Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 80 of 284
Found at i:26874226 original size:28 final size:30
Alignment explanation
Indices: 26874181--26874246 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 30
26874171 AAAAAGGGGC
26874181 AATTTACCAAAAAAAGCC-ATTTTTTTTA-
1 AATTTACCAAAAAAAGCCGATTTTTTTTAT
* **
26874209 AATTTACCGAAATGAGCCGATTTTTTTTAT
1 AATTTACCAAAAAAAGCCGATTTTTTTTAT
*
26874239 TATTTACC
1 AATTTACC
26874247 CGAATGGGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 15 0.47
29 10 0.31
30 7 0.22
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (30 bp):
AATTTACCAAAAAAAGCCGATTTTTTTTAT
Found at i:26874657 original size:14 final size:14
Alignment explanation
Indices: 26874634--26874663 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
26874624 ATTTGGCTTT
*
26874634 TTTTATAAAATTAA
1 TTTTAAAAAATTAA
26874648 TTTTAAAAAATTAA
1 TTTTAAAAAATTAA
26874662 TT
1 TT
26874664 AATTATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTAAAAAATTAA
Found at i:26874986 original size:23 final size:23
Alignment explanation
Indices: 26874960--26875092 Score: 96
Period size: 23 Copynumber: 5.8 Consensus size: 23
26874950 CATTTTTCTA
26874960 TTTTTTAATTTGTTTATTATTTG
1 TTTTTTAATTTGTTTATTATTTG
* *
26874983 TTTTTTAAATTATTTATTATTTG
1 TTTTTTAATTTGTTTATTATTTG
* * *
26875006 TTTTATAATAT-TTTA--A-ATG
1 TTTTTTAATTTGTTTATTATTTG
* **
26875025 TTTTATAATATTTGTTTATTCAAAT-
1 TTTT-TTA-ATTTGTTTATT-ATTTG
*
26875050 TTTTTTAATTTTTTTATTATTTG
1 TTTTTTAATTTGTTTATTATTTG
*
26875073 TTTTATAATATTTGTTTATT
1 TTTT-TTA-ATTTGTTTATT
26875093 CATACGTTTT
Statistics
Matches: 85, Mismatches: 15, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
19 6 0.07
20 2 0.02
21 3 0.04
22 10 0.12
23 43 0.51
24 4 0.05
25 15 0.18
26 2 0.02
ACGTcount: A:0.26, C:0.01, G:0.05, T:0.68
Consensus pattern (23 bp):
TTTTTTAATTTGTTTATTATTTG
Found at i:26875103 original size:48 final size:48
Alignment explanation
Indices: 26874961--26875103 Score: 147
Period size: 48 Copynumber: 3.1 Consensus size: 48
26874951 ATTTTTCTAT
* * * *
26874961 TTTTTAATTTGTTTATTATTTGTTTTTTAA-A-TTATTTATT-ATTTG
1 TTTTTAATTTTTTTATTATTTGTTTTATAATATTTGTTTATTCATATG
* * * *
26875006 TTTTATAA-TATTTTA--A-ATGTTTTATAATATTTGTTTATTCAAATT
1 TTTT-TAATTTTTTTATTATTTGTTTTATAATATTTGTTTATTCATATG
*
26875051 TTTTTAATTTTTTTATTATTTGTTTTATAATATTTGTTTATTCATACG
1 TTTTTAATTTTTTTATTATTTGTTTTATAATATTTGTTTATTCATATG
26875099 TTTTT
1 TTTTT
26875104 CAGAAAATAT
Statistics
Matches: 77, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
42 9 0.12
43 2 0.03
44 11 0.14
45 21 0.27
46 3 0.04
47 1 0.01
48 30 0.39
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (48 bp):
TTTTTAATTTTTTTATTATTTGTTTTATAATATTTGTTTATTCATATG
Found at i:26880931 original size:20 final size:20
Alignment explanation
Indices: 26880908--26880945 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
26880898 AATGTTAAAT
* *
26880908 TATATAAATTAAAATTAGCA
1 TATAAAAATGAAAATTAGCA
26880928 TATAAAAATGAAAATTAG
1 TATAAAAATGAAAATTAG
26880946 AAGGTAAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (20 bp):
TATAAAAATGAAAATTAGCA
Found at i:26882176 original size:22 final size:22
Alignment explanation
Indices: 26882141--26882183 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
26882131 ATTTTCTAAC
*
26882141 AGATTTAATAAATAAATTCAAG
1 AGATTAAATAAATAAATTCAAG
*
26882163 AGATTAAATGAATAAATTCAA
1 AGATTAAATAAATAAATTCAA
26882184 TGTTTCAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (22 bp):
AGATTAAATAAATAAATTCAAG
Found at i:26882900 original size:13 final size:14
Alignment explanation
Indices: 26882875--26882905 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
26882865 TGATGTGTTT
26882875 TAAACTAAATTTAC
1 TAAACTAAATTTAC
26882889 TAAACT-AATTTAC
1 TAAACTAAATTTAC
26882902 TAAA
1 TAAA
26882906 AACTCAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAACTAAATTTAC
Found at i:26889015 original size:23 final size:24
Alignment explanation
Indices: 26888971--26889016 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
26888961 TTTCTCACAT
* **
26888971 TTTCAAGTCAATCATTTTTCCACC
1 TTTCAAGTCAATAATTAATCCACC
26888995 TTTCAA-TCAATAATTAATCCAC
1 TTTCAAGTCAATAATTAATCCAC
26889017 AAACTCACAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (24 bp):
TTTCAAGTCAATAATTAATCCACC
Found at i:26889170 original size:3 final size:3
Alignment explanation
Indices: 26889162--26889187 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
26889152 TCACTCATCT
26889162 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
26889188 CTTACCTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:26889825 original size:17 final size:17
Alignment explanation
Indices: 26889791--26889824 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
26889781 GAATGGTCTC
*
26889791 TGTTTCTTTTCTTCTTT
1 TGTTTCTTTTATTCTTT
26889808 TGTTTCTTTTATT-TTT
1 TGTTTCTTTTATTCTTT
26889824 T
1 T
26889825 TATTTTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.79
Consensus pattern (17 bp):
TGTTTCTTTTATTCTTT
Found at i:26889878 original size:22 final size:24
Alignment explanation
Indices: 26889850--26889896 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
26889840 ATGTATTAGT
26889850 TAATAAT-A-ATAACAATATATTA
1 TAATAATCATATAACAATATATTA
* *
26889872 TAATAATCATATAATAATATTTTA
1 TAATAATCATATAACAATATATTA
26889896 T
1 T
26889897 TCACAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 1 0.05
24 13 0.62
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATAATCATATAACAATATATTA
Found at i:26904612 original size:72 final size:72
Alignment explanation
Indices: 26904495--26904662 Score: 223
Period size: 72 Copynumber: 2.3 Consensus size: 72
26904485 TCTCTAAATC
* *
26904495 TGTTTCTTCCCCTA-CTGCTGATGACTTTCTTTCTGCAGCCATTGAAGACGTTTCTTTTTCAGCC
1 TGTTTCTTCCCC-AGTTGCTGATGACCTTCTTTCTGCAGCCATTGAAGACGTTTCTTTTTCAGCC
26904559 ATTGAAGA
65 ATTGAAGA
* * * *
26904567 TGTTTCTTCCCCAGTTGCTGATGACGCTTGTTT-TTCAGTCATTGAAGGCGTTTCTTTTTCAGCC
1 TGTTTCTTCCCCAGTTGCTGATGAC-CTTCTTTCTGCAGCCATTGAAGACGTTTCTTTTTCAGCC
*
26904631 ATTGAAGT
65 ATTGAAGA
* *
26904639 TGTTTCTGCCCCTGTTGCTGATGA
1 TGTTTCTTCCCCAGTTGCTGATGA
26904663 GTCTCCTTTT
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
71 1 0.01
72 79 0.93
73 5 0.06
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (72 bp):
TGTTTCTTCCCCAGTTGCTGATGACCTTCTTTCTGCAGCCATTGAAGACGTTTCTTTTTCAGCCA
TTGAAGA
Found at i:26904645 original size:24 final size:24
Alignment explanation
Indices: 26904520--26904637 Score: 101
Period size: 24 Copynumber: 4.9 Consensus size: 24
26904510 TGCTGATGAC
*
26904520 TTTCTTTCTGCAGCCATTGAAGACG
1 TTTCTTT-TTCAGCCATTGAAGACG
*
26904545 TTTCTTTTTCAGCCATTGAAGATG
1 TTTCTTTTTCAGCCATTGAAGACG
*** **** *
26904569 TTTCTTCCCCAGTTGCTGATGACG
1 TTTCTTTTTCAGCCATTGAAGACG
* * * *
26904593 CTTGTTTTTCAGTCATTGAAGGCG
1 TTTCTTTTTCAGCCATTGAAGACG
26904617 TTTCTTTTTCAGCCATTGAAG
1 TTTCTTTTTCAGCCATTGAAG
26904638 TTGTTTCTGC
Statistics
Matches: 69, Mismatches: 24, Indels: 1
0.73 0.26 0.01
Matches are distributed among these distances:
24 62 0.90
25 7 0.10
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (24 bp):
TTTCTTTTTCAGCCATTGAAGACG
Found at i:26904673 original size:72 final size:72
Alignment explanation
Indices: 26904530--26904686 Score: 226
Period size: 72 Copynumber: 2.2 Consensus size: 72
26904520 TTTCTTTCTG
*
26904530 CAGCCATTGAAGACGTTTCTTTTTCAGCCATTGAAGATGTTTCTTCCCCAGTTGCTGATGACGCT
1 CAGCCATTGAAGACGTTTCTTTTTCAGCCATTGAAGATGTTTCTGCCCCAGTTGCTGATGACGCT
**
26904595 TGTTTTT
66 CCTTTTT
* * * *
26904602 CAGTCATTGAAGGCGTTTCTTTTTCAGCCATTGAAGTTGTTTCTGCCCCTGTTGCTGATGA-GTC
1 CAGCCATTGAAGACGTTTCTTTTTCAGCCATTGAAGATGTTTCTGCCCCAGTTGCTGATGACG-C
26904666 TCCTTTTT
65 TCCTTTTT
*
26904674 CAGCCATTTAAGA
1 CAGCCATTGAAGA
26904687 AGAAAAGAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
71 1 0.01
72 73 0.99
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (72 bp):
CAGCCATTGAAGACGTTTCTTTTTCAGCCATTGAAGATGTTTCTGCCCCAGTTGCTGATGACGCT
CCTTTTT
Found at i:26907090 original size:13 final size:13
Alignment explanation
Indices: 26907072--26907096 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26907062 TATTTTAATA
26907072 TTATTTTGTGTGT
1 TTATTTTGTGTGT
26907085 TTATTTTGTGTG
1 TTATTTTGTGTG
26907097 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:26908634 original size:114 final size:114
Alignment explanation
Indices: 26908508--26908729 Score: 417
Period size: 114 Copynumber: 1.9 Consensus size: 114
26908498 ATCAGCATAT
*
26908508 ATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAATATATGAATTGAAATTAGT
1 ATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAATATATAAATTGAAATTAGT
26908573 TAAGTATGAATGTTATATATATGCATAAATGAAGTTCGAATATATGTAA
66 TAAGTATGAATGTTATATATATGCATAAATGAAGTTCGAATATATGTAA
* *
26908622 ATATATATGTATATCTATTGTATATTTGATGAGCTATAATTGAAAGTATATAAATTGAAATTAGT
1 ATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAATATATAAATTGAAATTAGT
26908687 TAAGTATGAATGTTATATATATGCATAAATGAAGTTCGAATAT
66 TAAGTATGAATGTTATATATATGCATAAATGAAGTTCGAATAT
26908730 GTATATATGA
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 105 1.00
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.41
Consensus pattern (114 bp):
ATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAATATATAAATTGAAATTAGT
TAAGTATGAATGTTATATATATGCATAAATGAAGTTCGAATATATGTAA
Found at i:26909265 original size:41 final size:41
Alignment explanation
Indices: 26909216--26909319 Score: 172
Period size: 41 Copynumber: 2.5 Consensus size: 41
26909206 GACTTTACGT
*
26909216 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC
*
26909257 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC
* *
26909298 TTAGCAGGTTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
26909320 ATATGTTAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC
Found at i:26911213 original size:15 final size:16
Alignment explanation
Indices: 26911182--26911214 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
26911172 ATATCCTTTT
*
26911182 AAATTTCAAACACATA
1 AAATTTCAAACAAATA
26911198 AAATTTCAAA-AAATA
1 AAATTTCAAACAAATA
26911213 AA
1 AA
26911215 GGCAATATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATTTCAAACAAATA
Found at i:26912519 original size:17 final size:17
Alignment explanation
Indices: 26912465--26912523 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
26912455 GAAATTAATA
26912465 TTTTAAATATTTTTTAT
1 TTTTAAATATTTTTTAT
** *
26912482 ATTTATATAA-ATCATTGAT
1 -TTT-TA-AATATTTTTTAT
26912501 TTTTAAATATTTTTTAT
1 TTTTAAATATTTTTTAT
26912518 TTTTAA
1 TTTTAA
26912524 TAATTCATGA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
16 2 0.06
17 14 0.44
18 6 0.19
19 8 0.25
20 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTAAATATTTTTTAT
Found at i:26912535 original size:34 final size:36
Alignment explanation
Indices: 26912465--26912535 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
26912455 GAAATTAATA
26912465 TTTTAAATATTTTTTATATTTATATAAATCATTGAT
1 TTTTAAATATTTTTTATATTTATATAAATCATTGAT
* *
26912501 TTTTAAATATTTTTTATTTTTA-ATAATTCA-TGAT
1 TTTTAAATATTTTTTATATTTATATAAATCATTGAT
26912535 T
1 T
26912536 AAATTAGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 5 0.15
35 7 0.21
36 21 0.64
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (36 bp):
TTTTAAATATTTTTTATATTTATATAAATCATTGAT
Found at i:26929615 original size:21 final size:22
Alignment explanation
Indices: 26929577--26929618 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
26929567 AAAAACAAGA
*
26929577 ATAAATAATTGTCATCTTAATC
1 ATAAACAATTGTCATCTTAATC
26929599 ATAAACAATTG-CATCTTAAT
1 ATAAACAATTGTCATCTTAAT
26929619 TCCTTCAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (22 bp):
ATAAACAATTGTCATCTTAATC
Found at i:26935061 original size:37 final size:37
Alignment explanation
Indices: 26935011--26935102 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 37
26935001 TTAAACTTTT
* *
26935011 CCTCATGTTTCAAGTTATGACGGTCCGCTGGACTTGC
1 CCTCATGTTTCAAGTTATGACGATCCGCTAGACTTGC
** *
26935048 CCTCATGTTTCAAGTTATGACGATTTGCTAGACTTTC
1 CCTCATGTTTCAAGTTATGACGATCCGCTAGACTTGC
* *
26935085 CCACATATTTCAAGTTAT
1 CCTCATGTTTCAAGTTAT
26935103 AACAGTTCGT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (37 bp):
CCTCATGTTTCAAGTTATGACGATCCGCTAGACTTGC
Found at i:26935359 original size:26 final size:26
Alignment explanation
Indices: 26935330--26935436 Score: 117
Period size: 26 Copynumber: 4.1 Consensus size: 26
26935320 AATAGTCTAT
26935330 AAGGACTATTTCAAGTATGAGTCCGC
1 AAGGACTATTTCAAGTATGAGTCCGC
* *
26935356 AAGGACTATTTCATGTATGAGTCTGC
1 AAGGACTATTTCAAGTATGAGTCCGC
* * **
26935382 -AGATACTATTTCAAGCATGAGTCCAA
1 AAG-GACTATTTCAAGTATGAGTCCGC
* *
26935408 AAAGACTATTATCAAGTATGAGTCTGC
1 AAGGACTATT-TCAAGTATGAGTCCGC
26935435 AA
1 AA
26935437 AGATTTCTTA
Statistics
Matches: 64, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
25 2 0.03
26 47 0.73
27 15 0.23
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (26 bp):
AAGGACTATTTCAAGTATGAGTCCGC
Found at i:26935390 original size:52 final size:53
Alignment explanation
Indices: 26935334--26935435 Score: 152
Period size: 52 Copynumber: 1.9 Consensus size: 53
26935324 GTCTATAAGG
* ** * *
26935334 ACTATTTCAAGTATGAGTCCGCAAGGACTATT-TCATGTATGAGTCTGCAGAT
1 ACTATTTCAAGCATGAGTCCAAAAAGACTATTATCAAGTATGAGTCTGCAGAT
26935386 ACTATTTCAAGCATGAGTCCAAAAAGACTATTATCAAGTATGAGTCTGCA
1 ACTATTTCAAGCATGAGTCCAAAAAGACTATTATCAAGTATGAGTCTGCA
26935436 AAGATTTCTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 28 0.64
53 16 0.36
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (53 bp):
ACTATTTCAAGCATGAGTCCAAAAAGACTATTATCAAGTATGAGTCTGCAGAT
Found at i:26947044 original size:172 final size:175
Alignment explanation
Indices: 26946682--26947091 Score: 558
Period size: 184 Copynumber: 2.3 Consensus size: 175
26946672 AAAATACATA
* * * * *
26946682 TATAAAGTGTTTAAGAAAATATATTAATGGTTGAATTTTGATATTTTGATTTCATATATAAAACC
1 TATAAAGTCTTTAAGAAAACATATAAATGGTTAAATTTTGATATTTTGATTTGATATATAAAACC
*
26946747 ATTTGATCATGTCTTGTCTCTTGTACACGATGACTTAGTTGAGGATGGCCAGAACAACACGACTT
66 ATTTGATCATGTCTTGTCTCTTGTACACGATGACTTAGTCGAGGATGGCCAGAACAACACGACTT
* * *
26946812 TAGTGTAATGGATTAATTTGCTTTATTTACCAAAAAAAACCATATATATATATT
131 TAATGTAATGGATTAATTTACTTTATTT---------AACCATATATATATATC
*
26946866 TATAAAGTCTTTAAGAAAACATATAAATGGTTAAATTTTGATATTTTGATTTGATATATAAAATC
1 TATAAAGTCTTTAAGAAAACATATAAATGGTTAAATTTTGATATTTTGATTTGATATATAAAACC
* * *
26946931 ATTTGATTATGTCTTGTCTCTTGTTCATGATGACTT-GATCGAGGATGGCCAGAACAACACGACT
66 ATTTGATCATGTCTTGTCTCTTGTACACGATGACTTAG-TCGAGGATGGCCAGAACAACACGACT
*
26946995 TTAATTTAATGGATTAATTTACTTTATTT-A-CA-ATATATATATC
130 TTAATGTAATGGATTAATTTACTTTATTTAACCATATATATATATC
* *
26947038 TATAAAGTCTTTACGAAAGCATATAAATGGTTAAATTTTGATATTTTGATTTGA
1 TATAAAGTCTTTAAGAAAACATATAAATGGTTAAATTTTGATATTTTGATTTGA
26947092 AAATTTAAGT
Statistics
Matches: 209, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
172 62 0.30
173 2 0.01
174 1 0.00
183 1 0.00
184 143 0.68
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.40
Consensus pattern (175 bp):
TATAAAGTCTTTAAGAAAACATATAAATGGTTAAATTTTGATATTTTGATTTGATATATAAAACC
ATTTGATCATGTCTTGTCTCTTGTACACGATGACTTAGTCGAGGATGGCCAGAACAACACGACTT
TAATGTAATGGATTAATTTACTTTATTTAACCATATATATATATC
Found at i:26949513 original size:26 final size:26
Alignment explanation
Indices: 26949479--26949637 Score: 111
Period size: 26 Copynumber: 6.4 Consensus size: 26
26949469 TGGCTATCCG
*
26949479 GAGC-TCCTGATTAAAGGCTCTTCGT
1 GAGCTTCCTGATTAAAGGCTCTTTGT
* *
26949504 GAGCTTCCTGATTAAAAGTTCTTTGT
1 GAGCTTCCTGATTAAAGGCTCTTTGT
* * * *
26949530 GAACTTCCTGATT-ATGACTC-TTAT
1 GAGCTTCCTGATTAAAGGCTCTTTGT
****
26949554 GAGCTTCCTG-TTATATA-GC-CCGAAT
1 GAGCTTCCTGATTA-A-AGGCTCTTTGT
* *
26949579 AAGCTTTCTGA-T--AGGCTCTTTGT
1 GAGCTTCCTGATTAAAGGCTCTTTGT
*
26949602 GAGCTTCCTGATTAATGGCTCTTTGT
1 GAGCTTCCTGATTAAAGGCTCTTTGT
26949628 GAGCTTCCTG
1 GAGCTTCCTG
26949638 TTATATGGCT
Statistics
Matches: 100, Mismatches: 23, Indels: 21
0.69 0.16 0.15
Matches are distributed among these distances:
21 1 0.01
22 2 0.02
23 13 0.13
24 14 0.14
25 20 0.20
26 50 0.50
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (26 bp):
GAGCTTCCTGATTAAAGGCTCTTTGT
Found at i:26949607 original size:23 final size:26
Alignment explanation
Indices: 26949592--26949647 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
26949582 CTTTCTGATA
26949592 GGCTCTTTGTGAGCTTCCTGATTAAT
1 GGCTCTTTGTGAGCTTCCTGATTAAT
26949618 GGCTCTTTGTGAGCTTCCTG-TTATAT
1 GGCTCTTTGTGAGCTTCCTGATTA-AT
26949644 GGCT
1 GGCT
26949648 TGAGAGAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 3 0.10
26 26 0.90
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.43
Consensus pattern (26 bp):
GGCTCTTTGTGAGCTTCCTGATTAAT
Found at i:26950694 original size:74 final size:74
Alignment explanation
Indices: 26950566--26950709 Score: 207
Period size: 74 Copynumber: 1.9 Consensus size: 74
26950556 CTCGGATTTG
* * *
26950566 AAAACGGGATCATCCCCAGTCAGTTAGGACACAATCTTTTCTTAATTCCTGAGATCGTTTAAAAC
1 AAAACGGGATCATCCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATCGTTTAAAAC
26950631 TTGAGAAAA
66 TTGAGAAAA
* * ** * *
26950640 AAAAGGGGATCATGCCCAGTAAGTTAGGACATGATCTCTTCTTGATTCCCGAGATCGTTTAATAC
1 AAAACGGGATCATCCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATCGTTTAAAAC
26950705 TTGAG
66 TTGAG
26950710 TTTGAAAAGA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 61 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (74 bp):
AAAACGGGATCATCCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATCGTTTAAAAC
TTGAGAAAA
Found at i:26950917 original size:9 final size:9
Alignment explanation
Indices: 26950900--26950936 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
26950890 TGAGTTTTCG
26950900 AATTCGAAT
1 AATTCGAAT
*
26950909 AACTCGAAT
1 AATTCGAAT
26950918 AATTCGAAT
1 AATTCGAAT
26950927 AATTCGAAT
1 AATTCGAAT
26950936 A
1 A
26950937 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:26960905 original size:30 final size:30
Alignment explanation
Indices: 26960871--26961205 Score: 190
Period size: 30 Copynumber: 11.2 Consensus size: 30
26960861 GTATCCTGAA
**
26960871 TGGTGTGATAATGCAGCCCCATATCCGGCT
1 TGGTGTGATGGTGCAGCCCCATATCCGGCT
* * * * *
26960901 TGGTGTGACGGTGTAACCACATATCCGGGT
1 TGGTGTGATGGTGCAGCCCCATATCCGGCT
* *
26960931 TGGTGT-AGCGGTGCAGCCCCATATCCAGCT
1 TGGTGTGA-TGGTGCAGCCCCATATCCGGCT
* * * *
26960961 TGGTGCGATGGTACAGCTCCA-AACTCGGCT
1 TGGTGTGATGGTGCAGCCCCATATC-CGGCT
* *
26960991 TGGTGTGACGGTGC-GACTCCATATCCGGCT
1 TGGTGTGATGGTGCAG-CCCCATATCCGGCT
* * **
26961021 TGGTGCGACGGTGGGGCCCCATATCCAAGG--
1 TGGTGTGATGGTGCAGCCCCATATCC--GGCT
* * *
26961051 TGGTGTAATGATGCAGTCCCATATCCTGG-T
1 TGGTGTGATGGTGCAGCCCCATATCC-GGCT
26961081 TGGTGCTG-TGGTGCAGCCCCATATCCTGG-T
1 TGGTG-TGATGGTGCAGCCCCATATCC-GGCT
* ** *
26961111 TGGTGT-AGTAGTGTTGCCCCATATCCAGCT
1 TGGTGTGA-TGGTGCAGCCCCATATCCGGCT
* **
26961141 TGGTG-CATGGGTGCAGCAACATATCCGAG-T
1 TGGTGTGAT-GGTGCAGCCCCATATCCG-GCT
* * *
26961171 TGGTGCGGTGGTGCAGCACCATATCCAGG-T
1 TGGTGTGATGGTGCAGCCCCATATCC-GGCT
26961201 TGGTG
1 TGGTG
26961206 AGGCAATGGT
Statistics
Matches: 238, Mismatches: 49, Indels: 36
0.74 0.15 0.11
Matches are distributed among these distances:
29 9 0.04
30 219 0.92
31 8 0.03
32 2 0.01
ACGTcount: A:0.17, C:0.24, G:0.32, T:0.26
Consensus pattern (30 bp):
TGGTGTGATGGTGCAGCCCCATATCCGGCT
Found at i:26960965 original size:90 final size:89
Alignment explanation
Indices: 26960834--26961145 Score: 247
Period size: 90 Copynumber: 3.5 Consensus size: 89
26960824 CAGCTCTATC
* * * * * * ** *
26960834 TCCGAGTTGGTGAAGAGGTGCAACCCCGTATCCTGAATGGTGTGATAATGCAGCCCCATATCCGG
1 TCCGGGTTGGTGTAGCGGTGCAGCCCCATATCCAGCTTGGTGTGATGATGCAGCCCCATATCCGG
*
26960899 CTTGGTGTGACGGTGTAACCACATA
66 CTTGGTGTGACGGTGCAACC-CATA
* * * * *
26960924 TCCGGGTTGGTGTAGCGGTGCAGCCCCATATCCAGCTTGGTGCGATGGTACAGCTCCA-AACTCG
1 TCCGGGTTGGTGTAGCGGTGCAGCCCCATATCCAGCTTGGTGTGATGATGCAGCCCCATATC-CG
*
26960988 GCTTGGTGTGACGGTGCGACTCCATA
65 GCTTGGTGTGACGGTGCAAC-CCATA
* * ** * * *
26961014 TCCGGCTTGGTG-CGACGGTGGGGCCCCATATCCAAG-GTGGTGTAATGATGCAGTCCCATATCC
1 TCCGGGTTGGTGTAG-CGGTGCAGCCCCATATCC-AGCTTGGTGTGATGATGCAGCCCCATATCC
* *
26961077 TGG-TTGGTGCTG-TGGTGCAGCCCCATA
64 -GGCTTGGTG-TGACGGTGCA-ACCCATA
* ** **
26961104 TCCTGGTTGGTGTAGTAGTGTTGCCCCATATCCAGCTTGGTG
1 TCCGGGTTGGTGTAGCGGTGCAGCCCCATATCCAGCTTGGTG
26961146 CATGGGTGCA
Statistics
Matches: 173, Mismatches: 39, Indels: 20
0.75 0.17 0.09
Matches are distributed among these distances:
89 5 0.03
90 157 0.91
91 11 0.06
ACGTcount: A:0.18, C:0.25, G:0.31, T:0.26
Consensus pattern (89 bp):
TCCGGGTTGGTGTAGCGGTGCAGCCCCATATCCAGCTTGGTGTGATGATGCAGCCCCATATCCGG
CTTGGTGTGACGGTGCAACCCATA
Found at i:26963663 original size:82 final size:86
Alignment explanation
Indices: 26963571--26963743 Score: 273
Period size: 90 Copynumber: 2.0 Consensus size: 86
26963561 TGATGTAAAT
26963571 TTAAAACTTCTAACTATTTGTTTTATG-TAAAAAAAA-TCAACCGTTG-A-ATATATATATTAAT
1 TTAAAACTTCTAACTATTTGTTTTATGATAAAAAAAATTCAACCGTTGAATATATATATATTAAT
*
26963632 ATATTGAGTGCTTTAGATTAA
66 ATATTGAGTACTTTAGATTAA
26963653 TTAAAACTTCTAACTATTTGTTTTATGTAATAAAAAAAATTCAACCGTTGAATATATATATATAT
1 TTAAAACTTCTAACTATTTGTTTTATG--ATAAAAAAAATTCAACCGTTG-A-ATATATATATAT
26963718 TAATATATTGAGTACTTTAGATTAA
62 TAATATATTGAGTACTTTAGATTAA
26963743 T
1 T
26963744 ATGAAAGAGA
Statistics
Matches: 82, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
82 27 0.33
85 9 0.11
86 10 0.12
89 1 0.01
90 35 0.43
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (86 bp):
TTAAAACTTCTAACTATTTGTTTTATGATAAAAAAAATTCAACCGTTGAATATATATATATTAAT
ATATTGAGTACTTTAGATTAA
Found at i:26970581 original size:48 final size:48
Alignment explanation
Indices: 26970529--26970627 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
26970519 GGAGGATCTT
* *
26970529 GAATAAATCTATTGAGAAATATAAATATGGAATAAATTGGTTAAAATA
1 GAATAAATCTATTGAGAAATATAAATATGAAATAAATTGGTCAAAATA
*
26970577 GAATAAATCTATTGAGAAATATAGATATGAAATAAATTGGTCAAAATA
1 GAATAAATCTATTGAGAAATATAAATATGAAATAAATTGGTCAAAATA
26970625 GAA
1 GAA
26970628 AGACGCAACT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.29
Consensus pattern (48 bp):
GAATAAATCTATTGAGAAATATAAATATGAAATAAATTGGTCAAAATA
Found at i:26970615 original size:25 final size:25
Alignment explanation
Indices: 26970539--26970615 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
26970529 GAATAAATCT
* *
26970539 ATTGAGAAATATAAATATGGAATAA
1 ATTGAGAAATATAGATATGAAATAA
**
26970564 ATTG-GTTAAA-ATAGA-AT-AAATCT
1 ATTGAG--AAATATAGATATGAAATAA
26970587 ATTGAGAAATATAGATATGAAATAA
1 ATTGAGAAATATAGATATGAAATAA
26970612 ATTG
1 ATTG
26970616 GTCAAAATAG
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
22 3 0.08
23 12 0.30
24 6 0.15
25 16 0.40
26 3 0.08
ACGTcount: A:0.52, C:0.01, G:0.16, T:0.31
Consensus pattern (25 bp):
ATTGAGAAATATAGATATGAAATAA
Found at i:26970625 original size:25 final size:24
Alignment explanation
Indices: 26970553--26970626 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 24
26970543 AGAAATATAA
*
26970553 ATATGGAATAAATTGGTTAAAATAG
1 ATATGAAATAAATTGG-TAAAATAG
**
26970578 A-AT-AAATCTATTGAG-AAATATAG
1 ATATGAAATAAATTG-GTAAA-ATAG
26970601 ATATGAAATAAATTGGTCAAAATAG
1 ATATGAAATAAATTGGT-AAAATAG
26970626 A
1 A
26970627 AAGACGCAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
22 3 0.08
23 12 0.32
24 6 0.16
25 14 0.37
26 3 0.08
ACGTcount: A:0.51, C:0.03, G:0.16, T:0.30
Consensus pattern (24 bp):
ATATGAAATAAATTGGTAAAATAG
Found at i:26977012 original size:30 final size:30
Alignment explanation
Indices: 26976935--26977013 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
26976925 AATGTGTATG
*
26976935 ATTGAATCAAAATTAAAGTTTTATGTATACA
1 ATTGAA-CCAAATTAAAGTTTTATGTATACA
*
26976966 TTTGAACCACAATTAAAGTTTCGTATGTA-A-A
1 ATTGAACCA-AATTAAAGTTT--TATGTATACA
*
26976997 ATTGCACCAAATTAAAG
1 ATTGAACCAAATTAAAG
26977014 CTCGTGTATC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
30 10 0.24
31 24 0.59
32 1 0.02
33 6 0.15
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (30 bp):
ATTGAACCAAATTAAAGTTTTATGTATACA
Found at i:26981454 original size:74 final size:75
Alignment explanation
Indices: 26981342--26981517 Score: 189
Period size: 74 Copynumber: 2.4 Consensus size: 75
26981332 TTTGTGGAAG
* * * *
26981342 TCAAATTGTTTAACTTGATTAAAAC-CCTTAAGAGATTTAACTTTA-CTGATTAAGTGCAAGCAA
1 TCAAATTGTTTAACTTGATTACATCTCCTAAAGAGATTTAACTTTATC-GATTAAATGCAAGCAA
*
26981405 ATCTCTGAAAC
65 ATCTATGAAAC
* ** *
26981416 TCAAATTGTTTAACTTGATTACATCTCCTAAAGA-ATTTAGCTTTATCGATTAAATGGGAGCAAT
1 TCAAATTGTTTAACTTGATTACATCTCCTAAAGAGATTTAACTTTATCGATTAAATGCAAGCAAA
* * *
26981480 TTTATGGAAG
66 TCTATGAAAC
* *
26981490 TTAAATTGTTTGACTTGATTACAT-TCCT
1 TCAAATTGTTTAACTTGATTACATCTCCT
26981518 GTTAGCTCAA
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
73 4 0.05
74 74 0.86
75 8 0.09
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (75 bp):
TCAAATTGTTTAACTTGATTACATCTCCTAAAGAGATTTAACTTTATCGATTAAATGCAAGCAAA
TCTATGAAAC
Found at i:26984727 original size:17 final size:17
Alignment explanation
Indices: 26984700--26984745 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 17
26984690 AAAGTTTAGG
26984700 GGGGAAATAAAAAGTTTT
1 GGGGAAAT-AAAAGTTTT
26984718 GGGG-AATAAAAG-TTT
1 GGGGAAATAAAAGTTTT
26984733 GAGGGAAAGTAAA
1 G-GGGAAA-TAAA
26984746 TAGAGGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.16
16 8 0.32
17 5 0.20
18 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.33, T:0.22
Consensus pattern (17 bp):
GGGGAAATAAAAGTTTT
Found at i:26986696 original size:28 final size:29
Alignment explanation
Indices: 26986659--26986720 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
26986649 GAAAAAAATA
*
26986659 AAAATTTATTCT-AAAA-GAGAATAAAAG
1 AAAATTTATTCTAAAAATAAGAATAAAAG
*
26986686 AAAATTCTATTCTAAAAATAAGAATAAAAT
1 AAAATT-TATTCTAAAAATAAGAATAAAAG
26986716 AAAAT
1 AAAAT
26986721 AAAATAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 6 0.20
28 6 0.20
29 4 0.13
30 14 0.47
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.27
Consensus pattern (29 bp):
AAAATTTATTCTAAAAATAAGAATAAAAG
Found at i:26986716 original size:5 final size:5
Alignment explanation
Indices: 26986700--26986729 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
26986690 TTCTATTCTA
26986700 AAAAT AAGAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AA-AAT AAAAT AAAAT AAAAT AAAA
26986730 GAGAAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:26987757 original size:23 final size:22
Alignment explanation
Indices: 26987708--26987764 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
26987698 AGGACATTGC
*
26987708 CTTTCTCCATCTTCCATCAAAT
1 CTTTTTCCATCTTCCATCAAAT
26987730 CTTTTTCCATCTCTCCAT-AATAT
1 CTTTTTCCATCT-TCCATCAA-AT
*
26987753 -TTTTTCTATCTT
1 CTTTTTCCATCTT
26987765 GATTATGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 1 0.03
22 23 0.74
23 7 0.23
ACGTcount: A:0.19, C:0.30, G:0.00, T:0.51
Consensus pattern (22 bp):
CTTTTTCCATCTTCCATCAAAT
Found at i:26994182 original size:24 final size:24
Alignment explanation
Indices: 26994128--26994187 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
26994118 TTAAAATATC
* *
26994128 ATTTAAAATCTATTTATCTGAATT
1 ATTTAAAATCTATTTAACTAAATT
* *
26994152 CTGTAAAATCTATTTAACTAAATT
1 ATTTAAAATCTATTTAACTAAATT
26994176 ATTTAAATATCT
1 ATTTAAA-ATCT
26994188 TATATAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (24 bp):
ATTTAAAATCTATTTAACTAAATT
Found at i:26997029 original size:21 final size:21
Alignment explanation
Indices: 26996993--26997046 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
26996983 ATCATATATT
26996993 CCAAGATTGC--ATATCATAC
1 CCAAGATTGCATATATCATAC
*
26997012 CCAAGATTGCATATATCATAT
1 CCAAGATTGCATATATCATAC
* *
26997033 CTAAGATTGTATAT
1 CCAAGATTGCATAT
26997047 CCTTGAAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 10 0.33
21 20 0.67
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
CCAAGATTGCATATATCATAC
Found at i:26997473 original size:44 final size:44
Alignment explanation
Indices: 26997420--26997760 Score: 382
Period size: 44 Copynumber: 7.8 Consensus size: 44
26997410 ACCAGAATGG
* * * * *
26997420 GAAGACAAGATCTGCTACCTTTGATCTATTTCATGCCGAA-AAAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC-AATACAT
* *
26997464 GAAGACAAGATCTGTTTTCTTCGATCTACTT--CGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * ***
26997506 GAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCA-CGCCAATACAT
**
26997551 GAAGACAAGATCTATTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
26997595 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* *
26997639 GAAGACAAGATCTGCTATATTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * ***
26997683 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACAT
* *
26997728 GAAGACAATATCTGCTATCTTTGATCTACTTCA
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCA
26997761 TACTACGACC
Statistics
Matches: 254, Mismatches: 38, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
41 2 0.01
42 35 0.14
44 145 0.57
45 72 0.28
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
Found at i:26997726 original size:177 final size:175
Alignment explanation
Indices: 26997420--26997760 Score: 522
Period size: 177 Copynumber: 1.9 Consensus size: 175
26997410 ACCAGAATGG
* * * * *
26997420 GAAGACAAGATCTGCTACCTTTGATCTATTTCATGCCGAAAAATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTGCTACCTTTGATCTACTTCACGCCGAAAAATGAAGACAAGATCTGCTATATT
26997485 CGATCTACTTCGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTATG
66 CGATCTACTTCGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTATG
*
26997550 GGAAGACAAGATCTATTATCTTCGATCTACTTCACGCCAATACAT
131 GGAAGACAAGATCTACTATCTTCGATCTACTTCACGCCAATACAT
* *
26997595 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC-AATACATGAAGACAAGATCTGCTATAT
1 GAAGACAAGATCTGCTACCTTTGATCTACTTCACGCCGAA-AAATGAAGACAAGATCTGCTATAT
* * *
26997659 TTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGT
65 TCGATCTACTT--CGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGT
* * *
26997724 ATGGGAAGACAATATCTGCTATCTTTGATCTACTTCA
128 ATGGGAAGACAAGATCTACTATCTTCGATCTACTTCA
26997761 TACTACGACC
Statistics
Matches: 149, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
174 2 0.01
175 64 0.43
177 83 0.56
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (175 bp):
GAAGACAAGATCTGCTACCTTTGATCTACTTCACGCCGAAAAATGAAGACAAGATCTGCTATATT
CGATCTACTTCGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTATG
GGAAGACAAGATCTACTATCTTCGATCTACTTCACGCCAATACAT
Found at i:26997732 original size:133 final size:133
Alignment explanation
Indices: 26997464--26997760 Score: 368
Period size: 133 Copynumber: 2.2 Consensus size: 133
26997454 GCCGAAAAAT
* * * * *
26997464 GAAGACAAGATCTGTTTTCTTCGATCTACTT--CGCCAATACATGAAGACAAGATCTACTTTCTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTACTATATT
* ** *
26997527 CGATCTACTTCACCACCAGTATGGGAAGACAAGATCTATTATCTTCGATCTACTTCACGCCAATA
66 CGATCTACTTCACCACCAATACAGGAAGACAAGATCTATTATCTTCGATCTACTTCACACCAATA
*
26997592 CAT
131 CAG
*
26997595 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATATT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTACTATATT
* * * * * *
26997660 TGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTT-TCTTCGATCTACTTCGCCACCAG
66 CGATCTACTTCACCACCAATACAGGAAGACAAGATCT-ATTATCTTCGATCTACTTC-ACACCAA
**
26997723 TATGG
129 TACAG
*
26997728 GAAGACAATATCTGCTATCTTTGATCTACTTCA
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCA
26997761 TACTACGACC
Statistics
Matches: 142, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
131 28 0.20
132 34 0.24
133 80 0.56
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (133 bp):
GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTACTATATT
CGATCTACTTCACCACCAATACAGGAAGACAAGATCTATTATCTTCGATCTACTTCACACCAATA
CAG
Found at i:26997837 original size:45 final size:44
Alignment explanation
Indices: 26997419--26997839 Score: 341
Period size: 44 Copynumber: 9.5 Consensus size: 44
26997409 TACCAGAATG
* * * * * *
26997419 GGAAGACAAGATCTGCTACCTTTGATCTATTTCATGCCGAA-AAA
1 GGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCC-AATACA
* *
26997463 TGAAGACAAGATCTGTTTTCTTCGATCTACTT--CGCCAATACA
1 GGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACA
* * * * **
26997505 TGAAGACAAGATCTACTT-TCTTCGATCTACTTCACCACCAGTATG
1 GGAAGACAAGATCT-GTTATCTTCGATCTACTTCA-CGCCAATACA
*
26997550 GGAAGACAAGATCTATTATCTTCGATCTACTTCACGCCAATACA
1 GGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACA
* * *
26997594 TGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACA
1 GGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACA
* * * *
26997638 TGAAGACAAGATCTGCTATATTTGATCTACTTCACGCCAATACA
1 GGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACA
* * * * **
26997682 TGAAGACAAGATCTGCTT-TCTTCGATCTACTTCGCCACCAGTATG
1 GGAAGACAAGATCTG-TTATCTTCGATCTACTTC-ACGCCAATACA
* * * ** * **
26997727 GGAAGACAATATCTGCTATCTTTGATCTACTTCATACTACGACCCA
1 GGAAGACAAGATCTGTTATCTTCGATCTACTTC--ACGCCAATACA
* * * * * * *
26997773 GGGAGGCAAG-GCTGGTATCTTCGATCTGCTTCGCTGTCAATACA
1 GGAAGACAAGATCTGTTATCTTCGATCTACTTCAC-GCCAATACA
26997817 GGAAGACAAGATCTGTTATCTTC
1 GGAAGACAAGATCTGTTATCTTC
26997840 AACCTGCTCC
Statistics
Matches: 302, Mismatches: 63, Indels: 23
0.78 0.16 0.06
Matches are distributed among these distances:
41 2 0.01
42 33 0.11
43 3 0.01
44 158 0.52
45 97 0.32
46 9 0.03
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (44 bp):
GGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACA
Found at i:26998021 original size:88 final size:88
Alignment explanation
Indices: 26997762--26998312 Score: 784
Period size: 88 Copynumber: 6.3 Consensus size: 88
26997752 TCTACTTCAT
* * * *
26997762 ACTACGACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCAATACAGGAAGACAAG
1 ACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAG
*
26997827 ATCTGTTATCTTCAACCTGCTCC
66 ATCTGCTATCTTCAACCTGCTCC
* * *
26997850 ACTACAACCTAGGGAGGCAAGGCTGGTAT-TTCGATCTGCTTCACTGTCGATGCAGAAAGGCAAG
1 ACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAG
26997914 ATCTGCTATCTTCAACCTGCTCC
66 ATCTGCTATCTTCAACCTGCTCC
* * * * *
26997937 ACTACAACCCAGGGAGACAAGGCTGGTATATTCGATCAGCTACGCTGTCGATGTAGGAAGGCAAG
1 ACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAG
26998002 ATCTGCTATCTTCAACCTGCTCC
66 ATCTGCTATCTTCAACCTGCTCC
* * *
26998025 ACTACAACCCAGAGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAAGAAGGCAAG
1 ACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAG
* *
26998090 ATTTGCTATTTTCAACCTGCTCC
66 ATCTGCTATCTTCAACCTGCTCC
* *
26998113 ACTACAACCCAGAGAGGCAAGGCTGGTATCTTCGATCTGCTTCGATGTCGATGCAGGAAGGCAAG
1 ACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAG
*
26998178 ATCTGCTATCTTTAACCTGCTCC
66 ATCTGCTATCTTCAACCTGCTCC
* * * *
26998201 ACTACAACCCAGAGAGGCAAGGCTAGTATCTTCGATCTGCTTC-ATCGTC-AGTACAGGAAGGCA
1 ACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCT-GTCGA-TGCAGGAAGGCA
* *
26998264 AGATCTGTTATTTTCAACCTGCTCC
64 AGATCTGCTATCTTCAACCTGCTCC
* * * *
26998289 GCTGCAAACCAGGAAGGCAAGGCT
1 ACTACAACCCAGGGAGGCAAGGCT
26998313 TTGTGATTTC
Statistics
Matches: 419, Mismatches: 41, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
87 82 0.20
88 337 0.80
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.24
Consensus pattern (88 bp):
ACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAG
ATCTGCTATCTTCAACCTGCTCC
Found at i:26999702 original size:10 final size:9
Alignment explanation
Indices: 26999677--26999701 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
26999667 CCTGGAAGAG
26999677 TTTTTTTCT
1 TTTTTTTCT
26999686 TTTTTTTCT
1 TTTTTTTCT
26999695 TTTTTTT
1 TTTTTTT
26999702 TGCACCATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:27004702 original size:21 final size:21
Alignment explanation
Indices: 27004676--27004726 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
27004666 CATATCTTCC
27004676 AAGATTGCATATATCATATCT
1 AAGATTGCATATATCATATCT
*
27004697 AAGATTGC--ATGTCATATCT
1 AAGATTGCATATATCATATCT
*
27004716 AAAATTGCATA
1 AAGATTGCATA
27004727 CCTTTGAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 17 0.65
21 9 0.35
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (21 bp):
AAGATTGCATATATCATATCT
Found at i:27005857 original size:57 final size:57
Alignment explanation
Indices: 27005748--27005859 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 57
27005738 AAAAAAAAAG
* * *
27005748 AAAAAAAATTTGGGTGTTGGCCTATCAATGGCCGGCACCCAGTACGAAAAAAAGGAA
1 AAAAAAAATTTAGGTGCTGGCCTATCAATGGCCGGCACCCAGCACGAAAAAAAGGAA
* * *
27005805 AAAAAAAATTTAGGTGCTGGCCTGTTAATGGTCGGCACCCAGCACAGTAAAAAAA
1 AAAAAAAATTTAGGTGCTGGCCTATCAATGGCCGGCACCCAGCAC-G-AAAAAAA
27005860 TTTATTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 39 0.83
58 1 0.02
59 7 0.15
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (57 bp):
AAAAAAAATTTAGGTGCTGGCCTATCAATGGCCGGCACCCAGCACGAAAAAAAGGAA
Found at i:27006147 original size:212 final size:211
Alignment explanation
Indices: 27005790--27006192 Score: 657
Period size: 212 Copynumber: 1.9 Consensus size: 211
27005780 CGGCACCCAG
* *
27005790 TACGAAAAAAAGGAAAAAAAAAATTTAGGTGCTGGCCTGTTAATGGTCGGCACCCAGCACAGTAA
1 TACGAAAAAAAGGAAAAAAAAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAA
* * *
27005855 AAAAATTTATTTTTTTTCGTGTCAGTATCAGGTATCAGTATACGAAAAAAGTAATAAAAAAAAAT
66 AAAAATTTATCTTTTTTCATGTCAGTATCAAGTATCAGTATACGAAAAAAGTAATAAAAAAAAAT
*
27005920 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAAAAAAAATTATTTTTTTCGTGTC
131 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT-AAAAAAAATTACTTTTTTCGTGTC
27005985 AGTATCAGGTATCAGTA
195 AGTATCAGGTATCAGTA
* *
27006002 TACGAAAAAAAGGAAGAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCATAGT
1 TACGAAAAAAAGGAA-AAAAAAAA-TTTAGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
* *
27006067 AAAAAAATTTA-CTTTTTTCATGTCAGTATCAAGTATCAGTATACG-AAAAAGTAATAAAAATAT
64 AAAAAAATTTATCTTTTTTCATGTCAGTATCAAGTATCAGTATACGAAAAAAGTAATAAAAAAAA
* *
27006130 TTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAAAAAAATTACTTTTTTCGT
129 ATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAAAAAAATTACTTTTTTCGT
27006193 ATACTGATAC
Statistics
Matches: 177, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
211 20 0.11
212 71 0.40
213 39 0.22
214 47 0.27
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (211 bp):
TACGAAAAAAAGGAAAAAAAAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAA
AAAAATTTATCTTTTTTCATGTCAGTATCAAGTATCAGTATACGAAAAAAGTAATAAAAAAAAAT
TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAAAAAAATTACTTTTTTCGTGTCA
GTATCAGGTATCAGTA
Found at i:27006157 original size:105 final size:105
Alignment explanation
Indices: 27005790--27006192 Score: 587
Period size: 107 Copynumber: 3.8 Consensus size: 105
27005780 CGGCACCCAG
* * * *
27005790 TACGAAAAAAAGGAA-AAAAAAAA-TTTAGGTGCTGGCCTGTTAATGGTCGGCACCCAGCACAGT
1 TACG-AAAAAAGTAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
* *
27005853 AAAAAAATTTATTTTTTTTCGTGTCAGTATCAGGTATCAGTA
65 AAAAAAAATTA-CTTTTTTCGTGTCAGTATCAGGTATCAGTA
27005895 TACGAAAAAAGTAATAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
1 TACGAAAAAAGTAAT-AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
*
27005960 AAAAAAAAATTATTTTTTTCGTGTCAGTATCAGGTATCAGTA
65 -AAAAAAAATTACTTTTTTCGTGTCAGTATCAGGTATCAGTA
* * *
27006002 TACGAAAAAAAGGAAGAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCATAGT
1 TACG-AAAAAAGTAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
* * *
27006067 AAAAAAATTTACTTTTTTCATGTCAGTATCAAGTATCAGTA
65 AAAAAAAATTACTTTTTTCGTGTCAGTATCAGGTATCAGTA
** *
27006108 TACG-AAAAAGTAATAAAAATATTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
1 TACGAAAAAAGTAATAAAAA-AAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
27006172 AAAAAAAATTACTTTTTTCGT
65 AAAAAAAATTACTTTTTTCGT
27006193 ATACTGATAC
Statistics
Matches: 272, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
104 22 0.08
105 63 0.23
106 49 0.18
107 119 0.44
108 19 0.07
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (105 bp):
TACGAAAAAAGTAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTA
AAAAAAATTACTTTTTTCGTGTCAGTATCAGGTATCAGTA
Found at i:27010011 original size:3 final size:3
Alignment explanation
Indices: 27010003--27010041 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
27009993 TACTTCAAAA
*
27010003 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
27010042 GTTGGGGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:27020641 original size:13 final size:11
Alignment explanation
Indices: 27020610--27020638 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
27020600 CCATTGTACT
27020610 TTAAAAAGCAG
1 TTAAAAAGCAG
27020621 TTAAAAAGCAG
1 TTAAAAAGCAG
27020632 TTAAAAA
1 TTAAAAA
27020639 AAGTGAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.21
Consensus pattern (11 bp):
TTAAAAAGCAG
Found at i:27021277 original size:15 final size:16
Alignment explanation
Indices: 27021250--27021280 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
27021240 AAACCAAATA
27021250 GGACAAGAAAAGAAAC
1 GGACAAGAAAAGAAAC
27021266 GGACAA-AAAAGAAAC
1 GGACAAGAAAAGAAAC
27021281 AGAAATAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.65, C:0.13, G:0.23, T:0.00
Consensus pattern (16 bp):
GGACAAGAAAAGAAAC
Found at i:27021601 original size:12 final size:12
Alignment explanation
Indices: 27021584--27021608 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27021574 TGCTGGTGAG
27021584 AAAGGAAGGAAA
1 AAAGGAAGGAAA
27021596 AAAGGAAGGAAA
1 AAAGGAAGGAAA
27021608 A
1 A
27021609 TACTGAAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (12 bp):
AAAGGAAGGAAA
Found at i:27022907 original size:51 final size:52
Alignment explanation
Indices: 27022832--27022933 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 52
27022822 AGAGCCAATG
* **
27022832 AATGAAAATGAATAAAAATGATAAAGTAAC-AAAAATAGATCACACAAATCC
1 AATGAAAATAAATAAAAACAATAAAGTAACAAAAAATAGATCACACAAATCC
*
27022883 AATGGAAATAAATAAAAACAATAAAGTAACAAAAAATAGATCACACAAATC
1 AATGAAAATAAATAAAAACAATAAAGTAACAAAAAATAGATCACACAAATC
27022934 ACTATCCACA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 26 0.57
52 20 0.43
ACGTcount: A:0.63, C:0.12, G:0.09, T:0.17
Consensus pattern (52 bp):
AATGAAAATAAATAAAAACAATAAAGTAACAAAAAATAGATCACACAAATCC
Found at i:27023123 original size:16 final size:18
Alignment explanation
Indices: 27023096--27023128 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
27023086 TAGAATTTGG
27023096 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
27023113 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
27023129 GTTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:27024359 original size:9 final size:9
Alignment explanation
Indices: 27024341--27024391 Score: 75
Period size: 9 Copynumber: 5.4 Consensus size: 9
27024331 TTTGGTTAAA
27024341 AATTACCCG
1 AATTACCCG
*
27024350 AATTAACCG
1 AATTACCCG
27024359 AATTACCCG
1 AATTACCCG
27024368 AAAATTACCCG
1 --AATTACCCG
27024379 AATTACCCG
1 AATTACCCG
27024388 AATT
1 AATT
27024392 GAATCACATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
9 29 0.76
11 9 0.24
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:27024379 original size:20 final size:20
Alignment explanation
Indices: 27024341--27024389 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
27024331 TTTGGTTAAA
27024341 AATTACCCG--AATTAACCG
1 AATTACCCGAAAATTAACCG
*
27024359 AATTACCCGAAAATTACCCG
1 AATTACCCGAAAATTAACCG
27024379 AATTACCCGAA
1 AATTACCCGAA
27024390 TTGAATCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 9 0.32
20 19 0.68
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20
Consensus pattern (20 bp):
AATTACCCGAAAATTAACCG
Found at i:27028602 original size:28 final size:25
Alignment explanation
Indices: 27028535--27028586 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
27028525 AAAATTGGTA
27028535 AGACATTTTCCATTCTTCTCTAAGC
1 AGACATTTTCCATTCTTCTCTAAGC
27028560 AGACATTTTCCATTC-TCTTCTAAGC
1 AGACATTTTCCATTCTTC-TCTAAGC
27028585 AG
1 AG
27028587 CAAACATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (25 bp):
AGACATTTTCCATTCTTCTCTAAGC
Found at i:27030468 original size:14 final size:14
Alignment explanation
Indices: 27030451--27030478 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
27030441 AATATATATT
27030451 AATATATATTAATA
1 AATATATATTAATA
27030465 AATATATATTAATA
1 AATATATATTAATA
27030479 TATGTGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATTAATA
Found at i:27030481 original size:10 final size:10
Alignment explanation
Indices: 27030437--27030469 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
27030427 AAAAACAATT
27030437 TATTAATATA
1 TATTAATATA
27030447 TATTAATATA
1 TATTAATATA
*
27030457 TATTAATAAA
1 TATTAATATA
27030467 TAT
1 TAT
27030470 ATATTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TATTAATATA
Found at i:27030536 original size:32 final size:33
Alignment explanation
Indices: 27030500--27030584 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
27030490 AACTTTTCTG
* * *
27030500 GAAAATATTTT-CAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
27030532 GAAAATATTTTACA-CAGATTTACCAAACACCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
27030564 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGCAAATC
27030585 ATTTTACAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
32 37 0.88
33 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCTACCAAACACCA
Found at i:27030623 original size:34 final size:34
Alignment explanation
Indices: 27030565--27030630 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
27030555 CAAACACCAG
* *
27030565 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTACCAGTAAATCATTTTAC-GAAAAGT
*
27030600 AAAACATTTACCAG-AAATTATTTTACGAAAA
1 AAAACATTTACCAGTAAATCATTTTACGAAAA
27030631 ACATTTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 5 0.18
34 11 0.39
35 12 0.43
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (34 bp):
AAAACATTTACCAGTAAATCATTTTACGAAAAGT
Found at i:27033810 original size:39 final size:39
Alignment explanation
Indices: 27033734--27033892 Score: 183
Period size: 39 Copynumber: 4.1 Consensus size: 39
27033724 ACTTCCAATA
* * * * **
27033734 CACCGACACACAGCATGTTAGGCACAAAGCCCAAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAAT
** *
27033773 CATTGGCACAAAGCCTGCTAGGCACTTAGCCCGAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAAT
* * * * *
27033812 CACCAGCACAAAACCTGTTAGGCACTTAACCCGAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAAT
*
27033851 CACCGGCACAAAGCCTGCTAGGCGCTTAGCCCAAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAAT
27033890 CAC
1 CAC
27033893 AGTATTTCTA
Statistics
Matches: 99, Mismatches: 21, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
39 99 1.00
ACGTcount: A:0.35, C:0.31, G:0.17, T:0.16
Consensus pattern (39 bp):
CACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAAT
Found at i:27033879 original size:78 final size:78
Alignment explanation
Indices: 27033749--27033892 Score: 218
Period size: 78 Copynumber: 1.8 Consensus size: 78
27033739 ACACACAGCA
** *
27033749 TGTTAGGCACAAAGCCCAAATAATCATTGGCACAAAGCCTGCTAGGCACTTAGCCCGAATAATCA
1 TGTTAGGCACAAAGCCCAAATAATCACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAATCA
27033814 CCAGCACAAAACC
66 CCAGCACAAAACC
* * *
27033827 TGTTAGGCACTTAA-CCCGAATAATCACCGGCACAAAGCCTGCTAGGCGCTTAGCCCAAATAATC
1 TGTTAGGCAC-AAAGCCCAAATAATCACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAATC
27033891 AC
65 AC
27033893 AGTATTTCTA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
78 57 0.97
79 2 0.03
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.18
Consensus pattern (78 bp):
TGTTAGGCACAAAGCCCAAATAATCACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAATCA
CCAGCACAAAACC
Found at i:27044937 original size:14 final size:15
Alignment explanation
Indices: 27044920--27044948 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
27044910 ATTAGAAGTA
27044920 TTAAGAG-ATTTTAT
1 TTAAGAGTATTTTAT
27044934 TTAAGAGTATTTTAT
1 TTAAGAGTATTTTAT
27044949 GTCTTTAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (15 bp):
TTAAGAGTATTTTAT
Found at i:27049226 original size:30 final size:29
Alignment explanation
Indices: 27049200--27049279 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 29
27049190 TTGTTCTGGG
27049200 AAAAATAATTTTGACAAGATGGGTTCTGA
1 AAAAATAATTTTGACAAGATGGGTTCTGA
* * * *
27049229 AAAAATAAATTTAACATGATGTGTTCTGA
1 AAAAATAATTTTGACAAGATGGGTTCTGA
* *
27049258 AAAAATTATTTTGACGAGATGG
1 AAAAATAATTTTGACAAGATGG
27049280 ATTTTGTTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (29 bp):
AAAAATAATTTTGACAAGATGGGTTCTGA
Found at i:27049278 original size:29 final size:28
Alignment explanation
Indices: 27049191--27049278 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 28
27049181 TGCTAAGTAT
*
27049191 TGTTCTGGGAAAAATAATTTTGACAAGATG
1 TGTTCT-GAAAAAATAATTTTGAC-AGATG
* * *
27049221 GGTTCTGAAAAAATAAATTTAACATGATG
1 TGTTCTGAAAAAATAATTTTGACA-GATG
*
27049250 TGTTCTGAAAAAATTATTTTGACGAGATG
1 TGTTCTGAAAAAATAATTTTGAC-AGATG
27049279 GATTTTGTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.02
29 41 0.85
30 6 0.12
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (28 bp):
TGTTCTGAAAAAATAATTTTGACAGATG
Found at i:27051704 original size:16 final size:16
Alignment explanation
Indices: 27051683--27051722 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
27051673 ACCATTGGTA
*
27051683 TTGTCTAAGGTACGTT
1 TTGTCTAAGGTACATT
27051699 TTGTCTAAGGTACATT
1 TTGTCTAAGGTACATT
27051715 TTGTCTAA
1 TTGTCTAA
27051723 CTACTACGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (16 bp):
TTGTCTAAGGTACATT
Found at i:27052787 original size:59 final size:59
Alignment explanation
Indices: 27052692--27052928 Score: 388
Period size: 59 Copynumber: 4.0 Consensus size: 59
27052682 CCACATCGAG
* *
27052692 AGAACTTCTAATTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAA
1 AGAACTTCTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATTCAAA
*
27052751 AGAACTTTTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATTCAAA
1 AGAACTTCTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATTCAAA
*
27052810 AGAATTTCTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATT-AACA
1 AGAACTTCTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATTCAA-A
* *
27052869 ACAACTTCTATTTTATTAAATGAAACAAT-CTAAAATTAATTTGTACAAAAATATTCAAA
1 AGAACTTCTATTTTATTAAATGAAACAATATTAAAA-TAATTTGTACAAAAATATTCAAA
27052928 A
1 A
27052929 ATAAATCACT
Statistics
Matches: 167, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
58 7 0.04
59 158 0.95
60 2 0.01
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35
Consensus pattern (59 bp):
AGAACTTCTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATTCAAA
Found at i:27053328 original size:18 final size:18
Alignment explanation
Indices: 27053305--27053348 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
27053295 GTGGAAAAAA
* *
27053305 GATACATATAAGGGTTAG
1 GATACACATAAGAGTTAG
27053323 GATACACATAAGAGTTAG
1 GATACACATAAGAGTTAG
27053341 GATACACA
1 GATACACA
27053349 CCTTGTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (18 bp):
GATACACATAAGAGTTAG
Found at i:27057300 original size:3 final size:3
Alignment explanation
Indices: 27057279--27057341 Score: 54
Period size: 3 Copynumber: 21.0 Consensus size: 3
27057269 TTTAAGATTT
* * * ** * * *
27057279 TTA TTA TTG TTA TTG TTA TTA TTA ATA CCA TCA TCA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27057327 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
27057342 AATTGTTTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:27061493 original size:6 final size:6
Alignment explanation
Indices: 27061482--27061508 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
27061472 AGTGACTTTT
27061482 TTATAA TTATAA TTATAA TTATAA TTA
1 TTATAA TTATAA TTATAA TTATAA TTA
27061509 CTATGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTATAA
Found at i:27075601 original size:14 final size:14
Alignment explanation
Indices: 27075582--27075608 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27075572 AAAATAATAC
27075582 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
27075596 AAAAAAATAAAAA
1 AAAAAAATAAAAA
27075609 AAGGTGCAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:27075742 original size:4 final size:4
Alignment explanation
Indices: 27075725--27075768 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
27075715 GAATGAGAGG
*
27075725 GAAA G-AA G-AA GAAA GAAA GAAA GAAA G-AA -AAA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
27075769 ATGAAAGGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 10 0.29
4 25 0.71
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:27075750 original size:22 final size:22
Alignment explanation
Indices: 27075725--27075804 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 22
27075715 GAATGAGAGG
27075725 GAAAGAAGAAGAAAGAAAGAAA
1 GAAAGAAGAAGAAAGAAAGAAA
* *
27075747 GAAAGAAAAAGAAGGAAAGAAAA
1 GAAAGAAGAAGAAAGAAAG-AAA
* * *
27075770 TGAAAGGAGAAGAGAAAAAAAAAA
1 -GAAAGAAGAAGA-AAGAAAGAAA
*
27075794 G-AAGTAGAAGA
1 GAAAGAAGAAGA
27075805 GGGGAGGAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
22 26 0.55
23 4 0.09
24 13 0.28
25 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.03
Consensus pattern (22 bp):
GAAAGAAGAAGAAAGAAAGAAA
Found at i:27075768 original size:18 final size:19
Alignment explanation
Indices: 27075724--27075768 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
27075714 AGAATGAGAG
27075724 GGAAAG-AAGAAGAAAGAA
1 GGAAAGAAAGAAGAAAGAA
*
27075742 AGAAAGAAAGAA-AAAGAA
1 GGAAAGAAAGAAGAAAGAA
27075760 GGAAAGAAA
1 GGAAAGAAA
27075769 ATGAAAGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (19 bp):
GGAAAGAAAGAAGAAAGAA
Found at i:27075769 original size:14 final size:14
Alignment explanation
Indices: 27075740--27075796 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
27075730 AAGAAGAAAG
27075740 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
*
27075754 AAAGAAGGAAAGAA
1 AAAGAAAGAAAGAA
*
27075768 AATGAAAGGAGAAGAGA
1 AAAGAAA-GA-AAGA-A
27075785 AAA-AAA-AAAGAA
1 AAAGAAAGAAAGAA
27075797 GTAGAAGAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
12 1 0.03
13 4 0.11
14 19 0.53
15 2 0.06
16 7 0.19
17 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:27075775 original size:18 final size:17
Alignment explanation
Indices: 27075724--27075775 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
27075714 AGAATGAGAG
27075724 GGAAAGAAGAAGAAAGAA
1 GGAAAGAA-AAGAAAGAA
* *
27075742 AGAAAGAAAGAAAAAGAA
1 GGAAAGAAA-AGAAAGAA
27075760 GGAAAGAAAATGAAAG
1 GGAAAGAAAA-GAAAG
27075776 GAGAAGAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (17 bp):
GGAAAGAAAAGAAAGAA
Found at i:27076717 original size:284 final size:285
Alignment explanation
Indices: 27076204--27076870 Score: 1167
Period size: 284 Copynumber: 2.3 Consensus size: 285
27076194 AAAGTAAAAA
* *
27076204 TATAAAATTAGAAATTATGAAATTTTTTAAAGTAATAAAATACGGAGAAAAAAATACGAAGAAAT
1 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
* *
27076269 GGCCG-AGATAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTC
66 GGCCGAAG-TAAGAGTGTTTTACTAACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTC
*
27076333 AAACAAAATGTACCGAAATAATATAAAATAATAAAATACAAAAATAATTTTTTTATTGAAAGTAA
130 AAACAAAATGTACCGAAATAATATAAAATAATAAAATAAAAAAATAATTTTTTTATTGAAAGTAA
* *
27076398 TAAAATTCGGGAAAATAATACGAGCAAATGGCAGGAATAAGC-ATTTTTTTACACTAAATTAATT
195 TAAAATTCGGGAAAATAATACAAGCAAACGGCAGGAATAAGCGATTTTTTTACACTAAATTAATT
27076462 TAAAAAACACACTAAATTAATAAATT
260 TAAAAAACACACTAAATTAATAAATT
* *
27076488 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAACGCGGAGAAAAAAATAAGAAGAAAT
1 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
27076553 GGCCGAAGTAAGAGTGTTTTACTAACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCA
66 GGCCGAAGTAAGAGTGTTTTACTAACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCA
*
27076618 AACAAAATGTACTGAAATAATATAAAATAATAAAATAAAAAAATAATTTTTTTATTGAAAGTAAT
131 AACAAAATGTACCGAAATAATATAAAATAATAAAATAAAAAAATAATTTTTTTATTGAAAGTAAT
*
27076683 AAAATTCGGGAAAATAATACAAGCAAACGGCAGGAATAAGCGCTTTTTTTACACTAAATTAATTT
196 AAAATTCGGGAAAATAATACAAGCAAACGGCAGGAATAAGCGATTTTTTTACACTAAATTAATTT
27076748 AAAAAACACACTAAATTAATAAATT
261 AAAAAACACACTAAATTAATAAATT
* *
27076773 TATAAAATTAGAAATTATGATATTTTTTTAAGTAATAAAATGCGGAGAAAAGAATACGAAGAAAT
1 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
* *
27076838 GACTGAAGTAAGAGTGTTTTACTAACTATTTTT
66 GGCCGAAGTAAGAGTGTTTTACTAACT-TTTTT
27076871 TCAACATGCA
Statistics
Matches: 363, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
284 223 0.61
285 135 0.37
286 5 0.01
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (285 bp):
TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
GGCCGAAGTAAGAGTGTTTTACTAACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCA
AACAAAATGTACCGAAATAATATAAAATAATAAAATAAAAAAATAATTTTTTTATTGAAAGTAAT
AAAATTCGGGAAAATAATACAAGCAAACGGCAGGAATAAGCGATTTTTTTACACTAAATTAATTT
AAAAAACACACTAAATTAATAAATT
Found at i:27082036 original size:9 final size:9
Alignment explanation
Indices: 27082022--27082047 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
27082012 ATGAAAACCA
27082022 TAATAATAT
1 TAATAATAT
27082031 TAATAATAT
1 TAATAATAT
27082040 TAATAATA
1 TAATAATA
27082048 ATTTTATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAATAATAT
Found at i:27082080 original size:16 final size:18
Alignment explanation
Indices: 27082059--27082105 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
27082049 TTTTATACTC
27082059 AAAATAATACTAA-C-TA
1 AAAATAATACTAACCATA
27082075 AAAATAATAACTAACCATA
1 AAAATAAT-ACTAACCATA
*
27082094 ATAATAATACTA
1 AAAATAATACTA
27082106 GTTTTTTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 8 0.30
17 5 0.19
18 5 0.19
19 9 0.33
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATAATACTAACCATA
Found at i:27082387 original size:10 final size:10
Alignment explanation
Indices: 27082359--27082396 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
27082349 AAAATACCAT
27082359 TTTTTCTCTTC
1 TTTTTCTC-TC
*
27082370 TCTTTCTCTC
1 TTTTTCTCTC
27082380 TTTTTCTCTC
1 TTTTTCTCTC
27082390 TTTTTCT
1 TTTTTCT
27082397 GCAACAACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:27082505 original size:27 final size:27
Alignment explanation
Indices: 27082467--27082531 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
27082457 AACAAGACTA
*
27082467 GTGCCGCCCATGGGAAGGGCACCATTG
1 GTGCCGCCCATGGGAAGGGCACCATCG
*
27082494 GTGCCGCCCATGGGAATGGCACCATCG
1 GTGCCGCCCATGGGAAGGGCACCATCG
27082521 GTGCCGCCCAT
1 GTGCCGCCCAT
27082532 TAGTTAGGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.17, C:0.34, G:0.34, T:0.15
Consensus pattern (27 bp):
GTGCCGCCCATGGGAAGGGCACCATCG
Found at i:27083024 original size:20 final size:20
Alignment explanation
Indices: 27082996--27083034 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
27082986 CAAAAAATGC
*
27082996 AAAAGTATAAAAAATATTAT
1 AAAAATATAAAAAATATTAT
* *
27083016 AAAAATATATAAGATATTA
1 AAAAATATAAAAAATATTA
27083035 AATTTTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
AAAAATATAAAAAATATTAT
Found at i:27083042 original size:7 final size:7
Alignment explanation
Indices: 27083032--27083058 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
27083022 ATATAAGATA
27083032 TTAAATT
1 TTAAATT
27083039 TTAAATT
1 TTAAATT
27083046 TTAAATT
1 TTAAATT
27083053 TTAAAT
1 TTAAAT
27083059 ATATATGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:27084054 original size:21 final size:20
Alignment explanation
Indices: 27084030--27084069 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
27084020 TGGTTATAAA
*
27084030 AAAATATTAATATTTAAATTT
1 AAAATAATAA-ATTTAAATTT
*
27084051 AAAATAATAAATTTTAATT
1 AAAATAATAAATTTAAATT
27084070 ATTTTTTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATAATAAATTTAAATTT
Found at i:27084062 original size:28 final size:27
Alignment explanation
Indices: 27084004--27084073 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
27083994 TGTATAAATT
*
27084004 AATATTAATATTTAAATGGTTATAAAAA
1 AATATTAATATTTAAAT-GTTAAAAAAA
27084032 AATATTAATATTTAAAT-TTAAAATAATA
1 AATATTAATATTTAAATGTTAAAA-AA-A
*
27084060 AATTTTAATTATTT
1 AATATTAA-TATTT
27084074 TTTTGGTGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
26 5 0.14
27 2 0.05
28 25 0.68
29 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (27 bp):
AATATTAATATTTAAATGTTAAAAAAA
Found at i:27087877 original size:19 final size:18
Alignment explanation
Indices: 27087828--27087879 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
27087818 AAAATTTTGT
27087828 TTTTTAAATTAATTTTCA
1 TTTTTAAATTAATTTTCA
**
27087846 TTATTTATTTTAA-TTTCTA
1 TT-TTTAAATTAATTTTC-A
27087865 TATTTTAAATTAATT
1 T-TTTTAAATTAATT
27087880 CATATTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
18 6 0.23
19 18 0.69
20 2 0.08
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTAAATTAATTTTCA
Found at i:27088001 original size:14 final size:15
Alignment explanation
Indices: 27087978--27088007 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27087968 ATGAATTAAA
27087978 TGTTT-TTTTTATTT
1 TGTTTATTTTTATTT
27087992 TGTTTATTTTTATTT
1 TGTTTATTTTTATTT
27088007 T
1 T
27088008 TTATAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (15 bp):
TGTTTATTTTTATTT
Found at i:27088261 original size:9 final size:9
Alignment explanation
Indices: 27088242--27088278 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
27088232 TGAGCTTTCG
*
27088242 AATTTGAAT
1 AATTCGAAT
*
27088251 AACTCGAAT
1 AATTCGAAT
27088260 AATTCGAAT
1 AATTCGAAT
27088269 AATTCGAAT
1 AATTCGAAT
27088278 A
1 A
27088279 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:27095624 original size:102 final size:102
Alignment explanation
Indices: 27095506--27095705 Score: 319
Period size: 102 Copynumber: 2.0 Consensus size: 102
27095496 CCAGTGATTC
* * * *
27095506 GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGATTAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGATGGAATCAGCACTTAGCAACCA
*
27095571 CCAATGATTCAGGGAATCAACACTTAGCAACCCATCG
66 CCAATGAGTCAGGGAATCAACACTTAGCAACCCATCG
*
27095608 GGGGAATCATCACTTAGCAACCCCCTTCACATTTAAGATACGATGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGATGGAATCAGCACTTAGCAACCA
* * *
27095673 CCAATGAGTCGGGGAATTAGCACTTAGCAACCC
66 CCAATGAGTCAGGGAATCAACACTTAGCAACCC
27095706 CTTTCACAAT
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 89 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.21
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGATGGAATCAGCACTTAGCAACCA
CCAATGAGTCAGGGAATCAACACTTAGCAACCCATCG
Found at i:27095669 original size:42 final size:40
Alignment explanation
Indices: 27095610--27095746 Score: 117
Period size: 42 Copynumber: 3.5 Consensus size: 40
27095600 ACCCATCGGG
*
27095610 GGAATCATCACTTAGCAACCCCCTTCACATTTAAGATACGAT
1 GGAATCAGCACTTAGCAACCCCCTTCACA-TTAAGATACG-T
* * *
27095652 GGAATCAGCACTTAGCAA-CCAC--CA-A-TGAG-T-CGG
1 GGAATCAGCACTTAGCAACCCCCTTCACATTAAGATACGT
* *
27095685 GGAATTAGCACTTAGCAACCCCTTTCACAATTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCAC-ATTAAGATAC-GT
* *
27095727 GGGATCAACACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
27095747 ACCAATGAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
33 17 0.23
34 4 0.05
35 1 0.01
36 5 0.07
38 2 0.03
39 5 0.07
40 1 0.01
41 4 0.05
42 35 0.47
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (40 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTAAGATACGT
Found at i:27095704 original size:75 final size:75
Alignment explanation
Indices: 27095608--27095780 Score: 265
Period size: 75 Copynumber: 2.3 Consensus size: 75
27095598 CAACCCATCG
* * *
27095608 GGGGAATCATCACTTAGCAACCCCCTTCACATTTAAGATACGATGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACAATTAAGATACGATGGAATCAACACTTAGCAACCA
* *
27095673 CCAATGAGTC
66 CCAATGAATA
* * * *
27095683 GGGGAATTAGCACTTAGCAACCCCTTTCACAATTAAGATACGGTGGGATCAACACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACAATTAAGATACGATGGAATCAACACTTAGCAACCA
27095748 CCAATGAATA
66 CCAATGAATA
27095758 GGGGAATCAGCACTTAGCAACCC
1 GGGGAATCAGCACTTAGCAACCC
27095781 TTTGGAGGAA
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 88 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (75 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACAATTAAGATACGATGGAATCAACACTTAGCAACCA
CCAATGAATA
Found at i:27095775 original size:177 final size:177
Alignment explanation
Indices: 27095474--27095811 Score: 543
Period size: 177 Copynumber: 1.9 Consensus size: 177
27095464 CTGTTATCAG
* * * *
27095474 TGGATTCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATT
1 TGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCACAAT
* * *
27095539 TAAGATACGGTGGGATTAGCACTTAGCAACCACCAATGATTCAGGGAATCAACACTTAGCAACCC
66 TAAGATACGGTGGGATCAACACTTAGCAACCACCAATGAATCAGGGAATCAACACTTAGCAACCC
* *
27095604 ATCGGGGGAATCATCACTTAGCAACCCCCTTCACATTTAAGATACGA
131 ATCGGAGGAATCAACACTTAGCAACCCCCTTCACATTTAAGATACGA
*
27095651 TGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATTAGCACTTAGCAACCCCTTTCACAAT
1 TGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCACAAT
*
27095716 TAAGATACGGTGGGATCAACACTTAGCAACCACCAATGAAT-AGGGGAATCAGCACTTAGCAACC
66 TAAGATACGGTGGGATCAACACTTAGCAACCACCAATGAATCA-GGGAATCAACACTTAGCAACC
* *
27095780 CTTTGGAGGAATCAACACTTAGCAACCCCCTT
130 CATCGGAGGAATCAACACTTAGCAACCCCCTT
27095812 TATATTCAAT
Statistics
Matches: 147, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
176 1 0.01
177 146 0.99
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.22
Consensus pattern (177 bp):
TGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCACAAT
TAAGATACGGTGGGATCAACACTTAGCAACCACCAATGAATCAGGGAATCAACACTTAGCAACCC
ATCGGAGGAATCAACACTTAGCAACCCCCTTCACATTTAAGATACGA
Found at i:27095777 original size:33 final size:33
Alignment explanation
Indices: 27095652--27095779 Score: 112
Period size: 33 Copynumber: 3.6 Consensus size: 33
27095642 AAGATACGAT
* *
27095652 GGAATCAGCACTTAGCAACCACCAATGAGTCGG
1 GGAATCAGCACTTAGCAACCACCAATGAATAGG
* * *
27095685 GGAATTAGCACTTAGCAACCCCTTTCACAATTAAGATACGG
1 GGAATCAGCACTTAGCAA--CC--AC-CAA-TGA-ATA-GG
* *
27095726 TGGGATCAACACTTAGCAACCACCAATGAATAGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATAGG
27095760 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
27095780 CTTTGGAGGA
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
33 35 0.47
34 2 0.03
35 5 0.07
36 2 0.03
37 4 0.05
38 4 0.05
39 2 0.03
40 3 0.04
41 2 0.03
42 15 0.20
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATAGG
Found at i:27104336 original size:127 final size:127
Alignment explanation
Indices: 27104110--27104426 Score: 415
Period size: 127 Copynumber: 2.5 Consensus size: 127
27104100 TTTTATAACC
* * * *
27104110 AATTTTAGTATACCAAAATCATGTTATCCAAGACTTTACCAAGATTTCTAACGAAATACTAAAAA
1 AATTTTGGTATACCAAAATCATGTTATCCAAGCCTTTACCAATATTTATAACGAAATACTAAAAA
* * * * *
27104175 TTTTAAGTGCATATCTTAAGATATTTTGGTATATACCATAATTTTTATGGAATCTCGTTAAA
66 TTTTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
* * *
27104237 AATTTTGGTATACCAAAATCATGTTATCCAAGCCTTTACCAATATTTATAATGAAATTC-CAAAA
1 AATTTTGGTATACCAAAATCATGTTATCCAAGCCTTTACCAATATTTATAACGAAATACTAAAAA
27104301 TTTCTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
66 TTT-TAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
* * * * * *
27104364 AATTTTTGGCATACCAAAATCCA-GATT-TACAAGCCTATACCAATATTTTTAACAAAATGCTAA
1 AA-TTTTGGTATACCAAAAT-CATG-TTATCCAAGCCTTTACCAATATTTATAACGAAATACTAA
27104427 TTGTCTAATA
Statistics
Matches: 165, Mismatches: 20, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
126 7 0.04
127 109 0.66
128 44 0.27
129 5 0.03
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.36
Consensus pattern (127 bp):
AATTTTGGTATACCAAAATCATGTTATCCAAGCCTTTACCAATATTTATAACGAAATACTAAAAA
TTTTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
Found at i:27104434 original size:127 final size:127
Alignment explanation
Indices: 27104110--27104466 Score: 370
Period size: 127 Copynumber: 2.8 Consensus size: 127
27104100 TTTTATAACC
* * * * * * * * *
27104110 AATTTTAGTATACCAAAATCATGTTATCCAAGACTTTACCAAGATTTCTAA-CGAAATACTAAAA
1 AATTTTGGCATACCAAAATCATGTTATACAAGCCTATACCAATATTTATAATCAAAAT-C-CAAA
* * * * *
27104174 ATTT-TAAGTGCATATCTTAAGATATTTTGGTATATACCATAATTTTTATGGAATCTCGTTAAA
64 ATTTCTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
* * * * *
27104237 AATTTTGGTATACCAAAATCATGTTATCCAAGCCTTTACCAATATTTATAATGAAATTCCAAAAT
1 AATTTTGGCATACCAAAATCATGTTATACAAGCCTATACCAATATTTATAATCAAAATCCAAAAT
27104302 TTCTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
66 TTCTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
* * *
27104364 AATTTTTGGCATACCAAAATCCA-GATT-TACAAGCCTATACCAATATTTTTAA-CAAAATGC-T
1 AA-TTTTGGCATACCAAAAT-CATG-TTATACAAGCCTATACCAATATTTATAATCAAAATCCAA
* *
27104425 AATTGTCTAA-TAGCACATCCTCAA-ATATTTTGGTATATACCA
63 AATT-TCTAAGTA-CATAT-CTTAAGATATTTTGGTATATACCA
27104467 ACATTTACAA
Statistics
Matches: 199, Mismatches: 23, Indels: 16
0.84 0.10 0.07
Matches are distributed among these distances:
126 13 0.07
127 136 0.68
128 46 0.23
129 4 0.02
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (127 bp):
AATTTTGGCATACCAAAATCATGTTATACAAGCCTATACCAATATTTATAATCAAAATCCAAAAT
TTCTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
Found at i:27112072 original size:61 final size:63
Alignment explanation
Indices: 27111924--27112072 Score: 169
Period size: 63 Copynumber: 2.4 Consensus size: 63
27111914 AATATCCCTC
* * * * * *
27111924 ACACGGCCTGGACACACGCTCGTGTCTCTGGCCCTTGTGACTTTAAATCTAAAATAGTGAGTT
1 ACACGGCCTGGACACACGCTCGTGTCCCTGGCCCATGTGACTCTAAATCTAAAACAATGAGTA
* *
27111987 ACACGGCCTGGACACACGCCCGTGTCCCTGGCCCAT-TGACTCTAACT-TCAAAACAATGAGTA
1 ACACGGCCTGGACACACGCTCGTGTCCCTGGCCCATGTGACTCTAAATCT-AAAACAATGAGTA
* * *
27112049 ACATGG-CTTGACACACGGTCGTGT
1 ACACGGCCTGGACACACGCTCGTGT
27112073 GACCCACATG
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
61 16 0.22
62 24 0.33
63 33 0.45
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (63 bp):
ACACGGCCTGGACACACGCTCGTGTCCCTGGCCCATGTGACTCTAAATCTAAAACAATGAGTA
Found at i:27112662 original size:22 final size:23
Alignment explanation
Indices: 27112617--27112667 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
27112607 AAAATATGAT
27112617 AGAAAGAAAAATGAACAAAAAAG
1 AGAAAGAAAAATGAACAAAAAAG
* *
27112640 AGAAGGAAGAATGAAC-AAAAAG
1 AGAAAGAAAAATGAACAAAAAAG
27112662 A-AAAGA
1 AGAAAGA
27112668 GGAGGAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 4 0.16
22 7 0.28
23 14 0.56
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.04
Consensus pattern (23 bp):
AGAAAGAAAAATGAACAAAAAAG
Found at i:27116644 original size:28 final size:28
Alignment explanation
Indices: 27116565--27116644 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 28
27116555 AATTTTGGAC
* * *
27116565 AAAATTATAAAATATAAAAAATAAGGGA
1 AAAACTATAAAATCTAAAAAATAGGGGA
*
27116593 AAAACTATAAAATCTAAAAAATAGGGGC
1 AAAACTATAAAATCTAAAAAATAGGGGA
*
27116621 AAAACTGTAAAATCTAAAAAATAG
1 AAAACTATAAAATCTAAAAAATAG
27116645 TGGACATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.20
Consensus pattern (28 bp):
AAAACTATAAAATCTAAAAAATAGGGGA
Found at i:27120206 original size:16 final size:16
Alignment explanation
Indices: 27120180--27120219 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
27120170 TAACAGATCA
27120180 ACATCATACACATATAT
1 ACAT-ATACACATATAT
27120197 ACATATACACATATAT
1 ACATATACACATATAT
27120213 ATCATAT
1 A-CATAT
27120220 TAGAATTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (16 bp):
ACATATACACATATAT
Found at i:27122184 original size:3 final size:3
Alignment explanation
Indices: 27122170--27122224 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
27122160 AATTAAACAC
* * * *
27122170 TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TGA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
27122218 TAA TAA T
1 TAA TAA T
27122225 GAAATGTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:27131539 original size:98 final size:98
Alignment explanation
Indices: 27131370--27131620 Score: 457
Period size: 98 Copynumber: 2.6 Consensus size: 98
27131360 GCAAAAATGC
27131370 CACACCCAATACGTTTGGGCACGATCCCTTTAGAATCCCAAACTCGGAATATTTCATTTACTTTA
1 CACACCCAATACGTTTGGGCACGATCCCTTTAGAATCCCAAACTCGGAATATTTCATTTACTTTA
27131435 AAAGAACATCCACTCATCCAAGATTTAAGAAAT
66 AAAGAACATCCACTCATCCAAGATTTAAGAAAT
27131468 CACACCCAATACGTTTGGGCACGATCCCTTTAGAATCCCAAACTCGGAATATTTCATTTACTTTA
1 CACACCCAATACGTTTGGGCACGATCCCTTTAGAATCCCAAACTCGGAATATTTCATTTACTTTA
*
27131533 AAAGAACATCCACTTATCCAAGATTTAAGAAAT
66 AAAGAACATCCACTCATCCAAGATTTAAGAAAT
* * * *
27131566 CACACCCAATACGTTAGGGCACAATTCCTTTAGAATCTCAAACTCGGAATATTTC
1 CACACCCAATACGTTTGGGCACGATCCCTTTAGAATCCCAAACTCGGAATATTTC
27131621 CTTCATGATT
Statistics
Matches: 148, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 148 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (98 bp):
CACACCCAATACGTTTGGGCACGATCCCTTTAGAATCCCAAACTCGGAATATTTCATTTACTTTA
AAAGAACATCCACTCATCCAAGATTTAAGAAAT
Found at i:27131921 original size:15 final size:15
Alignment explanation
Indices: 27131903--27131935 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
27131893 CAAATGCTAT
27131903 AATAATAAATACAAC
1 AATAATAAATACAAC
*
27131918 AATAATAAATACATC
1 AATAATAAATACAAC
27131933 AAT
1 AAT
27131936 GACATATCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:27132424 original size:3 final size:3
Alignment explanation
Indices: 27132388--27132415 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
27132378 GCGCATGAAT
27132388 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
27132416 CGATAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:27133039 original size:12 final size:12
Alignment explanation
Indices: 27133022--27133052 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
27133012 ATTTGTTTGT
27133022 AAAAAATAAAAA
1 AAAAAATAAAAA
27133034 AAAAAATAAAAA
1 AAAAAATAAAAA
27133046 AATAAAA
1 AA-AAAA
27133053 GCTGTGAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAAAATAAAAA
Found at i:27134103 original size:19 final size:19
Alignment explanation
Indices: 27134079--27134129 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
27134069 TCTTGAAAAA
*
27134079 TAAAAAATTAAAT-ATTATT
1 TAAAAAATTAAATAACT-TT
*
27134098 TAAAAATTTAAATAACTTT
1 TAAAAAATTAAATAACTTT
*
27134117 TAAATAATTAAAT
1 TAAAAAATTAAAT
27134130 TATTTGTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 25 0.93
20 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAAAATTAAATAACTTT
Found at i:27134161 original size:30 final size:30
Alignment explanation
Indices: 27134116--27134192 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
27134106 TAAATAACTT
* *
27134116 TTAAATAATTAAATTATTTGTTAAATCTTAAA
1 TTAAAT-A-TAAATTACTTGTGAAATCTTAAA
*
27134148 TTAAATATAAATTACTTGTGAAATTTTAAA
1 TTAAATATAAATTACTTGTGAAATCTTAAA
*
27134178 TTAAA-ATAATTTACT
1 TTAAATATAAATTACT
27134193 AATTAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 9 0.22
30 25 0.61
31 1 0.02
32 6 0.15
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (30 bp):
TTAAATATAAATTACTTGTGAAATCTTAAA
Found at i:27134200 original size:29 final size:30
Alignment explanation
Indices: 27134136--27134202 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
27134126 AAATTATTTG
* **
27134136 TTAAATCTTAAATTAAATATAAATTACTTG
1 TTAAATTTTAAATTAAATATAAATTACTAA
* *
27134166 TGAAATTTTAAATTAAA-ATAATTTACTAA
1 TTAAATTTTAAATTAAATATAAATTACTAA
27134195 TTAAATTT
1 TTAAATTT
27134203 AATAAATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (30 bp):
TTAAATTTTAAATTAAATATAAATTACTAA
Found at i:27134818 original size:24 final size:25
Alignment explanation
Indices: 27134769--27134822 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
27134759 TTAAATTTTA
*
27134769 TATTTAATGTATCATTACATTAAAT
1 TATTTAATATATCATTACATTAAAT
*
27134794 TATTTAA-ATATCATATA-ATTTAAT
1 TATTTAATATATCAT-TACATTAAAT
27134818 TATTT
1 TATTT
27134823 TTAGTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (25 bp):
TATTTAATATATCATTACATTAAAT
Found at i:27137448 original size:46 final size:46
Alignment explanation
Indices: 27137381--27137473 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 46
27137371 GAGTTTGCCC
* ** *
27137381 AGGTTCCAAGCTCTTGCATATGTAGTGGACTCTAGAATACATGAAT
1 AGGTTCCAAGCTCCTGCATATGTAGCAGACTCAAGAATACATGAAT
* *
27137427 AGGTTCCGAGCTCCTGCATATGTTGCAGACTCAAGAATACATGAAT
1 AGGTTCCAAGCTCCTGCATATGTAGCAGACTCAAGAATACATGAAT
27137473 A
1 A
27137474 TTAAGCCCTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (46 bp):
AGGTTCCAAGCTCCTGCATATGTAGCAGACTCAAGAATACATGAAT
Found at i:27142981 original size:15 final size:17
Alignment explanation
Indices: 27142950--27142983 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
27142940 TTAAAGTGTA
27142950 AATTTACTTTAATTTAT
1 AATTTACTTTAATTTAT
27142967 AATTT-CTTT-ATTTAT
1 AATTTACTTTAATTTAT
27142982 AA
1 AA
27142984 GAGATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 4 0.24
17 5 0.29
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTTACTTTAATTTAT
Found at i:27150813 original size:20 final size:20
Alignment explanation
Indices: 27150788--27150833 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
27150778 CATTGGATGG
*
27150788 AAAATGAATGTATGAAATGA
1 AAAATGAATATATGAAATGA
**
27150808 AAAATGGTTATATGAAATGA
1 AAAATGAATATATGAAATGA
27150828 AAAATG
1 AAAATG
27150834 GTTGGAGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.26
Consensus pattern (20 bp):
AAAATGAATATATGAAATGA
Found at i:27150834 original size:20 final size:20
Alignment explanation
Indices: 27150798--27150836 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
27150788 AAAATGAATG
27150798 TATGAAATGAAAAATGGTTA
1 TATGAAATGAAAAATGGTTA
27150818 TATGAAATGAAAAATGGTT
1 TATGAAATGAAAAATGGTT
27150837 GGAGATGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.21, T:0.31
Consensus pattern (20 bp):
TATGAAATGAAAAATGGTTA
Found at i:27154874 original size:28 final size:28
Alignment explanation
Indices: 27154809--27154897 Score: 106
Period size: 28 Copynumber: 3.1 Consensus size: 28
27154799 ATACAATTCT
*
27154809 GGGTAAAATTATAAAAATTTAAAAAATAG
1 GGGTAAAATTAT-AAAATTTAAAAAATAA
* * *
27154838 GGGTAAAAACTATAAAATCTAAAAACTAA
1 GGGT-AAAATTATAAAATTTAAAAAATAA
* *
27154867 TGGTAAAATTGTAAAATTTAAAAAATAA
1 GGGTAAAATTATAAAATTTAAAAAATAA
27154895 GGG
1 GGG
27154898 ACACACGGCC
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
28 22 0.45
29 20 0.41
30 7 0.14
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (28 bp):
GGGTAAAATTATAAAATTTAAAAAATAA
Found at i:27158419 original size:50 final size:50
Alignment explanation
Indices: 27158352--27158590 Score: 225
Period size: 50 Copynumber: 4.8 Consensus size: 50
27158342 AGATTATGAC
* * *
27158352 AGGTCCCATGTAAGACCATGTTTAGGACATGGCGTTGGCACCGAGATAAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAG
* *
27158402 AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAG
** * * * * *
27158452 AGGTCCCCCGTAGGACCATGTCTGGGACATGGCATGGGCACCAATATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAG
** * * * * * *
27158502 AACTCCCATGTAAGGCCATATATGGGATATGGCATTGGCAGTAC-AGGA-AAC
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--CCGA-GATAAG
* *
27158553 A--TCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
27158591 TGTTATTATC
Statistics
Matches: 156, Mismatches: 30, Indels: 7
0.81 0.16 0.04
Matches are distributed among these distances:
49 31 0.20
50 120 0.77
51 3 0.02
52 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.21
Consensus pattern (50 bp):
AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAG
Done.