Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 133 of 171
Found at i:41397885 original size:4 final size:4
Alignment explanation
Indices: 41397860--41397927 Score: 50
Period size: 4 Copynumber: 17.0 Consensus size: 4
41397850 GGTTGTTTTT
* * * * *
41397860 ATTA ATTA AATA ATTA AATA ATTA ATTTA GTATA ATGA AATA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA A-TTA AT-TA ATTA ATTA ATTA ATTA
*
41397910 ATTA A--A ATTA AATA ATTA
1 ATTA ATTA ATTA ATTA ATTA
41397928 TATATATTTA
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
2 2 0.04
4 40 0.83
5 6 0.12
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (4 bp):
ATTA
Found at i:41397900 original size:22 final size:22
Alignment explanation
Indices: 41397860--41397927 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
41397850 GGTTGTTTTT
41397860 ATTAATTAA--ATAATTAAATA
1 ATTAATTAAGTATAATTAAATA
* *
41397880 ATTAATTTAGTATAATGAAATA
1 ATTAATTAAGTATAATTAAATA
* *
41397902 ATTAATTAATTAAAATTAAATA
1 ATTAATTAAGTATAATTAAATA
41397924 ATTA
1 ATTA
41397928 TATATATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.20
22 32 0.80
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (22 bp):
ATTAATTAAGTATAATTAAATA
Found at i:41397997 original size:78 final size:74
Alignment explanation
Indices: 41397892--41398050 Score: 158
Period size: 78 Copynumber: 2.1 Consensus size: 74
41397882 TAATTTAGTA
* * ** *
41397892 TAATGAAATAATTAATTAATTAAAATTAAATAA-TTATATATATTTATTTAGGAAAATATTTTAA
1 TAATTAAATAATTAATTAATTAAAATTAAATAATTTA-ATATAATTAAATAAGAAAATATTTTAA
41397956 ATTAAATATT
65 ATTAAATATT
* ** * ** *
41397966 TAATTAAATAATTAATTGATTTAATACAATTATTTACTTTAATATAATTAAATAATTAAATCTTT
1 TAATTAAATAATTAATT-AATT-A-A-AATTAAATAATTTAATATAATTAAATAAGAAAATATTT
41398031 TAAATTAAATATT
62 TAAATTAAATATT
41398044 TAATTAA
1 TAATTAA
41398051 TTGATACTGT
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
74 16 0.24
75 3 0.04
76 1 0.01
77 1 0.01
78 44 0.65
79 3 0.04
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.46
Consensus pattern (74 bp):
TAATTAAATAATTAATTAATTAAAATTAAATAATTTAATATAATTAAATAAGAAAATATTTTAAA
TTAAATATT
Found at i:41398115 original size:112 final size:112
Alignment explanation
Indices: 41397966--41398489 Score: 835
Period size: 112 Copynumber: 4.8 Consensus size: 112
41397956 ATTAAATATT
* *
41397966 TAATT-AA-ATAATTAATTGATTTAATACAATTATTTACTTTAATATAATTAAATAATTAAATCT
1 TAATTAAACATAATTAATTGATTTAATATAATCATTTACTTTAATATAATTAAATAATTAAATCT
41398029 TTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACA
66 TTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACA
**
41398076 TAAAGAAACATAATTAATTGATTTAATATAATCATTTACTTTAATATAATTAAATAATTAAATCT
1 TAATTAAACATAATTAATTGATTTAATATAATCATTTACTTTAATATAATTAAATAATTAAATCT
41398141 TTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACA
66 TTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACA
* *
41398188 TAATTAAACATAATTAATTGATTTAATATAATTATTTATTTTAATATAATTAAATAATTAAATCT
1 TAATTAAACATAATTAATTGATTTAATATAATCATTTACTTTAATATAATTAAATAATTAAATCT
41398253 TTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACA
66 TTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACA
*
41398300 TAATTAAACATAATTAATTGATTTAATAT-A--A-TTA---T--T-TACTT---TAATTAAATCT
1 TAATTAAACATAATTAATTGATTTAATATAATCATTTACTTTAATATAATTAAATAATTAAATCT
* *
41398352 TTTAAATTAAATATTTAATTAATTGATATTGTTTATAATTTAATACA
66 TTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACA
* *
41398399 TAATTAAACATAATTAATTGACTTAATATAATCATTTACTTTAATATAATTAAATAATTAAATAT
1 TAATTAAACATAATTAATTGATTTAATATAATCATTTACTTTAATATAATTAAATAATTAAATCT
*
41398464 TTTAAATTAATTATTTAATTAATTGA
66 TTTAAATTAAATATTTAATTAATTGA
41398490 GTAGAAAAAA
Statistics
Matches: 384, Mismatches: 15, Indels: 28
0.90 0.04 0.07
Matches are distributed among these distances:
99 84 0.22
100 1 0.00
102 5 0.01
103 4 0.01
105 1 0.00
106 1 0.00
108 4 0.01
109 5 0.01
110 3 0.01
111 3 0.01
112 273 0.71
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.47
Consensus pattern (112 bp):
TAATTAAACATAATTAATTGATTTAATATAATCATTTACTTTAATATAATTAAATAATTAAATCT
TTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACA
Found at i:41398220 original size:18 final size:19
Alignment explanation
Indices: 41398197--41398240 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
41398187 ATAATTAAAC
41398197 ATAATTAATTGA-TTTAAT
1 ATAATTAATTGATTTTAAT
*
41398215 ATAATT-ATTTATTTTAAT
1 ATAATTAATTGATTTTAAT
41398233 ATAATTAA
1 ATAATTAA
41398241 ATAATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 18 0.78
19 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATAATTAATTGATTTTAAT
Found at i:41398350 original size:99 final size:99
Alignment explanation
Indices: 41398242--41398443 Score: 368
Period size: 99 Copynumber: 2.0 Consensus size: 99
41398232 TATAATTAAA
41398242 TAATTAAATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAA
1 TAATTAAATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAA
* *
41398307 ACATAATTAATTGATTTAATATAATTATTTACTT
66 ACATAATTAATTGACTTAATATAATCATTTACTT
* *
41398341 TAATTAAATCTTTTAAATTAAATATTTAATTAATTGATATTGTTTATAATTTAATACATAATTAA
1 TAATTAAATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAA
41398406 ACATAATTAATTGACTTAATATAATCATTTACTT
66 ACATAATTAATTGACTTAATATAATCATTTACTT
41398440 TAAT
1 TAAT
41398444 ATAATTAAAT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (99 bp):
TAATTAAATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAA
ACATAATTAATTGACTTAATATAATCATTTACTT
Found at i:41398366 original size:211 final size:218
Alignment explanation
Indices: 41397966--41398489 Score: 832
Period size: 211 Copynumber: 2.4 Consensus size: 218
41397956 ATTAAATATT
*
41397966 TAATT-AA-ATAATTAATTGATTTAATACAATTATTTACTTTAATATAATTAAATAATTAAATCT
1 TAATTAAACATAATTAATTGATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCT
41398029 TTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAAAGAAACATAATTAAT
66 TTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAAAGAAACATAATTAAT
41398094 TGATTTAATATAATCATTTACTTTAATATAATTAAATAATTAAATCTTTTAAATTAAATATTTAA
131 TGATTTAATATAA-CATTTA--TT-ATATAATT--ATAATTAAATCTTTTAAATTAAATATTTAA
41398159 TTAATTGATACTGTTTACAATTTAATACA
190 TTAATTGATACTGTTTACAATTTAATACA
*
41398188 TAATTAAACATAATTAATTGATTTAATATAATTATTTATTTTAATATAATTAAATAATTAAATCT
1 TAATTAAACATAATTAATTGATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCT
**
41398253 TTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAAACATAATTAAT
66 TTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAAAGAAACATAATTAAT
*
41398318 TGATTTAATAT-A-A-TTA-T-T-TACTT-TAATTAAATCTTTTAAATTAAATATTTAATTAATT
131 TGATTTAATATAACATTTATTATATAATTATAATTAAATCTTTTAAATTAAATATTTAATTAATT
* *
41398376 GATATTGTTTATAATTTAATACA
196 GATACTGTTTACAATTTAATACA
* * *
41398399 TAATTAAACATAATTAATTGACTTAATATAATCATTTACTTTAATATAATTAAATAATTAAATAT
1 TAATTAAACATAATTAATTGATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCT
*
41398464 TTTAAATTAATTATTTAATTAATTGA
66 TTTAAATTAAATATTTAATTAATTGA
41398490 GTAGAAAAAA
Statistics
Matches: 288, Mismatches: 12, Indels: 15
0.91 0.04 0.05
Matches are distributed among these distances:
211 142 0.49
214 4 0.01
215 1 0.00
217 1 0.00
220 3 0.01
221 1 0.00
222 5 0.02
223 3 0.01
224 128 0.44
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.47
Consensus pattern (218 bp):
TAATTAAACATAATTAATTGATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCT
TTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAAAGAAACATAATTAAT
TGATTTAATATAACATTTATTATATAATTATAATTAAATCTTTTAAATTAAATATTTAATTAATT
GATACTGTTTACAATTTAATACA
Found at i:41398468 original size:99 final size:99
Alignment explanation
Indices: 41398242--41398475 Score: 339
Period size: 99 Copynumber: 2.4 Consensus size: 99
41398232 TATAATTAAA
**
41398242 TAATTAAATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAA
1 TAATTAAATCTAATAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAA
* *
41398307 ACATAATTAATTGATTTAATATAATTATTTACTT
66 ACATAATTAATTGACTTAATATAATCATTTACTT
** * *
41398341 TAATTAAATCTTTTAAATTAAATATTTAATTAATTGATATTGTTTATAATTTAATACATAATTAA
1 TAATTAAATCTAATAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAA
41398406 ACATAATTAATTGACTTAATATAATCATTTACTT
66 ACATAATTAATTGACTTAATATAATCATTTACTT
41398440 TAA-TATAAT-TAA-ATAATTAAATATTTTAAATTAATT
1 TAATTA-AATCTAATA-AATTAAATA-TTT-AATTAATT
41398476 ATTTAATTAA
Statistics
Matches: 125, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
97 1 0.01
98 12 0.10
99 104 0.83
100 8 0.06
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (99 bp):
TAATTAAATCTAATAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAA
ACATAATTAATTGACTTAATATAATCATTTACTT
Found at i:41401095 original size:41 final size:41
Alignment explanation
Indices: 41401042--41401220 Score: 261
Period size: 41 Copynumber: 4.4 Consensus size: 41
41401032 GCTTATATAT
* * * *
41401042 AAAGCGCTGCTAATGACCCGACCTTTAGCGACGCTTGAGGT
1 AAAGCGCCGCTAATGACCCTACCTTTAGCGGCGCTTGAGGA
* * *
41401083 AAAGCGCCGCTAATGATCTTACCTTTAGCGGCGCTTGAGGG
1 AAAGCGCCGCTAATGACCCTACCTTTAGCGGCGCTTGAGGA
*
41401124 AAAGCGCCGCTAATGATCCTACCTTTAGCGGCGCTTGAGGA
1 AAAGCGCCGCTAATGACCCTACCTTTAGCGGCGCTTGAGGA
41401165 AAAGCGCCGCTAATGATCCC-ACCTTTAGCGGCGCTTGAGGA
1 AAAGCGCCGCTAATGA-CCCTACCTTTAGCGGCGCTTGAGGA
*
41401206 AAAGAGCCGCTAATG
1 AAAGCGCCGCTAATG
41401221 CTTTACCATT
Statistics
Matches: 127, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
41 125 0.98
42 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.27, T:0.21
Consensus pattern (41 bp):
AAAGCGCCGCTAATGACCCTACCTTTAGCGGCGCTTGAGGA
Found at i:41405059 original size:3 final size:3
Alignment explanation
Indices: 41405051--41405075 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41405041 AGAGTGACTT
41405051 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
41405076 AATTTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41409111 original size:31 final size:31
Alignment explanation
Indices: 41409073--41409146 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
41409063 TGGCAATGAA
41409073 TCCTTTTCCCGTATAACCCCAATCTCATCTT
1 TCCTTTTCCCGTATAACCCCAATCTCATCTT
* *
41409104 TCCTTTTCCCGTATAACCTCTATCTCATCTT
1 TCCTTTTCCCGTATAACCCCAATCTCATCTT
41409135 TCCTTTTCCCGT
1 TCCTTTTCCCGT
41409147 TCACTTTAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.15, C:0.38, G:0.04, T:0.43
Consensus pattern (31 bp):
TCCTTTTCCCGTATAACCCCAATCTCATCTT
Found at i:41413901 original size:41 final size:41
Alignment explanation
Indices: 41413855--41413932 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
41413845 ATAAGGATAT
41413855 CGGGGTATTTATACATGTTTCTAATGGTATTATTATATGAA
1 CGGGGTATTTATACATGTTTCTAATGGTATTATTATATGAA
41413896 CGGGGTATTTATACATGTTTCTAATGGTATTATTATA
1 CGGGGTATTTATACATGTTTCTAATGGTATTATTATA
41413933 GTTTTTAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.28, C:0.08, G:0.19, T:0.45
Consensus pattern (41 bp):
CGGGGTATTTATACATGTTTCTAATGGTATTATTATATGAA
Found at i:41419355 original size:21 final size:21
Alignment explanation
Indices: 41419317--41419370 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
41419307 AAATGTTATG
* *
41419317 TTTCTTTTGAATCGATTGTATT
1 TTTC-TTTAAATCAATTGTATT
*
41419339 TTTCTTTAAATCAATTGTGTT
1 TTTCTTTAAATCAATTGTATT
* *
41419360 TATGTTTAAAT
1 TTTCTTTAAAT
41419371 TGATTAACTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.24, C:0.07, G:0.11, T:0.57
Consensus pattern (21 bp):
TTTCTTTAAATCAATTGTATT
Found at i:41424625 original size:22 final size:23
Alignment explanation
Indices: 41424584--41424629 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
41424574 AAGACTAAAC
41424584 ATATTATTATTTTTTAAATATTT
1 ATATTATTATTTTTTAAATATTT
41424607 ATATTA-TATTATTTT-AATATTT
1 ATATTATTATT-TTTTAAATATTT
41424629 A
1 A
41424630 ATAATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
ATATTATTATTTTTTAAATATTT
Found at i:41429623 original size:14 final size:15
Alignment explanation
Indices: 41429597--41429656 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 15
41429587 ACCTTCAAAA
41429597 ATTTTATAAATTATT
1 ATTTTATAAATTATT
41429612 ATTTTA-AAATTATT
1 ATTTTATAAATTATT
41429626 A-TTTATAAA-T-TT
1 ATTTTATAAATTATT
*
41429638 ATTTTA-ATATTATAT
1 ATTTTATAAATTAT-T
41429653 ATTT
1 ATTT
41429657 ATTTATTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
12 5 0.13
13 10 0.26
14 13 0.33
15 11 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTATAAATTATT
Found at i:41440192 original size:3 final size:3
Alignment explanation
Indices: 41440184--41440212 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
41440174 GCGCAAGGAC
41440184 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
41440213 TCATGACGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:41448002 original size:12 final size:12
Alignment explanation
Indices: 41447985--41448067 Score: 75
Period size: 12 Copynumber: 6.9 Consensus size: 12
41447975 TTTTAATAGT
41447985 TTAAATTTAATA
1 TTAAATTTAATA
41447997 TTAAATTTAATA
1 TTAAATTTAATA
41448009 TTAAATTTAAT-
1 TTAAATTTAATA
* *
41448020 TTAAGACTT-ATT
1 TTAA-ATTTAATA
*
41448032 TTAATAGTATT-TTA
1 TTAA-A-T-TTAATA
41448046 TT-AATTTAATA
1 TTAAATTTAATA
41448057 TTAAATTTAAT
1 TTAAATTTAAT
41448068 TTTATTTTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
10 2 0.03
11 11 0.19
12 40 0.68
13 1 0.02
14 5 0.08
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (12 bp):
TTAAATTTAATA
Found at i:41450608 original size:22 final size:21
Alignment explanation
Indices: 41450583--41450623 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41450573 GGAATTTGTA
* *
41450583 TTGTTTTGTATTTTTATTTTGG
1 TTGTATTGT-TTTGTATTTTGG
41450605 TTGTATTGTTTTGTATTTT
1 TTGTATTGTTTTGTATTTT
41450624 AAGCATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.00, G:0.17, T:0.73
Consensus pattern (21 bp):
TTGTATTGTTTTGTATTTTGG
Found at i:41464223 original size:22 final size:22
Alignment explanation
Indices: 41464197--41464242 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
41464187 ATTTGATATC
41464197 TTCTTAAGGGGATTTTTCAGAT
1 TTCTTAAGGGGATTTTTCAGAT
41464219 TTCTTAAGGGGATTTTTCAGAT
1 TTCTTAAGGGGATTTTTCAGAT
41464241 TT
1 TT
41464243 GAATTCTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.09, G:0.22, T:0.48
Consensus pattern (22 bp):
TTCTTAAGGGGATTTTTCAGAT
Found at i:41465372 original size:21 final size:22
Alignment explanation
Indices: 41465346--41465390 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
41465336 GGCCAACAAA
41465346 CCTTTGAACACAAAAA-ATATC
1 CCTTTGAACACAAAAACATATC
* *
41465367 CCTTTGATCGCAAAAACATATC
1 CCTTTGAACACAAAAACATATC
41465389 CC
1 CC
41465391 CCTTCATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.40, C:0.29, G:0.07, T:0.24
Consensus pattern (22 bp):
CCTTTGAACACAAAAACATATC
Found at i:41472729 original size:37 final size:37
Alignment explanation
Indices: 41472671--41472742 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
41472661 AAAAATAATA
41472671 TTATTTTAATAGTTTAATATTAAATTAAATTTAAAAC
1 TTATTTTAATAGTTTAATATTAAATTAAATTTAAAAC
* * *
41472708 TTATTTTAATAGTATT-TTATTAATTTAATTTTAAA
1 TTATTTTAATAGT-TTAATATTAAATTAAATTTAAA
41472743 GTGATTATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 29 0.94
38 2 0.06
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (37 bp):
TTATTTTAATAGTTTAATATTAAATTAAATTTAAAAC
Found at i:41472739 original size:25 final size:27
Alignment explanation
Indices: 41472710--41472768 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
41472700 TTTAAAACTT
*
41472710 ATTTTAATAGT-ATTTTATTAAT-TTA
1 ATTTTAATAGTGATTATATTAATATTA
*
41472735 ATTTTAA-AGTGATTATCTTAATATTA
1 ATTTTAATAGTGATTATATTAATATTA
*
41472761 AATTTAAT
1 ATTTTAAT
41472769 TTAATGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 3 0.11
25 16 0.57
26 9 0.32
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (27 bp):
ATTTTAATAGTGATTATATTAATATTA
Found at i:41476207 original size:10 final size:10
Alignment explanation
Indices: 41476194--41476240 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
41476184 ATTAATGGAA
41476194 TTTGTATTGT
1 TTTGTATTGT
*
41476204 TTTGTATTTT
1 TTTGTATTGT
* *
41476214 TTTTTTTTG-
1 TTTGTATTGT
*
41476223 GTTGTATTGT
1 TTTGTATTGT
41476233 TTTGTATT
1 TTTGTATT
41476241 TTAAGCATAA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
9 6 0.21
10 22 0.79
ACGTcount: A:0.09, C:0.00, G:0.17, T:0.74
Consensus pattern (10 bp):
TTTGTATTGT
Found at i:41477775 original size:17 final size:17
Alignment explanation
Indices: 41477753--41477787 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
41477743 ACACGCTGGG
41477753 AGGAATTGTTTTGGCGT
1 AGGAATTGTTTTGGCGT
41477770 AGGAATTGTTTTGGCGT
1 AGGAATTGTTTTGGCGT
41477787 A
1 A
41477788 AAGTTGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.20, C:0.06, G:0.34, T:0.40
Consensus pattern (17 bp):
AGGAATTGTTTTGGCGT
Found at i:41478674 original size:23 final size:23
Alignment explanation
Indices: 41478648--41478706 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
41478638 CTGACGTGGC
*
41478648 ATCCAGTCAGCAACTTCTAAAAG
1 ATCCAGTCAGCAACTTCCAAAAG
* *
41478671 ATCCAGTCAGCAGCTTCCAGAAG
1 ATCCAGTCAGCAACTTCCAAAAG
* *
41478694 GTCTAGTCAGCAA
1 ATCCAGTCAGCAA
41478707 GGATGGACGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (23 bp):
ATCCAGTCAGCAACTTCCAAAAG
Found at i:41483254 original size:15 final size:15
Alignment explanation
Indices: 41483234--41483272 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
41483224 TATGGAATGA
41483234 TATTGTTT-TCCATGC
1 TATTGTTTGT-CATGC
*
41483249 TATTGTTTGTCGTGC
1 TATTGTTTGTCATGC
41483264 TATTGTTTG
1 TATTGTTTG
41483273 CTCTTCGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 21 0.95
16 1 0.05
ACGTcount: A:0.10, C:0.13, G:0.21, T:0.56
Consensus pattern (15 bp):
TATTGTTTGTCATGC
Found at i:41485593 original size:20 final size:20
Alignment explanation
Indices: 41485564--41485609 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
41485554 TTAAACCTTG
* *
41485564 AACCTCAAATC-CAAATCCTA
1 AACCTTAAATCTCAAA-CCGA
41485584 AACCTTAAATCTCAAACCGA
1 AACCTTAAATCTCAAACCGA
41485604 AACCTT
1 AACCTT
41485610 GAACCTCGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.43, C:0.33, G:0.02, T:0.22
Consensus pattern (20 bp):
AACCTTAAATCTCAAACCGA
Found at i:41485600 original size:14 final size:14
Alignment explanation
Indices: 41485531--41485601 Score: 58
Period size: 14 Copynumber: 5.1 Consensus size: 14
41485521 GTTCAAGAAT
*
41485531 CTTAAACCCCAAAC
1 CTTAAACCTCAAAC
*
41485545 ACTTAAACCTTAAAC
1 -CTTAAACCTCAAAC
*
41485560 CTTGAACCTCAAATC
1 CTTAAACCTCAAA-C
41485575 C--AAATCCT-AAAC
1 CTTAAA-CCTCAAAC
*
41485587 CTTAAATCTCAAAC
1 CTTAAACCTCAAAC
41485601 C
1 C
41485602 GAAACCTTGA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
12 2 0.04
13 7 0.16
14 22 0.49
15 14 0.31
ACGTcount: A:0.42, C:0.34, G:0.01, T:0.23
Consensus pattern (14 bp):
CTTAAACCTCAAAC
Found at i:41485614 original size:27 final size:27
Alignment explanation
Indices: 41485549--41485615 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
41485539 CCAAACACTT
*
41485549 AAACCTTAAACCTTGAACCTCAAATCC
1 AAACCTTAAACCTTAAACCTCAAATCC
*
41485576 AAATCC-TAAACCTTAAATCTCAAA-CC
1 AAA-CCTTAAACCTTAAACCTCAAATCC
*
41485602 GAAACCTTGAACCT
1 -AAACCTTAAACCT
41485616 CGAGATTCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 4 0.12
27 28 0.82
28 2 0.06
ACGTcount: A:0.42, C:0.31, G:0.04, T:0.22
Consensus pattern (27 bp):
AAACCTTAAACCTTAAACCTCAAATCC
Found at i:41487678 original size:38 final size:37
Alignment explanation
Indices: 41487636--41487727 Score: 94
Period size: 37 Copynumber: 2.5 Consensus size: 37
41487626 AGGCATAAAA
*
41487636 CCCGATAACATCGGCACAAAGGCCTGCTAGACACATAG
1 CCCGATAACATCGGCACAAA-GCATGCTAGACACATAG
** * * * *
41487674 CCCGATCTCATTGGCACGAAGCATGTTAGGCACATAG
1 CCCGATAACATCGGCACAAAGCATGCTAGACACATAG
* *
41487711 CCCGATGACACCGGCAC
1 CCCGATAACATCGGCAC
41487728 TAACACGAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
37 27 0.63
38 16 0.37
ACGTcount: A:0.29, C:0.33, G:0.23, T:0.15
Consensus pattern (37 bp):
CCCGATAACATCGGCACAAAGCATGCTAGACACATAG
Found at i:41507687 original size:96 final size:96
Alignment explanation
Indices: 41507515--41507689 Score: 219
Period size: 96 Copynumber: 1.8 Consensus size: 96
41507505 TTCGATTACC
** * * * * * *
41507515 TCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGATAAGGAA
1 TCGATTTGAAGAAAAATTGCACATAGTAAGTTAAGGCACAAAATTTCAGAAACGAAAATAAAGAA
**
41507580 ACATTGTCTCGATTAAGGGTATTTGATTATT
66 ACATTACCTCGATTAAGGGTATTTGATTATT
41507611 TCGATTTGAAGAAAAATTGCACATAGTAAGTTAAGGCACAAAATTTC-GAAACTGAAAATAAA-A
1 TCGATTTGAAGAAAAATTGCACATAGTAAGTTAAGGCACAAAATTTCAGAAAC-GAAAATAAAGA
*
41507674 GAATATTACCTCGATT
65 -AACATTACCTCGATT
41507690 TTGAAGTTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
95 5 0.08
96 61 0.92
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.29
Consensus pattern (96 bp):
TCGATTTGAAGAAAAATTGCACATAGTAAGTTAAGGCACAAAATTTCAGAAACGAAAATAAAGAA
ACATTACCTCGATTAAGGGTATTTGATTATT
Found at i:41508123 original size:29 final size:30
Alignment explanation
Indices: 41508060--41508200 Score: 133
Period size: 29 Copynumber: 4.7 Consensus size: 30
41508050 CATCTGGGAT
* * *
41508060 AAAATGGTAATTTTTGAAAGTTTTAGGGTCA
1 AAAATGG-AATTTTTGGAAGTTTGAAGGTCA
**
41508091 AAAATGGAATTTTTGGAAGTTTGGGGGT-A
1 AAAATGGAATTTTTGGAAGTTTGAAGGTCA
** * *
41508120 AAAATATAATTTTTGTAAGTTTCAAGGTCA
1 AAAATGGAATTTTTGGAAGTTTGAAGGTCA
* * * *
41508150 AAAATAGAATTTTTCGAAATTTGGAGGT-A
1 AAAATGGAATTTTTGGAAGTTTGAAGGTCA
*
41508179 AAAATGTAATTTTTGGAAGTTT
1 AAAATGGAATTTTTGGAAGTTT
41508201 TCGAGGCCAA
Statistics
Matches: 90, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
29 42 0.47
30 41 0.46
31 7 0.08
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTGAAGGTCA
Found at i:41508213 original size:59 final size:60
Alignment explanation
Indices: 41508060--41508222 Score: 197
Period size: 59 Copynumber: 2.8 Consensus size: 60
41508050 CATCTGGGAT
* * * * *
41508060 AAAATGGTAATTTTTGAAAGTTTTAG-GGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTA
1 AAAAT-GTAATTTTTGAAAGTTTTCGAGGTCAAAAATAGAATTTTTCGAAATTTGGAGGTA
* * *
41508120 AAAATATAATTTTTGTAAG-TTTCAAGGTCAAAAATAGAATTTTTCGAAATTTGGAGGTA
1 AAAATGTAATTTTTGAAAGTTTTCGAGGTCAAAAATAGAATTTTTCGAAATTTGGAGGTA
* * *
41508179 AAAATGTAATTTTTGGAAGTTTTCGAGG-CCAAAATATAATTTTT
1 AAAATGTAATTTTTGAAAGTTTTCGAGGTCAAAAATAGAATTTTT
41508223 GGATAGTTAG
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
58 3 0.03
59 73 0.83
60 12 0.14
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (60 bp):
AAAATGTAATTTTTGAAAGTTTTCGAGGTCAAAAATAGAATTTTTCGAAATTTGGAGGTA
Found at i:41508219 original size:30 final size:30
Alignment explanation
Indices: 41508067--41508230 Score: 138
Period size: 30 Copynumber: 5.5 Consensus size: 30
41508057 GATAAAATGG
* * *
41508067 TAATTTTTGAAAGTTTTAG-GGTCAAAAATG
1 TAATTTTTGGAAGTTTTCGAGGT-AAAAATA
* * *
41508097 GAATTTTTGGAAG-TTTGGGGGTAAAAATA
1 TAATTTTTGGAAGTTTTCGAGGTAAAAATA
* *
41508126 TAATTTTTGTAAG-TTTCAAGGTCAAAAATA
1 TAATTTTTGGAAGTTTTCGAGGT-AAAAATA
* * * * *
41508156 GAATTTTTCGAA-ATTTGGAGGTAAAAATG
1 TAATTTTTGGAAGTTTTCGAGGTAAAAATA
**
41508185 TAATTTTTGGAAGTTTTCGAGGCCAAAATA
1 TAATTTTTGGAAGTTTTCGAGGTAAAAATA
41508215 TAATTTTTGGATAGTT
1 TAATTTTTGGA-AGTT
41508231 AGGGACCTTC
Statistics
Matches: 107, Mismatches: 22, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
29 43 0.40
30 60 0.56
31 4 0.04
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.39
Consensus pattern (30 bp):
TAATTTTTGGAAGTTTTCGAGGTAAAAATA
Found at i:41509284 original size:15 final size:15
Alignment explanation
Indices: 41509232--41509288 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
41509222 TTAATAATAT
* *
41509232 TTATTATTATTACCG
1 TTATTAATATTACTG
* *
41509247 TTATTATTATTAATTG
1 TTATTAATATT-ACTG
* *
41509263 TTGTTAATATTAGTG
1 TTATTAATATTACTG
41509278 TTATTAATATT
1 TTATTAATATT
41509289 CATTTAATAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 24 0.69
16 11 0.31
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.58
Consensus pattern (15 bp):
TTATTAATATTACTG
Found at i:41509619 original size:11 final size:11
Alignment explanation
Indices: 41509599--41509644 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
41509589 TTTAAAATAT
41509599 AATT-TTTTAA
1 AATTATTTTAA
41509609 AATTATTTTAA
1 AATTATTTTAA
*
41509620 AATTAATTTAA
1 AATTATTTTAA
* *
41509631 AATCATTTTTA
1 AATTATTTTAA
41509642 AAT
1 AAT
41509645 ATAAAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
10 4 0.13
11 27 0.87
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTATTTTAA
Found at i:41509628 original size:12 final size:12
Alignment explanation
Indices: 41509582--41509643 Score: 56
Period size: 11 Copynumber: 5.1 Consensus size: 12
41509572 AGCAGAAAAT
*
41509582 AATTATTTTTAA
1 AATTAATTTTAA
41509594 AATATAATTTTTTAA
1 AAT-TAA--TTTTAA
41509609 AATT-ATTTTAA
1 AATTAATTTTAA
41509620 AATTAA-TTTAA
1 AATTAATTTTAA
* *
41509631 AATCATTTTTAA
1 AATTAATTTTAA
41509643 A
1 A
41509644 TATAAAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
11 19 0.45
12 10 0.24
13 3 0.07
14 1 0.02
15 9 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (12 bp):
AATTAATTTTAA
Found at i:41510565 original size:15 final size:16
Alignment explanation
Indices: 41510545--41510576 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41510535 AAATAATTTT
41510545 AAATTAT-TTTTAAAA
1 AAATTATATTTTAAAA
41510560 AAATTATATTTTAAAA
1 AAATTATATTTTAAAA
41510576 A
1 A
41510577 CTAATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATTATATTTTAAAA
Found at i:41510571 original size:17 final size:18
Alignment explanation
Indices: 41510549--41510589 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
41510539 AATTTTAAAT
41510549 TATTTTTAAAAA-AATTA
1 TATTTTTAAAAACAATTA
41510566 TA-TTTTAAAAACTAATTA
1 TATTTTTAAAAAC-AATTA
41510584 -ATTTTT
1 TATTTTT
41510590 GCTGACGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 9 0.43
17 3 0.14
18 9 0.43
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTTTAAAAACAATTA
Found at i:41522143 original size:7 final size:7
Alignment explanation
Indices: 41522104--41522176 Score: 58
Period size: 8 Copynumber: 9.7 Consensus size: 7
41522094 CTTTATCCTC
41522104 TTTAAAA
1 TTTAAAA
41522111 TTATAAAA
1 TT-TAAAA
*
41522119 TTT-TAA
1 TTTAAAA
*
41522125 TTTAATAT
1 TTTAA-AA
41522133 TTTAAAA
1 TTTAAAA
41522140 TTTATAAAAA
1 -TT-T-AAAA
*
41522150 TATAAAA
1 TTTAAAA
41522157 TATTAAAA
1 T-TTAAAA
41522165 TTTAAAA
1 TTTAAAA
41522172 TTTAA
1 TTTAA
41522177 TTTTGGCCTT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
6 5 0.09
7 20 0.38
8 22 0.42
9 2 0.04
10 4 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TTTAAAA
Found at i:41523762 original size:18 final size:18
Alignment explanation
Indices: 41523739--41523781 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
41523729 ATTCAAGGTG
41523739 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
41523757 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
41523775 TAATTAA
1 TAATTAA
41523782 AAATTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:41523947 original size:15 final size:15
Alignment explanation
Indices: 41523913--41523959 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
41523903 AATAATAACG
* *
41523913 TAAATAACTAAAACA
1 TAAATAATTAAAATA
* *
41523928 T-AATATTTTAAATA
1 TAAATAATTAAAATA
41523942 TAAATAATTAAAATA
1 TAAATAATTAAAATA
41523957 TAA
1 TAA
41523960 TTTGAGGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAATAATTAAAATA
Found at i:41529143 original size:15 final size:15
Alignment explanation
Indices: 41529113--41529154 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
41529103 GATTTAAAAA
*
41529113 ATTATATAATTATTT
1 ATTATATATTTATTT
*
41529128 ATTATATATTTGTTT
1 ATTATATATTTATTT
*
41529143 AATATA-ATTTAT
1 ATTATATATTTAT
41529155 ATGAAACATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
ATTATATATTTATTT
Found at i:41529645 original size:12 final size:12
Alignment explanation
Indices: 41529624--41529656 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
41529614 ACAATGTAAT
*
41529624 CATGTCTCTAGA
1 CATGTTTCTAGA
41529636 CATGTTTCTAGA
1 CATGTTTCTAGA
41529648 CATGTTTCT
1 CATGTTTCT
41529657 CATGTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.42
Consensus pattern (12 bp):
CATGTTTCTAGA
Found at i:41539573 original size:31 final size:31
Alignment explanation
Indices: 41539538--41539623 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
41539528 TACTTTTCTC
* *
41539538 ATTCATTTTGATACTTAAACTTGTTAGTTAA
1 ATTCATTTTGATCCTTAAACTTGATAGTTAA
* *
41539569 ATTCATTTTGGTCCTTAAATTTGATAGTTAA
1 ATTCATTTTGATCCTTAAACTTGATAGTTAA
41539600 ATTCATTTTGATCCTTAAACTTGA
1 ATTCATTTTGATCCTTAAACTTGA
41539624 AAATTATAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (31 bp):
ATTCATTTTGATCCTTAAACTTGATAGTTAA
Found at i:41539882 original size:25 final size:27
Alignment explanation
Indices: 41539853--41539914 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 27
41539843 AATTAAAATG
41539853 AAATAAAAAT-AAAATT-TTATTCCAT
1 AAATAAAAATGAAAATTATTATTCCAT
41539878 AAAT-AAAATGAAAATTGAATTATTCCAT
1 AAATAAAAATGAAAATT--ATTATTCCAT
41539906 AAATAAAAA
1 AAATAAAAA
41539915 ACCTCCCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.16
25 10 0.31
28 13 0.41
29 4 0.12
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (27 bp):
AAATAAAAATGAAAATTATTATTCCAT
Found at i:41544560 original size:5 final size:5
Alignment explanation
Indices: 41544550--41544584 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
41544540 TCTGTTTTCA
41544550 CACTC CACTC CACTC CACTC CACTC CACTC CACTC
1 CACTC CACTC CACTC CACTC CACTC CACTC CACTC
41544585 TATCGTTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.20, C:0.60, G:0.00, T:0.20
Consensus pattern (5 bp):
CACTC
Found at i:41545625 original size:18 final size:18
Alignment explanation
Indices: 41545592--41545627 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41545582 TCTGTGTCTA
* *
41545592 CATCTGTATTTGTATTTG
1 CATCTGTATCTATATTTG
41545610 CATCTGTATCTATATTTG
1 CATCTGTATCTATATTTG
41545628 TATTAACATT
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:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (18 bp):
CATCTGTATCTATATTTG
Found at i:41550482 original size:2 final size:2
Alignment explanation
Indices: 41550475--41550500 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41550465 AGAAAGACAA
41550475 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
41550501 GGAAAGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41556387 original size:16 final size:15
Alignment explanation
Indices: 41556348--41556389 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
41556338 AAAAAGTCAC
41556348 AAATAATAAACAAAT
1 AAATAATAAACAAAT
*
41556363 AAATCAATAATACACAT
1 AAAT-AATAA-ACAAAT
41556380 AAATAATAAA
1 AAATAATAAA
41556390 TGTACATTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 5 0.21
16 10 0.42
17 9 0.38
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATAATAAACAAAT
Found at i:41556671 original size:17 final size:17
Alignment explanation
Indices: 41556618--41556676 Score: 75
Period size: 17 Copynumber: 3.4 Consensus size: 17
41556608 CAAGCCCATT
41556618 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
41556636 -TTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
41556653 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
41556670 TTTAAAT
1 TTTAAAT
41556677 AAATAAAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 22 0.61
18 14 0.39
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:41557344 original size:3 final size:3
Alignment explanation
Indices: 41557336--41557367 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41557326 TATATATTTA
41557336 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41557368 GAAAGTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41558263 original size:30 final size:30
Alignment explanation
Indices: 41558227--41558324 Score: 101
Period size: 30 Copynumber: 3.3 Consensus size: 30
41558217 AGAAATCATA
41558227 TTTTGACCCCCGAACTTTCCAAAATTTTAT
1 TTTTGACCCCCGAACTTTCCAAAATTTTAT
* * * **
41558257 TTTTGA-CCCCGAATTTTCTAAAAAATACAT
1 TTTTGACCCCCGAACTTTC-CAAAATTTTAT
* *
41558287 TTTT-ACCCTCGAACTTTTCAAAATTTTAT
1 TTTTGACCCCCGAACTTTCCAAAATTTTAT
*
41558316 TTTTAACCC
1 TTTTGACCC
41558325 TAAAAATTAC
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
29 23 0.43
30 30 0.57
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (30 bp):
TTTTGACCCCCGAACTTTCCAAAATTTTAT
Found at i:41558318 original size:59 final size:57
Alignment explanation
Indices: 41558226--41558488 Score: 270
Period size: 59 Copynumber: 4.6 Consensus size: 57
41558216 CAGAAATCAT
* * *
41558226 ATTTTGACCCCCGAACTTTCCAAAATTTTATTTTTGACCCCGAATTTTCTAAAAAATAC
1 ATTTTTACCCCCGAACTTTCCAAAATTCTATTTTTGA-CCC-AATTTTCCAAAAAATAC
* * * * *
41558285 ATTTTTACCCTCGAACTTTTCAAAATTTTATTTTTAACCC-----T--AAAAATTAC
1 ATTTTTACCCCCGAACTTTCCAAAATTCTATTTTTGACCCAATTTTCCAAAAAATAC
* * * *
41558335 AATTTTACCCCCAAACTTTCTAAAATTCAATTTTTGACCCTAATTTTTCCAAAAAATAC
1 ATTTTTACCCCCGAACTTTCCAAAATTCTATTTTTGACCC-AA-TTTTCCAAAAAATAC
* *
41558394 ATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCCCAAATTTTCCAAAAATTAC
1 ATTTTTACCCCCGAACTTTCCAAAATTCTATTTTTGA-CCC-AATTTTCCAAAAAATAC
* *
41558453 ATTTTTACCTCTCGAACTTTCCAAAATTCCATTTTT
1 ATTTTTACC-CCCGAACTTTCCAAAATTCTATTTTT
41558489 AACCTTGATT
Statistics
Matches: 172, Mismatches: 21, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
50 40 0.23
52 1 0.01
57 1 0.01
58 3 0.02
59 97 0.56
60 30 0.17
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (57 bp):
ATTTTTACCCCCGAACTTTCCAAAATTCTATTTTTGACCCAATTTTCCAAAAAATAC
Found at i:41558341 original size:50 final size:50
Alignment explanation
Indices: 41558274--41558377 Score: 129
Period size: 50 Copynumber: 2.1 Consensus size: 50
41558264 CCCGAATTTT
* * * **
41558274 CTAAAAAATACATTTTTACCCTCGAACTTT-TCAAAATTTTATTTTTAACC
1 CTAAAAAATACAATTTTACCCCCAAACTTTCT-AAAATTCAATTTTTAACC
* *
41558324 CTAAAAATTACAATTTTACCCCCAAACTTTCTAAAATTCAATTTTTGACC
1 CTAAAAAATACAATTTTACCCCCAAACTTTCTAAAATTCAATTTTTAACC
41558374 CTAA
1 CTAA
41558378 TTTTTCCAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
50 45 0.98
51 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (50 bp):
CTAAAAAATACAATTTTACCCCCAAACTTTCTAAAATTCAATTTTTAACC
Found at i:41558414 original size:30 final size:30
Alignment explanation
Indices: 41558326--41558638 Score: 170
Period size: 29 Copynumber: 10.6 Consensus size: 30
41558316 TTTTAACCCT
* *
41558326 AAAAATTACAATTTTACCCCCAAACTTT-C
1 AAAAATTACATTTTTACCCCCGAACTTTCC
* * *
41558355 TAAAATT-CAATTTTTGA--CCCTAATTTTTCC
1 AAAAATTAC-ATTTTT-ACCCCCGAA-CTTTCC
*
41558385 AAAAAATACATTTTTACCCCCGAACTTTCC
1 AAAAATTACATTTTTACCCCCGAACTTTCC
* * *
41558415 -AAAATTCCATTTTTGA-CCCCAAATTTTCC
1 AAAAATTACATTTTT-ACCCCCGAACTTTCC
*
41558444 AAAAATTACATTTTTACCTCTCGAACTTTCC
1 AAAAATTACATTTTTACC-CCCGAACTTTCC
* * ** **
41558475 -AAAATTCCATTTTTAACCTTGATTTTTCC
1 AAAAATTACATTTTTACCCCCGAACTTTCC
* *
41558504 -AAAATTACCA-TTTTACCCCCGAA-TGTCT
1 AAAAATTA-CATTTTTACCCCCGAACTTTCC
* * * * *
41558532 AAAAATTCCATTTTAAACCTCAAACTTTCC
1 AAAAATTACATTTTTACCCCCGAACTTTCC
* * *
41558562 -AAAATTACCA-TTTTACCCTCGAA-TGTCT
1 AAAAATTA-CATTTTTACCCCCGAACTTTCC
* **
41558590 AAAAATTCCATTTTTGA-CCTTGAACTTTCC
1 AAAAATTACATTTTT-ACCCCCGAACTTTCC
*
41558620 CAAAATTACCA-TTTTACCC
1 AAAAATTA-CATTTTTACCC
41558639 TCGAGTGTCC
Statistics
Matches: 215, Mismatches: 47, Indels: 43
0.70 0.15 0.14
Matches are distributed among these distances:
28 16 0.07
29 111 0.52
30 71 0.33
31 17 0.08
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAAATTACATTTTTACCCCCGAACTTTCC
Found at i:41558427 original size:109 final size:110
Alignment explanation
Indices: 41558226--41558433 Score: 294
Period size: 109 Copynumber: 1.9 Consensus size: 110
41558216 CAGAAATCAT
* ** *
41558226 ATTTTGACCCCCGAACTTTCCAAAATTTTATTTTTGACCCCGAATTTTCTAAAAAATACATTTTT
1 ATTTTGACCCCCAAACTTTCCAAAATTCAATTTTTGACCCCGAATTTTCCAAAAAATACATTTTT
* * **
41558291 ACCCTCGAACTTTTCAAAATTTTATTTTTAACCCTAAAAATTACA
66 ACCCCCGAACTTTCCAAAATTCCATTTTTAACCCTAAAAATTACA
* *
41558336 ATTTT-ACCCCCAAACTTTCTAAAATTCAATTTTTGA-CCCTAATTTTTCCAAAAAATACATTTT
1 ATTTTGACCCCCAAACTTTCCAAAATTCAATTTTTGACCCCGAA-TTTTCCAAAAAATACATTTT
*
41558399 TACCCCCGAACTTTCCAAAATTCCATTTTTGACCC
65 TACCCCCGAACTTTCCAAAATTCCATTTTTAACCC
41558434 CAAATTTTCC
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
108 5 0.06
109 76 0.88
110 5 0.06
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.39
Consensus pattern (110 bp):
ATTTTGACCCCCAAACTTTCCAAAATTCAATTTTTGACCCCGAATTTTCCAAAAAATACATTTTT
ACCCCCGAACTTTCCAAAATTCCATTTTTAACCCTAAAAATTACA
Found at i:41558561 original size:58 final size:58
Alignment explanation
Indices: 41558327--41558662 Score: 306
Period size: 59 Copynumber: 5.7 Consensus size: 58
41558317 TTTAACCCTA
* * * * * *
41558327 AAAATTACAATTTTACCCCCAAACTTTCTAAAATTCAATTTTTGACC-CTAATTTTTCC
1 AAAATTACCATTTTACCCCCGAACTGTCCAAAATTCCATTTTTGACCTC-AAATTTTCC
* * *
41558385 AAAAAATA-CATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCCCAAATTTTCC
1 -AAAATTACCA-TTTTACCCCCGAACTGTCCAAAATTCCATTTTTGACCTCAAATTTTCC
* * * ** *
41558444 AAAAATTA-CATTTTTACCTCTCGAACTTTCCAAAATTCCATTTTTAACCTTGATTTTTCC
1 -AAAATTACCA-TTTTACC-CCCGAACTGTCCAAAATTCCATTTTTGACCTCAAATTTTCC
* ** *
41558504 AAAATTACCATTTTACCCCCGAA-TGTCTAAAAATTCCATTTTAAACCTCAAACTTTCC
1 AAAATTACCATTTTACCCCCGAACTGTC-CAAAATTCCATTTTTGACCTCAAATTTTCC
* * * * *
41558562 AAAATTACCATTTTACCCTCGAA-TGTCTAAAAATTCCATTTTTGACCTTGAACTTTCCC
1 AAAATTACCATTTTACCCCCGAACTGTC-CAAAATTCCATTTTTGACC-TCAAATTTTCC
* *
41558621 AAAATTACCATTTTACCCTCG-AGTGTCCAAAATTACCATTTT
1 AAAATTACCATTTTACCCCCGAACTGTCCAAAATT-CCATTTT
41558663 ACCTCTAGGT
Statistics
Matches: 240, Mismatches: 29, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
57 3 0.01
58 81 0.34
59 118 0.49
60 38 0.16
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAACTGTCCAAAATTCCATTTTTGACCTCAAATTTTCC
Found at i:41558677 original size:28 final size:28
Alignment explanation
Indices: 41558619--41558680 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
41558609 TTGAACTTTC
* *
41558619 CCAAAATTACCATTTTACCCTCGAGTGT
1 CCAAAATTACCATTTTACCCTAGAGTAT
41558647 CCAAAATTACCATTTTACCTCTAG-GTAT
1 CCAAAATTACCATTTTACC-CTAGAGTAT
41558675 CCAAAA
1 CCAAAA
41558681 ATCTCATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 28 0.90
29 3 0.10
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCTAGAGTAT
Found at i:41560706 original size:7 final size:8
Alignment explanation
Indices: 41560689--41560714 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
41560679 TTTACTTTCG
41560689 AAAAATAA
1 AAAAATAA
41560697 AAAAATAA
1 AAAAATAA
41560705 AAAAATAA
1 AAAAATAA
41560713 AA
1 AA
41560715 TAGAAGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:41572238 original size:23 final size:23
Alignment explanation
Indices: 41572212--41572280 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
41572202 GAATTCTCTA
41572212 GCATGAACAATAAATATTCTTTG
1 GCATGAACAATAAATATTCTTTG
**
41572235 GCATGAACAATAAATATTCTCCG
1 GCATGAACAATAAATATTCTTTG
* * *
41572258 GCATGAACAGTGAATACTCTTTG
1 GCATGAACAATAAATATTCTTTG
41572281 AAAAATATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (23 bp):
GCATGAACAATAAATATTCTTTG
Found at i:41572909 original size:23 final size:22
Alignment explanation
Indices: 41572891--41572966 Score: 93
Period size: 21 Copynumber: 3.5 Consensus size: 22
41572881 ATAATTGTTG
41572891 CTTTTCATGCCAGAAAATTTTA
1 CTTTTCATGCCAGAAAATTTTA
*
41572913 -TTGTTCATGCCAGAGAATTTTTA
1 CTT-TTCATGCCAGA-AAATTTTA
*
41572936 CTATTCATGCCA-AAAATTTTA
1 CTTTTCATGCCAGAAAATTTTA
*
41572957 CTGTTCATGC
1 CTTTTCATGC
41572967 TAGAGAATCT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
21 18 0.38
22 12 0.26
23 16 0.34
24 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (22 bp):
CTTTTCATGCCAGAAAATTTTA
Found at i:41572919 original size:22 final size:22
Alignment explanation
Indices: 41572894--41572966 Score: 103
Period size: 23 Copynumber: 3.3 Consensus size: 22
41572884 ATTGTTGCTT
*
41572894 TTCATGCCAGAAAATTTTATTG
1 TTCATGCCAGAAAATTTTACTG
* *
41572916 TTCATGCCAGAGAATTTTTACTA
1 TTCATGCCAGA-AAATTTTACTG
41572939 TTCATGCCA-AAAATTTTACTG
1 TTCATGCCAGAAAATTTTACTG
41572960 TTCATGC
1 TTCATGC
41572967 TAGAGAATCT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
21 16 0.36
22 12 0.27
23 17 0.38
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (22 bp):
TTCATGCCAGAAAATTTTACTG
Found at i:41572987 original size:44 final size:45
Alignment explanation
Indices: 41572894--41572979 Score: 129
Period size: 44 Copynumber: 1.9 Consensus size: 45
41572884 ATTGTTGCTT
* * *
41572894 TTCATGCCAGAAAATTTTATTGTTCATGCCAGAGAATTTTTACTA
1 TTCATGCCAGAAAATTTTACTGTTCATGCCAGAGAATCTTCACTA
*
41572939 TTCATGCCA-AAAATTTTACTGTTCATGCTAGAGAATCTTCA
1 TTCATGCCAGAAAATTTTACTGTTCATGCCAGAGAATCTTCA
41572980 TTGTTCATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 28 0.76
45 9 0.24
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (45 bp):
TTCATGCCAGAAAATTTTACTGTTCATGCCAGAGAATCTTCACTA
Found at i:41576801 original size:20 final size:20
Alignment explanation
Indices: 41576751--41576801 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
41576741 AAGTTCTGGG
41576751 TCAATAAGTTCAGAATTTTA
1 TCAATAAGTTCAGAATTTTA
*
41576771 -AAATATA-TTCAGAATTTTA
1 TCAATA-AGTTCAGAATTTTA
41576790 TCAATAAGTTCA
1 TCAATAAGTTCA
41576802 TTTTCATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (20 bp):
TCAATAAGTTCAGAATTTTA
Found at i:41578753 original size:24 final size:24
Alignment explanation
Indices: 41578714--41578811 Score: 169
Period size: 24 Copynumber: 4.1 Consensus size: 24
41578704 TGATGTGGGA
41578714 CCAATAGAAAATGAAGATCCAACT
1 CCAATAGAAAATGAAGATCCAACT
* *
41578738 CCAGTAGAAAAAGAAGATCCAACT
1 CCAATAGAAAATGAAGATCCAACT
*
41578762 CTAATAGAAAATGAAGATCCAACT
1 CCAATAGAAAATGAAGATCCAACT
41578786 CCAATAGAAAATGAAGATCCAACT
1 CCAATAGAAAATGAAGATCCAACT
41578810 CC
1 CC
41578812 GTGTATGGTG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.49, C:0.21, G:0.13, T:0.16
Consensus pattern (24 bp):
CCAATAGAAAATGAAGATCCAACT
Found at i:41581862 original size:21 final size:21
Alignment explanation
Indices: 41581832--41581872 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
41581822 TTAATATTAC
41581832 TTACTACTAAC-AAATTAAAA
1 TTACTACTAACAAAATTAAAA
41581852 TTACTTACTAACAAAATTAAA
1 TTAC-TACTAACAAAATTAAA
41581873 TTAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 7 0.37
22 8 0.42
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.32
Consensus pattern (21 bp):
TTACTACTAACAAAATTAAAA
Found at i:41582262 original size:4 final size:4
Alignment explanation
Indices: 41582255--41582329 Score: 73
Period size: 4 Copynumber: 18.2 Consensus size: 4
41582245 TTCTCATTCA
* *
41582255 TTCT TTCT GTTCT CTCC TTCT TTCT TTCT TT-T TTCT CCTTC- TTCT TTCT
1 TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT TTCT --TTCT TTCT TTCT
*
41582304 TTCT TTTT TTCT TTCCT TTCT TTCT T
1 TTCT TTCT TTCT TT-CT TTCT TTCT T
41582330 ATTCTTGTCT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
3 6 0.10
4 42 0.71
5 8 0.14
6 3 0.05
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.71
Consensus pattern (4 bp):
TTCT
Found at i:41582279 original size:21 final size:19
Alignment explanation
Indices: 41582255--41582307 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 19
41582245 TTCTCATTCA
41582255 TTCTTTCTGTTCTCTCCTTC
1 TTCTTTCT-TTCTCTCCTTC
*
41582275 TTTCTTTCTTTTTTCTCCTTC
1 -TTCTTTC-TTTCTCTCCTTC
41582296 TTCTTTCTTTCT
1 TTCTTTCTTTCT
41582308 TTTTTTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 7 0.24
21 17 0.59
22 1 0.03
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (19 bp):
TTCTTTCTTTCTCTCCTTC
Found at i:41582303 original size:24 final size:22
Alignment explanation
Indices: 41582271--41582329 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 22
41582261 CTGTTCTCTC
41582271 CTTCTTTCTTTCTTTTTTCTCCTT
1 CTTCTTTCTTTCTTTTTT-T-CTT
41582295 CTTCTTTCTTTCTTTTTTTCTT
1 CTTCTTTCTTTCTTTTTTTCTT
*
41582317 -TCCTTTCTTTCTT
1 CTTCTTTCTTTCTT
41582330 ATTCTTGTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 12 0.35
22 3 0.09
23 1 0.03
24 18 0.53
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (22 bp):
CTTCTTTCTTTCTTTTTTTCTT
Found at i:41582498 original size:12 final size:13
Alignment explanation
Indices: 41582470--41582506 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
41582460 ATACACACCT
41582470 AAAAATAAATACA
1 AAAAATAAATACA
*
41582483 AAAAGTAAATACA
1 AAAAATAAATACA
41582496 AAAAA-AAATAC
1 AAAAATAAATAC
41582507 TTGACACGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.14
Consensus pattern (13 bp):
AAAAATAAATACA
Found at i:41582770 original size:4 final size:4
Alignment explanation
Indices: 41582750--41582814 Score: 58
Period size: 4 Copynumber: 15.2 Consensus size: 4
41582740 GGGAGAGAAG
* * * *
41582750 AAGA AGGA AAGGA AAGA AAGA AAGA AAGAA AAAA AAGA AAAA AAGGA GAGAA
1 AAGA AAGA AA-GA AAGA AAGA AAGA AAG-A AAGA AAGA AAGA AA-GA AAG-A
41582802 AAGA AAGA AAGA A
1 AAGA AAGA AAGA A
41582815 GGAGAATGAG
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
4 37 0.76
5 12 0.24
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:41582810 original size:9 final size:9
Alignment explanation
Indices: 41582745--41582811 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
41582735 GCTACGGGAG
41582745 AGAAGAAGAA
1 AGAA-AAGAA
* *
41582755 GGAAAGGAA
1 AGAAAAGAA
41582764 AG-AAAGAA
1 AGAAAAGAA
41582772 AG-AAAGAA
1 AGAAAAGAA
*
41582780 AAAAAAGAA
1 AGAAAAGAA
*
41582789 A-AAAAGGAG
1 AGAAAA-GAA
41582798 AGAAAAGAA
1 AGAAAAGAA
41582807 AGAAA
1 AGAAA
41582812 GAAGGAGAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
8 18 0.38
9 22 0.47
10 7 0.15
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (9 bp):
AGAAAAGAA
Found at i:41582814 original size:13 final size:13
Alignment explanation
Indices: 41582745--41582814 Score: 63
Period size: 13 Copynumber: 5.3 Consensus size: 13
41582735 GCTACGGGAG
*
41582745 AGAAGAAGAAGGAA
1 AGAA-AAGAAAGAA
*
41582759 AGGAAAGAAAGAA
1 AGAAAAGAAAGAA
*
41582772 AG-AAAGAAAAAAA
1 AGAAAAG-AAAGAA
*
41582785 AGAAAA-AAAGGAG
1 AGAAAAGAAA-GAA
41582798 AGAAAAGAAAGAA
1 AGAAAAGAAAGAA
41582811 AGAA
1 AGAA
41582815 GGAGAATGAG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
12 7 0.15
13 30 0.65
14 9 0.20
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAAGAA
Found at i:41582818 original size:21 final size:21
Alignment explanation
Indices: 41582747--41582819 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
41582737 TACGGGAGAG
* *
41582747 AAGAAGAAG-GAAAGGAAAGA
1 AAGAAGGAGAGAAAAGAAAGA
* * *
41582767 AAGAAAGAAAGAAAAAAAAGAA
1 AAGAAGGAGAGAAAAGAAAG-A
*
41582789 AAAAAGGAGAGAAAAGAAAGA
1 AAGAAGGAGAGAAAAGAAAGA
41582810 AAGAAGGAGA
1 AAGAAGGAGA
41582820 ATGAGGCTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
20 6 0.15
21 18 0.44
22 17 0.41
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (21 bp):
AAGAAGGAGAGAAAAGAAAGA
Found at i:41582882 original size:12 final size:12
Alignment explanation
Indices: 41582865--41582895 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
41582855 ATTTTGTGTG
41582865 TTTATTTTTAAA
1 TTTATTTTTAAA
41582877 TTTATTTTTAAA
1 TTTATTTTTAAA
*
41582889 GTTATTT
1 TTTATTT
41582896 AATTTGTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (12 bp):
TTTATTTTTAAA
Found at i:41583055 original size:5 final size:5
Alignment explanation
Indices: 41583047--41583075 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
41583037 TAATTTAAAG
41583047 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
41583076 GTTAGTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:41583116 original size:28 final size:26
Alignment explanation
Indices: 41583061--41583128 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 26
41583051 ATTTTATTTT
*
41583061 ATTTTATTTTATTTTGTTAGTAAGTA
1 ATTTTATTTTATTTTGTAAGTAAGTA
*
41583087 ATTTTATTTTGTTATTAGTAAGTAAGTA
1 ATTTTATTTTATT-TT-GTAAGTAAGTA
* *
41583115 ATATTAATTTATTT
1 ATTTTATTTTATTT
41583129 AAAAATTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 12 0.34
27 3 0.09
28 20 0.57
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (26 bp):
ATTTTATTTTATTTTGTAAGTAAGTA
Found at i:41586236 original size:24 final size:24
Alignment explanation
Indices: 41586209--41586258 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
41586199 CACCATAAAC
* *
41586209 GGAGTTGGATCTTCATTTTCTACT
1 GGAGTAGGATATTCATTTTCTACT
41586233 GGAGTAGGATATTCATTTTCTACT
1 GGAGTAGGATATTCATTTTCTACT
41586257 GG
1 GG
41586259 TTCCACATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.42
Consensus pattern (24 bp):
GGAGTAGGATATTCATTTTCTACT
Found at i:41586643 original size:16 final size:16
Alignment explanation
Indices: 41586619--41586656 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
41586609 AATTTGTTAA
41586619 AAAATAAATAA-AATTT
1 AAAA-AAATAATAATTT
41586635 CAAAAAAATAATAATTT
1 -AAAAAAATAATAATTT
41586652 AAAAA
1 AAAAA
41586657 TATACCCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAAAATAATAATTT
Found at i:41588241 original size:43 final size:42
Alignment explanation
Indices: 41588180--41588304 Score: 178
Period size: 42 Copynumber: 2.9 Consensus size: 42
41588170 TTAAGTGAGA
*
41588180 AAACGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGATCTTTAACGG-GCTTTTCCCAC
* * *
41588223 AAACGTCGCTATAGAACATGGTCTTTAACGGGGTTTTCCCAC
1 AAACGCCGCTATAGAACATGATCTTTAACGGGCTTTTCCCAC
* *
41588265 AAACGCCACTATAAAACATGATCTTTAACGGTGCTTTTCC
1 AAACGCCGCTATAGAACATGATCTTTAACGG-GCTTTTCC
41588305 TAGAAACACC
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 37 0.51
43 35 0.49
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (42 bp):
AAACGCCGCTATAGAACATGATCTTTAACGGGCTTTTCCCAC
Found at i:41588277 original size:42 final size:43
Alignment explanation
Indices: 41588180--41588318 Score: 172
Period size: 43 Copynumber: 3.3 Consensus size: 43
41588170 TTAAGTGAGA
* *
41588180 AAACGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCACTATAGAACATGATCTTTAACGGCGCTTTTCCCAC
* * * *
41588223 AAACGTCGCTATAGAACATGGTCTTTAACGG-GGTTTTCCCAC
1 AAACGCCACTATAGAACATGATCTTTAACGGCGCTTTTCCCAC
* * * *
41588265 AAACGCCACTATAAAACATGATCTTTAACGGTGCTTTTCCTAG
1 AAACGCCACTATAGAACATGATCTTTAACGGCGCTTTTCCCAC
*
41588308 AAACACCACTA
1 AAACGCCACTA
41588319 ACATTAACAG
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
42 37 0.45
43 46 0.55
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (43 bp):
AAACGCCACTATAGAACATGATCTTTAACGGCGCTTTTCCCAC
Found at i:41590390 original size:29 final size:29
Alignment explanation
Indices: 41590350--41590801 Score: 251
Period size: 29 Copynumber: 15.8 Consensus size: 29
41590340 AACGGAGTTA
* *
41590350 AAAATG-TAATTTTTGGATGTTCGGGGGT
1 AAAATGATAATTTTTGGAAGTTCGAGGGT
* * *
41590378 AAAATGATAATTTTTAGATGCTT-GAGGGA
1 AAAATGATAATTTTTGGAAG-TTCGAGGGT
* * * * *
41590407 AAAATGGTGATTTTAGGATGATT-GGGGCGT
1 AAAATGATAATTTTTGGAAG-TTCGAGG-GT
* ** *
41590437 AAAACGATAATTTTTGGACA-CCCGA-GGC
1 AAAATGATAATTTTTGGA-AGTTCGAGGGT
* * *
41590465 AAAATGGTGATTTTTGGACGTTC-AGGGGT
1 AAAATGATAATTTTTGGAAGTTCGA-GGGT
* * *
41590494 AAAACGATAATTTTTGGACA-CTCAAGGGT
1 AAAATGATAATTTTTGGA-AGTTCGAGGGT
* * * *
41590523 AAAATGATAATTTTTGAAAAATTTG-GGAT
1 AAAATGATAATTTTTG-GAAGTTCGAGGGT
*
41590552 CAAAAATG-TAATTTTTGGACA-TTCGATGGT
1 --AAAATGATAATTTTTGGA-AGTTCGAGGGT
* *
41590582 AAAATGGTAATTTTTGGATGTTCGAGGGT
1 AAAATGATAATTTTTGGAAGTTCGAGGGT
* * * *
41590611 AAAAAGGTAATTTTTGGATGTTCGAGAGT
1 AAAATGATAATTTTTGGAAGTTCGAGGGT
* * *
41590640 AAAATGGTAA-TTTTGGAAAGTTTGAGGTT
1 AAAATGATAATTTTTGG-AAGTTCGAGGGT
*
41590669 AAATAATG-TAATTTTTGGACA-TCCGAGGGT
1 -AA-AATGATAATTTTTGGA-AGTTCGAGGGT
* * *
41590699 AAAATGGTAATTTTTAGAAGTTCAAGGG-
1 AAAATGATAATTTTTGGAAGTTCGAGGGT
41590727 -----G-TAATTTTTGGAAGTTCGAGGGT
1 AAAATGATAATTTTTGGAAGTTCGAGGGT
* *
41590750 AAAACGATAATTTTTGGAAGTTCAAGGGT
1 AAAATGATAATTTTTGGAAGTTCGAGGGT
* *
41590779 AAAAACGATAATTTTTGAAAGTT
1 -AAAATGATAATTTTTGGAAGTT
41590802 TTTGAGAAGT
Statistics
Matches: 331, Mismatches: 60, Indels: 64
0.73 0.13 0.14
Matches are distributed among these distances:
22 19 0.06
23 1 0.00
27 1 0.00
28 41 0.12
29 186 0.56
30 66 0.20
31 17 0.05
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAATGATAATTTTTGGAAGTTCGAGGGT
Found at i:41590572 original size:59 final size:57
Alignment explanation
Indices: 41590444--41590713 Score: 240
Period size: 59 Copynumber: 4.6 Consensus size: 57
41590434 CGTAAAACGA
** * * * * * * *
41590444 TAATTTTTGGACACCCGA-GGCAAAATGGTGATTTTTGGACGTTCAGGGGT-AAAACG
1 TAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTT-TGAGGTAAAAATG
* * * *
41590500 ATAATTTTTGGACACTCAAGGGTAAAATGATAATTTTTGAAAAATTTG-GGATCAAAAATG
1 -TAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTG-AAAGTTTGAGG-T-AAAAATG
* * * * *
41590560 TAATTTTTGGACATTCGATGGTAAAATGGTAATTTTTGGATGTTCGAGGGTAAAAAGG
1 TAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTGA-GGTAAAAATG
** * *
41590618 TAATTTTTGGATGTTCGAGAGTAAAATGGTAATTTTGGAAAGTTTGAGGTTAAATAATG
1 TAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTGAGG-TAAA-AATG
*
41590677 TAATTTTTGGACATCCGAGGGTAAAATGGTAATTTTT
1 TAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTT
41590714 AGAAGTTCAA
Statistics
Matches: 171, Mismatches: 33, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
57 20 0.12
58 71 0.42
59 73 0.43
60 7 0.04
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.35
Consensus pattern (57 bp):
TAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTGAGGTAAAAATG
Found at i:41590583 original size:88 final size:89
Alignment explanation
Indices: 41590465--41590626 Score: 202
Period size: 88 Copynumber: 1.8 Consensus size: 89
41590455 CACCCGAGGC
* * *
41590465 AAAATGGTGATTTTTGGACGTTCAGGGGTAAAACGATAATTTTTGGACACTCAAGGGTAAAATGA
1 AAAATGGTAATTTTTGGACATTCAGGGGTAAAACGATAATTTTTGGACACTCAAGGGTAAAAAGA
41590530 TAATTTTTGAAAAATTTGGGATCA
66 TAATTTTTGAAAAATTTGGGATCA
* * * *** *
41590554 AAAAT-GTAATTTTTGGACATTC-GATGGTAAAATGGTAATTTTTGGATGTTCGAGGGTAAAAAG
1 AAAATGGTAATTTTTGGACATTCAG-GGGTAAAACGATAATTTTTGGACACTCAAGGGTAAAAAG
*
41590617 GTAATTTTTG
65 ATAATTTTTG
41590627 GATGTTCGAG
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
87 1 0.02
88 55 0.90
89 5 0.08
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (89 bp):
AAAATGGTAATTTTTGGACATTCAGGGGTAAAACGATAATTTTTGGACACTCAAGGGTAAAAAGA
TAATTTTTGAAAAATTTGGGATCA
Found at i:41590622 original size:117 final size:116
Alignment explanation
Indices: 41590444--41590730 Score: 337
Period size: 117 Copynumber: 2.4 Consensus size: 116
41590434 CGTAAAACGA
* * * *
41590444 TAATTTTTGGACACCCGAGGCAAAATGGTGATTTTTGGACGTTCAGGGGTAAAACGATAATTTTT
1 TAATTTTTGGACATCCGAGGTAAAATGGTAATTTTTGGACGTTCAGGGGTAAAAAGATAATTTTT
*
41590509 GGACACTCAAGGGTAAAATGATAATTTTTGAAAAATTTG-GGATCAAA-AATG
66 GGACACTCAAGAGTAAAATGATAA-TTTTGAAAAATTTGAGG-TCAAATAATG
* * *
41590560 TAATTTTTGGACATTCGATGGTAAAATGGTAATTTTTGGATGTTC-GAGGGTAAAAAGGTAATTT
1 TAATTTTTGGACATCCGA-GGTAAAATGGTAATTTTTGGACGTTCAG-GGGTAAAAAGATAATTT
*** * * * * *
41590624 TTGGATGTTCGAGAGTAAAATGGTAATTTTGGAAAGTTTGAGGTTAAATAATG
64 TTGGACACTCAAGAGTAAAATGATAATTTTGAAAAATTTGAGGTCAAATAATG
* *
41590677 TAATTTTTGGACATCCGAGGGTAAAATGGTAATTTTTAGAAGTTCAAGGGGTAA
1 TAATTTTTGGACATCCGA-GGTAAAATGGTAATTTTTGGACGTTC-AGGGGTAA
41590731 TTTTTGGAAG
Statistics
Matches: 145, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
116 33 0.23
117 105 0.72
118 6 0.04
119 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.25, T:0.34
Consensus pattern (116 bp):
TAATTTTTGGACATCCGAGGTAAAATGGTAATTTTTGGACGTTCAGGGGTAAAAAGATAATTTTT
GGACACTCAAGAGTAAAATGATAATTTTGAAAAATTTGAGGTCAAATAATG
Found at i:41590736 original size:51 final size:51
Alignment explanation
Indices: 41590676--41590777 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 51
41590666 GTTAAATAAT
* *
41590676 GTAATTTTTGGACA-TCCGAGGGTAAAATGGTAATTTTTAGAAGTTCAAGGG
1 GTAATTTTTGGA-AGTCCGAGGGTAAAACGATAATTTTTAGAAGTTCAAGGG
* *
41590727 GTAATTTTTGGAAGTTCGAGGGTAAAACGATAATTTTTGGAAGTTCAAGGG
1 GTAATTTTTGGAAGTCCGAGGGTAAAACGATAATTTTTAGAAGTTCAAGGG
41590778 TAAAAACGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 1 0.02
51 45 0.98
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.33
Consensus pattern (51 bp):
GTAATTTTTGGAAGTCCGAGGGTAAAACGATAATTTTTAGAAGTTCAAGGG
Found at i:41590751 original size:21 final size:22
Alignment explanation
Indices: 41590704--41590748 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
41590694 AGGGTAAAAT
41590704 GGTAATTTTTAGAAGTTCAAGG
1 GGTAATTTTTAGAAGTTCAAGG
* *
41590726 GGTAATTTTTGGAAGTTCGAGG
1 GGTAATTTTTAGAAGTTCAAGG
41590748 G
1 G
41590749 TAAAACGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.04, G:0.33, T:0.36
Consensus pattern (22 bp):
GGTAATTTTTAGAAGTTCAAGG
Found at i:41590833 original size:40 final size:40
Alignment explanation
Indices: 41590760--41590835 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 40
41590750 AAAACGATAA
41590760 TTTTTGGAAGTTCAAGGGTAAAAACGATAATTTTTGAAAG
1 TTTTTGGAAGTTCAAGGGTAAAAACGATAATTTTTGAAAG
* * *
41590800 TTTTTGAGAAGTTCAGGGGTCAAAAC-ATGATTTTTG
1 TTTTTG-GAAGTTCAAGGGTAAAAACGATAATTTTTG
41590836 GACAATTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 15 0.47
41 17 0.53
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.37
Consensus pattern (40 bp):
TTTTTGGAAGTTCAAGGGTAAAAACGATAATTTTTGAAAG
Found at i:41592561 original size:17 final size:17
Alignment explanation
Indices: 41592541--41592606 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
41592531 TAATTAAATT
*
41592541 ATAAATTTAAATTCAAA
1 ATAAATTTAAATTAAAA
*
41592558 ATAAATTTAAACTAAAAAA
1 ATAAATTTAAA-T-TAAAA
* *
41592577 ATAAGTTTAAATTTAAA
1 ATAAATTTAAATTAAAA
*
41592594 ATAAATTAAAATT
1 ATAAATTTAAATT
41592607 TAGAATTTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
17 25 0.62
18 2 0.05
19 13 0.32
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.35
Consensus pattern (17 bp):
ATAAATTTAAATTAAAA
Found at i:41595630 original size:3 final size:3
Alignment explanation
Indices: 41595622--41595660 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
41595612 GGTTATCCCT
*
41595622 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TGC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
41595661 GATATCATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:41605404 original size:29 final size:30
Alignment explanation
Indices: 41605371--41605463 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 30
41605361 TCAAAAAAGC
41605371 AATTTTTGA-ATGCTCGAGGCCAAAATGGT
1 AATTTTTGACATGCTCGAGGCCAAAATGGT
* * ** **
41605400 AATTTTTAGACAT--TTGGGGGTAAAACAGT
1 AATTTTT-GACATGCTCGAGGCCAAAATGGT
* *
41605429 AATTTTT-AGATGCTCGAGCCCAAAATGGT
1 AATTTTTGACATGCTCGAGGCCAAAATGGT
41605458 AATTTT
1 AATTTT
41605464 GGGATGATCG
Statistics
Matches: 46, Mismatches: 14, Indels: 8
0.68 0.21 0.12
Matches are distributed among these distances:
27 3 0.07
29 39 0.85
30 2 0.04
31 2 0.04
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (30 bp):
AATTTTTGACATGCTCGAGGCCAAAATGGT
Found at i:41605590 original size:29 final size:29
Alignment explanation
Indices: 41605504--41605825 Score: 171
Period size: 29 Copynumber: 11.0 Consensus size: 29
41605494 TGAACACAAA
* *
41605504 TAAAATGGTAATTTTTGAAAAGTTTGAGGTC
1 TAAAATGGTAATTTTTG-GAAGTTCGAGG-C
* ** * *
41605535 AAAAAT-GTAA-TTTTCAAACATCCGAGGC
1 TAAAATGGTAATTTTTGGAA-GTTCGAGGC
* * * *
41605563 TAAAATGGTAATATTTGGATGTTTGAGGG
1 TAAAATGGTAATTTTTGGAAGTTCGAGGC
* *
41605592 TAAAA-GGTGATTTTTGGATGTTCGA-GC
1 TAAAATGGTAATTTTTGGAAGTTCGAGGC
*
41605619 ATAAAATGGTAATTTTTGGAAAGTTTG-GGATC
1 -TAAAATGGTAATTTTTGG-AAGTTCGAGG--C
* *
41605651 AAAAAAT-GTAATTTTTGGACA-TTCG-GGTG
1 -TAAAATGGTAATTTTTGGA-AGTTCGAGG-C
* *
41605680 TAAAATGGTAATTTTTGGAAGTTTGAGGG
1 TAAAATGGTAATTTTTGGAAGTTCGAGGC
41605709 TAAAATGGTAATTTTTGGAAGTTCGAGGGC
1 TAAAATGGTAATTTTTGGAAGTTCGA-GGC
** * ** *
41605739 -AAAATAATAATTTTTGGAAATTTAAGGG
1 TAAAATGGTAATTTTTGGAAGTTCGAGGC
** *
41605767 TAAAAAT-GTAATTTTTGAGAAGTTTAAGGG
1 T-AAAATGGTAATTTTTG-GAAGTTCGAGGC
* *
41605797 TCAAAAT-ATACTTTTTGGAAAGTTCGAGG
1 T-AAAATGGTAATTTTTGG-AAGTTCGAGG
41605826 GTCAAAACAT
Statistics
Matches: 232, Mismatches: 41, Indels: 37
0.75 0.13 0.12
Matches are distributed among these distances:
27 1 0.00
28 39 0.17
29 106 0.46
30 62 0.27
31 17 0.07
32 7 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (29 bp):
TAAAATGGTAATTTTTGGAAGTTCGAGGC
Found at i:41605708 original size:117 final size:116
Alignment explanation
Indices: 41605503--41605784 Score: 347
Period size: 117 Copynumber: 2.4 Consensus size: 116
41605493 TTGAACACAA
* **
41605503 ATAAAATGGTAATTTTTGAAAAGTTTGAGGTCAAAAATGTAATTTTCAAACATCCGAGGCTAAAA
1 ATAAAATGGTAATTTTTGGAAAGTTTG-GGTCAAAAATGTAATTTTTGAACATCCGAGGCTAAAA
* * *
41605568 TGGTAATATTTGGATGTTTGAGGGTAAAA-GGTGATTTTTGGATGTTCGAGC
65 TGGTAATATTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGTTCGAGC
* * *
41605619 ATAAAATGGTAATTTTTGGAAAGTTTGGGATCAAAAAATGTAATTTTTGGACATTCG-GGTGTAA
1 ATAAAATGGTAATTTTTGGAAAGTTTGGG-TC-AAAAATGTAATTTTTGAACATCCGAGG-CTAA
* *
41605683 AATGGTAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGTTCGAGG
63 AATGGTAATATTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGTTCGAGC
** **
41605737 GCAAAATAATAATTTTTGGAAA-TTTAAGGGT-AAAAATGTAATTTTTGA
1 ATAAAATGGTAATTTTTGGAAAGTTT--GGGTCAAAAATGTAATTTTTGA
41605785 GAAGTTTAAG
Statistics
Matches: 144, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
115 2 0.01
116 46 0.32
117 55 0.38
118 38 0.26
119 3 0.02
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (116 bp):
ATAAAATGGTAATTTTTGGAAAGTTTGGGTCAAAAATGTAATTTTTGAACATCCGAGGCTAAAAT
GGTAATATTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGTTCGAGC
Found at i:41605713 original size:89 final size:91
Alignment explanation
Indices: 41605591--41605852 Score: 260
Period size: 89 Copynumber: 2.9 Consensus size: 91
41605581 ATGTTTGAGG
* * * ** *
41605591 GTAAAA-GGTGATTTTTGGATGTTCGAGCATAAAATGGTAATTTTTGGAAAGTTTG-GGATCAAA
1 GTAAAATGGTAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAAGTTCGAGG-TCAAA
*
41605654 AAATGTAATTTTTGGACA-TT-CGGGT
65 AAATGTAATTTTTGGACATTTAAGGGT
*
41605679 GTAAAATGGTAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGG-AAGTTCGAGGGCAAAA
1 GTAAAATGGTAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAA
*
41605743 TAA--TAATTTTTGGAAATTTAAGGGT
66 -AATGTAATTTTTGGACATTTAAGGGT
* * * *
41605768 -AAAAAT-GTAATTTTTGAGAAGTTTAAGGGTCAAAAT-ATACTTTTTGGAAAGTTCGAGGGTCA
1 GTAAAATGGTAATTTTTG-GAAGTTTGAGGGT-AAAATGGTAATTTTTGGAAAGTTCGA-GGTCA
*
41605830 AAACATG--ATTTTTGGACAATTTA
63 AAAAATGTAATTTTTGGAC-ATTTA
41605853 GGAACCTTCT
Statistics
Matches: 146, Mismatches: 16, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
87 22 0.15
88 45 0.31
89 67 0.46
90 12 0.08
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (91 bp):
GTAAAATGGTAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAA
AATGTAATTTTTGGACATTTAAGGGT
Found at i:41605842 original size:30 final size:29
Alignment explanation
Indices: 41605719--41605845 Score: 95
Period size: 30 Copynumber: 4.3 Consensus size: 29
41605709 TAAAATGGTA
* *
41605719 ATTTTTGG-AAGTTCGAGGG-CAAAATAATA
1 ATTTTTGGAAAGTTCAAGGGTC-AAA-AATG
*
41605748 ATTTTTGGAAA-TTTAAGGGT-AAAAATG
1 ATTTTTGGAAAGTTCAAGGGTCAAAAATG
*
41605775 TAATTTTT-GAGAAGTTTAAGGGTCAAAATAT-
1 --ATTTTTGGA-AAGTTCAAGGGTCAAAA-ATG
*
41605806 ACTTTTTGGAAAGTTCGAGGGTCAAAACATG
1 A-TTTTTGGAAAGTTCAAGGGTCAAAA-ATG
41605837 ATTTTTGGA
1 ATTTTTGGA
41605846 CAATTTAGGA
Statistics
Matches: 81, Mismatches: 6, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
27 3 0.04
28 5 0.06
29 23 0.28
30 41 0.51
31 7 0.09
32 2 0.02
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.35
Consensus pattern (29 bp):
ATTTTTGGAAAGTTCAAGGGTCAAAAATG
Found at i:41605984 original size:30 final size:29
Alignment explanation
Indices: 41605950--41606072 Score: 106
Period size: 30 Copynumber: 4.1 Consensus size: 29
41605940 AAAACTCATG
*
41605950 TTTTGAGCTCCAAACTTTCCAAAAATTACA
1 TTTTGACCTCCAAAC-TTCCAAAAATTACA
* * *
41605980 TTTTGACCCCCGAACTTATCAAAAATTACA
1 TTTTGACCTCCAAACTT-CCAAAAATTACA
* * *
41606010 TTTTTATCCT-TAAACTTCCAAAAATTAATA
1 TTTTGA-CCTCCAAACTTCCAAAAATT-ACA
* *
41606040 TTTTGCCCT-CGAACTTCCAAAAATTACCA
1 TTTTGACCTCCAAACTTCCAAAAATTA-CA
41606069 TTTT
1 TTTT
41606073 ACCCTTGAAT
Statistics
Matches: 74, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
28 1 0.01
29 32 0.43
30 39 0.53
31 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.37
Consensus pattern (29 bp):
TTTTGACCTCCAAACTTCCAAAAATTACA
Found at i:41606043 original size:29 final size:29
Alignment explanation
Indices: 41605966--41606252 Score: 171
Period size: 29 Copynumber: 9.8 Consensus size: 29
41605956 GCTCCAAACT
* **
41605966 TTCCAAAAATTACAT-TTTGACCCCCGAAC
1 TTCCAAAAATTA-ATATTTTACCCTTGAAC
* * *
41605995 TTATCAAAAATTACAT-TTTTATCCTTAAAC
1 TT-CCAAAAATTA-ATATTTTACCCTTGAAC
* *
41606025 TTCCAAAAATTAATATTTTGCCCTCGAAC
1 TTCCAAAAATTAATATTTTACCCTTGAAC
**
41606054 TTCCAAAAATTACCATTTTACCCTTGAA-
1 TTCCAAAAATTAATATTTTACCCTTGAAC
* *
41606082 TGTCCAAAAATTTCATTTTTTACCAC-T-AAC
1 T-TCCAAAAA-TTAATATTTTACC-CTTGAAC
* **
41606112 TTCCCAAAATTACCATTTTACCCTTGAAC
1 TTCCAAAAATTAATATTTTACCCTTGAAC
* * **
41606141 ATCCAAAAATTACCT-TTTTACCCTCAAAC
1 TTCCAAAAATTA-ATATTTTACCCTTGAAC
* * *
41606170 ATCCAAAAATTATTATTTTACCCTTTAA-
1 TTCCAAAAATTAATATTTTACCCTTGAAC
* *
41606198 TGTCTAAAAAGTACAT-TTTTAACCC-TGAAC
1 T-TCCAAAAATTA-ATATTTT-ACCCTTGAAC
*
41606228 TTTTCAAAAATT-ATCATTTTACCCT
1 -TTCCAAAAATTAAT-ATTTTACCCT
41606253 CGAGTGTCTA
Statistics
Matches: 200, Mismatches: 40, Indels: 35
0.73 0.15 0.13
Matches are distributed among these distances:
27 1 0.00
28 16 0.08
29 130 0.65
30 51 0.25
31 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (29 bp):
TTCCAAAAATTAATATTTTACCCTTGAAC
Found at i:41606089 original size:58 final size:57
Alignment explanation
Indices: 41605967--41606269 Score: 256
Period size: 58 Copynumber: 5.2 Consensus size: 57
41605957 CTCCAAACTT
* * * * *
41605967 TCCAAAAATTACATTTTGACCCCCGAACTTATCAAAAATTA-CATTTTTATCCTTAAACT-
1 TCCAAAAATTA-ATTTTTACCCTCGAACTT-CCAAAAATTACCA-TTTTACCCTTGAA-TG
*
41606026 TCCAAAAATTAATATTTTGCCCTCGAACTTCCAAAAATTACCATTTTACCCTTGAATG
1 TCCAAAAATTAAT-TTTTACCCTCGAACTTCCAAAAATTACCATTTTACCCTTGAATG
* * **
41606084 TCCAAAAATTTCATTTTTTACCACT--AACTTCCCAAAATTACCATTTTACCCTTGAACA
1 TCCAAAAA-TT-AATTTTTACC-CTCGAACTTCCAAAAATTACCATTTTACCCTTGAATG
* * * ** *
41606142 TCCAAAAATTACCTTTTTACCCTCAAACATCCAAAAATTATTATTTTACCCTTTAATG
1 TCCAAAAATTA-ATTTTTACCCTCGAACTTCCAAAAATTACCATTTTACCCTTGAATG
* * * * * *
41606200 TCTAAAAAGTACATTTTTAACCCT-GAACTTTTCAAAAATTATCATTTTACCCTCGAGTG
1 TCCAAAAATTA-ATTTTT-ACCCTCGAAC-TTCCAAAAATTACCATTTTACCCTTGAATG
*
41606259 TCTAAAAATTA
1 TCCAAAAATTA
41606270 TCGTTTTACC
Statistics
Matches: 203, Mismatches: 30, Indels: 22
0.80 0.12 0.09
Matches are distributed among these distances:
56 3 0.01
57 11 0.05
58 112 0.55
59 73 0.36
60 4 0.02
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.36
Consensus pattern (57 bp):
TCCAAAAATTAATTTTTACCCTCGAACTTCCAAAAATTACCATTTTACCCTTGAATG
Found at i:41606175 original size:87 final size:87
Alignment explanation
Indices: 41605967--41606180 Score: 220
Period size: 87 Copynumber: 2.4 Consensus size: 87
41605957 CTCCAAACTT
* * * *
41605967 TCCAAAAATTA-CATTTTGACCCCCGAACTTAT-CAAAAATTACA-TTTTTATCC-TTAAACTTC
1 TCCAAAAATTACCATTTT-ACCCTCAAAC--ATCCAAAAATTTCATTTTTTA-CCACT-AACTTC
* * *
41606028 CAAAAATTAATATTTTGCCCTCGAACT
61 CAAAAATTAACATTTTACCCTCGAACA
** ** *
41606055 TCCAAAAATTACCATTTTACCCTTGAATGTCCAAAAATTTCATTTTTTACCACTAACTTCCCAAA
1 TCCAAAAATTACCATTTTACCCTCAAACATCCAAAAATTTCATTTTTTACCACTAACTTCCAAAA
* *
41606120 ATTACCATTTTACCCTTGAACA
66 ATTAACATTTTACCCTCGAACA
*
41606142 TCCAAAAATTACCTTTTTACCCTCAAACATCCAAAAATT
1 TCCAAAAATTACCATTTTACCCTCAAACATCCAAAAATT
41606181 ATTATTTTAC
Statistics
Matches: 105, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
86 1 0.01
87 73 0.70
88 25 0.24
89 6 0.06
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (87 bp):
TCCAAAAATTACCATTTTACCCTCAAACATCCAAAAATTTCATTTTTTACCACTAACTTCCAAAA
ATTAACATTTTACCCTCGAACA
Found at i:41606381 original size:28 final size:28
Alignment explanation
Indices: 41606345--41606438 Score: 98
Period size: 28 Copynumber: 3.3 Consensus size: 28
41606335 ACCCCCGATT
* * *
41606345 ATCCCAAAATTACCATTTTCCCCCGGAC
1 ATCCAAAAATTATCATTTTCCCTCGGAC
* * * *
41606373 ATCTAAAAATTATCGTTTTACCTCGAAC
1 ATCCAAAAATTATCATTTTCCCTCGGAC
* *
41606401 GTCCAAAAATTATCATTTTACCCTCGGGC
1 ATCCAAAAATTATCATTTT-CCCTCGGAC
41606430 ATCCAAAAA
1 ATCCAAAAA
41606439 CTGCATTTTT
Statistics
Matches: 51, Mismatches: 14, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
28 37 0.73
29 14 0.27
ACGTcount: A:0.34, C:0.29, G:0.09, T:0.29
Consensus pattern (28 bp):
ATCCAAAAATTATCATTTTCCCTCGGAC
Found at i:41606434 original size:29 final size:29
Alignment explanation
Indices: 41606026--41606438 Score: 137
Period size: 29 Copynumber: 14.3 Consensus size: 29
41606016 TCCTTAAACT
* * *
41606026 TCCAAAAATTAAT-ATTTTGCCCTCGAACT
1 TCCAAAAATT-ATCATTTTACCCTCGGACA
* * * **
41606055 TCCAAAAATTACCATTTTACCCTTGAATG
1 TCCAAAAATTATCATTTTACCCTCGGACA
* *
41606084 TCCAAAAATT-TCATTTTTTACCACT--AACT
1 TCCAAAAATTATCA--TTTTACC-CTCGGACA
* * * *
41606113 TCCCAAAATTACCATTTTACCCTTGAACA
1 TCCAAAAATTATCATTTTACCCTCGGACA
* * **
41606142 TCCAAAAATTACCTTTTTACCCTCAAACA
1 TCCAAAAATTATCATTTTACCCTCGGACA
* *** **
41606171 TCCAAAAATTATTATTTTACCCTTTAATG
1 TCCAAAAATTATCATTTTACCCTCGGACA
* * * *
41606200 TCTAAAAAGTA-CATTTTTAACCCT-GAACTT
1 TCCAAAAATTATCA-TTTT-ACCCTCGGAC-A
* **
41606230 TTCAAAAATTATCATTTTACCCTC-GAGTG
1 TCCAAAAATTATCATTTTACCCTCGGA-CA
* * ** *
41606259 TCTAAAAATTATCGTTTTACCCTTAGATA
1 TCCAAAAATTATCATTTTACCCTCGGACA
** * * ** **
41606288 TTTAAAAATTACCATTTTGCCC-CCAAGTT
1 TCCAAAAATTATCATTTTACCCTCGGA-CA
** * * * *
41606317 TTAAAAAATTACCGTTTTACCC-CCGATTA
1 TCCAAAAATTATCATTTTACCCTCGGA-CA
* * *
41606346 TCCCAAAATTACCATTTT-CCCCCGGACA
1 TCCAAAAATTATCATTTTACCCTCGGACA
* * * *
41606374 TCTAAAAATTATCGTTTTA-CCTCGAACG
1 TCCAAAAATTATCATTTTACCCTCGGACA
*
41606402 TCCAAAAATTATCATTTTACCCTCGGGCA
1 TCCAAAAATTATCATTTTACCCTCGGACA
41606431 TCCAAAAA
1 TCCAAAAA
41606439 CTGCATTTTT
Statistics
Matches: 295, Mismatches: 71, Indels: 36
0.73 0.18 0.09
Matches are distributed among these distances:
27 2 0.01
28 53 0.18
29 208 0.71
30 28 0.09
31 4 0.01
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.35
Consensus pattern (29 bp):
TCCAAAAATTATCATTTTACCCTCGGACA
Found at i:41622752 original size:30 final size:30
Alignment explanation
Indices: 41622689--41622792 Score: 135
Period size: 29 Copynumber: 3.6 Consensus size: 30
41622679 CTATATGTGG
41622689 TTTTTGGAAG-TTCAGGGGT-AAAATGTAA
1 TTTTTGGAAGTTTCAGGGGTAAAAATGTAA
* * *
41622717 TTTTTGGAAGTTTCAAGGTTAAAAATGGAA
1 TTTTTGGAAGTTTCAGGGGTAAAAATGTAA
*
41622747 ATTTTGGAAGTTT-AGGGGTAAAAATGTAA
1 TTTTTGGAAGTTTCAGGGGTAAAAATGTAA
*
41622776 TTTTTAGAAGTTT-AGGG
1 TTTTTGGAAGTTTCAGGG
41622793 ACCTTTAATG
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
28 10 0.15
29 35 0.54
30 20 0.31
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.38
Consensus pattern (30 bp):
TTTTTGGAAGTTTCAGGGGTAAAAATGTAA
Found at i:41625369 original size:201 final size:202
Alignment explanation
Indices: 41624919--41625847 Score: 1280
Period size: 201 Copynumber: 4.6 Consensus size: 202
41624909 GTCTAGTTTC
* * * * *
41624919 ATTGACTTCGTCTTGCTTCTCAGTATCTCATCTAA-AAGCTAGGGATACGAAAATCTGCTCGTAT
1 ATTG-CTTCGACTTGCTTCTCAGTGTCTCATC-AAGAAGCTAGGGATTCGAAGATTTGCTCGTAT
* * * * *
41624983 CAAGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAAATGATCGTCTCACTTGTTTCAAT
64 CGAGCGTTGAATTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAAT
* *
41625048 TCGCCTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCT
129 TCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCT
41625113 AACCATTTT
194 AACCATTTT
* ** * * *
41625122 ATTGCTTCGACTTGCTTCTTAGTGTCTCATCCGGAAGTTGGGGATTCGAAGATTTACTCGTATCG
1 ATTGCTTCGACTTGCTTCTCAGTGTCTCATCAAGAAGCTAGGGATTCGAAGATTTGCTCGTATCG
41625187 AGCGTTGAATTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTC
66 AGCGTTGAATTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTC
* *
41625252 GCTTCTCTGTATCTCATCA-GAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGCTAA
131 GCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAA
41625316 CCATTTT
196 CCATTTT
* *
41625323 ATTGCTTCGACTTGCTTCTCAGTGTCTCATCAAGAAGCTAGGGATTCAAAGATTTAG-TCATATC
1 ATTGCTTCGACTTGCTTCTCAGTGTCTCATCAAGAAGCTAGGGATTCGAAGATTT-GCTCGTATC
* * * * *
41625387 GAGCATT-AAGTTGGTATACTTTTCTGTATCTCATCAGGAAGATTACCGCCTCATTTGTTTCGAT
65 GAGCGTTGAA-TTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAAT
* * *
41625451 TTGCTTCTCTGCATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGATGCT
129 TCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCT
41625516 AACCATTTT
194 AACCATTTT
* * * * * * **
41625525 ATTGCTTCGACTTGCTTCTTAATGTCTCATCAGGAAGCTAAGG-TTCAAAGATTTGCTCGCATTA
1 ATTGCTTCGACTTGCTTCTCAGTGTCTCATCAAGAAGCTAGGGATTCGAAGATTTGCTCGTATCG
* *
41625589 AGCGTT-AAGTTGGTATACTTCTATGTATCTCATCAGGAAGATGATCGCCTCACTTGTTTCAATT
66 AGCGTTGAA-TTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATT
* * *
41625653 CGCTTCTTTGTATCTCATGAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAAGAAGCTA
130 CGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTA
41625718 ACCATTTT
195 ACCATTTT
* * * * * *
41625726 ATTACTTCGACCTGCTTCTCAGTGTCTCATCAAGAAGCT-GGGGTTCGAAGATTTGTTTGTATTG
1 ATTGCTTCGACTTGCTTCTCAGTGTCTCATCAAGAAGCTAGGGATTCGAAGATTTGCTCGTATCG
* * * *
41625790 AGCGCTGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATAACCGCCTCAC-TGTTT
66 AGCGTTGAATTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTT
41625848 GTGTATAATC
Statistics
Matches: 645, Mismatches: 74, Indels: 17
0.88 0.10 0.02
Matches are distributed among these distances:
200 10 0.02
201 415 0.64
202 216 0.33
203 4 0.01
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (202 bp):
ATTGCTTCGACTTGCTTCTCAGTGTCTCATCAAGAAGCTAGGGATTCGAAGATTTGCTCGTATCG
AGCGTTGAATTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTC
GCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAA
CCATTTT
Found at i:41625680 original size:403 final size:403
Alignment explanation
Indices: 41624919--41625847 Score: 1332
Period size: 403 Copynumber: 2.3 Consensus size: 403
41624909 GTCTAGTTTC
* * * *
41624919 ATTGACTTCGTCTTGCTTCTCAGTATCTCATCTAA-AAGCTAGGGATACGAAA-ATCTGCTCGTA
1 ATTG-CTTCGACTTGCTTCTCAGTGTCTCATC-AAGAAGCTAGGGATTC-AAAGATTTGCTCGTA
* * * * *
41624982 TCAAGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAAATGATCGTCTCACTTGTTTCAA
63 TCGAGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATAACCGCCTCACTTGTTTCAA
* *
41625047 TTCGCCTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGC
128 TTCGCCTCTCTGCATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGC
* * * ** *
41625112 TAACCATTTTATTGCTTCGACTTGCTTCTTAGTGTCTCATCCGGAAGTTGGGGATTCGAAGATTT
193 TAACCATTTTATTGCTTCGACTTGCTTCTTAATGTCTCATCAGGAAGCTAAGGATTCAAAGATTT
* * *
41625177 ACTCGTATCGAGCGTTGAATTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTT
258 ACTCGCATCAAGCGTTGAATTGGTATACTTCTATGTATCTCATCAGGAAGATGACCGCCTCACTT
* *
41625242 GTTTCAATTCGCTTCTCTGTATCTCATCAGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCA
323 GTTTCAATTCGCTTCTCTGTATCTCATCAGAAGACGAATTTGGTCCACTTCTCAATATCTCATCA
*
41625307 GGAAGCTAACCATTTT
388 AGAAGCTAACCATTTT
*
41625323 ATTGCTTCGACTTGCTTCTCAGTGTCTCATCAAGAAGCTAGGGATTCAAAGATTTAG-TCATATC
1 ATTGCTTCGACTTGCTTCTCAGTGTCTCATCAAGAAGCTAGGGATTCAAAGATTT-GCTCGTATC
* * * * * *
41625387 GAGCATTAAGTTGGTATACTTTTCTGTATCTCATCAGGAAGATTACCGCCTCATTTGTTTCGATT
65 GAGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATAACCGCCTCACTTGTTTCAATT
* * *
41625452 TGCTTCTCTGCATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGATGCTA
130 CGCCTCTCTGCATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTA
*
41625517 ACCATTTTATTGCTTCGACTTGCTTCTTAATGTCTCATCAGGAAGCTAAGG-TTCAAAGATTTGC
195 ACCATTTTATTGCTTCGACTTGCTTCTTAATGTCTCATCAGGAAGCTAAGGATTCAAAGATTTAC
* *
41625581 TCGCATTAAGCGTT-AAGTTGGTATACTTCTATGTATCTCATCAGGAAGATGATCGCCTCACTTG
260 TCGCATCAAGCGTTGAA-TTGGTATACTTCTATGTATCTCATCAGGAAGATGACCGCCTCACTTG
* *
41625645 TTTCAATTCGCTTCTTTGTATCTCATGAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCA
324 TTTCAATTCGCTTCTCTGTATCTCATCA-GAAGACGAATTTGGTCCACTTCTCAATATCTCATCA
41625710 AGAAGCTAACCATTTT
388 AGAAGCTAACCATTTT
* * * * * * *
41625726 ATTACTTCGACCTGCTTCTCAGTGTCTCATCAAGAAGCT-GGGGTTCGAAGATTTGTTTGTATTG
1 ATTGCTTCGACTTGCTTCTCAGTGTCTCATCAAGAAGCTAGGGATTCAAAGATTTGCTCGTATCG
* *
41625790 AGCGCTGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATAACCGCCTCAC-TGTTT
66 AGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATAACCGCCTCACTTGTTT
41625848 GTGTATAATC
Statistics
Matches: 468, Mismatches: 51, Indels: 15
0.88 0.10 0.03
Matches are distributed among these distances:
401 8 0.02
402 162 0.35
403 293 0.63
404 5 0.01
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (403 bp):
ATTGCTTCGACTTGCTTCTCAGTGTCTCATCAAGAAGCTAGGGATTCAAAGATTTGCTCGTATCG
AGCGTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATAACCGCCTCACTTGTTTCAATTC
GCCTCTCTGCATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAA
CCATTTTATTGCTTCGACTTGCTTCTTAATGTCTCATCAGGAAGCTAAGGATTCAAAGATTTACT
CGCATCAAGCGTTGAATTGGTATACTTCTATGTATCTCATCAGGAAGATGACCGCCTCACTTGTT
TCAATTCGCTTCTCTGTATCTCATCAGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAAGA
AGCTAACCATTTT
Found at i:41633833 original size:17 final size:17
Alignment explanation
Indices: 41633813--41633877 Score: 94
Period size: 17 Copynumber: 3.8 Consensus size: 17
41633803 AATTAAATTC
*
41633813 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
41633830 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
41633847 TAAATTTATATTTAAAG
1 TAAATTTAAATTTAAAA
*
41633864 TAAATTAAAATTTA
1 TAAATTTAAATTTA
41633878 GAATTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:41633847 original size:7 final size:6
Alignment explanation
Indices: 41633805--41633906 Score: 66
Period size: 6 Copynumber: 17.0 Consensus size: 6
41633795 AACTTTTTAA
* * *
41633805 TTAAAT TCTAAAT TTAAAT TCAAA- ATAAAT TTAAAT TTAAA- ATAAAT
1 TTAAAT T-TAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * * * * *
41633852 TTATAT TTAAA- GTAAAT TAAAAT TTAGAATT TTAAAA TTGAGT TTAATT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTA-AA-T TTAAAT TTAAAT TTAAAT
41633901 TTAAAT
1 TTAAAT
41633907 GTTGGGTCCG
Statistics
Matches: 71, Mismatches: 19, Indels: 12
0.70 0.19 0.12
Matches are distributed among these distances:
5 11 0.15
6 46 0.65
7 10 0.14
8 4 0.06
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:41644677 original size:49 final size:49
Alignment explanation
Indices: 41644624--41645173 Score: 313
Period size: 49 Copynumber: 11.2 Consensus size: 49
41644614 GGCTTAAATA
* *
41644624 TTTCCCTTCATGCTTTCGAGGTACAAGGTTCGCCGTTGTGACTTAAACC
1 TTTCCCTTCATTCTTTCGAGGTACAAGGTTCGCCGTTGCGACTTAAACC
* * ** * * * *
41644673 TTTCCCTTTACA-TC-TTCGTGGCATTAGATTCGCCATTGCGGCTTAAATC
1 TTTCCC-TT-CATTCTTTCGAGGTACAAGGTTCGCCGTTGCGACTTAAACC
* * * *
41644722 TTACCCTTTATT-TTT-GAGGTACAAGGTTCACCGTTGCGGCTTAAACC
1 TTTCCCTTCATTCTTTCGAGGTACAAGGTTCGCCGTTGCGACTTAAACC
* ** * ** *
41644769 TTTCCCTTGACA-TCTTT-GTGGTACTTGATTTACCGTTGCGGCTTAAATCC
1 TTTCCCTT--CATTCTTTCGAGGTACAAGGTTCGCCGTTGCGACTTAAA-CC
* * *
41644819 TTT-CCTTCA-T-TTTCTGAGGTATAAGGTTCGTCATTGCGACTTAAACC
1 TTTCCCTTCATTCTTTC-GAGGTACAAGGTTCGCCGTTGCGACTTAAACC
* * * * * * * *
41644866 TTTTCCTCCATTATCTTCGAGGTAC-TGGATTCGCTGTTGTGGCTTAAATC
1 TTTCCCTTCATTCT-TTCGAGGTACAAGG-TTCGCCGTTGCGACTTAAACC
* * * *
41644916 TTTCCCTTCATTCTTCCGAGGTACCAGGTTCACCATTGCGACTTAAACC
1 TTTCCCTTCATTCTTTCGAGGTACAAGGTTCGCCGTTGCGACTTAAACC
* * * * * ** * * *
41644965 TTTTCCTCCATTATCTTCGAGGTAC-TGGATTTGCTATTGTGGCTTAAATC
1 TTTCCCTTCATTCT-TTCGAGGTACAAGG-TTCGCCGTTGCGACTTAAACC
* *
41645015 TTTCCCTTCATTC-TTCTGAGGTACCAGGTTCGCTGTTGCGACTTAAACC
1 TTTCCCTTCATTCTTTC-GAGGTACAAGGTTCGCCGTTGCGACTTAAACC
* * * * * *
41645064 TTTTCCTCCATTATCTTT-AAGGTACTGAA--TTCGCCGTTGTGCCTTAAATC
1 TTTCCCTTCA-T-TCTTTCGAGGTAC--AAGGTTCGCCGTTGCGACTTAAACC
*** * *
41645114 TTTCCCTTCATTC-TTCTGAGGTACAAGGTTCATTGTTGCAACTTAATCC
1 TTTCCCTTCATTCTTTC-GAGGTACAAGGTTCGCCGTTGCGACTTAAACC
41645163 TTTCCCTTCAT
1 TTTCCCTTCAT
41645174 ATTCCTGTGG
Statistics
Matches: 376, Mismatches: 96, Indels: 58
0.71 0.18 0.11
Matches are distributed among these distances:
46 3 0.01
47 44 0.12
48 36 0.10
49 172 0.46
50 111 0.30
51 7 0.02
52 3 0.01
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (49 bp):
TTTCCCTTCATTCTTTCGAGGTACAAGGTTCGCCGTTGCGACTTAAACC
Found at i:41644912 original size:50 final size:48
Alignment explanation
Indices: 41644856--41645137 Score: 226
Period size: 50 Copynumber: 5.7 Consensus size: 48
41644846 TCGTCATTGC
*
41644856 GACTTAAACCTTTTCCTCCATTATCTTCGAGGTACTGGATTCGCTGTTGT
1 GACTTAAACCTTTCCCTCCA-T-TCTTCGAGGTACTGGATTCGCTGTTGT
* * * * * ** *
41644906 GGCTTAAATCTTTCCCTTCATTCTTCCGAGGTACCAGG-TTCACCATTGC
1 GACTTAAACCTTTCCCTCCATTCTT-CGAGGTA-CTGGATTCGCTGTTGT
* * *
41644955 GACTTAAACCTTTTCCTCCATTATCTTCGAGGTACTGGATTTGCTATTGT
1 GACTTAAACCTTTCCCTCCA-T-TCTTCGAGGTACTGGATTCGCTGTTGT
* * * * *
41645005 GGCTTAAATCTTTCCCTTCATTCTTCTGAGGTACCAGG-TTCGCTGTTGC
1 GACTTAAACCTTTCCCTCCATTCTTC-GAGGTA-CTGGATTCGCTGTTGT
* ** * *
41645054 GACTTAAACCTTTTCCTCCATTATCTTTAAGGTACTGAATTCGCCGTTGT
1 GACTTAAACCTTTCCCTCCA-T-TCTTCGAGGTACTGGATTCGCTGTTGT
* * *
41645104 GCCTTAAATCTTTCCCTTCATTCTTCTGAGGTAC
1 GACTTAAACCTTTCCCTCCATTCTTC-GAGGTAC
41645138 AAGGTTCATT
Statistics
Matches: 179, Mismatches: 42, Indels: 23
0.73 0.17 0.09
Matches are distributed among these distances:
48 13 0.07
49 74 0.41
50 84 0.47
51 8 0.04
ACGTcount: A:0.18, C:0.26, G:0.16, T:0.39
Consensus pattern (48 bp):
GACTTAAACCTTTCCCTCCATTCTTCGAGGTACTGGATTCGCTGTTGT
Found at i:41644969 original size:99 final size:98
Alignment explanation
Indices: 41644601--41645228 Score: 638
Period size: 99 Copynumber: 6.4 Consensus size: 98
41644591 CATGGTATTA
* * * * *
41644601 GATTCGCCATTTCGGCTTAAATATTTCCCTTCATGCTT-TCGAGGTACAAGGTTCGCCGTTGTGA
1 GATTCGCCATTGCGGCTTAAATCTTTCCCTTCATTCTTCT-GAGGTACAAGGTTCACCGTTGCGA
** * * * * *
41644665 CTTAAACCTTTCCCTTTACATCTTCGTGGCATTA
65 CTTAAACCTTTCCCTCCATATCTTCGAGGTACTG
* * *
41644699 GATTCGCCATTGCGGCTTAAATCTTACCCTTTATT-TT-TGAGGTACAAGGTTCACCGTTGCGGC
1 GATTCGCCATTGCGGCTTAAATCTTTCCCTTCATTCTTCTGAGGTACAAGGTTCACCGTTGCGAC
** * * * *
41644762 TTAAACCTTTCCCTTGACATCTTTGTGGTACTT
66 TTAAACCTTTCCCTCCATATCTTCGAGGTACTG
** * * ** *
41644795 GATTTACCGTTGCGGCTTAAATCCTTT-CCTTCATT-TTCTGAGGTATAAGGTTCGTCATTGCGA
1 GATTCGCCATTGCGGCTTAAAT-CTTTCCCTTCATTCTTCTGAGGTACAAGGTTCACCGTTGCGA
*
41644858 CTTAAACCTTTTCCTCCATTATCTTCGAGGTACTG
65 CTTAAACCTTTCCCTCCA-TATCTTCGAGGTACTG
** * * * *
41644893 GATTCGCTGTTGTGGCTTAAATCTTTCCCTTCATTCTTCCGAGGTACCAGGTTCACCATTGCGAC
1 GATTCGCCATTGCGGCTTAAATCTTTCCCTTCATTCTTCTGAGGTACAAGGTTCACCGTTGCGAC
*
41644958 TTAAACCTTTTCCTCCATTATCTTCGAGGTACTG
66 TTAAACCTTTCCCTCCA-TATCTTCGAGGTACTG
* * * * * *
41644992 GATTTGCTATTGTGGCTTAAATCTTTCCCTTCATTCTTCTGAGGTACCAGGTTCGCTGTTGCGAC
1 GATTCGCCATTGCGGCTTAAATCTTTCCCTTCATTCTTCTGAGGTACAAGGTTCACCGTTGCGAC
* **
41645057 TTAAACCTTTTCCTCCATTATCTTTAAGGTACTG
66 TTAAACCTTTCCCTCCA-TATCTTCGAGGTACTG
* * * * ** *
41645091 AATTCGCCGTTGTGCCTTAAATCTTTCCCTTCATTCTTCTGAGGTACAAGGTTCATTGTTGCAAC
1 GATTCGCCATTGCGGCTTAAATCTTTCCCTTCATTCTTCTGAGGTACAAGGTTCACCGTTGCGAC
* * * *
41645156 TTAATCCTTTCCCTTCATAT-TCCTGTGGTACTG
66 TTAAACCTTTCCCTCCATATCTTC-GAGGTACTG
*
41645189 GATTCGCCATTGCGGCTTAAATCTTTCCCTTTATGTCTTC
1 GATTCGCCATTGCGGCTTAAATCTTTCCCTTCAT-TCTTC
41645229 ATGGTAATGC
Statistics
Matches: 455, Mismatches: 68, Indels: 13
0.85 0.13 0.02
Matches are distributed among these distances:
96 78 0.17
97 46 0.10
98 107 0.24
99 224 0.49
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.39
Consensus pattern (98 bp):
GATTCGCCATTGCGGCTTAAATCTTTCCCTTCATTCTTCTGAGGTACAAGGTTCACCGTTGCGAC
TTAAACCTTTCCCTCCATATCTTCGAGGTACTG
Found at i:41645059 original size:198 final size:197
Alignment explanation
Indices: 41644601--41645228 Score: 714
Period size: 198 Copynumber: 3.2 Consensus size: 197
41644591 CATGGTATTA
* * * * * *
41644601 GATTCGCCATTTCGGCTTAAATATTTCCCTTCATGCTT-TCGAGGTACAAGGTTCGCCGTTGTGA
1 GATTTGCCATTGCGGCTTAAATCTTTCCCTTCATTCTTCT-GAGGTACAAGGTTCGCTGTTGCGA
* ** * * * * * * * *
41644665 CTTAAACCTTTCCCTTTA-CATCTTCGTGGCATTAGATTCGCCATTGCGGCTTAAATCTTACCCT
65 CTTAAACCTTTTCCTCCATTATCTTCGAGGTACTGGATTCGCCGTTGTGGCTTAAATCTTTCCCT
* * * * *
41644729 TTATT-TT-TGAGGTACAAGGTTCACCGTTGCGGCTTAAACCTTTCCCTTGACATCTTTGTGGTA
130 TCATTCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTTCATATCTTCGTGGTA
*
41644792 CTT
195 CTG
* * * *
41644795 GATTTACCGTTGCGGCTTAAATCCTTT-CCTTCATT-TTCTGAGGTATAAGGTTCG-TCATTGCG
1 GATTTGCCATTGCGGCTTAAAT-CTTTCCCTTCATTCTTCTGAGGTACAAGGTTCGCT-GTTGCG
*
41644857 ACTTAAACCTTTTCCTCCATTATCTTCGAGGTACTGGATTCGCTGTTGTGGCTTAAATCTTTCCC
64 ACTTAAACCTTTTCCTCCATTATCTTCGAGGTACTGGATTCGCCGTTGTGGCTTAAATCTTTCCC
* * * * * *
41644922 TTCATTCTTCCGAGGTACCAGGTTCACCATTGCGACTTAAACCTTTTCCTCCATTATCTTCGAGG
129 TTCATTCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTTCA-TATCTTCGTGG
41644987 TACTG
193 TACTG
* * *
41644992 GATTTGCTATTGTGGCTTAAATCTTTCCCTTCATTCTTCTGAGGTACCAGGTTCGCTGTTGCGAC
1 GATTTGCCATTGCGGCTTAAATCTTTCCCTTCATTCTTCTGAGGTACAAGGTTCGCTGTTGCGAC
** * *
41645057 TTAAACCTTTTCCTCCATTATCTTTAAGGTACTGAATTCGCCGTTGTGCCTTAAATCTTTCCCTT
66 TTAAACCTTTTCCTCCATTATCTTCGAGGTACTGGATTCGCCGTTGTGGCTTAAATCTTTCCCTT
** * * *
41645122 CATTCTTCTGAGGTACAAGGTTCATTGTTGCAACTTAATCCTTTCCCTTCATAT-TCCTGTGGTA
131 CATTCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTTCATATCTTC-GTGGTA
41645186 CTG
195 CTG
* *
41645189 GATTCGCCATTGCGGCTTAAATCTTTCCCTTTATGTCTTC
1 GATTTGCCATTGCGGCTTAAATCTTTCCCTTCAT-TCTTC
41645229 ATGGTAATGC
Statistics
Matches: 361, Mismatches: 61, Indels: 20
0.82 0.14 0.05
Matches are distributed among these distances:
193 36 0.10
194 67 0.19
195 5 0.01
196 42 0.12
197 79 0.22
198 131 0.36
199 1 0.00
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.39
Consensus pattern (197 bp):
GATTTGCCATTGCGGCTTAAATCTTTCCCTTCATTCTTCTGAGGTACAAGGTTCGCTGTTGCGAC
TTAAACCTTTTCCTCCATTATCTTCGAGGTACTGGATTCGCCGTTGTGGCTTAAATCTTTCCCTT
CATTCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTTCATATCTTCGTGGTAC
TG
Found at i:41645234 original size:49 final size:48
Alignment explanation
Indices: 41644589--41645234 Score: 236
Period size: 49 Copynumber: 13.2 Consensus size: 48
41644579 TTGTAATGTT
* * * * * *
41644589 TTCATGGTATTAGATTCGCCATTTCGGCTTAAATATTTCCCTTCATGC
1 TTCATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATTC
* * * *
41644637 TTTCGA-GGTACAAGG-TTCGCCGTTGTGACTTAAACCTTTCCCTTTACA-TC
1 -TTC-ATGGTAC-TGGATTCGCCGTTGCGGCTTAAATCTTTCCC-TT-CATTC
* * * * * * * *
41644687 TTCGTGGCATTAGATTCGCCATTGCGGCTTAAATCTTACCCTTTATTT
1 TTCATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATTC
* * * *
41644735 TTGA-GGTACAAGG-TTCACCGTTGCGGCTTAAACCTTTCCCTTGACA-TC
1 TTCATGGTAC-TGGATTCGCCGTTGCGGCTTAAATCTTTCCCTT--CATTC
** * **
41644783 TTTGTGGTACTTGATTTACCGTTGCGGCTTAAATCCTTT-CCTTCATT-
1 TTCATGGTACTGGATTCGCCGTTGCGGCTTAAAT-CTTTCCCTTCATTC
* * * * * *
41644830 TTC-TGAGGTA-TAAGG-TTCGTCATTGCGACTTAAACCTTTTCCTCCATTATC
1 TTCAT--GGTACT--GGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCA-T-TC
* *
41644881 TTCGA-GGTACTGGATTCGCTGTTGTGGCTTAAATCTTTCCCTTCATTC
1 TTC-ATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATTC
* * * * * * *
41644929 TTCCGA-GGTACCAGG-TTCACCATTGCGACTTAAACCTTTTCCTCCATTATC
1 TT-C-ATGGTA-CTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCA-T-TC
* ** *
41644980 TTCGA-GGTACTGGATTTGCTATTGTGGCTTAAATCTTTCCCTTCATTC
1 TTC-ATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATTC
* * * * * *
41645028 TTC-TGAGGTACCAGG-TTCGCTGTTGCGACTTAAACCTTTTCCTCCATTATC
1 TTCAT--GGTA-CTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCA-T-TC
* * * * *
41645079 TTTAAGGTACTGAATTCGCCGTTGTGCCTTAAATCTTTCCCTTCATTC
1 TTCATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATTC
* *** **
41645127 TTC-TGAGGTACAAGG-TTCATTGTTGCAACTT-AATCCTTTCCCTTCATAT-
1 TTCAT--GGTAC-TGGATTCGCCGTTGCGGCTTAAAT-CTTTCCCTTCAT-TC
* * * *
41645176 TCCTGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTTATGTC
1 TTC-ATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT-TC
41645226 TTCATGGTA
1 TTCATGGTA
41645235 ATGCAAACTG
Statistics
Matches: 433, Mismatches: 115, Indels: 98
0.67 0.18 0.15
Matches are distributed among these distances:
46 1 0.00
47 38 0.09
48 53 0.12
49 215 0.50
50 111 0.26
51 15 0.03
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (48 bp):
TTCATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATTC
Found at i:41662746 original size:17 final size:17
Alignment explanation
Indices: 41662726--41662801 Score: 98
Period size: 17 Copynumber: 4.4 Consensus size: 17
41662716 AATTAAATTC
41662726 TAAATTTAAATTCAAAA
1 TAAATTTAAATTCAAAA
*
41662743 TAAATTTAAATTTAAAA
1 TAAATTTAAATTCAAAA
*
41662760 TAAATTTAAACTCAATAAA
1 TAAATTTAAATTC-A-AAA
* *
41662779 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTCAAAA
41662796 TAAATT
1 TAAATT
41662802 AAAAAATTGG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
17 35 0.70
18 2 0.04
19 13 0.26
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTCAAAA
Found at i:41662758 original size:36 final size:36
Alignment explanation
Indices: 41662726--41662801 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
41662716 AATTAAATTC
*
41662726 TAAATTTAAATTC-A-AAATAAATTTAAATTTAAAA
1 TAAATTTAAACTCAATAAATAAATTTAAATTTAAAA
*
41662760 TAAATTTAAACTCAATAAATAAGTTTAAATTTAAAA
1 TAAATTTAAACTCAATAAATAAATTTAAATTTAAAA
41662796 TAAATT
1 TAAATT
41662802 AAAAAATTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 12 0.32
35 1 0.03
36 25 0.66
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (36 bp):
TAAATTTAAACTCAATAAATAAATTTAAATTTAAAA
Found at i:41662760 original size:7 final size:6
Alignment explanation
Indices: 41662718--41662769 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
41662708 AACTTTTTAA
* * *
41662718 TTAAAT TCTAAAT TTAAAT TCAAA- ATAAAT TTAAAT TTAAA- ATAAAT
1 TTAAAT T-TAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
41662765 TTAAA
1 TTAAA
41662770 CTCAATAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 7 0.19
6 24 0.65
7 6 0.16
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:41665916 original size:48 final size:47
Alignment explanation
Indices: 41665841--41665932 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 47
41665831 TTAGGCTAAG
**
41665841 TTATACAATATTAACAAAATATTAATAAAATTAATAATAAA-ATAAGAA
1 TTATACAATATTAACAAAATAACAATAAAA-TAATAA-AAATATAAGAA
*
41665889 TTATACAATATCTAA-ATAATAACAATAAAATAATAAAAATATAA
1 TTATACAATAT-TAACAAAATAACAATAAAATAATAAAAATATAA
41665933 TAATAAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
46 3 0.08
47 10 0.26
48 23 0.59
49 3 0.08
ACGTcount: A:0.63, C:0.05, G:0.01, T:0.30
Consensus pattern (47 bp):
TTATACAATATTAACAAAATAACAATAAAATAATAAAAATATAAGAA
Found at i:41665921 original size:14 final size:14
Alignment explanation
Indices: 41665902--41665944 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
41665892 TACAATATCT
*
41665902 AAATAATAACAATA
1 AAATAATAAAAATA
41665916 AAATAATAAAAATA
1 AAATAATAAAAATA
*
41665930 TAATAATAAATAATA
1 AAATAATAAA-AATA
41665945 GCAAAACAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 22 0.85
15 4 0.15
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAATAAAAATA
Found at i:41669527 original size:12 final size:12
Alignment explanation
Indices: 41669510--41669540 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
41669500 GAATTAGGGT
41669510 AAATCATTGTAA
1 AAATCATTGTAA
41669522 AAATCATTGTAA
1 AAATCATTGTAA
41669534 AAATCAT
1 AAATCAT
41669541 CAATCGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (12 bp):
AAATCATTGTAA
Found at i:41675403 original size:20 final size:20
Alignment explanation
Indices: 41675378--41675416 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
41675368 GATTTGCAAC
*
41675378 TCATTTCTTTCAACTTGAAT
1 TCATTTCATTCAACTTGAAT
41675398 TCATTTCATTCAACTTGAA
1 TCATTTCATTCAACTTGAA
41675417 GAGATAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.46
Consensus pattern (20 bp):
TCATTTCATTCAACTTGAAT
Found at i:41683288 original size:20 final size:20
Alignment explanation
Indices: 41683243--41683289 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
41683233 GTGAAATTTA
*
41683243 ATTT-AATAATATATATAAT
1 ATTTAAATAAAATATATAAT
*
41683262 ATATAAATAAAAT-TATAATT
1 ATTTAAATAAAATATATAA-T
41683282 ATTTAAAT
1 ATTTAAAT
41683290 TTAATTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTAAATAAAATATATAAT
Done.