Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000692.1 Hibiscus syriacus cultivar Beakdansim tig00001349_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: 1095174
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 3 of 5
Found at i:366779 original size:16 final size:16
Alignment explanation
Indices: 366758--366790 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
366748 AAAAAAAATT
366758 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
366774 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
366790 T
1 T
366791 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:391863 original size:15 final size:15
Alignment explanation
Indices: 391823--391865 Score: 63
Period size: 13 Copynumber: 3.0 Consensus size: 15
391813 TCAATTTGTG
*
391823 TTTAATAAAATATTA
1 TTTATTAAAATATTA
391838 TTT-TT-AAATATTA
1 TTTATTAAAATATTA
391851 TTTATTAAAATATTA
1 TTTATTAAAATATTA
391866 AGTTTGTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 11 0.44
14 3 0.12
15 11 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTATTAAAATATTA
Found at i:394176 original size:30 final size:31
Alignment explanation
Indices: 394107--394177 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
394097 CTTCAGGGAT
* *
394107 CATATTGCAAACGAACTAAATGTTGAGGGGC
1 CATATTGCAAACGAACTAAATGTTGAGAGAC
* * *
394138 CGTATTGCAAACGGACTAAATGTTG-GAGAT
1 CATATTGCAAACGAACTAAATGTTGAGAGAC
*
394168 TATATTGCAA
1 CATATTGCAA
394178 GTTTTAAAAG
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
30 10 0.30
31 23 0.70
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (31 bp):
CATATTGCAAACGAACTAAATGTTGAGAGAC
Found at i:401419 original size:37 final size:36
Alignment explanation
Indices: 401377--401485 Score: 166
Period size: 35 Copynumber: 3.0 Consensus size: 36
401367 ATATTTCAAC
*
401377 AAACATCTACCAAACTTTGAAAAACTATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAAC-ATTTTTCAAAG
*
401414 AAACATTTACCAAACTTTGAAAATCA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
*
401449 AAACATTTACCAAACTTTGAAAACCATTTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAACA-TTTTTCAAAG
401486 TTAGTTGTCA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 34 0.51
36 1 0.01
37 32 0.48
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.31
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
Found at i:401441 original size:21 final size:20
Alignment explanation
Indices: 401414--401477 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
401404 TTTTTCAAAG
401414 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
401434 AAATCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
401449 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
401469 AAACCATTT
1 AAA-CATTT
401478 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:408042 original size:18 final size:19
Alignment explanation
Indices: 407991--408044 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 19
407981 TCTTATAACG
407991 TTTTATACATAATTTTAGAAA
1 TTTTATA-AT-ATTTTAGAAA
**
408012 CATTATGAATATTTTA-AAA
1 TTTTAT-AATATTTTAGAAA
408031 TTTTATAATATTTT
1 TTTTATAATATTTT
408045 TTTTCAATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 8 0.29
19 7 0.25
20 6 0.21
21 6 0.21
22 1 0.04
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (19 bp):
TTTTATAATATTTTAGAAA
Found at i:423321 original size:2 final size:2
Alignment explanation
Indices: 423316--423345 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
423306 ACACACACAC
423316 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
423346 TGACGGAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:431417 original size:23 final size:23
Alignment explanation
Indices: 431373--431417 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
431363 GACTAAAATA
* * **
431373 AAATTATATTAAATTAGTACATT
1 AAATTAAAATAAATTAAAACATT
431396 AAATTAAAATAAATTAAAACAT
1 AAATTAAAATAAATTAAAACAT
431418 GTTGTTCGGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (23 bp):
AAATTAAAATAAATTAAAACATT
Found at i:432608 original size:3 final size:3
Alignment explanation
Indices: 432602--432644 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
432592 ATTTATTATT
*
432602 TAA TAA TAA TAA T-A TAA -CA TAA TAA TAA TAA TAA TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
432645 TAAGCAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 3 0.09
3 29 0.83
4 3 0.09
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:432625 original size:16 final size:17
Alignment explanation
Indices: 432604--432644 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
432594 TTATTATTTA
432604 ATAATAATAAT-ATAAC
1 ATAATAATAATAATAAC
*
432620 ATAATAATAATAATAAT
1 ATAATAATAATAATAAC
432637 A-AATAATA
1 ATAATAATA
432645 TAAGCAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAATAATAATAATAAC
Found at i:432626 original size:19 final size:19
Alignment explanation
Indices: 432602--432644 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
432592 ATTTATTATT
432602 TAATAATAATAAT-ATAACA
1 TAATAATAATAATAATAA-A
432621 TAATAATAATAATAATAAA
1 TAATAATAATAATAATAAA
432640 TAATA
1 TAATA
432645 TAAGCAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAATAATAATAATAAA
Found at i:433165 original size:112 final size:112
Alignment explanation
Indices: 432965--433392 Score: 682
Period size: 112 Copynumber: 3.8 Consensus size: 112
432955 AGAATCAAAC
* * * *
432965 AAAGGCTGAATAAGTTATTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
433029 ATGAACACTTCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCA
66 ATGAACACTTCTGGCAATGATGATCCATCAAGTGATGGATTTGAGCA
*
433076 AAAGGTTGAACAAGTTCTTCTTATTATGAACTTCCTCTTCCTTCTTCAGATGAG-TCATTCTCAT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTC-TTCTCAT
*
433140 TATAAACACTTCTGGCAATGATGATCCATCAAGTGATGGATTTGAGCA
65 TATGAACACTTCTGGCAATGATGATCCATCAAGTGATGGATTTGAGCA
*
433188 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGACGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
433253 ATGAACACTTCTGGCAATGCTGATCCATCAAGTGAGGGATTTGAGCA
66 ATGAACACTTCTGGCAATGATGATCCATCAAGTGATGGATTTGAGCA
*
433300 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTTATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
433365 ATGAACTCTACCTGGC-ATGTTGATCCAT
66 ATGAACACT-TCTGGCAATGATGATCCAT
433393 TGAGTAATTG
Statistics
Matches: 295, Mismatches: 18, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
111 38 0.13
112 250 0.85
113 7 0.02
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (112 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACACTTCTGGCAATGATGATCCATCAAGTGATGGATTTGAGCA
Found at i:438506 original size:72 final size:72
Alignment explanation
Indices: 438343--438543 Score: 224
Period size: 72 Copynumber: 2.7 Consensus size: 72
438333 TAATTGAAAC
* * * ** * *
438343 TTATCCATAAAGCCAGGGCGATTAACCAATTACTCTAGAGGGACATTTTTATTGCAT-ATAATAG
1 TTATCCATAAAGCCGGGGCTATTAACCAATTGCTCTAGAGGGACA-ACTCA-AGCATAATAA-A-
*
438407 GTTAGCTGAATA
62 -CTAGCTGAATA
* *
438419 TTATTCATAAAGCCGGGGCTATTAACCAATTGCTCTAGAGGGATAACTCAAGCATAATAAACTAG
1 TTATCCATAAAGCCGGGGCTATTAACCAATTGCTCTAGAGGGACAACTCAAGCATAATAAACTAG
438484 CTGAATA
66 CTGAATA
* * * *
438491 TTATCCATAAAGCCGGGGCTATTGACCAATTGCTTTAGGGGGACAACTTAAGC
1 TTATCCATAAAGCCGGGGCTATTAACCAATTGCTCTAGAGGGACAACTCAAGC
438544 TTTATTGTAT
Statistics
Matches: 108, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
72 57 0.53
74 5 0.05
75 6 0.06
76 40 0.37
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (72 bp):
TTATCCATAAAGCCGGGGCTATTAACCAATTGCTCTAGAGGGACAACTCAAGCATAATAAACTAG
CTGAATA
Found at i:440925 original size:7 final size:7
Alignment explanation
Indices: 440916--440954 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
440906 TAAAAATGAA
*
440916 AAAATGA
1 AAAATGC
440923 AAAATGC
1 AAAATGC
440930 AAAATGC
1 AAAATGC
440937 AAAATGC
1 AAAATGC
440944 AAAATGC
1 AAAATGC
440951 AAAA
1 AAAA
440955 GTAAATATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.64, C:0.10, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAATGC
Found at i:440925 original size:14 final size:15
Alignment explanation
Indices: 440874--440947 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 15
440864 GCAAATATGC
440874 AAATGCAAAAAATGAA
1 AAATG-AAAAAATGAA
* *
440890 AATATAAATATAAACTTAA
1 AA-ATGAA-A-AAA-TGAA
440909 AAATGAAAAAATGAA
1 AAATGAAAAAATGAA
* *
440924 AAATG-CAAAATGCA
1 AAATGAAAAAATGAA
440938 AAATGCAAAA
1 AAATG-AAAA
440948 TGCAAAAGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
14 12 0.27
15 8 0.18
16 9 0.20
17 4 0.09
18 7 0.16
19 5 0.11
ACGTcount: A:0.66, C:0.07, G:0.09, T:0.18
Consensus pattern (15 bp):
AAATGAAAAAATGAA
Found at i:441203 original size:38 final size:39
Alignment explanation
Indices: 441130--441203 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 39
441120 TGCATCAAAC
* *
441130 AAAACTTTTACATGTAGGGGACAACTTTCAGTCCTATCT
1 AAAACTTTTACATATAGGGGACAACTTTCACTCCTATCT
* *
441169 AAAAC-TTTACATATAGGGGATAACTTTCCCTCCTA
1 AAAACTTTTACATATAGGGGACAACTTTCACTCCTA
441204 ACTTGGTCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 26 0.84
39 5 0.16
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (39 bp):
AAAACTTTTACATATAGGGGACAACTTTCACTCCTATCT
Found at i:442120 original size:46 final size:49
Alignment explanation
Indices: 442053--442143 Score: 127
Period size: 46 Copynumber: 1.9 Consensus size: 49
442043 AGGTATAAAT
* *
442053 CCTAACCTCATGCTTTCTAGTTC-CATGC-TTTGTTT-GGAAAAATTAA
1 CCTAACCTCATGATTTCTAGTTCGCATGCATTTATTTAGGAAAAATTAA
442099 CCTAA-CTGCATGATTTCTAGTTCGCATGCATTTATTTAGGAAAAA
1 CCTAACCT-CATGATTTCTAGTTCGCATGCATTTATTTAGGAAAAA
442144 GAAAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 2 0.05
46 19 0.49
47 5 0.13
48 6 0.15
49 7 0.18
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (49 bp):
CCTAACCTCATGATTTCTAGTTCGCATGCATTTATTTAGGAAAAATTAA
Found at i:454468 original size:31 final size:31
Alignment explanation
Indices: 454430--454493 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
454420 GTAATCTCTC
454430 ATTTGATGCATTGTTCTAAGCATTAACGATT
1 ATTTGATGCATTGTTCTAAGCATTAACGATT
454461 ATTTGATGCATTGTTCTAAGCATTAACGATT
1 ATTTGATGCATTGTTCTAAGCATTAACGATT
454492 AT
1 AT
454494 CTTATCCCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (31 bp):
ATTTGATGCATTGTTCTAAGCATTAACGATT
Found at i:455729 original size:3 final size:3
Alignment explanation
Indices: 455721--455761 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
455711 ATTCTAGAGG
455721 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
455762 CCCTAATAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:457334 original size:16 final size:16
Alignment explanation
Indices: 457313--457344 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
457303 TTTATTATTC
*
457313 AACGTCGGTAATCCAA
1 AACGTCAGTAATCCAA
457329 AACGTCAGTAATCCAA
1 AACGTCAGTAATCCAA
457345 CAATATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.19
Consensus pattern (16 bp):
AACGTCAGTAATCCAA
Found at i:459670 original size:43 final size:44
Alignment explanation
Indices: 459562--459676 Score: 124
Period size: 43 Copynumber: 2.6 Consensus size: 44
459552 AATTATTCAT
* * *
459562 TATTTTCATTTAAGGCATCCTTTCATGCCTTCAATGCACAATTATG
1 TATTTT-ATTTATGGCATCATTTCATGCATT-AATGCACAATTATG
* * * **
459608 CATTTCATTAATGGCATCATTTCATGCATT-ATGCACCGTTATG
1 TATTTTATTTATGGCATCATTTCATGCATTAATGCACAATTATG
*
459651 TATTTTATTTATGGAATCATTTCATG
1 TATTTTATTTATGGCATCATTTCATG
459677 TCTTTCATGC
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
43 33 0.58
45 20 0.35
46 4 0.07
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.43
Consensus pattern (44 bp):
TATTTTATTTATGGCATCATTTCATGCATTAATGCACAATTATG
Found at i:459878 original size:54 final size:54
Alignment explanation
Indices: 459820--460058 Score: 309
Period size: 54 Copynumber: 4.4 Consensus size: 54
459810 CATACGAAAA
* * * * * *
459820 TTCATAAACTTATTATGAATTCCGTGGGTTGCACACATAGTGTCGAAATGGTTG
1 TTCATCAACATATGATGAATTCCGTGGATTGCACACATAGTGCCGAAACGGTTG
* ** * *
459874 TTCATCAACATATGATAAATTTTGTAGATTGCATACATAGTGCCGAAACGGTTG
1 TTCATCAACATATGATGAATTCCGTGGATTGCACACATAGTGCCGAAACGGTTG
* *
459928 TTCATCAACATATGATGAATTCCGTGAATTACACACATAGTGCCGAAACGGTTG
1 TTCATCAACATATGATGAATTCCGTGGATTGCACACATAGTGCCGAAACGGTTG
* * * * *
459982 TTTA-CAACATATGATGAATTCTGTGGGTTGCACACATAGTGCCAAAATGGTTG
1 TTCATCAACATATGATGAATTCCGTGGATTGCACACATAGTGCCGAAACGGTTG
460035 TTCATCAACATATGATGAATTCCG
1 TTCATCAACATATGATGAATTCCG
460059 CGAAATGGTT
Statistics
Matches: 157, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
53 46 0.29
54 111 0.71
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (54 bp):
TTCATCAACATATGATGAATTCCGTGGATTGCACACATAGTGCCGAAACGGTTG
Found at i:460040 original size:107 final size:108
Alignment explanation
Indices: 459820--460058 Score: 327
Period size: 107 Copynumber: 2.2 Consensus size: 108
459810 CATACGAAAA
* * * ** * * *
459820 TTCATAAACTTATTATGAATTCCGTGGGTTGCACACATAGTGTCGAAATGGTTGTTCATCAACAT
1 TTCATCAACATATGATGAATTCCGTGAATTACACACATAGTGCCGAAACGGTTGTTCATCAACAT
* * *
459885 ATGATAAATTTTGTAGATTGCATACATAGTGCCGAAACGGTTG
66 ATGATAAATTCTGTAGATTGCACACATAGTGCCAAAACGGTTG
*
459928 TTCATCAACATATGATGAATTCCGTGAATTACACACATAGTGCCGAAACGGTTGTTTA-CAACAT
1 TTCATCAACATATGATGAATTCCGTGAATTACACACATAGTGCCGAAACGGTTGTTCATCAACAT
* * * *
459992 ATGATGAATTCTGTGGGTTGCACACATAGTGCCAAAATGGTTG
66 ATGATAAATTCTGTAGATTGCACACATAGTGCCAAAACGGTTG
460035 TTCATCAACATATGATGAATTCCG
1 TTCATCAACATATGATGAATTCCG
460059 CGAAATGGTT
Statistics
Matches: 115, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
107 66 0.57
108 49 0.43
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (108 bp):
TTCATCAACATATGATGAATTCCGTGAATTACACACATAGTGCCGAAACGGTTGTTCATCAACAT
ATGATAAATTCTGTAGATTGCACACATAGTGCCAAAACGGTTG
Found at i:460072 original size:35 final size:35
Alignment explanation
Indices: 460026--460093 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
460016 CATAGTGCCA
460026 AAATGGTTGTTCATCAACATATGATGAATTCCGCG
1 AAATGGTTGTTCATCAACATATGATGAATTCCGCG
460061 AAATGGTTGTTCATCAACATATGATGAATTCCG
1 AAATGGTTGTTCATCAACATATGATGAATTCCG
460094 TAGGTTGCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (35 bp):
AAATGGTTGTTCATCAACATATGATGAATTCCGCG
Found at i:460090 original size:89 final size:88
Alignment explanation
Indices: 459971--460146 Score: 280
Period size: 89 Copynumber: 2.0 Consensus size: 88
459961 CACATAGTGC
* * * * *
459971 CGAAACGGTTGTTTACAACATATGATGAATTCTGTGGGTTGCACACATAGTGCCAAAATGGTTGT
1 CGAAACGGTTGTTCACAACATATGATGAATTCCGTAGGTTGCACACATAGTGACAAAACGGTTGT
460036 TCATCAACATATGATGAATTCCG
66 TCATCAACATATGATGAATTCCG
* *
460059 CGAAATGGTTGTTCATCAACATATGATGAATTCCGTAGGTTGCACACATAGTGACGAAACGGTTG
1 CGAAACGGTTGTTCA-CAACATATGATGAATTCCGTAGGTTGCACACATAGTGACAAAACGGTTG
460124 TTCATCAACATATGATGAATTCC
65 TTCATCAACATATGATGAATTCC
460147 TTGGGTTGCA
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
88 13 0.16
89 67 0.84
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (88 bp):
CGAAACGGTTGTTCACAACATATGATGAATTCCGTAGGTTGCACACATAGTGACAAAACGGTTGT
TCATCAACATATGATGAATTCCG
Found at i:460124 original size:54 final size:54
Alignment explanation
Indices: 460059--460165 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
460049 ATGAATTCCG
*
460059 CGAAATGGTTGTTCATCAACATATGATGAATTCCGTAGGTTGCACACATAGTGA
1 CGAAACGGTTGTTCATCAACATATGATGAATTCCGTAGGTTGCACACATAGTGA
* * * *
460113 CGAAACGGTTGTTCATCAACATATGATGAATTCCTTGGGTTGCATACTTAGTG
1 CGAAACGGTTGTTCATCAACATATGATGAATTCCGTAGGTTGCACACATAGTG
460166 CCTATTAGGT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (54 bp):
CGAAACGGTTGTTCATCAACATATGATGAATTCCGTAGGTTGCACACATAGTGA
Found at i:460902 original size:23 final size:23
Alignment explanation
Indices: 460865--460925 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
460855 TACAGATAAA
* * *
460865 AAACGTACCAAAAAGATAGAGAT
1 AAACGTGCCACAAAGACAGAGAT
460888 AAACGTGCCACAAAG-CAGAGAT
1 AAACGTGCCACAAAGACAGAGAT
*
460910 AAACGTGTCACAAAGA
1 AAACGTGCCACAAAGA
460926 GATAATTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.51, C:0.18, G:0.20, T:0.11
Consensus pattern (23 bp):
AAACGTGCCACAAAGACAGAGAT
Found at i:464020 original size:18 final size:18
Alignment explanation
Indices: 463998--464121 Score: 176
Period size: 18 Copynumber: 6.9 Consensus size: 18
463988 TGTGTTATAT
* *
463998 GTGGTTCTTCGGGACATT
1 GTGGTCCTTCGGGACATA
*
464016 GTGGTCCTTCGGGACAGA
1 GTGGTCCTTCGGGACATA
*
464034 GTGGTCATTCGGGACATA
1 GTGGTCCTTCGGGACATA
* * *
464052 GTAGTCATTCGAGACATA
1 GTGGTCCTTCGGGACATA
464070 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
464088 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
464106 GTGGTCCTTTGGGACA
1 GTGGTCCTTCGGGACA
464122 AGTTTAAGTG
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 95 1.00
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:465219 original size:21 final size:21
Alignment explanation
Indices: 465192--465252 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
465182 GGTCATTCGG
*
465192 GACATATATGTGATCCTTTG-
1 GACATATATGTGGTCCTTTGT
*
465212 GAACATATATGCGGTCCTTTGT
1 G-ACATATATGTGGTCCTTTGT
*
465234 GATATATATGTGGTCCTTT
1 GACATATATGTGGTCCTTT
465253 AGACAATTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (21 bp):
GACATATATGTGGTCCTTTGT
Found at i:469687 original size:31 final size:33
Alignment explanation
Indices: 469651--469713 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
469641 ATAATCACAA
469651 TTAATATGAA-G-TAA-AATTAAGTATAAAATTG
1 TTAATATGAATGATAACAATTAA-TATAAAATTG
*
469682 TTAATATGAATGATAACAATTAATATCAAATT
1 TTAATATGAATGATAACAATTAATATAAAATT
469714 CTATGAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 10 0.36
32 1 0.04
33 11 0.39
34 6 0.21
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.37
Consensus pattern (33 bp):
TTAATATGAATGATAACAATTAATATAAAATTG
Found at i:470411 original size:11 final size:11
Alignment explanation
Indices: 470392--470421 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
470382 TGAATAAAAA
470392 TAAAATTTTAT
1 TAAAATTTTAT
*
470403 TATAATTTTAT
1 TAAAATTTTAT
470414 TAAAATTT
1 TAAAATTT
470422 AATAAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TAAAATTTTAT
Found at i:470546 original size:26 final size:26
Alignment explanation
Indices: 470492--470547 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
470482 ATTTATTTAT
* * * *
470492 GGTACATCGTTTTAGTAATATGTTTC
1 GGTACATCATTTTAATAATACGTTAC
*
470518 GGTACATCATTTTAATAGTACGTTAC
1 GGTACATCATTTTAATAATACGTTAC
470544 GGTA
1 GGTA
470548 TGCGACAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (26 bp):
GGTACATCATTTTAATAATACGTTAC
Found at i:473187 original size:24 final size:24
Alignment explanation
Indices: 473160--473213 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
473150 AATTTTCCAC
* * *
473160 CGAATGAAGTTGATTTTGATCATT
1 CGAATGAAGCTGACTTTAATCATT
*
473184 CGAATGATGCTGACTTTAATCATT
1 CGAATGAAGCTGACTTTAATCATT
*
473208 CAAATG
1 CGAATG
473214 GGACAAGTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (24 bp):
CGAATGAAGCTGACTTTAATCATT
Found at i:473662 original size:24 final size:24
Alignment explanation
Indices: 473635--473688 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
473625 AATTTTCCAC
* * *
473635 CGAATGAAGTTGATTTTGATCATT
1 CGAATGAAGCTGACTTTAATCATT
*
473659 CGAATGATGCTGACTTTAATCATT
1 CGAATGAAGCTGACTTTAATCATT
*
473683 CAAATG
1 CGAATG
473689 GGACAAGTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (24 bp):
CGAATGAAGCTGACTTTAATCATT
Found at i:477023 original size:76 final size:77
Alignment explanation
Indices: 476877--477318 Score: 475
Period size: 76 Copynumber: 5.7 Consensus size: 77
476867 CTAAAAATAC
* * * * *
476877 CATGTTTCACAAAGAAATAGGTTGCGATATAAAATGTTAATATTTTTATTAATAAAACT-GGTTG
1 CATGGTTCACTAAGAAATAAGTTGTGATCTAAAATGTTAATATTTTTATTAATAAAA-TGGGTTG
* *
476941 CACCCAAGAATAT
65 CGCCCAAGAATGT
** * * *
476954 CATGGTTCACTAAGAAATAAGTTACGATCTATAATGCTAATA-TTTTATTAATAAATTGGGTTGC
1 CATGGTTCACTAAGAAATAAGTTGTGATCTAAAATGTTAATATTTTTATTAATAAAATGGGTTGC
477018 GCCCAAGAATGT
66 GCCCAAGAATGT
* ** * *
477030 CATGTTTCACTAAGAAAT-AGATTGTGATCTGTAATGTTAATATTTTTATTAATAAAATGGGCTA
1 CATGGTTCACTAAGAAATAAG-TTGTGATCTAAAATGTTAATATTTTTATTAATAAAATGGGTTG
*
477094 CACACACAAGAATGT
65 CGC-C-CAAGAATGT
* * * *
477109 CGTGGTTAACTAAGAAATATGTTGTGATCTAAAATGTTAATATTTTTATTAATAAAATCGGTCT-
1 CATGGTTCACTAAGAAATAAGTTGTGATCTAAAATGTTAATATTTTTATTAATAAAATGGGT-TG
*
477173 CGCACAA-AATGT
65 CGCCCAAGAATGT
* * **
477185 CATGATTCACTAAGAAAT-AGATTGTGATATGGAATGTTAATATTTTTATTAATAAAATGGGTTG
1 CATGGTTCACTAAGAAATAAG-TTGTGATCTAAAATGTTAATATTTTTATTAATAAAATGGGTTG
* *
477249 CGTCCAAGAATTT
65 CGCCCAAGAATGT
* * * *
477262 TATGGTTCACTAAGAAAGTAAGTTGTGATCTAGAATGATAATATTTTTGTT-ATAAAA
1 CATGGTTCACTAAGAAA-TAAGTTGTGATCTAAAATGTTAATATTTTTATTAATAAAA
477319 AATCAAAAAT
Statistics
Matches: 307, Mismatches: 46, Indels: 24
0.81 0.12 0.06
Matches are distributed among these distances:
75 5 0.02
76 125 0.41
77 83 0.27
78 27 0.09
79 65 0.21
80 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (77 bp):
CATGGTTCACTAAGAAATAAGTTGTGATCTAAAATGTTAATATTTTTATTAATAAAATGGGTTGC
GCCCAAGAATGT
Found at i:477185 original size:155 final size:154
Alignment explanation
Indices: 476877--477318 Score: 552
Period size: 155 Copynumber: 2.9 Consensus size: 154
476867 CTAAAAATAC
* * * *
476877 CATGTTTCACAAAGAAATAGGTTGCGATATAAAATGTTAATATTTTTATTAATAAAACT-GGTTG
1 CATGTTTCACTAAGAAATAGATTGTGATATGAAATGTTAATATTTTTATTAATAAAA-TGGGTTG
** * *
476941 CACCCAAGAATATCATGGTTCACTAAGAAATAAGTTACGATCTATAATGCTAATA-TTTTATTAA
65 CACCCAAGAATATCATGGTTCACTAAGAAATAAGTTGTGATCTAAAATGATAATATTTTTATTAA
* * *
477005 TAAATTGGGTTGCGCCCAAGAATGT
130 TAAAATCGGTTGCGCACAAGAATGT
* * * *
477030 CATGTTTCACTAAGAAATAGATTGTGATCTGTAATGTTAATATTTTTATTAATAAAATGGGCTAC
1 CATGTTTCACTAAGAAATAGATTGTGATATGAAATGTTAATATTTTTATTAATAAAATGGGTTGC
* * * * *
477095 ACACACAAGAATGTCGTGGTTAACTAAGAAATATGTTGTGATCTAAAATGTTAATATTTTTATTA
66 AC-C-CAAGAATATCATGGTTCACTAAGAAATAAGTTGTGATCTAAAATGATAATATTTTTATTA
477160 ATAAAATCGGTCT-CGCACAA-AATGT
129 ATAAAATCGGT-TGCGCACAAGAATGT
* *
477185 CATGATTCACTAAGAAATAGATTGTGATATGGAATGTTAATATTTTTATTAATAAAATGGGTTGC
1 CATGTTTCACTAAGAAATAGATTGTGATATGAAATGTTAATATTTTTATTAATAAAATGGGTTGC
** * * * *
477250 GTCCAAGAATTTTATGGTTCACTAAGAAAGTAAGTTGTGATCTAGAATGATAATATTTTTGTT-A
66 ACCCAAGAATATCATGGTTCACTAAGAAA-TAAGTTGTGATCTAAAATGATAATATTTTTATTAA
477314 TAAAA
130 TAAAA
477319 AATCAAAAAT
Statistics
Matches: 249, Mismatches: 34, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
152 1 0.00
153 85 0.34
154 31 0.12
155 108 0.43
156 23 0.09
157 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (154 bp):
CATGTTTCACTAAGAAATAGATTGTGATATGAAATGTTAATATTTTTATTAATAAAATGGGTTGC
ACCCAAGAATATCATGGTTCACTAAGAAATAAGTTGTGATCTAAAATGATAATATTTTTATTAAT
AAAATCGGTTGCGCACAAGAATGT
Found at i:478025 original size:73 final size:74
Alignment explanation
Indices: 477903--478104 Score: 250
Period size: 73 Copynumber: 2.8 Consensus size: 74
477893 ATAACATATT
* * * * *
477903 TATCGATATTTTAACTATCGATCATATTTATCAACTTGTTCAATATTTAAAAGTATCGATCATCA
1 TATCAATATTTTAAATTTCGATCTTATTTATCAACTTTTTCAATATTTAAAAGTATCGATCATCA
*
477968 -TCACATAAG
66 CT-ACATAAA
* * * *
477977 TATCAATATTTTAAATTTTGATCTT-TTTATCAACTTTTTCAATTTTTAAAAGTATCGATCGTTA
1 TATCAATATTTTAAATTTCGATCTTATTTATCAACTTTTTCAATATTTAAAAGTATCGATCATCA
478041 CTACATAAA
66 CTACATAAA
* * *
478050 TATCGATATTTTAACTTTCGATCTTATCT-TCAACTTTTTC-ATATTTAAAAGTATC
1 TATCAATATTTTAAATTTCGATCTTATTTATCAACTTTTTCAATATTTAAAAGTATC
478105 TATGATAATA
Statistics
Matches: 111, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
72 14 0.13
73 74 0.67
74 23 0.21
ACGTcount: A:0.34, C:0.15, G:0.06, T:0.45
Consensus pattern (74 bp):
TATCAATATTTTAAATTTCGATCTTATTTATCAACTTTTTCAATATTTAAAAGTATCGATCATCA
CTACATAAA
Found at i:478406 original size:78 final size:77
Alignment explanation
Indices: 478157--478399 Score: 227
Period size: 81 Copynumber: 3.1 Consensus size: 77
478147 CTTTTTTTTT
* ** * * * *
478157 GCGCAACTTATTTTAATTAATAAAAATATTAACATAACATGTTATAACCTATTTATTAGTGAACT
1 GCGCAACTTATTTT-ATTAATAAAAATATTAACATTACAAATTACAACATATTTCTTAGTGAACC
*
478222 ATGATATTTTTGG
65 ATGATATTATTGG
* * * *
478235 GCACAACTTATTTTATTAAAAAAATATAACTTTAA-ATTACAAATTACATCATATTTTCTTAGTT
1 GCGCAACTTATTTTATTAATAAAA-AT-A--TTAACATTACAAATTACAACATA-TTTCTTAGTG
* * * *
478299 AACCATAACATTCTTTG
61 AACCATGATATTATTGG
* * * * * *
478316 GTGTAACCTATTTTACTAATAAAAATATTAACATTACAAATTGCAACATATTTCTTAATGAACCA
1 GCGCAACTTATTTTATTAATAAAAATATTAACATTACAAATTACAACATATTTCTTAGTGAACCA
478381 TGATATTATTGG
66 TGATATTATTGG
478393 GCGCAAC
1 GCGCAAC
478400 AATATTTCTT
Statistics
Matches: 128, Mismatches: 31, Indels: 13
0.74 0.18 0.08
Matches are distributed among these distances:
77 39 0.30
78 31 0.24
79 2 0.02
80 14 0.11
81 42 0.33
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.39
Consensus pattern (77 bp):
GCGCAACTTATTTTATTAATAAAAATATTAACATTACAAATTACAACATATTTCTTAGTGAACCA
TGATATTATTGG
Found at i:479394 original size:20 final size:19
Alignment explanation
Indices: 479369--479407 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
479359 AATTTTTTCA
*
479369 TATAAAGTTATAATACTTTT
1 TATAAAATTATAATA-TTTT
479389 TATAAAATTATAATATTTT
1 TATAAAATTATAATATTTT
479408 AAAATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (19 bp):
TATAAAATTATAATATTTT
Found at i:479929 original size:92 final size:93
Alignment explanation
Indices: 479772--479958 Score: 286
Period size: 92 Copynumber: 2.0 Consensus size: 93
479762 CATGTCACAT
* *
479772 TCTTAATTCTTCTTAAGGTTCATCTTTCATTTGTATGGCGAAGTTTGTTTATTGCTATCCCAGAA
1 TCTTAATTCTTCTTAAGGTTCACCCTTCATTTGTATGGCGAAGTTTGTTTATTGCTATCCCAGAA
*
479837 CT-GAGAGGATTTTTTCCGGCGAGTTGG
66 CTCGAGAGGATTTTTTCCGACGAGTTGG
* * *
479864 TCTTAGTTCTTCTTAAGGTTCACCCTTCATTTTTATGGCGAAGTTTGTTTATTGCTATCCGAGAA
1 TCTTAATTCTTCTTAAGGTTCACCCTTCATTTGTATGGCGAAGTTTGTTTATTGCTATCCCAGAA
* *
479929 CTGCGGGAGGATTTTTTCTGACGAGTTGG
66 CT-CGAGAGGATTTTTTCCGACGAGTTGG
479958 T
1 T
479959 ATCAACAGTA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
92 62 0.73
94 23 0.27
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (93 bp):
TCTTAATTCTTCTTAAGGTTCACCCTTCATTTGTATGGCGAAGTTTGTTTATTGCTATCCCAGAA
CTCGAGAGGATTTTTTCCGACGAGTTGG
Found at i:483498 original size:57 final size:57
Alignment explanation
Indices: 483427--483541 Score: 187
Period size: 57 Copynumber: 2.0 Consensus size: 57
483417 GGCAATTCTT
*
483427 GATTTTCTTGCGAAATCAGTTTGGTGTATCCAACTAGACTGACGTTATGCAGCAGTC
1 GATTTTCTTGCGAAATCAGTTTGGTGTATCCAACCAGACTGACGTTATGCAGCAGTC
* *
483484 GATTTTCTCT-CGAAATCAGTTTGGTGTATCCAACCAGACTGACGTTCTGCTGCAGTC
1 GATTTTCT-TGCGAAATCAGTTTGGTGTATCCAACCAGACTGACGTTATGCAGCAGTC
483541 G
1 G
483542 TGAATTAGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
57 53 0.98
58 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (57 bp):
GATTTTCTTGCGAAATCAGTTTGGTGTATCCAACCAGACTGACGTTATGCAGCAGTC
Found at i:493203 original size:233 final size:235
Alignment explanation
Indices: 492796--493264 Score: 924
Period size: 233 Copynumber: 2.0 Consensus size: 235
492786 TAAATTATGA
492796 AATATATGTTAGAAATGGTGGATTGCCATCACATGTTAACTGGGACTATTATTATGTAAATGAGA
1 AATATATGTTAGAAATGGTGGATTGCCATCACATGTTAACTGGGACTATTATTATGTAAATGAGA
492861 CAAACAGTAGTAACTCCATGTTTTTTGAATTATGCAATTCAAGTGCTGAAAAGGTCGAATTTTAC
66 CAAACAGTAGTAACTCCATGTTTTTTGAATTATGCAATTCAAGTGCTGAAAAGGTCGAATTTTAC
492926 ATCTTATATGTTAGAGAAGGAATCTGGAGTATCGCATTAAGGCATCTAAACGGAACTGGTGGCAT
131 ATCTTATATGTTAGAGAAGGAATCTGGAGTATCGCATTAAGGCATCTAAACGGAACTGGTGGCAT
492991 TTCCGATGGTC-GACTACT-ATATCTATTTCACTTGAAAG
196 TTCCGATGGTCAGACTACTAATATCTATTTCACTTGAAAG
493029 AATATATGTTAGAAATGGTGGATTGCCATCACATGTTAACTGGGACTATTATTATGTAAATGAGA
1 AATATATGTTAGAAATGGTGGATTGCCATCACATGTTAACTGGGACTATTATTATGTAAATGAGA
493094 CAAACAGTAGTAACTCCATGTTTTTTGAATTATGCAATTCAAGTGCTGAAAAGGTCGAATTTTAC
66 CAAACAGTAGTAACTCCATGTTTTTTGAATTATGCAATTCAAGTGCTGAAAAGGTCGAATTTTAC
493159 ATCTTATATGTTAGAGAAGGAATCTGGAGTATCGCATTAAGGCATCTAAACGGAACTGGTGGCAT
131 ATCTTATATGTTAGAGAAGGAATCTGGAGTATCGCATTAAGGCATCTAAACGGAACTGGTGGCAT
493224 TTCCGATGGTCAGACTACTAATATCTATTTCACTTGAAAG
196 TTCCGATGGTCAGACTACTAATATCTATTTCACTTGAAAG
493264 A
1 A
493265 TGCCCAAAAA
Statistics
Matches: 234, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
233 206 0.88
234 7 0.03
235 21 0.09
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.32
Consensus pattern (235 bp):
AATATATGTTAGAAATGGTGGATTGCCATCACATGTTAACTGGGACTATTATTATGTAAATGAGA
CAAACAGTAGTAACTCCATGTTTTTTGAATTATGCAATTCAAGTGCTGAAAAGGTCGAATTTTAC
ATCTTATATGTTAGAGAAGGAATCTGGAGTATCGCATTAAGGCATCTAAACGGAACTGGTGGCAT
TTCCGATGGTCAGACTACTAATATCTATTTCACTTGAAAG
Found at i:512301 original size:27 final size:27
Alignment explanation
Indices: 512263--512317 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
512253 GTTGGAGCAA
512263 TATACTGTGCTGACAAATGAACTCAAG
1 TATACTGTGCTGACAAATGAACTCAAG
512290 TATACTGTGCTGACAAATGAACTCAAG
1 TATACTGTGCTGACAAATGAACTCAAG
512317 T
1 T
512318 TTTCTCTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (27 bp):
TATACTGTGCTGACAAATGAACTCAAG
Found at i:517111 original size:3 final size:3
Alignment explanation
Indices: 517097--517161 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
517087 TTTATTCGGG
*
517097 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
517145 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
517162 CAGGCATAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:525221 original size:36 final size:35
Alignment explanation
Indices: 525171--525291 Score: 134
Period size: 36 Copynumber: 3.3 Consensus size: 35
525161 ACTCATAATC
*
525171 ATCTCACTTAAGATTACTTTTCTTAAAACATATTTT
1 ATCTCACTTGAGATTA-TTTTCTTAAAACATATTTT
* * *
525207 ACCTCACTTGAGATTGTTTTTCTTAAAACAAATTTT
1 ATCTCACTTGAGATT-ATTTTCTTAAAACATATTTT
* * * *
525243 ATTTCACTTGAGATTATTTTTTCTAAAAAATAAATTT
1 ATCTCACTTGAGATTATTTTCT-TAAAACAT-ATTTT
525280 ATCTCACTTGAG
1 ATCTCACTTGAG
525292 GTTGTTTTAC
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
35 5 0.07
36 50 0.71
37 15 0.21
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (35 bp):
ATCTCACTTGAGATTATTTTCTTAAAACATATTTT
Found at i:527216 original size:12 final size:12
Alignment explanation
Indices: 527196--527233 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
527186 TTAAAAATAA
527196 TTTTT-AGGAAT
1 TTTTTCAGGAAT
527207 TTTTTCAGGAAT
1 TTTTTCAGGAAT
527219 TTTTTCAGGAAT
1 TTTTTCAGGAAT
527231 TTT
1 TTT
527234 CCGATACCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 5 0.19
12 21 0.81
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.55
Consensus pattern (12 bp):
TTTTTCAGGAAT
Found at i:530790 original size:218 final size:216
Alignment explanation
Indices: 530265--530929 Score: 1048
Period size: 218 Copynumber: 3.1 Consensus size: 216
530255 ATCGTTGCAA
* * ** *
530265 CAGGTTCCTTTGATGTGTGCAAGGGTAAGCCTTACAATTT-CCCTAGGTTATTTTGCTGTGTGTA
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCTAGGTCCTTTTGCTGTGTGCA
*
530329 AGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
66 AGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTCCC
* * *
530394 CAGGTTCATTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCTAGGTCCCTTTTGCTGTGTGC
131 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC-AGGTTCC-TTTGTTGTGTGC
530459 AAGGGTAAGCCTTACAGTTTCCCC
194 AAGGGTAAGCCTTACAGTTT-CCC
*
530483 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC-AGGTTCC-TTTGCTGTGTGC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCTAGG-TCCTTTTGCTGTGTGC
* *
530546 AAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTCTGTGAAAGGGTAAGCCTTACAGTTTCC
65 AAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTCC
* *
530611 CCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTTCCTTTGTTATGTGCA
130 CCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCA
530676 AGGGTAAGCCTTACAGTTTCCC
195 AGGGTAAGCCTTACAGTTTCCC
* * *
530698 CAGGTTCATTTGTTGTGTGCAAGGGTAAGCTTTACAGTTTCCCCTAGGTCCCTTTTGCTGTATGC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCTAGGT-CCTTTTGCTGTGTGC
* *
530763 AAGGGTAAGCTTTACAGTTTCCCCCAGGTCCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTC
65 AAGGGTAAGCCTTACAGTTT-CCCCAGGTTCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTC
* *
530828 CCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCTAGGTTCATTTGTTGTGTGC
129 CCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTGTGTGC
530893 AAGGGTAAGCCTTACAGTTTCCC
194 AAGGGTAAGCCTTACAGTTTCCC
* *
530916 CAGGCTCTTTTGTT
1 CAGGTTCCTTTGTT
530930 ATATGCAATG
Statistics
Matches: 414, Mismatches: 27, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
215 45 0.11
216 35 0.08
217 35 0.08
218 295 0.71
219 4 0.01
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (216 bp):
CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCTAGGTCCTTTTGCTGTGTGCA
AGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTCCC
CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAA
GGGTAAGCCTTACAGTTTCCC
Found at i:530814 original size:304 final size:304
Alignment explanation
Indices: 530265--530919 Score: 1157
Period size: 304 Copynumber: 2.2 Consensus size: 304
530255 ATCGTTGCAA
* * * * *
530265 CAGGTTCCTTTGATGTGTGCAAGGGTAAGCCTTACAATTTCCCTAGGTTATTTTGCTGTGTGTAA
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTACTTTGCTGTGTGCAA
* *
530330 GGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
66 GGGTAAGCCTTACAGTTTCCCCAAGTTCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTCCCC
*
530395 AGGTTCATTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCTAGGTCCCTTTTGCTGTGTGCA
131 AGGTTCATTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCTAGGTCCCTTTTGCTGTATGCA
*
530460 AGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCC
196 AGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTCC
530525 CCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
261 CCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* * *
530569 CAGGTTCCTTTGTTCTGTGAAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAA
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTACTTTGCTGTGTGCAA
530634 GGGTAAGCCTTACAGTTTCCCCAAGTTCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTCCCC
66 GGGTAAGCCTTACAGTTTCCCCAAGTTCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTCCCC
* *
530699 AGGTTCATTTGTTGTGTGCAAGGGTAAGCTTTACAGTTTCCCCTAGGTCCCTTTTGCTGTATGCA
131 AGGTTCATTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCTAGGTCCCTTTTGCTGTATGCA
*
530764 AGGGTAAGCTTTACAGTTTCCCCCAGGTCCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTCC
196 AGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTCC
530829 CCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
261 CCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
530873 TAGGTTCATTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGG
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGG
530920 CTCTTTTGTT
Statistics
Matches: 332, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
304 332 1.00
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.34
Consensus pattern (304 bp):
CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTACTTTGCTGTGTGCAA
GGGTAAGCCTTACAGTTTCCCCAAGTTCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTCCCC
AGGTTCATTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCTAGGTCCCTTTTGCTGTATGCA
AGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTCC
CCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
Found at i:530937 original size:43 final size:43
Alignment explanation
Indices: 530265--530929 Score: 997
Period size: 43 Copynumber: 15.3 Consensus size: 43
530255 ATCGTTGCAA
* *
530265 CAGGTTCCTTTGATGTGTGCAAGGGTAAGCCTTACAATTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* ** * *
530308 TAGGTTATTTTGCTGTGTGTAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
530351 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
530394 CAGGTTCATTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
530437 CTAGGTCCCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
1 C-AGGTTCC-TTTGTTGTGTGCAAGGGTAAGCCTTACAGTTT-CCC
*
530483 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
*
530526 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
530569 CAGGTTCCTTTGTTCTGTGAAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
*
530612 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
530655 CAAGTTCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
530698 CAGGTTCATTTGTTGTGTGCAAGGGTAAGCTTTACAGTTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* * * *
530741 CTAGGTCCCTTTTGCTGTATGCAAGGGTAAGCTTTACAGTTTCCCC
1 C-AGGTTCC-TTTGTTGTGTGCAAGGGTAAGCCTTACAGTTT-CCC
* *
530787 CAGGTCCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
*
530830 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
530873 TAGGTTCATTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
530916 CAGGCTCTTTTGTT
1 CAGGTTCCTTTGTT
530930 ATATGCAATG
Statistics
Matches: 568, Mismatches: 48, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
43 415 0.73
44 69 0.12
45 76 0.13
46 8 0.01
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (43 bp):
CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
Found at i:533636 original size:24 final size:24
Alignment explanation
Indices: 533595--533651 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
533585 TGCTCCACAT
*
533595 TTCTTA-ATG-ATATGCCCTGAGC
1 TTCTTATATGAATATACCCTGAGC
533617 TTCTTATATGAATATACCCTGAGC
1 TTCTTATATGAATATACCCTGAGC
*
533641 TTCATATATGA
1 TTCTTATATGA
533652 TGTTAACATC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 6 0.19
23 3 0.10
24 22 0.71
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (24 bp):
TTCTTATATGAATATACCCTGAGC
Found at i:535167 original size:15 final size:15
Alignment explanation
Indices: 535147--535186 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
535137 TAAAGTTGAT
535147 AAAAAATTTAATAAC
1 AAAAAATTTAATAAC
* *
535162 AAAAAAATTCATAAC
1 AAAAAATTTAATAAC
535177 AAAAAATTTA
1 AAAAAATTTA
535187 TTTTAGTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAAAATTTAATAAC
Found at i:535433 original size:21 final size:21
Alignment explanation
Indices: 535407--535453 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
535397 AAAACTTATA
535407 TGACAA-TCTACAATATTGATG
1 TGACAATTC-ACAATATTGATG
* *
535428 TGACAATTCACGATATTGTTG
1 TGACAATTCACAATATTGATG
535449 TGACA
1 TGACA
535454 GTACTTGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (21 bp):
TGACAATTCACAATATTGATG
Found at i:535627 original size:42 final size:43
Alignment explanation
Indices: 535536--535632 Score: 105
Period size: 42 Copynumber: 2.3 Consensus size: 43
535526 TAAAAAATTA
*
535536 AAAAATAAATTAAAATATAAAATATAAACAATTATTAAGATATT
1 AAAAATAAATT-AAATATAAAATATAAACAATAATTAAGATATT
*
535580 --CAATAAATTAAATATAAAA-ATAATACAA-AATTAA-ATTATT
1 AAAAATAAATTAAATATAAAATATAA-ACAATAATTAAGA-TATT
*
535620 AAAAATAATTTAA
1 AAAAATAAATTAA
535633 GGATTACATT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
39 1 0.02
40 13 0.29
41 14 0.31
42 17 0.38
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (43 bp):
AAAAATAAATTAAATATAAAATATAAACAATAATTAAGATATT
Found at i:536071 original size:22 final size:22
Alignment explanation
Indices: 536046--536095 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
536036 AAAATTAAAC
536046 TTAAAATGTA-ATTATTAT-TTAA
1 TTAAAATGTATATT-TTATATT-A
536068 TT-AAATGTATATTTTATATTA
1 TTAAAATGTATATTTTATATTA
536089 TTAAAAT
1 TTAAAAT
536096 TATTTATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TTAAAATGTATATTTTATATTA
Found at i:536578 original size:60 final size:60
Alignment explanation
Indices: 536500--536624 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 60
536490 GAACAAATGA
* * *
536500 ATAGTTGAGTGACAATTTTGTAACTTTTAATAGTCGA-GAGACTCAGCAAAATAATATCCT
1 ATAGTTGAGGGACAATTTTATAACTTTTAATAGTCGAGGA-ACTCAACAAAATAATATCCT
* * * * *
536560 ATAGTTGGGGGACTATTTTATAACTTTTAATAGTTGAGGAACTCAACAAAATAATTTCTT
1 ATAGTTGAGGGACAATTTTATAACTTTTAATAGTCGAGGAACTCAACAAAATAATATCCT
536620 ATAGT
1 ATAGT
536625 CGGGAACCAT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 54 0.96
61 2 0.04
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (60 bp):
ATAGTTGAGGGACAATTTTATAACTTTTAATAGTCGAGGAACTCAACAAAATAATATCCT
Found at i:559549 original size:20 final size:19
Alignment explanation
Indices: 559505--559551 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
559495 GGTTTTAAAA
* *
559505 TTTTATTTTCCTTTTTCTT
1 TTTTATTTTCCATTTGCTT
*
559524 TCTTATTTTCTCATTTGCTT
1 TTTTATTTTC-CATTTGCTT
559544 TTTTATTT
1 TTTTATTT
559552 ATGCTCTCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.09, C:0.15, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTATTTTCCATTTGCTT
Found at i:559582 original size:7 final size:7
Alignment explanation
Indices: 559570--559646 Score: 118
Period size: 7 Copynumber: 11.0 Consensus size: 7
559560 CTTCTCTCTC
*
559570 TGCGCTT
1 TGCGTTT
*
559577 TGCGCTT
1 TGCGTTT
*
559584 TGCGCTT
1 TGCGTTT
*
559591 TGCGCTT
1 TGCGTTT
559598 TGCGTTT
1 TGCGTTT
559605 TGCGTTT
1 TGCGTTT
559612 TGCGTTT
1 TGCGTTT
559619 TGCGTTT
1 TGCGTTT
559626 TGCGTTT
1 TGCGTTT
559633 TGCGTTT
1 TGCGTTT
559640 TGCGTTT
1 TGCGTTT
559647 GGTGCTTATT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
7 69 1.00
ACGTcount: A:0.00, C:0.19, G:0.29, T:0.52
Consensus pattern (7 bp):
TGCGTTT
Found at i:559944 original size:21 final size:21
Alignment explanation
Indices: 559918--559957 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
559908 ATAAAAGTAA
*
559918 TAAAATATTATTATTTTTACT
1 TAAAATATTAATATTTTTACT
559939 TAAAATATTAATATTTTTA
1 TAAAATATTAATATTTTTA
559958 ACATTTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TAAAATATTAATATTTTTACT
Found at i:560004 original size:21 final size:21
Alignment explanation
Indices: 559978--560029 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
559968 TAAAGTACGT
559978 AATAATAATAAAATTGATAAA
1 AATAATAATAAAATTGATAAA
*
559999 AATAATAACAAAATTGATAAA
1 AATAATAATAAAATTGATAAA
560020 AATAATAATA
1 AATAATAATA
560030 TTTATAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (21 bp):
AATAATAATAAAATTGATAAA
Found at i:560861 original size:2 final size:2
Alignment explanation
Indices: 560854--560884 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
560844 AGCTTTTAGA
560854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
560885 GGGTCGGCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:561090 original size:73 final size:72
Alignment explanation
Indices: 560958--561098 Score: 210
Period size: 73 Copynumber: 1.9 Consensus size: 72
560948 TTTTAAATTT
* * * * *
560958 AATAATTAAAAAATATTTTTAAATATACTTTTTATTTCAAATACTCTAAAATATAGTAATTTAGT
1 AATAATTAAAAAATATTTTTAAACATACTTTTTATTTAAAAAACTCGAAAATATAGTAATTCAGT
561023 GGGCCTC
66 GGGCCTC
* *
561030 AATAATTAAAAAATATTTTTAAACATCATTTTTTATTTAAAAAACTCGAAAATATGGTAATTCAG
1 AATAATTAAAAAATATTTTTAAACAT-ACTTTTTATTTAAAAAACTCGAAAATATAGTAATTCAG
561095 TGGG
65 TGGG
561099 TCCTATTTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
72 25 0.41
73 36 0.59
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (72 bp):
AATAATTAAAAAATATTTTTAAACATACTTTTTATTTAAAAAACTCGAAAATATAGTAATTCAGT
GGGCCTC
Found at i:563118 original size:3 final size:3
Alignment explanation
Indices: 563112--563174 Score: 81
Period size: 3 Copynumber: 20.3 Consensus size: 3
563102 TTTAAAAAAA
* *
563112 TAT TAT TAT TAT ATAT TAT TAT TAT TAT TAT TAT TGT TAT TTT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
563158 TAA TAT TATT TAT TAT T
1 TAT TAT TA-T TAT TAT T
563175 GTTGCAGGCC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:564761 original size:2 final size:2
Alignment explanation
Indices: 564754--564792 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
564744 CATGAACAAG
564754 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
564793 GTTTATGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:564905 original size:2 final size:2
Alignment explanation
Indices: 564898--564930 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
564888 TTTAAAACAA
564898 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
564931 TTCTTTGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:580504 original size:64 final size:65
Alignment explanation
Indices: 580418--580542 Score: 191
Period size: 64 Copynumber: 1.9 Consensus size: 65
580408 TGCACTAAGA
* *
580418 GTGCATCGATGCATCAACTGCATTCGATG-TTTCA-AAATAGCCAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCCACAGTGCATCGATGCATGGCT
580481 G
65 G
* *
580482 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATG
580543 AAATGCATTC
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
64 28 0.51
65 24 0.44
66 3 0.05
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGCTG
Found at i:580555 original size:64 final size:64
Alignment explanation
Indices: 580419--580556 Score: 165
Period size: 64 Copynumber: 2.2 Consensus size: 64
580409 GCACTAAGAG
* * ***
580419 TGCATCGATGCATCAACTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCAAA
* *
580483 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCAT-G-AA
1 TGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGGCAA
580545 A
64 A
580546 TGCATTCGATG
1 TGCA-TCGATG
580557 TTCAATTTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
63 4 0.06
64 34 0.53
65 23 0.36
66 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCAAA
Found at i:581720 original size:30 final size:30
Alignment explanation
Indices: 581661--581756 Score: 149
Period size: 30 Copynumber: 3.2 Consensus size: 30
581651 CCCGAAGGAC
* *
581661 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
581690 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
581720 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
581750 CTGTCCA
1 CTATCCA
581757 TATGTTCCTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
29 19 0.30
30 44 0.70
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:581787 original size:31 final size:31
Alignment explanation
Indices: 581745--581840 Score: 176
Period size: 31 Copynumber: 3.1 Consensus size: 31
581735 AAAGATCCTC
581745 GGTA-ACTGTCCATATGTTCCTTAGAACATA
1 GGTATACTGTCCATATGTTCCTTAGAACATA
581775 GGTATACTGTCCATATGTTCCTTAGAACATA
1 GGTATACTGTCCATATGTTCCTTAGAACATA
*
581806 GGTATACTGTCCATATGTTCCGTAGAACATA
1 GGTATACTGTCCATATGTTCCTTAGAACATA
581837 GGTA
1 GGTA
581841 AACCCTCGAC
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
30 4 0.06
31 60 0.94
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (31 bp):
GGTATACTGTCCATATGTTCCTTAGAACATA
Found at i:582638 original size:21 final size:21
Alignment explanation
Indices: 582608--582652 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
582598 GAATTCTCGT
* *
582608 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
582629 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
582650 TTG
1 TTG
582653 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:584289 original size:188 final size:189
Alignment explanation
Indices: 583972--584349 Score: 749
Period size: 188 Copynumber: 2.0 Consensus size: 189
583962 CCGGTTCTGA
583972 TGCAGGCTCATCGTCTGGAACGTGATCGTTGATATCTTGCATAAGTTGTTGAAACTCAGGATCAT
1 TGCAGGCTCATCGTCTGGAACGTGATCGTTGATATCTTGCATAAGTTGTTGAAACTCAGGATCAT
584037 CGTCAGCAGCCAGTGCCGGAGAAGGAGGATGAGGAGCACGAGAAGAGCTAGGAGTAGCTCGTGAA
66 CGTCAGCAGCCAGTGCCGGAGAAGGAGGATGAGGAGCACGAGAAGAGCTAGGAGTAGCTCGTGAA
584102 GAGCTAGCTCCCGGGGTTTGCTTACCGGGTC-AAATACCCAAAGATCAGTTTCCTCGTC
131 GAGCTAGCTCCCGGGGTTTGCTTACCGGGTCAAAATACCCAAAGATCAGTTTCCTCGTC
584160 TGCAGGCTCATCGTCTGGAACGTGATCGTTGATATCTTGCATAAGTTGTTGAAACTCAGGATCAT
1 TGCAGGCTCATCGTCTGGAACGTGATCGTTGATATCTTGCATAAGTTGTTGAAACTCAGGATCAT
584225 CGTCAGCAGCCAGTGCCGGAGAAGGAGGATGAGGAGCACGAGAAGAGCTAGGAGTAGCTCGTGAA
66 CGTCAGCAGCCAGTGCCGGAGAAGGAGGATGAGGAGCACGAGAAGAGCTAGGAGTAGCTCGTGAA
584290 GAGCTAGCTCCCGGGGTTTGCTTACCGGGTCAAAATACCCAAAGATCAGTTTCCTCGTC
131 GAGCTAGCTCCCGGGGTTTGCTTACCGGGTCAAAATACCCAAAGATCAGTTTCCTCGTC
584349 T
1 T
584350 TGTTTCCAAT
Statistics
Matches: 189, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
188 161 0.85
189 28 0.15
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.23
Consensus pattern (189 bp):
TGCAGGCTCATCGTCTGGAACGTGATCGTTGATATCTTGCATAAGTTGTTGAAACTCAGGATCAT
CGTCAGCAGCCAGTGCCGGAGAAGGAGGATGAGGAGCACGAGAAGAGCTAGGAGTAGCTCGTGAA
GAGCTAGCTCCCGGGGTTTGCTTACCGGGTCAAAATACCCAAAGATCAGTTTCCTCGTC
Found at i:585857 original size:23 final size:22
Alignment explanation
Indices: 585830--585909 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
585820 GCATGGGCTT
585830 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
585852 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
585874 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
585896 ATGCATCGATGCAC
1 GTGCATCGATGCAC
585910 TGTTAGGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 15 0.32
22 16 0.34
23 16 0.34
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:585883 original size:44 final size:42
Alignment explanation
Indices: 585834--585928 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 42
585824 GGGCTTGTGC
* *
585834 ATCGATGCACATTCAAGGCGTGCATCGGTGCACCT-TCATGGTGT
1 ATCGATGCACATTCAAGG-ATGCATCGATGCA-CTGTCA-GGTGT
*
585878 ATCGATGCACATTCAAGGATGCATCGATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGT
585920 ATCGATGCA
1 ATCGATGCA
585929 TGAAGCACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
42 16 0.34
43 13 0.28
44 18 0.38
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGT
Found at i:585925 original size:20 final size:21
Alignment explanation
Indices: 585834--585928 Score: 86
Period size: 21 Copynumber: 4.4 Consensus size: 21
585824 GGGCTTGTGC
*
585834 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* * *
585857 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
*
585878 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
585900 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
585920 ATCGATGCA
1 ATCGATGCA
585929 TGAAGCACAA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 11 0.18
21 22 0.37
22 14 0.23
23 13 0.22
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:590355 original size:24 final size:23
Alignment explanation
Indices: 590327--590384 Score: 100
Period size: 22 Copynumber: 2.5 Consensus size: 23
590317 TCCAGAGGGA
590327 ACCGATTCCCTCCCCCAAGGGGGT
1 ACCGATTCCC-CCCCCAAGGGGGT
590351 ACCGATT-CCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCCAAGGGGGT
590373 ACCGATTCCCCC
1 ACCGATTCCCCC
590385 TGAATGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
22 20 0.61
23 6 0.18
24 7 0.21
ACGTcount: A:0.17, C:0.45, G:0.22, T:0.16
Consensus pattern (23 bp):
ACCGATTCCCCCCCCAAGGGGGT
Found at i:596242 original size:22 final size:21
Alignment explanation
Indices: 596216--596273 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
596206 TTAGTGCAGA
*
596216 GGGAATCGATACCCCCTTGA-AG
1 GGGAATCGATACCCCC--CACAG
* *
596238 GGGAACCGATTCCCCCCACAG
1 GGGAATCGATACCCCCCACAG
596259 GGGAATCGATACCCC
1 GGGAATCGATACCCC
596274 ATGAGAGTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 1 0.03
21 15 0.50
22 14 0.47
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.14
Consensus pattern (21 bp):
GGGAATCGATACCCCCCACAG
Found at i:597861 original size:18 final size:19
Alignment explanation
Indices: 597835--597882 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
597825 GACGACTCTG
* *
597835 ACGATGAACCAGAAC-AGC
1 ACGAGGAACAAGAACGAGC
*
597853 ACGAGGAACAAGCACGAGC
1 ACGAGGAACAAGAACGAGC
597872 A-GAGGAACAAG
1 ACGAGGAACAAG
597883 CACAACCAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.46, C:0.23, G:0.29, T:0.02
Consensus pattern (19 bp):
ACGAGGAACAAGAACGAGC
Found at i:597883 original size:18 final size:18
Alignment explanation
Indices: 597850--597895 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
597840 GAACCAGAAC
*
597850 AGCACGAGGAACAAGCACG
1 AGCA-GAGGAACAAGCACA
597869 AGCAGAGGAACAAGCACA
1 AGCAGAGGAACAAGCACA
*
597887 ACCAGAGGA
1 AGCAGAGGA
597896 TCAAATGCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.46, C:0.24, G:0.30, T:0.00
Consensus pattern (18 bp):
AGCAGAGGAACAAGCACA
Found at i:601290 original size:19 final size:20
Alignment explanation
Indices: 601266--601312 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 20
601256 AAAATAGCCA
601266 GAGTGCATCGATGCATGG-T
1 GAGTGCATCGATGCATGGCT
601285 GAGTGCATCGATGCATGGCT
1 GAGTGCATCGATGCATGGCT
601305 G-GTGCATC
1 GAGTGCATC
601313 AAATGCATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 25 0.93
20 2 0.07
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.26
Consensus pattern (20 bp):
GAGTGCATCGATGCATGGCT
Found at i:601371 original size:75 final size:75
Alignment explanation
Indices: 601232--601372 Score: 171
Period size: 75 Copynumber: 1.9 Consensus size: 75
601222 AGTGCAACGA
* * * * *
601232 TGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGTGAGTGCATCGAT
1 TGCATCAAATGCATTCAATGTTTCAAAATAGCCACAGTGCATCGATGCATGGTAAATGCATCGAT
601297 GCATGGCTGG
66 GCATGGCTGG
* *
601307 TGCATCAAATGCATTCAATGTTTTCATAAA-ATCCTCAGTGCATCGATGCAT-G-AAATGCATTC
1 TGCATCAAATGCATTCAATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGGTAAATGCA-TC
601369 GATG
63 GATG
601373 TTCAATTTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
74 5 0.09
75 25 0.45
76 23 0.41
77 3 0.05
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.29
Consensus pattern (75 bp):
TGCATCAAATGCATTCAATGTTTCAAAATAGCCACAGTGCATCGATGCATGGTAAATGCATCGAT
GCATGGCTGG
Found at i:606390 original size:18 final size:19
Alignment explanation
Indices: 606362--606397 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
606352 TCTTCTTATT
*
606362 TTTACTTTAATTGCTTTTA
1 TTTACTTTAATCGCTTTTA
606381 TTTA-TTTAATCGCTTTT
1 TTTACTTTAATCGCTTTT
606398 TATTATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.19, C:0.11, G:0.06, T:0.64
Consensus pattern (19 bp):
TTTACTTTAATCGCTTTTA
Found at i:609211 original size:5 final size:6
Alignment explanation
Indices: 609195--609234 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
609185 TTTCCGTTAA
*
609195 ATTTTT ATTTTT ATTTTT ATTTTC ACTTTTT ATTTTT ATT
1 ATTTTT ATTTTT ATTTTT ATTTTT A-TTTTT ATTTTT ATT
609235 CGATCAAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (6 bp):
ATTTTT
Found at i:612715 original size:18 final size:18
Alignment explanation
Indices: 612687--612729 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
612677 TCTTCTTATT
*
612687 TTTACTTTAATTGCTTTTA
1 TTTA-TTTAATCGCTTTTA
*
612706 TTTATTTAATCGTTTTTA
1 TTTATTTAATCGCTTTTA
612724 -TTATTT
1 TTTATTT
612730 TAATATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 12 0.55
19 4 0.18
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTATTTAATCGCTTTTA
Found at i:623929 original size:59 final size:59
Alignment explanation
Indices: 623816--623931 Score: 141
Period size: 59 Copynumber: 2.0 Consensus size: 59
623806 TTTAAATTGG
* *
623816 TCCTTACACTTTTGATATTCTAATCTTATCCTCAAACTATGATACTCGTTCTAAACTAA
1 TCCTTACACTTTTGACATTCTAATCTTATCCTCAAACTATGACACTCGTTCTAAACTAA
*
623875 TCCTTA-ACTTTTGAGCATTCTAAT-TTCATCC-CTAAACTATGACCCTC-TTACTAAACT
1 TCCTTACACTTTTGA-CATTCTAATCTT-ATCCTC-AAACTATGACACTCGTT-CTAAACT
623932 GGTTCCAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
58 13 0.26
59 37 0.74
ACGTcount: A:0.29, C:0.26, G:0.05, T:0.40
Consensus pattern (59 bp):
TCCTTACACTTTTGACATTCTAATCTTATCCTCAAACTATGACACTCGTTCTAAACTAA
Found at i:624479 original size:2 final size:2
Alignment explanation
Indices: 624472--624498 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
624462 ATAGATAACT
624472 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 T
624499 CTCACAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:625307 original size:26 final size:26
Alignment explanation
Indices: 625277--625378 Score: 96
Period size: 26 Copynumber: 3.8 Consensus size: 26
625267 TTGAGGTAAT
* *
625277 ATTTATTTATTTATATATTTCGAATA
1 ATTTATTTATTTATATATTTTGAAAA
*
625303 ATTTATTTATCTATATATTTTGAAAA
1 ATTTATTTATTTATATATTTTGAAAA
* * * *
625329 ATTAATTTACGTATATGTTTATTTTGAACA
1 ATTTATTTA--T-T-TATATATTTTGAAAA
*
625359 ATTTATTTATTTATTTATTT
1 ATTTATTTATTTATATATTT
625379 ATCTATTTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
26 39 0.63
27 1 0.02
28 2 0.03
30 20 0.32
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (26 bp):
ATTTATTTATTTATATATTTTGAAAA
Found at i:625380 original size:30 final size:30
Alignment explanation
Indices: 625276--625380 Score: 92
Period size: 30 Copynumber: 3.6 Consensus size: 30
625266 CTTGAGGTAA
* * *
625276 TATTTATTTATTTATATATTTCGAATAATT
1 TATTTATTTATTTATTTATTTTGAAAAATT
*
625306 TATTTATCTA--TA--TATTTTGAAAAATT
1 TATTTATTTATTTATTTATTTTGAAAAATT
* ** * * *
625332 AATTTACGTATATGTTTATTTTGAACAATT
1 TATTTATTTATTTATTTATTTTGAAAAATT
625362 TATTTATTTATTTATTTAT
1 TATTTATTTATTTATTTAT
625381 CTATTTTAAG
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
26 19 0.33
28 3 0.05
30 36 0.62
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (30 bp):
TATTTATTTATTTATTTATTTTGAAAAATT
Found at i:625692 original size:19 final size:20
Alignment explanation
Indices: 625653--625692 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
625643 TAAGTGTTAA
*
625653 TGAATTTTAAGATTTTATAT
1 TGAATTTTAAGATTATATAT
625673 TGAATTTTAA-ATTATATAT
1 TGAATTTTAAGATTATATAT
625692 T
1 T
625693 CGATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TGAATTTTAAGATTATATAT
Found at i:626107 original size:19 final size:20
Alignment explanation
Indices: 626083--626130 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
626073 AACGATTTTC
*
626083 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
626102 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
626122 TTTTGAAAA
1 TTTTGAAAA
626131 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:627904 original size:17 final size:17
Alignment explanation
Indices: 627861--627896 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
627851 TTATTTCATC
627861 TTTCTCTTGTAAATATT
1 TTTCTCTTGTAAATATT
627878 TTTCTCTTGTAAATATT
1 TTTCTCTTGTAAATATT
627895 TT
1 TT
627897 GTTCTTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.11, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTCTCTTGTAAATATT
Found at i:629455 original size:25 final size:26
Alignment explanation
Indices: 629408--629461 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
629398 AATTTAGATT
*
629408 TATTTTTATAAAAGTAATATTTTTAA
1 TATTTTTATAAAAGTAATATTTTAAA
*
629434 TATTTTTA-AAAA-TATATTTTTTAAA
1 TATTTTTATAAAAGTA-ATATTTTAAA
629459 TAT
1 TAT
629462 AATAGTAACG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 2 0.08
25 15 0.60
26 8 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
TATTTTTATAAAAGTAATATTTTAAA
Found at i:629457 original size:24 final size:26
Alignment explanation
Indices: 629408--629454 Score: 73
Period size: 23 Copynumber: 1.9 Consensus size: 26
629398 AATTTAGATT
629408 TATTTTTATAAAAGTAATATTTTTAA
1 TATTTTTATAAAAGTAATATTTTTAA
629434 TATTTTTA-AAAA-T-ATATTTTT
1 TATTTTTATAAAAGTAATATTTTT
629455 TAAATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.38
24 1 0.05
25 4 0.19
26 8 0.38
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TATTTTTATAAAAGTAATATTTTTAA
Found at i:636044 original size:26 final size:26
Alignment explanation
Indices: 636008--636059 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
635998 ACATAACACG
636008 TGTCACATGTAAATTTCTTTTTATTA
1 TGTCACATGTAAATTTCTTTTTATTA
636034 TGTCACATGTAAATTTCTTTTTATTA
1 TGTCACATGTAAATTTCTTTTTATTA
636060 AAAAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.54
Consensus pattern (26 bp):
TGTCACATGTAAATTTCTTTTTATTA
Found at i:637028 original size:21 final size:21
Alignment explanation
Indices: 637002--637052 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
636992 TAAAGTGTCC
637002 AAAAAATAACAAAATCGATAG
1 AAAAAATAACAAAATCGATAG
** *
637023 AAAAAATAGTAAAATCGGTAG
1 AAAAAATAACAAAATCGATAG
*
637044 AAATAATAA
1 AAAAAATAA
637053 TATTTTTGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (21 bp):
AAAAAATAACAAAATCGATAG
Found at i:642280 original size:6 final size:6
Alignment explanation
Indices: 642269--642299 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
642259 GCCTTGTAAA
642269 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC T
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC T
642300 ATTTGACCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCC
Found at i:646076 original size:2 final size:2
Alignment explanation
Indices: 646069--646098 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
646059 ATCAACCTGA
646069 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
646099 TGAATAAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:648823 original size:42 final size:42
Alignment explanation
Indices: 648777--648863 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
648767 TCCTCCAACT
* * *
648777 AAATACTGAAAAATATTTTCCTGAAAACGAATTACATGAAAC
1 AAATACAGAAAAACATTTTCCGGAAAACGAATTACATGAAAC
648819 AAATACAGAAAAACATTTTCCGGAAAACGAATTACATGAAAC
1 AAATACAGAAAAACATTTTCCGGAAAACGAATTACATGAAAC
648861 AAA
1 AAA
648864 CACAAAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.53, C:0.15, G:0.10, T:0.22
Consensus pattern (42 bp):
AAATACAGAAAAACATTTTCCGGAAAACGAATTACATGAAAC
Found at i:649931 original size:16 final size:17
Alignment explanation
Indices: 649910--649952 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
649900 ATGTAAAAAT
649910 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
** *
649926 AAATATAAAAATTTATT
1 AAATATTTAAATTTATA
649943 AAATATTTAA
1 AAATATTTAA
649953 TTAAGTAGGG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:652059 original size:19 final size:19
Alignment explanation
Indices: 652019--652058 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
652009 ATAATTTAAA
652019 TTAATTAATTTTATTTATT
1 TTAATTAATTTTATTTATT
652038 TTAA-TAATATTTATTTTATT
1 TTAATTAAT-TTTA-TTTATT
652058 T
1 T
652059 AGGGTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 8 0.42
20 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTAATTAATTTTATTTATT
Found at i:652116 original size:2 final size:2
Alignment explanation
Indices: 652111--652150 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
652101 AATGTAGTAT
652111 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
652151 CTGTCTATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:652710 original size:31 final size:31
Alignment explanation
Indices: 652672--652750 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
652662 AAAAAACCCA
*
652672 TAAGTTTTGGTCACTTACGTTATTATTTTAT
1 TAAGTTTTGGTCACTTACGTTATCATTTTAT
* * *
652703 TAAGTTTTGGCCACTTATGTTATCGTTTTAT
1 TAAGTTTTGGTCACTTACGTTATCATTTTAT
* * *
652734 AAAATTTTGGTTACTTA
1 TAAGTTTTGGTCACTTA
652751 GTAGTTGAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACGTTATCATTTTAT
Found at i:654391 original size:14 final size:14
Alignment explanation
Indices: 654372--654404 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
654362 CGACACAAAT
654372 GAACAAATATAAAC
1 GAACAAATATAAAC
*
654386 GAACAAATGTAAAC
1 GAACAAATATAAAC
654400 GAACA
1 GAACA
654405 CAACAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.61, C:0.15, G:0.12, T:0.12
Consensus pattern (14 bp):
GAACAAATATAAAC
Found at i:654474 original size:23 final size:23
Alignment explanation
Indices: 654448--654496 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
654438 AATCTGCACA
* *
654448 AACATAACAAATGAACATAATCG
1 AACACAACAAATGAACATAAACG
* *
654471 AACACAATAAATGAACTTAAACG
1 AACACAACAAATGAACATAAACG
654494 AAC
1 AAC
654497 GTAAACAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.57, C:0.18, G:0.08, T:0.16
Consensus pattern (23 bp):
AACACAACAAATGAACATAAACG
Found at i:656725 original size:39 final size:39
Alignment explanation
Indices: 656671--656748 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
656661 TTATCCTTAT
* *
656671 GCCCATAAGGACTTACCCAATGCATATAGTAGAAGAGCC
1 GCCCATAAGGACTTACCCAATGCATATAGCAAAAGAGCC
656710 GCCCATAAGGACTTACCCAATGCATATAGCAAAAGAGCC
1 GCCCATAAGGACTTACCCAATGCATATAGCAAAAGAGCC
656749 ACCCTAAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (39 bp):
GCCCATAAGGACTTACCCAATGCATATAGCAAAAGAGCC
Found at i:657063 original size:21 final size:22
Alignment explanation
Indices: 657023--657065 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
657013 TTATCAAAGA
*
657023 GGAATCGATTCCCCTGCTACAG
1 GGAATCGATTACCCTGCTACAG
*
657045 GGAATCGA-TACCTTGCTACAG
1 GGAATCGATTACCCTGCTACAG
657066 TACTGCTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (22 bp):
GGAATCGATTACCCTGCTACAG
Found at i:660411 original size:20 final size:20
Alignment explanation
Indices: 660361--660412 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
660351 ACCGATTCAG
* * *
660361 GTTGACTCAGGTTGGTTCGG
1 GTTGACTCAGTTTGGTCCGA
*
660381 GTTGATTCAGTTTGGTCCGA
1 GTTGACTCAGTTTGGTCCGA
660401 GTTGACTCAGTT
1 GTTGACTCAGTT
660413 CGATCTGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.13, C:0.15, G:0.33, T:0.38
Consensus pattern (20 bp):
GTTGACTCAGTTTGGTCCGA
Found at i:662342 original size:2 final size:2
Alignment explanation
Indices: 662335--662365 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
662325 ACTTAAATTA
662335 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
662366 ATTTTAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:663450 original size:3 final size:3
Alignment explanation
Indices: 663431--663470 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
663421 TTAAGACATA
663431 TAT TA- TAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT T
663471 GGTTTGGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:680728 original size:36 final size:36
Alignment explanation
Indices: 680649--680735 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 36
680639 TTATCCCATT
* *
680649 ATCATTTTTC-AACAAACATCTATCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATCTACCAAACTTTGAAA
* *
680684 AACTATTTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATC-ATTTTTCAAAGAAACATCTACCAAACTTTGAAA
680721 ATCATTTTTTCAAAG
1 ATCA-TTTTTCAAAG
680736 TTGGTTACCA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
35 2 0.05
36 8 0.18
37 34 0.77
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (36 bp):
ATCATTTTTCAAAGAAACATCTACCAAACTTTGAAA
Found at i:684818 original size:16 final size:16
Alignment explanation
Indices: 684794--684832 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
684784 TATCGCCGAT
*
684794 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
684810 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
684826 CGTAAAT
1 CG-AAAT
684833 AGTAACCTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:685282 original size:37 final size:36
Alignment explanation
Indices: 685223--685342 Score: 163
Period size: 35 Copynumber: 3.3 Consensus size: 36
685213 ATCCCATTAT
* *
685223 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
685258 CTATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
* *
685295 CA-TTTTCAAAGAAACATTCACCAAACTTTGAAAAT
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
685330 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
685343 TTGGTTACGA
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
35 34 0.45
36 8 0.11
37 34 0.45
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
Found at i:688246 original size:13 final size:13
Alignment explanation
Indices: 688228--688254 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
688218 TCTCAACACA
688228 TAACTACTCAAAT
1 TAACTACTCAAAT
688241 TAACTACTCAAAT
1 TAACTACTCAAAT
688254 T
1 T
688255 TAAGACCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (13 bp):
TAACTACTCAAAT
Found at i:694442 original size:24 final size:25
Alignment explanation
Indices: 694414--694496 Score: 75
Period size: 24 Copynumber: 3.3 Consensus size: 25
694404 ATATAATATA
694414 ATTTTATATTTA-TTAAATTAAAAT
1 ATTTTATATTTACTTAAATTAAAAT
694438 ATTTT-TATGTTAACTT--ATTAAATAT
1 ATTTTATAT-TT-ACTTAAATTAAA-AT
* *
694463 ATTTTATTATTAACTTAATTTCAAAAT
1 ATTTTA-TATTTACTTAAATT-AAAAT
694490 ATTTTAT
1 ATTTTAT
694497 TTTCATTTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
23 3 0.06
24 13 0.27
25 12 0.25
26 4 0.08
27 13 0.27
28 3 0.06
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (25 bp):
ATTTTATATTTACTTAAATTAAAAT
Found at i:694475 original size:25 final size:24
Alignment explanation
Indices: 694434--694535 Score: 84
Period size: 25 Copynumber: 4.1 Consensus size: 24
694424 TATTAAATTA
*
694434 AAATAT-TTTTATGTTAACTTATT
1 AAATATATTTTATTTTAACTTATT
694457 AAATATATTTTATTATTAACTTAATTT
1 AAATATATTTTATT-TTAACTT-A-TT
* * *
694484 CAAA-ATATTTTATTTTCATTTA-A
1 -AAATATATTTTATTTTAACTTATT
*
694507 AAATATATAATTTATTTTAATTTATT
1 AAATATAT--TTTATTTTAACTTATT
694533 AAA
1 AAA
694536 AGTATGAATA
Statistics
Matches: 64, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
22 3 0.05
23 10 0.16
24 6 0.09
25 21 0.33
26 9 0.14
27 12 0.19
28 3 0.05
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (24 bp):
AAATATATTTTATTTTAACTTATT
Found at i:694519 original size:21 final size:21
Alignment explanation
Indices: 694480--694519 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
694470 TATTAACTTA
* * *
694480 ATTTCAAAATATTTTATTTTC
1 ATTTAAAAATATATAATTTTC
694501 ATTTAAAAATATATAATTT
1 ATTTAAAAATATATAATTT
694520 ATTTTAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAAAAATATATAATTTTC
Found at i:695008 original size:23 final size:23
Alignment explanation
Indices: 694959--695022 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
694949 GTTTTATATT
* *
694959 TTTATAAAAAGTATA-TGAAATA
1 TTTATAAAAAATATATTTAAATA
694981 TTTATAAAAAATATATTTACAATA
1 TTTATAAAAAATATATTTA-AATA
* *
695005 -TTATAAAATATTTATTTA
1 TTTATAAAAAATATATTTA
695023 TTTTTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 14 0.39
23 18 0.50
24 4 0.11
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (23 bp):
TTTATAAAAAATATATTTAAATA
Found at i:695062 original size:23 final size:24
Alignment explanation
Indices: 695016--695062 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
695006 TATAAAATAT
*
695016 TTATTTATTTTTAAAATCCAACTAA
1 TTATTTA-TTTTAAAATACAACTAA
*
695041 TTATTTA-TTTAAAATACTACTA
1 TTATTTATTTTAAAATACAACTA
695063 TTTTCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
25 7 0.35
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (24 bp):
TTATTTATTTTAAAATACAACTAA
Found at i:695240 original size:23 final size:23
Alignment explanation
Indices: 695178--695243 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
695168 TAGATAATTT
* *
695178 TAAAGTAATATTATTTCAAATAAA
1 TAAA-TAATATGATTTTAAATAAA
*
695202 TAAATAATATTG-TTTTAGATAAA
1 TAAATAATA-TGATTTTAAATAAA
695225 TAAATAATATGATTTTAAA
1 TAAATAATATGATTTTAAA
695244 AGTTAAACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 2 0.06
23 29 0.81
24 5 0.14
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (23 bp):
TAAATAATATGATTTTAAATAAA
Found at i:695851 original size:42 final size:40
Alignment explanation
Indices: 695796--695880 Score: 125
Period size: 42 Copynumber: 2.1 Consensus size: 40
695786 ATCAGGCCTG
695796 ATATATATATTTAAATTAAATATATAAATATTATATATAT
1 ATATATATATTTAAATTAAATATATAAATATTATATATAT
* * *
695836 ATATATATGAATTTAAATTTAATTTATTAATATTATATATAT
1 ATATATAT--ATTTAAATTAAATATATAAATATTATATATAT
695878 ATA
1 ATA
695881 ATAATTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 8 0.20
42 32 0.80
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (40 bp):
ATATATATATTTAAATTAAATATATAAATATTATATATAT
Found at i:695922 original size:12 final size:13
Alignment explanation
Indices: 695902--695935 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
695892 TAATATTTAG
*
695902 CGGGTCGGGT-AT
1 CGGGGCGGGTAAT
695914 CGGGGCGGGTAAT
1 CGGGGCGGGTAAT
695927 CGGGGCGGG
1 CGGGGCGGG
695936 GATTACCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.09, C:0.18, G:0.59, T:0.15
Consensus pattern (13 bp):
CGGGGCGGGTAAT
Found at i:696000 original size:35 final size:36
Alignment explanation
Indices: 695950--696019 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 36
695940 ACCAAACCCG
* *
695950 TCCCCGTTTAGCATAAATGG-TTTTTCCCGTCCCCA
1 TCCCCGTTTAACATAAACGGTTTTTTCCCGTCCCCA
*
695985 TCCCCGTTTAACATAAACGGTTTTTTCTCGTCCCC
1 TCCCCGTTTAACATAAACGGTTTTTTCCCGTCCCC
696020 GTTTAATTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 18 0.58
36 13 0.42
ACGTcount: A:0.17, C:0.34, G:0.13, T:0.36
Consensus pattern (36 bp):
TCCCCGTTTAACATAAACGGTTTTTTCCCGTCCCCA
Done.