAAGGTAAAATTATGTCATTTCGATAAATGTTTACCTATTAAGTTAAAAGGCAAAACCATTAT
1 AAAAGGCAAAACTACATCATTTCGATAAATGTTTACCTATTAAGTTAAAAGGCAAAACCATTAT
38013621 ATTGTTTATG
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
67 22 0.39
68 1 0.02
69 4 0.07
70 29 0.52
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (67 bp):
AAAAGGCAAAACTACATCATTTCGATAAATGTTTACCTATTAAGTTAAAAGGCAAAACCATTATG
TT
Found at i:38015820 original size:19 final size:20
Alignment explanation
Indices: 38015781--38015821 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
38015771 ATATCAAAGT
38015781 GAGAAAAATGATATACTTTAA
1 GAGAAAAATGA-ATACTTTAA
*
38015802 GAGAAAAATG-ATGCTTTAA
1 GAGAAAAATGAATACTTTAA
38015821 G
1 G
38015822 CCTATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
21 10 0.53
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.27
Consensus pattern (20 bp):
GAGAAAAATGAATACTTTAA
Found at i:38015940 original size:2 final size:2
Alignment explanation
Indices: 38015933--38015978 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
38015923 AGTTCGAAAG
38015933 AT AT AT 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
38015975 AT AT
1 AT AT
38015979 TAGTTTATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38017175 original size:29 final size:29
Alignment explanation
Indices: 38017137--38017205 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
38017127 TTTAATAGTT
* * * *
38017137 TATATTTTTATAATTTTTAAAGAGTTAAAT
1 TATAATTTTATAA-TTTTAAAGAATCAAAA
*
38017167 TA-AATTTTATTATTTTAAAGAATCAAAA
1 TATAATTTTATAATTTTAAAGAATCAAAA
38017195 TATAATTTTAT
1 TATAATTTTAT
38017206 CATTACTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 15 0.45
29 16 0.48
30 2 0.06
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (29 bp):
TATAATTTTATAATTTTAAAGAATCAAAA
Found at i:38020247 original size:11 final size:9
Alignment explanation
Indices: 38020231--38020257 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
38020221 AATTTCAATT
38020231 TATATATAA
1 TATATATAA
38020240 TATATATAA
1 TATATATAA
38020249 TATATATAA
1 TATATATAA
38020258 GTTTTGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TATATATAA
Found at i:38025090 original size:18 final size:18
Alignment explanation
Indices: 38025062--38025105 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
38025052 AGTGAAATTT
*
38025062 ATATGAAAATCCCTAAAGG
1 ATAT-AAAATCCCAAAAGG
*
38025081 ATTTAAAATCCCAAAAGG
1 ATATAAAATCCCAAAAGG
38025099 ATATAAA
1 ATATAAA
38025106 GTTTATTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.23
Consensus pattern (18 bp):
ATATAAAATCCCAAAAGG
Found at i:38027328 original size:15 final size:15
Alignment explanation
Indices: 38027308--38027336 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38027298 AAACACACGA
38027308 GATGTTAGATAGAAG
1 GATGTTAGATAGAAG
38027323 GATGTTAGATAGAA
1 GATGTTAGATAGAA
38027337 CAACGTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (15 bp):
GATGTTAGATAGAAG
Found at i:38038537 original size:16 final size:16
Alignment explanation
Indices: 38038516--38038546 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38038506 ATAATGTGAA
38038516 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
38038532 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
38038547 AGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:38039510 original size:37 final size:37
Alignment explanation
Indices: 38039469--38039541 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
38039459 ATATTCCTGC
* * *
38039469 GACGACAGTTTTTGGTGCAATCTGGAAGTGCTCATGT
1 GACGACAGTTTTGGGCGCAATCTAGAAGTGCTCATGT
* *
38039506 GACGATAGTTTTGGGCGTAATCTAGAAGTGCTCATG
1 GACGACAGTTTTGGGCGCAATCTAGAAGTGCTCATG
38039542 CAGTGACATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (37 bp):
GACGACAGTTTTGGGCGCAATCTAGAAGTGCTCATGT
Found at i:38040859 original size:22 final size:22
Alignment explanation
Indices: 38040831--38040875 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
38040821 CTATTTGTGT
*
38040831 TTACTATCTTAGTGAACTTATC
1 TTACTATCCTAGTGAACTTATC
*
38040853 TTACTATCCTAGTGGACTTATC
1 TTACTATCCTAGTGAACTTATC
38040875 T
1 T
38040876 CTGTTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (22 bp):
TTACTATCCTAGTGAACTTATC
Found at i:38047756 original size:3 final size:3
Alignment explanation
Indices: 38047748--38047787 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
38047738 AAGTTTTGAA
38047748 AAT AAT AAT AAT AAT -AT AAT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38047788 GAATGGATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:38048555 original size:13 final size:13
Alignment explanation
Indices: 38048539--38048563 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38048529 AAACCACTAA
38048539 GGAAAATTTTAAT
1 GGAAAATTTTAAT
38048552 GGAAAATTTTAA
1 GGAAAATTTTAA
38048564 AATAATAAAA
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:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (13 bp):
GGAAAATTTTAAT
Found at i:38049421 original size:27 final size:27
Alignment explanation
Indices: 38049391--38049443 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
38049381 GAGTAAACAA
38049391 ATAGGGTGCGCATGTATGACATGTAAT
1 ATAGGGTGCGCATGTATGACATGTAAT
*
38049418 ATAGGGTTCGCATGTATGACATGTAA
1 ATAGGGTGCGCATGTATGACATGTAA
38049444 GGTTCCTGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.30
Consensus pattern (27 bp):
ATAGGGTGCGCATGTATGACATGTAAT
Found at i:38049617 original size:16 final size:16
Alignment explanation
Indices: 38049596--38049634 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
38049586 GTTTGCTCCT
38049596 AGGGTTCTCATTCATA
1 AGGGTTCTCATTCATA
38049612 AGGGTTCTCATTCATA
1 AGGGTTCTCATTCATA
38049628 AGGGTTC
1 AGGGTTC
38049635 ACATACAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (16 bp):
AGGGTTCTCATTCATA
Found at i:38049678 original size:14 final size:14
Alignment explanation
Indices: 38049609--38049786 Score: 140
Period size: 14 Copynumber: 12.5 Consensus size: 14
38049599 GTTCTCATTC
*
38049609 ATAAGGGTTCTCATT
1 ATAAGGGTTCGCA-T
*
38049624 CATAAGGGTTCACAT
1 -ATAAGGGTTCGCAT
* * *
38049639 ACAAGTGTTCGCCT
1 ATAAGGGTTCGCAT
* *
38049653 ATAGGAGGTTCGTAT
1 ATAAG-GGTTCGCAT
38049668 ATAAGGGTTCGCAT
1 ATAAGGGTTCGCAT
* *
38049682 ATAGGGGTTCACAT
1 ATAAGGGTTCGCAT
* ** *
38049696 ATAATGGTTTACTT
1 ATAAGGGTTCGCAT
38049710 ATAAGGGTTCGCAT
1 ATAAGGGTTCGCAT
* *
38049724 ATAGGGGTTCGCTT
1 ATAAGGGTTCGCAT
*
38049738 ATAAGGGTTCGTAT
1 ATAAGGGTTCGCAT
* * *
38049752 ACAGGGGTTCGCCT
1 ATAAGGGTTCGCAT
* *
38049766 ATATGGGTTCACAT
1 ATAAGGGTTCGCAT
38049780 ATAAGGG
1 ATAAGGG
38049787 GGGTTGTACA
Statistics
Matches: 125, Mismatches: 36, Indels: 4
0.76 0.22 0.02
Matches are distributed among these distances:
14 102 0.82
15 11 0.09
16 12 0.10
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (14 bp):
ATAAGGGTTCGCAT
Found at i:38062814 original size:12 final size:12
Alignment explanation
Indices: 38062797--38062826 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
38062787 ATGTCGGAAC
38062797 AATTAATACTGA
1 AATTAATACTGA
38062809 AATTAATACTGA
1 AATTAATACTGA
38062821 AATTAA
1 AATTAA
38062827 GTAAAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (12 bp):
AATTAATACTGA
Found at i:38064466 original size:12 final size:12
Alignment explanation
Indices: 38064434--38064466 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
38064424 AAATTTTCTT
38064434 TCTTTTT-TTTC
1 TCTTTTTCTTTC
*
38064445 TCTTTCTCTTTC
1 TCTTTTTCTTTC
38064457 TCTTTTTCTT
1 TCTTTTTCTT
38064467 ATTACTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTTTTCTTTC
Found at i:38064491 original size:12 final size:12
Alignment explanation
Indices: 38064427--38064492 Score: 51
Period size: 13 Copynumber: 5.2 Consensus size: 12
38064417 TTTATCAAAA
38064427 TTTTCTTTCTTTT
1 TTTTCTTT-TTTT
*
38064440 TTTTCTCTTTCTCT
1 TTTTCT-TTT-TTT
*
38064454 TTCTCTTTTTCTT
1 TTTTCTTTTT-TT
* * *
38064467 ATTACTTTGTTT
1 TTTTCTTTTTTT
38064479 TTTTCTTTTTTT
1 TTTTCTTTTTTT
38064491 TT
1 TT
38064493 CAAATGACTG
Statistics
Matches: 40, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
12 14 0.35
13 17 0.43
14 9 0.22
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.79
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:38067946 original size:23 final size:23
Alignment explanation
Indices: 38067920--38067967 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
38067910 CCTAGATGAG
38067920 TTAACCACCTTTTCAAGTATGCT
1 TTAACCACCTTTTCAAGTATGCT
38067943 TTAACCACCTTTTCAAGTATGCT
1 TTAACCACCTTTTCAAGTATGCT
38067966 TT
1 TT
38067968 TAATTTGTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.42
Consensus pattern (23 bp):
TTAACCACCTTTTCAAGTATGCT
Found at i:38072767 original size:3 final size:3
Alignment explanation
Indices: 38072761--38072786 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
38072751 TGGTAAATTA
38072761 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
38072787 ACCAGCCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:38077989 original size:26 final size:26
Alignment explanation
Indices: 38077960--38078011 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
38077950 GTTACATTTG
38077960 ATCACCGAAGTGATCTTGTAAAGTCT
1 ATCACCGAAGTGATCTTGTAAAGTCT
38077986 ATCACCGAAGTGATCTTGTAAAGTCT
1 ATCACCGAAGTGATCTTGTAAAGTCT
38078012 TTCTTTTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (26 bp):
ATCACCGAAGTGATCTTGTAAAGTCT
Found at i:38079231 original size:22 final size:21
Alignment explanation
Indices: 38079206--38079277 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 21
38079196 AGTAAACAAA
38079206 TAAGGTATGCATGTATAACATG
1 TAAGGT-TGCATGTATAACATG
* * *
38079228 TAAGGTTTGCATGAAAAACATA
1 TAAGG-TTGCATGTATAACATG
*
38079250 TAAGGTTCGAATGTATAACATG
1 TAAGGTT-GCATGTATAACATG
38079272 TAAGGT
1 TAAGGT
38079278 GCACATGAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
21 2 0.05
22 38 0.93
23 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (21 bp):
TAAGGTTGCATGTATAACATG
Found at i:38079254 original size:44 final size:43
Alignment explanation
Indices: 38079186--38079301 Score: 142
Period size: 44 Copynumber: 2.6 Consensus size: 43
38079176 ACACATTTAG
* *
38079186 GGTTTGCATGAGTAAACAAATAAGGTATGCATGTATAACATGTAA
1 GGTTTGCATGA-AAAACATATAAGGT-TGCATGTATAACATGTAA
*
38079231 GGTTTGCATGAAAAACATATAAGGTTCGAATGTATAACATGTAA
1 GGTTTGCATGAAAAACATATAAGGTT-GCATGTATAACATGTAA
***
38079275 GGTGCACATGAATAAACATATAAGGTT
1 GGTTTGCATGAA-AAACATATAAGGTT
38079302 TGCAAATTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
43 1 0.02
44 37 0.59
45 25 0.40
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (43 bp):
GGTTTGCATGAAAAACATATAAGGTTGCATGTATAACATGTAA
Found at i:38079289 original size:22 final size:22
Alignment explanation
Indices: 38079215--38079301 Score: 77
Period size: 22 Copynumber: 3.9 Consensus size: 22
38079205 ATAAGGTATG
* * **
38079215 CATGTATAACATGTAAGGTTTG
1 CATGAATAACATATAAGGTTCA
*
38079237 CATGAAAAACATATAAGGTTCGA
1 CATGAATAACATATAAGGTTC-A
* * *
38079260 -ATGTATAACATGTAAGGTGCA
1 CATGAATAACATATAAGGTTCA
38079281 CATGAATAAACATATAAGGTT
1 CATGAAT-AACATATAAGGTT
38079302 TGCAAATTAA
Statistics
Matches: 50, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
21 1 0.02
22 38 0.76
23 11 0.22
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (22 bp):
CATGAATAACATATAAGGTTCA
Found at i:38079507 original size:14 final size:14
Alignment explanation
Indices: 38079488--38079574 Score: 50
Period size: 14 Copynumber: 6.1 Consensus size: 14
38079478 TCTCATTCAT
38079488 AAGGGTTTGCATAC
1 AAGGGTTTGCATAC
* *
38079502 AAGGGTTTGCCTAT
1 AAGGGTTTGCATAC
* * *
38079516 AGGGGGTT-CATATAT
1 AAGGGTTTGC--ATAC
* * *
38079531 AAGGGTTCGCCTAT
1 AAGGGTTTGCATAC
*
38079545 AAGGGGTTTGTATAC
1 AA-GGGTTTGCATAC
*
38079560 AAGGGTTCGCATAC
1 AAGGGTTTGCATAC
38079574 A
1 A
38079575 GGGGGTCATA
Statistics
Matches: 54, Mismatches: 15, Indels: 8
0.70 0.19 0.10
Matches are distributed among these distances:
13 1 0.02
14 34 0.63
15 18 0.33
16 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (14 bp):
AAGGGTTTGCATAC
Found at i:38079522 original size:29 final size:29
Alignment explanation
Indices: 38079490--38079580 Score: 110
Period size: 29 Copynumber: 3.1 Consensus size: 29
38079480 TCATTCATAA
* *
38079490 GGGTTTGCATACAAGGGTTTGCCTATAGG
1 GGGTTTGTATACAAGGGTTCGCCTATAGG
** * *
38079519 GGGTTCATATATAAGGGTTCGCCTATAAG
1 GGGTTTGTATACAAGGGTTCGCCTATAGG
* *
38079548 GGGTTTGTATACAAGGGTTCGCATACAGG
1 GGGTTTGTATACAAGGGTTCGCCTATAGG
38079577 GGGT
1 GGGT
38079581 CATACACAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (29 bp):
GGGTTTGTATACAAGGGTTCGCCTATAGG
Found at i:38079549 original size:43 final size:43
Alignment explanation
Indices: 38079455--38079554 Score: 107
Period size: 43 Copynumber: 2.3 Consensus size: 43
38079445 ATAACAATTT
* *
38079455 ATATAAGGGTTTGCTCATAGGGTTCTCATTCATAAGGGTTTGC
1 ATATAAGGGTTTGCTCATAGGGGTCTCATTCATAAGGGTTCGC
*
38079498 ATACAAGGGTTTGC-CTATAGGGGGT-TCATAT-ATAAGGGTTCGC
1 ATATAAGGGTTTGCTC-ATA-GGGGTCTCAT-TCATAAGGGTTCGC
*
38079541 CTATAAGGGGTTTG
1 ATATAA-GGGTTTG
38079555 TATACAAGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
42 1 0.02
43 35 0.73
44 12 0.25
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (43 bp):
ATATAAGGGTTTGCTCATAGGGGTCTCATTCATAAGGGTTCGC
Found at i:38081005 original size:16 final size:17
Alignment explanation
Indices: 38080984--38081017 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
38080974 ATGAATAATA
38080984 ATAATTA-ATTAAAAAT
1 ATAATTACATTAAAAAT
38081000 ATAATTACATTAAAAAT
1 ATAATTACATTAAAAAT
38081017 A
1 A
38081018 AACAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATTACATTAAAAAT
Found at i:38084093 original size:18 final size:18
Alignment explanation
Indices: 38084070--38084104 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38084060 AAAAATTTGT
38084070 AAAAATAATTAAAAAATA
1 AAAAATAATTAAAAAATA
**
38084088 AAAAATTGTTAAAAAAT
1 AAAAATAATTAAAAAAT
38084105 TATAAAAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATAATTAAAAAATA
Found at i:38093851 original size:23 final size:25
Alignment explanation
Indices: 38093825--38093900 Score: 75
Period size: 28 Copynumber: 2.9 Consensus size: 25
38093815 GTGTTACAGA
38093825 TAGTTTTTAGTTAAATTAATTATTAGTT
1 TAGTTTTTAGTTAAATTAA--ATTAG-T
38093853 TAGTTTTTAGTTAAATT-AATTA-T
1 TAGTTTTTAGTTAAATTAAATTAGT
* *
38093876 TAGTTTATTTAGTTAATTTCAATTA
1 TAG-TT-TTTAGTTAAATTAAATTA
38093901 CAATTTAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
23 4 0.09
24 2 0.05
25 15 0.34
26 5 0.11
27 1 0.02
28 17 0.39
ACGTcount: A:0.33, C:0.01, G:0.09, T:0.57
Consensus pattern (25 bp):
TAGTTTTTAGTTAAATTAAATTAGT
Found at i:38093852 original size:16 final size:16
Alignment explanation
Indices: 38093831--38093880 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
38093821 CAGATAGTTT
38093831 TTAGTTAAATTAATTA
1 TTAGTTAAATTAATTA
* *
38093847 TTAG-T---TTAGTTT
1 TTAGTTAAATTAATTA
38093859 TTAGTTAAATTAATTA
1 TTAGTTAAATTAATTA
38093875 TTAGTT
1 TTAGTT
38093881 TATTTAGTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
12 9 0.35
13 1 0.04
15 1 0.04
16 15 0.58
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (16 bp):
TTAGTTAAATTAATTA
Found at i:38093865 original size:28 final size:28
Alignment explanation
Indices: 38093825--38093882 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
38093815 GTGTTACAGA
38093825 TAGTTTTTAGTTAAATTAATTATTAGTT
1 TAGTTTTTAGTTAAATTAATTATTAGTT
38093853 TAGTTTTTAGTTAAATTAATTATTAGTT
1 TAGTTTTTAGTTAAATTAATTATTAGTT
38093881 TA
1 TA
38093883 TTTAGTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (28 bp):
TAGTTTTTAGTTAAATTAATTATTAGTT
Found at i:38099707 original size:29 final size:29
Alignment explanation
Indices: 38099674--38099731 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
38099664 AGGATGAAAC
38099674 TTAGGCAAATGATGAACAATGTGGATCTA
1 TTAGGCAAATGATGAACAATGTGGATCTA
38099703 TTAGGCAAATGATGAACAATGTGGATCTA
1 TTAGGCAAATGATGAACAATGTGGATCTA
38099732 AGGACCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (29 bp):
TTAGGCAAATGATGAACAATGTGGATCTA
Found at i:38100308 original size:147 final size:147
Alignment explanation
Indices: 38100070--38100438 Score: 465
Period size: 147 Copynumber: 2.5 Consensus size: 147
38100060 CCTAACATAC
* **
38100070 TAAAATCGAAGAGGAAAAGATTGAAGTCGCAACAATGGATCTTACACCTTAAAATTGAAGAGGGA
1 TAAAATCGAAGAGGGAAAGATTGAAGTCGCAACGGTGGATCTTACACCTTAAAATTGAAGAGGGA
* * * * * *
38100135 TGGGTTGAAGTCGTAATGGCAGACCTAACACCCTAAAATCGAATAAGGAAAGATTGAAGTCGCAA
66 TAGGTTGAAGTCGTAACGACAGACCTAACACCCTAAAATCAAAGAAGGAAAGATTAAAGTCGCAA
38100200 -CAGTGGATC-CTACACCT
131 TCA-TGGATCTC-ACACCT
* * *
38100217 TAAAATCGAATAGGGAAAGATTGAAGTCGCAATGGTGGATCTTACACCTTAAAACTGAAGAGGGA
1 TAAAATCGAAGAGGGAAAGATTGAAGTCGCAACGGTGGATCTTACACCTTAAAATTGAAGAGGGA
* * *
38100282 TAGGTTGAAGTCGTAACGATAGACCTAACACCCTAAAATCAAAGAGGGAAAGATTAAAGTTGCAA
66 TAGGTTGAAGTCGTAACGACAGACCTAACACCCTAAAATCAAAGAAGGAAAGATTAAAGTCGCAA
*
38100347 TTATGGATCTCACACCT
131 TCATGGATCTCACACCT
* * * * * * * *
38100364 TAAAATTGAAGAGGGACAGGTTGAAG-CTGTAACGGCGGACCTAACACCTTAAAATTGAATAGGG
1 TAAAATCGAAGAGGGAAAGATTGAAGTC-GCAACGGTGGATCTTACACCTTAAAATTGAAGAGGG
*
38100428 ATAGGCTGAAG
65 ATAGGTTGAAG
38100439 CTATAATAAC
Statistics
Matches: 191, Mismatches: 28, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
146 1 0.01
147 188 0.98
148 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (147 bp):
TAAAATCGAAGAGGGAAAGATTGAAGTCGCAACGGTGGATCTTACACCTTAAAATTGAAGAGGGA
TAGGTTGAAGTCGTAACGACAGACCTAACACCCTAAAATCAAAGAAGGAAAGATTAAAGTCGCAA
TCATGGATCTCACACCT
Found at i:38100457 original size:147 final size:144
Alignment explanation
Indices: 38100070--38100641 Score: 445
Period size: 147 Copynumber: 3.9 Consensus size: 144
38100060 CCTAACATAC
* * **** * * *
38100070 TAAAATCGAAGAGGAAAAGATTGAAGTCGCAACAATGGATCTTACACCTTAAAATTGAAGAGGGA
1 TAAAATCGAAGAGGGAAAGGTTGAAGT-GCAATGGCGGACCTAACACCTTAAAATTGAATAGGGA
* * * * * * *
38100135 TGGGTTGAAGTCGT-AAT-GGCAGACCTAACACCCTAAAATCGAATAAGGAAAGATTGAAGTCGC
65 TAGGTTGAAG-C-TAAATAAG-A-ATCTAACACCCTAAAACCAAAGAGGGAAAGATTGAAGTCGC
38100198 AA-CAGTGGATC-CTACACCT
126 AATCA-TGGATCTC-ACACCT
* * * * * * *
38100217 TAAAATCGAATAGGGAAAGATTGAAGTCGCAATGGTGGATCTTACACCTTAAAACTGAAGAGGGA
1 TAAAATCGAAGAGGGAAAGGTTGAAGT-GCAATGGCGGACCTAACACCTTAAAATTGAATAGGGA
* * * *
38100282 TAGGTTGAAGTCGTAACGAT-AG-ACCTAACACCCTAAAATCAAAGAGGGAAAGATTAAAGTTGC
65 TAGGTTGAAG-C-TAA--ATAAGAATCTAACACCCTAAAACCAAAGAGGGAAAGATTGAAGTCGC
*
38100345 AATTATGGATCTCACACCT
126 AATCATGGATCTCACACCT
* * * *
38100364 TAAAATTGAAGAGGGACAGGTTGAAGCTGTAACGGCGGACCTAACACCTTAAAATTGAATAGGGA
1 TAAAATCGAAGAGGGAAAGGTTGAAG-TGCAATGGCGGACCTAACACCTTAAAATTGAATAGGGA
* * * * * *
38100429 TAGGCTGAAGCTATAATAACGAATCTAACACTCTAAAACCAAAGAGGTAAAAAATGAAGCCGCAA
65 TAGGTTGAAGCTA-AATAA-GAATCTAACACCCTAAAACCAAAGAGGGAAAGATTGAAGTCGCAA
*** * *
38100494 TGGCGGATCTTACACAT
128 TCATGGATCTCACACCT
* * ** *
38100511 TAAAATCGAAGAGGGATAGGTTGAAGTTGCAATGGCAGACCTAACACCCCAAAATCGAATAGGGA
1 TAAAATCGAAGAGGGAAAGGTTGAAG-TGCAATGGCGGACCTAACACCTTAAAATTGAATAGGGA
* * * * * *
38100576 TAGATTGAAGCCACAATAATAGATCTACCACCCTAAAACCAAAGAGGGAACAAATTGAAGCCGCA
65 TAGGTTGAAGCTA-AATAAGA-ATCTAACACCCTAAAACCAAAGAGGGAA-AGATTGAAGTCGCA
38100641 A
127 A
38100642 CGACGAATCT
Statistics
Matches: 355, Mismatches: 58, Indels: 23
0.81 0.13 0.05
Matches are distributed among these distances:
144 2 0.01
145 3 0.01
146 4 0.01
147 325 0.92
148 18 0.05
150 3 0.01
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (144 bp):
TAAAATCGAAGAGGGAAAGGTTGAAGTGCAATGGCGGACCTAACACCTTAAAATTGAATAGGGAT
AGGTTGAAGCTAAATAAGAATCTAACACCCTAAAACCAAAGAGGGAAAGATTGAAGTCGCAATCA
TGGATCTCACACCT
Found at i:38100536 original size:49 final size:49
Alignment explanation
Indices: 38100070--38100585 Score: 313
Period size: 49 Copynumber: 10.5 Consensus size: 49
38100060 CCTAACATAC
* * **** *
38100070 TAAAATCGAAGAGGAAAAGATTGAAGTCGCAACAATGGATCTTACACCT
1 TAAAATCGAAGAGGGATAGATTGAAGTCGCAATGGCGGATCTAACACCT
* * * * * * *
38100119 TAAAATTGAAGAGGGATGGGTTGAAGTCGTAATGGCAGACCTAACACCC
1 TAAAATCGAAGAGGGATAGATTGAAGTCGCAATGGCGGATCTAACACCT
* * * ** *
38100168 TAAAATCGAATAAGGAAAGATTGAAGTCGCAACAGTGGATCCT-ACACCT
1 TAAAATCGAAGAGGGATAGATTGAAGTCGCAATGGCGGAT-CTAACACCT
* * * *
38100217 TAAAATCGAATAGGGAAAGATTGAAGTCGCAATGGTGGATCTTACACCT
1 TAAAATCGAAGAGGGATAGATTGAAGTCGCAATGGCGGATCTAACACCT
* * * *** * *
38100266 TAAAA-CTGAAGAGGGATAGGTTGAAGTCGTAACGATAGACCTAACACCC
1 TAAAATC-GAAGAGGGATAGATTGAAGTCGCAATGGCGGATCTAACACCT
* * * * *** *
38100315 TAAAATCAAAGAGGGAAAGATTAAAGTTGCAATTATGGATCTCACACCT
1 TAAAATCGAAGAGGGATAGATTGAAGTCGCAATGGCGGATCTAACACCT
* * * * * *
38100364 TAAAATTGAAGAGGGACAGGTTGAAG-CTGTAACGGCGGACCTAACACCT
1 TAAAATCGAAGAGGGATAGATTGAAGTC-GCAATGGCGGATCTAACACCT
* * ** ** ** *
38100413 TAAAATTGAATAGGGATAGGCTGAAG-CTATAATAACGAATCTAACA-CT
1 TAAAATCGAAGAGGGATAGATTGAAGTC-GCAATGGCGGATCTAACACCT
* * * * * * * * *
38100461 CTAAAACCAAAGAGGTAAAAAATGAAGCCGCAATGGCGGATCTTACACAT
1 -TAAAATCGAAGAGGGATAGATTGAAGTCGCAATGGCGGATCTAACACCT
* * * * *
38100511 TAAAATCGAAGAGGGATAGGTTGAAGTTGCAATGGCAGACCTAACACCC
1 TAAAATCGAAGAGGGATAGATTGAAGTCGCAATGGCGGATCTAACACCT
* *
38100560 CAAAATCGAATAGGGATAGATTGAAG
1 TAAAATCGAAGAGGGATAGATTGAAG
38100586 CCACAATAAT
Statistics
Matches: 352, Mismatches: 107, Indels: 16
0.74 0.23 0.03
Matches are distributed among these distances:
48 5 0.01
49 342 0.97
50 5 0.01
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (49 bp):
TAAAATCGAAGAGGGATAGATTGAAGTCGCAATGGCGGATCTAACACCT
Found at i:38100586 original size:98 final size:98
Alignment explanation
Indices: 38100028--38100587 Score: 402
Period size: 98 Copynumber: 5.7 Consensus size: 98
38100018 ACATAGAGTT
* * * ** *
38100028 GAAGAGTGATAGGTTGAAGCTGGAATGACGGACCTAACATACTAAAATCGAAGAGGAAAAGATTG
1 GAAGAGGGATAGGTTGAAGTTGCAATGACGGACCTAACACCCTAAAATCGAAGAGGGAAAGATTG
* ** *
38100093 AAGTCGCAACAATGGATCTTACACCTTAAAATT
66 AAGCCGCAACGGTGGATCTTACACCTTAAAATC
* * * * * * *
38100126 GAAGAGGGATGGGTTGAAGTCGTAATGGCAGACCTAACACCCTAAAATCGAATAAGGAAAGATTG
1 GAAGAGGGATAGGTTGAAGTTGCAATGACGGACCTAACACCCTAAAATCGAAGAGGGAAAGATTG
* * *
38100191 AAGTCGCAACAGTGGATCCTACACCTTAAAATC
66 AAGCCGCAACGGTGGATCTTACACCTTAAAATC
* * * * ** * * * * *
38100224 GAATAGGGAAAGATTGAAGTCGCAATGGTGGATCTTACACCTTAAAA-CTGAAGAGGGATAGGTT
1 GAAGAGGGATAGGTTGAAGTTGCAATGACGGACCTAACACCCTAAAATC-GAAGAGGGAAAGATT
* * * * * * *
38100288 GAAGTCGTAACGATAGACCTAACACCCTAAAATC
65 GAAGCCGCAACGGTGGATCTTACACCTTAAAATC
* * * * * * * * * * * *
38100322 AAAGAGGGAAAGATTAAAGTTGCAATTATGGATCTCACACCTTAAAATTGAAGAGGGACAGGTTG
1 GAAGAGGGATAGGTTGAAGTTGCAATGACGGACCTAACACCCTAAAATCGAAGAGGGAAAGATTG
* * * * * *
38100387 AAGCTGTAACGGCGGACCTAACACCTTAAAATT
66 AAGCCGCAACGGTGGATCTTACACCTTAAAATC
* * * ** * * * * * * * * *
38100420 GAATAGGGATAGGCTGAAGCTATAATAACGAATCTAACACTCTAAAACCAAAGAGGTAAAAAATG
1 GAAGAGGGATAGGTTGAAGTTGCAATGACGGACCTAACACCCTAAAATCGAAGAGGGAAAGATTG
* * *
38100485 AAGCCGCAATGGCGGATCTTACACATTAAAATC
66 AAGCCGCAACGGTGGATCTTACACCTTAAAATC
* * * * *
38100518 GAAGAGGGATAGGTTGAAGTTGCAATGGCAGACCTAACACCCCAAAATCGAATAGGGATAGATTG
1 GAAGAGGGATAGGTTGAAGTTGCAATGACGGACCTAACACCCTAAAATCGAAGAGGGAAAGATTG
38100583 AAGCC
66 AAGCC
38100588 ACAATAATAG
Statistics
Matches: 358, Mismatches: 102, Indels: 4
0.77 0.22 0.01
Matches are distributed among these distances:
97 1 0.00
98 357 1.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.20
Consensus pattern (98 bp):
GAAGAGGGATAGGTTGAAGTTGCAATGACGGACCTAACACCCTAAAATCGAAGAGGGAAAGATTG
AAGCCGCAACGGTGGATCTTACACCTTAAAATC
Found at i:38102014 original size:31 final size:28
Alignment explanation
Indices: 38101950--38102036 Score: 86
Period size: 27 Copynumber: 3.0 Consensus size: 28
38101940 CCCCTTTATA
* *
38101950 TTTTATTTATTTATTTATTTTTCAAGA-
1 TTTTATTTATTTATTTATTTTGCATGAT
38101977 TTTTATTTATTTATTTATTTTGCATGAT
1 TTTTATTTATTTATTTATTTTGCATGAT
* * * *
38102005 CTTCATTATTTTTTTGTTTAATTGGCATGAT
1 -TT--TTATTTATTTATTTATTTTGCATGAT
38102036 T
1 T
38102037 GTAAAATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
27 25 0.50
29 2 0.04
30 1 0.02
31 22 0.44
ACGTcount: A:0.22, C:0.06, G:0.08, T:0.64
Consensus pattern (28 bp):
TTTTATTTATTTATTTATTTTGCATGAT
Found at i:38102105 original size:23 final size:23
Alignment explanation
Indices: 38102078--38102123 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
38102068 ATTTTAATTA
38102078 TTTATTC-TAT-TTATTATATATTT
1 TTTATTCATATATT-TTAT-TATTT
38102101 TTTATTCATATATTTTATTATTT
1 TTTATTCATATATTTTATTATTT
38102124 ACGTATTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 12 0.57
24 7 0.33
25 2 0.10
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTATTCATATATTTTATTATTT
Found at i:38102113 original size:15 final size:14
Alignment explanation
Indices: 38102087--38102122 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
38102077 ATTTATTCTA
38102087 TTTATTATATATTT
1 TTTATTATATATTT
38102101 TTTATTCATATATTT
1 TTTATT-ATATATTT
38102116 TATTATT
1 T-TTATT
38102123 TACGTATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 9 0.45
16 5 0.25
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTATTATATATTT
Found at i:38104858 original size:13 final size:13
Alignment explanation
Indices: 38104840--38104874 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
38104830 TAAAGTGGTG
38104840 TAAGCCAAGGCCT
1 TAAGCCAAGGCCT
38104853 TAAGCCAAGGCCT
1 TAAGCCAAGGCCT
38104866 TAAGCCAAG
1 TAAGCCAAG
38104875 TAGTGCCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.34, C:0.29, G:0.23, T:0.14
Consensus pattern (13 bp):
TAAGCCAAGGCCT
Found at i:38106181 original size:13 final size:13
Alignment explanation
Indices: 38106162--38106227 Score: 69
Period size: 13 Copynumber: 5.0 Consensus size: 13
38106152 TTAAACCAAG
38106162 CTTTTCAAAAGTA
1 CTTTTCAAAAGTA
* *
38106175 ATTTTCAAAAATCA
1 CTTTTCAAAAGT-A
* *
38106189 CTTTTCCAAAGCA
1 CTTTTCAAAAGTA
*
38106202 CTTTTTAAAAGTA
1 CTTTTCAAAAGTA
*
38106215 CTTCTCAAAAGTA
1 CTTTTCAAAAGTA
38106228 ATGTTAAATT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
13 32 0.78
14 9 0.22
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (13 bp):
CTTTTCAAAAGTA
Found at i:38106552 original size:21 final size:20
Alignment explanation
Indices: 38106528--38106580 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
38106518 TTTTAAATCA
38106528 TATTATATT-TTTAATTTTAAG
1 TATTA-ATTATTT-ATTTTAAG
*
38106549 TATTAATTATTTATTTTATAT
1 TATTAATTATTTATTTTA-AG
38106570 TATTAAATTAT
1 TATT-AATTAT
38106581 CAAAGGGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 9 0.32
21 13 0.46
22 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTAATTATTTATTTTAAG
Found at i:38110590 original size:29 final size:31
Alignment explanation
Indices: 38110524--38110594 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 31
38110514 TTTAATAATT
* *
38110524 TATATTTTTATAATTTTTAAAACAGTTAAAT
1 TATAATTTTATAATTTTTAAAACAGTTAAAA
*
38110555 TAAAATTTTATAA-TTTTAAAA-AGTTAAAA
1 TATAATTTTATAATTTTTAAAACAGTTAAAA
38110584 TATAATTTTAT
1 TATAATTTTAT
38110595 TTTTATTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 17 0.47
30 8 0.22
31 11 0.31
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (31 bp):
TATAATTTTATAATTTTTAAAACAGTTAAAA
Found at i:38111128 original size:86 final size:86
Alignment explanation
Indices: 38110965--38111128 Score: 258
Period size: 86 Copynumber: 1.9 Consensus size: 86
38110955 AAAAGTTATA
* * **
38110965 AAAAAATCTAAAGCATTTGTCACTTTGTATGTCTTTTCCCCAACATAACTCCCAGAGTATTTAGT
1 AAAAAATCTAAAGCATTTGTCACTTTGTATGTCTTTTCCCCAACATAACTCCCAAAATATTTAAC
*
38111030 CATTTGACAAAAAAATCTAAT
66 CATTCGACAAAAAAATCTAAT
* *
38111051 AAAAAATCTAAAGCATTTGTCATTTTGTATGTCTTTTCCCCCACATAACTCCCAAAATATTTAAC
1 AAAAAATCTAAAGCATTTGTCACTTTGTATGTCTTTTCCCCAACATAACTCCCAAAATATTTAAC
38111116 CA-TCGACAAAAAA
66 CATTCGACAAAAAA
38111129 TCGGGTTTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
85 10 0.14
86 61 0.86
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.32
Consensus pattern (86 bp):
AAAAAATCTAAAGCATTTGTCACTTTGTATGTCTTTTCCCCAACATAACTCCCAAAATATTTAAC
CATTCGACAAAAAAATCTAAT
Found at i:38111672 original size:59 final size:57
Alignment explanation
Indices: 38111590--38111756 Score: 198
Period size: 56 Copynumber: 2.9 Consensus size: 57
38111580 GCTAACACCT
* * *
38111590 CTTTATCAAATAAAAAA-ATATTTTTTGGGTGTCTGTCAAGCCATGATCGACACT-C
1 CTTTATCAGATAAAAAATATATTTTTTGGGTGTCTGCCAAGCCATGACCGACACTCC
* *
38111645 CTTTTTCAGATACAGAAAAATATATTTTTTGGGT-TCGGCCAAGCCATGACCGACACTCC
1 CTTTATCAGAT--A-AAAAATATATTTTTTGGGTGTCTGCCAAGCCATGACCGACACTCC
* * * *
38111704 CTTTATCTGATAAAAAATAT-TTTTTTTGGTGTCTGCCAAGCAATGGCCGACAC
1 CTTTATCAGATAAAAAATATATTTTTTGGGTGTCTGCCAAGCCATGACCGACAC
38111757 CAACTTTTCC
Statistics
Matches: 95, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
55 18 0.19
56 27 0.28
57 2 0.02
58 25 0.26
59 23 0.24
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (57 bp):
CTTTATCAGATAAAAAATATATTTTTTGGGTGTCTGCCAAGCCATGACCGACACTCC
Found at i:38112260 original size:21 final size:21
Alignment explanation
Indices: 38112236--38112280 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38112226 TCCTTGAGGG
38112236 TGGCCAAGAATTTCATGAAGT
1 TGGCCAAGAATTTCATGAAGT
* * *
38112257 TGGCCAGGAATTTCTTGATGT
1 TGGCCAAGAATTTCATGAAGT
38112278 TGG
1 TGG
38112281 TCTCGTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.33
Consensus pattern (21 bp):
TGGCCAAGAATTTCATGAAGT
Found at i:38115642 original size:29 final size:31
Alignment explanation
Indices: 38115576--38115646 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 31
38115566 TTTAATAATT
* *
38115576 TATATTTTTATAATTTTTAAAACAGTTAAAT
1 TATAATTTTATAATTTTTAAAACAGTTAAAA
*
38115607 TAAAATTTTATAA-TTTTAAAA-AGTTAAAA
1 TATAATTTTATAATTTTTAAAACAGTTAAAA
38115636 TATAATTTTAT
1 TATAATTTTAT
38115647 TTTTATTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 17 0.47
30 8 0.22
31 11 0.31
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (31 bp):
TATAATTTTATAATTTTTAAAACAGTTAAAA
Found at i:38116158 original size:86 final size:85
Alignment explanation
Indices: 38116014--38116175 Score: 270
Period size: 86 Copynumber: 1.9 Consensus size: 85
38116004 AAAAAGTTAT
*
38116014 AAAAAAATCTTAAAAAAATCTAAAGCATTTGTCACTTTGTATGTCTTTTCCCCAACATAACTCCC
1 AAAAAAATCTAAAAAAAATCTAAAGCATTTGTCACTTTGTATGTCTTTTCCCCAACATAACTCCC
* *
38116079 AGAGTATTTAATCATTTGAC
66 AAAATATTTAATCATTTGAC
* *
38116099 AAAAAAATCTAATAAAAAATCTAAAGCATTTGTCATTTTGTATGTCTTTTCCCCCACATAACTCC
1 AAAAAAATCTAA-AAAAAATCTAAAGCATTTGTCACTTTGTATGTCTTTTCCCCAACATAACTCC
38116164 CAAAATATTTAA
65 CAAAATATTTAA
38116176 CATCCAAAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
85 11 0.15
86 60 0.85
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.34
Consensus pattern (85 bp):
AAAAAAATCTAAAAAAAATCTAAAGCATTTGTCACTTTGTATGTCTTTTCCCCAACATAACTCCC
AAAATATTTAATCATTTGAC
Found at i:38118506 original size:13 final size:13
Alignment explanation
Indices: 38118488--38118515 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
38118478 ATTTTAATTA
38118488 TTATAGTTTAAAT
1 TTATAGTTTAAAT
38118501 TTATAGTTTAAAT
1 TTATAGTTTAAAT
38118514 TT
1 TT
38118516 GAAATCTAAA
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:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (13 bp):
TTATAGTTTAAAT
Found at i:38118634 original size:23 final size:22
Alignment explanation
Indices: 38118536--38118712 Score: 79
Period size: 23 Copynumber: 7.4 Consensus size: 22
38118526 TTATAGATTT
*
38118536 TTAAATTAAAATTGAAATGAAA
1 TTAAATTAAAATTGAAATTAAA
*
38118558 TTAACATTCAAAGTTGAAATTGAAA
1 TTAA-ATT-AAAATTGAAATT-AAA
* * *
38118583 TTAAA-TAATACTTTAAATTAAG
1 TTAAATTAA-AATTGAAATTAAA
* *
38118605 TGCAAATTAAAATTGAAATTAAG
1 T-TAAATTAAAATTGAAATTAAA
* *
38118628 TTGAAATTTAATTTCGAAATTTAAACCCA
1 TT-AAATTAAAATT-GAAA-TT-AA---A
* *
38118657 TTTGAAATGAAAATT-AAATGAAA
1 -TT-AAATTAAAATTGAAATTAAA
* *
38118680 TTTAAATTAAAGTTGAAATGAAAA
1 -TTAAATTAAAATTGAAAT-TAAA
38118704 TTAAATTAA
1 TTAAATTAA
38118713 TAAAAATTTA
Statistics
Matches: 120, Mismatches: 19, Indels: 31
0.71 0.11 0.18
Matches are distributed among these distances:
22 18 0.15
23 53 0.44
24 21 0.17
25 9 0.08
26 4 0.03
27 1 0.01
28 3 0.03
30 11 0.09
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (22 bp):
TTAAATTAAAATTGAAATTAAA
Found at i:38118677 original size:11 final size:11
Alignment explanation
Indices: 38118661--38118709 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
38118651 AACCCATTTG
38118661 AAATGAAAATT
1 AAATGAAAATT
*
38118672 AAATGAAATTT
1 AAATGAAAATT
* *
38118683 AAATTAAAGTT
1 AAATGAAAATT
38118694 GAAATGAAAATT
1 -AAATGAAAATT
38118706 AAAT
1 AAAT
38118710 TAATAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 23 0.72
12 9 0.28
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (11 bp):
AAATGAAAATT
Found at i:38118698 original size:18 final size:16
Alignment explanation
Indices: 38118659--38118709 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
38118649 TAAACCCATT
38118659 TGAAATGAAAATTAAA
1 TGAAATGAAAATTAAA
**
38118675 TGAAATTTAAATTAAA
1 TGAAATGAAAATTAAA
38118691 GTTGAAATGAAAATTAAA
1 --TGAAATGAAAATTAAA
38118709 T
1 T
38118710 TAATAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 15 0.52
18 14 0.48
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.31
Consensus pattern (16 bp):
TGAAATGAAAATTAAA
Found at i:38118804 original size:24 final size:26
Alignment explanation
Indices: 38118777--38118829 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
38118767 TGAATTGAAA
38118777 TTTAAAA-T-TAAAGTGTAATAAAAT
1 TTTAAAACTATAAAGTGTAATAAAAT
38118801 TTTAAAACTAATAAAGTGTAATAAAAT
1 TTTAAAACT-ATAAAGTGTAATAAAAT
38118828 TT
1 TT
38118830 AATTTTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 7 0.27
25 1 0.04
27 18 0.69
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.38
Consensus pattern (26 bp):
TTTAAAACTATAAAGTGTAATAAAAT
Found at i:38119126 original size:14 final size:15
Alignment explanation
Indices: 38119102--38119155 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
38119092 TAATAATATC
*
38119102 AAAATTCAAATTTAA
1 AAAATTAAAATTTAA
*
38119117 AAAA-TAAAATTAAA
1 AAAATTAAAATTTAA
*
38119131 AAAATTATAATTTAA
1 AAAATTAAAATTTAA
*
38119146 AAACTTAAAA
1 AAAATTAAAA
38119156 AATGAACTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATTAAAATTTAA
Found at i:38122596 original size:33 final size:32
Alignment explanation
Indices: 38122545--38122608 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
38122535 TGTTTTAAAA
38122545 ATATTTTTTATTTCTTCGAAATAATTT-TTTAC
1 ATATTTTTTATTTCTTCGAAAT-ATTTGTTTAC
38122577 ATATATTTTTATATT-TTCGAAATATTTGTTTA
1 ATAT-TTTTTAT-TTCTTCGAAATATTTGTTTA
38122609 TATTTTAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 8 0.28
33 19 0.66
34 2 0.07
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.59
Consensus pattern (32 bp):
ATATTTTTTATTTCTTCGAAATATTTGTTTAC
Found at i:38122629 original size:21 final size:21
Alignment explanation
Indices: 38122577--38122629 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
38122567 AATTTTTTAC
* *
38122577 ATATATTTTTATATTTTCGAA
1 ATATTTTTTTATATTTTAGAA
*
38122598 ATATTTGTTTATATTTTAGAA
1 ATATTTTTTTATATTTTAGAA
38122619 ATATTTTTTTA
1 ATATTTTTTTA
38122630 CAAATGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (21 bp):
ATATTTTTTTATATTTTAGAA
Found at i:38123671 original size:30 final size:30
Alignment explanation
Indices: 38123620--38123740 Score: 156
Period size: 30 Copynumber: 4.1 Consensus size: 30
38123610 TTTTGATTTT
* *
38123620 TTTCGTTTAT-TTTTTAATTTAATTTATAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
*
38123649 TTTCGTTTATATTTTAAATTTAATTTCTCA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
* * *
38123679 TTTTGTTT-TATATTTAAAATTAATTTCTCA
1 TTTCGTTTATAT-TTTAAATTTAATTTCTAA
*
38123709 TTTCGTTTATATTTTAAATTTAATTTGTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
38123739 TT
1 TT
38123741 ATTATTTTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
29 13 0.16
30 64 0.80
31 3 0.04
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (30 bp):
TTTCGTTTATATTTTAAATTTAATTTCTAA
Found at i:38124693 original size:18 final size:18
Alignment explanation
Indices: 38124666--38124701 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
38124656 ACATGAAAAA
38124666 ATTAAATTTTTTATTCGT
1 ATTAAATTTTTTATTCGT
*
38124684 ATTAATTTTTTTATTCGT
1 ATTAAATTTTTTATTCGT
38124702 CCATGACTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.64
Consensus pattern (18 bp):
ATTAAATTTTTTATTCGT
Found at i:38124761 original size:55 final size:54
Alignment explanation
Indices: 38124702--38124845 Score: 157
Period size: 54 Copynumber: 2.6 Consensus size: 54
38124692 TTTTATTCGT
*
38124702 CCATGACTTGGCAGACACCTAAAAAATATTTTTTATCTGATAAAAGAAGTGTCGA
1 CCATGGCTTGGCAGACACCT-AAAAATATTTTTTATCTGATAAAAGAAGTGTCGA
** * * ** * *
38124757 CCATGGCTTGATAGACA-CTCAAAAATATTTTTTATTTGATAAAGGGGGTGTTGG
1 CCATGGCTTGGCAGACACCT-AAAAATATTTTTTATCTGATAAAAGAAGTGTCGA
*
38124811 CCATGGCTTGGCTGACATCC-AAAAATATTTTTTAT
1 CCATGGCTTGGCAGACA-CCTAAAAATATTTTTTAT
38124846 TCGTATTTTT
Statistics
Matches: 74, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
54 59 0.80
55 14 0.19
56 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (54 bp):
CCATGGCTTGGCAGACACCTAAAAATATTTTTTATCTGATAAAAGAAGTGTCGA
Found at i:38132549 original size:28 final size:28
Alignment explanation
Indices: 38132518--38132576 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
38132508 ATAATGTTAG
*
38132518 TTTT-TATTTTAT-TTTATGAGTACTAATA
1 TTTTATATTTTATATTT-TGA-TAATAATA
*
38132546 TTTTATTTTTTATATTTTGATAATAATA
1 TTTTATATTTTATATTTTGATAATAATA
38132574 TTT
1 TTT
38132577 AGTATGCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 14 0.52
29 10 0.37
30 3 0.11
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (28 bp):
TTTTATATTTTATATTTTGATAATAATA
Found at i:38135663 original size:11 final size:11
Alignment explanation
Indices: 38135632--38135673 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
38135622 CCCAACTTGG
38135632 ATTTTAAATTA
1 ATTTTAAATTA
* *
38135643 AGTTTGAATTA
1 ATTTTAAATTA
*
38135654 ATTTTAAATTT
1 ATTTTAAATTA
38135665 A-TTTAAATT
1 ATTTTAAATT
38135674 TAAAATTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:38135673 original size:17 final size:17
Alignment explanation
Indices: 38135653--38135695 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
38135643 AGTTTGAATT
38135653 AATTTTAAATT-TATTTA
1 AATTTTAAATTGT-TTTA
*
38135670 AATTTAAAATTGTTTTA
1 AATTTTAAATTGTTTTA
38135687 AA-TTTAAAT
1 AATTTTAAAT
38135696 ACATTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.26
17 16 0.70
18 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATTTTAAATTGTTTTA
Found at i:38135676 original size:22 final size:22
Alignment explanation
Indices: 38135632--38135673 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
38135622 CCCAACTTGG
*
38135632 ATTTTAAATTAAGTTTGAATTA
1 ATTTTAAATTAAGTTTAAATTA
*
38135654 ATTTTAAATTTA-TTTAAATT
1 ATTTTAAATTAAGTTTAAATT
38135674 TAAAATTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTTTAAATTAAGTTTAAATTA
Found at i:38135685 original size:27 final size:27
Alignment explanation
Indices: 38135655--38135706 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
38135645 TTTGAATTAA
**
38135655 TTTTAAATTTATTTAAATTTAAAATTG
1 TTTTAAATTTAAATAAATTTAAAATTG
*
38135682 TTTTAAATTTAAATACATTTAAAAT
1 TTTTAAATTTAAATAAATTTAAAAT
38135707 AATTTAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (27 bp):
TTTTAAATTTAAATAAATTTAAAATTG
Found at i:38135702 original size:16 final size:16
Alignment explanation
Indices: 38135651--38135704 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
38135641 TAAGTTTGAA
* *
38135651 TTAATTTTAAATTTAT
1 TTAAATTTAAATTCAT
**
38135667 TTAAATTTAAAATTGTT
1 TTAAATTT-AAATTCAT
*
38135684 TTAAATTTAAATACAT
1 TTAAATTTAAATTCAT
38135700 TTAAA
1 TTAAA
38135705 ATAATTTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (16 bp):
TTAAATTTAAATTCAT
Found at i:38137620 original size:30 final size:30
Alignment explanation
Indices: 38137585--38137708 Score: 123
Period size: 30 Copynumber: 4.2 Consensus size: 30
38137575 TTGAACTGTT
*
38137585 TAAAAATTA-TATTTTGACCCCAAAACTTTC
1 TAAAAATTACCATTTT-ACCCCAAAACTTTC
*
38137615 TAAAAATTACCATTTTACCCCCAAACTTTC
1 TAAAAATTACCATTTTACCCCAAAACTTTC
*
38137645 T-AAAATT-CCATTCTTAACCCC--AATTTTAC
1 TAAAAATTACCATT-TT-ACCCCAAAACTTT-C
* *
38137674 CAAAAATTACCATTTTACCCCTAAACTTTC
1 TAAAAATTACCATTTTACCCCAAAACTTTC
*
38137704 CAAAA
1 TAAAA
38137709 TCCCATTTTA
Statistics
Matches: 81, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
28 10 0.12
29 14 0.17
30 42 0.52
31 15 0.19
ACGTcount: A:0.39, C:0.27, G:0.01, T:0.34
Consensus pattern (30 bp):
TAAAAATTACCATTTTACCCCAAAACTTTC
Found at i:38137748 original size:58 final size:59
Alignment explanation
Indices: 38137616--38137976 Score: 428
Period size: 59 Copynumber: 6.1 Consensus size: 59
38137606 AAAACTTTCT
* * * * * *
38137616 AAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTCTTAACCCCAATTTTACC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
*
38137675 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCA-TTTTAACCTCGATTTCACC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
* * *
38137733 AAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATCCTATTTTTAACCCTGATTTCACC
1 AAAAATTACCATTTTACCCCT-AAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
* *
38137792 AAAAATTACCATTTCACACCCTGAACTTTCCAAAATCCCATTTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTAC-CCCTAAACTTTCCAAAATCCCA-TTTTTAACCCCGATTTCACC
* * * * *
38137853 AAAAAATACCATTTTACCCCTGAACTTTCCAAAA-CCTTATTTTTAGCCCCGATTTTACC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATCC-CATTTTTAACCCCGATTTCACC
* * * * **
38137912 -AAAATTACCGTTTTACCCGC-AAAC-TTCCAAAATTCTATTTTTGACCCTAATTTCACC
1 AAAAATTACCATTTTACCC-CTAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
38137969 AAAAATTA
1 AAAAATTA
38137977 TATTTTTACC
Statistics
Matches: 265, Mismatches: 28, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
57 29 0.11
58 74 0.28
59 89 0.34
60 35 0.13
61 38 0.14
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
Found at i:38137885 original size:30 final size:30
Alignment explanation
Indices: 38137608--38137886 Score: 121
Period size: 30 Copynumber: 9.4 Consensus size: 30
38137598 TTGACCCCAA
* * **
38137608 AACTTTCTAAAAATTACCATTTTACCCCCA
1 AACTTTCCAAAAAATACCATTTTACCCCTG
* *
38137638 AACTTT-C-TAAAATTCCATTCTTAACCCC--
1 AACTTTCCAAAAAATACCATT-TT-ACCCCTG
* * *
38137666 AATTTTACCAAAAATTACCATTTTACCCCTA
1 AACTTT-CCAAAAAATACCATTTTACCCCTG
* *
38137697 AACTTTCC--AAAATCCCATTTTA-ACCTCG
1 AACTTTCCAAAAAATACCATTTTACCCCT-G
*
38137725 -A-TTTCACCAAAAATTACCATTTTA-CCCTCG
1 AACTTT--CCAAAAAATACCATTTTACCCCT-G
*
38137755 AACTTTCC--AAAAT-CCTATTTTTAACCCTG
1 AACTTTCCAAAAAATACC-A-TTTTACCCCTG
* *
38137784 -A-TTTCACCAAAAATTACCATTTCACACCCTG
1 AACTTT--CCAAAAAATACCATTTTAC-CCCTG
*
38137815 AACTTTCC--AAAATCCCATTTTTTAACCCC-G
1 AACTTTCCAAAAAATACCA--TTTT-ACCCCTG
38137845 -A-TTTCACCAAAAAATACCATTTTACCCCTG
1 AACTTT--CCAAAAAATACCATTTTACCCCTG
38137875 AACTTTCCAAAA
1 AACTTTCCAAAA
38137887 CCTTATTTTT
Statistics
Matches: 190, Mismatches: 24, Indels: 70
0.67 0.08 0.25
Matches are distributed among these distances:
26 3 0.02
27 9 0.05
28 37 0.19
29 28 0.15
30 57 0.30
31 34 0.18
32 19 0.10
33 3 0.02
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (30 bp):
AACTTTCCAAAAAATACCATTTTACCCCTG
Found at i:38153698 original size:20 final size:20
Alignment explanation
Indices: 38153673--38153746 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
38153663 AGTCTTCAAG
*
38153673 GTATCGATAGAAGTGGAGTT
1 GTATCGGTAGAAGTGGAGTT
38153693 GTATCGGTAGAAGTGGAGTT
1 GTATCGGTAGAAGTGGAGTT
*
38153713 GTATAGGTAGAAGTGGAGTT
1 GTATCGGTAGAAGTGGAGTT
* * *
38153733 CTACCGGTAAAAGT
1 GTATCGGTAGAAGT
38153747 CTCACTAGAG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.30, C:0.07, G:0.35, T:0.28
Consensus pattern (20 bp):
GTATCGGTAGAAGTGGAGTT
Done.