Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_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: 10425128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 51
Found at i:2752878 original size:11 final size:11
Alignment explanation
Indices: 2752862--2752893 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2752852 TTTTTATAAA
2752862 AAAATATATAT
1 AAAATATATAT
*
2752873 AAAATAAATAT
1 AAAATATATAT
2752884 AAAATATATA
1 AAAATATATA
2752894 ATAATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATATATAT
Found at i:2757304 original size:2 final size:2
Alignment explanation
Indices: 2757297--2757374 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
2757287 TTTCAACATA
2757297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2757339 AT AT AT AT AT AT AT AT -T 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 AT AT AT A
2757375 CATTTAAAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2760790 original size:27 final size:27
Alignment explanation
Indices: 2760699--2760798 Score: 155
Period size: 27 Copynumber: 3.7 Consensus size: 27
2760689 CTTGGATGAG
* *
2760699 AAATTATGAAAATACCCTTATAGGGTA
1 AAATTACGAAAATACCCTTATGGGGTA
*
2760726 AAATTACAAAAATACCCTTATGGGGTA
1 AAATTACGAAAATACCCTTATGGGGTA
2760753 AAATTACGAAAATACCCTTATGGGGTA
1 AAATTACGAAAATACCCTTATGGGGTA
* *
2760780 AAATTATGAAAACACCCTT
1 AAATTACGAAAATACCCTT
2760799 GAGTTGTAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (27 bp):
AAATTACGAAAATACCCTTATGGGGTA
Found at i:2764746 original size:22 final size:22
Alignment explanation
Indices: 2764718--2764809 Score: 139
Period size: 22 Copynumber: 4.2 Consensus size: 22
2764708 ACTTTTTCGG
* *
2764718 TCAAAGTCAACGGTCAGACCGA
1 TCAAAGTCAACGGTCTGATCGA
2764740 TCAAAGTCAACGGTCTGATCGA
1 TCAAAGTCAACGGTCTGATCGA
2764762 TCAAAGTCAACGGTCTGATCGA
1 TCAAAGTCAACGGTCTGATCGA
* * *
2764784 TCAAAGTCAACAGTCTAATCGG
1 TCAAAGTCAACGGTCTGATCGA
2764806 TCAA
1 TCAA
2764810 TGGTCAACTG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (22 bp):
TCAAAGTCAACGGTCTGATCGA
Found at i:2769396 original size:24 final size:24
Alignment explanation
Indices: 2769364--2769409 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
2769354 GCATGATATG
2769364 GTACATAGATGTTTTATACATCGT
1 GTACATAGATGTTTTATACATCGT
2769388 GTACATAGATGTTTTATACATC
1 GTACATAGATGTTTTATACATC
2769410 ATCTGGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCGT
Found at i:2778178 original size:15 final size:15
Alignment explanation
Indices: 2778158--2778186 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2778148 AACTCCTACT
2778158 TATATATTGATAATA
1 TATATATTGATAATA
2778173 TATATATTGATAAT
1 TATATATTGATAAT
2778187 TGTAATTTTT
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:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
TATATATTGATAATA
Found at i:2778218 original size:2 final size:2
Alignment explanation
Indices: 2778213--2778239 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2778203 CATTCCTACT
2778213 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
2778240 TGGAGATAAA
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:2780497 original size:3 final size:3
Alignment explanation
Indices: 2780489--2780514 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2780479 CAATTGAAAA
2780489 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
2780515 AGTAGATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2780532 original size:96 final size:96
Alignment explanation
Indices: 2780418--2780610 Score: 377
Period size: 96 Copynumber: 2.0 Consensus size: 96
2780408 TTTTAGTAAT
*
2780418 TAGTAGATTGATTTTCAAGATCGAGTAAAGTCTCTCAACTTTACATGATGCATGTATATCACAAT
1 TAGTAGATTGATTTTCAAGATCGAGTAAAGTCTCTCAACTTTACATGATGCATGTATATCACAAA
2780483 TGAAAAATTATTATTATTATTATTATTATTA
66 TGAAAAATTATTATTATTATTATTATTATTA
2780514 TAGTAGATTGATTTTCAAGATCGAGTAAAGTCTCTCAACTTTACATGATGCATGTATATCACAAA
1 TAGTAGATTGATTTTCAAGATCGAGTAAAGTCTCTCAACTTTACATGATGCATGTATATCACAAA
2780579 TGAAAAATTATTATTATTATTATTATTATTA
66 TGAAAAATTATTATTATTATTATTATTATTA
2780610 T
1 T
2780611 TATTATTATT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.41
Consensus pattern (96 bp):
TAGTAGATTGATTTTCAAGATCGAGTAAAGTCTCTCAACTTTACATGATGCATGTATATCACAAA
TGAAAAATTATTATTATTATTATTATTATTA
Found at i:2780593 original size:3 final size:3
Alignment explanation
Indices: 2780585--2780622 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2780575 CAAATGAAAA
2780585 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2780623 ATATCATAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2788531 original size:24 final size:24
Alignment explanation
Indices: 2788504--2788549 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
2788494 CCTTCTCCTT
2788504 CCACCATGACAATTCCTCCCCCTC
1 CCACCATGACAATTCCTCCCCCTC
2788528 CCACCATGACAATTCCTCCCCC
1 CCACCATGACAATTCCTCCCCC
2788550 CTTTAGACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.54, G:0.04, T:0.20
Consensus pattern (24 bp):
CCACCATGACAATTCCTCCCCCTC
Found at i:2791917 original size:304 final size:304
Alignment explanation
Indices: 2791368--2791975 Score: 1031
Period size: 304 Copynumber: 2.0 Consensus size: 304
2791358 AGAGAAGAAA
2791368 ATATTTGTTCATTCATAACATATGGGAAATATCATCTCAGCCGTTTTTATTTAATTACAATGCTA
1 ATATTTGTTCATTCATAACATATGGGAAATATCATCTCAGCCGTTTTTATTTAATTACAATGCTA
*
2791433 ATAGAAAATAGCCAGCTAGCGGTCCTTTCTAACAGAATATAACGACTCATTTAACCACCTTCTTT
66 ATAGAAAATAGCCAGCTAGCGGTCCTTTCTAACAGAATATAACAACTCATTTAACCACCTTCTTT
*
2791498 TGCAGATATTGAACTAGTGTACTTGGGCTGCTTTACTTCTTCTTGGGTCTGCTCCAGCTTCTTCG
131 TGCAGATATTGAACTAGTGTACTCGGGCTGCTTTACTTCTTCTTGGGTCTGCTCCAGCTTCTTCG
* * * *
2791563 AATTCGGTTCGGCCTGCTCCAAATCAGAAGGTAAGTGATTAACCTCTCCCTCATGTTCCTCAATC
196 AATCCGGTTCGGCATGCTCCAAATCAGAAGGTAAGTGATTAACCTCTCCCTCACGTGCCTCAATC
* *
2791628 CCCAATCTTTCATGCTCATTCCCTAACCCTCACATTTCTTCCCC
261 CCCAATCTTTCATGCCCAATCCCTAACCCTCACATTTCTTCCCC
* *
2791672 ATATTTGTTCATTCATAACATATGTGAAATATCCTCTCAGCCGTTTTTATTTAATTACAATGCTA
1 ATATTTGTTCATTCATAACATATGGGAAATATCATCTCAGCCGTTTTTATTTAATTACAATGCTA
* **
2791737 ATAGAAAATAGCCAGATTA-CGGTCCTTTCTAACAGAATATAACAACTCATTTAACCTTCTTCTT
66 ATAGAAAATAGCCAG-CTAGCGGTCCTTTCTAACAGAATATAACAACTCATTTAACCACCTTCTT
*
2791801 TTGTAGATATTGAACTAGTGTACTCGGGCTGCTTTACTTCTTCTTGGGTCTGCTCCAGCTTCTTC
130 TTGCAGATATTGAACTAGTGTACTCGGGCTGCTTTACTTCTTCTTGGGTCTGCTCCAGCTTCTTC
*
2791866 -AGATCCGGTTCGGCATGCTCCACATCAGAAGGTAAGTGATTAACCTCTCCCTCACGTGCCTCAA
195 GA-ATCCGGTTCGGCATGCTCCAAATCAGAAGGTAAGTGATTAACCTCTCCCTCACGTGCCTCAA
**
2791930 TCCCCAATCTTTCATGCCCAATCCCTAACCCTTGCATTTCTTCCCC
259 TCCCCAATCTTTCATGCCCAATCCCTAACCCTCACATTTCTTCCCC
2791976 CAATTCGTCT
Statistics
Matches: 285, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
303 1 0.00
304 282 0.99
305 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (304 bp):
ATATTTGTTCATTCATAACATATGGGAAATATCATCTCAGCCGTTTTTATTTAATTACAATGCTA
ATAGAAAATAGCCAGCTAGCGGTCCTTTCTAACAGAATATAACAACTCATTTAACCACCTTCTTT
TGCAGATATTGAACTAGTGTACTCGGGCTGCTTTACTTCTTCTTGGGTCTGCTCCAGCTTCTTCG
AATCCGGTTCGGCATGCTCCAAATCAGAAGGTAAGTGATTAACCTCTCCCTCACGTGCCTCAATC
CCCAATCTTTCATGCCCAATCCCTAACCCTCACATTTCTTCCCC
Found at i:2793833 original size:26 final size:25
Alignment explanation
Indices: 2793790--2793842 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
2793780 TATTATTACC
* * *
2793790 AAAATTTTTTTTACAAAATCTAATAA
1 AAAATTTCTTTAAAAAAAT-TAATAA
*
2793816 AAAATTTCTTTAAAAAAATTCATAA
1 AAAATTTCTTTAAAAAAATTAATAA
2793841 AA
1 AA
2793843 TTTATATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38
Consensus pattern (25 bp):
AAAATTTCTTTAAAAAAATTAATAA
Found at i:2797804 original size:3 final size:3
Alignment explanation
Indices: 2797796--2797823 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2797786 TGATATATAG
2797796 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2797824 TTTTCATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2804170 original size:47 final size:47
Alignment explanation
Indices: 2804099--2804237 Score: 190
Period size: 47 Copynumber: 3.0 Consensus size: 47
2804089 GAATAAATGT
*
2804099 ATGCGAACTAGAAATCATGAGGTTAGGTTTATTTTTCTCGAACAAGC
1 ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTCTCGAACAAGC
** * *
2804146 ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTT-TTTAACATGT
1 ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTCTCGAACAAGC
* * *
2804192 ATACGAACTAGAAATCATGCTGTTATGTTTATTTTTTCTCGAACAA
1 ATGCGAACTAGAAATCATGCGGTTAGGTTTA-TTTTTCTCGAACAA
2804238 TTATGCAAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
46 34 0.43
47 40 0.51
48 5 0.06
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (47 bp):
ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTCTCGAACAAGC
Found at i:2804211 original size:46 final size:46
Alignment explanation
Indices: 2804095--2804229 Score: 189
Period size: 46 Copynumber: 2.9 Consensus size: 46
2804085 TTTTGAATAA
*
2804095 ATGTATGCGAACTAGAAATCATGAGGTTAGGTTTATTTTTCTCGAAC
1 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTT-TCGAAC
* * **
2804142 AAGCATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTTTAAC
1 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTCGAAC
* * *
2804188 ATGTATACGAACTAGAAATCATGCTGTTATGTTTATTTTTTC
1 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTC
2804230 TCGAACAATT
Statistics
Matches: 77, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
46 40 0.52
47 37 0.48
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (46 bp):
ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTCGAAC
Found at i:2809009 original size:99 final size:99
Alignment explanation
Indices: 2808894--2809080 Score: 286
Period size: 99 Copynumber: 1.9 Consensus size: 99
2808884 TTATTATATT
* * *
2808894 ATATGTATACAATAAAGCTTGAACTGTCACTCTAGAGCAATTGATTAAACGCCCCGACTTTATGG
1 ATATATATACAATAAAGCTTGAAATGTCACTCTAGAGAAATTGATTAAACGCCCCGACTTTATGG
*
2808959 ATAAGATTCAA-CTAGTCTGATAACTGTGATTATA
66 ATAAGATT-AAGCTAGCCTGATAACTGTGATTATA
* * * *
2808993 ATATATATACAATAAAGCTTGAAATGTCCCTTTAGAGAAATTGGTTAAACGCCCCGGCTTTATGG
1 ATATATATACAATAAAGCTTGAAATGTCACTCTAGAGAAATTGATTAAACGCCCCGACTTTATGG
2809058 ATAAGATTAAGCTAGCCTGATAA
66 ATAAGATTAAGCTAGCCTGATAA
2809081 AGACAAATTA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
98 2 0.03
99 77 0.97
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (99 bp):
ATATATATACAATAAAGCTTGAAATGTCACTCTAGAGAAATTGATTAAACGCCCCGACTTTATGG
ATAAGATTAAGCTAGCCTGATAACTGTGATTATA
Found at i:2811136 original size:113 final size:113
Alignment explanation
Indices: 2810989--2811193 Score: 322
Period size: 113 Copynumber: 1.8 Consensus size: 113
2810979 GTCGGGCTTT
* *
2810989 CGAGCAAGATGATAAGTCCTCCGGACCATCTTAAGCCTTCACGGAAGAGTAGTAAAGCAAA-CAT
1 CGAGCAAGATGATAAGTCCTCCGGACCATCTTAAGCCTTCACGAAAGAGTAGTAAAGAAAACCAT
* *
2811053 CTTAAGCCTTGACGGAAGAGTAGTGAAGTAAGAAATTAGTAAGTCTTC
66 CTTAAGCCATCACGGAAGAGTAGTGAAGTAAGAAATTAGTAAGTCTTC
* * *
2811101 CGAGCATGATGATTAAGTCCTCCGGGCCATCTTAAGCCTTCACGAAAGAGTAGTGAAGAAAACCA
1 CGAGCAAGATGA-TAAGTCCTCCGGACCATCTTAAGCCTTCACGAAAGAGTAGTAAAGAAAACCA
*
2811166 TCTTAAGCCATCACGTAAGAGTAGTGAA
65 TCTTAAGCCATCACGGAAGAGTAGTGAA
2811194 ACAAACAATC
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
112 11 0.13
113 45 0.54
114 27 0.33
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (113 bp):
CGAGCAAGATGATAAGTCCTCCGGACCATCTTAAGCCTTCACGAAAGAGTAGTAAAGAAAACCAT
CTTAAGCCATCACGGAAGAGTAGTGAAGTAAGAAATTAGTAAGTCTTC
Found at i:2811174 original size:36 final size:36
Alignment explanation
Indices: 2811127--2811490 Score: 241
Period size: 36 Copynumber: 9.9 Consensus size: 36
2811117 GTCCTCCGGG
*
2811127 CCATCTTAAGCCTTCACGAAAGAGTAGTGAAGAAAA
1 CCATCTTAAGCCTTCACGGAAGAGTAGTGAAGAAAA
* *
2811163 CCATCTTAAGCCATCACGTAAGAGTAGTGAA-ACAAA
1 CCATCTTAAGCCTTCACGGAAGAGTAGTGAAGA-AAA
* * * *
2811199 CAATCTCAAGACTTCACGGAAGAGTAGTGAAGAAAT
1 CCATCTTAAGCCTTCACGGAAGAGTAGTGAAGAAAA
* * * * **
2811235 CCATCAGTAAGCCTTC-CGAGCATGA-T-GATTAAGTCATC
1 CCATC-TTAAGCCTTCACG-G-AAGAGTAG-TGAAG-AAAA
* *
2811273 CGGGCATCTTAAACCTTCACGGAAGAGTAGTGAAGCAAA
1 C---CATCTTAAGCCTTCACGGAAGAGTAGTGAAGAAAA
* * * *
2811312 CCATCTTAAGCATTCACAGAAGAGCAGTGAAGCAAA
1 CCATCTTAAGCCTTCACGGAAGAGTAGTGAAGAAAA
* * * * *
2811348 TCATCCTAAGTCTTAACGGAAGAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCACGGAAGAGTAGTGAAG-AAAA
* * * * **
2811385 CAATCTCAAGCCTTCACGAAAAAGTAGTGAAGCGAA
1 CCATCTTAAGCCTTCACGGAAGAGTAGTGAAGAAAA
* * * ** *
2811421 TCATTTTAAGTCTTCACGGAAGAGTAGACAATGCAAAT
1 CCATCTTAAGCCTTCACGGAAGAGTAGTGAA-G-AAAA
* **
2811459 CAATCCCAAGCCTTCACGGAAGAGTAGTGAAG
1 CCATCTTAAGCCTTCACGGAAGAGTAGTGAAG
2811491 CAAATCAAGA
Statistics
Matches: 245, Mismatches: 67, Indels: 31
0.71 0.20 0.09
Matches are distributed among these distances:
35 1 0.00
36 146 0.60
37 42 0.17
38 29 0.12
39 6 0.02
40 14 0.06
41 7 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (36 bp):
CCATCTTAAGCCTTCACGGAAGAGTAGTGAAGAAAA
Found at i:2811299 original size:149 final size:148
Alignment explanation
Indices: 2811013--2811389 Score: 483
Period size: 149 Copynumber: 2.5 Consensus size: 148
2811003 AGTCCTCCGG
* * * *
2811013 ACCATCTTAAGCCTTCACGGAAGAGTAGT-AAAGCAAACATCTTAAGCCTTGACGGAAGAGTAGT
1 ACCATCTTAAGCCATCAC-GAAGAGTAGTGAAA-CAAACATCTCAAGACTTAACGGAAGAGTAGT
* ** * * * *
2811077 GAAGTAAGAAATTAGTAAGTCTTCCGAGCATGATGATTAAGTCCTCCGGGCCATCTTAAGCCTTC
64 GAAGAAATCAATCAGTAAGCCTTCCGAGCATGATGATTAAGTCATCCGGGCCATCTTAAACCTTC
2811142 ACGAAAGAGTAGTGAAGAAA
129 ACGAAAGAGTAGTGAAGAAA
*
2811162 ACCATCTTAAGCCATCACGTAAGAGTAGTGAAACAAACAATCTCAAGACTTCACGGAAGAGTAGT
1 ACCATCTTAAGCCATCACG-AAGAGTAGTGAAACAAAC-ATCTCAAGACTTAACGGAAGAGTAGT
*
2811227 GAAGAAATCCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCATCCGGG-CATCTTAAACCTTC
64 GAAGAAATCAATCAGTAAGCCTTCCGAGCATGATGATTAAGTCATCCGGGCCATCTTAAACCTTC
* *
2811291 ACGGAAGAGTAGTGAAGCAA
129 ACGAAAGAGTAGTGAAGAAA
* * *
2811311 ACCATCTTAAG-CATTCACAGAAGAGCAGTGAAGCAAATCATC-CTAAGTCTTAACGGAAGAGTA
1 ACCATCTTAAGCCA-TCAC-GAAGAGTAGTGAAACAAA-CATCTC-AAGACTTAACGGAAGAGTA
2811374 GTGAAGCAAATCAATC
62 GTGAAG-AAATCAATC
2811390 TCAAGCCTTC
Statistics
Matches: 201, Mismatches: 19, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
148 4 0.02
149 118 0.59
150 79 0.39
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (148 bp):
ACCATCTTAAGCCATCACGAAGAGTAGTGAAACAAACATCTCAAGACTTAACGGAAGAGTAGTGA
AGAAATCAATCAGTAAGCCTTCCGAGCATGATGATTAAGTCATCCGGGCCATCTTAAACCTTCAC
GAAAGAGTAGTGAAGAAA
Found at i:2811430 original size:109 final size:111
Alignment explanation
Indices: 2811286--2811498 Score: 288
Period size: 109 Copynumber: 1.9 Consensus size: 111
2811276 GCATCTTAAA
* * **
2811286 CCTTCACGGAAGAGTAGTGAAGCAAACCATCTTAAG-CATTCACAGAAGAGCAGTGAA-GCAAAT
1 CCTTCACGAAAAAGTAGTGAAGCAAACCATCTTAAGTC-TTCACAGAAGAGCAGACAATGCAAAT
* *
2811349 C-ATCCTAAGTCTTAACGGAAGAGTAGTGAAGCAAATCAATCTCAAG
65 CAATCCCAAGCCTTAACGGAAGAGTAGTGAAGCAAATCAATCTCAAG
* * * * *
2811395 CCTTCACGAAAAAGTAGTGAAGCGAATCATTTTAAGTCTTCACGGAAGAGTAGACAATGCAAATC
1 CCTTCACGAAAAAGTAGTGAAGCAAACCATCTTAAGTCTTCACAGAAGAGCAGACAATGCAAATC
*
2811460 AATCCCAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAA
66 AATCCCAAGCCTTAACGGAAGAGTAGTGAAGCAAATCAA
2811499 GATCGGGCCT
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
109 46 0.52
110 8 0.09
111 35 0.39
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (111 bp):
CCTTCACGAAAAAGTAGTGAAGCAAACCATCTTAAGTCTTCACAGAAGAGCAGACAATGCAAATC
AATCCCAAGCCTTAACGGAAGAGTAGTGAAGCAAATCAATCTCAAG
Found at i:2811431 original size:73 final size:73
Alignment explanation
Indices: 2811291--2811497 Score: 265
Period size: 73 Copynumber: 2.8 Consensus size: 73
2811281 TTAAACCTTC
* * * *
2811291 ACGGAAGAGTAGTGAAGCAAA-CCATCTTAAGCATTCAC-AGAAGAGCAGTGAAGCAAATCATCC
1 ACGGAAGAGTAGTGAAGCAAATCAATCTCAAGCCTTCACGA-AAGAGTAGTGAAGCAAATCATCC
2811354 TAAGTCTTA
65 TAAGTCTTA
* * **
2811363 ACGGAAGAGTAGTGAAGCAAATCAATCTCAAGCCTTCACGAAAAAGTAGTGAAGCGAATCATTTT
1 ACGGAAGAGTAGTGAAGCAAATCAATCTCAAGCCTTCACGAAAGAGTAGTGAAGCAAATCATCCT
*
2811428 AAGTCTTC
66 AAGTCTTA
** * *
2811436 ACGGAAGAGTAGACAATGCAAATCAATCCCAAGCCTTCACGGAAGAGTAGTGAAGCAAATCA
1 ACGGAAGAGTAGTGAA-GCAAATCAATCTCAAGCCTTCACGAAAGAGTAGTGAAGCAAATCA
2811498 AGATCGGGCC
Statistics
Matches: 117, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
72 21 0.18
73 54 0.46
74 42 0.36
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (73 bp):
ACGGAAGAGTAGTGAAGCAAATCAATCTCAAGCCTTCACGAAAGAGTAGTGAAGCAAATCATCCT
AAGTCTTA
Found at i:2811733 original size:15 final size:16
Alignment explanation
Indices: 2811693--2811733 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2811683 TTTATCCGGG
2811693 ATTTTTAT-TTTATTT
1 ATTTTTATATTTATTT
2811708 ATTTGTT-TATTT-TTT
1 ATTT-TTATATTTATTT
2811723 ATTTTTATATT
1 ATTTTTATATT
2811734 ATTAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 2 0.09
15 16 0.70
16 5 0.22
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (16 bp):
ATTTTTATATTTATTT
Found at i:2819877 original size:3 final size:3
Alignment explanation
Indices: 2819869--2819906 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2819859 CAAATGAAAA
* *
2819869 ATT ATT ATT ATT ATT ATA ATT AAT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2819907 ATATCATAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:2826024 original size:23 final size:21
Alignment explanation
Indices: 2825977--2826056 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
2825967 AGAACCCCAG
* ***
2825977 GGGGGTATCGATTCCCCTGTG
1 GGGGGAATCGATTCCCCTCAA
2825998 GGGGGAATCGATTCCCCTTCAAA
1 GGGGGAATCGATTCCCC-TC-AA
* *
2826021 GGGGGAATCGGTT-CCCTCAT
1 GGGGGAATCGATTCCCCTCAA
*
2826041 GGGGGGATCGATTCCC
1 GGGGGAATCGATTCCC
2826057 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 12 0.25
21 20 0.42
22 4 0.08
23 12 0.25
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCTCAA
Found at i:2826050 original size:20 final size:20
Alignment explanation
Indices: 2825998--2826058 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
2825988 TTCCCCTGTG
*
2825998 GGGGGAATCGATTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TC-AT
*
2826021 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
2826041 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
2826059 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 12 0.35
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:2829908 original size:22 final size:21
Alignment explanation
Indices: 2829866--2829905 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2829856 GAGTTTGTTT
*
2829866 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2829887 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2829906 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2832492 original size:29 final size:29
Alignment explanation
Indices: 2832433--2832489 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
2832423 CCAAATTTTG
*
2832433 TTTAGTGACTAAAATGTAAGTTTTGAAAA
1 TTTAGTGACTAAAATGTAAATTTTGAAAA
2832462 TTTAGTGACTAAAATG-AAATTTTGAAAA
1 TTTAGTGACTAAAATGTAAATTTTGAAAA
2832490 ATTAAAGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.37
Consensus pattern (29 bp):
TTTAGTGACTAAAATGTAAATTTTGAAAA
Found at i:2834353 original size:36 final size:38
Alignment explanation
Indices: 2834298--2834373 Score: 129
Period size: 36 Copynumber: 2.1 Consensus size: 38
2834288 TAGTTGAGTA
*
2834298 GTTATCCATTATCAGCTTTGATACATTCGTGTATCAAT
1 GTTATCCATTATCAACTTTGATACATTCGTGTATCAAT
2834336 GTTAT-CA-TATCAACTTTGATACATTCGTGTATCAAT
1 GTTATCCATTATCAACTTTGATACATTCGTGTATCAAT
2834372 GT
1 GT
2834374 CCAGCACTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
36 30 0.81
37 2 0.05
38 5 0.14
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (38 bp):
GTTATCCATTATCAACTTTGATACATTCGTGTATCAAT
Found at i:2834548 original size:178 final size:178
Alignment explanation
Indices: 2834249--2834605 Score: 689
Period size: 178 Copynumber: 2.0 Consensus size: 178
2834239 TAGCCCATTG
2834249 TATGTTAATTGAGAATTGTTGGTACACTTGGCATGCCATTAGTTGAGTAGTTATCCATTATCAGC
1 TATGTTAATTGAGAATTGTTGGTACACTTGGCATGCCATTAGTTGAGTAGTTATCCATTATCAGC
*
2834314 TTTGATACATTCGTGTATCAATGTTATCATATCAACTTTGATACATTCGTGTATCAATGTCCAGC
66 TTTGATACATTCGTGTATCAATGCTATCATATCAACTTTGATACATTCGTGTATCAATGTCCAGC
2834379 ACTGTTGGTGCTTATTCAGGTTATGATGGCACTGAAGTGCATCATATC
131 ACTGTTGGTGCTTATTCAGGTTATGATGGCACTGAAGTGCATCATATC
2834427 TATGTTAATTGAGAATTGTTGGTACACTTGGCATGCCATTAGTTGAGTAGTTATCCATTATCAGC
1 TATGTTAATTGAGAATTGTTGGTACACTTGGCATGCCATTAGTTGAGTAGTTATCCATTATCAGC
2834492 TTTGATACATTCGTGTATCAATGCTATCATAT-AACCTTTGATACATTCGTGTATCAATGTCCAG
66 TTTGATACATTCGTGTATCAATGCTATCATATCAA-CTTTGATACATTCGTGTATCAATGTCCAG
2834556 CACTGTTGGTGCTTATTCAGGTTATGATGGCACTGAAGTGCATCATATC
130 CACTGTTGGTGCTTATTCAGGTTATGATGGCACTGAAGTGCATCATATC
2834605 T
1 T
2834606 CATTATCAGT
Statistics
Matches: 177, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
177 2 0.01
178 175 0.99
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (178 bp):
TATGTTAATTGAGAATTGTTGGTACACTTGGCATGCCATTAGTTGAGTAGTTATCCATTATCAGC
TTTGATACATTCGTGTATCAATGCTATCATATCAACTTTGATACATTCGTGTATCAATGTCCAGC
ACTGTTGGTGCTTATTCAGGTTATGATGGCACTGAAGTGCATCATATC
Found at i:2839357 original size:19 final size:19
Alignment explanation
Indices: 2839333--2839384 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
2839323 TTTAAACAGG
2839333 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
2839352 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
2839371 TGCATCGATGCACT
1 TGCATCGATGCACT
2839385 AATTGCATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:2843273 original size:29 final size:28
Alignment explanation
Indices: 2843212--2843360 Score: 126
Period size: 29 Copynumber: 5.4 Consensus size: 28
2843202 CATTTTACAC
* * * *
2843212 AAATAGCACCCTTTTAAAATAATTACCG
1 AAATAGCACCCTTTTGAATTAATTCCCA
2843240 AAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTT-GAATTAATTCCCA
* *
2843269 AAATAACACCAATTTTGAATTAATTCCCA
1 AAATAGCACC-CTTTTGAATTAATTCCCA
* ** *
2843298 TAATA--A--CTTTTGAAAAAATTACCA
1 AAATAGCACCCTTTTGAATTAATTCCCA
* * *
2843322 AAATAGCACTCATTTCGAATTAATTCTCA
1 AAATAGCAC-CCTTTTGAATTAATTCCCA
2843351 AAATAGCACC
1 AAATAGCACC
2843361 AAAATCAAAT
Statistics
Matches: 96, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
24 18 0.19
26 1 0.01
27 1 0.01
28 16 0.17
29 56 0.58
30 4 0.04
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (28 bp):
AAATAGCACCCTTTTGAATTAATTCCCA
Found at i:2843317 original size:24 final size:24
Alignment explanation
Indices: 2843281--2843326 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
2843271 ATAACACCAA
** * *
2843281 TTTTGAATTAATTCCCATAATAAC
1 TTTTGAAAAAATTACCAAAATAAC
2843305 TTTTGAAAAAATTACCAAAATA
1 TTTTGAAAAAATTACCAAAATA
2843327 GCACTCATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (24 bp):
TTTTGAAAAAATTACCAAAATAAC
Found at i:2843376 original size:82 final size:82
Alignment explanation
Indices: 2843222--2843384 Score: 211
Period size: 82 Copynumber: 2.0 Consensus size: 82
2843212 AAATAGCACC
* * ** **
2843222 CTTTTAAAATAATTACCGAAATAGCACCCTTTTCGAATTAATTCCCAAAATAACACCAATTTTGA
1 CTTTTAAAATAATTACCAAAATAGCACCCATTTCGAATTAATTCCCAAAATAACACCAAAATCAA
* *
2843287 ATTAATTCCCATAATAA
66 ATAAATTCCCAGAATAA
* * *
2843304 CTTTTGAAAA-AATTACCAAAATAGCACTCATTTCGAATTAATTCTCAAAATAGCACCAAAATCA
1 CTTTT-AAAATAATTACCAAAATAGCACCCATTTCGAATTAATTCCCAAAATAACACCAAAATCA
2843368 AATAAATTCCCAGAATA
65 AATAAATTCCCAGAATA
2843385 GTACCAGTCA
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
82 65 0.94
83 4 0.06
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (82 bp):
CTTTTAAAATAATTACCAAAATAGCACCCATTTCGAATTAATTCCCAAAATAACACCAAAATCAA
ATAAATTCCCAGAATAA
Found at i:2843423 original size:13 final size:13
Alignment explanation
Indices: 2843401--2843437 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2843391 GTCAACGGGT
2843401 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
2843414 CGGGTTGGGTCAA
1 CGGGTCGGGTCAA
*
2843427 CGGGTCAGGTC
1 CGGGTCGGGTC
2843438 GTGACCGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.14, C:0.22, G:0.46, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:2850116 original size:28 final size:29
Alignment explanation
Indices: 2850074--2850136 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
2850064 CATTTTACAC
* *
2850074 AAATAGCA-CCTTTTTAAAATAATTACCA
1 AAATAGAACCCTTTTGAAAATAATTACCA
* * *
2850102 AAATAGAACCCTTTTGGAATTAATTCCCA
1 AAATAGAACCCTTTTGAAAATAATTACCA
2850131 AAATAG
1 AAATAG
2850137 CACAATTTCG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.30
Consensus pattern (29 bp):
AAATAGAACCCTTTTGAAAATAATTACCA
Found at i:2851125 original size:25 final size:27
Alignment explanation
Indices: 2851096--2851148 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2851086 CCACTAGGGG
2851096 CTATG-AAAGT-TTTGTCCCGAAGGAC
1 CTATGTAAAGTATTTGTCCCGAAGGAC
* *
2851121 CTATGTAATGTATTTGTCCCGAATGAC
1 CTATGTAAAGTATTTGTCCCGAAGGAC
2851148 C
1 C
2851149 ACTCCTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 4 0.17
27 15 0.62
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (27 bp):
CTATGTAAAGTATTTGTCCCGAAGGAC
Found at i:2851877 original size:19 final size:19
Alignment explanation
Indices: 2851853--2851904 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
2851843 TTTAAACAGG
2851853 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
2851872 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
2851891 TGCATCGATGCACT
1 TGCATCGATGCACT
2851905 AATTGCATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:2855036 original size:29 final size:29
Alignment explanation
Indices: 2854994--2855053 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
2854984 CCAAATTTTG
*
2854994 TTTAGTGACTAAAATGTAAGTTTT-GAAAA
1 TTTAGTGACTAAAATG-AAATTTTGGAAAA
2855023 TTTAGTGACTAAAATGAAATTTTGGAAAA
1 TTTAGTGACTAAAATGAAATTTTGGAAAA
2855052 TT
1 TT
2855054 GAAAGGTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.38
Consensus pattern (29 bp):
TTTAGTGACTAAAATGAAATTTTGGAAAA
Found at i:2856926 original size:36 final size:36
Alignment explanation
Indices: 2856885--2857023 Score: 233
Period size: 36 Copynumber: 3.9 Consensus size: 36
2856875 ATTTATCCAT
2856885 TATCAACTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAACTTTGATACATTCGTGTATCAATGTTATCA
*
2856921 TATCAACTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAACTTTGATACATTCGTGTATCAATGTTATCA
* *
2856957 TATCATCTTTGATACATTTGTGTATCAATGTTATCA
1 TATCAACTTTGATACATTCGTGTATCAATGTTATCA
* *
2856993 TATCAACTTTGGTACATTCATGTATCAATGT
1 TATCAACTTTGATACATTCGTGTATCAATGT
2857024 CCAGCACCAT
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 95 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (36 bp):
TATCAACTTTGATACATTCGTGTATCAATGTTATCA
Found at i:2859023 original size:35 final size:35
Alignment explanation
Indices: 2858930--2859025 Score: 138
Period size: 35 Copynumber: 2.7 Consensus size: 35
2858920 AACATAGTAA
* *
2858930 TCAATTACATTCTAAACCCCAAAATCCAAAATATT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
*
2858965 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
* **
2859000 TCAATTACATGCCCAACCCCAAATTC
1 TCAATTACATTCTAAACCCCAAATTC
2859026 ATAATCCATT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.42, C:0.29, G:0.01, T:0.28
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATACT
Found at i:2860224 original size:24 final size:24
Alignment explanation
Indices: 2860197--2860261 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
2860187 CTTCTAATAT
*
2860197 AATTTG-CACCGAAGTACCACATAG
1 AATTTGTC-CCGAAGGACCACATAG
* *
2860221 AATTTGTCCCTAAGGACCACGTAG
1 AATTTGTCCCGAAGGACCACATAG
*
2860245 AA-TTGTCCCGAAAGACC
1 AATTTGTCCCGAAGGACC
2860262 CCGTAGAACC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 13 0.37
24 21 0.60
25 1 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (24 bp):
AATTTGTCCCGAAGGACCACATAG
Found at i:2860261 original size:23 final size:24
Alignment explanation
Indices: 2860212--2860269 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
2860202 GCACCGAAGT
* * *
2860212 ACCACATAGAATTTGTCCCTAAGG
1 ACCACGTAGAATTTGTCCCGAAAG
2860236 ACCACGTAGAA-TTGTCCCGAAAG
1 ACCACGTAGAATTTGTCCCGAAAG
*
2860259 ACCCCGTAGAA
1 ACCACGTAGAA
2860270 CCCTCGACTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (24 bp):
ACCACGTAGAATTTGTCCCGAAAG
Found at i:2863774 original size:31 final size:31
Alignment explanation
Indices: 2863736--2863885 Score: 248
Period size: 31 Copynumber: 4.8 Consensus size: 31
2863726 GATTCGAGGG
2863736 TTACCTATGTTCTTCGGGACATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
*
2863767 TTACCTATGTTCTTCGGGACATATGGATAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
*
2863798 TTACTTATGTTCTTCGGGACATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
* *
2863829 TTATCTATGTTCTTCGGGACGTATGGACA-T
1 TTACCTATGTTCTTCGGGACATATGGACAGT
2863859 ATTACCTATGTTCTTCGGGACATATGG
1 -TTACCTATGTTCTTCGGGACATATGG
2863886 CAGATTATTA
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
30 1 0.01
31 109 0.99
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACAGT
Found at i:2864089 original size:31 final size:31
Alignment explanation
Indices: 2864054--2864123 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
2864044 TCTATATGTT
2864054 ACAGATTACCTATGTTCTTCGGGACATATGG
1 ACAGATTACCTATGTTCTTCGGGACATATGG
2864085 ACAGATTACCTATGTTCTTCGGGACATATGG
1 ACAGATTACCTATGTTCTTCGGGACATATGG
*
2864116 ATAGATTA
1 ACAGATTA
2864124 TTGTATGAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (31 bp):
ACAGATTACCTATGTTCTTCGGGACATATGG
Found at i:2868164 original size:33 final size:31
Alignment explanation
Indices: 2868127--2868188 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
2868117 AAAATTGAAA
2868127 ATAAAATGCTAACAAATATATTTTTTAAAAAGT
1 ATAAAAT-CTAA-AAATATATTTTTTAAAAAGT
* *
2868160 ATAAAATTTTAAAATATATTTTTTAAAAA
1 ATAAAATCTAAAAATATATTTTTTAAAAA
2868189 ATATTATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 18 0.67
32 2 0.07
33 7 0.26
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (31 bp):
ATAAAATCTAAAAATATATTTTTTAAAAAGT
Found at i:2871137 original size:106 final size:100
Alignment explanation
Indices: 2871007--2871199 Score: 260
Period size: 106 Copynumber: 1.9 Consensus size: 100
2870997 AGTATTGTTC
**
2871007 TGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGTTCTGAAACTGGGAAATTATTTGTTGACA
1 TGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGACA
*
2871072 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCATGTGCTGTCT
60 ATCAGCCGCCCCTTCGCTGTGAAGTTGAGCATGTGCTGTCT
* * *
2871113 TGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAATTTTGTTGACAATCAGC
1 TGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGACTCTGAATGAAATTTTGTTGACAATCAGC
* *
2871178 CGCCCTTTCGTTGTGAAGTTGA
66 CGCCCCTTCGCTGTGAAGTTGA
2871200 AATTGGTTAT
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
100 35 0.44
101 1 0.01
102 4 0.05
104 1 0.01
105 2 0.03
106 36 0.46
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (100 bp):
TGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGACTCTGAATGAAATTTTGTTGACAATCAGC
CGCCCCTTCGCTGTGAAGTTGAGCATGTGCTGTCT
Found at i:2872329 original size:17 final size:15
Alignment explanation
Indices: 2872297--2872347 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
2872287 ACCCACCTTA
2872297 TTTTTC-TTTT-TCT
1 TTTTTCTTTTTCTCT
2872310 TTTTTCTTCTGTTCTCT
1 TTTTTCTT-T-TTCTCT
*
2872327 TTTCTCTTTTTCTCT
1 TTTTTCTTTTTCTCT
2872342 TTTTTC
1 TTTTTC
2872348 AATTTAAGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 6 0.19
14 1 0.03
15 12 0.38
16 3 0.09
17 10 0.31
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTTCTTTTTCTCT
Found at i:2872347 original size:9 final size:8
Alignment explanation
Indices: 2872297--2872345 Score: 52
Period size: 7 Copynumber: 6.5 Consensus size: 8
2872287 ACCCACCTTA
2872297 TTTT-TCT
1 TTTTCTCT
2872304 TTTTCT-T
1 TTTTCTCT
2872311 TTTTCT-T
1 TTTTCTCT
*
2872318 CTGTTCTC-
1 -TTTTCTCT
2872326 TTTTCTCT
1 TTTTCTCT
2872334 TTTTCTCT
1 TTTTCTCT
2872342 TTTT
1 TTTT
2872346 TCAATTTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
7 18 0.50
8 18 0.50
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTCTCT
Found at i:2872433 original size:7 final size:7
Alignment explanation
Indices: 2872386--2872434 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
2872376 CCTAAACGTC
2872386 TTTTTCT
1 TTTTTCT
*
2872393 CTTTTTGT
1 -TTTTTCT
*
2872401 TTTTTGT
1 TTTTTCT
*
2872408 TTTTCCT
1 TTTTTCT
*
2872415 TTTTCCT
1 TTTTTCT
2872422 TTTTTCT
1 TTTTTCT
2872429 TTTTTC
1 TTTTTC
2872435 GACTTAAGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
7 31 0.84
8 6 0.16
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (7 bp):
TTTTTCT
Found at i:2881732 original size:22 final size:21
Alignment explanation
Indices: 2881689--2881734 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2881679 AAAAATAAAT
*
2881689 AAATAAAAAATGACGAAAGAA
1 AAATAAAAAATGAAGAAAGAA
* *
2881710 AAATAAAAAGATTAAGAAGGAA
1 AAATAAAAA-ATGAAGAAAGAA
2881732 AAA
1 AAA
2881735 CATGGTTAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11
Consensus pattern (21 bp):
AAATAAAAAATGAAGAAAGAA
Found at i:2886309 original size:18 final size:18
Alignment explanation
Indices: 2886280--2886321 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2886270 ATTTAAAAAA
*
2886280 TAAAAT-TATATATATTT
1 TAAAATATATATAAATTT
2886297 TAAAATATATATAAATTT
1 TAAAATATATATAAATTT
*
2886315 TGAAATA
1 TAAAATA
2886322 ACCCCAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TAAAATATATATAAATTT
Found at i:2886866 original size:29 final size:29
Alignment explanation
Indices: 2886824--2886888 Score: 130
Period size: 29 Copynumber: 2.2 Consensus size: 29
2886814 TTTGTAACGT
2886824 TAGGCACATGGATGTGCCAAAAAATATTA
1 TAGGCACATGGATGTGCCAAAAAATATTA
2886853 TAGGCACATGGATGTGCCAAAAAATATTA
1 TAGGCACATGGATGTGCCAAAAAATATTA
2886882 TAGGCAC
1 TAGGCAC
2886889 CAATTTAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (29 bp):
TAGGCACATGGATGTGCCAAAAAATATTA
Found at i:2891419 original size:42 final size:42
Alignment explanation
Indices: 2891324--2891412 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
2891314 AGTATTTAAG
* * * *
2891324 AGTATGTACACTCAACTAGGGAGTATGGATACTCAAACGAAA
1 AGTATGAATACTCAACTAGGGAGTATGAATACTCAAACAAAA
* * *
2891366 TGTATGAATACTCAAAC-AGGGAGTTTGAATATTCAAACAAAA
1 AGTATGAATACTC-AACTAGGGAGTATGAATACTCAAACAAAA
2891408 AGTAT
1 AGTAT
2891413 AGATACTTGA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
42 35 0.92
43 3 0.08
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (42 bp):
AGTATGAATACTCAACTAGGGAGTATGAATACTCAAACAAAA
Found at i:2892116 original size:79 final size:80
Alignment explanation
Indices: 2892024--2892182 Score: 284
Period size: 79 Copynumber: 2.0 Consensus size: 80
2892014 ATATTATCTC
* *
2892024 ATTCAACCCAAATTGATGATCAATATCATAAAATTGATTCTTTTCAATCTTAGGGACTAGGATTT
1 ATTCAACCCAAATTAATGATCAATATCATAAAATTGATTCTTTTCAATATTAGGGACTAGGATTT
2892089 CAATG-AAAAAATAT
66 CAATGCAAAAAATAT
2892103 ATTCAACCCAAATTAATGATCAATATCATAAAATTGATTCTTTTCAATATTAGGGACTAGGATTT
1 ATTCAACCCAAATTAATGATCAATATCATAAAATTGATTCTTTTCAATATTAGGGACTAGGATTT
*
2892168 CTATGCAAAAAATAT
66 CAATGCAAAAAATAT
2892183 GAGGAGGAGA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 67 0.88
80 9 0.12
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.35
Consensus pattern (80 bp):
ATTCAACCCAAATTAATGATCAATATCATAAAATTGATTCTTTTCAATATTAGGGACTAGGATTT
CAATGCAAAAAATAT
Found at i:2893035 original size:51 final size:50
Alignment explanation
Indices: 2892968--2893085 Score: 123
Period size: 51 Copynumber: 2.3 Consensus size: 50
2892958 CACCCGTAGC
* * * * *
2892968 AGTAAAGCGCGCCCCCTGA-ACCGCACTATATGCTTATTTGG-CACCACGTGG
1 AGTATAGCGCG-CCCCT-ATACCGCACTATACGCTGACTGGGTCA-CACGTGG
* *
2893019 AGTATAGCGCGTCCCCTATACCGCGCTATACGCTGACTGGGTTACACGTGG
1 AGTATAGCGCG-CCCCTATACCGCACTATACGCTGACTGGGTCACACGTGG
2893070 AGTATAGCGCGCCCCT
1 AGTATAGCGCGCCCCT
2893086 TGCTCCGCGC
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
50 6 0.11
51 50 0.88
52 1 0.02
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.22
Consensus pattern (50 bp):
AGTATAGCGCGCCCCTATACCGCACTATACGCTGACTGGGTCACACGTGG
Found at i:2896782 original size:35 final size:34
Alignment explanation
Indices: 2896697--2896783 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
2896687 ATTTGGTATT
*
2896697 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
2896731 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
2896769 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
2896784 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:2899051 original size:111 final size:111
Alignment explanation
Indices: 2898914--2899357 Score: 816
Period size: 111 Copynumber: 4.0 Consensus size: 111
2898904 ATTACAAAAA
2898914 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * *
2898979 AATTAAAACGTTAAAATATTAACATATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
2899025 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
2899090 AATTAAAACGTTAAAATTTTATCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
2899136 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
2899201 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
2899247 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
2899312 AATTAAAACGTTAAAATGTTACCGTATCAGCAAATTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
2899358 ATGATTTCCA
Statistics
Matches: 325, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 325 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:2899441 original size:17 final size:18
Alignment explanation
Indices: 2899419--2899459 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2899409 GAATTATATT
*
2899419 AGTAAAGTA-TTAAATAA
1 AGTAAAATACTTAAATAA
2899436 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
2899454 ATTAAA
1 AGTAAA
2899460 TACATAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:2900219 original size:5 final size:5
Alignment explanation
Indices: 2900206--2900684 Score: 949
Period size: 5 Copynumber: 95.8 Consensus size: 5
2900196 TATTCGATAA
*
2900206 TTATA TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
2900256 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
2900306 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
2900356 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
2900406 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
2900456 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
2900506 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
2900556 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
2900606 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
2900656 TTATG TTATG TTATG TTATG TTATG TTAT
1 TTATG TTATG TTATG TTATG TTATG TTAT
2900685 ATTAACTACT
Statistics
Matches: 473, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 473 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
TTATG
Found at i:2901040 original size:20 final size:20
Alignment explanation
Indices: 2901015--2901052 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2901005 TTTGGTTCAC
2901015 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
2901035 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
2901053 AGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:2906499 original size:2 final size:2
Alignment explanation
Indices: 2906492--2906521 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2906482 TTTACCCTAC
2906492 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
2906522 GTATTTTTTG
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:2907924 original size:19 final size:18
Alignment explanation
Indices: 2907870--2907917 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 18
2907860 AGCAGCACCA
2907870 ACTATCTCCACTACAAGC
1 ACTATCTCCACTACAAGC
*
2907888 ACCATGCTCCACTACAAGC
1 ACTAT-CTCCACTACAAGC
2907907 ACTATCTCCAC
1 ACTATCTCCAC
2907918 CAACAAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.31, C:0.42, G:0.06, T:0.21
Consensus pattern (18 bp):
ACTATCTCCACTACAAGC
Found at i:2909485 original size:6 final size:6
Alignment explanation
Indices: 2909474--2909500 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2909464 GGTTTTTTTA
2909474 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
2909501 TATACTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:2909509 original size:22 final size:22
Alignment explanation
Indices: 2909468--2909509 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2909458 TTGATAGGTT
*
2909468 TTTTTATTTATTTTTATTTTTA
1 TTTTTATTTATTTATATTTTTA
*
2909490 TTTTTATTT-TTTATACTTTT
1 TTTTTATTTATTTATATTTTT
2909510 GCATGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTATTTATTTATATTTTTA
Found at i:2909945 original size:17 final size:17
Alignment explanation
Indices: 2909923--2909959 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2909913 TGTCTTTCAA
* *
2909923 ATTAAAATTAATATTTT
1 ATTAAAATGAAAATTTT
2909940 ATTAAAATGAAAATTTT
1 ATTAAAATGAAAATTTT
2909957 ATT
1 ATT
2909960 TTTGGGTGTC
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:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
ATTAAAATGAAAATTTT
Found at i:2912890 original size:64 final size:62
Alignment explanation
Indices: 2912804--2913013 Score: 190
Period size: 64 Copynumber: 3.2 Consensus size: 62
2912794 TGCACTAAGA
* *
2912804 GTGCAACGATGCATGAAGTGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATGAAATGCATTCGATGTTT-AAAAATAG-CTGGTGCATCGATGCATGGATT
* * *
2912868 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAG--AGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTAA--AAAT-AGCTGGTGCATCGATGCATGGAT
*
2912931 A
62 T
* * * ** * *
2912932 GTGCATCGGTGCATGGAATGCATTCGATGTTTCAATTTATTCATTGATGCATCGATGCATGGTAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTAAAAATA-GC--TGGTGCATCGATGCATGG-AT
2912997 T
62 T
2912998 GATGCATCGATGCATG
1 G-TGCATCGATGCATG
2913014 CCTTTGAAAA
Statistics
Matches: 117, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
60 1 0.01
61 2 0.02
63 4 0.03
64 71 0.61
65 18 0.15
66 6 0.05
67 15 0.13
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (62 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTAAAAATAGCTGGTGCATCGATGCATGGATT
Found at i:2912934 original size:19 final size:19
Alignment explanation
Indices: 2912910--2912960 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2912900 TAATTAAATC
2912910 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2912929 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2912948 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2912961 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2912998 original size:21 final size:21
Alignment explanation
Indices: 2912974--2913013 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2912964 CAATTTATTC
2912974 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
2912995 ATTGATGCATCGATGCATG
1 ATTGATGCATCGATGCATG
2913014 CCTTTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:2915086 original size:13 final size:15
Alignment explanation
Indices: 2915060--2915092 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2915050 CAAGGTTTTA
2915060 AAAATAACTGTTTG-
1 AAAATAACTGTTTGT
2915074 AAAATAA-TGTTTGT
1 AAAATAACTGTTTGT
2915088 AAAAT
1 AAAAT
2915093 TATAAGATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36
Consensus pattern (15 bp):
AAAATAACTGTTTGT
Found at i:2915656 original size:44 final size:44
Alignment explanation
Indices: 2915563--2915663 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 44
2915553 GCATGGTCTT
* *
2915563 GTGCATCGATGCACATTCAAGGCATGCATCGGTGCATCATGCGGA
1 GTGCATCGATGCACATTCAAGGAATGCATCGGTGCAT-ATGCGAA
**
2915608 -TGCATCGATGCACATTCAAAGGAATGCATCGGTGCAT-TGTTAA
1 GTGCATCGATGCACATTC-AAGGAATGCATCGGTGCATATGCGAA
*
2915651 GTGCATCGGTGCA
1 GTGCATCGATGCA
2915664 TTAAGCATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
43 3 0.06
44 28 0.57
45 18 0.37
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (44 bp):
GTGCATCGATGCACATTCAAGGAATGCATCGGTGCATATGCGAA
Found at i:2921498 original size:18 final size:17
Alignment explanation
Indices: 2921444--2921492 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2921434 TTGGACTCCT
* *
2921444 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
2921462 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
2921480 AGTGCATTCGATG
1 AGTGCA-TCGATG
2921493 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:2921599 original size:64 final size:64
Alignment explanation
Indices: 2921444--2921651 Score: 174
Period size: 64 Copynumber: 3.2 Consensus size: 64
2921434 TTGGACTCCT
* * *
2921444 AGTGCATCGGTGCACTA-AGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA--AAAT-AG
1 AGTGCATCGATGCA-TAGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG
* * *** * * * * *
2921505 CCTGGTGCATCGATGCATGGATTTTACATCGATGCATCAAATGAATTCTATGTTTTAATTAAATC
1 ---AGTGCATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATC
2921570 AG
63 AG
* * * *
2921572 AGTGCATCGATGCATAGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTTCAATTTATTCATT
1 AGTGCATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCA--
2921637 G
64 G
2921638 A-TGCATCGATGCAT
1 AGTGCATCGATGCAT
2921652 GGTATTGATG
Statistics
Matches: 112, Mismatches: 26, Indels: 11
0.75 0.17 0.07
Matches are distributed among these distances:
63 1 0.01
64 90 0.80
65 13 0.12
66 6 0.05
67 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.32
Consensus pattern (64 bp):
AGTGCATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG
Found at i:2921658 original size:21 final size:21
Alignment explanation
Indices: 2921634--2921673 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2921624 CAATTTATTC
2921634 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
2921655 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
2921674 CCTTTGAAAA
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:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:2923305 original size:5 final size:5
Alignment explanation
Indices: 2923295--2923319 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2923285 GTTAAAAGAG
2923295 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
2923320 GAAGAAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:2924806 original size:94 final size:95
Alignment explanation
Indices: 2924645--2924854 Score: 280
Period size: 94 Copynumber: 2.2 Consensus size: 95
2924635 ATACCGAAGA
* * *
2924645 GGTAGTGTCGATACCATGGTAAGGGTATCGATACCAGGAATCATCGAATCTAAAATTGGTATTGA
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAATCATCGAACCTAAAATTGGTATCGA
** *
2924710 TACCGGAA-GGGGTATCAATACCATAGCAT
66 TACCAAAAGGGGGTATCAATACCATAACAT
*
2924739 GGTAGTATCGATACCATGGTAAGGGTATCGATATCAGGCAA-CATCGAACCTAAAATTGGTATCG
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGG-AATCATCGAACCTAAAATTGGTATCG
**
2924803 ATACCAAAAGGGGGTATCGGTACCATAACAT
65 ATACCAAAAGGGGGTATCAATACCATAACAT
* * * *
2924834 AGAAGTATCGGTACCAGGGTA
1 GGTAGTATCGATACCATGGTA
2924855 GTAGTATAGA
Statistics
Matches: 101, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
94 64 0.63
95 37 0.37
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.24
Consensus pattern (95 bp):
GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAATCATCGAACCTAAAATTGGTATCGA
TACCAAAAGGGGGTATCAATACCATAACAT
Found at i:2925279 original size:59 final size:59
Alignment explanation
Indices: 2925208--2925361 Score: 254
Period size: 59 Copynumber: 2.6 Consensus size: 59
2925198 TGCGCAAAGT
*
2925208 TAAGAAATTCATACTAAGTGTATGAATTTTCGTATTAGGCACTTTGTGTGCTAAAATGA
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCACTTTGTGTGCTAAAATGA
*
2925267 TAAGAAATTCATACTAAGTGTATGAATTTCCGCATTAGGCACTTTGTGTGCTAAAATGA
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCACTTTGTGTGCTAAAATGA
* * *
2925326 TAAGAAATCCATACTAATTGAATGAAATTTCCGTAT
1 TAAGAAATTCATACTAAGTGTATG-AATTTCCGTAT
2925362 GGGAAATATA
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 78 0.89
60 10 0.11
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (59 bp):
TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCACTTTGTGTGCTAAAATGA
Found at i:2925812 original size:68 final size:68
Alignment explanation
Indices: 2925703--2926248 Score: 822
Period size: 68 Copynumber: 8.0 Consensus size: 68
2925693 AAATAAAATA
* * * *
2925703 TTTGAGGCCTAAATGTGCATTTGACAGAAATGTATCAATTATGCCAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGT
2925768 GCC
66 GCC
* * *
2925771 TTTGAGGCCTAACTGTGCATTTGATAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGT
2925836 GCC
66 GCC
* * *
2925839 TTTAAGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGT
2925904 GCC
66 GCC
* *
2925907 TTTGAGGCCTAACTGTGCATTTGACAGAAAGATGTCAATCATGCCAGTTAGATAAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGT
2925972 GCC
66 GCC
* ** **
2925975 TTTGAGGCCTAACTGTGCATTTGATAGAAAGGTGGAAATCATGTTAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGT
*
2926040 TCC
66 GCC
* * * *
2926043 TTTGAGGCCTAACTGTGCATTTGAAAAAAAGGTGTCAATTATGCCAGTTAGATAAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGT
2926108 GCC
66 GCC
* * * *
2926111 TTTGAGGCCTATCTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGACGAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGT
*
2926176 GTC
66 GCC
* * *
2926179 TTTGAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAAT
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGT
2926244 GCC
66 GCC
2926247 TT
1 TT
2926249 GAGTAAAAGA
Statistics
Matches: 435, Mismatches: 43, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 435 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (68 bp):
TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGT
GCC
Found at i:2926348 original size:46 final size:45
Alignment explanation
Indices: 2926263--2926455 Score: 224
Period size: 46 Copynumber: 4.2 Consensus size: 45
2926253 AAAAGACTAG
** *
2926263 ATGTATAACAGTGTATAAAAGGCATGAAAAGATGTCATAAATAAA
1 ATGTATAATGGTGTATAAAAGGCATGAAAAGATGCCATAAATAAA
** * *
2926308 ATGTATAATGGTGTATAAAAAAACATGAAAAGATGTCATAAATGAA
1 ATGTATAATGGTGTAT-AAAAGGCATGAAAAGATGCCATAAATAAA
* *
2926354 ATGTATAACGGTGTATAAAAGGCATGAAATGATGCCATAAATAAA
1 ATGTATAATGGTGTATAAAAGGCATGAAAAGATGCCATAAATAAA
* * * ** *
2926399 ATATATAATAGTATATAAAAAGGCATGAACGGTTGCCATAAATGAAA
1 ATGTATAATGGTGTAT-AAAAGGCATGAAAAGATGCCATAAAT-AAA
2926446 ATGTATAATG
1 ATGTATAATG
2926456 ATGCATTATA
Statistics
Matches: 125, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
45 50 0.40
46 64 0.51
47 11 0.09
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (45 bp):
ATGTATAATGGTGTATAAAAGGCATGAAAAGATGCCATAAATAAA
Found at i:2926371 original size:23 final size:23
Alignment explanation
Indices: 2926290--2926372 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 23
2926280 AAAGGCATGA
*
2926290 AAAGATGTCATAAATAAAATGTAT
1 AAAGGTGT-ATAAATAAAATGTAT
* *
2926314 AATGGTGTATAAAAAAACATG-A-
1 AAAGGTGTATAAATAAA-ATGTAT
* *
2926336 AAAGATGTCATAAATGAAATGTAT
1 AAAGGTGT-ATAAATAAAATGTAT
*
2926360 AACGGTGTATAAA
1 AAAGGTGTATAAA
2926373 AGGCATGAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
22 9 0.20
23 22 0.48
24 15 0.33
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.27
Consensus pattern (23 bp):
AAAGGTGTATAAATAAAATGTAT
Found at i:2926418 original size:91 final size:92
Alignment explanation
Indices: 2926263--2926453 Score: 267
Period size: 91 Copynumber: 2.1 Consensus size: 92
2926253 AAAAGACTAG
* * * *
2926263 ATGTATAACAGTGTATAAAAGGCATGAAAAGATGTCATAAATAAAATGTATAATGGTGTATAAAA
1 ATGTATAACAGTGTATAAAAGGCATGAAAAGATGCCATAAATAAAATATATAATAGTATATAAAA
*
2926328 AAACATGAAAAGATGTCATAAATG-AA
66 AAACATGAAAAGATGCCATAAATGAAA
* *
2926354 ATGTATAACGGTGTATAAAAGGCATGAAATGATGCCATAAATAAAATATATAATAGTATATAAAA
1 ATGTATAACAGTGTATAAAAGGCATGAAAAGATGCCATAAATAAAATATATAATAGTATATAAAA
** ** *
2926419 AGGCATGAACGGTTGCCATAAATGAAA
66 AAACATGAAAAGATGCCATAAATGAAA
2926446 ATGTATAA
1 ATGTATAA
2926454 TGATGCATTA
Statistics
Matches: 87, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
91 77 0.89
92 10 0.11
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.26
Consensus pattern (92 bp):
ATGTATAACAGTGTATAAAAGGCATGAAAAGATGCCATAAATAAAATATATAATAGTATATAAAA
AAACATGAAAAGATGCCATAAATGAAA
Found at i:2927749 original size:9 final size:9
Alignment explanation
Indices: 2927730--2927777 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
2927720 ACTTAAACCA
2927730 AAATGAAAAT
1 AAAT-AAAAT
2927740 AAATAAAAT
1 AAATAAAAT
2927749 AAAT-AAAT
1 AAATAAAAT
*
2927757 AAA-ATAAT
1 AAATAAAAT
2927765 AAAATAAAAT
1 -AAATAAAAT
2927775 AAA
1 AAA
2927778 ATATAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
8 10 0.30
9 15 0.45
10 8 0.24
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2927750 original size:5 final size:5
Alignment explanation
Indices: 2927729--2927780 Score: 60
Period size: 5 Copynumber: 11.2 Consensus size: 5
2927719 GACTTAAACC
2927729 AAAAT GAAAAT -AAAT AAAAT -AAAT -AAAT AAAAT --AAT AAAAT AAAAT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
2927775 AAAAT A
1 AAAAT A
2927781 TAAAATATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
3 3 0.07
4 12 0.29
5 22 0.52
6 5 0.12
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:2927754 original size:13 final size:13
Alignment explanation
Indices: 2927736--2927787 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
2927726 ACCAAAATGA
2927736 AAATAAATAAAAT
1 AAATAAATAAAAT
2927749 AAATAAATAAAAT
1 AAATAAATAAAAT
2927762 -AATAAAATAAAAT
1 AAAT-AAATAAAAT
*
2927775 AAA-ATATAAAAT
1 AAATAAATAAAAT
2927787 A
1 A
2927788 TATGTATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
12 12 0.33
13 22 0.61
14 2 0.06
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:2927783 original size:17 final size:18
Alignment explanation
Indices: 2927729--2927787 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
2927719 GACTTAAACC
*
2927729 AAAATGAAAAT-AAATAAA
1 AAAAT-AAAATAAAATAAT
2927747 ATAAAT-AAATAAAATAAT
1 A-AAATAAAATAAAATAAT
2927765 AAAATAAAATAAAAT-AT
1 AAAATAAAATAAAATAAT
2927782 AAAATA
1 AAAATA
2927788 TATGTATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
17 16 0.43
18 17 0.46
19 4 0.11
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (18 bp):
AAAATAAAATAAAATAAT
Found at i:2927855 original size:22 final size:21
Alignment explanation
Indices: 2927808--2927856 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
2927798 AGCTATATAA
2927808 TATATAATATATTTCAAAAAC
1 TATATAATATATTTCAAAAAC
* * *
2927829 AATATAATATATTTTCAAAGAT
1 TATATAATATA-TTTCAAAAAC
2927851 TATATA
1 TATATA
2927857 TATTTTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (21 bp):
TATATAATATATTTCAAAAAC
Found at i:2927887 original size:23 final size:23
Alignment explanation
Indices: 2927856--2927900 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2927846 AAGATTATAT
* *
2927856 ATATTTTATATGTTTTCAAAACC
1 ATATATTATATGCTTTCAAAACC
2927879 ATATATTATATGCTTTCAAAAC
1 ATATATTATATGCTTTCAAAAC
2927901 TGTTTTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.44
Consensus pattern (23 bp):
ATATATTATATGCTTTCAAAACC
Found at i:2928023 original size:17 final size:17
Alignment explanation
Indices: 2927998--2928036 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2927988 AAATATATAT
*
2927998 TATACGTTTTAAAAAAA
1 TATATGTTTTAAAAAAA
* *
2928015 TATATGTTTTCAAAAAT
1 TATATGTTTTAAAAAAA
2928032 TATAT
1 TATAT
2928037 TATATATGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (17 bp):
TATATGTTTTAAAAAAA
Found at i:2928074 original size:38 final size:39
Alignment explanation
Indices: 2927863--2928096 Score: 184
Period size: 38 Copynumber: 6.1 Consensus size: 39
2927853 TATATATTTT
** * *
2927863 ATATGTTTTC-AAAACCATATATTATATGCTTTCAAAAC
1 ATATGTTTTCAAAAAATATATATTATACGTTTTCAAAAC
* *
2927901 -TGT-TTTTCAAAAAAAACTATATATTATACGTTTTCGAAAC
1 ATATGTTTTC--AAAAAA-TATATATTATACGTTTTCAAAAC
* * *
2927941 --CT-TTTT-AAAAAACTATATATTGTATGTTTTCAAAAC
1 ATATGTTTTCAAAAAA-TATATATTATACGTTTTCAAAAC
* * *
2927977 -TAT-TTTTAAAAAAATATATATTATACGTTTTAAAAAAAT
1 ATATGTTTTCAAAAAATATATATTATACGTTTT--CAAAAC
* *
2928016 ATATGTTTTCAAAAATTATAT-TATATATGTTTTCAAAA-
1 ATATGTTTTCAAAAAATATATAT-TATACGTTTTCAAAAC
* *
2928054 ATATGTTTTCAATAACTATATATTATACGTTTTCAAAAC
1 ATATGTTTTCAAAAAATATATATTATACGTTTTCAAAAC
2928093 ATAT
1 ATAT
2928097 ATTATATACT
Statistics
Matches: 161, Mismatches: 22, Indels: 25
0.77 0.11 0.12
Matches are distributed among these distances:
36 32 0.20
37 22 0.14
38 39 0.24
39 22 0.14
40 23 0.14
41 23 0.14
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (39 bp):
ATATGTTTTCAAAAAATATATATTATACGTTTTCAAAAC
Found at i:2928097 original size:24 final size:23
Alignment explanation
Indices: 2928058--2928113 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
2928048 TCAAAAATAT
2928058 GTTTTCAATAACTATA-TATTATAC
1 GTTTTCAA-AACTATATTA-TATAC
2928082 GTTTTCAAAACATATATTATATAC
1 GTTTTCAAAAC-TATATTATATAC
2928106 --TTTCAAAA
1 GTTTTCAAAA
2928114 ATTACGTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.27
23 3 0.10
24 17 0.57
25 2 0.07
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (23 bp):
GTTTTCAAAACTATATTATATAC
Found at i:2928099 original size:22 final size:24
Alignment explanation
Indices: 2928058--2928102 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
2928048 TCAAAAATAT
2928058 GTTTTCAATAACTATATATTATAC
1 GTTTTCAATAACTATATATTATAC
2928082 GTTTTCAA-AAC-ATATATTATA
1 GTTTTCAATAACTATATATTATA
2928103 TACTTTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.48
23 3 0.14
24 8 0.38
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.44
Consensus pattern (24 bp):
GTTTTCAATAACTATATATTATAC
Found at i:2928109 original size:22 final size:23
Alignment explanation
Indices: 2928060--2928113 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
2928050 AAAAATATGT
**
2928060 TTTCAATAACTATATATTATACGT
1 TTTCAA-AACTATATATTATACAC
*
2928084 TTTCAAAAC-ATATATTATATAC
1 TTTCAAAACTATATATTATACAC
2928106 TTTCAAAA
1 TTTCAAAA
2928114 ATTACGTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 18 0.67
23 3 0.11
24 6 0.22
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTCAAAACTATATATTATACAC
Found at i:2930401 original size:35 final size:35
Alignment explanation
Indices: 2930349--2930415 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
2930339 CAACAGAGTC
*
2930349 TTCAATTTCATTCTAAACCCCAAATTCTAAAATAA
1 TTCAATTACATTCTAAACCCCAAATTCTAAAATAA
*
2930384 TTCAATTACATTTTAAACCCCAAATTCTAAAA
1 TTCAATTACATTCTAAACCCCAAATTCTAAAA
2930416 GTTTAGATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.34
Consensus pattern (35 bp):
TTCAATTACATTCTAAACCCCAAATTCTAAAATAA
Found at i:2931833 original size:35 final size:35
Alignment explanation
Indices: 2931793--2931867 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
2931783 TTCATGTTCA
*
2931793 AAATTCCAAAACACTTCAATTATATTCTAAACCCC
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCC
* * * *
2931828 AAATTCTAAAATACTTTAATTACATTCTAAACCCT
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCC
2931863 AAATT
1 AAATT
2931868 GAATAATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCTAAACCCC
Found at i:2931938 original size:35 final size:35
Alignment explanation
Indices: 2931863--2931939 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
2931853 TCTAAACCCT
*
2931863 AAATTGAATAATTTTAGAATTTAGGGCTTAAAATG
1 AAATTGAATAATTTTAGAATTTAGGGCTTAAAATA
* * * * *
2931898 TAATTGAATTATTTT-GAAATTTGGGGTTTAGAATA
1 AAATTGAATAATTTTAG-AATTTAGGGCTTAAAATA
2931933 AAATTGA
1 AAATTGA
2931940 GGAATGTGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
34 1 0.03
35 33 0.97
ACGTcount: A:0.40, C:0.01, G:0.18, T:0.40
Consensus pattern (35 bp):
AAATTGAATAATTTTAGAATTTAGGGCTTAAAATA
Found at i:2940643 original size:13 final size:15
Alignment explanation
Indices: 2940607--2940648 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
2940597 ATCTCTAAGC
2940607 TGAATATATCATTGT
1 TGAATATATCATTGT
2940622 TGAATATATCATTGT
1 TGAATATATCATTGT
2940637 TGAATATATCAT
1 TGAATATATCAT
2940649 GCAATCACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (15 bp):
TGAATATATCATTGT
Found at i:2944833 original size:16 final size:15
Alignment explanation
Indices: 2944812--2944843 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
2944802 CCAAGATGTC
2944812 ACATTGACTTTTCAAA
1 ACATTGACTTTT-AAA
2944828 ACATTGACTTTTAAA
1 ACATTGACTTTTAAA
2944843 A
1 A
2944844 GATAGTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.38
Consensus pattern (15 bp):
ACATTGACTTTTAAA
Found at i:2945419 original size:24 final size:24
Alignment explanation
Indices: 2945392--2945448 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
2945382 CACCACAGCT
* *
2945392 CGTATAAATTGCACTGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
*
2945416 CGTAGAAATTGCACCGAAGTGCTA
1 CGTAGAAATTGCACCGAAGTGCCA
*
2945440 CATAGAAAT
1 CGTAGAAAT
2945449 GTCTCGAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:2945463 original size:23 final size:23
Alignment explanation
Indices: 2945429--2945502 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
2945419 AGAAATTGCA
2945429 CCGAAGTG-CTACATAGAAATGTC
1 CCGAA-TGACTACATAGAAATGTC
* * *
2945452 TCGAATGACTACATAGTATTGTC
1 CCGAATGACTACATAGAAATGTC
**
2945475 CCGAATGACCGCATAGAAATGTC
1 CCGAATGACTACATAGAAATGTC
2945498 CCGAA
1 CCGAA
2945503 GGACCACGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 2 0.05
23 40 0.95
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (23 bp):
CCGAATGACTACATAGAAATGTC
Found at i:2945496 original size:46 final size:46
Alignment explanation
Indices: 2945440--2945538 Score: 117
Period size: 46 Copynumber: 2.2 Consensus size: 46
2945430 CGAAGTGCTA
* * * ** *
2945440 CATAGAAATGTCTCGAATGACTACATAGTATTGTCCCGAATGACCG
1 CATAGAAATGTCCCGAAGGACCACATAAAATTGTCCCGAAGGACCG
* *
2945486 CATAGAAATGTCCCGAAGGACCACGTAAAATTGTCCTGAAGGACCG
1 CATAGAAATGTCCCGAAGGACCACATAAAATTGTCCCGAAGGACCG
*
2945532 CGTAGAA
1 CATAGAA
2945539 CCCTCGACAT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (46 bp):
CATAGAAATGTCCCGAAGGACCACATAAAATTGTCCCGAAGGACCG
Found at i:2945507 original size:23 final size:23
Alignment explanation
Indices: 2945439--2945530 Score: 87
Period size: 23 Copynumber: 4.0 Consensus size: 23
2945429 CCGAAGTGCT
* * *
2945439 ACATAGAAATGTCTCGAATGACT
1 ACATAGAAATGTCCCGAAGGACC
* * *
2945462 ACATAGTATTGTCCCGAATGACC
1 ACATAGAAATGTCCCGAAGGACC
*
2945485 GCATAGAAATGTCCCGAAGGACC
1 ACATAGAAATGTCCCGAAGGACC
* *
2945508 ACGTA-AAATTGTCCTGAAGGACC
1 ACATAGAAA-TGTCCCGAAGGACC
2945531 GCGTAGAACC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
22 3 0.05
23 54 0.95
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (23 bp):
ACATAGAAATGTCCCGAAGGACC
Found at i:2945535 original size:23 final size:24
Alignment explanation
Indices: 2945469--2945538 Score: 90
Period size: 23 Copynumber: 3.0 Consensus size: 24
2945459 ACTACATAGT
* *
2945469 ATTGTCCCGAATGACCGCATAGAA
1 ATTGTCCCGAAGGACCGCGTAGAA
*
2945493 A-TGTCCCGAAGGACCACGTA-AA
1 ATTGTCCCGAAGGACCGCGTAGAA
*
2945515 ATTGTCCTGAAGGACCGCGTAGAA
1 ATTGTCCCGAAGGACCGCGTAGAA
2945539 CCCTCGACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
22 3 0.08
23 33 0.85
24 3 0.08
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (24 bp):
ATTGTCCCGAAGGACCGCGTAGAA
Found at i:2949519 original size:20 final size:20
Alignment explanation
Indices: 2949491--2949546 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
2949481 TTAACTGATT
* *
2949491 TTTTTTCAAATTCCAACTGG
1 TTTTATCAAATTCCAACTAG
* **
2949511 TTTTGTCAAATTTTAACTAG
1 TTTTATCAAATTCCAACTAG
*
2949531 TTTTATCAATTTCCAA
1 TTTTATCAAATTCCAA
2949547 TCGATTTTGT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.48
Consensus pattern (20 bp):
TTTTATCAAATTCCAACTAG
Found at i:2949556 original size:40 final size:42
Alignment explanation
Indices: 2949470--2949563 Score: 113
Period size: 40 Copynumber: 2.3 Consensus size: 42
2949460 ATACCGATAC
* * *
2949470 TTTGTAAAATTTTAACTGATTTTTTTTCAAATTCCAACTGGT
1 TTTGTAAAATTTTAACTGATGTTTTATCAAATTCCAACTGAT
* *
2949512 TTTGTCAAATTTTAACT-A-GTTTTATCAATTTCCAA-TCGAT
1 TTTGTAAAATTTTAACTGATGTTTTATCAAATTCCAACT-GAT
2949552 TTTGTAAAATTT
1 TTTGTAAAATTT
2949564 GTTACCTGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.02
40 27 0.60
41 1 0.02
42 16 0.36
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.50
Consensus pattern (42 bp):
TTTGTAAAATTTTAACTGATGTTTTATCAAATTCCAACTGAT
Found at i:2949878 original size:20 final size:21
Alignment explanation
Indices: 2949853--2949891 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2949843 AGATGCATAT
2949853 TGGAATAA-AAATATCGATTC
1 TGGAATAATAAATATCGATTC
*
2949873 TGGAATAATAAGTATCGAT
1 TGGAATAATAAATATCGAT
2949892 ACTTTATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.31
Consensus pattern (21 bp):
TGGAATAATAAATATCGATTC
Found at i:2956778 original size:16 final size:16
Alignment explanation
Indices: 2956757--2956788 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2956747 GTTTGTCTAG
2956757 AAATTGAATTGCAATT
1 AAATTGAATTGCAATT
2956773 AAATTGAATTGCAATT
1 AAATTGAATTGCAATT
2956789 TCAAGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (16 bp):
AAATTGAATTGCAATT
Found at i:2959538 original size:20 final size:20
Alignment explanation
Indices: 2959513--2959560 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2959503 GTCAGAGTGT
*
2959513 GGCGGCGGACGGCTGACGGC
1 GGCGGCGGACGGCGGACGGC
* *
2959533 GGCGGCAGACGGCGGGCGGC
1 GGCGGCGGACGGCGGACGGC
*
2959553 GGCAGCGG
1 GGCGGCGG
2959561 CCAGCAGGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.10, C:0.29, G:0.58, T:0.02
Consensus pattern (20 bp):
GGCGGCGGACGGCGGACGGC
Found at i:2959550 original size:17 final size:16
Alignment explanation
Indices: 2959530--2959561 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2959520 GACGGCTGAC
2959530 GGCGGCGGCAGACGGCG
1 GGCGGCGGCAG-CGGCG
2959547 GGCGGCGGCAGCGGC
1 GGCGGCGGCAGCGGC
2959562 CAGCAGGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.31, G:0.59, T:0.00
Consensus pattern (16 bp):
GGCGGCGGCAGCGGCG
Found at i:2985597 original size:28 final size:28
Alignment explanation
Indices: 2985503--2985597 Score: 136
Period size: 28 Copynumber: 3.4 Consensus size: 28
2985493 AATTGGGTTG
* *
2985503 GGGTCGGGGTTTTTTAAGTGTGGTATTC
1 GGGTCGGGTTTTTTTAAGTGTGATATTC
* * *
2985531 AGTTCGGATTTTTTTAAGTGTGATATTC
1 GGGTCGGGTTTTTTTAAGTGTGATATTC
2985559 GGGTCGGGTTTTTTTAAGTGTGATATTC
1 GGGTCGGGTTTTTTTAAGTGTGATATTC
*
2985587 GGGTCGTGTTT
1 GGGTCGGGTTT
2985598 GGGTTTAGGA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.14, C:0.07, G:0.33, T:0.46
Consensus pattern (28 bp):
GGGTCGGGTTTTTTTAAGTGTGATATTC
Found at i:2986197 original size:16 final size:16
Alignment explanation
Indices: 2986173--2986222 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
2986163 AGGTTTCAGA
2986173 TTCAGATTCCAATTCC
1 TTCAGATTCCAATTCC
* *
2986189 TTCAAATTCCAATTCAT
1 TTCAGATTCCAATTC-C
2986206 TTACAGATTCCAATTCC
1 TT-CAGATTCCAATTCC
2986223 CTGAGAAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 14 0.50
17 2 0.07
18 12 0.43
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (16 bp):
TTCAGATTCCAATTCC
Found at i:2988745 original size:12 final size:13
Alignment explanation
Indices: 2988728--2988771 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
2988718 TATAAATTAA
2988728 ATTATTAATA-AT
1 ATTATTAATATAT
2988740 ATTATTAATATAT
1 ATTATTAATATAT
2988753 A-TA-T-ATATAT
1 ATTATTAATATAT
2988763 A-TATTAATA
1 ATTATTAATA
2988772 AAAAATTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.31
11 2 0.07
12 15 0.52
13 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTATTAATATAT
Found at i:2990639 original size:3 final size:3
Alignment explanation
Indices: 2990631--2990660 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2990621 GATTATATTA
2990631 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2990661 TTAAGCTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3002531 original size:31 final size:31
Alignment explanation
Indices: 3002493--3002617 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
3002483 AGGGTCGAGG
3002493 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
3002524 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3002555 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
3002586 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
3002617 G
1 G
3002618 GTCATTCGGG
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:3003282 original size:21 final size:21
Alignment explanation
Indices: 3003257--3003307 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
3003247 TTACGAAAAT
*
3003257 CACTGTAGCAGTGCATCAATA
1 CACTGTAGCAATGCATCAATA
* *
3003278 TACTGTAGCAATGCATCAATG
1 CACTGTAGCAATGCATCAATA
3003299 CACTGTAGC
1 CACTGTAGC
3003308 CATTTGAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (21 bp):
CACTGTAGCAATGCATCAATA
Found at i:3003347 original size:21 final size:21
Alignment explanation
Indices: 3003321--3003362 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3003311 TTGAAGTTTT
3003321 ATGCATCGATGCAATGTAGCA
1 ATGCATCGATGCAATGTAGCA
* *
3003342 ATGCATTGATGCACTGTAGCA
1 ATGCATCGATGCAATGTAGCA
3003363 GGTTACTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (21 bp):
ATGCATCGATGCAATGTAGCA
Found at i:3005662 original size:14 final size:14
Alignment explanation
Indices: 3005643--3005669 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3005633 CACAATAGAT
3005643 ATTCTATAACAATG
1 ATTCTATAACAATG
3005657 ATTCTATAACAAT
1 ATTCTATAACAAT
3005670 CTCGTTCATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (14 bp):
ATTCTATAACAATG
Found at i:3013250 original size:15 final size:15
Alignment explanation
Indices: 3013230--3013265 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3013220 TTCCAGAAAA
3013230 TGAATTACTGCAATT
1 TGAATTACTGCAATT
*
3013245 TGAATTACTGGAATT
1 TGAATTACTGCAATT
3013260 TGAATT
1 TGAATT
3013266 CTGGAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (15 bp):
TGAATTACTGCAATT
Found at i:3013277 original size:14 final size:15
Alignment explanation
Indices: 3013225--3013281 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
3013215 TGGTTTTCCA
3013225 GAAAATGAATTACTG
1 GAAAATGAATTACTG
* **
3013240 CAATTTGAATTACTG
1 GAAAATGAATTACTG
**
3013255 GAATTTGAATT-CTG
1 GAAAATGAATTACTG
3013269 GAAAATGAATTAC
1 GAAAATGAATTAC
3013282 ATTTCTGGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 12 0.34
15 23 0.66
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:3013287 original size:20 final size:21
Alignment explanation
Indices: 3013264--3013316 Score: 90
Period size: 20 Copynumber: 2.5 Consensus size: 21
3013254 GGAATTTGAA
3013264 TTCTGGAAAATGAATT-ACAT
1 TTCTGGAAAATGAATTAACAT
3013284 TTCTGGAAAATGAATTACACAT
1 TTCTGGAAAATGAATTA-ACAT
3013306 TTCTGGAAAAT
1 TTCTGGAAAAT
3013317 ATCTGAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 16 0.52
22 15 0.48
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (21 bp):
TTCTGGAAAATGAATTAACAT
Found at i:3013693 original size:27 final size:26
Alignment explanation
Indices: 3013639--3013701 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
3013629 TTTACTAAAA
*
3013639 TATTATTTAAATATATAAATAATATAT
1 TATTA-TTAAATATATAAAAAATATAT
3013666 TCATTATTAAATATATAAAAAA-ATTAT
1 T-ATTATTAAATATATAAAAAATA-TAT
3013693 TATATATTA
1 TAT-TATTA
3013702 TTAAAATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 3 0.09
27 25 0.78
28 4 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
TATTATTAAATATATAAAAAATATAT
Done.