Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 96 of 207
Found at i:28474157 original size:13 final size:13
Alignment explanation
Indices: 28474139--28474174 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
28474129 CTACAGTATG
28474139 ATAAAAATTTCGT
1 ATAAAAATTTCGT
28474152 ATAAAAATTTCGT
1 ATAAAAATTTCGT
28474165 -TAAGAAATTT
1 ATAA-AAATTT
28474175 TACCGTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 3 0.14
13 19 0.86
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (13 bp):
ATAAAAATTTCGT
Found at i:28475299 original size:25 final size:25
Alignment explanation
Indices: 28475265--28475354 Score: 119
Period size: 25 Copynumber: 3.6 Consensus size: 25
28475255 GACACACCAT
*
28475265 AGCTCGCATGAGCTTCCTGTTACTC
1 AGCTCGCATGAGCTTCCCGTTACTC
*
28475290 AGCTCGCATGAGCTTCCCGTTATTC
1 AGCTCGCATGAGCTTCCCGTTACTC
*
28475315 AGCTCGCATGAGCTTCCCATTA-TAC
1 AGCTCGCATGAGCTTCCCGTTACT-C
* *
28475340 AGCTCGGAGGAGCTT
1 AGCTCGCATGAGCTT
28475355 ACTATTTACA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
24 1 0.02
25 58 0.98
ACGTcount: A:0.19, C:0.30, G:0.22, T:0.29
Consensus pattern (25 bp):
AGCTCGCATGAGCTTCCCGTTACTC
Found at i:28495628 original size:64 final size:64
Alignment explanation
Indices: 28495527--28495654 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
28495517 CATTAACCAC
28495527 AGGTAAATGCACTACCCATCCAAAAGGGCCCTAAGAGTGAGTAAAAGGAAAGAAATAAAATCTA
1 AGGTAAATGCACTACCCATCCAAAAGGGCCCTAAGAGTGAGTAAAAGGAAAGAAATAAAATCTA
*
28495591 AGGTAAATGCACTACCCATCCAAAAGGGCCTTAAGAGTGAGTAAAAGGAAAGAAATAAAATCTA
1 AGGTAAATGCACTACCCATCCAAAAGGGCCCTAAGAGTGAGTAAAAGGAAAGAAATAAAATCTA
28495655 TCTAAAAATC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.16
Consensus pattern (64 bp):
AGGTAAATGCACTACCCATCCAAAAGGGCCCTAAGAGTGAGTAAAAGGAAAGAAATAAAATCTA
Found at i:28500568 original size:3 final size:3
Alignment explanation
Indices: 28500560--28500598 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
28500550 TCAGAAACAC
28500560 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28500599 CAGTACTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:28504417 original size:29 final size:29
Alignment explanation
Indices: 28504380--28504448 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
28504370 CAATATATTA
* *
28504380 GATATCACTTGGTTCAAACCAACAGTTC-
1 GATACCACTTGGTTCAAACCAACAGCTCT
*
28504408 GAATACCACTTGGTTCGAACCAACAGCTCT
1 G-ATACCACTTGGTTCAAACCAACAGCTCT
28504438 GATACCACTTG
1 GATACCACTTG
28504449 TTACGAGACT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.03
29 34 0.94
30 1 0.03
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (29 bp):
GATACCACTTGGTTCAAACCAACAGCTCT
Found at i:28507203 original size:20 final size:20
Alignment explanation
Indices: 28507178--28507217 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28507168 CTTAGATGAG
*
28507178 TTGTAAGATATTTTGTTATT
1 TTGTAAGATATTTTATTATT
*
28507198 TTGTAAGGTATTTTATTATT
1 TTGTAAGATATTTTATTATT
28507218 AACTTTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.15, T:0.60
Consensus pattern (20 bp):
TTGTAAGATATTTTATTATT
Found at i:28514365 original size:2 final size:2
Alignment explanation
Indices: 28514358--28514394 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
28514348 AGAATTCAGA
*
28514358 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
28514395 ATTTTCAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.46, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:28518487 original size:13 final size:13
Alignment explanation
Indices: 28518469--28518499 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28518459 CACATGACTA
28518469 ATTTCATATAGCC
1 ATTTCATATAGCC
*
28518482 ATTTCATATATCC
1 ATTTCATATAGCC
28518495 ATTTC
1 ATTTC
28518500 CATTTATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.45
Consensus pattern (13 bp):
ATTTCATATAGCC
Found at i:28524070 original size:25 final size:25
Alignment explanation
Indices: 28524026--28524098 Score: 103
Period size: 25 Copynumber: 3.0 Consensus size: 25
28524016 TGATGCTTCG
28524026 AAGAACTAT-TAACGGGAAGCTCGC
1 AAGAACTATATAACGGGAAGCTCGC
** *
28524050 AAGAACTATATAACGAAAAGCTCGT
1 AAGAACTATATAACGGGAAGCTCGC
*
28524075 AAGAACCATATAACGGGAAGCTCG
1 AAGAACTATATAACGGGAAGCTCG
28524099 AGAGGGCCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 9 0.21
25 33 0.79
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.16
Consensus pattern (25 bp):
AAGAACTATATAACGGGAAGCTCGC
Found at i:28525762 original size:16 final size:16
Alignment explanation
Indices: 28525739--28525776 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
28525729 TTTAGTTTGA
28525739 CCCAATCTGTTAATGG
1 CCCAATCTGTTAATGG
*
28525755 CTCAATCTGTTAATGG
1 CCCAATCTGTTAATGG
28525771 CCCAAT
1 CCCAAT
28525777 TAATAAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (16 bp):
CCCAATCTGTTAATGG
Found at i:28525859 original size:23 final size:22
Alignment explanation
Indices: 28525799--28525868 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
28525789 TCAAGTCAAG
28525799 TTGTCTTCCACAATTTTAGGGAT
1 TTGTCTTCCACAATTTTA-GGAT
* *
28525822 TTGT-TTGGCTA-AATTGTAGGTAT
1 TTGTCTT--CCACAATTTTAGG-AT
28525845 TTGTCTTCCACAATTTTAGGAT
1 TTGTCTTCCACAATTTTAGGAT
28525867 TT
1 TT
28525869 TGTTTCTCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
22 10 0.26
23 24 0.63
24 4 0.11
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (22 bp):
TTGTCTTCCACAATTTTAGGAT
Found at i:28528297 original size:69 final size:67
Alignment explanation
Indices: 28528176--28528337 Score: 161
Period size: 69 Copynumber: 2.4 Consensus size: 67
28528166 GGTTTAAGGT
* * * * *
28528176 GTAAGACCATAGCTGGGCTATGGCAACTAGTAGAGTATGCCAGGATAGTAAACG-CGTGA-ATCA
1 GTAAGACCATAGCTCGACTATGGCAACTAATAGAGTACGCCAGGATAGTAAACGTAG-GATAT-A
28528239 CGAGGC
64 C--GGC
* *
28528245 GTAAGACCATAGCTCGACTATGGCAA-TCAATAGAGTCCGCCAGGA-CGTTAAACGTAGGATATA
1 GTAAGACCATAGCTCGACTATGGCAACT-AATAGAGTACGCCAGGATAG-TAAACGTAGGATATA
* *
28528308 CTGT
64 CGGC
28528312 GTAAGACCATAGCTCGACTATGGCAA
1 GTAAGACCATAGCTCGACTATGGCAA
28528338 GATAGAAGGT
Statistics
Matches: 80, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
67 27 0.34
68 2 0.03
69 48 0.60
70 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (67 bp):
GTAAGACCATAGCTCGACTATGGCAACTAATAGAGTACGCCAGGATAGTAAACGTAGGATATACG
GC
Found at i:28528390 original size:27 final size:27
Alignment explanation
Indices: 28528346--28528401 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
28528336 AAGATAGAAG
28528346 GTTTGCCAAGATAATAAACAC-GGGATA
1 GTTTGCCAAGATAATAAACACAGGG-TA
*
28528373 GTTTGCCAGGA-AACTAAACACAGGGTA
1 GTTTGCCAAGATAA-TAAACACAGGGTA
28528400 GT
1 GT
28528402 CTGCTGTGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 2 0.08
27 21 0.81
28 3 0.12
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (27 bp):
GTTTGCCAAGATAATAAACACAGGGTA
Found at i:28533590 original size:19 final size:20
Alignment explanation
Indices: 28533547--28533588 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28533537 AGATTTGCTC
28533547 AAACAGAAAGCAAGATGCAA
1 AAACAGAAAGCAAGATGCAA
*
28533567 AAACAGAAAAGGAAGA-GCAA
1 AAACAG-AAAGCAAGATGCAA
28533587 AA
1 AA
28533589 CAAATGACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.64, C:0.12, G:0.21, T:0.02
Consensus pattern (20 bp):
AAACAGAAAGCAAGATGCAA
Found at i:28541400 original size:15 final size:16
Alignment explanation
Indices: 28541367--28541411 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
28541357 GCTATTATGA
28541367 AATAGAGTTGTAATAG
1 AATAGAGTTGTAATAG
*
28541383 AATAGAGTT-TAATGG
1 AATAGAGTTGTAATAG
*
28541398 AATAAAGTTGTAAT
1 AATAGAGTTGTAAT
28541412 CAGTAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (16 bp):
AATAGAGTTGTAATAG
Found at i:28541656 original size:6 final size:6
Alignment explanation
Indices: 28541645--28541669 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28541635 AAATATAATT
28541645 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
28541670 TAATTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:28554508 original size:19 final size:21
Alignment explanation
Indices: 28554484--28554522 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
28554474 TATCTCTTGA
28554484 ATTTTA-TTTATT-TTATAAT
1 ATTTTATTTTATTATTATAAT
28554503 ATTTTATTTTATTATTATAA
1 ATTTTATTTTATTATTATAA
28554523 AAACCCTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 6 0.33
21 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTTATTTTATTATTATAAT
Found at i:28558678 original size:15 final size:15
Alignment explanation
Indices: 28558660--28558700 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
28558650 CGAGGACTAA
28558660 CAGGTGTAGGATTGG
1 CAGGTGTAGGATTGG
*
28558675 CAGGTGTAAGATTGG
1 CAGGTGTAGGATTGG
28558690 CAGGTGTAGGA
1 CAGGTGTAGGA
28558701 ATAGGGTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.24, C:0.07, G:0.44, T:0.24
Consensus pattern (15 bp):
CAGGTGTAGGATTGG
Found at i:28561999 original size:22 final size:22
Alignment explanation
Indices: 28561974--28562016 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28561964 AAAATGTCAT
* *
28561974 TGATTTGTATATAAACTACCAC
1 TGATTTGCAAATAAACTACCAC
*
28561996 TGATTTGCAAATAAATTACCA
1 TGATTTGCAAATAAACTACCA
28562017 TTCATAACAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (22 bp):
TGATTTGCAAATAAACTACCAC
Found at i:28565452 original size:14 final size:14
Alignment explanation
Indices: 28565424--28565452 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28565414 GCTTAGTGGC
28565424 TTTTGACTTGATTT
1 TTTTGACTTGATTT
28565438 TTTTG-CTTGATTT
1 TTTTGACTTGATTT
28565451 TT
1 TT
28565453 AAGTAATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.10, C:0.07, G:0.14, T:0.69
Consensus pattern (14 bp):
TTTTGACTTGATTT
Found at i:28573198 original size:46 final size:46
Alignment explanation
Indices: 28573131--28573219 Score: 178
Period size: 46 Copynumber: 1.9 Consensus size: 46
28573121 AGGTCCTTAT
28573131 TCAAGTATTATTGTTGGATACGACAACAATAATGCATTAAGACTAG
1 TCAAGTATTATTGTTGGATACGACAACAATAATGCATTAAGACTAG
28573177 TCAAGTATTATTGTTGGATACGACAACAATAATGCATTAAGAC
1 TCAAGTATTATTGTTGGATACGACAACAATAATGCATTAAGAC
28573220 AAACATGTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (46 bp):
TCAAGTATTATTGTTGGATACGACAACAATAATGCATTAAGACTAG
Found at i:28582753 original size:31 final size:31
Alignment explanation
Indices: 28582687--28582745 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
28582677 TGTCAATAAA
* *
28582687 CTTTTCTTAAACTCTCTATTTCAATCCAAGG
1 CTTTTCTTAAACTCTCTATTTCAAACCAAGC
28582718 CTTTTCTTAAACTCTCTATTTCAAACCA
1 CTTTTCTTAAACTCTCTATTTCAAACCA
28582746 TTCCTTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.27, G:0.03, T:0.42
Consensus pattern (31 bp):
CTTTTCTTAAACTCTCTATTTCAAACCAAGC
Found at i:28587194 original size:62 final size:62
Alignment explanation
Indices: 28587124--28587247 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
28587114 GATATAAGGT
28587124 AGACCTGACTTCAATAGGTCATGCCAAGGAAAAATCCTTTTGTTTCAATAGAGTGACCATCG
1 AGACCTGACTTCAATAGGTCATGCCAAGGAAAAATCCTTTTGTTTCAATAGAGTGACCATCG
28587186 AGACCTGACTTCAATAGGTCATGCCAAGGAAAAATCCTTTTGTTTCAATAGAGTGACCATCG
1 AGACCTGACTTCAATAGGTCATGCCAAGGAAAAATCCTTTTGTTTCAATAGAGTGACCATCG
28587248 GGTGGTGGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (62 bp):
AGACCTGACTTCAATAGGTCATGCCAAGGAAAAATCCTTTTGTTTCAATAGAGTGACCATCG
Found at i:28589775 original size:39 final size:40
Alignment explanation
Indices: 28589732--28589807 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
28589722 ATTAAACAAT
* *
28589732 CAGAGATACCAAAGTG-TAACAGAGGCACCGAAGTGCGAA
1 CAGAGACACCAAAGTGCAAACAGAGGCACCGAAGTGCGAA
* * *
28589771 CAGAGGCACCGAAGTGCAAACGGAGGCACCGAAGTGC
1 CAGAGACACCAAAGTGCAAACAGAGGCACCGAAGTGC
28589808 AAACGGAGGC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 13 0.42
40 18 0.58
ACGTcount: A:0.37, C:0.24, G:0.32, T:0.08
Consensus pattern (40 bp):
CAGAGACACCAAAGTGCAAACAGAGGCACCGAAGTGCGAA
Found at i:28589837 original size:20 final size:20
Alignment explanation
Indices: 28589753--28589851 Score: 126
Period size: 20 Copynumber: 5.0 Consensus size: 20
28589743 AAGTGTAACA
* *
28589753 GAGGCACCGAAGTGCGAACA
1 GAGGCACCGAAGTGCAAACG
28589773 GAGGCACCGAAGTGCAAACG
1 GAGGCACCGAAGTGCAAACG
28589793 GAGGCACCGAAGTGCAAACG
1 GAGGCACCGAAGTGCAAACG
* * *
28589813 GAGGCACTGAAGAGCAAATG
1 GAGGCACCGAAGTGCAAACG
* * *
28589833 AAGGCACTGAAGTGAAAAC
1 GAGGCACCGAAGTGCAAAC
28589852 TCTTACAAGT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.38, C:0.21, G:0.33, T:0.07
Consensus pattern (20 bp):
GAGGCACCGAAGTGCAAACG
Found at i:28589879 original size:21 final size:21
Alignment explanation
Indices: 28589855--28589919 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
28589845 TGAAAACTCT
*
28589855 TACAAGTGCACGTTCAAACCC
1 TACAAGCGCACGTTCAAACCC
*
28589876 TACAAGCACACGTTCAAACCC
1 TACAAGCGCACGTTCAAACCC
*
28589897 TATAAGCGCACGTTCAAACCC
1 TACAAGCGCACGTTCAAACCC
28589918 TA
1 TA
28589920 TTGGCATGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.35, C:0.34, G:0.12, T:0.18
Consensus pattern (21 bp):
TACAAGCGCACGTTCAAACCC
Found at i:28592246 original size:18 final size:18
Alignment explanation
Indices: 28592225--28592260 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28592215 TTCTTTTAAG
28592225 TTAGAAAATTTCAAGGGC
1 TTAGAAAATTTCAAGGGC
28592243 TTAGAAAATTTCAAGGGC
1 TTAGAAAATTTCAAGGGC
28592261 GAAATTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (18 bp):
TTAGAAAATTTCAAGGGC
Found at i:28600853 original size:86 final size:86
Alignment explanation
Indices: 28600708--28600873 Score: 314
Period size: 86 Copynumber: 1.9 Consensus size: 86
28600698 ATTCGTTCTG
28600708 TATTTTGGGAATTTAGAGGTATCCTAAACCCCTCCTCTAAATTCCAAGTGGAAGTGTTATTTTAC
1 TATTTTGGGAATTTAGAGGTATCCTAAACCCCTCCTCTAAATTCCAAGTGGAAGTGTTATTTTAC
28600773 CTATGCTAAATATGTGATAAA
66 CTATGCTAAATATGTGATAAA
* *
28600794 TATTTTGGGAATTTAGAGGTATCCTAATCCCCTCCTCTAAATTCCAAGTGTAAGTGTTATTTTAC
1 TATTTTGGGAATTTAGAGGTATCCTAAACCCCTCCTCTAAATTCCAAGTGGAAGTGTTATTTTAC
28600859 CTATGCTAAATATGT
66 CTATGCTAAATATGT
28600874 TTGTGAATTC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
86 78 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.38
Consensus pattern (86 bp):
TATTTTGGGAATTTAGAGGTATCCTAAACCCCTCCTCTAAATTCCAAGTGGAAGTGTTATTTTAC
CTATGCTAAATATGTGATAAA
Found at i:28603775 original size:20 final size:20
Alignment explanation
Indices: 28603752--28603814 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
28603742 TGGGCCTTCA
*
28603752 TGGCATTCTATTAGCCTTTG
1 TGGCATTATATTAGCCTTTG
* * *
28603772 TGGCATTTTGTTAGCCGTTG
1 TGGCATTATATTAGCCTTTG
*
28603792 CGGCATTATATT-GCCTTTG
1 TGGCATTATATTAGCCTTTG
28603811 TGGC
1 TGGC
28603815 GTACTTTGTA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 9 0.26
20 26 0.74
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TGGCATTATATTAGCCTTTG
Found at i:28614292 original size:29 final size:29
Alignment explanation
Indices: 28614250--28614382 Score: 106
Period size: 29 Copynumber: 4.6 Consensus size: 29
28614240 CGATAGTCGT
* * *
28614250 AACCGTCCCTTTTCATATTCAATGGCCGA
1 AACCATCCCTTTTCATAATCGATGGCCGA
** *
28614279 AACCATCCCTTTTCATTAATCGATGTTCGT
1 AACCATCCCTTTTCA-TAATCGATGGCCGA
* * * *
28614309 CACCAACCCTTTTCATAATCGATAGCTGA
1 AACCATCCCTTTTCATAATCGATGGCCGA
* * * *
28614338 AGCTATCCCTTTTCATATTCGATGGTC-A
1 AACCATCCCTTTTCATAATCGATGGCCGA
*
28614366 TCACCATCCCTTTTCAT
1 -AACCATCCCTTTTCAT
28614383 TAGTCAATGA
Statistics
Matches: 78, Mismatches: 24, Indels: 4
0.74 0.23 0.04
Matches are distributed among these distances:
28 1 0.01
29 55 0.71
30 22 0.28
ACGTcount: A:0.24, C:0.30, G:0.11, T:0.35
Consensus pattern (29 bp):
AACCATCCCTTTTCATAATCGATGGCCGA
Found at i:28614349 original size:59 final size:58
Alignment explanation
Indices: 28614256--28614382 Score: 155
Period size: 59 Copynumber: 2.2 Consensus size: 58
28614246 TCGTAACCGT
* * * *
28614256 CCCTTTTCATATTCAATGGCCGAAACCATCCCTTTTCATTAATCGATGTTCGTCACCAA
1 CCCTTTTCATAATCAATAGCCGAAACCATCCCTTTTCA-TAATCGATGGTCATCACCAA
* * * * * *
28614315 CCCTTTTCATAATCGATAGCTGAAGCTATCCCTTTTCATATTCGATGGTCATCACCAT
1 CCCTTTTCATAATCAATAGCCGAAACCATCCCTTTTCATAATCGATGGTCATCACCAA
28614373 CCCTTTTCAT
1 CCCTTTTCAT
28614383 TAGTCAATGA
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
58 26 0.45
59 32 0.55
ACGTcount: A:0.24, C:0.30, G:0.10, T:0.36
Consensus pattern (58 bp):
CCCTTTTCATAATCAATAGCCGAAACCATCCCTTTTCATAATCGATGGTCATCACCAA
Found at i:28627896 original size:13 final size:13
Alignment explanation
Indices: 28627878--28627905 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28627868 AACATCACAT
28627878 GTTTTATGTAAAA
1 GTTTTATGTAAAA
28627891 GTTTTATGTAAAA
1 GTTTTATGTAAAA
28627904 GT
1 GT
28627906 GAGTTGAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (13 bp):
GTTTTATGTAAAA
Found at i:28628191 original size:31 final size:29
Alignment explanation
Indices: 28628153--28628223 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
28628143 AATATTAAAA
* *
28628153 TTATACATGAATTTTAATTTAATGTGTAATG
1 TTATACATGAACTTTAATTT--TGTGCAATG
* *
28628184 TTATACATGAACTTTGATTTTGTGCAATT
1 TTATACATGAACTTTAATTTTGTGCAATG
28628213 TTATACATGAA
1 TTATACATGAA
28628224 AATTTGATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 18 0.50
31 18 0.50
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (29 bp):
TTATACATGAACTTTAATTTTGTGCAATG
Found at i:28628217 original size:29 final size:30
Alignment explanation
Indices: 28628153--28628233 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
28628143 AATATTAAAA
* * *
28628153 TTATACATGAATTTTAATTTAATGTGTAATG
1 TTATACATGAAATTTGATTT-ATGTGCAATG
* *
28628184 TTATACATGAACTTTGATTT-TGTGCAATT
1 TTATACATGAAATTTGATTTATGTGCAATG
28628213 TTATACATGAAAATTTGATTT
1 TTATACATG-AAATTTGATTT
28628234 GATTCAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 16 0.36
30 10 0.23
31 18 0.41
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (30 bp):
TTATACATGAAATTTGATTTATGTGCAATG
Found at i:28643129 original size:19 final size:20
Alignment explanation
Indices: 28643087--28643129 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
28643077 TCATGCTTTC
*
28643087 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
*
28643107 -ATTCACATTTTTAAATT-A
1 TATTCACATTTTCAAATTCA
28643125 TATTC
1 TATTC
28643130 CACAATCACG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:28652328 original size:16 final size:16
Alignment explanation
Indices: 28652275--28652330 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
28652265 TACATAATAG
*
28652275 TCCATTCCAA-TGATA
1 TCCATTTCAATTGATA
* * *
28652290 TCCTTTTCATTTGAAA
1 TCCATTTCAATTGATA
28652306 T-CATTTCAATTGATA
1 TCCATTTCAATTGATA
28652321 TCCATTTCAA
1 TCCATTTCAA
28652331 CCTTTTCATT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
15 19 0.59
16 13 0.41
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.43
Consensus pattern (16 bp):
TCCATTTCAATTGATA
Found at i:28655037 original size:27 final size:28
Alignment explanation
Indices: 28655007--28655062 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
28654997 ACTCAACTCT
28655007 TGTTCAAACAACCCATTTAGACAA-ACC
1 TGTTCAAACAACCCATTTAGACAAGACC
* * *
28655034 TGTTTAAACAATCTATTTAGACAAGACC
1 TGTTCAAACAACCCATTTAGACAAGACC
28655062 T
1 T
28655063 TTGAGACAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.29
Consensus pattern (28 bp):
TGTTCAAACAACCCATTTAGACAAGACC
Found at i:28656645 original size:16 final size:17
Alignment explanation
Indices: 28656624--28656660 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
28656614 AAGGGGATTA
28656624 AAATAAATTT-TTAATT
1 AAATAAATTTATTAATT
28656640 AAATAAATTTGATTAATT
1 AAATAAATTT-ATTAATT
28656658 AAA
1 AAA
28656661 ATTTTTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATAAATTTATTAATT
Found at i:28663089 original size:13 final size:13
Alignment explanation
Indices: 28663058--28663091 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
28663048 TTTGAATTTC
28663058 AATTT-ATTTAAT
1 AATTTAATTTAAT
28663070 AATTTTAATTTAAT
1 AA-TTTAATTTAAT
28663084 AATTTAAT
1 AATTTAAT
28663092 CCAAGGACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 2 0.10
13 9 0.45
14 9 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTTAATTTAAT
Found at i:28664788 original size:23 final size:24
Alignment explanation
Indices: 28664761--28664810 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
28664751 GTATAAGTAC
28664761 ATAATT-AGTTATATATAACGCAT
1 ATAATTAAGTTATATATAACGCAT
* *
28664784 ATAATTGAATTTATATATAATGCAT
1 ATAATT-AAGTTATATATAACGCAT
28664809 AT
1 AT
28664811 TTTCTTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 6 0.26
25 17 0.74
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (24 bp):
ATAATTAAGTTATATATAACGCAT
Found at i:28664832 original size:8 final size:8
Alignment explanation
Indices: 28664819--28664876 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
28664809 ATTTTCTTTC
28664819 TATATTAT
1 TATATTAT
28664827 TATATTAT
1 TATATTAT
28664835 TAATATTAT
1 T-ATATTAT
28664844 T-TATATAT
1 TATAT-TAT
28664852 TAT-TTA-
1 TATATTAT
28664858 TATATT-T
1 TATATTAT
*
28664865 TA-ATTTT
1 TATATTAT
28664872 TATAT
1 TATAT
28664877 ATTTAAATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
6 6 0.14
7 12 0.28
8 16 0.37
9 9 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATATTAT
Found at i:28664850 original size:20 final size:19
Alignment explanation
Indices: 28664827--28664881 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 19
28664817 TCTATATTAT
28664827 TATATTATTAATATTATTTA
1 TATATTATTAATA-TATTTA
*
28664847 TATATTATTTATATATTT-
1 TATATTATTAATATATTTA
*
28664865 TA-ATT-TTTATATATTTA
1 TATATTATTAATATATTTA
28664882 AATTATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 11 0.33
17 3 0.09
18 2 0.06
19 5 0.15
20 12 0.36
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATATTATTAATATATTTA
Found at i:28664851 original size:11 final size:11
Alignment explanation
Indices: 28664827--28664863 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
28664817 TCTATATTAT
28664827 TATATTA-TTA
1 TATATTATTTA
28664837 -ATATTATTTA
1 TATATTATTTA
28664847 TATATTATTTA
1 TATATTATTTA
28664858 TATATT
1 TATATT
28664864 TTAATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 6 0.24
10 3 0.12
11 16 0.64
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATTATTTA
Found at i:28664875 original size:16 final size:16
Alignment explanation
Indices: 28664854--28664897 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 16
28664844 TTATATATTA
*
28664854 TTTATATATTTTAATT
1 TTTATATATTTAAATT
28664870 TTTATATATTTAAA--
1 TTTATATATTTAAATT
28664884 -TTATATATTTAAAT
1 TTTATATATTTAAAT
28664898 GATAAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 13 0.50
16 13 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATATATTTAAATT
Found at i:28664877 original size:29 final size:29
Alignment explanation
Indices: 28664819--28664893 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
28664809 ATTTTCTTTC
*
28664819 TATATTATTATAT-TATTAATATTATTTA
1 TATATTATTATATATTTTAATATTATTTA
28664847 TATATTATTTATATATTTT-A-ATT-TTTA
1 TATATTA-TTATATATTTTAATATTATTTA
28664874 TATATTTAAATTATATATTT
1 TATA-TT--ATTATATATTT
28664894 AAATGATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
27 8 0.20
28 12 0.29
29 17 0.41
30 4 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
TATATTATTATATATTTTAATATTATTTA
Found at i:28665083 original size:21 final size:21
Alignment explanation
Indices: 28665043--28665081 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28665033 AAATCATGGA
28665043 TAAATCCAAGCGACTCTTTCT
1 TAAATCCAAGCGACTCTTTCT
28665064 TAAATCCAAGCGAC-CTTT
1 TAAATCCAAGCGACTCTTT
28665082 TCGTAGGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (21 bp):
TAAATCCAAGCGACTCTTTCT
Found at i:28667616 original size:12 final size:12
Alignment explanation
Indices: 28667599--28667623 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28667589 ATTTTATAAC
28667599 ATAAATATTGTT
1 ATAAATATTGTT
28667611 ATAAATATTGTT
1 ATAAATATTGTT
28667623 A
1 A
28667624 ATAGCCTCTG
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATAAATATTGTT
Found at i:28672865 original size:307 final size:308
Alignment explanation
Indices: 28672305--28673231 Score: 1429
Period size: 307 Copynumber: 3.0 Consensus size: 308
28672295 AATTACAAAA
* *
28672305 GAATAAAAAGGAAAGCCCTTTTCACCAGCAGTAACATGCATAGC-AAAGAAATAAAATGATTTTA
1 GAATAAAAAGGAAGGCCCTTTTCACCAGCAGTAACATGCAGAGCGAAA-AAATAAAATGATTTTA
* * *
28672369 GATCCAAATTTGAGTAAAACCAAGTTCTTAGCAAAAATTATGCAAAACCCACATCAGATTTACAA
65 GATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGATATACAA
* *
28672434 TTAATCATGTAGAGTCTCCAAGTACCAA-CAGATAAAACTAATAACATAGAGATATAATTTAAAG
130 TTAATAATGTA-AGTCTCCAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAATTTAAAG
* *
28672498 AAAACAAAAGCTACTAATCAATTAGCTCTGAACCAAAATTTACCCAAGACCAGC--AAAAGAAAA
194 AAAACAAAAGCTACTAACCAATTAGCTCTGAACCAAAACTTACCCAAGACCAGCAAAAAAGAAAA
* *
28672561 AAATTGCAAGGTAGTTTAACACAAAATCAACAGTAAGAAAGAATAATCTG
259 AAATTGCAAGGTAATTCAACACAAAATCAACAGTAAGAAAGAATAATCTG
* *
28672611 GAATAAAAAAGGAAGGCCCTTTTCACTAGCAATAACATGCAGAGCGAAAAAATAAAATGATTTTA
1 GAAT-AAAAAGGAAGGCCCTTTTCACCAGCAGTAACATGCAGAGCGAAAAAATAAAATGATTTTA
* *
28672676 GATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATACAAAACCTACATCAGATATACAA
65 GATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGATATACAA
* * *
28672741 TTAATAATGT-AGTCTCAAAGTACCAAGTAGATAAAACTAATAACATAGAAATATAGTTTAAAGA
130 TTAATAATGTAAGTCTCCAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAATTTAAAGA
*
28672805 ATACAAAAGCTACTAACCAATTAGCT-TGAACCAAAACTTACCCAAGACCAGCAAAAAAG--AAA
195 AAACAAAAGCTACTAACCAATTAGCTCTGAACCAAAACTTACCCAAGACCAGCAAAAAAGAAAAA
* * * *
28672867 GATTGTAAGGTAATTCAACACAAAAATCAACAATAAGAAAGAATAATTTG
260 AATTGCAAGGTAATTCAACAC-AAAATCAACAGTAAGAAAGAATAATCTG
* * * *
28672917 GAATAAAAAGGAAGGCCCTTTTCACCAGCAGTAATATGCAGAACGAAGAAATAAAACGATTTTAG
1 GAATAAAAAGGAAGGCCCTTTTCACCAGCAGTAACATGCAGAGCGAAAAAATAAAATGATTTTAG
*
28672982 ATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGAAATACAAT
66 ATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGATATACAAT
* *
28673047 TAATAATGTAGAGTCTCCAAGTACTAAGCAGATAAAACTAATAACATAGAAATATAATTTAAATA
131 TAATAATGTA-AGTCTCCAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAATTTAAAGA
* * *
28673112 AAACACAAGCTACTAACCAATTAGCTCTAAACCAAAACTTACCCAAGACCAGCAAAAAAAAAAAA
195 AAACAAAAGCTACTAACCAATTAGCTCTGAACCAAAACTTACCCAAGACCAGCAAAAAAGAAAAA
* *
28673177 AGATTGCAAGGTAATTCAACACAGAATCAGCAGTAAGAAAGAATAATCTG
260 A-ATTGCAAGGTAATTCAACACAAAATCAACAGTAAGAAAGAATAATCTG
28673227 GAATA
1 GAATA
28673232 CCCACAAAGA
Statistics
Matches: 562, Mismatches: 47, Indels: 20
0.89 0.07 0.03
Matches are distributed among these distances:
305 186 0.33
306 92 0.16
307 199 0.35
308 34 0.06
310 32 0.06
311 19 0.03
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (308 bp):
GAATAAAAAGGAAGGCCCTTTTCACCAGCAGTAACATGCAGAGCGAAAAAATAAAATGATTTTAG
ATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGATATACAAT
TAATAATGTAAGTCTCCAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAATTTAAAGAA
AACAAAAGCTACTAACCAATTAGCTCTGAACCAAAACTTACCCAAGACCAGCAAAAAAGAAAAAA
ATTGCAAGGTAATTCAACACAAAATCAACAGTAAGAAAGAATAATCTG
Found at i:28689231 original size:16 final size:16
Alignment explanation
Indices: 28689207--28689237 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28689197 TTACTTTATA
*
28689207 TTTTTCTTTTGTAAAC
1 TTTTCCTTTTGTAAAC
28689223 TTTTCCTTTTGTAAA
1 TTTTCCTTTTGTAAA
28689238 AAAGAGTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.61
Consensus pattern (16 bp):
TTTTCCTTTTGTAAAC
Found at i:28690010 original size:16 final size:15
Alignment explanation
Indices: 28689989--28690018 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28689979 TAGACTCTTT
28689989 TTTACAAAAGGAAAAG
1 TTTACAAAA-GAAAAG
28690005 TTTACAAAAGAAAA
1 TTTACAAAAGAAAA
28690019 CTATAAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (15 bp):
TTTACAAAAGAAAAG
Found at i:28690549 original size:16 final size:17
Alignment explanation
Indices: 28690522--28690553 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28690512 TACATTTTAG
28690522 TTTTCTCTTTTGTAAAC
1 TTTTCTCTTTTGTAAAC
28690539 TTTTC-CTTTTGTAAA
1 TTTTCTCTTTTGTAAA
28690554 AAAGAGTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.59
Consensus pattern (17 bp):
TTTTCTCTTTTGTAAAC
Found at i:28691848 original size:16 final size:15
Alignment explanation
Indices: 28691823--28691852 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28691813 TACTTTATAG
28691823 TTTTCTTTTGTAAAC
1 TTTTCTTTTGTAAAC
28691838 TTTTCCTTTTGTAAA
1 TTTT-CTTTTGTAAA
28691853 AAAAAGTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (15 bp):
TTTTCTTTTGTAAAC
Found at i:28692363 original size:16 final size:15
Alignment explanation
Indices: 28692342--28692371 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28692332 TAGACTCTTT
28692342 TTTACAAAAGGAAAAG
1 TTTACAAAA-GAAAAG
28692358 TTTACAAAAGAAAA
1 TTTACAAAAGAAAA
28692372 CTATAAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (15 bp):
TTTACAAAAGAAAAG
Found at i:28692625 original size:27 final size:27
Alignment explanation
Indices: 28692595--28692650 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
28692585 TCTTGAATTA
28692595 ATGGCTGCTTCCATCACCGCTTGTGTC
1 ATGGCTGCTTCCATCACCGCTTGTGTC
* **
28692622 ATGGTTGCTTCCATCACTTCTTGTGTC
1 ATGGCTGCTTCCATCACCGCTTGTGTC
28692649 AT
1 AT
28692651 CATTGCTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.12, C:0.29, G:0.20, T:0.39
Consensus pattern (27 bp):
ATGGCTGCTTCCATCACCGCTTGTGTC
Found at i:28692656 original size:27 final size:27
Alignment explanation
Indices: 28692600--28692658 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
28692590 AATTAATGGC
**
28692600 TGCTTCCATCACCGCTTGTGTCATGGT
1 TGCTTCCATCACCGCTTGTGTCATCAT
**
28692627 TGCTTCCATCACTTCTTGTGTCATCAT
1 TGCTTCCATCACCGCTTGTGTCATCAT
28692654 TGCTT
1 TGCTT
28692659 TGATGATAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.12, C:0.29, G:0.17, T:0.42
Consensus pattern (27 bp):
TGCTTCCATCACCGCTTGTGTCATCAT
Found at i:28694312 original size:27 final size:27
Alignment explanation
Indices: 28694280--28694335 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
28694270 GCTTGAATTA
*
28694280 ATGGTTGCTTCCATCACTGCTTGTGTC
1 ATGGTTGCTTCCATCACTGCTTGCGTC
*
28694307 ATGGTTGCTTCCATCATTGCTTGCGTC
1 ATGGTTGCTTCCATCACTGCTTGCGTC
28694334 AT
1 AT
28694336 CATTGCTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.41
Consensus pattern (27 bp):
ATGGTTGCTTCCATCACTGCTTGCGTC
Found at i:28694341 original size:27 final size:27
Alignment explanation
Indices: 28694284--28694343 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
28694274 GAATTAATGG
* **
28694284 TTGCTTCCATCACTGCTTGTGTCATGG
1 TTGCTTCCATCACTGCTTGCGTCATCA
*
28694311 TTGCTTCCATCATTGCTTGCGTCATCA
1 TTGCTTCCATCACTGCTTGCGTCATCA
28694338 TTGCTT
1 TTGCTT
28694344 TGATGATAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.12, C:0.27, G:0.18, T:0.43
Consensus pattern (27 bp):
TTGCTTCCATCACTGCTTGCGTCATCA
Found at i:28699334 original size:21 final size:22
Alignment explanation
Indices: 28699310--28699357 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
28699300 AAAAAACCAG
*
28699310 AAAAAT-GCAAAA-AATCAGAA
1 AAAAATAGCAAAATAATAAGAA
*
28699330 AAAAATAGCAAAATAATAATAA
1 AAAAATAGCAAAATAATAAGAA
28699352 AAAAAT
1 AAAAAT
28699358 CTCACTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.25
21 6 0.25
22 12 0.50
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.15
Consensus pattern (22 bp):
AAAAATAGCAAAATAATAAGAA
Found at i:28700601 original size:16 final size:18
Alignment explanation
Indices: 28700570--28700609 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
28700560 ATTATGAAAA
28700570 AAAATATATAATTTATAT
1 AAAATATATAATTTATAT
28700588 AAAA-ATAT-ATTTATAT
1 AAAATATATAATTTATAT
*
28700604 ATAATA
1 AAAATA
28700610 CATTCATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 11 0.55
17 5 0.25
18 4 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATATATAATTTATAT
Found at i:28700664 original size:20 final size:20
Alignment explanation
Indices: 28700639--28700676 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28700629 AAATATACAT
*
28700639 ATAGAAATTATAAAATATGG
1 ATAGAAAGTATAAAATATGG
*
28700659 ATAGAAAGTATAATATAT
1 ATAGAAAGTATAAAATAT
28700677 ATATATACGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (20 bp):
ATAGAAAGTATAAAATATGG
Found at i:28700763 original size:52 final size:55
Alignment explanation
Indices: 28700631--28700803 Score: 169
Period size: 56 Copynumber: 3.2 Consensus size: 55
28700621 ATAAAGAAAA
* * *
28700631 ATATACATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATATACGT
1 ATATATATATAGAAATTATAAAATAT-GATAGAAAGTATAAGATATATATATACAT
* * * *
28700687 ACATATATATATAAGTTA-ATAAATAT-ATAGATCA-TA-AAGATA-ATGAT-TACAT
1 ATATATATATAGAAATTATA-AAATATGATAGA-AAGTATAAGATATAT-ATATACAT
* **
28700739 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATACGTACAT
1 ATATATATATAGAAATTATAAAATATG-ATAGAAAGTATAAGATATATATATACAT
28700795 ATATATATA
1 ATATATATA
28700804 AGGTAATAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
52 27 0.29
53 9 0.10
54 14 0.15
55 8 0.09
56 36 0.38
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (55 bp):
ATATATATATAGAAATTATAAAATATGATAGAAAGTATAAGATATATATATACAT
Found at i:28700769 original size:20 final size:20
Alignment explanation
Indices: 28700741--28700787 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
28700731 GATTACATAT
*
28700741 ATATATATAGAAATTATAAA
1 ATATATATAGAAAGTATAAA
* *
28700761 ATATGTATAGAAAGTATAAT
1 ATATATATAGAAAGTATAAA
28700781 ATATATA
1 ATATATA
28700788 CGTACATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:28700815 original size:52 final size:52
Alignment explanation
Indices: 28700651--28700816 Score: 142
Period size: 52 Copynumber: 3.1 Consensus size: 52
28700641 AGAAATTATA
* *
28700651 AAATATGGATAGAAAGTATAATATATATATATACGTACATATATATATAAGTTAAT
1 AAATATGTATAGAAAG--T-ATA-ATATATATACGTACATATATATATAAGATAAT
* * * * * * *
28700707 AAATATATAGATCATAAAG-ATAAT-GAT-TACATATATATATATAGAA-ATTAT
1 AAATATGT--AT-AGAAAGTATAATATATATACGTACATATATATATAAGATAAT
*
28700758 AAAATATGTATAGAAAGTATAATATATATACGTACATATATATATAAGGTAAT
1 -AAATATGTATAGAAAGTATAATATATATACGTACATATATATATAAGATAAT
28700811 AAATAT
1 AAATAT
28700817 ATAAAACATA
Statistics
Matches: 85, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
49 5 0.06
50 7 0.08
51 5 0.06
52 45 0.53
53 5 0.06
54 2 0.02
55 3 0.04
56 6 0.07
58 2 0.02
59 5 0.06
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.35
Consensus pattern (52 bp):
AAATATGTATAGAAAGTATAATATATATACGTACATATATATATAAGATAAT
Found at i:28700816 original size:16 final size:17
Alignment explanation
Indices: 28700778--28700820 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
28700768 TAGAAAGTAT
28700778 AATATATATACGTACATA
1 AATATATA-ACGTACATA
* *
28700796 TATATATAAGGTA-ATA
1 AATATATAACGTACATA
28700812 AATATATAA
1 AATATATAA
28700821 AACATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 11 0.50
17 4 0.18
18 7 0.32
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (17 bp):
AATATATAACGTACATA
Found at i:28700817 original size:104 final size:107
Alignment explanation
Indices: 28700631--28700847 Score: 341
Period size: 104 Copynumber: 2.0 Consensus size: 107
28700621 ATAAAGAAAA
28700631 ATATACATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATATACGTACATATATA
1 ATATACATATAGAAATTATAAAATATGGATAGAAAG-ATAATATATATATATACGTACATATATA
* * * * *
28700696 TATAAGTTAATAAATATATAGATCATAAAGATAATGATTACAT
65 TATAAGGTAATAAATATATAAAACATAAAAATAATAATTACAT
* *
28700739 ATATATATATAGAAATTATAAAATATGTATAGAAAG-T-ATA-ATATATATACGTACATATATAT
1 ATATACATATAGAAATTATAAAATATGGATAGAAAGATAATATATATATATACGTACATATATAT
28700801 ATAAGGTAATAAATATATAAAACATAAAAATAATAATTACAT
66 ATAAGGTAATAAATATATAAAACATAAAAATAATAATTACAT
28700843 ATATA
1 ATATA
28700848 AACTTAAAAA
Statistics
Matches: 102, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
104 64 0.63
105 3 0.03
106 1 0.01
108 34 0.33
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.34
Consensus pattern (107 bp):
ATATACATATAGAAATTATAAAATATGGATAGAAAGATAATATATATATATACGTACATATATAT
ATAAGGTAATAAATATATAAAACATAAAAATAATAATTACAT
Found at i:28701432 original size:19 final size:19
Alignment explanation
Indices: 28701408--28701499 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
28701398 AATCATATAT
28701408 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
28701427 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
28701446 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
28701465 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
28701484 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
28701500 CCTGAAGATT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 63 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:28701455 original size:38 final size:38
Alignment explanation
Indices: 28701408--28701499 Score: 175
Period size: 38 Copynumber: 2.4 Consensus size: 38
28701398 AATCATATAT
28701408 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
*
28701446 TCTAAGATTGCATATCATATCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28701484 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
28701500 CCTGAAGATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTATATATCATA
Found at i:28701941 original size:44 final size:44
Alignment explanation
Indices: 28701893--28702635 Score: 159
Period size: 44 Copynumber: 16.8 Consensus size: 44
28701883 CTGTAACCAC
* *
28701893 AGGGAGGTAAAATCTGCTATCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * ** * **
28701937 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTG-TCT
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCT-T
* * * ** * * *
28701981 AGGGAAGTAGAAT-TACTGGCTTCAATGTACTCCACTA-TAATCAT
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACT--GCTT
* * * *
28702025 AGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * * ** * ** *
28702069 CGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTG-TCC
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCT-T
* * * ** * **
28702113 AGGGAAGTAGAAT-TACTGGCTTCAATGTACTCCACTGTAAC--CAC
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCAC--T-ACTGCTT
* * * *
28702157 AGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * * ** * ** **
28702201 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCC
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * * * **
28702245 AGGGAAGTAGAATTACTGGCT-TC-ACAATGTACTCCACTGTAAC--CAC
1 AGGGAGGTA-AAAT-CT-GCTATCTTCAATCTACTCCAC--T-ACTGCTT
* * *
28702291 AGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * * ** * * ** *
28702335 AAGGAGATAAGATCTGAAATCTTCAATTTATTCCACTGTTGTTT
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * * ** * **
28702379 AGGGAAGTAGAAT-TACTGGCTTCAATGTACTCCACTGTAAC--CAC
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCAC--T-ACTGCTT
** * ** **
28702423 AGGGAGGTAAAATCCACCATCTTTGATCTGTTCCACTACTGCTT
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * * *** * ** **
28702467 AGGGAGATAAGATATAAAATCTTCAATCTATTCCACTGTTGCCC
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * ** ** * * **
28702511 AGGGAAGTAGAAT-TATTGGCTTCAATGTACTCCACTA-TAACCAC
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACT--GCTT
* * * * *
28702555 AGGGCGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * ** *
28702599 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACT
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACT
28702636 GTTGTCCAAG
Statistics
Matches: 464, Mismatches: 201, Indels: 68
0.63 0.27 0.09
Matches are distributed among these distances:
42 8 0.02
43 70 0.15
44 283 0.61
45 85 0.18
46 16 0.03
47 2 0.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (44 bp):
AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
Found at i:28702047 original size:132 final size:132
Alignment explanation
Indices: 28701822--28702718 Score: 1458
Period size: 132 Copynumber: 6.8 Consensus size: 132
28701812 TAGGACTTAC
* * *
28701822 AATCTTCAACCTATTCCACTGCTGAT-TAGGG-AGATATG-ATTACTGGCTTCAATGTACTCCAC
1 AATCTTCAATCTATTCCACTGTTG-TCCAGGGAAG-TA-GAATTACTGGCTTCAATGTACTCCAC
* *
28701884 TGTAACCACAGGGAGGTAAAATCTGCTATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGA
63 TGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGA
28701949 TCTGA
128 TCTGA
* *
28701954 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
* * *
28702019 AATCATAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTCGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
28702084 GA
131 GA
28702086 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
*
28702151 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
28702216 GA
131 GA
*
28702218 AATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCTTCACAATGTACTCCACT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTT--CAATGTACTCCACT
* *
28702283 GTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGAT
64 GTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAT
28702348 CTGA
129 CTGA
* **
28702352 AATCTTCAATTTATTCCACTGTTGTTTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
* * * *
28702417 AACCACAGGGAGGTAAAATCCACCATCTTTGATCTGTTCCACTACTGCTTAGGGAGATAAGATAT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
*
28702482 AA
131 GA
* * *
28702484 AATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTATTGGCTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
*
28702549 AACCACAGGGCGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
28702614 GA
131 GA
* * *
28702616 AATCTTCAATCTATTCCACTGTTGTCCAAGGAAGTAGAATTACTGGCTTTAATGTATTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
*
28702681 AACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
28702719 TCACAGTCAA
Statistics
Matches: 711, Mismatches: 49, Indels: 10
0.92 0.06 0.01
Matches are distributed among these distances:
131 2 0.00
132 582 0.82
133 2 0.00
134 125 0.18
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (132 bp):
AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
GA
Found at i:28702607 original size:398 final size:396
Alignment explanation
Indices: 28701860--28702718 Score: 1502
Period size: 398 Copynumber: 2.2 Consensus size: 396
28701850 GGGAGATATG
*
28701860 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCTATCTTCGATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCT
*
28701925 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTA
66 CCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTA
* * *
28701990 GAATTACTGGCTTCAATGTACTCCACTATAATCATAGGGAGGTAAAATCCGCCATCTTCGATCTG
131 GAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCACCATCTTCGATCTG
* * * *
28702055 CTCCACTACTGCTTCGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAG
196 CTCCACTACTGCTTAGGGAGATAAGATATAAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAG
*
28702120 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATC
261 TAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATC
*
28702185 TGCTCCACTACTGCTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGA
326 TGCTCCACTACTGCTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCCAAGGA
28702250 AGTAGA
391 AGTAGA
28702256 ATTACTGGCTTCACAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTG
1 ATTACTGGCTT--CAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTG
* *
28702321 CTCCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATTTATTCCACTGTTGTTTAGGGAAG
64 CTCCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCTAGGGAAG
* *
28702386 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTTGATC
129 TAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCACCATCTTCGATC
*
28702451 TGTTCCACTACTGCTTAGGGAGATAAGATATAAAATCTTCAATCTATTCCACTGTTGCCCAGGGA
194 TGCTCCACTACTGCTTAGGGAGATAAGATATAAAATCTTCAATCTATTCCACTGTTGCCCAGGGA
* *
28702516 AGTAGAATTATTGGCTTCAATGTACTCCACTATAACCACAGGGCGGTAAAATCCGCCATCTTCGA
259 AGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGA
* *
28702581 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAAG
324 TCTGCTCCACTACTGCTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCCAAG
28702646 GAAGTAGA
389 GAAGTAGA
* *
28702654 ATTACTGGCTTTAATGTATTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCT
28702719 TCACAGTCAA
Statistics
Matches: 439, Mismatches: 22, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
396 63 0.14
398 376 0.86
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (396 bp):
ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCT
CCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTA
GAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCACCATCTTCGATCTG
CTCCACTACTGCTTAGGGAGATAAGATATAAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAG
TAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATC
TGCTCCACTACTGCTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCCAAGGA
AGTAGA
Found at i:28706518 original size:24 final size:24
Alignment explanation
Indices: 28706490--28706535 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
28706480 ATCATTTTTT
*
28706490 GCTGCTCATTCATTTACTTTTGAA
1 GCTGCTCATGCATTTACTTTTGAA
* *
28706514 GCTGCTCCTGCATTTCCTTTTG
1 GCTGCTCATGCATTTACTTTTG
28706536 GGATTGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.46
Consensus pattern (24 bp):
GCTGCTCATGCATTTACTTTTGAA
Found at i:28708795 original size:20 final size:20
Alignment explanation
Indices: 28708770--28708807 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28708760 AAATATACAT
*
28708770 ATAGAAATTATAAAATATGG
1 ATAGAAAGTATAAAATATGG
*
28708790 ATAGAAAGTATAATATAT
1 ATAGAAAGTATAAAATAT
28708808 ATACGTACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (20 bp):
ATAGAAAGTATAAAATATGG
Found at i:28708818 original size:48 final size:48
Alignment explanation
Indices: 28708765--28708924 Score: 151
Period size: 54 Copynumber: 3.2 Consensus size: 48
28708755 AAGAAAAATA
*
28708765 TACATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATACG
1 TACATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATG
* * * * * *
28708813 TACATATATATATAAGTTAATAAATATATAGATCATAAA-AATAATGATTACATATA
1 TAC--ATATAGA-AA-TT-ATAAA-ATATGGAT-AGAAAGTATAAT-A-TATATATG
* *
28708869 TATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATATG
1 TACATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATG
28708917 TACATATA
1 TACATATA
28708925 TATATAAGGT
Statistics
Matches: 86, Mismatches: 16, Indels: 20
0.70 0.13 0.16
Matches are distributed among these distances:
48 16 0.19
49 5 0.06
50 17 0.20
51 7 0.08
52 4 0.05
53 7 0.08
54 18 0.21
55 5 0.06
56 7 0.08
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.35
Consensus pattern (48 bp):
TACATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATG
Found at i:28708839 original size:52 final size:51
Alignment explanation
Indices: 28708782--28708943 Score: 161
Period size: 52 Copynumber: 3.1 Consensus size: 51
28708772 AGAAATTATA
28708782 AAATATGGATAGAAAGTATAATATATATACGTACATATATATATAAGTTAAT
1 AAATAT-GATAGAAAGTATAATATATATACGTACATATATATATAAGTTAAT
* * * * * *
28708834 AAATAT-ATAGATCA-TA-AAAATAATGATTACATATATATATATAGAAATT-AT
1 AAATATGATAGA-AAGTATAATAT-AT-A-TACGTACATATATATATAAGTTAAT
* *
28708885 AAAATATGTATAGAAAGTATAATATATATATGTACATATATATATAAGGTAAT
1 -AAATATG-ATAGAAAGTATAATATATATACGTACATATATATATAAGTTAAT
28708938 AAATAT
1 AAATAT
28708944 ATAAATCATA
Statistics
Matches: 86, Mismatches: 14, Indels: 20
0.72 0.12 0.17
Matches are distributed among these distances:
49 4 0.05
50 9 0.10
51 4 0.05
52 52 0.60
53 4 0.05
54 9 0.10
55 4 0.05
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.35
Consensus pattern (51 bp):
AAATATGATAGAAAGTATAATATATATACGTACATATATATATAAGTTAAT
Found at i:28708876 original size:104 final size:104
Alignment explanation
Indices: 28708762--28708974 Score: 372
Period size: 104 Copynumber: 2.0 Consensus size: 104
28708752 ATAAAGAAAA
28708762 ATATACATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATACGTACATATATATATA
1 ATATACATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATACGTACATATATATATA
* * *
28708827 AGTTAATAAATATATAGATCATAAAAATAATGATTACAT
66 AGGTAATAAATATATAAATCATAAAAATAATAATTACAT
* * *
28708866 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATATGTACATATATATATA
1 ATATACATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATACGTACATATATATATA
28708931 AGGTAATAAATATATAAATCATAAAAATAATAATTACAT
66 AGGTAATAAATATATAAATCATAAAAATAATAATTACAT
28708970 ATATA
1 ATATA
28708975 AACTTAAAAA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
104 103 1.00
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.35
Consensus pattern (104 bp):
ATATACATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATACGTACATATATATATA
AGGTAATAAATATATAAATCATAAAAATAATAATTACAT
Found at i:28708896 original size:20 final size:20
Alignment explanation
Indices: 28708868--28708915 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
28708858 GATTACATAT
*
28708868 ATATATATAGAAATTATAAA
1 ATATATATAGAAAGTATAAA
* *
28708888 ATATGTATAGAAAGTATAAT
1 ATATATATAGAAAGTATAAA
28708908 ATATATAT
1 ATATATAT
28708916 GTACATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:28708943 original size:16 final size:17
Alignment explanation
Indices: 28708905--28708947 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
28708895 TAGAAAGTAT
*
28708905 AATATATATATGTACATA
1 AATATATA-AGGTACATA
*
28708923 TATATATAAGGTA-ATA
1 AATATATAAGGTACATA
28708939 AATATATAA
1 AATATATAA
28708948 ATCATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 11 0.50
17 4 0.18
18 7 0.32
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (17 bp):
AATATATAAGGTACATA
Found at i:28709592 original size:19 final size:19
Alignment explanation
Indices: 28709535--28709592 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
28709525 TACAAAATCA
28709535 TATATTCTAAGATTGCATAT
1 TATA-TCTAAGATTGCATAT
* * **
28709555 CATATCTAAAATTATATAT
1 TATATCTAAGATTGCATAT
28709574 TATATCTAAGATTGCATAT
1 TATATCTAAGATTGCATAT
28709593 CCCTGAAGAT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
19 27 0.90
20 3 0.10
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (19 bp):
TATATCTAAGATTGCATAT
Found at i:28710401 original size:17 final size:17
Alignment explanation
Indices: 28710381--28710414 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28710371 AAATAAATTT
* *
28710381 AAAAATCAAATTTTCAA
1 AAAAATAAAAATTTCAA
28710398 AAAAATAAAAATTTCAA
1 AAAAATAAAAATTTCAA
28710415 GGCTAATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAATAAAAATTTCAA
Found at i:28710500 original size:23 final size:21
Alignment explanation
Indices: 28710451--28710502 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
28710441 TGTATATGTA
*
28710451 TATTATTTTGTGTTTTTTTTC
1 TATTATTTTATGTTTTTTTTC
28710472 TA-TATTTTAATGATTTTTTCTT-
1 TATTATTTT-ATG-TTTTTT-TTC
28710494 TATTATTTT
1 TATTATTTT
28710503 TCATTGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 6 0.23
21 4 0.15
22 8 0.31
23 8 0.31
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.73
Consensus pattern (21 bp):
TATTATTTTATGTTTTTTTTC
Found at i:28710503 original size:24 final size:23
Alignment explanation
Indices: 28710476--28710529 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
28710466 TTTTTCTATA
*
28710476 TTTTAATGATTTTTT-CTTTATTAT
1 TTTTAATG-TTTTTTGCATT-TTAT
*
28710500 TTTTCATTGTTTTTTGCATTTTAT
1 TTTT-AATGTTTTTTGCATTTTAT
28710524 TTTTAA
1 TTTTAA
28710530 AAAAGAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 1 0.04
24 18 0.72
25 6 0.24
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.70
Consensus pattern (23 bp):
TTTTAATGTTTTTTGCATTTTAT
Found at i:28715071 original size:40 final size:40
Alignment explanation
Indices: 28715010--28715085 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
28715000 GCGGGCATGA
* *
28715010 CTTGCGACCTCGTCTCTGTGAGGCTTACAC-GAGCTCTGCT
1 CTTGCGACCTCGTCCCCGTGAGGCTTAC-CTGAGCTCTGCT
*
28715050 CTTGCGCCCTCGTCCCCGTGAGGCTTACCTGAGCTC
1 CTTGCGACCTCGTCCCCGTGAGGCTTACCTGAGCTC
28715086 ACTATACTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 1 0.03
40 31 0.97
ACGTcount: A:0.11, C:0.37, G:0.25, T:0.28
Consensus pattern (40 bp):
CTTGCGACCTCGTCCCCGTGAGGCTTACCTGAGCTCTGCT
Found at i:28727715 original size:18 final size:17
Alignment explanation
Indices: 28727674--28727712 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
28727664 ATCTTAAAGC
28727674 GTTTTATGCCAAACATA
1 GTTTTATGCCAAACATA
28727691 GTTTTATGCCAAACATA
1 GTTTTATGCCAAACATA
*
28727708 ATTTT
1 GTTTT
28727713 TATTTCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (17 bp):
GTTTTATGCCAAACATA
Found at i:28728971 original size:20 final size:20
Alignment explanation
Indices: 28728946--28729010 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
28728936 TCATTTTGCA
**
28728946 ATAAAAATACATAAGATTTT
1 ATAAAAATACATAAGAAATT
* **
28728966 ATAAAAATATATATTAAATT
1 ATAAAAATACATAAGAAATT
28728986 ATAAAAATACATACA-AAATT
1 ATAAAAATACATA-AGAAATT
28729006 ATAAA
1 ATAAA
28729011 TAAATGAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (20 bp):
ATAAAAATACATAAGAAATT
Found at i:28735043 original size:24 final size:26
Alignment explanation
Indices: 28734972--28735045 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 26
28734962 AGCTCCATAT
* * *
28734972 TATTTTTTTTAAATAAAAATATATTTA
1 TATTATTTTT-AATAATATTATATTTA
*
28734999 TATTATTTTTAATAATTTTATATTT-
1 TATTATTTTTAATAATATTATATTTA
28735024 T-TTATTTATTAA-AATATTATAT
1 TATTATTT-TTAATAATATTATAT
28735046 ATAATCATCT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 15 0.37
25 5 0.12
26 12 0.29
27 9 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TATTATTTTTAATAATATTATATTTA
Found at i:28735046 original size:26 final size:27
Alignment explanation
Indices: 28734990--28735047 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 27
28734980 TTAAATAAAA
28734990 ATATATTTATATTATTTTTAATAATTT
1 ATATATTTATATTATTTTTAATAATTT
28735017 -TATATTT-T-TTATTTATTAA-AATATT
1 ATATATTTATATTATTT-TTAATAAT-TT
28735042 ATATAT
1 ATATAT
28735048 AATCATCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
24 9 0.32
25 7 0.25
26 12 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
ATATATTTATATTATTTTTAATAATTT
Found at i:28735609 original size:10 final size:10
Alignment explanation
Indices: 28735596--28735655 Score: 63
Period size: 9 Copynumber: 6.2 Consensus size: 10
28735586 ATATTCTATT
*
28735596 AAAATGATTA
1 AAAATCATTA
28735606 AAAATCA-TA
1 AAAATCATTA
28735615 AAAAGTCATTA
1 AAAA-TCATTA
*
28735626 AAAATTA-TA
1 AAAATCATTA
*
28735635 AAAATCATAA
1 AAAATCATTA
28735645 AAAAT-ATTA
1 AAAATCATTA
28735654 AA
1 AA
28735656 GATTATAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
9 19 0.45
10 17 0.40
11 6 0.14
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (10 bp):
AAAATCATTA
Found at i:28735626 original size:29 final size:27
Alignment explanation
Indices: 28735592--28735666 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 27
28735582 TAATATATTC
*
28735592 TATTAAAATGATTAAAAATCATAAAAAG
1 TATTAAAATGA-TAAAAATCATAAAAAA
*
28735620 TCATTAAAAATTATAAAAATCATAAAAAA
1 T-ATT-AAAATGATAAAAATCATAAAAAA
*
28735649 TATTAAAGATTATAAAAA
1 TATTAAA-ATGATAAAAA
28735667 ATAAGGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 3 0.07
28 14 0.33
29 19 0.45
30 6 0.14
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (27 bp):
TATTAAAATGATAAAAATCATAAAAAA
Found at i:28735627 original size:20 final size:19
Alignment explanation
Indices: 28735596--28735649 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
28735586 ATATTCTATT
*
28735596 AAAATGATTAAAAATCATA
1 AAAATCATTAAAAATCATA
*
28735615 AAAAGTCATTAAAAATTATA
1 AAAA-TCATTAAAAATCATA
*
28735635 AAAATCATAAAAAAT
1 AAAATCATTAAAAAT
28735650 ATTAAAGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.26
Consensus pattern (19 bp):
AAAATCATTAAAAATCATA
Found at i:28735664 original size:9 final size:9
Alignment explanation
Indices: 28735604--28736029 Score: 122
Period size: 9 Copynumber: 44.7 Consensus size: 9
28735594 TTAAAATGAT
*
28735604 TAAAAATCA
1 TAAAAATTA
*
28735613 TAAAAAGTCA
1 TAAAAA-TTA
28735623 TTAAAAATTA
1 -TAAAAATTA
*
28735633 TAAAAATCA
1 TAAAAATTA
*
28735642 TAAAAAATA
1 TAAAAATTA
*
28735651 TTAAAGATTA
1 -TAAAAATTA
*
28735661 TAAAAAATAA
1 T-AAAAATTA
*
28735671 GGAAAAAATTA
1 --TAAAAATTA
28735682 TAAAATATT-
1 TAAAA-ATTA
28735691 TAAAATATT-
1 TAAAA-ATTA
28735700 TAAAAA-TA
1 TAAAAATTA
*
28735708 TTAAAATTAA
1 TAAAAATT-A
*
28735718 TATAAACTTA
1 TA-AAAATTA
* *
28735728 TAATACTTA
1 TAAAAATTA
*
28735737 TAAAAGCTTA
1 TAAAA-ATTA
*
28735747 TAAATATTA
1 TAAAAATTA
*
28735756 TAAAAACATA
1 TAAAAA-TTA
28735766 TAATAAATCTA
1 TAA-AAAT-TA
**
28735777 -ATTAATTA
1 TAAAAATTA
28735785 TAAAAATATA
1 TAAAAAT-TA
28735795 TAAAAATTAA
1 TAAAAATT-A
*
28735805 TAAACA-TA
1 TAAAAATTA
*
28735813 TTAAATATT-
1 -TAAAAATTA
**
28735822 TAAATTTTTA
1 TAAA-AATTA
*
28735832 TAAAAACCTA
1 TAAAAA-TTA
*
28735842 T-AAAATTCT
1 TAAAAATT-A
28735851 TAAAAATTA
1 TAAAAATTA
*
28735860 T-TAAA-TA
1 TAAAAATTA
* *
28735867 TTAAAACTA
1 TAAAAATTA
*
28735876 TTAAAATTGA
1 TAAAAATT-A
*
28735886 TATAAATTA
1 TAAAAATTA
*
28735895 TAATAA-TA
1 TAAAAATTA
28735903 TAATAAATTA
1 TAA-AAATTA
28735913 TAAATAGATT-
1 TAAA-A-ATTA
28735923 TATAAAATTAA
1 TA-AAAATT-A
*
28735934 TAAAATATATT
1 TAAAA-AT-TA
28735945 TAAAATATT-
1 TAAAA-ATTA
*
28735954 TAATAATTTA
1 TAA-AAATTA
* *
28735964 TAACAAGTAA
1 TAA-AAATTA
28735974 TAAAAATTCA
1 TAAAAATT-A
28735984 TAAAAAACTTA
1 T-AAAAA-TTA
28735995 TAAATAA-TA
1 TAAA-AATTA
*
28736004 TAATAAATTC
1 TAA-AAATTA
*
28736014 TAATAAATTG
1 TAA-AAATTA
28736024 TAAAAA
1 TAAAAA
28736030 AATTATAAAT
Statistics
Matches: 321, Mismatches: 51, Indels: 90
0.69 0.11 0.19
Matches are distributed among these distances:
7 4 0.01
8 25 0.08
9 120 0.37
10 120 0.37
11 49 0.15
12 3 0.01
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:28735676 original size:28 final size:27
Alignment explanation
Indices: 28735604--28735687 Score: 71
Period size: 28 Copynumber: 2.9 Consensus size: 27
28735594 TTAAAATGAT
**
28735604 TAAAAATCATAAAAAGTCATTAAAAATTA
1 TAAAAA-CATAAAAA-AAATTAAAAATTA
* *
28735633 TAAAAATCATAAAAAATATTAAAGATTA
1 TAAAAA-CATAAAAAAAATTAAAAATTA
28735661 TAAAAA-ATAAGGAAAAAATTATAAAAT
1 TAAAAACATAA--AAAAAATTA-AAAAT
28735688 ATTTAAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
26 4 0.09
28 24 0.51
29 19 0.40
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.26
Consensus pattern (27 bp):
TAAAAACATAAAAAAAATTAAAAATTA
Found at i:28735686 original size:10 final size:10
Alignment explanation
Indices: 28735605--28735710 Score: 67
Period size: 10 Copynumber: 10.8 Consensus size: 10
28735595 TAAAATGATT
*
28735605 AAAAATCATA
1 AAAAATTATA
* * *
28735615 AAAAGTCATT
1 AAAAATTATA
28735625 AAAAATTAT-
1 AAAAATTATA
*
28735634 AAAAATCATA
1 AAAAATTATA
*
28735644 AAAAA-TATT
1 AAAAATTATA
*
28735653 AAAGATTATA
1 AAAAATTATA
* *
28735663 AAAAATAAGGA
1 AAAAATTA-TA
28735674 AAAAATTATA
1 AAAAATTATA
*
28735684 AAATATT-TA
1 AAAAATTATA
*
28735693 AAATATT-TA
1 AAAAATTATA
28735702 AAAATATTA
1 AAAA-ATTA
28735711 AAATTAATAT
Statistics
Matches: 75, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
9 28 0.37
10 39 0.52
11 8 0.11
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (10 bp):
AAAAATTATA
Found at i:28735802 original size:19 final size:19
Alignment explanation
Indices: 28735605--28736038 Score: 97
Period size: 19 Copynumber: 22.6 Consensus size: 19
28735595 TAAAATGATT
*
28735605 AAAAATCATAAAAAGTCAT-T
1 AAAAATTATAAAAA-T-ATAT
28735625 AAAAATTATAAAAATCATA-
1 AAAAATTATAAAAAT-ATAT
*
28735644 AAAAA-TATTAAAGAT-TAT
1 AAAAATTA-TAAAAATATAT
* *
28735662 AAAAAATA-AGGAAAAAATTAT
1 AAAAATTATA--AAAATA-TAT
*
28735683 AAAATATT-T-AAAATATTT
1 AAAA-ATTATAAAAATATAT
*
28735701 AAAAA-TATTAAAAT-TAAT
1 AAAAATTATAAAAATAT-AT
* * *
28735719 ATAAACTTATAATACT-TAT
1 A-AAAATTATAAAAATATAT
* *
28735738 AAAAGCTTATAAATAT-TAT
1 AAAA-ATTATAAAAATATAT
* *
28735757 AAAAACATATAATAAATCTA-
1 AAAAA-TTATAA-AAATATAT
**
28735777 ATTAATTATAAAAATATAT
1 AAAAATTATAAAAATATAT
*
28735796 AAAAATTAATAAACATAT-T
1 AAAAATT-ATAAAAATATAT
* ** *
28735815 AAATATT-TAAATTTTTAT
1 AAAAATTATAAAAATATAT
* * *
28735833 AAAAACCTATAAAATTCT-T
1 AAAAA-TTATAAAAATATAT
*
28735852 AAAAATTAT-TAAATAT-T
1 AAAAATTATAAAAATATAT
* *
28735869 -AAAACTATTAAAAT-TGAT
1 AAAAATTATAAAAATAT-AT
* *
28735887 ATAAATTATAATAATATA-
1 AAAAATTATAAAAATATAT
* *
28735905 ATAAATTATAAATAGATTTAT
1 AAAAATTATAAA-A-ATATAT
*
28735926 -AAAATTAATAAAATATATTT
1 AAAAATT-ATAAAA-ATATAT
* *
28735946 AAAATATT-TAATAATTTAT
1 AAAA-ATTATAAAAATATAT
* *
28735965 AACAAGTAATAAAAAT-TCAT
1 AA-AAATTATAAAAATAT-AT
28735985 AAAAAACTTATAAATAATATA-
1 -AAAAA-TTATAAA-AATATAT
* * * *
28736006 ATAAATTCTAATAAATTGTAA
1 AAAAATTATAA-AAA-TATAT
28736027 AAAAATTATAAA
1 AAAAATTATAAA
28736039 TTATACCCCT
Statistics
Matches: 307, Mismatches: 62, Indels: 90
0.67 0.14 0.20
Matches are distributed among these distances:
16 9 0.03
17 21 0.07
18 49 0.16
19 102 0.33
20 82 0.27
21 34 0.11
22 9 0.03
23 1 0.00
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAAATTATAAAAATATAT
Found at i:28735805 original size:27 final size:29
Alignment explanation
Indices: 28735752--28735805 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
28735742 GCTTATAAAT
28735752 ATTATAAAAACATATAATAAATCTAATTA
1 ATTATAAAAACATATAATAAATCTAATTA
*
28735781 ATTATAAAAATATATAA-AAAT-TAAT
1 ATTATAAAAACATATAATAAATCTAAT
28735806 AAACATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 4 0.17
28 4 0.17
29 16 0.67
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (29 bp):
ATTATAAAAACATATAATAAATCTAATTA
Found at i:28735900 original size:10 final size:10
Alignment explanation
Indices: 28735887--28736037 Score: 57
Period size: 10 Copynumber: 15.1 Consensus size: 10
28735877 TAAAATTGAT
28735887 ATAAATTATA
1 ATAAATTATA
28735897 AT-AA-TATA
1 ATAAATTATA
28735905 ATAAATTATAA
1 ATAAATTAT-A
*
28735916 ATAGATT-T-
1 ATAAATTATA
*
28735924 ATAAAAT-TA
1 ATAAATTATA
*
28735933 ATAAAATATA
1 ATAAATTATA
* *
28735943 TTTAAAATATTTA
1 -AT-AAAT-TATA
*
28735956 ATAATTTATA
1 ATAAATTATA
* * *
28735966 ACAAGTAATA
1 ATAAATTATA
28735976 A-AAATTCATA
1 ATAAATT-ATA
*
28735986 AAAAACTTATA
1 ATAAA-TTATA
28735997 A-ATAA-TATA
1 ATA-AATTATA
*
28736006 ATAAATTCTA
1 ATAAATTATA
*
28736016 ATAAATTGTAA
1 ATAAATTAT-A
*
28736027 AAAAATTATA
1 ATAAATTATA
28736037 A
1 A
28736038 ATTATACCCC
Statistics
Matches: 108, Mismatches: 18, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
8 12 0.11
9 21 0.19
10 38 0.35
11 28 0.26
12 6 0.06
13 3 0.03
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (10 bp):
ATAAATTATA
Found at i:28735932 original size:20 final size:19
Alignment explanation
Indices: 28735889--28736002 Score: 60
Period size: 22 Copynumber: 5.7 Consensus size: 19
28735879 AAATTGATAT
*
28735889 AAATTAT-AATAATATA-A
1 AAATTATAAATAATTTATA
28735906 TAAATTATAAATAGATTTATA
1 -AAATTATAAATA-ATTTATA
28735927 AAATTAATAAAATATATTTA-A
1 AAATT-AT-AAATA-ATTTATA
28735948 AATATT-T-AATAATTTATA
1 AA-ATTATAAATAATTTATA
* *
28735966 ACAAGTAATAAA-AATTCATAAA
1 A-AA-TTATAAATAATT--TATA
28735988 AAACTTATAAATAAT
1 AAA-TTATAAATAAT
28736003 ATAATAAATT
Statistics
Matches: 76, Mismatches: 6, Indels: 24
0.72 0.06 0.23
Matches are distributed among these distances:
17 5 0.07
18 14 0.18
19 6 0.08
20 15 0.20
21 16 0.21
22 20 0.26
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (19 bp):
AAATTATAAATAATTTATA
Found at i:28736028 original size:50 final size:51
Alignment explanation
Indices: 28735892--28736029 Score: 124
Period size: 50 Copynumber: 2.7 Consensus size: 51
28735882 TTGATATAAA
* *
28735892 TTAT-AATAATATAATAAATTATAAATAGATTTATAAAATTAATAAAATATAT
1 TTATAAATAATATAATAAATTAT-AATAAATTTA-AAAATTAATAAAATATAC
* * * * * *
28735944 TTA-AAAT-ATTTAATAATTTATAACAAGTAATAAAAATTCATAAAA-A-AC
1 TTATAAATAATATAATAAATTATAATAAAT-TTAAAAATTAATAAAATATAC
*
28735992 TTATAAATAATATAATAAATTCTAATAAATTGTAAAAA
1 TTATAAATAATATAATAAATTATAATAAATT-TAAAAA
28736030 AATTATAAAT
Statistics
Matches: 67, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
48 4 0.06
49 5 0.07
50 38 0.57
51 14 0.21
52 6 0.09
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (51 bp):
TTATAAATAATATAATAAATTATAATAAATTTAAAAATTAATAAAATATAC
Found at i:28736773 original size:28 final size:25
Alignment explanation
Indices: 28736730--28736788 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 25
28736720 ATTTCATATT
*
28736730 TTTTTATAATTTATTAGATTTT-TTA
1 TTTTTATAATTTATTA-ATTTTAATA
28736755 TTTTTATAAGTTTGTATTAATTTTAATA
1 TTTTTATAA--TT-TATTAATTTTAATA
28736783 TTTTTA
1 TTTTTA
28736789 ATTTTTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 9 0.31
27 7 0.24
28 13 0.45
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (25 bp):
TTTTTATAATTTATTAATTTTAATA
Found at i:28736813 original size:26 final size:26
Alignment explanation
Indices: 28736719--28736814 Score: 70
Period size: 27 Copynumber: 3.6 Consensus size: 26
28736709 ATGTTTTGTT
* * * *
28736719 AATTTCATATTTTTTTATAATTTATTA
1 AATTTTATATTTTTTAAT-TTTTAATA
* * * *
28736746 GATTTTTTATTTTTATAAGTTTGT-ATT
1 AATTTTATATTTTT-TAA-TTTTTAATA
28736773 AATTTTA-ATATTTTTAATTTTTAATA
1 AATTTTATAT-TTTTTAATTTTTAATA
28736799 AATTTTATATTTTTTA
1 AATTTTATATTTTTTA
28736815 TGATTTTTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 11
0.69 0.16 0.15
Matches are distributed among these distances:
25 4 0.08
26 20 0.38
27 23 0.44
28 4 0.08
29 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (26 bp):
AATTTTATATTTTTTAATTTTTAATA
Found at i:28737047 original size:37 final size:37
Alignment explanation
Indices: 28736997--28737068 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
28736987 ATGCATGGGC
*
28736997 TGTTAGAATTAAGTGACCCGAATCCTTATTTAAATAT
1 TGTTAGAATTAAGTGACCCAAATCCTTATTTAAATAT
* *
28737034 TGTTAGAATTAAGTGACTCAAATTCTTATTTAAAT
1 TGTTAGAATTAAGTGACCCAAATCCTTATTTAAAT
28737069 CAAATACAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.40
Consensus pattern (37 bp):
TGTTAGAATTAAGTGACCCAAATCCTTATTTAAATAT
Found at i:28743932 original size:33 final size:33
Alignment explanation
Indices: 28743860--28743968 Score: 150
Period size: 33 Copynumber: 3.3 Consensus size: 33
28743850 AATTTTTTTA
*
28743860 AAAATTAATTAAATTAGGTTTTAGGGGTTTTAAG
1 AAAATTAATTAAATTAGGGTTTA-GGGTTTTAAG
* *
28743894 TAAATTAATTAAATTAGGGTTTAGTGTTTTAAG
1 AAAATTAATTAAATTAGGGTTTAGGGTTTTAAG
*
28743927 AAAATTAACTAAATTAGGGTTTAGGGTTTTTAA-
1 AAAATTAATTAAATTAGGGTTTAGGG-TTTTAAG
28743960 AAAA-TAATT
1 AAAATTAATT
28743969 TTGTGTTTAG
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
32 4 0.06
33 36 0.54
34 27 0.40
ACGTcount: A:0.40, C:0.01, G:0.17, T:0.41
Consensus pattern (33 bp):
AAAATTAATTAAATTAGGGTTTAGGGTTTTAAG
Found at i:28744314 original size:124 final size:125
Alignment explanation
Indices: 28744052--28744316 Score: 374
Period size: 124 Copynumber: 2.1 Consensus size: 125
28744042 ATTTTGTGTT
*
28744052 TTTTTCTACT-GTAGTTTCTGAAAAAATAAATTTGAGAAGACGATTTTGAAAAAATAGTGACAAA
1 TTTTTCTA-TAGTAGTTTCTGAAAAAATAAATTTGAGAAGACGATTCTGAAAAAATAGTGACAAA
* * *
28744116 AATGCTTCAAGCAGGATGCACTGTCAGCTAAAGTACTAAAAAAGCTCCCACATTGACGCTC
65 AATGCTTCAAACAGGATGCACTGTCAGCAAAAGTACTAAAAAAGCTCCCACATGGACGCTC
* * * *
28744177 TTTTTCTACAGTAGTTTCTG-AAAAATAATTTTGAGAAGACGGTTCT-AAAAAATAGTGTCAAAA
1 TTTTTCTATAGTAGTTTCTGAAAAAATAAATTTGAGAAGACGATTCTGAAAAAATAGTGACAAAA
* * * * *
28744240 ATGCTTCAAACAGGATGCATTGTCAGCAAAATTATTGAAAAAAGCTCGCACGTGGACGCTC
66 ATGCTTCAAACAGGATGCACTGTCAGCAAAAGTACT-AAAAAAGCTCCCACATGGACGCTC
28744301 TTTTTCTATAGTAGTT
1 TTTTTCTATAGTAGTT
28744317 CTTGCTTGGC
Statistics
Matches: 124, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
123 47 0.38
124 59 0.48
125 18 0.15
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (125 bp):
TTTTTCTATAGTAGTTTCTGAAAAAATAAATTTGAGAAGACGATTCTGAAAAAATAGTGACAAAA
ATGCTTCAAACAGGATGCACTGTCAGCAAAAGTACTAAAAAAGCTCCCACATGGACGCTC
Found at i:28747814 original size:18 final size:18
Alignment explanation
Indices: 28747788--28747830 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
28747778 GACTGGGAAA
* *
28747788 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
*
28747806 AGGATACATATGAGGGCT
1 AGGATACATATAAGGGCT
28747824 AGGATAC
1 AGGATAC
28747831 TCACCTAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.30, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:28750282 original size:51 final size:51
Alignment explanation
Indices: 28750209--28750424 Score: 222
Period size: 51 Copynumber: 4.3 Consensus size: 51
28750199 TATGAACATG
* * * *
28750209 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-GATAGATAATGGTCACA
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAT-GACAATGGTCACA
* * ** *
28750260 TGTGTAGTACTATGTGTAGGCTACCATGTGTACCGGATGACCTTGGTCACG
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATGACAATGGTCACA
* * * * * *
28750311 TGTGTAGTACTATGTGTAGGCTACTACGTGAACCAGA-AAGC-TTGATCACG
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATGA-CAATGGTCACA
**
28750361 TGTGTAGTACTATGTGTAGGCTACTACGTGTTTCGGATGACAATGGTCACA
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATGACAATGGTCACA
* *
28750412 TGGGTGGTACTAT
1 TGTGTAGTACTAT
28750425 ATGCAAACCA
Statistics
Matches: 136, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
50 43 0.32
51 90 0.66
52 3 0.02
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATGACAATGGTCACA
Found at i:28750398 original size:101 final size:101
Alignment explanation
Indices: 28750208--28750429 Score: 257
Period size: 101 Copynumber: 2.2 Consensus size: 101
28750198 CTATGAACAT
* * * * *
28750208 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAGATAATGGTCACATGTGTAGTACTAT
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGAAAGAT-ATGATCACATGTGTAGTACTAT
* **
28750273 GTGTAGGCTACCATGTGTACCGGATGACCTTGGTCAC
65 GTGTAGGCTACCACGTGTACCGGATGACAATGGTCAC
* * *
28750310 GTGTGTAGTACTATGTGTAGGCTACTACGTGAACCAGAAAGCT-TGATCACGTGTGTAGTACTAT
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGAACC-GAAAGATATGATCACATGTGTAGTACTAT
* **
28750374 GTGTAGGCTACTACGTGTTTCGGATGACAATGGTCAC
65 GTGTAGGCTACCACGTGTACCGGATGACAATGGTCAC
* * * *
28750411 ATGGGTGGTACTATATGCA
1 GTGTGTAGTACTATGTGCA
28750430 AACCACCGAA
Statistics
Matches: 100, Mismatches: 19, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
101 64 0.64
102 31 0.31
103 5 0.05
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (101 bp):
GTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGAAAGATATGATCACATGTGTAGTACTATG
TGTAGGCTACCACGTGTACCGGATGACAATGGTCAC
Found at i:28756251 original size:10 final size:10
Alignment explanation
Indices: 28756209--28756263 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
28756199 AAAAAATTCG
*
28756209 TTATTTGTAA
1 TTATTTATAA
28756219 TT-TTTAATAA
1 TTATTT-ATAA
28756229 TT-TTCTATAA
1 TTATT-TATAA
28756239 TTATTTATAA
1 TTATTTATAA
*
28756249 TTATTGATAA
1 TTATTTATAA
28756259 -TATTT
1 TTATTT
28756264 CTTGTCAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
9 7 0.18
10 29 0.74
11 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (10 bp):
TTATTTATAA
Found at i:28757876 original size:83 final size:87
Alignment explanation
Indices: 28757778--28757962 Score: 225
Period size: 83 Copynumber: 2.2 Consensus size: 87
28757768 TAATAAAGTG
* * * * * *
28757778 CAGGGGTCACACGGCCAAGCCACACACCCGTGTGTTAGGCCGTGTGAATAA-TTTGAGCATTCTG
1 CAGGGGACACACGGCCAAACCACACACCCGTGCGATAAGCCGTGTGAACAATTTTGAGCATTCTG
*
28757842 AC-T-TGC-AATTTATAAGATG
66 ACTTGTGCAAATTTATAAGATA
* ** *
28757861 TAGGGGACACACGGCCAAACCACACGTCCGTGCGATAAGCCGTGTGAACAATTTTGAGTATTCTG
1 CAGGGGACACACGGCCAAACCACACACCCGTGCGATAAGCCGTGTGAACAATTTTGAGCATTCTG
* *
28757926 ACTTGTGCAAATTTTTAAGTTA
66 ACTTGTGCAAATTTATAAGATA
28757948 CAGGGGACACACGGC
1 CAGGGGACACACGGC
28757963 TGAGGCACAC
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
83 42 0.50
84 14 0.17
85 1 0.01
86 3 0.04
87 24 0.29
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (87 bp):
CAGGGGACACACGGCCAAACCACACACCCGTGCGATAAGCCGTGTGAACAATTTTGAGCATTCTG
ACTTGTGCAAATTTATAAGATA
Found at i:28758699 original size:21 final size:21
Alignment explanation
Indices: 28758661--28758752 Score: 73
Period size: 21 Copynumber: 4.5 Consensus size: 21
28758651 ACATCGTTTC
*
28758661 CAGAAGC-C-TGAAAGCTAAA
1 CAGAAGCTCATGAGAGCTAAA
28758680 CAGAAGCTCATGAGAGCTAAA
1 CAGAAGCTCATGAGAGCTAAA
* * * * *
28758701 CAGAAACCCAT-ATGGGTTGAA
1 CAGAAGCTCATGA-GAGCTAAA
* * *
28758722 CAGAAGCTCGTAAGAGCTGAA
1 CAGAAGCTCATGAGAGCTAAA
28758743 CAGAAGCTCA
1 CAGAAGCTCA
28758753 AAAGAACTGG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 7 0.12
20 2 0.04
21 47 0.82
22 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.14
Consensus pattern (21 bp):
CAGAAGCTCATGAGAGCTAAA
Found at i:28758757 original size:21 final size:21
Alignment explanation
Indices: 28758673--28758757 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
28758663 GAAGCCTGAA
*
28758673 AGCTAAACAGAAGCTCATGAG
1 AGCTAAACAGAAGCTCATAAG
* * *
28758694 AGCTAAACAGAAACCCATATG
1 AGCTAAACAGAAGCTCATAAG
* * * *
28758715 GGTTGAACAGAAGCTCGTAAG
1 AGCTAAACAGAAGCTCATAAG
* *
28758736 AGCTGAACAGAAGCTCAAAAG
1 AGCTAAACAGAAGCTCATAAG
28758757 A
1 A
28758758 ACTGGGCAGA
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.14
Consensus pattern (21 bp):
AGCTAAACAGAAGCTCATAAG
Found at i:28762854 original size:16 final size:16
Alignment explanation
Indices: 28762833--28762866 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
28762823 TCTTTTTCAC
28762833 AAACCCTTGGTCTAAT
1 AAACCCTTGGTCTAAT
28762849 AAACCCTTGGTCTAAT
1 AAACCCTTGGTCTAAT
28762865 AA
1 AA
28762867 CTCTTGCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (16 bp):
AAACCCTTGGTCTAAT
Found at i:28766427 original size:42 final size:42
Alignment explanation
Indices: 28766381--28766467 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
28766371 AGCTAAAAAG
*
28766381 AAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTGAACAA
1 AAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTGAACAA
* * * *
28766423 AAGCTCGTACGAGCTGAACAGAAACTCATAAGAGTTGAACAA
1 AAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTGAACAA
28766465 AAG
1 AAG
28766468 ATCGAAAGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (42 bp):
AAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTGAACAA
Found at i:28766461 original size:21 final size:21
Alignment explanation
Indices: 28766350--28766463 Score: 95
Period size: 21 Copynumber: 5.4 Consensus size: 21
28766340 GAAGCCCGAA
* * *
28766350 AGCTGAACAGAAGCTCGTGAG
1 AGCTGAACAGAAACTCATAAG
* * *
28766371 AGCTAAAAAGAAGCTCATAAG
1 AGCTGAACAGAAACTCATAAG
* *
28766392 AGCTAAACAGAAACCCATAAG
1 AGCTGAACAGAAACTCATAAG
* * * *
28766413 GGTTGAACA-AAAGCTCGTACG
1 AGCTGAACAGAAA-CTCATAAG
28766434 AGCTGAACAGAAACTCATAAG
1 AGCTGAACAGAAACTCATAAG
*
28766455 AGTTGAACA
1 AGCTGAACA
28766464 AAAGATCGAA
Statistics
Matches: 73, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
20 3 0.04
21 67 0.92
22 3 0.04
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (21 bp):
AGCTGAACAGAAACTCATAAG
Found at i:28769276 original size:57 final size:59
Alignment explanation
Indices: 28769198--28769319 Score: 176
Period size: 57 Copynumber: 2.1 Consensus size: 59
28769188 CATTTTCATT
**
28769198 TTTTCATTTTTCATTTTGGAGAAAACCACCTTCATTTCCAAATGAGTC-CATTTCTCCA
1 TTTTCATTTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGAGTCTCATTTCTCCA
* * **
28769256 TTTTCA-TTTTCATTTTGGAGAAAATCATAATCATTTCCAAATGTTTCTCATTTCTCCA
1 TTTTCATTTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGAGTCTCATTTCTCCA
28769314 TTTTCA
1 TTTTCA
28769320 CTATTTTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 35 0.61
58 22 0.39
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.45
Consensus pattern (59 bp):
TTTTCATTTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGAGTCTCATTTCTCCA
Found at i:28772367 original size:17 final size:18
Alignment explanation
Indices: 28772349--28772383 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28772339 GCTGTGTCGG
28772349 CCACACGAGCGTGTGGGC
1 CCACACGAGCGTGTGGGC
* *
28772367 CCACATGGGCGTGTGGG
1 CCACACGAGCGTGTGGG
28772384 ATTATTGGGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.29, G:0.43, T:0.14
Consensus pattern (18 bp):
CCACACGAGCGTGTGGGC
Found at i:28772439 original size:33 final size:34
Alignment explanation
Indices: 28772396--28772471 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
28772386 TATTGGGCCA
28772396 GGCTGTGTGATCCACACGGCCAAGGCCA-TTTAG
1 GGCTGTGTGATCCACACGGCCAAGGCCATTTTAG
* * *
28772429 TGCTGTGTGATCTACATGGCCAAGGCCATTTTAG
1 GGCTGTGTGATCCACACGGCCAAGGCCATTTTAG
28772463 GGCTGTGTG
1 GGCTGTGTG
28772472 GGCCACACTG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
33 25 0.66
34 13 0.34
ACGTcount: A:0.18, C:0.22, G:0.32, T:0.28
Consensus pattern (34 bp):
GGCTGTGTGATCCACACGGCCAAGGCCATTTTAG
Found at i:28773785 original size:25 final size:25
Alignment explanation
Indices: 28773757--28773844 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
28773747 TTGTTTTTGA
* *
28773757 TAGTATATCCTGAAACTGCTATAGG
1 TAGTATATACTGAAACTACTATAGG
* *
28773782 TAGTATATACTGAGACTACTATAGA
1 TAGTATATACTGAAACTACTATAGG
* *
28773807 TAG-ACTATACTGAAAATACTCA-AGT
1 TAGTA-TATACTGAAACTACT-ATAGG
*
28773832 TAGTGTATACTGA
1 TAGTATATACTGA
28773845 TACTGTAGTA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.02
25 50 0.96
26 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (25 bp):
TAGTATATACTGAAACTACTATAGG
Found at i:28778416 original size:11 final size:11
Alignment explanation
Indices: 28778343--28778417 Score: 50
Period size: 11 Copynumber: 6.7 Consensus size: 11
28778333 ATTCCAAAAA
28778343 TAATATTATTT
1 TAATATTATTT
*
28778354 TAATAGTTTAATAT
1 TAATA--TT-ATTT
*
28778368 TAA-ATTAAATT
1 TAATATT-ATTT
28778379 TAATACTTATTT
1 TAATA-TTATTT
*
28778391 TAATAGTA-TT
1 TAATATTATTT
28778401 T--TATTATTT
1 TAATATTATTT
28778410 TAATATTA
1 TAATATTA
28778418 AAGTGATTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 3 0.06
11 20 0.40
12 9 0.18
13 5 0.10
14 6 0.12
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (11 bp):
TAATATTATTT
Found at i:28778502 original size:62 final size:59
Alignment explanation
Indices: 28778429--28778544 Score: 187
Period size: 62 Copynumber: 1.9 Consensus size: 59
28778419 AGTGATTGTC
*
28778429 TTAATATTAAATTTAATTTAATATTTATCTTGTAGATAAACATTATATTATTTTAATCAGAT
1 TTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAACATTATATTATTTTAATCAGAT
*
28778491 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTATTTTAAT
1 TTAATATTAAATTTAATCTAATATTTATCTTGATAAACATTATATTATTTTAAT
28778545 ATTAAAGTGA
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
59 22 0.42
60 1 0.02
61 1 0.02
62 28 0.54
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTGATAAACATTATATTATTTTAATCAGAT
Found at i:28779403 original size:41 final size:40
Alignment explanation
Indices: 28779353--28779538 Score: 291
Period size: 41 Copynumber: 4.5 Consensus size: 40
28779343 TTTAACATAT
* *
28779353 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTTAGA
1 TCACCGGCACTTAGCCTGCTAGG-TTATAACCTGATTCAGA
*
28779394 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGG-TTATAACCTGATTCAGA
*
28779435 TCACCGGCACTTAGCCTGCTAGGTTCATAACCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTT-ATAACCTGATTCAGA
*
28779476 TCACCGGCACTTAGCCTGCTAGGTTCATAACCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTT-ATAACCTGATTCAGA
28779517 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
28779539 ACTTAAAGTC
Statistics
Matches: 138, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
40 2 0.01
41 136 0.99
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (40 bp):
TCACCGGCACTTAGCCTGCTAGGTTATAACCTGATTCAGA
Found at i:28779562 original size:82 final size:81
Alignment explanation
Indices: 28779353--28779568 Score: 276
Period size: 82 Copynumber: 2.6 Consensus size: 81
28779343 TTTAACATAT
* * *
28779353 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTTAGATCACCGGCACGTAGCCTGCTAGGT
1 TCACCGGCACTTAGCCTGCTA-GCTTAAAGCCTGAATTAGATCACCGGCACTTAGCCTGCTAGGT
*
28779418 TTATAACCTGATTCAGA
65 TCATAACCTGATTCAGA
* *
28779435 TCACCGGCACTTAGCCTGCTAGGTTCATAA-CCTG-GTTCAGATCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAGCTT-A-AAGCCTGAATT-AGATCACCGGCACTTAGCCTGCTAG
*
28779498 GTTCATAACCTGGTTCAGA
63 GTTCATAACCTGATTCAGA
* *
28779517 TCACCGGCACTTAGCCTGCTAGACTTAAAGTCTGAATTA-ATTCACCGACACT
1 TCACCGGCACTTAGCCTGCTAG-CTTAAAGCCTGAATTAGA-TCACCGGCACT
28779569 ACATCTGCTA
Statistics
Matches: 117, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
81 8 0.07
82 104 0.89
83 5 0.04
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.27
Consensus pattern (81 bp):
TCACCGGCACTTAGCCTGCTAGCTTAAAGCCTGAATTAGATCACCGGCACTTAGCCTGCTAGGTT
CATAACCTGATTCAGA
Done.