Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 86 of 279
Found at i:28432104 original size:21 final size:21
Alignment explanation
Indices: 28432078--28432119 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28432068 AAATGCTGGG
28432078 AAAGAGGAAAAAGTCTGAAAC
1 AAAGAGGAAAAAGTCTGAAAC
*
28432099 AAAGAGTAAAAAGTCTGAAAC
1 AAAGAGGAAAAAGTCTGAAAC
28432120 TGCCCGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.57, C:0.10, G:0.21, T:0.12
Consensus pattern (21 bp):
AAAGAGGAAAAAGTCTGAAAC
Found at i:28436286 original size:33 final size:33
Alignment explanation
Indices: 28436216--28436288 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
28436206 TATGTAATAT
* * *
28436216 TTTAATTGGTACAAATGTATGTATAGATATGAT
1 TTTACTTGGTAAAAATGTATGTATAGATATGAA
*
28436249 TTTACTTGGTAAAAATGTATGTATATATATGAA
1 TTTACTTGGTAAAAATGTATGTATAGATATGAA
28436282 TTTACTT
1 TTTACTT
28436289 ATTATATAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (33 bp):
TTTACTTGGTAAAAATGTATGTATAGATATGAA
Found at i:28436456 original size:11 final size:11
Alignment explanation
Indices: 28436419--28436457 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
28436409 GAATGAGCAG
28436419 GGAAAGAAATAA
1 GGAAAGAAA-AA
28436431 GGAAA-AAAAA
1 GGAAAGAAAAA
*
28436441 AGAAAGAAAAA
1 GGAAAGAAAAA
28436452 GGAAAG
1 GGAAAG
28436458 GGAAAATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 6 0.25
11 13 0.54
12 5 0.21
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.03
Consensus pattern (11 bp):
GGAAAGAAAAA
Found at i:28437261 original size:6 final size:6
Alignment explanation
Indices: 28437250--28437279 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
28437240 GTACCAGTAT
*
28437250 TGTTAC TGTTAC TGTTAC TGTTAG TGTTAC
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC
28437280 CCTTACGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.13, G:0.20, T:0.50
Consensus pattern (6 bp):
TGTTAC
Found at i:28442911 original size:23 final size:23
Alignment explanation
Indices: 28442884--28442931 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
28442874 ATACTTTATC
28442884 ATACATTCACCAA-GCAATAACAT
1 ATACA-TCACCAAGGCAATAACAT
* *
28442907 ATACATCATCAAGGCACTAACAT
1 ATACATCACCAAGGCAATAACAT
28442930 AT
1 AT
28442932 GCATGCATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.46, C:0.25, G:0.06, T:0.23
Consensus pattern (23 bp):
ATACATCACCAAGGCAATAACAT
Found at i:28446807 original size:131 final size:129
Alignment explanation
Indices: 28446381--28446862 Score: 384
Period size: 130 Copynumber: 3.7 Consensus size: 129
28446371 TTGCCTCACC
* * ** * **
28446381 TTAGAAAATACGAGTGAAATTCCGAA-GAGATATTCGATTATTTTGAACAAAC-AGGAAATTGCA
1 TTAGAAAACATGAGTGAAATTTTGAAGGA-ATATTCGATTGTTTTGAACAAACGA-GAAATCACA
*** * * ** * * * ** *
28446444 ACCCAGCACGATAGGGTACTATTCCCTGAATTGCCAAACATCAAATATCACCTTCATTTTAAAGG
64 ACCCAGCGTAATAGGGCACGATT-CC-GAATTATCAAACACCGAGTATTGCCTTCATTTCAAA-G
28446509 GTTT
126 GTTT
* * *
28446513 TTAGAAAACGTGAGTGAAATTTTGAAGGAATCTTCGATTGTTTTGAAAAAACGAGAAATCACAAC
1 TTAGAAAACATGAGTGAAATTTTGAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCACAAC
* * ** * * **
28446578 CTAACGTGTTAGGGCACGATTCCGAATTATCAAACACCGAGTATTGTCTTCTTTTTGGAAGGTTT
66 CCAGCGTAATAGGGCACGATTCCGAATTATCAAACACCGAGTATTGCCTTC-ATTTCAAAGGTTT
* *** * *
28446643 TTA-ATAAACACGAGTGAAAACCTAAAGGAATATTCAATTGTTTTGAACAAACGAGAAATCACAA
1 TTAGA-AAACATGAGTGAAATTTTGAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCACAA
* * *
28446707 CCCAGC-TCAATAGGGCATGGTTCTCGAATTATCAAACACCGAGTATTGCCTTCAGTTCAAAGGA
65 CCCAGCGT-AATAGGGCACGATTC-CGAATTATCAAACACCGAGTATTGCCTTCATTTCAAAGG-
28446771 TTT
127 TTT
* * * * **
28446774 TTAGAAGACATGAGTGAAATTTTGAAGGGATATTTGATTATTTT-AAGCAAACGAGAAATTGCAA
1 TTAGAAAACATGAGTGAAATTTTGAAGGAATATTCGATTGTTTTGAA-CAAACGAGAAATCACAA
28446838 CCCAGCACGT--TAGGGCACGATTCCG
65 CCCAG--CGTAATAGGGCACGATTCCG
28446863 TGAATTACCA
Statistics
Matches: 276, Mismatches: 62, Indels: 26
0.76 0.17 0.07
Matches are distributed among these distances:
129 2 0.01
130 103 0.37
131 101 0.37
132 65 0.24
133 4 0.01
134 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (129 bp):
TTAGAAAACATGAGTGAAATTTTGAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCACAAC
CCAGCGTAATAGGGCACGATTCCGAATTATCAAACACCGAGTATTGCCTTCATTTCAAAGGTTT
Found at i:28446900 original size:131 final size:131
Alignment explanation
Indices: 28446381--28446907 Score: 442
Period size: 131 Copynumber: 4.0 Consensus size: 131
28446371 TTGCCTCACC
* * * **
28446381 TTAGAAAATACGAGTGAAATTCCGAA-GAGATATTCGATTATTTTGAACAAAC-AGGAAATTGCA
1 TTAGAAAACATGAGTGAAATTCTGAAGGA-ATATTCGATTATTTTGAACAAACGA-GAAATCACA
* * * * * * * *
28446444 ACCCAGCACGATAGGGTACTATTCCCTGAATTGCCAAACATCAAATATCACCTTCATTTTAAAGG
64 ACCCAGCACGATAGGGCACGATT-CCTGAATTACCAAACACCGAGTATCGCCTTCAGTTTAAAGG
*
28446509 GTTT
128 ATTT
* * * * *
28446513 TTAGAAAACGTGAGTGAAATTTTGAAGGAATCTTCGATTGTTTTGAAAAAACGAGAAATCACAAC
1 TTAGAAAACATGAGTGAAATTCTGAAGGAATATTCGATTATTTTGAACAAACGAGAAATCACAAC
* * ** * * * * ** *
28446578 CTAACGTGTTAGGGCACGATTCC-GAATTATCAAACACCGAGTATTGTCTTCTTTTTGGAAGG-T
66 CCAGCACGATAGGGCACGATTCCTGAATTACCAAACACCGAGTATCGCCTTCAGTTT-AAAGGAT
28446641 TT
130 TT
* ** * * *
28446643 TTA-ATAAACACGAGTGAAAACCTAAAGGAATATTCAATTGTTTTGAACAAACGAGAAATCACAA
1 TTAGA-AAACATGAGTGAAATTCTGAAGGAATATTCGATTATTTTGAACAAACGAGAAATCACAA
* * * * * * *
28446707 CCCAGCTCAATAGGGCATGGTT-CTCGAATTATCAAACACCGAGTATTGCCTTCAGTTCAAAGGA
65 CCCAGCACGATAGGGCACGATTCCT-GAATTACCAAACACCGAGTATCGCCTTCAGTTTAAAGGA
28446771 TTT
129 TTT
* * * * **
28446774 TTAGAAGACATGAGTGAAATTTTGAAGGGATATTTGATTATTTT-AAGCAAACGAGAAATTGCAA
1 TTAGAAAACATGAGTGAAATTCTGAAGGAATATTCGATTATTTTGAA-CAAACGAGAAATCACAA
* * *
28446838 CCCAGCACGTTAGGGCACGATTCCGTGAATTACCAAATATCGCA-TATCGCCTTC-GTTTAAAGG
65 CCCAGCACGATAGGGCACGATTCC-TGAATTACCAAACACCG-AGTATCGCCTTCAGTTTAAAGG
28446901 ATTT
128 ATTT
28446905 TTA
1 TTA
28446908 ATAATTGTGA
Statistics
Matches: 312, Mismatches: 71, Indels: 25
0.76 0.17 0.06
Matches are distributed among these distances:
129 2 0.01
130 100 0.32
131 117 0.38
132 88 0.28
133 5 0.02
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (131 bp):
TTAGAAAACATGAGTGAAATTCTGAAGGAATATTCGATTATTTTGAACAAACGAGAAATCACAAC
CCAGCACGATAGGGCACGATTCCTGAATTACCAAACACCGAGTATCGCCTTCAGTTTAAAGGATT
T
Found at i:28447256 original size:21 final size:23
Alignment explanation
Indices: 28447206--28447256 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 23
28447196 ATGATAATGT
* *
28447206 ACATAGCATGATATAGAATAACC
1 ACATAGCAAGATATAGAATAACA
28447229 A-AT-GCAAGATATA-AA-AACA
1 ACATAGCAAGATATAGAATAACA
28447248 ACATAGCAA
1 ACATAGCAA
28447257 TTAGAAGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 13 0.54
22 2 0.08
23 1 0.04
ACGTcount: A:0.55, C:0.16, G:0.12, T:0.18
Consensus pattern (23 bp):
ACATAGCAAGATATAGAATAACA
Found at i:28455573 original size:27 final size:27
Alignment explanation
Indices: 28455543--28455639 Score: 131
Period size: 27 Copynumber: 3.6 Consensus size: 27
28455533 TAGGGCAAAT
*
28455543 CAGTCATATTACCTTACAAGGGTATTA
1 CAGTCATTTTACCTTACAAGGGTATTA
*
28455570 CAGTCATTTTACCATACAAGGGTATTA
1 CAGTCATTTTACCTTACAAGGGTATTA
* *** *
28455597 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCTTACAAGGGTATTA
28455624 CAGTCATTTTACCTTA
1 CAGTCATTTTACCTTA
28455640 TGGGGGCATT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (27 bp):
CAGTCATTTTACCTTACAAGGGTATTA
Found at i:28455641 original size:27 final size:27
Alignment explanation
Indices: 28455562--28455785 Score: 288
Period size: 27 Copynumber: 8.3 Consensus size: 27
28455552 TACCTTACAA
* * ***
28455562 GGGTATTACAGTCATTTTACCATACAA
1 GGGTATTTCAGTCATTTTACCCTATGG
*
28455589 GGGTATTACAGTCATTTTACCCTATGG
1 GGGTATTTCAGTCATTTTACCCTATGG
*
28455616 GGGTATTTCAGTCATTTTACCTTATGG
1 GGGTATTTCAGTCATTTTACCCTATGG
* **
28455643 GGGCATTTTGGTCATTTTACCCTATGG
1 GGGTATTTCAGTCATTTTACCCTATGG
* * *
28455670 AGATATTTCAGTCATTTTACCCTTTGG
1 GGGTATTTCAGTCATTTTACCCTATGG
*
28455697 GGGTATTTCAGTTATTTTACCCTATAGG
1 GGGTATTTCAGTCATTTTACCCTAT-GG
28455725 GGG-ATTTCAGTCATTTTACCCTATGG
1 GGGTATTTCAGTCATTTTACCCTATGG
* *
28455751 GGGTATTTCGGTCATTTTACCCTATGA
1 GGGTATTTCAGTCATTTTACCCTATGG
28455778 GGGTATTT
1 GGGTATTT
28455786 GGGCCCAACA
Statistics
Matches: 172, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 5 0.03
27 162 0.94
28 5 0.03
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (27 bp):
GGGTATTTCAGTCATTTTACCCTATGG
Found at i:28458204 original size:19 final size:19
Alignment explanation
Indices: 28458180--28458219 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
28458170 ATGTAATTTG
28458180 TTAAGAAT-AAATTTTCTAA
1 TTAAGAATAAAATTTT-TAA
*
28458199 TTAAGATTAAAATTTTTAA
1 TTAAGAATAAAATTTTTAA
28458218 TT
1 TT
28458220 TTCATTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (19 bp):
TTAAGAATAAAATTTTTAA
Found at i:28466364 original size:54 final size:54
Alignment explanation
Indices: 28466270--28466441 Score: 231
Period size: 54 Copynumber: 3.2 Consensus size: 54
28466260 TGTACCTAGA
* * *
28466270 CCCCATATATGGTAAAATGACTCTTTTGCCCCTATATGGTAAAATGACTGTTTTG
1 CCCC-TATGTGGTAAAATGACTATTTTGCCCTTATATGGTAAAATGACTGTTTTG
* * *
28466325 CCCCTATGTTGTAAAATGA-TGATTTTGCCCTTATGTGGTAAAATGACTATTTTG
1 CCCCTATGTGGTAAAATGACT-ATTTTGCCCTTATATGGTAAAATGACTGTTTTG
* * *
28466379 CCCCTATGTGGTGAAATGACTATTTTGCCCTTATATGGTAAGATGACTGCTTTG
1 CCCCTATGTGGTAAAATGACTATTTTGCCCTTATATGGTAAAATGACTGTTTTG
28466433 -CCCTATGTG
1 CCCCTATGTG
28466442 ATATATATAT
Statistics
Matches: 103, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
53 10 0.10
54 88 0.85
55 5 0.05
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (54 bp):
CCCCTATGTGGTAAAATGACTATTTTGCCCTTATATGGTAAAATGACTGTTTTG
Found at i:28466433 original size:81 final size:80
Alignment explanation
Indices: 28466279--28466441 Score: 220
Period size: 81 Copynumber: 2.0 Consensus size: 80
28466269 ACCCCATATA
* * * *
28466279 TGGTAAAATGACTCTTTTGCCCCTATATGGTAAAATGACTGTTTTGCCCCTATGTTGTAAAATGA
1 TGGTAAAATGACTATTTTGCCCCTATATGGTAAAATGACTATTTTGCCCCTATATGGTAAAATGA
*
28466344 TGATTTTGCCCTTATG
66 TGACTTTGCCC-TATG
* * * *
28466360 TGGTAAAATGACTATTTTGCCCCTATGTGGTGAAATGACTATTTTGCCCTTATATGGTAAGATGA
1 TGGTAAAATGACTATTTTGCCCCTATATGGTAAAATGACTATTTTGCCCCTATATGGTAAAATGA
28466425 CTG-CTTTGCCCTATG
66 -TGACTTTGCCCTATG
28466440 TG
1 TG
28466442 ATATATATAT
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
80 6 0.08
81 64 0.89
82 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (80 bp):
TGGTAAAATGACTATTTTGCCCCTATATGGTAAAATGACTATTTTGCCCCTATATGGTAAAATGA
TGACTTTGCCCTATG
Found at i:28466436 original size:27 final size:27
Alignment explanation
Indices: 28466270--28466435 Score: 199
Period size: 27 Copynumber: 6.1 Consensus size: 27
28466260 TGTACCTAGA
*
28466270 CCCCATATATGGTAAAATGACTCTTTTG
1 CCCC-TATATGGTAAAATGACTGTTTTG
28466298 CCCCTATATGGTAAAATGACTGTTTTG
1 CCCCTATATGGTAAAATGACTGTTTTG
* *
28466325 CCCCTATGTTGTAAAATGA-TGATTTTG
1 CCCCTATATGGTAAAATGACTG-TTTTG
* * *
28466352 CCCTTATGTGGTAAAATGACTATTTTG
1 CCCCTATATGGTAAAATGACTGTTTTG
* * *
28466379 CCCCTATGTGGTGAAATGACTATTTTG
1 CCCCTATATGGTAAAATGACTGTTTTG
* * *
28466406 CCCTTATATGGTAAGATGACTGCTTTG
1 CCCCTATATGGTAAAATGACTGTTTTG
28466433 CCC
1 CCC
28466436 TATGTGATAT
Statistics
Matches: 122, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
26 2 0.02
27 115 0.94
28 5 0.04
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (27 bp):
CCCCTATATGGTAAAATGACTGTTTTG
Found at i:28470134 original size:26 final size:27
Alignment explanation
Indices: 28470101--28470247 Score: 143
Period size: 27 Copynumber: 5.5 Consensus size: 27
28470091 ATACCCCATG
* * *
28470101 TGTGGTAAAGTTACT-TTTTTCCCCTA
1 TGTGGTAAAATGACTGTTTTGCCCCTA
* * * *
28470127 TGTGGTAAAATAACTATTTTTCCCTTA
1 TGTGGTAAAATGACTGTTTTGCCCCTA
*
28470154 TGTGGTAAAATGACTGTTTTGCCCTTA
1 TGTGGTAAAATGACTGTTTTGCCCCTA
*
28470181 TATGGTAAAATGACTGTTTTGCCCCTA
1 TGTGGTAAAATGACTGTTTTGCCCCTA
* * * * *
28470208 TATGGTAAAAAGACTATTTTTCCCGTA
1 TGTGGTAAAATGACTGTTTTGCCCCTA
* *
28470235 TATGGTAAGATGA
1 TGTGGTAAAATGA
28470248 TTGTGTAACA
Statistics
Matches: 106, Mismatches: 14, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
26 13 0.12
27 93 0.88
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (27 bp):
TGTGGTAAAATGACTGTTTTGCCCCTA
Found at i:28470191 original size:54 final size:53
Alignment explanation
Indices: 28470101--28470242 Score: 158
Period size: 54 Copynumber: 2.6 Consensus size: 53
28470091 ATACCCCATG
* * * * *
28470101 TGTGGTAAAGTTACTTTTTTCCCCTATGTGGTAAAATAACTATTTTTCCCTTA
1 TGTGGTAAAATGACTTTTTTCCCCTATATGGTAAAATAACTATTTTGCCCCTA
* * * *
28470154 TGTGGTAAAATGACTGTTTTGCCCTTATATGGTAAAATGACTGTTTTGCCCCTA
1 TGTGGTAAAATGACT-TTTTTCCCCTATATGGTAAAATAACTATTTTGCCCCTA
* * *
28470208 TATGGTAAAAAGACTATTTTTCCCGTATATGGTAA
1 TGTGGTAAAATGACT-TTTTTCCCCTATATGGTAA
28470243 GATGATTGTG
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
53 13 0.18
54 61 0.82
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (53 bp):
TGTGGTAAAATGACTTTTTTCCCCTATATGGTAAAATAACTATTTTGCCCCTA
Found at i:28478021 original size:30 final size:30
Alignment explanation
Indices: 28477963--28478021 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
28477953 ATTTTCAGGC
* **
28477963 CTAGGGGTAAAATGGTCATTTTGTCAAAGT
1 CTAGGGGCAAAATGGTCATTTTACCAAAGT
28477993 CTAGGGGCAAAATGGTCATTTTACCAAAG
1 CTAGGGGCAAAATGGTCATTTTACCAAAG
28478022 ATATAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (30 bp):
CTAGGGGCAAAATGGTCATTTTACCAAAGT
Found at i:28478422 original size:47 final size:44
Alignment explanation
Indices: 28478357--28478528 Score: 168
Period size: 46 Copynumber: 3.7 Consensus size: 44
28478347 GGATTATTGT
28478357 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATT-ATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGG---CATTGATGA
*
28478403 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGGGATGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATT--GATGA
* * * *
28478451 GTGCTAGTGTAAGACATGTCTGGCACATGCATCGACCTTGA-GA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGATGA
* **
28478494 CGTAAGCCAGTGTAAGACATGTCTCAGACATGCAT
1 -G--AGCTAGTGTAAGACATGTCTGGGACATGCAT
28478529 TACGAAATGT
Statistics
Matches: 107, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
43 2 0.02
44 3 0.03
45 4 0.04
46 48 0.45
47 27 0.25
48 23 0.21
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (44 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGATGA
Found at i:28482352 original size:696 final size:690
Alignment explanation
Indices: 28480953--28483643 Score: 3273
Period size: 696 Copynumber: 4.0 Consensus size: 690
28480943 GGGTGTTACA
* * *
28480953 AAATTGC-GCTCACATTGGTCTGGACCTTTCAAAGTTGTCGAAGTATTTCCTCATGGTGCAGTCA
1 AAATTGCAG-TCACATTGGTTTGGACCTTTCGAAGTTGTCGAAGTATTTCTTCATGGTGCAGTCA
* * * *
28481017 CAATCAGAGATTTACATGATGGACACTAGTTCAAAGTGAATGGACAATGGTTGAAGCA-CTTTAT
65 CAATCAGAGATTTACATGATGGACACCAGTTCAAAGTGAATGGACAACGGTTGAAACACCATT-T
* *
28481081 TGGGAATATTAATCAAAAGCAAGAAGAGACCATTAAATTAGTCTAAAAATTTTAATTTTTATTGA
129 TGGGAATATTAATCAAAAGCAAGAAGAGACCATTAAATTGGTC-AAAATTTTTAATTTTTATTGA
* * *
28481146 ATTTATCATCATGTGATTTTATTTTA-TTT-TATTG-TTTTTGTTCAAGTTTGTTTTAC-TTCTT
193 ATTTATCATTATGTGATTTTATTTTATTTTGTTTTGTTTTTTGTTCAAGTTTGTTTTACTTTTTT
* * * *
28481207 TTTTTTCCAGAATAATTTGGTACCATTGTCGATGCACTTGGGCTTTATTGTCAACGCAGTTCCTA
258 TTTTTTTCAGAATAATTAGGTACCATTGTCGACGCACTTGGGCTTTATTGTCAACGCAGTTCGTA
* * * *
28481272 CTATTGTATTGTCACTTATGACTCATCAAGAAAGAGGGCATATAAAAAATTTCAGATCTCATCAT
323 CTATTGTACTGTCACTTATGACTCATCAAGAATGAGGGCATATAAAAAATTTCAGATCCCATCGT
* * *
28481337 TTGATCAAAAGTTACCTAGCCGTCTGATCTGTCTCAGCGGGCGCAATTCTCATTGGACATATTTA
388 TTGATCAAAAGTGACCTAGCCGTCTGATCTGTCTGAGCGGGCGCAATTCTCATTCGACATATTTA
* * *
28481402 TTCCTGCCAGCTTTATATCCCTTCACAAAACTCACGCCTTTCCATCTTCTTCCGTTACTGGAAAG
453 TTCCTGCCAACTTTATATCCCTTCACAAAAGTCACGCCTTTCCATCTTCTTCCGCTACTGGAAAG
* * * * *
28481467 AAAAGGTTGTTGGATATCACTGAACTAGAGGAGATTAGACGAAATGCCTATGTAAACT-CTACAA
518 AAAAGGCTGTTGGATATCACTAAACTAGAGAAGATTAGGCGAAATGCCTATG-AAAATGCTACAA
* * * * * *
28481531 TTTACAAGGAAAAGACCAGACAATGGCAGGATAGAAGTATTTTGTAGCAAAAATTTATCGCGGGT
582 TTTACAAGGAAAAGACCAAACAATGGCATGACAGAATTATTTTGCAGCAACAATTTATCGCGGGT
* * *
28481596 CAACAAGTTTTATTATTCAATTCTAGACTGAATTTGTACTCAAGT
647 CAACAAGTTTTATTATTCAATTCTAGACTGAAATTGCAC-CCAGT
* * *
28481641 AAATTGTACTCACATTGGTTTGGACCTTTCGAAGTTGTC-AAGATATTTCTTCATGGTG-AGTTA
1 AAATTGCAGTCACATTGGTTTGGACCTTTCGAAGTTGTCGAAG-TATTTCTTCATGGTGCAGTCA
* * * *
28481704 GAATTAGAGATTTACATGATTGACACCAGTTCAAAGTGAATGGATAACGGTTGAAACACCATTTT
65 CAATCAGAGATTTACATGATGGACACCAGTTCAAAGTGAATGGACAACGGTTGAAACACCATTTT
* *
28481769 GGGAATATTAATCAAAAGCAGGCAA-AGACAATTAAATTGGTCAAAATTTTTTAATTTTTATTGA
130 GGGAATATTAATCAAAAGCAAG-AAGAGACCATTAAATTGGTCAAAA-TTTTTAATTTTTATTGA
* *
28481833 ATTTATGATTATGTGATTTTATTTTATTTTGTTTTGTTTTTTGTTCAAGTTTGTTTTTCTTCTTC
193 ATTTATCATTATGTGATTTTATTTTATTTTGTTTTGTTTTTTGTTCAAGTTTG--TTT-TACTT-
*
28481898 TTTCTTTTTTTTTAGAATAATTAGGTACCATTGTCGACGCACTTGGGCTTTATTGTCAACGCAGT
254 TTT-TTTTTTTTCAGAATAATTAGGTACCATTGTCGACGCACTTGGGCTTTATTGTCAACGCAGT
* * * * *
28481963 TCGTACTATTGTACTGTAACTTATGAATCATCAAGAATGAGGGCATATTAGAAATTTTAGATCCC
318 TCGTACTATTGTACTGTCACTTATGACTCATCAAGAATGAGGGCATATAAAAAATTTCAGATCCC
* * * * * *
28482028 ATCGTTTGATCAAAATTGACCTATCCATCTGATTTGTCTGAGCGGGCGTAATTGTCATTCGACAT
383 ATCGTTTGATCAAAAGTGACCTAGCCGTCTGATCTGTCTGAGCGGGCGCAATTCTCATTCGACAT
* *
28482093 ATTTATT-CTCGTCAATTTTATATCCCTTCACAAAAGTCACGCCTTTCCATCTTCTTCCGCTACT
448 ATTTATTCCT-GCCAACTTTATATCCCTTCACAAAAGTCACGCCTTTCCATCTTCTTCCGCTACT
* *
28482157 GGAAAGAAAAGGCTGTTGGATATCACTGAACTAGAGAAGATTAGGCGAAATGCCTATGAAAATGA
512 GGAAAGAAAAGGCTGTTGGATATCACTAAACTAGAGAAGATTAGGCGAAATGCCTATGAAAATGC
* * *
28482222 TGCAATTTACAAGGAAAAGACCAAACAATGGCATGATAGAATTATTTTGCAGCAACAATTTATCA
577 TACAATTTACAAGGAAAAGACCAAACAATGGCATGACAGAATTATTTTGCAGCAACAATTTATCG
* *
28482287 CAGGTCAACAAGTTTTATTATTCAATTC-ACAACTGAAATTGCACCCAGGT
642 CGGGTCAACAAGTTTTATTATTCAATTCTA-GACTGAAATTGCACCCA-GT
28482337 AAATTGCAGTCACATTGGTTTGGACCTTTCGAAGTTGTCGAAGTATTTCCTT-ATGGTGCAGTCA
1 AAATTGCAGTCACATTGGTTTGGACCTTTCGAAGTTGTCGAAGTATTT-CTTCATGGTGCAGTCA
* **
28482401 CAATCAGAGATTTACGTGATGGACACCAGTTCAAAGTGAATGGACAACGGTTGAAACATTATTTT
65 CAATCAGAGATTTACATGATGGACACCAGTTCAAAGTGAATGGACAACGGTTGAAACACCATTTT
* * * ** *
28482466 GGGAATATTAATCAAAAGCAGGTAGAGACCATTAAATTTGTTGAAATTTTTAATTTTTATTAAAT
130 GGGAATATTAATCAAAAGCAAGAAGAGACCATTAAATTGGTCAAAATTTTTAATTTTTATTGAAT
* * * * *
28482531 TTTTAATTATGTGATTTTATTTTATTTTATTTTGTTTTGTTTTCGTTCAAGTTTGTTTAAC-TTG
195 TTATCATTATGTGATTTTATTTTATTTTGTTTTG--TT-TTTT-GTTCAAGTTTGTTTTACTTTT
*
28482595 TTTTTTTTTCAGAATAAGTAGGTACCATTGT-------C----G----A---T----GCAGTTCG
256 TTTTTTTTTCAGAATAATTAGGTACCATTGTCGACGCACTTGGGCTTTATTGTCAACGCAGTTCG
** * * *
28482638 TACTATTGTACTACCACTTATGACTCGTCAAGAATTAGGGCATATAAAAAATTTTAGATCCCA-C
321 TACTATTGTACTGTCACTTATGACTCATCAAGAATGAGGGCATATAAAAAATTTCAGATCCCATC
* * *
28482702 AGTTTGATCAAAAGTGACCTAGCCGTCTGATCTGTCTGAGCGGACACAATTCTCATTGGACATAT
386 -GTTTGATCAAAAGTGACCTAGCCGTCTGATCTGTCTGAGCGGGCGCAATTCTCATTCGACATAT
* *
28482767 TTATTCCTGCCAACTTTATATCCCTTCACAAAAGTCATGCCTTTCCATCTTCTT-CGTTACTGGA
450 TTATTCCTGCCAACTTTATATCCCTTCACAAAAGTCACGCCTTTCCATCTTCTTCCGCTACTGGA
* * * * *
28482831 AAGAAAAGGTTGTTGGATATCACTAAACTAGAGGAGATTAGGCGAAATGCATATAAAAATGCTGC
515 AAGAAAAGGCTGTTGGATATCACTAAACTAGAGAAGATTAGGCGAAATGCCTATGAAAATGCTAC
** * * * *
28482896 AATTTACAAGGAAAAGACCAAATGATAGCATGACAGAATTATTTTCCAGCGACAATTTATCGTGG
580 AATTTACAAGGAAAAGACCAAACAATGGCATGACAGAATTATTTTGCAGCAACAATTTATCGCGG
* *
28482961 GTCAACAAGTTTTATTATTCAATTCTAGACTAAAATTGCATCCAG-
645 GTCAACAAGTTTTATTATTCAATTCTAGACTGAAATTGCACCCAGT
* * *
28483006 -----GCAGTCACATCGGTTTGGACCTTTCGAAGTTGTCAAAGTATTT-TCTCATGGTGTAGTCA
1 AAATTGCAGTCACATTGGTTTGGACCTTTCGAAGTTGTCGAAGTATTTCT-TCATGGTGCAGTCA
* ** *
28483065 CAATCAGAGATTTACATGATGGACATCAGTTCAAAGTGAATGGA-AAGCGAATGAAACACTATTT
65 CAATCAGAGATTTACATGATGGACACCAGTTCAAAGTGAATGGACAA-CGGTTGAAACACCATTT
*
28483129 TGGGAATATTAATCAAAAGAAAGAAGAGACCATTAAATTGGTCAAAA-----AA---TTA--GAA
129 TGGGAATATTAATCAAAAGCAAGAAGAGACCATTAAATTGGTCAAAATTTTTAATTTTTATTGAA
* * * * * ** *
28483184 ATTACCATTATGTGATGTT-TTTTGTTTT-TTTTATTCAAATTGTTTC-ACTTCT-TTTTA--TT
194 TTTATCATTATGTGATTTTATTTTATTTTGTTTTGTT--TTTTG-TTCAAGTT-TGTTTTACTTT
* * * * * *
28483243 TTTATTTTTGCTGAATAATTAGGAACCATTGTCGACTCACTTGGGCTTTATTGTCAACGCAATTC
255 TTTTTTTTTTCAGAATAATTAGGTACCATTGTCGACGCACTTGGGCTTTATTGTCAACGCAGTTC
* ** * * *
28483308 GTACTATTGTACT-TCCCTTATGACTCATTGAGAATGAGGGCA-ATTAGAAATTTCAGATCCCAC
320 GTACTATTGTACTGTCACTTATGACTCATCAAGAATGAGGGCATATAAAAAATTTCAGATCCCAT
* *
28483371 CGTTTGATCAAAAGTGACCTAGCTGTCTGATCTGTCTGAGCGGGCGCAATTCTCATTCAACATAT
385 CGTTTGATCAAAAGTGACCTAGCCGTCTGATCTGTCTGAGCGGGCGCAATTCTCATTCGACATAT
** *
28483436 TTATTCCCACCAGCTTTATATATCCCTTCACAAAAGTCACGCCTTTCCATCTTCTTCCGCTACTG
450 TTATTCCTGCCAAC-TT-TATATCCCTTCACAAAAGTCACGCCTTTCCATCTTCTTCCGCTACTG
* * *
28483501 GAAAGAAAAGGCTATTAGATATCACTAAACTAGAGAAGATTAGGTGAAATGCCTATGAAAATGCT
513 GAAAGAAAAGGCTGTTGGATATCACTAAACTAGAGAAGATTAGGCGAAATGCCTATGAAAATGCT
* * * * *
28483566 ACAATTTACAAGG-AAAGACAAAACGATGGCATGACAGAATTATTTTGTA-CTGATAATTTATCG
578 ACAATTTACAAGGAAAAGACCAAACAATGGCATGACAGAATTATTTTGCAGC-AACAATTTATCG
*
28483629 GGGGTCAACAAGTTT
642 CGGGTCAACAAGTTT
28483644 GTGGGTGCAA
Statistics
Matches: 1742, Mismatches: 199, Indels: 141
0.84 0.10 0.07
Matches are distributed among these distances:
649 28 0.02
650 10 0.01
651 6 0.00
652 4 0.00
653 8 0.00
654 16 0.01
656 4 0.00
659 2 0.00
660 1 0.00
662 1 0.00
663 3 0.00
664 150 0.09
667 1 0.00
669 87 0.05
670 28 0.02
671 276 0.16
672 244 0.14
673 2 0.00
676 1 0.00
679 1 0.00
683 1 0.00
686 4 0.00
687 137 0.08
688 56 0.03
689 4 0.00
690 16 0.01
692 3 0.00
693 2 0.00
694 29 0.02
695 13 0.01
696 476 0.27
697 108 0.06
698 5 0.00
699 4 0.00
700 11 0.01
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (690 bp):
AAATTGCAGTCACATTGGTTTGGACCTTTCGAAGTTGTCGAAGTATTTCTTCATGGTGCAGTCAC
AATCAGAGATTTACATGATGGACACCAGTTCAAAGTGAATGGACAACGGTTGAAACACCATTTTG
GGAATATTAATCAAAAGCAAGAAGAGACCATTAAATTGGTCAAAATTTTTAATTTTTATTGAATT
TATCATTATGTGATTTTATTTTATTTTGTTTTGTTTTTTGTTCAAGTTTGTTTTACTTTTTTTTT
TTTTCAGAATAATTAGGTACCATTGTCGACGCACTTGGGCTTTATTGTCAACGCAGTTCGTACTA
TTGTACTGTCACTTATGACTCATCAAGAATGAGGGCATATAAAAAATTTCAGATCCCATCGTTTG
ATCAAAAGTGACCTAGCCGTCTGATCTGTCTGAGCGGGCGCAATTCTCATTCGACATATTTATTC
CTGCCAACTTTATATCCCTTCACAAAAGTCACGCCTTTCCATCTTCTTCCGCTACTGGAAAGAAA
AGGCTGTTGGATATCACTAAACTAGAGAAGATTAGGCGAAATGCCTATGAAAATGCTACAATTTA
CAAGGAAAAGACCAAACAATGGCATGACAGAATTATTTTGCAGCAACAATTTATCGCGGGTCAAC
AAGTTTTATTATTCAATTCTAGACTGAAATTGCACCCAGT
Found at i:28488026 original size:55 final size:54
Alignment explanation
Indices: 28487888--28488094 Score: 256
Period size: 53 Copynumber: 3.8 Consensus size: 54
28487878 TTCCTTTTTA
* *
28487888 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * *
28487941 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAG
1 AACTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * *
28487995 TAGTTTACCAGTGCCATGCCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAG
1 -AACTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* *
28488050 AACTTACCAATGCCATGCCTT-AGCATGGTCTTACTTGGTATCCTT
1 AACTTACCATTGCCATGCCTTGA-CATGGTCTTACATGGTATCCTT
28488095 AAACCCTAAT
Statistics
Matches: 129, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
53 47 0.36
54 38 0.29
55 44 0.34
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (54 bp):
AACTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:28495518 original size:47 final size:47
Alignment explanation
Indices: 28495461--28495717 Score: 347
Period size: 47 Copynumber: 5.4 Consensus size: 47
28495451 ATTGATGTAC
* * *
28495461 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
28495508 AAGTATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATAT--GTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
28495557 ACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
28495604 ACA-TGCATATGTGAGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
28495651 AAGTGTATATATGTGATAAGACCGAATGGCCAATGTGATGGATGTGG
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
28495698 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
28495718 TCCCGAAGGG
Statistics
Matches: 191, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
46 1 0.01
47 149 0.78
49 40 0.21
50 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.27
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:28495595 original size:22 final size:22
Alignment explanation
Indices: 28495568--28495642 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 22
28495558 CATGTGTATG
28495568 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* *
28495590 TGTGATGAATG-TGAACAT-G-CATA
1 TGTGAT-AAGGCCG-A-ATGGCCA-A
28495613 TGTGAGATAAGGCCGAATGGCCAA
1 TGT--GATAAGGCCGAATGGCCAA
28495637 TGTGAT
1 TGTGAT
28495643 GAATGTGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 12 0.30
23 11 0.28
24 11 0.28
25 6 0.15
ACGTcount: A:0.32, C:0.13, G:0.31, T:0.24
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:28498212 original size:38 final size:38
Alignment explanation
Indices: 28498148--28498222 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
28498138 AATCCGAGTT
*
28498148 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
28498186 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
28498223 ATTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:28498344 original size:40 final size:40
Alignment explanation
Indices: 28498276--28498556 Score: 393
Period size: 40 Copynumber: 7.0 Consensus size: 40
28498266 AGGTCTCGAC
* *
28498276 GATG-ATCCGAGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * *
28498315 GATGTACCCGGGCTAAGTCCCGAAAAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
28498355 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
28498395 GATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
28498435 GATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * ** *
28498475 GATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * * * *
28498515 GTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
28498555 GA
1 GA
28498557 CGTGTATTCG
Statistics
Matches: 215, Mismatches: 26, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
39 4 0.02
40 211 0.98
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
Found at i:28503106 original size:27 final size:26
Alignment explanation
Indices: 28503054--28503112 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
28503044 CCACATATAT
*
28503054 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
28503080 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
28503107 ATATCT
1 ATATCT
28503113 AGCAACCTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.36
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:28510446 original size:27 final size:26
Alignment explanation
Indices: 28510402--28510453 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
28510392 CTCGTTGCAA
*
28510402 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
28510429 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
28510454 GCAGCCTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:28510532 original size:27 final size:26
Alignment explanation
Indices: 28510492--28510551 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
28510482 CCACATATAT
*
28510492 ATATCTATTCTGGTGACCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
28510518 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
28510545 ATATCTG
1 ATATCTG
28510552 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:28516352 original size:33 final size:31
Alignment explanation
Indices: 28516271--28516358 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 31
28516261 AATTGCATTA
* * *
28516271 CACTGTACTAATACTGTATTGGGCTTAGGCC
1 CACTGTACTGATACTGTATAGGGCTAAGGCC
*
28516302 CAC---ACTGTTACTGTATAGGGCTAAGGCC
1 CACTGTACTGATACTGTATAGGGCTAAGGCC
28516330 CTGACTGTACTGATACTGTATAGGGCTAA
1 C--ACTGTACTGATACTGTATAGGGCTAA
28516359 AGCCTATACT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
28 22 0.47
30 2 0.04
31 3 0.06
33 20 0.43
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.30
Consensus pattern (31 bp):
CACTGTACTGATACTGTATAGGGCTAAGGCC
Found at i:28544832 original size:14 final size:14
Alignment explanation
Indices: 28544809--28544839 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28544799 GTTTTGTTGT
28544809 TTCGACTTTCTTTC
1 TTCGACTTTCTTTC
*
28544823 TTCGATTTTCTTTC
1 TTCGACTTTCTTTC
28544837 TTC
1 TTC
28544840 CTCAACTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.26, G:0.06, T:0.61
Consensus pattern (14 bp):
TTCGACTTTCTTTC
Found at i:28551996 original size:27 final size:26
Alignment explanation
Indices: 28551959--28552073 Score: 97
Period size: 27 Copynumber: 4.3 Consensus size: 26
28551949 AGCATGACTG
* *
28551959 CCAGAACAGATATTGTGATAGAGTCA
1 CCAGAACAGATATTGTGACAGAGCCA
* *
28551985 CCAGATACAGATAATGTGGCAGAGCCA
1 CCAGA-ACAGATATTGTGACAGAGCCA
* *
28552012 CCAGAATAGATATTTGTGGC-GTAGCCA
1 CCAGAACAGATA-TTGTGACAG-AGCCA
* * *
28552039 CTAGAAACAGATATTTGTGGCATAGCCA
1 CCAG-AACAGATA-TTGTGACAGAGCCA
28552067 CCAGAAC
1 CCAGAAC
28552074 GCTTCCTCCA
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
26 12 0.16
27 39 0.53
28 23 0.31
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (26 bp):
CCAGAACAGATATTGTGACAGAGCCA
Found at i:28552058 original size:28 final size:28
Alignment explanation
Indices: 28551983--28552072 Score: 112
Period size: 28 Copynumber: 3.3 Consensus size: 28
28551973 GTGATAGAGT
* * *
28551983 CACCAGATACAGATA-ATGTGGCAGAGC
1 CACCAGAAACAGATATTTGTGGCATAGC
* *
28552010 CACCAG-AATAGATATTTGTGGCGTAGC
1 CACCAGAAACAGATATTTGTGGCATAGC
*
28552037 CACTAGAAACAGATATTTGTGGCATAGC
1 CACCAGAAACAGATATTTGTGGCATAGC
28552065 CACCAGAA
1 CACCAGAA
28552073 CGCTTCCTCC
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
26 6 0.12
27 20 0.38
28 26 0.50
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (28 bp):
CACCAGAAACAGATATTTGTGGCATAGC
Found at i:28554862 original size:15 final size:14
Alignment explanation
Indices: 28554844--28554934 Score: 74
Period size: 15 Copynumber: 5.9 Consensus size: 14
28554834 AGATTGAAAA
28554844 ATAATATATAAATAG
1 ATAATATA-AAATAG
28554859 ATAATATAAAAATAG
1 ATAATAT-AAAATAG
*
28554874 ATAATATAATAATAA
1 ATAATATAA-AATAG
* *
28554889 ATAATAGAATAATTG
1 ATAATATAA-AATAG
*
28554904 ATAGAATAATAAAATAA
1 AT--AAT-ATAAAATAG
28554921 ATAATATAGAAATA
1 ATAATATA-AAATA
28554935 TAGATTTATA
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
14 5 0.08
15 46 0.73
16 1 0.02
17 8 0.13
18 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (14 bp):
ATAATATAAAATAG
Found at i:28554867 original size:20 final size:20
Alignment explanation
Indices: 28554844--28554983 Score: 67
Period size: 20 Copynumber: 7.5 Consensus size: 20
28554834 AGATTGAAAA
28554844 ATAATATATAAATAGAT-A-
1 ATAATATATAAATAGATAAT
28554862 AT-ATA-A-AAATAGATAAT
1 ATAATATATAAATAGATAAT
28554879 ATAATA-ATAAATA-ATAGA-
1 ATAATATATAAATAGATA-AT
*
28554897 ATAAT-TGATAGAATA-ATAAA
1 ATAATAT-ATA-AATAGATAAT
*
28554917 ATAA-ATA-ATATAGA-AAT
1 ATAATATATAAATAGATAAT
* *
28554934 ATAGATTTATAAATCGA-AAT
1 ATA-ATATATAAATAGATAAT
* *
28554954 ATATTAATATAAATATAATAAT
1 ATAAT-ATATAAATA-GATAAT
28554976 ATAA-ATAT
1 ATAATATAT
28554984 TATTAATTAC
Statistics
Matches: 95, Mismatches: 10, Indels: 32
0.69 0.07 0.23
Matches are distributed among these distances:
15 8 0.08
16 2 0.02
17 13 0.14
18 17 0.18
19 14 0.15
20 34 0.36
21 1 0.01
22 6 0.06
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.33
Consensus pattern (20 bp):
ATAATATATAAATAGATAAT
Found at i:28554878 original size:30 final size:30
Alignment explanation
Indices: 28554844--28554939 Score: 88
Period size: 30 Copynumber: 3.1 Consensus size: 30
28554834 AGATTGAAAA
*
28554844 ATAATATATAAATAGATAATATAAAAATAG
1 ATAATATATAAATAAATAATATAAAAATAG
* * *
28554874 ATAATATA-ATAATAAATAATAGAATAATTG
1 ATAATATATA-AATAAATAATATAAAAATAG
28554904 ATAGA-ATAATAAAATAAATAATATAGAAATATAG
1 ATA-ATAT-AT-AAATAAATAATATA-AAA-ATAG
28554938 AT
1 AT
28554940 TTATAAATCG
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
29 1 0.02
30 29 0.56
31 2 0.04
32 12 0.23
33 3 0.06
34 5 0.10
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (30 bp):
ATAATATATAAATAAATAATATAAAAATAG
Found at i:28554899 original size:12 final size:11
Alignment explanation
Indices: 28554842--28554926 Score: 54
Period size: 12 Copynumber: 7.7 Consensus size: 11
28554832 ATAGATTGAA
*
28554842 AAATAATATAT
1 AAATAATAAAT
28554853 AAATAGATAATAT
1 AAATA-ATAA-AT
*
28554866 AAA-AATAGAT
1 AAATAATAAAT
28554876 AATATAAT-AAT
1 AA-ATAATAAAT
28554887 AAATAATAGAAT
1 AAATAATA-AAT
* *
28554899 AATTGATAGAAT
1 AAATAATA-AAT
28554911 -AAT-A-AAAT
1 AAATAATAAAT
28554919 AAATAATA
1 AAATAATA
28554927 TAGAAATATA
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
8 3 0.05
9 4 0.07
10 11 0.19
11 16 0.27
12 20 0.34
13 5 0.08
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:28554969 original size:14 final size:14
Alignment explanation
Indices: 28554950--28554990 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
28554940 TTATAAATCG
28554950 AAATATATTAATAT
1 AAATATATTAATAT
*
28554964 AAATATAATAATAT
1 AAATATATTAATAT
28554978 AAATATTATTAAT
1 AAATA-TATTAAT
28554991 TACTTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATATTAATAT
Found at i:28565959 original size:27 final size:26
Alignment explanation
Indices: 28565890--28566004 Score: 97
Period size: 27 Copynumber: 4.3 Consensus size: 26
28565880 AGCATGGCTG
** *
28565890 CCAGAACAGATATTGTGATAGAGTCA
1 CCAGAACAGATATTGTGGCAGAGCCA
* *
28565916 CCAGATATAGATATTGTAGCAGAGCCA
1 CCAGA-ACAGATATTGTGGCAGAGCCA
28565943 CCAGAACAGATATTTGTGGC-GTAGCCA
1 CCAGAACAGATA-TTGTGGCAG-AGCCA
* * *
28565970 CCAAAAACAGATGTTTGTGGCATAGCCA
1 CC-AGAACAGAT-ATTGTGGCAGAGCCA
*
28565998 CTAGAAC
1 CCAGAAC
28566005 GCTTCCTCCA
Statistics
Matches: 71, Mismatches: 12, Indels: 11
0.76 0.13 0.12
Matches are distributed among these distances:
26 12 0.17
27 38 0.54
28 21 0.30
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCAGAGCCA
Found at i:28565986 original size:28 final size:27
Alignment explanation
Indices: 28565924--28565998 Score: 89
Period size: 28 Copynumber: 2.8 Consensus size: 27
28565914 CACCAGATAT
* * *
28565924 AGATA-TTGTAGCAGAGCCACCAGAAC
1 AGATATTTGTGGCATAGCCACCAAAAC
*
28565950 AGATATTTGTGGCGTAGCCACCAAAAAC
1 AGATATTTGTGGCATAGCCACC-AAAAC
*
28565978 AGATGTTTGTGGCATAGCCAC
1 AGATATTTGTGGCATAGCCAC
28565999 TAGAACGCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.12
27 13 0.32
28 23 0.56
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (27 bp):
AGATATTTGTGGCATAGCCACCAAAAC
Found at i:28566323 original size:21 final size:22
Alignment explanation
Indices: 28566292--28566332 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28566282 GAATGTGTTG
*
28566292 TGATGTATGTGGAAATGAAATA
1 TGATGTATGTGCAAATGAAATA
*
28566314 TGAT-TATGTGCCAATGAAA
1 TGATGTATGTGCAAATGAAA
28566333 CATAAATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (22 bp):
TGATGTATGTGCAAATGAAATA
Found at i:28583322 original size:42 final size:43
Alignment explanation
Indices: 28583263--28583376 Score: 131
Period size: 53 Copynumber: 2.4 Consensus size: 43
28583253 AATACTCAAT
28583263 ATCTCGCACACTAAGTGCCGAAGC-ATAGCTGAAGCTATTATA
1 ATCTCGCACACTAAGTGCCGAAGCTATAGCTGAAGCTATTATA
28583305 ATCTCGCACACTAAGTGCCTTTCATAGCCGAAGCTATAGCTGAAGCTATTATA
1 ATCTCGCACACTAA--G-------T-GCCGAAGCTATAGCTGAAGCTATTATA
28583358 ATCTCGCACACTAAGTGCC
1 ATCTCGCACACTAAGTGCC
28583377 TTTCATAGCC
Statistics
Matches: 61, Mismatches: 0, Indels: 21
0.74 0.00 0.26
Matches are distributed among these distances:
42 14 0.23
43 3 0.05
44 2 0.03
51 2 0.03
52 8 0.13
53 32 0.52
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
ATCTCGCACACTAAGTGCCGAAGCTATAGCTGAAGCTATTATA
Found at i:28583358 original size:53 final size:53
Alignment explanation
Indices: 28583279--28583394 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
28583269 CACACTAAGT
28583279 GCCGAAGC-ATAGCTGAAGCTATTATAATCTCGCACACTAAGTGCCTTTCATA
1 GCCGAAGCTATAGCTGAAGCTATTATAATCTCGCACACTAAGTGCCTTTCATA
28583331 GCCGAAGCTATAGCTGAAGCTATTATAATCTCGCACACTAAGTGCCTTTCATA
1 GCCGAAGCTATAGCTGAAGCTATTATAATCTCGCACACTAAGTGCCTTTCATA
28583384 GCCGAAGCTAT
1 GCCGAAGCTAT
28583395 CTCAGTCTCA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 8 0.13
53 55 0.87
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (53 bp):
GCCGAAGCTATAGCTGAAGCTATTATAATCTCGCACACTAAGTGCCTTTCATA
Found at i:28585306 original size:23 final size:25
Alignment explanation
Indices: 28585280--28585334 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
28585270 ACCATAAATA
28585280 ATAT-TAAAT-AAATTTTTACACAT
1 ATATATAAATGAAATTTTTACACAT
**
28585303 ATATATTCATGAAATTTTTACACAT
1 ATATATAAATGAAATTTTTACACAT
28585328 ATATATA
1 ATATATA
28585335 TTTACATGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 4 0.15
24 3 0.11
25 20 0.74
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (25 bp):
ATATATAAATGAAATTTTTACACAT
Found at i:28586711 original size:42 final size:42
Alignment explanation
Indices: 28586590--28586777 Score: 146
Period size: 42 Copynumber: 4.4 Consensus size: 42
28586580 TGATTTCTGA
* * * * * *
28586590 TATTTGATTTCATGTAAGACTATGTCTGGGACGTTGGCATC-
1 TATTTGATTACGTGTAAGGCTTTGTCTGGGACATCGGCATCG
* * * * * *
28586631 AATTTGAGATTATGTGTAAGACTATGTCCGGGACATCGGCATTG
1 TATTT--GATTACGTGTAAGGCTTTGTCTGGGACATCGGCATCG
*
28586675 TATTTGATTACGTGTAAGGCTTTGTCTGGGAGATCGGCATCG
1 TATTTGATTACGTGTAAGGCTTTGTCTGGGACATCGGCATCG
* * * * *
28586717 TATTTGATTTCGTGTTAGGCCTTGTCTAGGATAGT-GGCATCG
1 TATTTGATTACGTGTAAGGCTTTGTCTGGGACA-TCGGCATCG
* *
28586759 ATATTTAATTACATGTAAG
1 -TATTTGATTACGTGTAAG
28586778 ACCACGTCTG
Statistics
Matches: 118, Mismatches: 24, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
41 4 0.03
42 66 0.56
43 44 0.37
44 4 0.03
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.37
Consensus pattern (42 bp):
TATTTGATTACGTGTAAGGCTTTGTCTGGGACATCGGCATCG
Found at i:28588518 original size:29 final size:28
Alignment explanation
Indices: 28588477--28588622 Score: 145
Period size: 29 Copynumber: 5.1 Consensus size: 28
28588467 GTGAGCATGA
28588477 ATAT-AATGTGATTTGGGCCAGATGGGCC
1 ATATAAATGTGA-TTGGGCCAGATGGGCC
* *
28588505 ATATAAATGAGATTGGGTCTA-ATGGGCC
1 ATATAAATGTGATTGGG-CCAGATGGGCC
*
28588533 ATATAAATGTGAATTGGGCCTGATGGGCC
1 ATATAAATGTG-ATTGGGCCAGATGGGCC
* * * * *
28588562 AAATGAACGTGAATTGGCCCGGATGGGCC
1 ATATAAATGTG-ATTGGGCCAGATGGGCC
*
28588591 ATATAAATGAGATTGGGCCTAG-TGGGCC
1 ATATAAATGTGATTGGGCC-AGATGGGCC
28588619 ATAT
1 ATAT
28588623 GCATGTATGT
Statistics
Matches: 97, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
28 44 0.45
29 53 0.55
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCAGATGGGCC
Found at i:28596229 original size:29 final size:29
Alignment explanation
Indices: 28596144--28596290 Score: 128
Period size: 29 Copynumber: 5.2 Consensus size: 29
28596134 GTGAGCATGA
*
28596144 ATATG-ATGTGATTTGGG-CTGGATGGGCC
1 ATATGAATGTGAATTGGGCCT-GATGGGCC
* * * **
28596172 ATATAAATGAG-ATTGGGCCTAATAAGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
28596200 ATATGAATGTGAATTGGGCCTGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
*
28596229 ATA-GAAACGTGAATT-GGCCTGAATGGGCC
1 ATATG-AATGTGAATTGGGCCTG-ATGGGCC
* *
28596258 ATATAAATGAG-ATTGGGCCT-AGTGGGCC
1 ATATGAATGTGAATTGGGCCTGA-TGGGCC
28596286 ATATG
1 ATATG
28596291 CAGGTATGTA
Statistics
Matches: 95, Mismatches: 16, Indels: 16
0.75 0.13 0.13
Matches are distributed among these distances:
27 1 0.01
28 43 0.45
29 51 0.54
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.27
Consensus pattern (29 bp):
ATATGAATGTGAATTGGGCCTGATGGGCC
Found at i:28596231 original size:57 final size:57
Alignment explanation
Indices: 28596144--28596289 Score: 151
Period size: 57 Copynumber: 2.6 Consensus size: 57
28596134 GTGAGCATGA
*
28596144 ATATG-ATGTGATTTGGG-CTGGATGGGCCATATAAA-TGAGATTGGGCCT-AATAAGCC
1 ATATGAATGTGAATTGGGCCT-GATGGGCCATATAAACTGA-ATT-GGCCTGAATAAGCC
* **
28596200 ATATGAATGTGAATTGGGCCTGATGGGCCATAGAAACGTGAATTGGCCTGAATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCCATATAAAC-TGAATTGGCCTGAATAAGCC
* *
28596258 ATATAAATGAG-ATTGGGCCT-AGTGGGCCATAT
1 ATATGAATGTGAATTGGGCCTGA-TGGGCCATAT
28596290 GCAGGTATGT
Statistics
Matches: 77, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
56 6 0.08
57 48 0.62
58 20 0.26
59 3 0.04
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.27
Consensus pattern (57 bp):
ATATGAATGTGAATTGGGCCTGATGGGCCATATAAACTGAATTGGCCTGAATAAGCC
Found at i:28600122 original size:18 final size:19
Alignment explanation
Indices: 28600099--28600141 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
28600089 TGTGAGTTGG
*
28600099 CCGTGTGGG-TTCACATGC
1 CCGTGTGGGATGCACATGC
*
28600117 CCGTGTGGGATGGACATGC
1 CCGTGTGGGATGCACATGC
28600136 CCGTGT
1 CCGTGT
28600142 CTTCAGCCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.12, C:0.26, G:0.37, T:0.26
Consensus pattern (19 bp):
CCGTGTGGGATGCACATGC
Found at i:28602159 original size:46 final size:45
Alignment explanation
Indices: 28602054--28602176 Score: 162
Period size: 46 Copynumber: 2.7 Consensus size: 45
28602044 ATATTCGTAC
*
28602054 CGATGCATGTCCCAGACATGTCTTACACTAGC-ACATCTCGTAGCT
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTACATCTC-TAGCT
* * *
28602099 -GATGTATTTCCCAGACATGTCTTACACTGGCTTACATCT-TAAGGT
1 CGATGCATGTCCCAGACATGTCTTACACTGGC-TACATCTCT-AGCT
28602144 CGATGCATGTCCCAGACATGTCTTACACTGGCT
1 CGATGCATGTCCCAGACATGTCTTACACTGGCT
28602177 CACGTAACAG
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
44 29 0.43
45 4 0.06
46 35 0.51
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.30
Consensus pattern (45 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTACATCTCTAGCT
Found at i:28605355 original size:16 final size:16
Alignment explanation
Indices: 28605334--28605370 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
28605324 ATGAATCTCC
*
28605334 ATTATCAATGCACATG
1 ATTATCAATCCACATG
*
28605350 ATTATCAATCCAGATG
1 ATTATCAATCCACATG
28605366 ATTAT
1 ATTAT
28605371 ATTTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (16 bp):
ATTATCAATCCACATG
Found at i:28608179 original size:14 final size:14
Alignment explanation
Indices: 28608160--28608192 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
28608150 ATTTATGCGA
28608160 TTAATTCCTTTTAT
1 TTAATTCCTTTTAT
28608174 TTAATTCCTTTTAT
1 TTAATTCCTTTTAT
28608188 TTAAT
1 TTAAT
28608193 CGGACACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (14 bp):
TTAATTCCTTTTAT
Found at i:28617998 original size:30 final size:30
Alignment explanation
Indices: 28617903--28617999 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
28617893 AGCTCACTCC
** * *
28617903 TAGCTCATTTTCAACTCGCGAGCTAAACCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * * * *
28617933 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
28617963 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
28617993 TAGCTCA
1 TAGCTCA
28618000 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:28620393 original size:16 final size:16
Alignment explanation
Indices: 28620374--28620415 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
28620364 AAGAGAAAAC
28620374 AAAGAAAAGAAAAGAA
1 AAAGAAAAGAAAAGAA
* *
28620390 AAAGAAAACAAAATAA
1 AAAGAAAAGAAAAGAA
28620406 AAAGAAAAGA
1 AAAGAAAAGA
28620416 GCGGCAAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (16 bp):
AAAGAAAAGAAAAGAA
Found at i:28620539 original size:30 final size:30
Alignment explanation
Indices: 28620497--28620577 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
28620487 TTGGAAAACA
*
28620497 AAAAAG-GAAATGAAAAAGAAAATGAGATTG
1 AAAAAGAG-AATGAAAAAGAAAATGAGAGTG
* ***
28620527 AAAAAGAGAATGAAGAAGAGTTTGAGAGTG
1 AAAAAGAGAATGAAAAAGAAAATGAGAGTG
28620557 AAAAAGA-AGATGAAAAAGAAA
1 AAAAAGAGA-ATGAAAAAGAAA
28620578 TTGAAACAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 1 0.02
30 39 0.95
31 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (30 bp):
AAAAAGAGAATGAAAAAGAAAATGAGAGTG
Found at i:28628537 original size:21 final size:21
Alignment explanation
Indices: 28628513--28628566 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
28628503 AAAACAGGGC
28628513 ACACGCCCGTGTGGAAGGGTA
1 ACACGCCCGTGTGGAAGGGTA
*
28628534 ACACGCCCGTGTTGAAGGGTA
1 ACACGCCCGTGTGGAAGGGTA
* *
28628555 ACATGCTCGTGT
1 ACACGCCCGTGT
28628567 CCCACATCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.20
Consensus pattern (21 bp):
ACACGCCCGTGTGGAAGGGTA
Found at i:28629867 original size:26 final size:26
Alignment explanation
Indices: 28629838--28629911 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 26
28629828 AATGCTTGGA
28629838 TATTATATAAATTGTATATACGTGAC
1 TATTATATAAATTGTATATACGTGAC
*
28629864 TATTGT-T--A-TGT-T-TGAC--GA-
1 TATTATATAAATTGTATAT-ACGTGAC
28629882 TATTATATAAATTGTATATACGTGAC
1 TATTATATAAATTGTATATACGTGAC
28629908 TATT
1 TATT
28629912 GTTATGTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 20
0.62 0.03 0.34
Matches are distributed among these distances:
18 5 0.14
19 3 0.08
20 1 0.03
21 4 0.11
22 6 0.17
23 4 0.11
24 1 0.03
25 3 0.08
26 9 0.25
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.46
Consensus pattern (26 bp):
TATTATATAAATTGTATATACGTGAC
Found at i:28629885 original size:44 final size:44
Alignment explanation
Indices: 28629836--28629925 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
28629826 TTAATGCTTG
*
28629836 GATATTATATAAATTGTATATACGTGACTATTGTTATGTTTGAC
1 GATATTATATAAATTGTATATACGTGACTATTGTTATGTTTAAC
28629880 GATATTATATAAATTGTATATACGTGACTATTGTTATGTTTAAC
1 GATATTATATAAATTGTATATACGTGACTATTGTTATGTTTAAC
28629924 GA
1 GA
28629926 CATATCGACT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (44 bp):
GATATTATATAAATTGTATATACGTGACTATTGTTATGTTTAAC
Found at i:28630078 original size:28 final size:28
Alignment explanation
Indices: 28630047--28630103 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
28630037 AATGTGAAAA
* * *
28630047 ATATTAAGAATGGTACTTGGTGTGCGAG
1 ATATTAAGAATGGCACTTAGTGTACGAG
* *
28630075 ATATTGAGTATGGCACTTAGTGTACGAG
1 ATATTAAGAATGGCACTTAGTGTACGAG
28630103 A
1 A
28630104 CATCGAAGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32
Consensus pattern (28 bp):
ATATTAAGAATGGCACTTAGTGTACGAG
Found at i:28633609 original size:28 final size:30
Alignment explanation
Indices: 28633578--28633638 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
28633568 AAAGTGATTT
*
28633578 TTGACAAAAATGTCAATT-A-GGGATTAAA
1 TTGACAAAAATGTAAATTGAGGGGATTAAA
* * *
28633606 TTGAGAAAAGTGTAAATTGAGGGGGTTAAA
1 TTGACAAAAATGTAAATTGAGGGGATTAAA
28633636 TTG
1 TTG
28633639 TGAAATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 15 0.56
29 1 0.04
30 11 0.41
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.30
Consensus pattern (30 bp):
TTGACAAAAATGTAAATTGAGGGGATTAAA
Found at i:28634275 original size:43 final size:43
Alignment explanation
Indices: 28634117--28634283 Score: 142
Period size: 43 Copynumber: 3.9 Consensus size: 43
28634107 GGTTATTGAG
* * *
28634117 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTG-T
1 ATGTGATTACATGTAAGACCATATCTGGGACAATGGCATCGAT
* * * *
28634159 ATTGAGATTACGTGTAAGACCATGTCTGGGACATTGGCATC-ATT
1 A-TGTGATTACATGTAAGACCATATCTGGGACAATGGCATCGA-T
* * * * * * * *
28634203 ATTTAATTTCGTATAAGTCCCTATTTGGGACAATGGCATCGAT
1 ATGTGATTACATGTAAGACCATATCTGGGACAATGGCATCGAT
* *
28634246 ATGTGATAACATGTAAGACCATATCTGGGA-TATGGCAT
1 ATGTGATTACATGTAAGACCATATCTGGGACAATGGCAT
28634284 TGTATGAACT
Statistics
Matches: 98, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
42 8 0.08
43 87 0.89
44 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (43 bp):
ATGTGATTACATGTAAGACCATATCTGGGACAATGGCATCGAT
Found at i:28636822 original size:79 final size:80
Alignment explanation
Indices: 28636654--28636835 Score: 210
Period size: 79 Copynumber: 2.3 Consensus size: 80
28636644 GCTACTCGTT
* * *
28636654 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAA-GCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAG
* *
28636719 ATTTAGTAACTCGCAC
65 ATATAGTAACTAGCAC
* **
28636735 CAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCA
1 CAAAGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCA
* *
28636797 GATATGGTCACTTAGCA-
64 GATATAGTAAC-TAGCAC
28636814 CAAAGCCTTCGGGACTTAGCCC
1 CAAAGCCTTCGGGACTTAGCCC
28636836 AGACATCATT
Statistics
Matches: 86, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
78 4 0.05
79 58 0.67
80 21 0.24
81 3 0.03
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGA
TATAGTAACTAGCAC
Found at i:28636838 original size:40 final size:40
Alignment explanation
Indices: 28636635--28636835 Score: 223
Period size: 40 Copynumber: 5.0 Consensus size: 40
28636625 CAGAATTTAA
** *
28636635 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28636675 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28636715 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
28636754 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * * *
28636794 CCAGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
28636834 CC
1 CC
28636836 AGACATCATT
Statistics
Matches: 137, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 90 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:28637999 original size:56 final size:56
Alignment explanation
Indices: 28637932--28638051 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
28637922 TATTAGTTTA
28637932 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
28637988 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
28638044 TTGCCCAT
1 TTGCCCAT
28638052 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:28639264 original size:17 final size:17
Alignment explanation
Indices: 28639224--28639267 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
28639214 AAATAAACAT
*
28639224 AAAAATAAACACCTAAA
1 AAAAATAAACAACTAAA
28639241 AAGAAATAAA-AACTAAA
1 AA-AAATAAACAACTAAA
28639258 GAAAAATAAA
1 -AAAAATAAA
28639268 TTCCCCCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.75, C:0.09, G:0.05, T:0.11
Consensus pattern (17 bp):
AAAAATAAACAACTAAA
Found at i:28641695 original size:19 final size:20
Alignment explanation
Indices: 28641658--28641695 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28641648 ATAAGGTGGT
28641658 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
28641678 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
28641696 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:28649954 original size:29 final size:29
Alignment explanation
Indices: 28649894--28650085 Score: 228
Period size: 29 Copynumber: 6.6 Consensus size: 29
28649884 GATAGTCAAA
*
28649894 ACCATCCCTTTTTCATATTCGATAGT-TGTC
1 ACCATCCC-TTTTCATATTTGATAGTCT-TC
*
28649924 ACCATCCCTTTTCATATTTGATGGTCTTC
1 ACCATCCCTTTTCATATTTGATAGTCTTC
* * **
28649953 ACCATCCATTTTCATATTTGATGGTC-GA
1 ACCATCCCTTTTCATATTTGATAGTCTTC
* * *
28649981 AACATCCCTTTTCATATTCGACAGT-TGTC
1 ACCATCCCTTTTCATATTTGATAGTCT-TC
* *
28650010 ACCATCCCTTTTCATATTTGATGGTCATC
1 ACCATCCCTTTTCATATTTGATAGTCTTC
*
28650039 ACCATCCCTTTTCATATTTGATAGTCGTC
1 ACCATCCCTTTTCATATTTGATAGTCTTC
28650068 ACCATCCCTTTTCATATT
1 ACCATCCCTTTTCATATT
28650086 GATTGGCGTC
Statistics
Matches: 139, Mismatches: 19, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
28 20 0.14
29 110 0.79
30 9 0.06
ACGTcount: A:0.21, C:0.27, G:0.10, T:0.42
Consensus pattern (29 bp):
ACCATCCCTTTTCATATTTGATAGTCTTC
Found at i:28650051 original size:86 final size:87
Alignment explanation
Indices: 28649883--28650085 Score: 311
Period size: 86 Copynumber: 2.3 Consensus size: 87
28649873 GTGTGCTAAA
* *
28649883 TGATAGTC-AAAACCATCCCTTTTTCATATTCGATAGTTGTCACCATCCCTTTTCATATTTGATG
1 TGATAGTCGTAAA-CATCCC-TTTTCATATTCGACAGTTGTCACCATCCCTTTTCATATTTGATG
*
28649947 GTCTTCACCATCCATTTTCATATT
64 GTCATCACCATCCATTTTCATATT
*
28649971 TGATGGTCG-AAACATCCCTTTTCATATTCGACAGTTGTCACCATCCCTTTTCATATTTGATGGT
1 TGATAGTCGTAAACATCCCTTTTCATATTCGACAGTTGTCACCATCCCTTTTCATATTTGATGGT
*
28650035 CATCACCATCCCTTTTCATATT
66 CATCACCATCCATTTTCATATT
* *
28650057 TGATAGTCGTCACCATCCCTTTTCATATT
1 TGATAGTCGTAAACATCCCTTTTCATATT
28650086 GATTGGCGTC
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
86 73 0.69
87 23 0.22
88 10 0.09
ACGTcount: A:0.23, C:0.26, G:0.10, T:0.41
Consensus pattern (87 bp):
TGATAGTCGTAAACATCCCTTTTCATATTCGACAGTTGTCACCATCCCTTTTCATATTTGATGGT
CATCACCATCCATTTTCATATT
Found at i:28652452 original size:37 final size:37
Alignment explanation
Indices: 28652402--28652477 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
28652392 ATGAAAGCCT
28652402 TATAGAACAAATCTTACAACAACTTCTTTTTATCTGG
1 TATAGAACAAATCTTACAACAACTTCTTTTTATCTGG
28652439 TATAGAACAAATCTTACAACAACTTCTTTTTATCTGG
1 TATAGAACAAATCTTACAACAACTTCTTTTTATCTGG
28652476 TA
1 TA
28652478 AACTTAAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (37 bp):
TATAGAACAAATCTTACAACAACTTCTTTTTATCTGG
Found at i:28656570 original size:51 final size:51
Alignment explanation
Indices: 28656510--28656612 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
28656500 CTTGACATCT
** * *
28656510 TGTAATAGCCTGTTTTCAGTGAAATT-GAAACAGTGGTTCTGGGACCACAAA
1 TGTAATAGCCCATTTTCAGTCAAATTAG-AACAGTGGTTCTGAGACCACAAA
* * *
28656561 TGTAATAGCCCATTTTTAGTCAAATTAGAATAGTGGTTTTGAGACCACAAA
1 TGTAATAGCCCATTTTCAGTCAAATTAGAACAGTGGTTCTGAGACCACAAA
28656612 T
1 T
28656613 TCGACGTCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (51 bp):
TGTAATAGCCCATTTTCAGTCAAATTAGAACAGTGGTTCTGAGACCACAAA
Found at i:28659403 original size:21 final size:20
Alignment explanation
Indices: 28659374--28659413 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
28659364 CTTTGAAACA
* *
28659374 GGGCACACGTCTGTGTGGAT
1 GGGCACACGCCCGTGTGGAT
28659394 GGGCAACACGCCCGTGTGGA
1 GGGC-ACACGCCCGTGTGGA
28659414 ACTTGAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.17, C:0.25, G:0.40, T:0.17
Consensus pattern (20 bp):
GGGCACACGCCCGTGTGGAT
Found at i:28671701 original size:41 final size:41
Alignment explanation
Indices: 28671641--28671723 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
28671631 TATATAGGAC
28671641 TTAAATTAAAGTTTAGAAGACAATTGATTCAAACTTTTTTT
1 TTAAATTAAAGTTTAGAAGACAATTGATTCAAACTTTTTTT
*
28671682 TTAAATTAAAGTTTGGAAGACAATTGATTCAAACTTTTTTT
1 TTAAATTAAAGTTTAGAAGACAATTGATTCAAACTTTTTTT
28671723 T
1 T
28671724 CCTTATTTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (41 bp):
TTAAATTAAAGTTTAGAAGACAATTGATTCAAACTTTTTTT
Found at i:28671815 original size:23 final size:23
Alignment explanation
Indices: 28671789--28671838 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
28671779 ATGCAATATA
*
28671789 TGAATTAAAAGCATTTATTATGT
1 TGAAGTAAAAGCATTTATTATGT
* *
28671812 TGAAGTACAATCATTTATTATGT
1 TGAAGTAAAAGCATTTATTATGT
28671835 TGAA
1 TGAA
28671839 AATAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (23 bp):
TGAAGTAAAAGCATTTATTATGT
Found at i:28682619 original size:5 final size:5
Alignment explanation
Indices: 28682609--28682634 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28682599 ACACTAGAAC
28682609 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
28682635 TAATTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:28682878 original size:2 final size:2
Alignment explanation
Indices: 28682873--28682903 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28682863 AGGGGGAAGG
28682873 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
28682904 GGGAGCGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28687558 original size:19 final size:19
Alignment explanation
Indices: 28687552--28687588 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28687542 TGAAAAAAAT
28687552 AGAAAAAACTAAAAAATAA
1 AGAAAAAACTAAAAAATAA
* *
28687571 AGAAAAAATTTAAAAATA
1 AGAAAAAACTAAAAAATA
28687589 TTTTTTTGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (19 bp):
AGAAAAAACTAAAAAATAA
Found at i:28690848 original size:20 final size:20
Alignment explanation
Indices: 28690815--28690874 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
28690805 GAAAACTATA
28690815 AATTTA-AC-TAATAATTAT
1 AATTTATACATAATAATTAT
*
28690833 AATTTATACATAATAA-GAT
1 AATTTATACATAATAATTAT
*
28690852 AAATTGATA-ATAA-AATTAT
1 -AATTTATACATAATAATTAT
28690871 AATT
1 AATT
28690875 ATTTTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 12 0.34
19 10 0.29
20 13 0.37
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (20 bp):
AATTTATACATAATAATTAT
Found at i:28699552 original size:49 final size:49
Alignment explanation
Indices: 28699495--28699592 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
28699485 ATAAGATTTC
*
28699495 ATCCTAGACTAATGAAATTATTAAACTATTGCTTGTGAATAGACCAAGT
1 ATCCTAGACTAATGAAATTATTAAACTACTGCTTGTGAATAGACCAAGT
* * *
28699544 ATCCTAGACTACTGAAATTATTAACCTACTGCTTGTGAATAGACTAAGT
1 ATCCTAGACTAATGAAATTATTAAACTACTGCTTGTGAATAGACCAAGT
28699593 GCTTGGAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (49 bp):
ATCCTAGACTAATGAAATTATTAAACTACTGCTTGTGAATAGACCAAGT
Found at i:28700439 original size:15 final size:17
Alignment explanation
Indices: 28700414--28700448 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
28700404 TAAAATATAT
28700414 AAAGTAAAT-AAAAGAA
1 AAAGTAAATAAAAAGAA
28700430 AAAG-AAATAAAAAGAA
1 AAAGTAAATAAAAAGAA
28700446 AAA
1 AAA
28700449 AAGCAAGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (17 bp):
AAAGTAAATAAAAAGAA
Found at i:28704651 original size:18 final size:18
Alignment explanation
Indices: 28704614--28704652 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28704604 TTGGAAATCA
*
28704614 AAATTATTAAAAGATGAT
1 AAATTATTAAAAGATAAT
28704632 AAATTATTAAATAGA-AAT
1 AAATTATTAAA-AGATAAT
28704650 AAA
1 AAA
28704653 AATCATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (18 bp):
AAATTATTAAAAGATAAT
Found at i:28705444 original size:7 final size:7
Alignment explanation
Indices: 28705434--28705460 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28705424 GATAATGTCC
28705434 GATAAAT
1 GATAAAT
28705441 GATAAAT
1 GATAAAT
28705448 GATAAAT
1 GATAAAT
28705455 GATAAA
1 GATAAA
28705461 AATGTTACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (7 bp):
GATAAAT
Found at i:28706323 original size:60 final size:60
Alignment explanation
Indices: 28706250--28706491 Score: 475
Period size: 60 Copynumber: 4.0 Consensus size: 60
28706240 ATATAAGAGA
28706250 TGATTTATACATGTTAAGTGAATACATGTTATGGAAAGCATATGTGCATGGAAACTTAAT
1 TGATTTATACATGTTAAGTGAATACATGTTATGGAAAGCATATGTGCATGGAAACTTAAT
28706310 TGATTTATACATGTTAAGTGAATACATGTTATGGAAAGCATATGTGCATGGAAACTTAAT
1 TGATTTATACATGTTAAGTGAATACATGTTATGGAAAGCATATGTGCATGGAAACTTAAT
28706370 TGATTTATACATGTTAAGTGAATACATGTTATGGAAAGCATATGTGCATGGAAACTTAAT
1 TGATTTATACATGTTAAGTGAATACATGTTATGGAAAGCATATGTGCATGGAAACTTAAT
*
28706430 TGATTTATACATGTTAAGTGAATACATGTTATGGAAAGCATATGTGCATGGAAACTTGAT
1 TGATTTATACATGTTAAGTGAATACATGTTATGGAAAGCATATGTGCATGGAAACTTAAT
28706490 TG
1 TG
28706492 TTTGTTGAGC
Statistics
Matches: 181, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 181 1.00
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (60 bp):
TGATTTATACATGTTAAGTGAATACATGTTATGGAAAGCATATGTGCATGGAAACTTAAT
Found at i:28710173 original size:43 final size:42
Alignment explanation
Indices: 28710106--28710282 Score: 185
Period size: 43 Copynumber: 4.1 Consensus size: 42
28710096 ATTTTGTACA
* * * *
28710106 ATGCCAACGTCCCTGACGTGGTCTTACATGTAATCTCATACCG
1 ATGCCAACGTCCCAGAC-AGGTCTTACATGTAATCACATATCG
* * *
28710149 ATGCC-ACTGTCCCAGACAGAGTCTTACTTTTAAACACATATCG
1 ATGCCAAC-GTCCCAGACAG-GTCTTACATGTAATCACATATCG
* * *
28710192 ATGCCAACGTCCCAGACGTGGTCTTAAACGTAATCACATATCG
1 ATGCCAACGTCCCAGAC-AGGTCTTACATGTAATCACATATCG
* * *
28710235 ATGCCAACGTCCCAGACATGGTCTTACACGAAATCACATATCA
1 ATGCCAACGTCCCAGACA-GGTCTTACATGTAATCACATATCG
28710278 ATGCC
1 ATGCC
28710283 TCATATACAT
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
42 3 0.03
43 106 0.95
44 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACAGGTCTTACATGTAATCACATATCG
Found at i:28710273 original size:86 final size:86
Alignment explanation
Indices: 28710104--28710282 Score: 229
Period size: 86 Copynumber: 2.1 Consensus size: 86
28710094 ATATTTTGTA
* * * *
28710104 CAATGCCAACGTCCCTGACGTGGTCTTACATGTAATCTCATACCGATGCCACTGTCCCAGACAGA
1 CAATGCCAACGTCCCAGACGTGGTCTTAAACGTAATCACATACCGATGCCACTGTCCCAGACAGA
***
28710169 GTCTTACTTTTAAACACATAT
66 GTCTTACTACGAAACACATAT
* *
28710190 CGATGCCAACGTCCCAGACGTGGTCTTAAACGTAATCACATATCGATGCCAAC-GTCCCAGACAT
1 CAATGCCAACGTCCCAGACGTGGTCTTAAACGTAATCACATACCGATGCC-ACTGTCCCAGACA-
28710254 G-GTCTTAC-ACGAAATCACATAT
64 GAGTCTTACTACGAAA-CACATAT
28710276 CAATGCC
1 CAATGCC
28710283 TCATATACAT
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
85 3 0.04
86 74 0.93
87 3 0.04
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.25
Consensus pattern (86 bp):
CAATGCCAACGTCCCAGACGTGGTCTTAAACGTAATCACATACCGATGCCACTGTCCCAGACAGA
GTCTTACTACGAAACACATAT
Found at i:28711056 original size:15 final size:15
Alignment explanation
Indices: 28711033--28711063 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28711023 TCAAAAATTC
28711033 CAATACAAAACATAT
1 CAATACAAAACATAT
*
28711048 CAATCCAAAACATAT
1 CAATACAAAACATAT
28711063 C
1 C
28711064 TTTCATATTT
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:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (15 bp):
CAATACAAAACATAT
Found at i:28715738 original size:48 final size:50
Alignment explanation
Indices: 28715622--28715752 Score: 185
Period size: 48 Copynumber: 2.7 Consensus size: 50
28715612 CGAAATCGAG
* * * * *
28715622 GCCGACGCCATGTCCCAGACATGGTCTTATACTAGCTCTCACATATTCGT
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCACTCACATATGCGT
* *
28715672 GCCGATGCTATGTCCCAAACATGGTCTTACACTAGCAC-CTC-TATGCGT
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCACTCACATATGCGT
28715720 GCCGATGCCATGTCCCAAACATGGTCTTACACT
1 GCCGATGCCATGTCCCAAACATGGTCTTACACT
28715753 GACACATCTC
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
48 38 0.52
49 2 0.03
50 33 0.45
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (50 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCACTCACATATGCGT
Found at i:28715820 original size:46 final size:46
Alignment explanation
Indices: 28715720--28715934 Score: 172
Period size: 46 Copynumber: 4.7 Consensus size: 46
28715710 CTCTATGCGT
* * * *
28715720 GCCGATGCCATGTCCCAAACATGGTCTTACACT-G-ACACATCTCGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATCTC-AAG
* *
28715766 GCCAATGCATGTCCTAGACATGTCTTACACTGGCT-TACATCTCAAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATCTCAAG
* * * * *
28715812 GCCGATGCATGTCCCAAAAATGTCTTACACTAGCTCTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAAG
* * * * * *
28715858 GCCGA-CCATGTCCAAGACATGGTCTTGCATTGGCTCTCATAAT-ATG
1 GCCGATGCATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTCAAG
*
28715904 GTCGATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
28715935 AGCGCACAAA
Statistics
Matches: 132, Mismatches: 29, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
44 10 0.08
45 25 0.19
46 82 0.62
47 15 0.11
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAAG
Found at i:28721574 original size:9 final size:9
Alignment explanation
Indices: 28721562--28721596 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
28721552 AGGAATCAGA
28721562 GGAGGTGGG
1 GGAGGTGGG
28721571 GGAGGTGGG
1 GGAGGTGGG
28721580 GGAGGTGGG
1 GGAGGTGGG
28721589 GGAGGTGG
1 GGAGGTGG
28721597 AGTGTTCGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.11, C:0.00, G:0.77, T:0.11
Consensus pattern (9 bp):
GGAGGTGGG
Found at i:28723385 original size:49 final size:51
Alignment explanation
Indices: 28723313--28723443 Score: 171
Period size: 49 Copynumber: 2.6 Consensus size: 51
28723303 AGGGTGTAAT
*
28723313 GCCGATGCCATGTCCCAAACATGGTCTTACACTGA-CTATCA-AAATCGAG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGAGCTATCACAAATCCAG
* * * *
28723362 GCCGATGCCATGTCCCAAACATGGTCTTACA-TTAGCTCTCACAGATCCAT
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGAGCTATCACAAATCCAG
* *
28723412 GCCGATGGCAT-TCCCAAACAGGGTCTTACACT
1 GCCGATGCCATGTCCCAAACATGGTCTTACACT
28723444 AGAATCTCTA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
48 2 0.03
49 54 0.75
50 16 0.22
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (51 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTGAGCTATCACAAATCCAG
Found at i:28723546 original size:46 final size:46
Alignment explanation
Indices: 28723476--28723633 Score: 182
Period size: 46 Copynumber: 3.4 Consensus size: 46
28723466 CCTTGTCCCT
*
28723476 GACATGGTCTTACACTGAC--ACATCTCGTAGCCGATGCATGTCCTA
1 GACATGGTCTTACACTGGCTTACATCTCG-AGCCGATGCATGTCCTA
* *
28723521 GACAT-GTCTTACACTGGCTTACATCTCGAGTCCGATACATGTCCAA
1 GACATGGTCTTACACTGGCTTACATCTCGAG-CCGATGCATGTCCTA
* * *
28723567 GACAT-GTCTTACACTAGCTCT-CATCTCAATGCCGATGCCATGTCGTA
1 GACATGGTCTTACACTGGCT-TACATCTCGA-GCCGATG-CATGTCCTA
28723614 GACATGGTCTTACACTGGCT
1 GACATGGTCTTACACTGGCT
28723634 CTCATAATTT
Statistics
Matches: 97, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
44 12 0.12
45 7 0.07
46 51 0.53
47 14 0.14
48 13 0.13
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (46 bp):
GACATGGTCTTACACTGGCTTACATCTCGAGCCGATGCATGTCCTA
Found at i:28723635 original size:48 final size:45
Alignment explanation
Indices: 28723496--28723675 Score: 168
Period size: 46 Copynumber: 3.9 Consensus size: 45
28723486 TACACTGACA
*
28723496 CATCTCGTAGCCGATGCATGTCCTAGACATGTCTTACACTGGCT-T
1 CATCTCAT-GCCGATGCATGTCCTAGACATGTCTTACACTGGCTCT
* * *
28723541 ACATCTCGA-GTCCGATACATGTCCAAGACATGTCTTACACTAGCTCT
1 -CATCTC-ATG-CCGATGCATGTCCTAGACATGTCTTACACTGGCTCT
*
28723588 CATCTCAATGCCGATGCCATGTCGTAGACATGGTCTTACACTGGCTCT
1 CATCTC-ATGCCGATG-CATGTCCTAGACAT-GTCTTACACTGGCTCT
* * * * *
28723636 CATAAT-TTGGTCGGTGCATGTCCCAGACATGTCTTACACT
1 CAT-CTCAT-GCCGATGCATGTCCTAGACATGTCTTACACT
28723676 AGCGCACAAA
Statistics
Matches: 111, Mismatches: 15, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
45 1 0.01
46 59 0.53
47 27 0.24
48 23 0.21
49 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (45 bp):
CATCTCATGCCGATGCATGTCCTAGACATGTCTTACACTGGCTCT
Found at i:28726168 original size:5 final size:5
Alignment explanation
Indices: 28726158--28726283 Score: 184
Period size: 5 Copynumber: 25.2 Consensus size: 5
28726148 AAGTATAACT
* * * *
28726158 TATCA TATCA TAACA TAT-A GTATCA TACCA TA-CAA TACCA TATCA TACCA
1 TATCA TATCA TATCA TATCA -TATCA TATCA TATC-A TATCA TATCA TATCA
28726208 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
28726258 TATCA TATCA TATCA TATCA TATCA T
1 TATCA TATCA TATCA TATCA TATCA T
28726284 GTCCTAGCCC
Statistics
Matches: 111, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
4 2 0.02
5 107 0.96
6 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (5 bp):
TATCA
Found at i:28726855 original size:20 final size:19
Alignment explanation
Indices: 28726826--28726863 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
28726816 GTATAGAAAA
28726826 AGAAAAGGGAACAAAAGAG
1 AGAAAAGGGAACAAAAGAG
*
28726845 AGAACAAGGGAATAAAAGA
1 AGAA-AAGGGAACAAAAGA
28726864 TATGTGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.63, C:0.05, G:0.29, T:0.03
Consensus pattern (19 bp):
AGAAAAGGGAACAAAAGAG
Found at i:28733532 original size:29 final size:28
Alignment explanation
Indices: 28733491--28733545 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
28733481 ATCCGACATA
**
28733491 CTGATATCATGGCCTGAAGCCAAATCAG
1 CTGATATCATGGCCCAAAGCCAAATCAG
28733519 CTGATATTCATGGCCCAAAGCCAAATC
1 CTGATA-TCATGGCCCAAAGCCAAATC
28733546 GCTATAACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (28 bp):
CTGATATCATGGCCCAAAGCCAAATCAG
Found at i:28733587 original size:77 final size:77
Alignment explanation
Indices: 28733494--28733667 Score: 260
Period size: 77 Copynumber: 2.3 Consensus size: 77
28733484 CGACATACTG
*
28733494 ATATCATGGCCTGAAGCCAAATCAG-CTGATATTCATGGCCCAAAGCCAAATCGCTATAACTCGC
1 ATATCATGGCCCGAAGCCAAATCAGCCT-ATATTCATGGCCCAAAGCCAAATCGCTATAACTCGC
* **
28733558 ATCTGAATTGCTA
65 ACCTGAAGAGCTA
* * * *
28733571 ATATTATGTCCCGAAGCCAAATCAGCCTATATTCATGGCCCAAAGCCAAATCGGTATAACTTGCA
1 ATATCATGGCCCGAAGCCAAATCAGCCTATATTCATGGCCCAAAGCCAAATCGCTATAACTCGCA
28733636 CCTGAAGAGCTA
66 CCTGAAGAGCTA
28733648 ATATCATGGCCCGAAGCCAA
1 ATATCATGGCCCGAAGCCAA
28733668 CTCAATGTAT
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
77 84 0.98
78 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.23
Consensus pattern (77 bp):
ATATCATGGCCCGAAGCCAAATCAGCCTATATTCATGGCCCAAAGCCAAATCGCTATAACTCGCA
CCTGAAGAGCTA
Found at i:28740202 original size:17 final size:17
Alignment explanation
Indices: 28740180--28740213 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28740170 TACAAAATGA
28740180 GAGATTTATCCCAAGCC
1 GAGATTTATCCCAAGCC
28740197 GAGATTTATCCCAAGCC
1 GAGATTTATCCCAAGCC
28740214 AACACATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (17 bp):
GAGATTTATCCCAAGCC
Found at i:28740798 original size:47 final size:45
Alignment explanation
Indices: 28740733--28740857 Score: 132
Period size: 47 Copynumber: 2.7 Consensus size: 45
28740723 TCTCGTAGCC
*
28740733 GATGCATGTCCCAGACATGTCTTACACTAGCACTCGTC-TCAATGCT-
1 GATGCATGTCCCAAACATGTCTTACACTAGCACTC-TCAT-AATG-TG
*
28740779 GATGCCATGTCCCAAACATGGTCTTACACT-G-GCTCTCATAATGTG
1 GATG-CATGTCCCAAACAT-GTCTTACACTAGCACTCTCATAATGTG
28740824 GCCTATGCATGTCCCAAACATGTCTTACACTAGC
1 G---ATGCATGTCCCAAACATGTCTTACACTAGC
28740858 TCACACAAGT
Statistics
Matches: 68, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
44 1 0.01
45 7 0.10
46 18 0.26
47 29 0.43
48 13 0.19
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (45 bp):
GATGCATGTCCCAAACATGTCTTACACTAGCACTCTCATAATGTG
Found at i:28754624 original size:18 final size:20
Alignment explanation
Indices: 28754592--28754642 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 20
28754582 GTTAATTTCA
*
28754592 ATTTTTTAATATTATTTAAT
1 ATTTTTTAATATTATGTAAT
28754612 ATTTTTT-AT-TTATGTAAT
1 ATTTTTTAATATTATGTAAT
*
28754630 -TTTAATTAATATT
1 ATTT-TTTAATATT
28754643 TTTTTATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 3 0.12
18 10 0.38
19 4 0.15
20 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
ATTTTTTAATATTATGTAAT
Found at i:28755468 original size:45 final size:45
Alignment explanation
Indices: 28755392--28755480 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 45
28755382 GCTAAAATTT
* * ** *
28755392 TATTTAATTAGGTGGAAACTTTTTGTCAGTTATGGGGGAATACCA
1 TATTTAAATAGGTGGAAACATTCGGTCAGTTACGGGGGAATACCA
* * *
28755437 TATTTAAATAGGTGGAACCATTCGGTGAGTTACGGGGTAATACC
1 TATTTAAATAGGTGGAAACATTCGGTCAGTTACGGGGGAATACC
28755481 TACCGCTCTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.34
Consensus pattern (45 bp):
TATTTAAATAGGTGGAAACATTCGGTCAGTTACGGGGGAATACCA
Found at i:28756201 original size:18 final size:18
Alignment explanation
Indices: 28756178--28756213 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28756168 TGCCAGGTGC
28756178 GTATCCTAGCCATTATAT
1 GTATCCTAGCCATTATAT
* *
28756196 GTATCCTTGCCCTTATAT
1 GTATCCTAGCCATTATAT
28756214 ATTTCCTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.25, G:0.11, T:0.42
Consensus pattern (18 bp):
GTATCCTAGCCATTATAT
Found at i:28758467 original size:43 final size:44
Alignment explanation
Indices: 28758318--28758476 Score: 177
Period size: 43 Copynumber: 3.7 Consensus size: 44
28758308 TATGTGTTAT
* * *
28758318 CATGTAAGACCACGTCTGGGAAGTTGGCATTGACT-TATGATTTA
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGA-TATTTGATTTA
* * *
28758362 CGTATAAGACCACATCTGGGACGTTGGCATCG-TATTTGATTT-
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTTA
* *
28758404 CGTGTAAGACC-CTGTTTGGGACAG-TGGCATCGATATTTG-TTTA
1 CATGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTTGATTTA
28758447 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CATGTAAGACCACGTCTGGGACGTTGGCAT
28758477 TGTGCGAGCT
Statistics
Matches: 97, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
41 1 0.01
42 30 0.31
43 38 0.39
44 28 0.29
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (44 bp):
CATGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTTA
Found at i:28771937 original size:36 final size:36
Alignment explanation
Indices: 28771897--28772181 Score: 173
Period size: 36 Copynumber: 7.7 Consensus size: 36
28771887 TAACTCTCAA
* * *
28771897 AATTATTCAATAACAGTCAGTTATTCGGTAACAATC
1 AATTATTCAGTAACAATCAGTTATTCAGTAACAATC
* * * * *
28771933 AATTATTCAATAATAACCAGTTATTCAATATCGATCAATT
1 AATTATTCAGTAACAATCAGTTATTCAGTA---A-CAATC
* * *
28771973 AATTGGTTATCTAGTAACAGTCAATTATTCAGTAA-AATC
1 AATT--AT-TC-AGTAACAATCAGTTATTCAGTAACAATC
* * ****
28772012 AGA-TATTTAGTAACAATTAAGTTATTCAGTAGTTGTC
1 A-ATTATTCAGTAACAA-TCAGTTATTCAGTAACAATC
* *
28772049 -ATTCATTCAGTGACAATCAGTTATTCAGTAATAATC
1 AATT-ATTCAGTAACAATCAGTTATTCAGTAACAATC
* * *
28772085 AATTATTCAGTAATATTCAGTTATTCAGTAACAGTC
1 AATTATTCAGTAACAATCAGTTATTCAGTAACAATC
* * * * * *
28772121 TAA-TATCCAGTAACAGTCAATTATCCGGTAACAGTC
1 -AATTATTCAGTAACAATCAGTTATTCAGTAACAATC
*
28772157 AATTATTCAGTAATAATCAGTTATT
1 AATTATTCAGTAACAATCAGTTATT
28772182 TTATACCTTT
Statistics
Matches: 189, Mismatches: 44, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
35 10 0.05
36 126 0.67
37 18 0.10
39 6 0.03
40 9 0.05
41 1 0.01
42 1 0.01
43 2 0.01
44 16 0.08
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.36
Consensus pattern (36 bp):
AATTATTCAGTAACAATCAGTTATTCAGTAACAATC
Found at i:28772006 original size:18 final size:18
Alignment explanation
Indices: 28771985--28772169 Score: 144
Period size: 18 Copynumber: 10.3 Consensus size: 18
28771975 TTGGTTATCT
28771985 AGTAACAGTCAATTATTC
1 AGTAACAGTCAATTATTC
* *
28772003 AGTAA-AATCAGA-TATTT
1 AGTAACAGTCA-ATTATTC
* *
28772020 AGTAACAATTAAGTTATTC
1 AGTAACAGTCAA-TTATTC
***
28772039 AGTAGTTGTC-ATTCATTC
1 AGTAACAGTCAATT-ATTC
* * *
28772057 AGTGACAATCAGTTATTC
1 AGTAACAGTCAATTATTC
* *
28772075 AGTAATAATCAATTATTC
1 AGTAACAGTCAATTATTC
* * *
28772093 AGTAATATTCAGTTATTC
1 AGTAACAGTCAATTATTC
*
28772111 AGTAACAGTCTAA-TATCC
1 AGTAACAGTC-AATTATTC
*
28772129 AGTAACAGTCAATTATCC
1 AGTAACAGTCAATTATTC
*
28772147 GGTAACAGTCAATTATTC
1 AGTAACAGTCAATTATTC
28772165 AGTAA
1 AGTAA
28772170 TAATCAGTTA
Statistics
Matches: 132, Mismatches: 27, Indels: 16
0.75 0.15 0.09
Matches are distributed among these distances:
17 18 0.14
18 102 0.77
19 12 0.09
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
AGTAACAGTCAATTATTC
Found at i:28772114 original size:72 final size:71
Alignment explanation
Indices: 28771980--28772181 Score: 192
Period size: 72 Copynumber: 2.8 Consensus size: 71
28771970 ATTAATTGGT
* * * * * *
28771980 TATCTAGTAACAGTCAATTATTCAGTAAAATCAGA-TATTTAGTAACAATTAAGTTATTCAGTAG
1 TATCCAGTAACAATCAATTATTCAGTAAAATCA-ATTATTCAGTAA-TATTCAGTTATTCAGTAA
** *
28772044 TTGTC-AT
64 CAGTCTAA
* * *
28772051 TCATTCAGTGACAATCAGTTATTCAGTAATAATCAATTATTCAGTAATATTCAGTTATTCAGTAA
1 T-ATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATTCAGTAA
28772116 CAGTCTAA
64 CAGTCTAA
* * * * *
28772124 TATCCAGTAACAGTCAATTATCCGGTAACAGTCAATTATTCAGTAATAATCAGTTATT
1 TATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATT
28772182 TTATACCTTT
Statistics
Matches: 106, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
71 1 0.01
72 89 0.84
73 16 0.15
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (71 bp):
TATCCAGTAACAATCAATTATTCAGTAAAATCAATTATTCAGTAATATTCAGTTATTCAGTAACA
GTCTAA
Found at i:28772180 original size:18 final size:18
Alignment explanation
Indices: 28771899--28772181 Score: 133
Period size: 18 Copynumber: 15.3 Consensus size: 18
28771889 ACTCTCAAAA
* *
28771899 TTATTCAATAACAGTCAG
1 TTATTCAGTAACAATCAG
* *
28771917 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAG
* * *
28771935 TTATTCAATAATAACCAG
1 TTATTCAGTAACAATCAG
* *
28771953 TTATTCAATATCGATCAATTAATTGG
1 TTATTCAGTA---A-CAA-TCA---G
* *
28771979 TTA-TCTAGTAACAGTCAA
1 TTATTC-AGTAACAATCAG
28771997 TTATTCAGTAA-AATCAG
1 TTATTCAGTAACAATCAG
* * *
28772014 ATATTTAGTAACAATTAAG
1 TTATTCAGTAACAA-TCAG
****
28772033 TTATTCAGTAGTTGTCA-
1 TTATTCAGTAACAATCAG
*
28772050 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAACAATCAG
* *
28772069 TTATTCAGTAATAATCAA
1 TTATTCAGTAACAATCAG
* *
28772087 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAATCAG
*
28772105 TTATTCAGTAACAGTCTA-
1 TTATTCAGTAACAATC-AG
* * * *
28772123 ATATCCAGTAACAGTCAA
1 TTATTCAGTAACAATCAG
* * * *
28772141 TTATCCGGTAACAGTCAA
1 TTATTCAGTAACAATCAG
*
28772159 TTATTCAGTAATAATCAG
1 TTATTCAGTAACAATCAG
28772177 TTATT
1 TTATT
28772182 TTATACCTTT
Statistics
Matches: 200, Mismatches: 49, Indels: 32
0.71 0.17 0.11
Matches are distributed among these distances:
17 16 0.08
18 150 0.75
19 16 0.08
21 3 0.01
22 4 0.02
23 2 0.01
25 2 0.01
26 7 0.04
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (18 bp):
TTATTCAGTAACAATCAG
Found at i:28772362 original size:47 final size:47
Alignment explanation
Indices: 28772292--28772408 Score: 155
Period size: 47 Copynumber: 2.5 Consensus size: 47
28772282 CCGGAACAGT
* * *
28772292 AACAGTAGCAGTATGGTACACAGAATACCTCATCGGAACAAATCCGG
1 AACAGTAACAGTACGGTACACAGAATACCTCATCGGAACAAATCCGA
* * * *
28772339 GACAGTAATAGTACGGTACACAGAGTACCTCATCGGAACAAATCTGA
1 AACAGTAACAGTACGGTACACAGAATACCTCATCGGAACAAATCCGA
28772386 AACAGTAACAGTAACGGTA-ACAG
1 AACAGTAACAGT-ACGGTACACAG
28772409 TATTCAACAC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
47 54 0.90
48 6 0.10
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (47 bp):
AACAGTAACAGTACGGTACACAGAATACCTCATCGGAACAAATCCGA
Found at i:28772495 original size:12 final size:12
Alignment explanation
Indices: 28772478--28772502 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28772468 AGTGCCGAAT
28772478 CGGTAACAGTAA
1 CGGTAACAGTAA
28772490 CGGTAACAGTAA
1 CGGTAACAGTAA
28772502 C
1 C
28772503 AGTAGTCGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:28772496 original size:45 final size:45
Alignment explanation
Indices: 28772390--28772500 Score: 150
Period size: 45 Copynumber: 2.5 Consensus size: 45
28772380 ATCTGAAACA
*
28772390 GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGCTAAATCG
1 GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGCCAAATCG
* ** ** * *
28772435 ATAATGGTAATAGTAACAGTATTCGACACACAAAGTGCCGAATCG
1 GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGCCAAATCG
28772480 GTAACAGTAACGGTAACAGTA
1 GTAACAGTAACGGTAACAGTA
28772501 ACAGTAGTCG
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (45 bp):
GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGCCAAATCG
Found at i:28774042 original size:20 final size:18
Alignment explanation
Indices: 28774008--28774052 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
28773998 AAACTTTCAA
28774008 TTTTCCCTTTCTTCTTTC
1 TTTTCCCTTTCTTCTTTC
28774026 TTTTCTCCTTTCTTTCTTTC
1 TTTTC-CCTTTC-TTCTTTC
28774046 -TTTCCCT
1 TTTTCCCT
28774053 GCTTTTCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTCCCTTTCTTCTTTC
Found at i:28782402 original size:88 final size:86
Alignment explanation
Indices: 28782246--28782468 Score: 250
Period size: 88 Copynumber: 2.6 Consensus size: 86
28782236 CTTAATGGTG
* *** * * *
28782246 TAAAAAACCCTTAAATTTTTTCAAAAACTTCAATTAAGCCCCTACTTTTTTTGCAGTCACTTGAG
1 TAAAAAACCCTCAAATTTTTTCAAAAAAAACAATTAAGCCCCTGCTTTTTTTGCACTCAATTGAG
28782311 TACTTAAACTTGCACAA-TACA
66 TACTTAAACTTGCA-AATTACA
* * **
28782332 TCAAAAAGACCGTCAATTTTTTTCAAAAAAAACAATTAAGCCCCTGCTTTTTTTTTACTCAATTG
1 T-AAAAA-ACCCTCAAATTTTTTCAAAAAAAACAATTAAGCCCCTGCTTTTTTTGCACTCAATTG
* * *
28782397 GGTACTTAAACTTTCAAATTGCA
64 AGTACTTAAACTTGCAAATTACA
* * * *
28782420 TAAAAAACCCTCAAACTTTTTCAAAAAAAGCAACTAAGTCCCTGCTTTT
1 TAAAAAACCCTCAAATTTTTTCAAAAAAAACAATTAAGCCCCTGCTTTT
28782469 CCTTCTTTTT
Statistics
Matches: 114, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
86 38 0.33
87 12 0.11
88 64 0.56
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.34
Consensus pattern (86 bp):
TAAAAAACCCTCAAATTTTTTCAAAAAAAACAATTAAGCCCCTGCTTTTTTTGCACTCAATTGAG
TACTTAAACTTGCAAATTACA
Found at i:28782617 original size:19 final size:18
Alignment explanation
Indices: 28782595--28782653 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
28782585 AAATCAATAA
*
28782595 AAAATATTAAATTTTAAT
1 AAAATATTAAATATTAAT
*
28782613 GAAAATATAAAAATATTAAT
1 -AAAATAT-TAAATATTAAT
* *
28782633 AAATTATTAAAAATT-AT
1 AAAATATTAAATATTAAT
28782650 AAAA
1 AAAA
28782654 ATTCAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 5 0.15
18 6 0.18
19 13 0.39
20 9 0.27
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAATATTAAATATTAAT
Found at i:28782626 original size:20 final size:20
Alignment explanation
Indices: 28782595--28782647 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
28782585 AAATCAATAA
28782595 AAAATATT--AAATTTTAAT
1 AAAATATTAAAAATTTTAAT
*
28782613 GAAAATA-TAAAAATATTAAT
1 -AAAATATTAAAAATTTTAAT
*
28782633 AAATTATTAAAAATT
1 AAAATATTAAAAATT
28782648 ATAAAAATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.04
19 11 0.39
20 16 0.57
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAATATTAAAAATTTTAAT
Found at i:28782646 original size:10 final size:10
Alignment explanation
Indices: 28782620--28782656 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
28782610 AATGAAAATA
28782620 TAAAAA-TAT
1 TAAAAATTAT
28782629 TAATAAATTAT
1 TAA-AAATTAT
28782640 TAAAAATTA-
1 TAAAAATTAT
28782649 TAAAAATT
1 TAAAAATT
28782657 CAAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 11 0.42
10 9 0.35
11 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:28782684 original size:31 final size:31
Alignment explanation
Indices: 28782646--28782775 Score: 113
Period size: 32 Copynumber: 4.0 Consensus size: 31
28782636 TTATTAAAAA
28782646 TTATAAAAATTC-AAAAAAAAT-TCATAAAATT
1 TTATAAAAA-TCGAAAAAAAATCT-ATAAAATT
28782677 TTATAAAAATCGTAAAAAAAATCTATAAAA-T
1 TTATAAAAATCG-AAAAAAAATCTATAAAATT
* * **
28782708 ATATAGAAATATAGAAATACAGAAAAAATATAAAATT
1 TTATA-AAA-ATCG-AA-A-A-AAAATCTATAAAATT
28782745 TTATAAAAATCGTAAAAAAAATCTATAAAAT
1 TTATAAAAATCG-AAAAAAAATCTATAAAAT
28782776 ATATAGAAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
30 2 0.03
31 14 0.17
32 30 0.38
33 7 0.09
34 2 0.03
35 6 0.08
36 14 0.17
37 5 0.06
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.28
Consensus pattern (31 bp):
TTATAAAAATCGAAAAAAAATCTATAAAATT
Found at i:28782686 original size:68 final size:68
Alignment explanation
Indices: 28782581--28782819 Score: 290
Period size: 68 Copynumber: 3.5 Consensus size: 68
28782571 TTGATAAAAA
* * * * *
28782581 ATAAAAAT-CAATAAAAAATATTAAATTTTAATGAAAAT-AT-AAAAATAT-TAATAAATTAT-T
1 ATAAAAATACAA-AAAAAATATAAAATTTT-ATAAAAATCGTAAAAAAAATCT-ATAAAATATAT
*
28782641 AAAAATT
63 AGAAA-T
*
28782648 ATAAAAATTCAAAAAAAATTCATAAAATTTTATAAAAATCGTAAAAAAAATCTATAAAATATATA
1 ATAAAAATACAAAAAAAA-T-ATAAAATTTTATAAAAATCGTAAAAAAAATCTATAAAATATATA
28782713 GAAAT
64 GAAAT
* *
28782718 ATAGAAATACAGAAAAAATATAAAATTTTATAAAAATCGTAAAAAAAATCTATAAAATATATAGA
1 ATAAAAATACAAAAAAAATATAAAATTTTATAAAAATCGTAAAAAAAATCTATAAAATATATAGA
28782783 AAT
66 AAT
* *
28782786 ATAGAAATACAGAAAAAATATAAAATTTTATAAA
1 ATAAAAATACAAAAAAAATATAAAATTTTATAAA
28782820 TTTGTAAGAA
Statistics
Matches: 156, Mismatches: 9, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
67 14 0.09
68 94 0.60
69 11 0.07
70 31 0.20
71 6 0.04
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (68 bp):
ATAAAAATACAAAAAAAATATAAAATTTTATAAAAATCGTAAAAAAAATCTATAAAATATATAGA
AAT
Found at i:28782852 original size:19 final size:20
Alignment explanation
Indices: 28782830--28782878 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
28782820 TTTGTAAGAA
28782830 AATTATAAAAAAT-ATAAAG
1 AATTATAAAAAATCATAAAG
* *
28782849 AATTAT-AAAATTCGTAAAG
1 AATTATAAAAAATCATAAAG
28782868 AATTATAAAAA
1 AATTATAAAAA
28782879 TGATCGTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 5 0.19
19 17 0.65
20 4 0.15
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (20 bp):
AATTATAAAAAATCATAAAG
Found at i:28782855 original size:10 final size:9
Alignment explanation
Indices: 28782828--28782879 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
28782818 AATTTGTAAG
28782828 AAAATTATA
1 AAAATTATA
*
28782837 AAAAATATA
1 AAAATTATA
28782846 AAGAATTAT-
1 AA-AATTATA
*
28782855 AAAATTCGTA
1 AAAATT-ATA
28782865 AAGAATTATA
1 AA-AATTATA
28782875 AAAAT
1 AAAAT
28782880 GATCGTACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
8 4 0.11
9 16 0.46
10 11 0.31
11 4 0.11
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (9 bp):
AAAATTATA
Found at i:28782855 original size:38 final size:38
Alignment explanation
Indices: 28782798--28782878 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 38
28782788 AGAAATACAG
* *
28782798 AAAAAATATAAAATTTTAT-AAATTTGTAAGAAAATTAT
1 AAAAAATATAAAATATTATAAAATTCGTAA-AAAATTAT
*
28782836 AAAAAATATAAAGA-ATTATAAAATTCGTAAAGAATTAT
1 AAAAAATATAAA-ATATTATAAAATTCGTAAAAAATTAT
28782874 AAAAA
1 AAAAA
28782879 TGATCGTACT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 28 0.74
39 10 0.26
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (38 bp):
AAAAAATATAAAATATTATAAAATTCGTAAAAAATTAT
Found at i:28783128 original size:19 final size:19
Alignment explanation
Indices: 28783061--28783129 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
28783051 TTTTGATACA
* *
28783061 TTTTATAATTTTTTATGAT
1 TTTTATAAATTTTTACGAT
* * *
28783080 TTGTATAAAATTTTACAAT
1 TTTTATAAATTTTTACGAT
*
28783099 ACTTTAT-AATTTTTACGAT
1 -TTTTATAAATTTTTACGAT
28783118 TTTTATAAATTT
1 TTTTATAAATTT
28783130 GTTTCTAATT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
18 5 0.13
19 29 0.76
20 4 0.11
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (19 bp):
TTTTATAAATTTTTACGAT
Found at i:28783157 original size:30 final size:30
Alignment explanation
Indices: 28783123--28783184 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
28783113 ACGATTTTTA
28783123 TAAATTTGTTTCTA-ATTTTTTAAT-AAATTT
1 TAAATTT-TTT-TATATTTTTTAATAAAATTT
* *
28783153 TAAATTTTTTTATCTTTTTTATTAAAATTT
1 TAAATTTTTTTATATTTTTTAATAAAATTT
28783183 TA
1 TA
28783185 TTTTTATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.07
29 11 0.39
30 15 0.54
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (30 bp):
TAAATTTTTTTATATTTTTTAATAAAATTT
Found at i:28783189 original size:29 final size:30
Alignment explanation
Indices: 28783138--28783195 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
28783128 TTGTTTCTAA
28783138 TTTTTTAATAAATTTTAAATTTT-TTTATC
1 TTTTTTAATAAATTTTAAATTTTATTTATC
* *
28783167 TTTTTTATTAAAATTTT-ATTTTTATTTAT
1 TTTTTTAAT-AAATTTTAAATTTTATTTAT
28783196 TATATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (30 bp):
TTTTTTAATAAATTTTAAATTTTATTTATC
Found at i:28783204 original size:21 final size:20
Alignment explanation
Indices: 28783159--28783204 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
28783149 ATTTTAAATT
28783159 TTTTTATCTTTTTTATTAAA
1 TTTTTATCTTTTTTATTAAA
* * *
28783179 ATTTTATTTTTATTTATTATA
1 TTTTTATCTTT-TTTATTAAA
28783200 TTTTT
1 TTTTT
28783205 TGCCACATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTATCTTTTTTATTAAA
Done.