Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 82 of 325
Found at i:28016236 original size:16 final size:16
Alignment explanation
Indices: 28016211--28016242 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28016201 AAAACAATCG
28016211 TCAATAAATCAATATA
1 TCAATAAATCAATATA
*
28016227 TCAATTAATCAATATA
1 TCAATAAATCAATATA
28016243 CATAATGGAG
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:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (16 bp):
TCAATAAATCAATATA
Found at i:28016940 original size:19 final size:20
Alignment explanation
Indices: 28016908--28016950 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
28016898 GGAAGATAAT
28016908 ATTTGGGATGGTTAGAAAGA
1 ATTTGGGATGGTTAGAAAGA
*
28016928 ATTT-GGATTGTTAGAAAGA
1 ATTTGGGATGGTTAGAAAGA
28016947 ATTT
1 ATTT
28016951 TAAAAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.28, T:0.37
Consensus pattern (20 bp):
ATTTGGGATGGTTAGAAAGA
Found at i:28017452 original size:965 final size:972
Alignment explanation
Indices: 28015556--28017499 Score: 2777
Period size: 965 Copynumber: 2.0 Consensus size: 972
28015546 TGATTGTGGC
*
28015556 TTTAAAATGTCTTAATTATCCATCTTAGGACTTTCAAATTGTGTAAGAGTTTGAACATAAGCCAT
1 TTTAAAATGTCTTAATTATCCATCTTAGGACTTTCAAATTGTGTAAGAGTTTGAACATAAACCAT
* * * *
28015621 CTAGTGTTTATGCAAGTTTATATGGAAATTCCAGCGATACCATGCTGCCTTTGTTCACATTAAGT
66 CTAGTGCTAATGCAAGTTTATAAGGAAATTCAAGCGATACCATGCTGCCTTTGTTCACATTAAGT
*
28015686 ATGGAAGTAACATAGTATTCTTTTTTAGGACATATACTCTGTAGATGCTGATGGTGCTCTTTTCG
131 ATGGAAGTAACATAGTATTCTTTTTTAGGACATATACTCTGTAGATGCAGATGGTGCTCTTTTCG
* * * * *
28015751 ACACTGCATTACTCTCAGTAGTTTCTGTCTTTTCTCATTGTAAGCGTTTCTCTCATTTTTATCAA
196 ACACTACATTACTCTCAGTAGTTGCTGCCTTTTCTCATTGTAAGCGCTTCTCTCATTTTCATCAA
* *
28015816 ATATTGTAACATCAATTCACCATGCCACTAAATATGATAATACTTGTCGAAAACAACCAACCTCT
261 ATATTGTAACACCAATTCACCATGCCACTAAATATGATAATACTTGCCGAAAACAACCAACCTCT
* * *
28015881 TCCGTGAGAAAGAAGATTGACAATTAGAGGGAAAAAAATATTTGAGATGGCTAGGAAGAATTTAG
326 TCCATGAGAAAGAAGATTGACAATCAGAGGGAAAAAAATATTTGAGATGGCTAGAAAGAATTTAG
* * *
28015946 ATTGCTAGGAAGAATTCTAAAAAAAGGACAAGACATTAAAGCTTCTTTCATATAGTTTGGCATGA
391 ATTGCTAGAAAGAATTCTAAAAAAAGGACAAGACATTAAAACATCTTTCATATAGTTTGGCATGA
28016011 CAAATCCATTTCATCTTACTTTAAATACTTATAAAAATGTTCTCTCAATTTTGCATTCAATTAAA
456 CAAATCCATTTCATCTTACTTTAAATACTTATAAAAATGTTCTCTCAATTTTGCATTCAATTAAA
* * * *
28016076 TTTTGGCATGATAGTTTGGCATCTTAATTTTACATTTAATCTAAATTTGTTTGGCAGGGCAGTTT
521 TTTTGGCATGATAGTTTAGAATCTTAATTTTACATTCAATCTAAATTTGTTT-G-A-GGAAG-TT
* * *
28016141 GGCATTTTGGCATGACAATCTCCAACACAAAGTCTAAATAAACCTTATCTCAAGCAATGTAAAAC
582 GGCAGTTTGGCATGACAATCTCCAACACAAAGTCTAAATAAACCCTATCTCAAGCAATGCAAAAC
28016206 AATCGTCAATAAATCAATATATCAATTAATCAATATACATAATGGAGGAGAAACCAGGGGTGTTG
647 AA-C-TC----AATC-A-ATATCAA-TAATCAATATACATAATGGAGGAGAAACCAGGGGTGTTG
* ** * **
28016271 ATGTTCTGTTTACTGTTGGGGATCCTTGTTAGTCCCTTACGTCAAGATGTTACAGCACTCGTCCC
703 ATGTTCTATTTACTGTCAGGGATCCATGTTAGTCCCACACGTCAAGATGTTACAGCACTCGTCCC
*
28016336 AATTGGGTTAAAGTATACGTTTTGCTTAACTACTTGCGTCACCAACGGAACTTCCCTTAAAGATT
768 AATTGGGTTAAAGTATACATTTTGCTTAACTACTTGCGTCACCAACGGAACTTCCCTTAAAGATT
* * * * * *
28016401 GTATTCAATATTGTCTGGTGTCGGAAGCACTAGTGGAGACTCTGGAGGAAATCTACCTCACGAGT
833 GTATTCAATATTGCCTGGTGACGGAAGCACTAGTGGAGACTCTAGAGGAAACCCACCTCACGAGC
* * * *
28016466 AGCTTTAGATTTTGCATAGTTGGGTGTGCCACCATGACATTTTCGAGGCTAAGCAGCCAAGGGAG
898 AGCTTTAGATTTTGCATAGTTGGGTGTGCCACCACGACATGTTCAAGGCTAAGCAGCCAAAGGAG
28016531 GACTCTTGAT
963 GACTCTTGAT
** *
28016541 TTTAAAATGTCTTAATTATCTGTCTTAGGACTTTCAACTTGTGTAAGAGTTTGAACATAAACCAT
1 TTTAAAATGTCTTAATTATCCATCTTAGGACTTTCAAATTGTGTAAGAGTTTGAACATAAACCAT
* * * * *
28016606 CTAGTGCTAATGCAA-TTTGATAAGGAAATTCAAGTGATACTATGGTGCCTTTGTTCTCATTGAG
66 CTAGTGCTAATGCAAGTTT-ATAAGGAAATTCAAGCGATACCATGCTGCCTTTGTTCACATTAAG
* *
28016670 TATTGAAGTAACATAGTATTCTGTTTTTTCAGGACATATACTAC-GTAGATGCAGATGGTGTTCT
130 TATGGAAGTAACATAGTATTC--TTTTTT-AGGACATATACT-CTGTAGATGCAGATGGTGCTCT
* * * *
28016734 TTTTGGCACTACATTACTCTCAGTTGTTGCTGCCTTTTCTCATTGTTAGCGCTTCTCTCATTTTC
191 TTTCGACACTACATTACTCTCAGTAGTTGCTGCCTTTTCTCATTGTAAGCGCTTCTCTCATTTTC
28016799 ATCAAATATTGTAACACCAATTCACCATGCCACTAAATATGATAATACTTGCCGAAAACAACCAA
256 ATCAAATATTGTAACACCAATTCACCATGCCACTAAATATGATAATACTTGCCGAAAACAACCAA
* * * *
28016864 CCTCTTCCATGAGAAAGAAGATTGACAATCAGAGGGAAGATAATATTTGGGATGGTTAGAAAGAA
321 CCTCTTCCATGAGAAAGAAGATTGACAATCAGAGGGAAAAAAATATTTGAGATGGCTAGAAAGAA
* * * *
28016929 TTTGGATTGTTAGAAAGAATTTTAAAAAAAAGGACAAGACATTAAAACAT-TTTCAATGTAGTTT
386 TTTAGATTGCTAGAAAGAATTCT-AAAAAAAGGACAAGACATTAAAACATCTTTC-ATATAGTTT
* * *
28016993 GGCATGACAAATCCATTTCATCTTACTTTAATTACTTATAAAAATGTTCTTTTAATTTTGCATTC
449 GGCATGACAAATCCATTTCATCTTACTTTAAATACTTATAAAAATGTTCTCTCAATTTTGCATTC
* *
28017058 AATTAAATTTTGGCATGATAGTTTAGAATCTTAATTTTACATTCAATGTAATTTTGTTT-A-GAA
514 AATTAAATTTTGGCATGATAGTTTAGAATCTTAATTTTACATTCAATCTAAATTTGTTTGAGGAA
* *
28017121 G-T-GCAGTTTGGCATGACAATCTCCCACAC-AAGTTCTATATAAACCCTATCTCAAGCAATGCA
579 GTTGGCAGTTTGGCATGACAATCTCCAACACAAAG-TCTAAATAAACCCTATCTCAAGCAATGCA
* *
28017183 AAACAA-TC-ATC-A-A-C-A-AATCAATATACATAATGGGGGAGAAATCAGGGGTGTTGATGTT
643 AAACAACTCAATCAATATCAATAATCAATATACATAATGGAGGAGAAACCAGGGGTGTTGATGTT
** *
28017241 CTATTTGGTGTCAGGGATCCATGTTAGTCCCACAGGTCAAGATGTTACAGCACTCGTCCCAATTG
708 CTATTTACTGTCAGGGATCCATGTTAGTCCCACACGTCAAGATGTTACAGCACTCGTCCCAATTG
* * * * *
28017306 GGTTAAGGTATACATTTTGCTTAACTACTTGTGTCACCAATGGAACTTCCCTTGAGGATTGTATT
773 GGTTAAAGTATACATTTTGCTTAACTACTTGCGTCACCAACGGAACTTCCCTTAAAGATTGTATT
*
28017371 CAATATTGCCTGGT-ACAGGAAGCACTAGTGGAGACTCTAGAGGAAACCCACCTTACGAGCAGCT
838 CAATATTGCCTGGTGAC-GGAAGCACTAGTGGAGACTCTAGAGGAAACCCACCTCACGAGCAGCT
* * * ** *
28017435 TTGGGTTTTGTATAGTTGGGTGTGCCACCACGATGTGTTCAAGGCTAAGCAGCCAAATGAGGACT
902 TTAGATTTTGCATAGTTGGGTGTGCCACCACGACATGTTCAAGGCTAAGCAGCCAAAGGAGGACT
28017500 GATAGTTTTT
Statistics
Matches: 861, Mismatches: 89, Indels: 38
0.87 0.09 0.04
Matches are distributed among these distances:
964 1 0.00
965 266 0.31
967 1 0.00
968 1 0.00
969 1 0.00
970 1 0.00
973 3 0.00
978 2 0.00
980 3 0.00
981 57 0.07
982 1 0.00
984 6 0.01
985 132 0.15
986 1 0.00
987 6 0.01
988 230 0.27
989 149 0.17
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (972 bp):
TTTAAAATGTCTTAATTATCCATCTTAGGACTTTCAAATTGTGTAAGAGTTTGAACATAAACCAT
CTAGTGCTAATGCAAGTTTATAAGGAAATTCAAGCGATACCATGCTGCCTTTGTTCACATTAAGT
ATGGAAGTAACATAGTATTCTTTTTTAGGACATATACTCTGTAGATGCAGATGGTGCTCTTTTCG
ACACTACATTACTCTCAGTAGTTGCTGCCTTTTCTCATTGTAAGCGCTTCTCTCATTTTCATCAA
ATATTGTAACACCAATTCACCATGCCACTAAATATGATAATACTTGCCGAAAACAACCAACCTCT
TCCATGAGAAAGAAGATTGACAATCAGAGGGAAAAAAATATTTGAGATGGCTAGAAAGAATTTAG
ATTGCTAGAAAGAATTCTAAAAAAAGGACAAGACATTAAAACATCTTTCATATAGTTTGGCATGA
CAAATCCATTTCATCTTACTTTAAATACTTATAAAAATGTTCTCTCAATTTTGCATTCAATTAAA
TTTTGGCATGATAGTTTAGAATCTTAATTTTACATTCAATCTAAATTTGTTTGAGGAAGTTGGCA
GTTTGGCATGACAATCTCCAACACAAAGTCTAAATAAACCCTATCTCAAGCAATGCAAAACAACT
CAATCAATATCAATAATCAATATACATAATGGAGGAGAAACCAGGGGTGTTGATGTTCTATTTAC
TGTCAGGGATCCATGTTAGTCCCACACGTCAAGATGTTACAGCACTCGTCCCAATTGGGTTAAAG
TATACATTTTGCTTAACTACTTGCGTCACCAACGGAACTTCCCTTAAAGATTGTATTCAATATTG
CCTGGTGACGGAAGCACTAGTGGAGACTCTAGAGGAAACCCACCTCACGAGCAGCTTTAGATTTT
GCATAGTTGGGTGTGCCACCACGACATGTTCAAGGCTAAGCAGCCAAAGGAGGACTCTTGAT
Found at i:28017720 original size:45 final size:45
Alignment explanation
Indices: 28017669--28017759 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
28017659 ATGAAATTAT
* *
28017669 AATAAAATGCCTTGAATTACATTTAGCCTGAATGAAGAAAACATA
1 AATAAAAGGCCTTGAACTACATTTAGCCTGAATGAAGAAAACATA
28017714 AATAAAAGGCCTTGAACTACATTTAGCCTGAATGAAGAAAACATA
1 AATAAAAGGCCTTGAACTACATTTAGCCTGAATGAAGAAAACATA
28017759 A
1 A
28017760 TTGGGTTGCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (45 bp):
AATAAAAGGCCTTGAACTACATTTAGCCTGAATGAAGAAAACATA
Found at i:28018995 original size:19 final size:20
Alignment explanation
Indices: 28018963--28019004 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
28018953 GTAAAAGAAT
*
28018963 ATTTGGGATGGTTATAAAGA
1 ATTTGGGATGGTTAGAAAGA
*
28018983 ATTT-GGATTGTTAGAAAGA
1 ATTTGGGATGGTTAGAAAGA
28019002 ATT
1 ATT
28019005 CTAAAAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (20 bp):
ATTTGGGATGGTTAGAAAGA
Found at i:28023602 original size:46 final size:46
Alignment explanation
Indices: 28023546--28023721 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
28023536 TGGTTGAGCA
*
28023546 TCCGAACTCGTTGAGTTGAGTCCGAGTCCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
28023592 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
28023637 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28023685 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCTCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28023722 GCGGGTTTCA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28023702 original size:93 final size:93
Alignment explanation
Indices: 28023543--28023713 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
28023533 GGATGGTTGA
* **
28023543 GCATCCGAACTCGTTGAGTTGAGTCCGAGTCCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTCCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28023608 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
28023636 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTCCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28023701 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
28023714 TCTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTCCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28033841 original size:30 final size:30
Alignment explanation
Indices: 28033805--28033865 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
28033795 ATTTTATTGT
* *
28033805 TAATTTTTTTATTATTTTAAAGACATTTGC
1 TAATTTTGTTACTATTTTAAAGACATTTGC
* *
28033835 TAATTTTGTTACTATTTTAGAGGCATTTGC
1 TAATTTTGTTACTATTTTAAAGACATTTGC
28033865 T
1 T
28033866 TGTTAAATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.54
Consensus pattern (30 bp):
TAATTTTGTTACTATTTTAAAGACATTTGC
Found at i:28034989 original size:16 final size:17
Alignment explanation
Indices: 28034970--28035012 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
28034960 ATTTAAAAAC
*
28034970 TTTTATTTTT-AGTATA
1 TTTTATTTTTAAATATA
*
28034986 TTTTATCTTTTAAATATT
1 TTTTAT-TTTTAAATATA
28035004 TTTTATTTT
1 TTTTATTTT
28035013 GATTCATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.26
17 7 0.30
18 10 0.43
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTTATTTTTAAATATA
Found at i:28048467 original size:20 final size:20
Alignment explanation
Indices: 28048442--28048479 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28048432 ATAAAATTTG
28048442 AAAAAAACGAATCAATTCAA
1 AAAAAAACGAATCAATTCAA
*
28048462 AAAAAAATGAATCAATTC
1 AAAAAAACGAATCAATTC
28048480 GTTCTCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.63, C:0.13, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAAAAACGAATCAATTCAA
Found at i:28049143 original size:21 final size:21
Alignment explanation
Indices: 28049109--28049155 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
28049099 CATGTTAATA
28049109 TATTTTTATCATGTTTT-TAT
1 TATTTTTATCATGTTTTGTAT
* *
28049129 TATTTTTAATTATGTTTTGTTT
1 TATTTTT-ATCATGTTTTGTAT
28049151 TATTT
1 TATTT
28049156 ATTTTATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 9 0.39
22 7 0.30
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.72
Consensus pattern (21 bp):
TATTTTTATCATGTTTTGTAT
Found at i:28050211 original size:18 final size:18
Alignment explanation
Indices: 28050190--28050224 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28050180 AATCAGTAAT
* *
28050190 CAGTAACGGTAGCAGTAG
1 CAGTAACAGTAACAGTAG
28050208 CAGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTA
28050225 TTCAACACAC
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:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (18 bp):
CAGTAACAGTAACAGTAG
Found at i:28050299 original size:39 final size:39
Alignment explanation
Indices: 28050210--28050302 Score: 143
Period size: 39 Copynumber: 2.4 Consensus size: 39
28050200 AGCAGTAGCA
* *
28050210 GTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCT
1 GTAACAGTAACGGTATTCAACACACAAAGTGCTGAATCG
*
28050249 GTAACAGTAACGGTATTCGACACACAAAGTG-TCGAATCG
1 GTAACAGTAACGGTATTCAACACACAAAGTGCT-GAATCG
28050288 GTAACAGTAACGGTA
1 GTAACAGTAACGGTA
28050303 ATAGTAACAG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
38 1 0.02
39 49 0.98
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (39 bp):
GTAACAGTAACGGTATTCAACACACAAAGTGCTGAATCG
Found at i:28051594 original size:33 final size:32
Alignment explanation
Indices: 28051536--28051598 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
28051526 ATTATTTAAT
28051536 TAATAAATATCTCTTAATTATAATAATAATAAA
1 TAATAAATATCTCTTAATTATAATAA-AATAAA
28051569 TAATAAATATCTAC-TAATT-TAAATAAAATA
1 TAATAAATATCT-CTTAATTAT-AATAAAATA
28051599 TTATAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 5 0.18
33 22 0.79
34 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (32 bp):
TAATAAATATCTCTTAATTATAATAAAATAAA
Found at i:28053271 original size:13 final size:13
Alignment explanation
Indices: 28053253--28053277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28053243 AATAAATTTA
28053253 TAAAAAAAAAAGT
1 TAAAAAAAAAAGT
28053266 TAAAAAAAAAAG
1 TAAAAAAAAAAG
28053278 CGCTCTAGAT
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:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
TAAAAAAAAAAGT
Found at i:28054699 original size:21 final size:21
Alignment explanation
Indices: 28054670--28054713 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28054660 AAACTCTAAA
*
28054670 AAAATAAATTAAAATCCTAATT
1 AAAATAAATTAAAAT-ATAATT
*
28054692 AAAA-AAATTCAAATATAATT
1 AAAATAAATTAAAATATAATT
28054712 AA
1 AA
28054714 GATTATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 9 0.45
22 4 0.20
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAATAAATTAAAATATAATT
Found at i:28060883 original size:24 final size:25
Alignment explanation
Indices: 28060850--28060910 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
28060840 AAAATTATAT
28060850 TTAAAA-ATTAAACAAT-TAAATTA
1 TTAAAATATTAAACAATATAAATTA
*
28060873 TTAAAATATT-AACTATATAAATTA
1 TTAAAATATTAAACAATATAAATTA
**
28060897 CAAAAATATGTAAA
1 TTAAAATAT-TAAA
28060911 AACTCATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 11 0.35
24 17 0.55
25 1 0.03
26 2 0.06
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (25 bp):
TTAAAATATTAAACAATATAAATTA
Found at i:28062638 original size:33 final size:33
Alignment explanation
Indices: 28062582--28062666 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 33
28062572 AAACTTGGGA
*
28062582 GGACAGACA--AACAACCTAGGACAAAG-AAAT
1 GGACAGACATTAACAACCTAAGACAAAGAAAAT
28062612 GGACAGACATTAAGCAACCTAAGACAAAGAAAAT
1 GGACAGACATTAA-CAACCTAAGACAAAGAAAAT
*
28062646 -GACAGACATTAATCCACCTAA
1 GGACAGACATTAA-CAACCTAA
28062667 ATAATAATGA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
30 9 0.19
32 2 0.04
33 33 0.69
34 4 0.08
ACGTcount: A:0.51, C:0.21, G:0.16, T:0.12
Consensus pattern (33 bp):
GGACAGACATTAACAACCTAAGACAAAGAAAAT
Found at i:28063019 original size:14 final size:14
Alignment explanation
Indices: 28062973--28063013 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
28062963 ATTTTATTCT
28062973 TAATAAATATTTGAA
1 TAATAAATATTT-AA
28062988 T--TAAATATTTAA
1 TAATAAATATTTAA
28063000 TAATAAA-ATTTAA
1 TAATAAATATTTAA
28063013 T
1 T
28063014 TGATAATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.12
13 16 0.67
14 4 0.17
15 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
TAATAAATATTTAA
Found at i:28064736 original size:19 final size:19
Alignment explanation
Indices: 28064712--28064751 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
28064702 TCAAGTCTGT
*
28064712 AAATAATTTA-AAATTAAAA
1 AAATAAATTATAAA-TAAAA
28064731 AAATAAATTATAAATAAAA
1 AAATAAATTATAAATAAAA
28064750 AA
1 AA
28064752 TAAGTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATAAATTATAAATAAAA
Found at i:28067722 original size:30 final size:30
Alignment explanation
Indices: 28067688--28067795 Score: 80
Period size: 33 Copynumber: 3.4 Consensus size: 30
28067678 ATAACTTGTT
28067688 AATA-TTTTAATATATAAAATATAAATTTTA
1 AATATTTTTAATATAT-AAATATAAATTTTA
*
28067718 AATATTTTTAATCTATAAATATTAATTATTTATA
1 AATATTTTTAATATATAAATA-TAA--ATTT-TA
28067752 AA-ATTTAATTAGAATATATAAACTAT--ATTTTA
1 AATATTT--TT--AATATATAAA-TATAAATTTTA
*
28067784 AATATTTGTAAT
1 AATATTTTTAAT
28067796 TAGTATTTTA
Statistics
Matches: 64, Mismatches: 3, Indels: 23
0.71 0.03 0.26
Matches are distributed among these distances:
29 3 0.05
30 9 0.14
31 14 0.22
32 4 0.06
33 16 0.25
34 4 0.06
35 2 0.03
37 10 0.16
38 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (30 bp):
AATATTTTTAATATATAAATATAAATTTTA
Found at i:28069809 original size:24 final size:25
Alignment explanation
Indices: 28069762--28069812 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
28069752 ACACATGTTC
*
28069762 ATAATATATAAAACATACATATAAT
1 ATAATATATAAAACATACACATAAT
**
28069787 ATAATAT-TAAAACATTTACATAAT
1 ATAATATATAAAACATACACATAAT
28069811 AT
1 AT
28069813 GTACACACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (25 bp):
ATAATATATAAAACATACACATAAT
Found at i:28069919 original size:21 final size:21
Alignment explanation
Indices: 28069885--28069924 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28069875 AAGATATACT
*
28069885 TATATAAACATATATTAAAGA
1 TATATAAACATATAATAAAGA
* *
28069906 TATATACATATATAATAAA
1 TATATAAACATATAATAAA
28069925 ATACATGAAT
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:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (21 bp):
TATATAAACATATAATAAAGA
Found at i:28070012 original size:29 final size:27
Alignment explanation
Indices: 28069977--28070038 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 27
28069967 AATAATAATA
28069977 ATAATATACATA-ATATATACAAAATACAC
1 ATAATATACATATATATA-AC-AAA-ACAC
* *
28070006 ATAATATATATGTATATAACAAAACAC
1 ATAATATACATATATATAACAAAACAC
28070033 ATAATA
1 ATAATA
28070039 GTGATGGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 10 0.33
28 3 0.10
29 12 0.40
30 5 0.17
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (27 bp):
ATAATATACATATATATAACAAAACAC
Found at i:28071999 original size:4 final size:4
Alignment explanation
Indices: 28071990--28072016 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
28071980 ATAATAATAA
28071990 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
28072017 GCCCTCCACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:28072609 original size:31 final size:31
Alignment explanation
Indices: 28072548--28072609 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
28072538 TATTTACATA
* *
28072548 AAATTTTAATTATAGTTCAAATGTAGATATT
1 AAATTTTAATTATAATTCAAATATAGATATT
* *
28072579 AAATTTTAATTATAATTCAATTATATATATT
1 AAATTTTAATTATAATTCAAATATAGATATT
28072610 TAAAAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (31 bp):
AAATTTTAATTATAATTCAAATATAGATATT
Found at i:28074933 original size:31 final size:31
Alignment explanation
Indices: 28074898--28074959 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
28074888 TTAACGGATA
28074898 CAAAATTTTCTACAATTTATTCAATTTAATT
1 CAAAATTTTCTACAATTTATTCAATTTAATT
*
28074929 CAAAATTTTCTATAATTTATTCAATTTAATT
1 CAAAATTTTCTACAATTTATTCAATTTAATT
28074960 TGATGTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (31 bp):
CAAAATTTTCTACAATTTATTCAATTTAATT
Found at i:28076736 original size:19 final size:19
Alignment explanation
Indices: 28076694--28076738 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
28076684 GGTACTAAAA
28076694 AAATTAATTTTAAATTAATT
1 AAATT-ATTTTAAATTAATT
*
28076714 -AATTATTTTAAATTTATT
1 AAATTATTTTAAATTAATT
28076732 AAATTAT
1 AAATTAT
28076739 GAATTGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATTATTTTAAATTAATT
Found at i:28083902 original size:44 final size:44
Alignment explanation
Indices: 28083853--28084070 Score: 283
Period size: 44 Copynumber: 4.9 Consensus size: 44
28083843 CCTTTGAAAT
* * *
28083853 AGATTGAGGCCACAAATATTATCTCCCTGAAGTTGCAGTGGAAC
1 AGATTGAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
*
28083897 AGATTGAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGT
1 AGATTGAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
* * * * *
28083941 AGATTGAAACCACTAACCTTATCTCCCTAAAGTTGTAGTGGAGC
1 AGATTGAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
* ** *
28083985 AGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGC
1 AGATTGAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
* **
28084029 AAATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGG
1 AGATTGAAGCCA-CAAATCTTATCTCCCTGAAGTTGCAGTGG
28084071 GGTATATTGA
Statistics
Matches: 150, Mismatches: 23, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
44 122 0.81
45 28 0.19
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
AGATTGAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
Found at i:28085552 original size:42 final size:45
Alignment explanation
Indices: 28085489--28085791 Score: 250
Period size: 49 Copynumber: 6.6 Consensus size: 45
28085479 CTTCGTTTTC
** *
28085489 TCGATGCCATAGTTCAACTATGGTCTTACAC-ATC-T-TCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACAATCATATCACAT-A
*
28085532 T-GATGCCATAGCCCAGCTATGGTCTTACAC-AT-AT-TCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACAATCATATCACATA
28085573 TCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC--AAT--CATATCACATA
*
28085622 TCGATGCCATAGCTCAGCTATGGTCTTACACGTAATCAAATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC--AATC--ATATCACATA
* *
28085671 TCGATGCCATAGCCCAGCTATGATCTTACACGAATCACATATCTCACTA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-AAT--CATATCACA-TA
* * * * *
28085720 ---ATGCCATATCCCAGATATGGTCTTATACAGTAGCATAT-ATCACA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACA--ATCATATCA-CATA
* * *
28085764 CCGATGCCATATCCCAGATATGGTCTTA
1 TCGATGCCATAGCCCAGCTATGGTCTTA
28085792 TACGGAAATC
Statistics
Matches: 223, Mismatches: 17, Indels: 36
0.81 0.06 0.13
Matches are distributed among these distances:
41 2 0.01
42 63 0.28
43 1 0.00
44 1 0.00
45 10 0.04
46 24 0.11
47 27 0.12
48 12 0.05
49 82 0.37
50 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (45 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACAATCATATCACATA
Found at i:28085632 original size:49 final size:49
Alignment explanation
Indices: 28085559--28085791 Score: 273
Period size: 49 Copynumber: 4.8 Consensus size: 49
28085549 TATGGTCTTA
*
28085559 CACATATTCATATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
1 CACATA-TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
*
28085609 CACATATCACATATCGATGCCATAGCTCAGCTATGGTCTTACACGTAAT
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
* *
28085658 CAAATATCACATATCGATGCCATAGCCCAGCTATGATCTTACACG-AAT
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
* * * * *
28085706 CACATATCTCACTA---ATGCCATATCCCAGATATGGTCTTATACAGT-AG
1 CACATATCACA-TATCGATGCCATAGCCCAGCTATGGTCTTACAC-GTAAT
* * * *
28085753 CATATATCAC--ACCGATGCCATATCCCAGATATGGTCTTA
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTA
28085792 TACGGAAATC
Statistics
Matches: 163, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
44 1 0.01
46 24 0.15
47 35 0.21
48 12 0.07
49 85 0.52
50 6 0.04
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (49 bp):
CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
Found at i:28085640 original size:91 final size:93
Alignment explanation
Indices: 28085524--28085744 Score: 276
Period size: 98 Copynumber: 2.4 Consensus size: 93
28085514 TTACACATCT
*
28085524 TCACATAATGATGCCATAGCCCAGCTATGGTCTTACAC-AT-AT-TCATATATCGATGCCATAGC
1 TCACATAATGATGCCATAGCCCAGCTATGGTCTTACACAATAATATCACATATCGATGCCATAGC
*
28085586 CCAGCTATGGTCTTACACGTAATCACATA
66 CCAGCTATGATCTTACACG-AATCACATA
*
28085615 TCACAT-ATCGATGCCATAGCTCAGCTATGGTCTTACACGTAATCAAATATCACATATCGATGCC
1 TCACATAAT-GATGCCATAGCCCAGCTATGGTCTTACAC--AAT--AATATCACATATCGATGCC
28085679 ATAGCCCAGCTATGATCTTACACGAATCACATA
61 ATAGCCCAGCTATGATCTTACACGAATCACATA
* * *
28085712 TCTCACT-A--ATGCCATATCCCAGATATGGTCTTA
1 TCACA-TAATGATGCCATAGCCCAGCTATGGTCTTA
28085745 TACAGTAGCA
Statistics
Matches: 114, Mismatches: 7, Indels: 14
0.84 0.05 0.10
Matches are distributed among these distances:
90 2 0.02
91 34 0.30
94 2 0.02
95 22 0.19
97 15 0.13
98 39 0.34
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.29
Consensus pattern (93 bp):
TCACATAATGATGCCATAGCCCAGCTATGGTCTTACACAATAATATCACATATCGATGCCATAGC
CCAGCTATGATCTTACACGAATCACATA
Found at i:28085803 original size:95 final size:94
Alignment explanation
Indices: 28085574--28085791 Score: 262
Period size: 95 Copynumber: 2.3 Consensus size: 94
28085564 ATTCATATAT
*
28085574 CGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATATCGATGCCATAGCTCAG
1 CGATGCCATAGCCCAGCTATGGTCTTACACG-AATCACATATCACATA-C-ATGCCATAGCCCAG
* * *
28085639 CTATGGTCTTACACGTAATCAAATATCACATAT
63 ATATGGTCTTACACGTAAGCAAATATCACA-AC
* * *
28085672 CGATGCCATAGCCCAGCTATGATCTTACACGAATCACATATCTCACTA-ATGCCATATCCCAGAT
1 CGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCACA-TACATGCCATAGCCCAGAT
* *
28085736 ATGGTCTTATACAGT-AGCATATATCAC-AC
65 ATGGTCTTACAC-GTAAGCAAATATCACAAC
* *
28085765 CGATGCCATATCCCAGATATGGTCTTA
1 CGATGCCATAGCCCAGCTATGGTCTTA
28085792 TACGGAAATC
Statistics
Matches: 106, Mismatches: 12, Indels: 9
0.83 0.09 0.07
Matches are distributed among these distances:
93 25 0.24
95 34 0.32
96 2 0.02
97 13 0.12
98 32 0.30
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (94 bp):
CGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCACATACATGCCATAGCCCAGATA
TGGTCTTACACGTAAGCAAATATCACAAC
Found at i:28085856 original size:31 final size:32
Alignment explanation
Indices: 28085813--28085930 Score: 165
Period size: 31 Copynumber: 3.8 Consensus size: 32
28085803 CTTGTCACTT
28085813 GTAGCC-GAAGCTACCACTATTT-ACTGATCAG
1 GTAGCCAGAAGCTACCACT-TTTCACTGATCAG
28085844 GTAGCCAG-AGCTACCACTTTTCACTGATCAG
1 GTAGCCAGAAGCTACCACTTTTCACTGATCAG
* *
28085875 GTAGCC-GGAGCTGCCACTTTTCACTGATCAG
1 GTAGCCAGAAGCTACCACTTTTCACTGATCAG
*
28085906 GTAG-TAGAAGCTACCACTTTTCACT
1 GTAGCCAGAAGCTACCACTTTTCACT
28085931 TGTCATTTGT
Statistics
Matches: 79, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
30 4 0.05
31 74 0.94
32 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (32 bp):
GTAGCCAGAAGCTACCACTTTTCACTGATCAG
Found at i:28086000 original size:50 final size:51
Alignment explanation
Indices: 28085912--28086034 Score: 221
Period size: 50 Copynumber: 2.4 Consensus size: 51
28085902 TCAGGTAGTA
* *
28085912 GAAGCTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTGTCATTTGTCCTTGATCAGATAAGTGTAGCC
28085963 GAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTGTCATTTGTCCTTGATCAGATAAGTGTAGCC
28086013 GAAGCTATCACTTATCACTTGT
1 GAAGCTATCACTTATCACTTGT
28086035 TGCCATGGTC
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
50 50 0.72
51 19 0.28
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (51 bp):
GAAGCTATCACTTATCACTTGTCATTTGTCCTTGATCAGATAAGTGTAGCC
Found at i:28092000 original size:44 final size:44
Alignment explanation
Indices: 28091911--28092094 Score: 188
Period size: 44 Copynumber: 4.2 Consensus size: 44
28091901 CGAATCTTAA
* * ** *
28091911 CCACAAATCTTATCTCCCTAAAGCTGCAGTGGAACATATTGAAG
1 CCACAAATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAG
* * * *
28091955 CCATAAATCTTATCTCCCTGAAGTTACAGTAGAGTAGATTTAAG
1 CCACAAATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAG
* * *
28091999 CCACTAATCTTATCTCCCTAAAGTTGTAGTAGAGTAGGTTGAAG
1 CCACAAATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAG
** * * * * *
28092043 TTACAAGTCTTATCTCCCTGAAGTTGCAGTAGGGTATATTGAAA
1 CCACAAATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAG
*
28092087 CAACAAAT
1 CCACAAAT
28092095 TCTATACCTC
Statistics
Matches: 111, Mismatches: 29, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
44 111 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (44 bp):
CCACAAATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAG
Found at i:28093081 original size:16 final size:17
Alignment explanation
Indices: 28093050--28093082 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28093040 TTCATAAGTA
28093050 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
28093067 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
28093083 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:28093428 original size:46 final size:46
Alignment explanation
Indices: 28093363--28093864 Score: 650
Period size: 46 Copynumber: 11.0 Consensus size: 46
28093353 TTATCTTTGA
* * * * *
28093363 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
* *** *
28093409 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* ** ** ***
28093455 TACATTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *** *
28093500 CATGTTGCCATGGTATCTTTCAACTATGGTCTTGTTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* ** ** ***
28093546 TACATTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
28093591 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
28093637 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
28093683 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
28093729 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
28093775 CATGTTGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
28093821 CATGTTGTCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
28093865 TTCAGAAAGC
Statistics
Matches: 410, Mismatches: 43, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
45 80 0.20
46 330 0.80
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:28097133 original size:3 final size:3
Alignment explanation
Indices: 28097127--28097156 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
28097117 GTGTTGTTTC
28097127 TTA TTA TTA TTA TTA TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
28097157 CATGCATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28097256 original size:4 final size:4
Alignment explanation
Indices: 28097247--28097283 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
28097237 TTTTCTTCTA
* *
28097247 TATT TATT TATT TATG TATT TATG TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT T
28097284 CCTCGTCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:28100542 original size:30 final size:30
Alignment explanation
Indices: 28100508--28100566 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
28100498 CAATAATTCG
*
28100508 TCAATCAACTCATCATCATAATCGATATCA
1 TCAATCAACTCATCATCATAATCAATATCA
*
28100538 TCAATCAACTCATTATCATAATCAATATC
1 TCAATCAACTCATCATCATAATCAATATC
28100567 GTCATCCTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.25, G:0.02, T:0.32
Consensus pattern (30 bp):
TCAATCAACTCATCATCATAATCAATATCA
Found at i:28101072 original size:41 final size:41
Alignment explanation
Indices: 28101015--28101097 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
28101005 ACATTTATAG
28101015 ATAGATGTCTTTTAATTATACTCTAATTAGGAATCCAATAC
1 ATAGATGTCTTTTAATTATACTCTAATTAGGAATCCAATAC
* *
28101056 ATAGATGTGTTTTAATTATACTCTATTTAGGAATCCAATAC
1 ATAGATGTCTTTTAATTATACTCTAATTAGGAATCCAATAC
28101097 A
1 A
28101098 GAAGTGGAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (41 bp):
ATAGATGTCTTTTAATTATACTCTAATTAGGAATCCAATAC
Found at i:28115676 original size:107 final size:108
Alignment explanation
Indices: 28115562--28115777 Score: 380
Period size: 107 Copynumber: 2.0 Consensus size: 108
28115552 TAAACAAAAT
*
28115562 ATTAGTTTAACAAAATAATGATATGTTAAATTAGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAATTAGAATAAGTTTTAAATAATAAAATTTCTAACAA
*
28115627 AATTGTATTAAAATTTTTGTTAATTACTCT-ATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAAATTTTG
* *
28115669 ATTAGTTTAACAAAACAATGATATGTTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAATTAGAATAAGTTTTAAATAATAAAATTTCTAACAA
*
28115734 AATTGTATTAAATTTTTTGTTAATTACTCTGATAAAAATTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAAATTTTG
28115777 A
1 A
28115778 CGTGTTTTTT
Statistics
Matches: 103, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
107 91 0.88
108 12 0.12
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (108 bp):
ATTAGTTTAACAAAACAATGATATGTTAAATTAGAATAAGTTTTAAATAATAAAATTTCTAACAA
AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAAATTTTG
Found at i:28118248 original size:65 final size:64
Alignment explanation
Indices: 28118132--28118312 Score: 310
Period size: 65 Copynumber: 2.8 Consensus size: 64
28118122 CCATATGTTC
*
28118132 TCGAGTTAACTTATGAAACTAACTT-ATCGACAACATTATTAATATATACAATCTTGAGTTGGTG
1 TCGAGTTAACTTATGAAAC-AACTTAATCAACAACATTATTAATATATACAATCTTGAGTTGGTG
*
28118196 TCGAGTTAACTTGTGAAATCAACTTAATCAACAACATTATTAATATATACAATCTTGAGTTGGTG
1 TCGAGTTAACTTATGAAA-CAACTTAATCAACAACATTATTAATATATACAATCTTGAGTTGGTG
28118261 TCGAGTTAACTTATGAAACCAACTTAATCAACAACATTATTAATATATACAA
1 TCGAGTTAACTTATGAAA-CAACTTAATCAACAACATTATTAATATATACAA
28118313 CTGATGAAGG
Statistics
Matches: 111, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
64 22 0.20
65 89 0.80
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (64 bp):
TCGAGTTAACTTATGAAACAACTTAATCAACAACATTATTAATATATACAATCTTGAGTTGGTG
Found at i:28121298 original size:17 final size:19
Alignment explanation
Indices: 28121265--28121301 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
28121255 ATAAATTACA
28121265 ATAATAACAATAATAAAAG
1 ATAATAACAATAATAAAAG
28121284 ATAA-AACAA-AATAAAAG
1 ATAATAACAATAATAAAAG
28121301 A
1 A
28121302 ATATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 5 0.28
19 4 0.22
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.16
Consensus pattern (19 bp):
ATAATAACAATAATAAAAG
Found at i:28127975 original size:16 final size:15
Alignment explanation
Indices: 28127954--28128001 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
28127944 TTTTAAAGAA
*
28127954 AATATATACGTAAAAT
1 AATATATACAT-AAAT
*
28127970 AATATA-ACATCAAT
1 AATATATACATAAAT
28127984 AATATATACATAGAAT
1 AATATATACATA-AAT
28128000 AA
1 AA
28128002 GAAAATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 9 0.33
15 7 0.26
16 11 0.41
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.29
Consensus pattern (15 bp):
AATATATACATAAAT
Found at i:28128739 original size:7 final size:8
Alignment explanation
Indices: 28128722--28128746 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28128712 TTAAAAGCAT
28128722 AAATAAAA
1 AAATAAAA
28128730 AAATAAAA
1 AAATAAAA
28128738 AAATAAAA
1 AAATAAAA
28128746 A
1 A
28128747 CTAAACACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAATAAAA
Found at i:28128947 original size:10 final size:10
Alignment explanation
Indices: 28128932--28128961 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
28128922 TTTGCAAATG
28128932 GAAAAAAAAA
1 GAAAAAAAAA
28128942 GAAAAAAAAA
1 GAAAAAAAAA
*
28128952 CAAAAAAAAA
1 GAAAAAAAAA
28128962 AACAAGAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:28128950 original size:12 final size:13
Alignment explanation
Indices: 28128933--28128968 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
28128923 TTGCAAATGG
28128933 AAAAAAA-AAGAA
1 AAAAAAACAAGAA
28128945 AAAAAAACAA-AA
1 AAAAAAACAAGAA
28128957 AAAAAAACAAGA
1 AAAAAAACAAGA
28128969 GGAGAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 19 0.86
13 3 0.14
ACGTcount: A:0.89, C:0.06, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAGAA
Found at i:28130752 original size:20 final size:20
Alignment explanation
Indices: 28130729--28130771 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
28130719 TTTAAATTCT
28130729 AAAATCTGAAAAGTAAGACC
1 AAAATCTGAAAAGTAAGACC
* *
28130749 AAAATTTGAAAAGTAATACC
1 AAAATCTGAAAAGTAAGACC
28130769 AAA
1 AAA
28130772 TTCTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (20 bp):
AAAATCTGAAAAGTAAGACC
Found at i:28135935 original size:31 final size:30
Alignment explanation
Indices: 28135881--28135968 Score: 140
Period size: 31 Copynumber: 2.9 Consensus size: 30
28135871 GTCATTAAGG
*
28135881 TATTTGAAAGTTTTTATTAAGTCACTAAAC
1 TATTTGAAAGTTTTTTTTAAGTCACTAAAC
28135911 TATTTGAAAGTTTTTCTTTAAGTCACTAAAC
1 TATTTGAAAGTTTTT-TTTAAGTCACTAAAC
* *
28135942 TATTCGAAAGTTTTTTTAAAGTCACTA
1 TATTTGAAAGTTTTTTTTAAGTCACTA
28135969 GACGATTAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
30 26 0.48
31 28 0.52
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (30 bp):
TATTTGAAAGTTTTTTTTAAGTCACTAAAC
Found at i:28136097 original size:65 final size:65
Alignment explanation
Indices: 28136001--28136132 Score: 167
Period size: 65 Copynumber: 2.0 Consensus size: 65
28135991 TTCGATTAAT
* * * *
28136001 TAGCTCTAAGCGACTATTCAACAATCGGTACAGTAGATCAGCATTCATC-AATAAGTAGAAGAAC
1 TAGCTCCAAGCGACTAGTCAACAATCAGTACAGTAGATCAGCATTCATCGAA-AAGAAGAAGAAC
28136065 A
65 A
* * * **
28136066 TAGCTCCAAGTGACTAGTCGACAATTAGTACAGTAGATCAGTTTTCATCGAAAAGAAGAAGAACA
1 TAGCTCCAAGCGACTAGTCAACAATCAGTACAGTAGATCAGCATTCATCGAAAAGAAGAAGAACA
28136131 TA
1 TA
28136133 CCTTAGATTC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 55 0.96
66 2 0.04
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.23
Consensus pattern (65 bp):
TAGCTCCAAGCGACTAGTCAACAATCAGTACAGTAGATCAGCATTCATCGAAAAGAAGAAGAACA
Found at i:28137455 original size:42 final size:42
Alignment explanation
Indices: 28137395--28137475 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
28137385 CATGAATTTA
* *
28137395 ATGTAATTATATGCATTAAATTTGAATT-TTGATTTATATGCG
1 ATGTAATTATATACATTAAATTTAAATTATT-ATTTATATGCG
*
28137437 ATGTAATTATATATATTAAATTTAAATTATTATTTATAT
1 ATGTAATTATATACATTAAATTTAAATTATTATTTATAT
28137476 ATATGCATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (42 bp):
ATGTAATTATATACATTAAATTTAAATTATTATTTATATGCG
Found at i:28142941 original size:23 final size:23
Alignment explanation
Indices: 28142915--28142962 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
28142905 TAGTGTTCTT
28142915 TTGGCCTCATATCAAAGTCACTA
1 TTGGCCTCATATCAAAGTCACTA
28142938 TTGGCCTCATATCAAAGTCACTA
1 TTGGCCTCATATCAAAGTCACTA
28142961 TT
1 TT
28142963 AAGGTTTATT
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:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (23 bp):
TTGGCCTCATATCAAAGTCACTA
Found at i:28151986 original size:45 final size:45
Alignment explanation
Indices: 28151937--28152200 Score: 420
Period size: 45 Copynumber: 5.9 Consensus size: 45
28151927 TCGGCCATGG
* * * * *
28151937 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
28151982 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
28152027 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
28152072 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
28152117 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * **
28152162 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
28152201 TCCACCTCTT
Statistics
Matches: 205, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 205 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:28155441 original size:53 final size:53
Alignment explanation
Indices: 28155360--28155515 Score: 217
Period size: 53 Copynumber: 3.0 Consensus size: 53
28155350 GACAAAAAAT
* *
28155360 ATGTGATAAGTGTG-C-CCGTTTAAGACCATATCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATATCTGGGCTATGGCATCGGTACA
* *
28155412 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATATCTGGGCTATGGCATCGGTACA
* * * *
28155465 ATGTGATAATGTGATTCCGTATAAGACCATGTCTGGGATATGGCTTCGGTA
1 ATGTGATAATGTGACTCCGTATAAGACCATATCTGGGCTATGGCATCGGTA
28155516 TGATATGTGA
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
51 4 0.04
52 10 0.11
53 79 0.85
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATATCTGGGCTATGGCATCGGTACA
Found at i:28166892 original size:21 final size:21
Alignment explanation
Indices: 28166866--28166906 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28166856 AGACGAGCAA
* *
28166866 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
28166887 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
28166907 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:28169775 original size:22 final size:21
Alignment explanation
Indices: 28169750--28169794 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
28169740 TAAGCAATAG
28169750 AATTAAATATCAAG-AAAAGAAA
1 AATTAAA-A-CAAGAAAAAGAAA
28169772 AATTAAAACAAGAAAAAGAAA
1 AATTAAAACAAGAAAAAGAAA
28169793 AA
1 AA
28169795 CATGAACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.18
21 11 0.50
22 7 0.32
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.13
Consensus pattern (21 bp):
AATTAAAACAAGAAAAAGAAA
Found at i:28174455 original size:38 final size:38
Alignment explanation
Indices: 28174413--28174487 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
28174403 TAGTCCGATG
*
28174413 TTTACTTGCAAGTGTTAATTTCATTTTCATGTTTATTT
1 TTTACTTGCAAGTGCTAATTTCATTTTCATGTTTATTT
*
28174451 TTTACTTGCAAGTGCTATTTTCATTTTCATGTTTATT
1 TTTACTTGCAAGTGCTAATTTCATTTTCATGTTTATT
28174488 GCATCAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.20, C:0.12, G:0.11, T:0.57
Consensus pattern (38 bp):
TTTACTTGCAAGTGCTAATTTCATTTTCATGTTTATTT
Found at i:28174606 original size:14 final size:14
Alignment explanation
Indices: 28174587--28174615 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28174577 ACTTTTCTTG
28174587 GGTTGTTTTAATTT
1 GGTTGTTTTAATTT
28174601 GGTTGTTTTAATTT
1 GGTTGTTTTAATTT
28174615 G
1 G
28174616 AAGAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.24, T:0.62
Consensus pattern (14 bp):
GGTTGTTTTAATTT
Found at i:28175965 original size:13 final size:15
Alignment explanation
Indices: 28175947--28175980 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
28175937 TCTCGATATG
28175947 TATCAAACAT-G-AA
1 TATCAAACATGGAAA
28175960 TATCAAACATGGAAA
1 TATCAAACATGGAAA
28175975 TATCAA
1 TATCAA
28175981 GAAAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 1 0.05
15 8 0.42
ACGTcount: A:0.53, C:0.15, G:0.09, T:0.24
Consensus pattern (15 bp):
TATCAAACATGGAAA
Found at i:28181762 original size:25 final size:23
Alignment explanation
Indices: 28181722--28181769 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
28181712 ATTTTTTATA
* *
28181722 TTTAAATTTAATCTTTATATATTTT
1 TTTAAATTAAACCTTT-TAT-TTTT
28181747 TTTAAATTAAACCTTTTATTTTT
1 TTTAAATTAAACCTTTTATTTTT
28181770 AGAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 3 0.14
25 14 0.67
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTAAATTAAACCTTTTATTTTT
Found at i:28182743 original size:14 final size:14
Alignment explanation
Indices: 28182708--28182746 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
28182698 CTACTGATAT
28182708 AATATTTATATTTTAA
1 AATA-TTAT-TTTTAA
28182724 AA-ATTATTTTTAA
1 AATATTATTTTTAA
28182737 AATATTATTT
1 AATATTATTT
28182747 ATTTAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.36
14 11 0.50
15 1 0.05
16 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATATTATTTTTAA
Found at i:28184709 original size:105 final size:105
Alignment explanation
Indices: 28184577--28184782 Score: 315
Period size: 105 Copynumber: 2.0 Consensus size: 105
28184567 TGCTAGTTAC
* * * *
28184577 CCTACCGTACTCATTCCAAATTCAACTTTTACGAGGTCAATAAATTCTTAAAAAGCTTTTGAA-G
1 CCTACCATACTCATTCCAAATTCAACTTTCACGAGATCAACAAATTCTTAAAAAGCTTTTGAATG
28184641 AAGTGAAATAAAAGAAAAATGCCATCCACATAGATTTTTCA
66 -AGTGAAATAAAAGAAAAATGCCATCCACATAGATTTTTCA
* * * *
28184682 CCTACCATACTCATTTCAAATTCAACTTTCACGAGATCTACAAATTCTTAAGAAGTTTTTGAATG
1 CCTACCATACTCATTCCAAATTCAACTTTCACGAGATCAACAAATTCTTAAAAAGCTTTTGAATG
*
28184747 AGTGAAATAAAAGAAAAATGTCATCCACATAGATTT
66 AGTGAAATAAAAGAAAAATGCCATCCACATAGATTT
28184783 GTCCTAAATT
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
105 90 0.99
106 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (105 bp):
CCTACCATACTCATTCCAAATTCAACTTTCACGAGATCAACAAATTCTTAAAAAGCTTTTGAATG
AGTGAAATAAAAGAAAAATGCCATCCACATAGATTTTTCA
Found at i:28186515 original size:22 final size:22
Alignment explanation
Indices: 28186485--28186529 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
28186475 TGGGAGTGTT
*
28186485 TTTGTATCAAAACGATACCAGG
1 TTTGCATCAAAACGATACCAGG
*
28186507 TTTGCATCAAAATGATACCAGG
1 TTTGCATCAAAACGATACCAGG
28186529 T
1 T
28186530 GTGTACTCGA
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:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (22 bp):
TTTGCATCAAAACGATACCAGG
Found at i:28188496 original size:18 final size:18
Alignment explanation
Indices: 28188473--28188509 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28188463 TAGTGAAATG
28188473 ATGTTAGAGGTTAACCCA
1 ATGTTAGAGGTTAACCCA
28188491 ATGTTAGAGGTTAACCCA
1 ATGTTAGAGGTTAACCCA
28188509 A
1 A
28188510 CTCTTTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (18 bp):
ATGTTAGAGGTTAACCCA
Found at i:28211368 original size:15 final size:15
Alignment explanation
Indices: 28211337--28211367 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28211327 AATACTAAAA
28211337 TTATATTTTAACATT
1 TTATATTTTAACATT
28211352 TTATATTTTAA-ATT
1 TTATATTTTAACATT
28211366 TT
1 TT
28211368 TTTCTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATTTTAACATT
Found at i:28213735 original size:11 final size:11
Alignment explanation
Indices: 28213721--28213776 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
28213711 AGATAAATAT
28213721 TATTTTATTAA
1 TATTTTATTAA
*
28213732 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
28213745 TATTTTATTAT
1 TATTTTATTAA
*
28213756 TATTTTATTAT
1 TATTTTATTAA
28213767 TATTTTATTA
1 TATTTTATTA
28213777 GTATATAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
11 27 0.68
12 6 0.15
13 7 0.17
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:28215984 original size:45 final size:46
Alignment explanation
Indices: 28215918--28216093 Score: 239
Period size: 46 Copynumber: 3.8 Consensus size: 46
28215908 GCTCTCTGAT
** *
28215918 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
28215964 ATGAAATG-ATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* *
28216009 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* * * * *
28216055 A-GAAAATGAGTAAGACCGTAGTTGAAAGACACTATGGCA
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCA
28216094 TCATGTCAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
45 43 0.36
46 75 0.64
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
Found at i:28216116 original size:91 final size:90
Alignment explanation
Indices: 28215928--28216098 Score: 236
Period size: 91 Copynumber: 1.9 Consensus size: 90
28215918 ATGAAATGTG
* * * *
28215928 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGATAAGACCATGGTTGAAAGAT
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGATAAGACCATAGTTGAAAGAC
*
28215993 ACCATGGCAACGTGACATGAAAAGAA
66 ACCATGGCAACATGACA-GAAAAGAA
*
28216019 TAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACCGTAGTTGAAAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATG-AAATGA-TAAGACCATAGTTGAAAG
* *
28216083 ACACTATGGCATCATG
64 ACACCATGGCAACATG
28216099 TCAAAGATAA
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
90 1 0.01
91 41 0.59
92 28 0.40
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (90 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGATAAGACCATAGTTGAAAGAC
ACCATGGCAACATGACAGAAAAGAA
Found at i:28217497 original size:15 final size:15
Alignment explanation
Indices: 28217479--28217509 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28217469 TCAAATTAGT
28217479 TATTTACTATTATTA
1 TATTTACTATTATTA
*
28217494 TATTTATTATTATTA
1 TATTTACTATTATTA
28217509 T
1 T
28217510 TGTTTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTACTATTATTA
Found at i:28217527 original size:18 final size:18
Alignment explanation
Indices: 28217482--28217528 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
28217472 AATTAGTTAT
28217482 TTACTATTATTATATTTA
1 TTACTATTATTATATTTA
* * *
28217500 TTATTATTATTGTTTTTA
1 TTACTATTATTATATTTA
*
28217518 TTACTGTTATT
1 TTACTATTATT
28217529 TTTATTATCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (18 bp):
TTACTATTATTATATTTA
Found at i:28217608 original size:22 final size:22
Alignment explanation
Indices: 28217583--28217624 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28217573 TACTTTCTAT
*
28217583 TATTGTAATTATTAACATATAC
1 TATTATAATTATTAACATATAC
* *
28217605 TATTATTATTATTAATATAT
1 TATTATAATTATTAACATAT
28217625 TATTATTACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTATAATTATTAACATATAC
Found at i:28217628 original size:20 final size:22
Alignment explanation
Indices: 28217580--28217642 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 22
28217570 TATTACTTTC
* *
28217580 TATTATTGTAATTATTAACATA
1 TATTATTATTATTATTAACATA
*
28217602 TACTATTATTATTATT-A-ATA
1 TATTATTATTATTATTAACATA
* *
28217622 TATTATTATTACTATTTACAT
1 TATTATTATTATTATTAACAT
28217643 GTTATCATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 15 0.44
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (22 bp):
TATTATTATTATTATTAACATA
Found at i:28217682 original size:3 final size:3
Alignment explanation
Indices: 28217674--28217908 Score: 95
Period size: 3 Copynumber: 77.7 Consensus size: 3
28217664 TATTACGGTT
* * * *
28217674 TTA TTA TTA TTA CTA TTA TTA CTA TTT TTA TT- TTCA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
* * * * * *
28217719 TTA TCA TCCTA TT- TTA TTA CTA TTA TCA CTT- TTG TAA TTA CTA TTA
1 TTA TTA T--TA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* ** * *
28217765 TTA TTG TT- TTA TTA TTA TTTA TTTA GCA -TA TTA TTA GTA TTA TTG
1 TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA
** * * * * *
28217810 CCA TCA TTA TTA TTA TTA TTA TTA CTTT TTA CTA TTA CTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* * * * * *
28217856 CTA TTA ATA TCA TTA GTA TTA TTA TTA TTA CTG TT- TTCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
28217901 TTG TTA TT
1 TTA TTA TT
28217909 TTTTGTAATA
Statistics
Matches: 169, Mismatches: 50, Indels: 26
0.69 0.20 0.11
Matches are distributed among these distances:
2 11 0.07
3 143 0.85
4 13 0.08
5 2 0.01
ACGTcount: A:0.29, C:0.10, G:0.03, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:28219126 original size:46 final size:47
Alignment explanation
Indices: 28219066--28219301 Score: 248
Period size: 46 Copynumber: 5.0 Consensus size: 47
28219056 TTTGATATGA
* * * * * *
28219066 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
*** *
28219112 TGCCATGGTATCTTTCAACCATGGTCTTGTTCA-TTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
*
28219158 TGCTATGGTATCTTTCAACCATTCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATC--T------TTCAACCATGGTCTTACACATTTTCATATCAGGT
* *
28219212 TGCCATGGTATCTTTCAACCATGGTCTTACATA-TTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
28219258 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAG
28219302 AGAGCACACT
Statistics
Matches: 165, Mismatches: 16, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
45 4 0.02
46 119 0.72
48 1 0.01
52 1 0.01
54 40 0.24
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.39
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
Found at i:28219252 original size:100 final size:100
Alignment explanation
Indices: 28219079--28219279 Score: 289
Period size: 100 Copynumber: 2.0 Consensus size: 100
28219069 CATAGTGTCT
* * * * **
28219079 TTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTGTTC
1 TTCAACCATGGTCTTACACATTTTCTATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTCATC
* *
28219144 ATTTCATATCACGTTGCTATGGTATCTTTCAACCA
66 ATTTCATATCACGCTGCCATGGTATCTTTCAACCA
28219179 TTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
1 TTCAACCATGGTCTTACACATTTTC-TATCAGGTTGCCATGGTATCTTTCAACCATGGTCTT-CA
*
28219243 T-ATTTCATATCAGGCTGCCATGGTATCTTTCAACCA
64 TCATTTCATATCACGCTGCCATGGTATCTTTCAACCA
28219279 T
1 T
28219280 GGTCTTACAC
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
99 4 0.04
100 85 0.94
101 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (100 bp):
TTCAACCATGGTCTTACACATTTTCTATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTCATC
ATTTCATATCACGCTGCCATGGTATCTTTCAACCA
Found at i:28222170 original size:19 final size:19
Alignment explanation
Indices: 28222146--28222194 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
28222136 TTTTACACTA
28222146 AGGTACTAATTAATCAACT
1 AGGTACTAATTAATCAACT
28222165 AGGTACTAATTAATCAACT
1 AGGTACTAATTAATCAACT
*
28222184 AGGTACCAATT
1 AGGTACTAATT
28222195 TTTGGGCGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (19 bp):
AGGTACTAATTAATCAACT
Found at i:28222315 original size:22 final size:21
Alignment explanation
Indices: 28222273--28222316 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
28222263 TCGCGGACCA
*
28222273 AAATCATTGTTTAAATAAATC
1 AAATCATTGTTTAAAAAAATC
28222294 AAATCATT-TATTAAAAACAATC
1 AAATCATTGT-TTAAAAA-AATC
28222316 A
1 A
28222317 CTTTTACGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 14 0.70
22 5 0.25
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (21 bp):
AAATCATTGTTTAAAAAAATC
Found at i:28224670 original size:23 final size:23
Alignment explanation
Indices: 28224616--28224676 Score: 94
Period size: 21 Copynumber: 2.8 Consensus size: 23
28224606 GATACATAAA
28224616 GTGCCT-AAA-ACGACACACGAG
1 GTGCCTGAAATACGACACACGAG
28224637 GTGCCTG--ATACGACACACGAG
1 GTGCCTGAAATACGACACACGAG
28224658 GTGCCTGAAATACGACACA
1 GTGCCTGAAATACGACACA
28224677 TAAAGTGCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.03
21 25 0.69
23 10 0.28
ACGTcount: A:0.34, C:0.28, G:0.25, T:0.13
Consensus pattern (23 bp):
GTGCCTGAAATACGACACACGAG
Found at i:28224684 original size:23 final size:23
Alignment explanation
Indices: 28224602--28224688 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
28224592 CCTGATCAGT
* *
28224602 ATACGATACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
28224624 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
28224644 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
28224667 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
28224689 TCGATAAAGC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.02
21 33 0.61
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:28227878 original size:18 final size:18
Alignment explanation
Indices: 28227857--28227891 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28227847 AATCAGTAAT
*
28227857 CAGTAACGGTAGCAGTAG
1 CAGTAACGGTAACAGTAG
28227875 CAGTAACGGTAACAGTA
1 CAGTAACGGTAACAGTA
28227892 TTTGACACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (18 bp):
CAGTAACGGTAACAGTAG
Found at i:28228892 original size:17 final size:17
Alignment explanation
Indices: 28228866--28228902 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
28228856 ATCTCTAGTT
* *
28228866 TTTCCTTTTTCTTTTTC
1 TTTCCCTTTTCTTTCTC
28228883 TTTCCCTTTTCTTTCTC
1 TTTCCCTTTTCTTTCTC
28228900 TTT
1 TTT
28228903 TTCTCCCCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTCCCTTTTCTTTCTC
Found at i:28230149 original size:28 final size:28
Alignment explanation
Indices: 28230109--28230165 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
28230099 ATAAGGAGCC
28230109 GTCGGGTATGATCCTCTGCTCATGTTAA
1 GTCGGGTATGATCCTCTGCTCATGTTAA
28230137 GTCGGGTATGATCCTCTGCTCATGTTAA
1 GTCGGGTATGATCCTCTGCTCATGTTAA
28230165 G
1 G
28230166 ATAGTATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (28 bp):
GTCGGGTATGATCCTCTGCTCATGTTAA
Found at i:28238825 original size:38 final size:38
Alignment explanation
Indices: 28238782--28238976 Score: 327
Period size: 38 Copynumber: 5.1 Consensus size: 38
28238772 AAAGGCTCGA
* * *
28238782 ATATAATACCAGCACTAGGCCTGCAGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
28238820 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* *
28238858 ATATATTACCAGCACGAAGCCTGTGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
28238896 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* *
28238934 ATATAATACCAGCACGAAACCTACGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
28238972 ATATA
1 ATATA
28238977 CATCAAATAT
Statistics
Matches: 148, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 148 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.21
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
Found at i:28244570 original size:38 final size:38
Alignment explanation
Indices: 28244528--28244835 Score: 510
Period size: 38 Copynumber: 8.1 Consensus size: 38
28244518 AAAGGCTCGA
* * *
28244528 ATATAATACCAGCACTAGGCCTGTGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
28244566 ATATAATACCAGCACGAAGCCTGCAGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
28244604 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
28244642 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* *
28244680 ATATAATACCAGCACGAAGCCTGTGGGATTTAACCCAG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* * *
28244718 ACATATTACCAGCACGAAGCCTGCGGGATTT-ACCCAG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
28244755 ATATAATACCAGCACGAAGCCTGCGGGATTTAACTCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
28244793 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
28244831 ATATA
1 ATATA
28244836 CATCAAATAT
Statistics
Matches: 252, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
37 35 0.14
38 217 0.86
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.20
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
Found at i:28246163 original size:2 final size:2
Alignment explanation
Indices: 28246151--28246179 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28246141 CACTTTCAAA
28246151 AT AT A- 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
28246180 TCGACTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28249398 original size:88 final size:88
Alignment explanation
Indices: 28249239--28249723 Score: 702
Period size: 88 Copynumber: 5.5 Consensus size: 88
28249229 CATGTCCCTA
* * * * * *
28249239 GAAGACGGTGAGCCTTAACTCCCTAAGCAGTAGGGTAATAGGCTGGAAACTAAAGATCTTATCTC
1 GAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTC
* *
28249304 CTTAAGCAGTAGTGGAGTAGATC
66 CCTAAGCAGTAGTGGAGCAGATC
*
28249327 GAAGGCAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTC
1 GAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTC
*
28249392 CCTAAGCAGTAGTGGAGTAGATC
66 CCTAAGCAGTAGTGGAGCAGATC
* * * *
28249415 GAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTAGAAATTACATATGTTATCTC
1 GAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTC
* *
28249480 CCTAAGCAATAGTGGAGCAGATT
66 CCTAAGCAGTAGTGGAGCAGATC
* * *
28249503 GAAGACGGTAAGCCTTAACCCCTTAAGGAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTC
1 GAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTC
* *
28249568 CCTAAGCAGTAATGGAGCAGATT
66 CCTAAGCAGTAGTGGAGCAGATC
* * *
28249591 GAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTATAGATCTTATCAC
1 GAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTC
*
28249656 CCTAAGCAGTAGGGGAGCAGATC
66 CCTAAGCAGTAGTGGAGCAGATC
* * *
28249679 AAAGACGGTGAGCCTTAACCCCCTCAA-CAGTAGGGTAACAGGCTG
1 GAAGACAGTAAGCCTTAACCCCCT-AAGCAGTAGGGTAACAGGCTG
28249724 AAGATCAAAA
Statistics
Matches: 359, Mismatches: 37, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
88 357 0.99
89 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (88 bp):
GAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTC
CCTAAGCAGTAGTGGAGCAGATC
Found at i:28249659 original size:44 final size:42
Alignment explanation
Indices: 28249252--28249669 Score: 168
Period size: 44 Copynumber: 9.5 Consensus size: 42
28249242 GACGGTGAGC
* * * *
28249252 CTTAACTCCCTAAGCAGTAGGGTAATAGGCTGGAAACTAAAGAT
1 CTTATCTCCCTAAGCAGTAGGG-AACAGGCT-GAAAATTAAGAT
* ** * * * *
28249296 CTTATCTCCTTAAGCAGTAGTGGAGTA-GATCGAAGGCAGTAAG-C
1 CTTATCTCCCTAAGCAGTAG-GGAACAGGCT-GAA--AATTAAGAT
* * *
28249340 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGAT
1 CTTATCTCCCTAAGCAGTAGGG-AACAGGCTGAAAATTA-AGAT
** * * *
28249384 CTTATCTCCCTAAGCAGTAGTGGAGTA-GATCGAAGACAGTAAG-C
1 CTTATCTCCCTAAGCAGTAG-GGAACAGGCT-GAA-A-ATTAAGAT
* * *
28249428 CTTAACCCCCTAAGCAGTAGGGAAACAGGCT-AGAAATTACATAT
1 CTTATCTCCCTAAGCAGTAGGG-AACAGGCTGA-AAATTA-AGAT
* * * ** ** *
28249472 GTTATCTCCCTAAGCAATAGTGGAGCAGATTGAAGACGGTAAG-C
1 CTTATCTCCCTAAGCAGTAG-GGAACAGGCTGAA-A-ATTAAGAT
* * *
28249516 CTTAAC-CCCTTAAGGAGTAGGGTAACAGGCTGGAAATTACAGAT
1 CTTATCTCCC-TAAGCAGTAGGG-AACAGGCTGAAAATTA-AGAT
* * ** * *
28249560 CTTATCTCCCTAAGCAGTAATGGAGCAGATTGAAGACAGTAAG-C
1 CTTATCTCCCTAAGCAGT-AGGGAACAGGCTGAA-A-ATTAAGAT
* *
28249604 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTATAGAT
1 CTTATCTCCCTAAGCAGTAGGG-AACAGGCTGAAAATTA-AGAT
*
28249648 CTTATCACCCTAAGCAGTAGGG
1 CTTATCTCCCTAAGCAGTAGGG
28249670 GAGCAGATCA
Statistics
Matches: 266, Mismatches: 77, Indels: 62
0.66 0.19 0.15
Matches are distributed among these distances:
42 11 0.04
43 30 0.11
44 189 0.71
45 28 0.11
46 8 0.03
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.22
Consensus pattern (42 bp):
CTTATCTCCCTAAGCAGTAGGGAACAGGCTGAAAATTAAGAT
Found at i:28249985 original size:45 final size:42
Alignment explanation
Indices: 28249872--28249994 Score: 140
Period size: 41 Copynumber: 2.9 Consensus size: 42
28249862 AGCTATGAAT
*
28249872 AAACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA-GATCA
1 AAACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGATCA
* * *
28249913 AAACAAACCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGA
1 AAACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGATCA
* * * *
28249955 AGTCACCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
1 A---AACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAG
28249995 ACTAAAACAC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 34 0.49
42 4 0.06
45 31 0.45
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (42 bp):
AAACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGATCA
Found at i:28250348 original size:19 final size:19
Alignment explanation
Indices: 28250295--28250348 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
28250285 AAGCCCAAAT
28250295 CAAA-CCAAAACCCAGATTA
1 CAAACCCAAAACCCA-ATTA
* ** *
28250314 AAAACCCATCAGCCAATTA
1 CAAACCCAAAACCCAATTA
28250333 CAAACCCAAAACCCAA
1 CAAACCCAAAACCCAA
28250349 ACCTAAATCA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.52, C:0.35, G:0.04, T:0.09
Consensus pattern (19 bp):
CAAACCCAAAACCCAATTA
Found at i:28251486 original size:28 final size:27
Alignment explanation
Indices: 28251426--28251487 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
28251416 ATCATTTTTC
*
28251426 ATTATTTTGCTATTTTATTTTTAAATT
1 ATTATTTTGCTATTTTATATTTAAATT
*
28251453 AGTTATTTT-CTATTATTATATTTATTATT
1 A-TTATTTTGCTATT-TTATATTTA-AATT
28251482 ATTATT
1 ATTATT
28251488 GTTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 6 0.20
28 20 0.67
29 4 0.13
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.66
Consensus pattern (27 bp):
ATTATTTTGCTATTTTATATTTAAATT
Found at i:28251495 original size:15 final size:15
Alignment explanation
Indices: 28251456--28251497 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
28251446 TTAAATTAGT
*
28251456 TATTTTCTATTATTA
1 TATTTTTTATTATTA
*
28251471 TATTTATTATTATTA
1 TATTTTTTATTATTA
28251486 T-TGTTTTTATTA
1 TAT-TTTTTATTA
28251498 CTGTTATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 1 0.04
15 22 0.96
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (15 bp):
TATTTTTTATTATTA
Found at i:28251586 original size:22 final size:22
Alignment explanation
Indices: 28251561--28251602 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
28251551 TACTTTCGAT
28251561 TATTATCATTATTAACATATAC
1 TATTATCATTATTAACATATAC
* *
28251583 TATTATTATTATTAATATAT
1 TATTATCATTATTAACATAT
28251603 TATTATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTATCATTATTAACATATAC
Found at i:28251606 original size:20 final size:20
Alignment explanation
Indices: 28251559--28251625 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
28251549 ATTACTTTCG
*
28251559 ATTATTATCATTATTAACATAT
1 ATTATTATTATTATT-A-ATAT
*
28251581 ACTATTATTATTATTAATAT
1 ATTATTATTATTATTAATAT
* *
28251601 ATTATTATTACTATTTATAT
1 ATTATTATTATTATTAATAT
*
28251621 GTTAT
1 ATTAT
28251626 CATTTCTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 25 0.64
21 1 0.03
22 13 0.33
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.55
Consensus pattern (20 bp):
ATTATTATTATTATTAATAT
Found at i:28251792 original size:41 final size:41
Alignment explanation
Indices: 28251711--28251792 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 41
28251701 TATCATCCTA
* * *
28251711 TTTTATTACTATTATCACTTTTGTAATTACTATTACTATTG
1 TTTTATTACTATTATCACTTTAGCAATTACTACTACTATTG
* * *
28251752 TTTTATTACTATTATTA-TTTAGCATATTATTACTATTATTG
1 TTTTATTACTATTATCACTTTAGCA-ATTACTACTACTATTG
28251793 CCATCATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 5 0.15
41 29 0.85
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57
Consensus pattern (41 bp):
TTTTATTACTATTATCACTTTAGCAATTACTACTACTATTG
Found at i:28251890 original size:3 final size:3
Alignment explanation
Indices: 28251652--28251874 Score: 87
Period size: 3 Copynumber: 74.0 Consensus size: 3
28251642 TATTACGGTT
* * * * *
28251652 TTA TTA TTA TTA CTA TTA TTA CTA TTT TTA TT- TTCA TCA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
* * * * * *
28251697 TTA TTA TCA TCCTA TT- TTA TTA CTA TTA TCA CTT- TTG TAA TTA CTA
1 TTA TTA TTA T--TA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * * ** *
28251743 TTA CTA TTG TT- TTA TTA CTA TTA TTA TTTA GCA -TA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* ** * * * *
28251787 TTA TTG CCA TCA TTA TTA TTA TTA TTA TTA CTTT TTA CTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * * * * *
28251833 TTA CTA CTA TTA ATA TCA TTA GTA TTA GTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28251875 CTGTTTTCAT
Statistics
Matches: 158, Mismatches: 51, Indels: 22
0.68 0.22 0.10
Matches are distributed among these distances:
2 9 0.06
3 140 0.89
4 7 0.04
5 2 0.01
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:28251946 original size:12 final size:12
Alignment explanation
Indices: 28251918--28251966 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
28251908 TTTTATATTT
*
28251918 TTATTTATTTAC
1 TTATTTATTTGC
*
28251930 CTATTTATTTGC
1 TTATTTATTTGC
*
28251942 TTATTTCACTTTTC
1 TTATTT-A-TTTGC
28251956 TTATTTATTTG
1 TTATTTATTTG
28251967 TTTAAGTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
12 18 0.60
13 2 0.07
14 10 0.33
ACGTcount: A:0.18, C:0.12, G:0.04, T:0.65
Consensus pattern (12 bp):
TTATTTATTTGC
Found at i:28253449 original size:23 final size:23
Alignment explanation
Indices: 28253418--28253466 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
28253408 AAATGAGATG
28253418 TTTAAAAAT-TAATTTTAA-ATATT
1 TTTAAAAATAT-ATTTTAATA-ATT
*
28253441 TTTATAAATATATTTTAATAATT
1 TTTAAAAATATATTTTAATAATT
28253464 TTT
1 TTT
28253467 CGATTCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTAAAAATATATTTTAATAATT
Found at i:28254649 original size:21 final size:21
Alignment explanation
Indices: 28254625--28254668 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
28254615 CTTGGTATGA
* *
28254625 TGCAAGGTGAGCTTACTCAGT
1 TGCAAGCTGAACTTACTCAGT
*
28254646 TGCAAGCTGAATTTACTCAGT
1 TGCAAGCTGAACTTACTCAGT
28254667 TG
1 TG
28254669 GATGCTAGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (21 bp):
TGCAAGCTGAACTTACTCAGT
Found at i:28258651 original size:15 final size:15
Alignment explanation
Indices: 28258631--28258660 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28258621 TATTTTATTT
*
28258631 ATATTAGGATAATTA
1 ATATTAAGATAATTA
28258646 ATATTAAGATAATTA
1 ATATTAAGATAATTA
28258661 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:28262419 original size:8 final size:8
Alignment explanation
Indices: 28262401--28262455 Score: 56
Period size: 9 Copynumber: 6.2 Consensus size: 8
28262391 GGCAACCCAA
28262401 TTTTTATTT
1 TTTTTA-TT
28262410 TTTTTATT
1 TTTTTATT
28262418 TTTTTATTT
1 TTTTTA-TT
28262427 TTTCTTATT
1 TTT-TTATT
*
28262436 ATTTTATT
1 TTTTTATT
28262444 ATTTATTATT
1 -TTT-TTATT
28262454 TT
1 TT
28262456 CAGATATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 13 0.32
9 19 0.47
10 8 0.20
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTATT
Found at i:28262420 original size:15 final size:15
Alignment explanation
Indices: 28262400--28262455 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
28262390 AGGCAACCCA
28262400 ATTTTTATTTTTTTT
1 ATTTTTATTTTTTTT
28262415 ATTTTT-TTATTTTTT
1 ATTTTTATT-TTTTTT
* * *
28262430 CTTATTA-TTTTATT
1 ATTTTTATTTTTTTT
28262444 ATTTATTATTTT
1 ATTT-TTATTTT
28262456 CAGATATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
14 9 0.28
15 20 0.62
16 3 0.09
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (15 bp):
ATTTTTATTTTTTTT
Found at i:28262428 original size:18 final size:18
Alignment explanation
Indices: 28262401--28262455 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
28262391 GGCAACCCAA
28262401 TTTTTATTTTTT-TTATT
1 TTTTTATTTTTTATTATT
*
28262418 TTTTTATTTTTTCTTATT
1 TTTTTATTTTTTATTATT
* *
28262436 ATTTTATTATTTATTATT
1 TTTTTATTTTTTATTATT
28262454 TT
1 TT
28262456 CAGATATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
17 12 0.36
18 21 0.64
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTATTTTTTATTATT
Found at i:28263403 original size:11 final size:11
Alignment explanation
Indices: 28263380--28263421 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
28263370 ACACATACAT
*
28263380 AAAT-AAAATA
1 AAATAAAAAGA
28263390 AAATAAAAAGA
1 AAATAAAAAGA
28263401 AAA-AAAAAGA
1 AAATAAAAAGA
*
28263411 AAAAAAAAAGA
1 AAATAAAAAGA
28263422 GAAAATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 14 0.48
11 15 0.52
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (11 bp):
AAATAAAAAGA
Found at i:28263408 original size:21 final size:21
Alignment explanation
Indices: 28263384--28263426 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28263374 ATACATAAAT
* *
28263384 AAAATAAAATAAAAAGAAAAA
1 AAAAGAAAAAAAAAAGAAAAA
*
28263405 AAAAGAAAAAAAAAAGAGAAA
1 AAAAGAAAAAAAAAAGAAAAA
28263426 A
1 A
28263427 TATATGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.05
Consensus pattern (21 bp):
AAAAGAAAAAAAAAAGAAAAA
Found at i:28263426 original size:11 final size:10
Alignment explanation
Indices: 28263384--28263418 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
28263374 ATACATAAAT
*
28263384 AAAATAAAATA
1 AAAAGAAAA-A
28263395 AAAAGAAAAA
1 AAAAGAAAAA
28263405 AAAAGAAAAA
1 AAAAGAAAAA
28263415 AAAA
1 AAAA
28263419 AGAGAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.65
11 8 0.35
ACGTcount: A:0.89, C:0.00, G:0.06, T:0.06
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:28264071 original size:10 final size:10
Alignment explanation
Indices: 28264052--28264083 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
28264042 ATTTAGGATT
28264052 TTAT-TTTAA
1 TTATCTTTAA
28264061 TTATCTTTAA
1 TTATCTTTAA
28264071 TTATCTTTAA
1 TTATCTTTAA
28264081 TTA
1 TTA
28264084 AATGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:28264891 original size:6 final size:7
Alignment explanation
Indices: 28264876--28264900 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28264866 AGATTCTTAA
28264876 TTTTATT
1 TTTTATT
28264883 TTTTATT
1 TTTTATT
28264890 TTTTATT
1 TTTTATT
28264897 TTTT
1 TTTT
28264901 CAAGAACGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:28265826 original size:44 final size:44
Alignment explanation
Indices: 28265763--28265851 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
28265753 TAAACGAGTC
28265763 GTTTTGGCTGGAACACTGCTTAAATTCTACTGCTGCTGTTAGAA
1 GTTTTGGCTGGAACACTGCTTAAATTCTACTGCTGCTGTTAGAA
28265807 GTTTTGGCTGGAACACTGCTTAAATTCTACTGCTGCTGTTAGAA
1 GTTTTGGCTGGAACACTGCTTAAATTCTACTGCTGCTGTTAGAA
28265851 G
1 G
28265852 AATCCGTTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (44 bp):
GTTTTGGCTGGAACACTGCTTAAATTCTACTGCTGCTGTTAGAA
Found at i:28267033 original size:9 final size:9
Alignment explanation
Indices: 28267019--28267047 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
28267009 TTTATTCATT
28267019 AAAATTAAA
1 AAAATTAAA
28267028 AAAATTAAA
1 AAAATTAAA
28267037 AAAATTAAA
1 AAAATTAAA
28267046 AA
1 AA
28267048 CAAAAACACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAATTAAA
Found at i:28280521 original size:43 final size:41
Alignment explanation
Indices: 28280430--28280592 Score: 148
Period size: 43 Copynumber: 3.9 Consensus size: 41
28280420 ACCGAGATGA
* * * *
28280430 GATTACATGTAAAACCATGTCTGGGAAATTGGAATTGTATT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATT
*
28280471 GATATTACATGTAAGACCATGTTTGGGACATTGGCATCGTTAATT
1 G--ATTACATGTAAGACCATGTCTGGGACATTGGCATCG-T-ATT
* * * * *
28280516 GATTACGTGTACGACCTTGTCTAGGACAGTGGCATCGATATGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCG-TAT-T
* * *
28280559 GATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCAT
28280593 TGTACAAGCT
Statistics
Matches: 98, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
41 1 0.01
42 8 0.08
43 84 0.86
44 1 0.01
45 4 0.04
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (41 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATT
Found at i:28281062 original size:36 final size:36
Alignment explanation
Indices: 28281015--28281088 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
28281005 AGATTAAAGT
28281015 GAATGGAAGCTGTGCACCAGGTAGAAAGCCAGAAAA
1 GAATGGAAGCTGTGCACCAGGTAGAAAGCCAGAAAA
28281051 GAATGGAAGCTGTGCACCAGGTAGAAAGCCAGAAAA
1 GAATGGAAGCTGTGCACCAGGTAGAAAGCCAGAAAA
28281087 GA
1 GA
28281089 GGAGGTGAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.42, C:0.16, G:0.31, T:0.11
Consensus pattern (36 bp):
GAATGGAAGCTGTGCACCAGGTAGAAAGCCAGAAAA
Found at i:28281742 original size:60 final size:59
Alignment explanation
Indices: 28281622--28281758 Score: 143
Period size: 60 Copynumber: 2.3 Consensus size: 59
28281612 CAGTGTTAAC
* *
28281622 TGGGCCTTAGCCCATATCAATATTAATCTAGGCCATAGCCCCTTACAGTATCAGAGTATAT
1 TGGGCC-TAGCCCATATCAATATCAATCTAGGCCATAGCCCATTACAG-ATCAGAGTATAT
* * * *
28281683 TGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCTTATTACA-AGTC-GAGATATAT
1 TGGGCCTAGCCCATATCAATATCAATCTAGGCCATAGCC-CATTACAGA-TCAGAG-TATAT
* *
28281743 TGGGTCTTGCCCATAT
1 TGGGCCTAGCCCATAT
28281759 TAACATAGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
59 4 0.06
60 50 0.77
61 11 0.17
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (59 bp):
TGGGCCTAGCCCATATCAATATCAATCTAGGCCATAGCCCATTACAGATCAGAGTATAT
Found at i:28284173 original size:15 final size:15
Alignment explanation
Indices: 28284136--28284164 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28284126 TTTCCCTATC
28284136 TAATAATAATAATTA
1 TAATAATAATAATTA
28284151 TAATAATAATAATT
1 TAATAATAATAATT
28284165 TTATAAATAT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:28286352 original size:28 final size:28
Alignment explanation
Indices: 28286302--28286356 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
28286292 GTCCACTTCT
** * *
28286302 CCCAAATTGGTACTTATAGTTTTTTTTC
1 CCCAAATTGGTACCCAAACTTTTTTTTC
28286330 CCCAAATTGGTACCCAAACTTTTTTTT
1 CCCAAATTGGTACCCAAACTTTTTTTT
28286357 GTTAACAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (28 bp):
CCCAAATTGGTACCCAAACTTTTTTTTC
Found at i:28287554 original size:21 final size:21
Alignment explanation
Indices: 28287490--28287556 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
28287480 GGCCAGCCCA
*
28287490 TGTGGCTACCCCACACA-CTCG
1 TGTGGATACCCCACACAGC-CG
* * *
28287511 TATAGATACCCCACA-TGCCCG
1 TGTGGATACCCCACACAG-CCG
28287532 TGTGGATACCCCACACAGCCG
1 TGTGGATACCCCACACAGCCG
28287553 TGTG
1 TGTG
28287557 CTCAAATCGT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
21 34 0.94
22 2 0.06
ACGTcount: A:0.22, C:0.37, G:0.21, T:0.19
Consensus pattern (21 bp):
TGTGGATACCCCACACAGCCG
Found at i:28287779 original size:21 final size:21
Alignment explanation
Indices: 28287723--28287782 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
28287713 ATCAAAATCA
*
28287723 ACCCCACACGCCCGTATGGAT
1 ACCCCACACGCCCGTGTGGAT
* *
28287744 ACCCTACATGCCCGTGTGGAT
1 ACCCCACACGCCCGTGTGGAT
28287765 ACCCCACACAG-CCGTGTG
1 ACCCCACAC-GCCCGTGTG
28287783 CTCAAATCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 32 0.97
22 1 0.03
ACGTcount: A:0.22, C:0.40, G:0.22, T:0.17
Consensus pattern (21 bp):
ACCCCACACGCCCGTGTGGAT
Found at i:28288600 original size:13 final size:13
Alignment explanation
Indices: 28288582--28288611 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28288572 TTCCTGTAAA
28288582 CATTTCACATAAC
1 CATTTCACATAAC
*
28288595 CATTTCATATAAC
1 CATTTCACATAAC
28288608 CATT
1 CATT
28288612 CCATCTGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (13 bp):
CATTTCACATAAC
Found at i:28288781 original size:46 final size:46
Alignment explanation
Indices: 28288705--28289202 Score: 674
Period size: 46 Copynumber: 10.8 Consensus size: 46
28288695 TGATGTCATA
* * * * *
28288705 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATATCACGTTGCCATG
* * *** * *
28288751 GTATCTTTCAACCATGATCTTATTCATTTTCCCGTCATGTTGCCATT
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGTTGCCATG
* * *
28288798 ATATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
*
28288844 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
* *** *
28288890 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGTTGCCATG
* *
28288937 ATATCTTTCAACCATGGTCTTACTCATTTCATATCAAGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
*
28288983 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
*
28289029 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
*
28289075 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
* * * *
28289121 GTATCTTTCAACCATAGTCTTACACATTTCATATCAGGTTGTCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
* *
28289167 GTATCTTTCAACCATGGTCTTACACATTCCATATCA
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCA
28289203 GAGAGCACAC
Statistics
Matches: 411, Mismatches: 38, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
46 335 0.82
47 76 0.18
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
Done.