Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 127 of 144
Found at i:31062732 original size:2 final size:2
Alignment explanation
Indices: 31062725--31062770 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
31062715 ACCAAAACAA
31062725 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31062767 AT AT
1 AT AT
31062771 TTGTCGACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31066006 original size:23 final size:23
Alignment explanation
Indices: 31065976--31066065 Score: 92
Period size: 23 Copynumber: 3.8 Consensus size: 23
31065966 CAAAAGTACT
*
31065976 GAGCACACAAAGTGCTAATTAGA
1 GAGCACACAAAGTGCTAATCAGA
*
31065999 GAGCACACGAAGTGCTAATAACAGA
1 GAGCACACAAAGTGCTAAT--CAGA
* * *
31066024 GAGCATGA-AACGTGCTAAACAGA
1 GAGCA-CACAAAGTGCTAATCAGA
*
31066047 GAGCACACACAGTGCTAAT
1 GAGCACACAAAGTGCTAAT
31066066 AATCAGATAG
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
22 1 0.02
23 35 0.66
25 16 0.30
26 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.14
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCAGA
Found at i:31066048 original size:48 final size:49
Alignment explanation
Indices: 31065987--31066091 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 49
31065977 AGCACACAAA
** *
31065987 GTGCTAATTAGAGAGCACACGA-AGTGCTAATAA-CAGAGAGCATGAA-AC
1 GTGCTAAACAGAGAGCACAC-ACAGTGCTAATAATCAGAGAGCA-CAATAC
*
31066035 GTGCTAAACAGAGAGCACACACAGTGCTAATAATCAGATAGCACAATAC
1 GTGCTAAACAGAGAGCACACACAGTGCTAATAATCAGAGAGCACAATAC
31066084 GTGCTAAA
1 GTGCTAAA
31066092 ACAACAGAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
47 1 0.02
48 31 0.62
49 18 0.36
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (49 bp):
GTGCTAAACAGAGAGCACACACAGTGCTAATAATCAGAGAGCACAATAC
Found at i:31066087 original size:26 final size:24
Alignment explanation
Indices: 31065981--31066094 Score: 89
Period size: 23 Copynumber: 4.8 Consensus size: 24
31065971 GTACTGAGCA
*
31065981 CACAAA-GTGCTAAT--TAGAGAG
1 CACAAACGTGCTAATAACAGAGAG
31066002 CACACGAA-GTGCTAATAACAGAGAG
1 CACA--AACGTGCTAATAACAGAGAG
*
31066027 CATGAAACGTGCT-A-AACAGAGAG
1 CA-CAAACGTGCTAATAACAGAGAG
* *
31066050 CACACACAGTGCTAATAATCAGATAG
1 CACAAAC-GTGCTAATAA-CAGAGAG
31066076 CACAATACGTGCTAA-AACA
1 CACAA-ACGTGCTAATAACA
31066095 ACAGAGAGAG
Statistics
Matches: 76, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
21 4 0.05
22 3 0.04
23 26 0.34
24 6 0.08
25 17 0.22
26 18 0.24
27 2 0.03
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.16
Consensus pattern (24 bp):
CACAAACGTGCTAATAACAGAGAG
Found at i:31068203 original size:22 final size:21
Alignment explanation
Indices: 31068161--31068203 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
31068151 TATATTATTT
**
31068161 TTAATTTTTTATTTATTTTAA
1 TTAATTTTTTATTTAACTTAA
31068182 TTAATCTTTTTATTTAACTTAA
1 TTAAT-TTTTTATTTAACTTAA
31068204 AACAACATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
TTAATTTTTTATTTAACTTAA
Found at i:31072275 original size:13 final size:14
Alignment explanation
Indices: 31072233--31072269 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
31072223 TAAATTAATA
*
31072233 TTTATTATAACTTT
1 TTTATTAAAACTTT
31072247 TTTATTAAAACTTT
1 TTTATTAAAACTTT
31072261 TTTA-TAAAA
1 TTTATTAAAA
31072270 TATTTTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATTAAAACTTT
Found at i:31072786 original size:36 final size:36
Alignment explanation
Indices: 31072736--31072807 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
31072726 AAAAAAATTC
* *
31072736 AAAATTTATATTTTT-AATTTTTTTAAAAATATATAA
1 AAAAGTTAAATTTTTAAATTTTTTTAAAAATA-ATAA
*
31072772 AAAAGTTAAATTTTTAAATTTTTTTTAAAATAATAA
1 AAAAGTTAAATTTTTAAATTTTTTTAAAAATAATAA
31072808 TTTAGGAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 17 0.53
37 15 0.47
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (36 bp):
AAAAGTTAAATTTTTAAATTTTTTTAAAAATAATAA
Found at i:31076075 original size:1 final size:1
Alignment explanation
Indices: 31076069--31076101 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
31076059 AACTAGAGTC
31076069 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
31076102 CATTAAACGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:31080144 original size:72 final size:72
Alignment explanation
Indices: 31080027--31080170 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
31080017 AATTTGTATT
*
31080027 GAATTCCGATCCCTATCCATCTCAGGCCTCAGCCACCAAACAAAGAATATGCATGCTTTGACAGA
1 GAATTCCGATCCCTATCCATCTCAGGCCTCAGCCACCAAACAAAGAATATGCATGCTTCGACAGA
31080092 ATTTTCA
66 ATTTTCA
31080099 GAATTCCGATCCCTATCCATCTCAGGCCTCAGCCACCAAACAAAGAATATGCATGCTTCGACAGA
1 GAATTCCGATCCCTATCCATCTCAGGCCTCAGCCACCAAACAAAGAATATGCATGCTTCGACAGA
31080164 ATTTTCA
66 ATTTTCA
31080171 TTCTTATTTC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (72 bp):
GAATTCCGATCCCTATCCATCTCAGGCCTCAGCCACCAAACAAAGAATATGCATGCTTCGACAGA
ATTTTCA
Found at i:31081774 original size:2 final size:2
Alignment explanation
Indices: 31081767--31081797 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
31081757 AAACTTAATG
31081767 TC TC TC TC TC TC TC T- TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31081798 CTTCTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:31081787 original size:15 final size:15
Alignment explanation
Indices: 31081767--31081796 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31081757 AAACTTAATG
31081767 TCTCTCTCTCTCTCT
1 TCTCTCTCTCTCTCT
31081782 TCTCTCTCTCTCTCT
1 TCTCTCTCTCTCTCT
31081797 CCTTCTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (15 bp):
TCTCTCTCTCTCTCT
Found at i:31088943 original size:3 final size:3
Alignment explanation
Indices: 31088935--31088966 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
31088925 ACAAGAGCAA
*
31088935 GAT GAT GAT GAT GAT GAT GAT GAT GAT AAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
31088967 GCATGAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:31100337 original size:18 final size:18
Alignment explanation
Indices: 31100314--31100348 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31100304 TTTCATGTTG
31100314 TTTTTAACTT-TTATTTTA
1 TTTTTAA-TTATTATTTTA
31100332 TTTTTAATTATTATTTT
1 TTTTTAATTATTATTTT
31100349 TAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTAATTATTATTTTA
Found at i:31100695 original size:2 final size:2
Alignment explanation
Indices: 31100688--31100712 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31100678 CGAATTGAAC
31100688 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
31100713 ATTGGATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31105634 original size:5 final size:5
Alignment explanation
Indices: 31105624--31105651 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
31105614 AAAGAGTCAA
31105624 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
31105652 GTTGAACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:31135365 original size:129 final size:129
Alignment explanation
Indices: 31135133--31135389 Score: 399
Period size: 129 Copynumber: 2.0 Consensus size: 129
31135123 TTATAGGGTC
* *
31135133 ACAGTTATTGACCCTGGATCTTTCTTGTAATTGCCGGTTTGCTTCAGACTGACAGTTCCTATCTG
1 ACAGTTATCGACCCAGGATCTTTCTTGTAATTGCCGGTTTGCTTCAGACTGACAGTTCCTATCTG
31135198 ATTGTTCAATTGGCTGGAGTAAGGGCAGGGCCTGTTGATCAATAATGACAGCATGGTTATGACT
66 ATTGTTCAATTGGCTGGAGTAAGGGCAGGGCCTGTTGATCAATAATGACAGCATGGTTATGACT
* * ** *
31135262 ACAGTTATCGATCCAGGA-CTTTGCTTGTAATTGCTGGTTTGCTTCAGGGTGACTGTTCCTATCT
1 ACAGTTATCGACCCAGGATCTTT-CTTGTAATTGCCGGTTTGCTTCAGACTGACAGTTCCTATCT
* * * *
31135326 GGTTGTTCAATTGGCTGGGGTAGGGGCAGGGCCTTTTGATCAATAATGACAGCATGGTTATGAC
65 GATTGTTCAATTGGCTGGAGTAAGGGCAGGGCCTGTTGATCAATAATGACAGCATGGTTATGAC
31135390 CAGGTGTTCT
Statistics
Matches: 116, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
128 4 0.03
129 112 0.97
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (129 bp):
ACAGTTATCGACCCAGGATCTTTCTTGTAATTGCCGGTTTGCTTCAGACTGACAGTTCCTATCTG
ATTGTTCAATTGGCTGGAGTAAGGGCAGGGCCTGTTGATCAATAATGACAGCATGGTTATGACT
Found at i:31139203 original size:39 final size:39
Alignment explanation
Indices: 31139160--31139291 Score: 201
Period size: 39 Copynumber: 3.4 Consensus size: 39
31139150 AGAGAACAAG
31139160 TGCATTCTGCTCTTTGTATCTCATATTGTAGGGGACGAT
1 TGCATTCTGCTCTTTGTATCTCATATTGTAGGGGACGAT
* * *
31139199 TGCATTCTGCTCCTTGTATCCCATATTGTAAGGGACGAT
1 TGCATTCTGCTCTTTGTATCTCATATTGTAGGGGACGAT
* * *
31139238 TGCATTCTGCTTTTTGTATCTCGTATTGTAGGGGATGAT
1 TGCATTCTGCTCTTTGTATCTCATATTGTAGGGGACGAT
*
31139277 TGCCTTCTGCTCTTT
1 TGCATTCTGCTCTTT
31139292 ATGTATAATA
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (39 bp):
TGCATTCTGCTCTTTGTATCTCATATTGTAGGGGACGAT
Found at i:31143436 original size:5 final size:5
Alignment explanation
Indices: 31143426--31143450 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31143416 AATAGTCAAT
31143426 GTTGG GTTGG GTTGG GTTGG GTTGG
1 GTTGG GTTGG GTTGG GTTGG GTTGG
31143451 TGTTTTAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (5 bp):
GTTGG
Found at i:31145571 original size:2 final size:2
Alignment explanation
Indices: 31145564--31145589 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31145554 TCGCATATGG
31145564 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
31145590 GTACTGATTT
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:31153433 original size:14 final size:15
Alignment explanation
Indices: 31153416--31153445 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31153406 ATTAATAAAA
31153416 TAAAT-ATTTAAAGT
1 TAAATAATTTAAAGT
31153430 TAAATAATTTAAAGT
1 TAAATAATTTAAAGT
31153445 T
1 T
31153446 TTTAAAAATT
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:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
TAAATAATTTAAAGT
Found at i:31158843 original size:30 final size:31
Alignment explanation
Indices: 31158785--31158845 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
31158775 AATTAACTAC
* *
31158785 CGGTGACTAATATGATTAAAGTATGTAACAG
1 CGGTGACTAAAATGATAAAAGTATGTAACAG
31158816 CGGTGACTAAAATGATAAAAG-ATGTAACAG
1 CGGTGACTAAAATGATAAAAGTATGTAACAG
31158846 TAGTGCTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 9 0.32
31 19 0.68
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.25
Consensus pattern (31 bp):
CGGTGACTAAAATGATAAAAGTATGTAACAG
Found at i:31179686 original size:26 final size:26
Alignment explanation
Indices: 31179651--31179709 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
31179641 AAAATTATTC
*
31179651 TAATATT-TTAATTTA-AATAATTAA
1 TAATATTATTTATTTAGAATAATTAA
*
31179675 TAATATTATTTATTTAGACTAATTAA
1 TAATATTATTTATTTAGAATAATTAA
31179701 TAATATTAT
1 TAATATTAT
31179710 AAAAATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 7 0.23
25 7 0.23
26 17 0.55
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (26 bp):
TAATATTATTTATTTAGAATAATTAA
Found at i:31183196 original size:26 final size:30
Alignment explanation
Indices: 31183167--31183236 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 30
31183157 TGACATTGTT
*
31183167 AATTATTATATT-CATT-G-CT-TTAAAAA
1 AATTATTATATTACATTAGTATATTAAAAA
31183193 AATTATTATATTTACATTAGTATATTAAAAA
1 AATTATTATA-TTACATTAGTATATTAAAAA
31183224 AATTATTATATTA
1 AATTATTATATTA
31183237 ACAATTGATA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
26 10 0.26
27 2 0.05
28 4 0.11
29 1 0.03
30 4 0.11
31 17 0.45
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (30 bp):
AATTATTATATTACATTAGTATATTAAAAA
Found at i:31183233 original size:17 final size:17
Alignment explanation
Indices: 31183186--31183237 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
31183176 ATTCATTGCT
31183186 TTAAAAAAATTATTATA
1 TTAAAAAAATTATTATA
* * *
31183203 TT---TACATTAGTATA
1 TTAAAAAAATTATTATA
31183217 TTAAAAAAATTATTATA
1 TTAAAAAAATTATTATA
31183234 TTAA
1 TTAA
31183238 CAATTGATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
14 11 0.42
17 15 0.58
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TTAAAAAAATTATTATA
Found at i:31183499 original size:19 final size:18
Alignment explanation
Indices: 31183475--31183525 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
31183465 ATCATAAATC
31183475 ATTATTATAATTTATGTAT
1 ATTATTATAATTTAT-TAT
* *
31183494 ATTATT-TTATTTAATTTT
1 ATTATTATAATTT-ATTAT
*
31183512 AATATTATAATTTA
1 ATTATTATAATTTA
31183526 CTTTCTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTATTATAATTTATTAT
Found at i:31184202 original size:21 final size:22
Alignment explanation
Indices: 31184164--31184212 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
31184154 GAATAATTTT
31184164 TTTAAAAAAACAATAAT-AAAA
1 TTTAAAAAAACAATAATAAAAA
*
31184185 TTTAAAATATACAA-AATAGAAAA
1 TTTAAAA-AAACAATAATA-AAAA
31184208 TTTAA
1 TTTAA
31184213 TTTCATGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 10 0.42
22 5 0.21
23 9 0.38
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (22 bp):
TTTAAAAAAACAATAATAAAAA
Found at i:31192752 original size:9 final size:9
Alignment explanation
Indices: 31192734--31192780 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
31192724 ATCCACTGCC
31192734 TCGTCCTCA
1 TCGTCCTCA
*
31192743 TCGTCGTCA
1 TCGTCCTCA
* *
31192752 TCCTCCTCC
1 TCGTCCTCA
31192761 TCGTCCTCA
1 TCGTCCTCA
*
31192770 TCGTCGTCA
1 TCGTCCTCA
31192779 TC
1 TC
31192781 CTCATCCTCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.09, C:0.45, G:0.13, T:0.34
Consensus pattern (9 bp):
TCGTCCTCA
Found at i:31192762 original size:27 final size:27
Alignment explanation
Indices: 31192732--31192795 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
31192722 CCATCCACTG
*
31192732 CCTCGTCCTCATCGTCGTCATCCTCCT
1 CCTCGTCCTCATCGTCGTCATCCTCAT
31192759 CCTCGTCCTCATCGTCGTCATCCTCAT
1 CCTCGTCCTCATCGTCGTCATCCTCAT
*
31192786 CCTCATCCTC
1 CCTCGTCCTC
31192796 TTCTTCACTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.09, C:0.48, G:0.09, T:0.33
Consensus pattern (27 bp):
CCTCGTCCTCATCGTCGTCATCCTCAT
Found at i:31194064 original size:15 final size:15
Alignment explanation
Indices: 31194024--31194074 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
31194014 AAGATAGGCG
31194024 AAGAGATATAGAAGGCA
1 AAGAGATATAGAA-G-A
31194041 AA-AGA-ATAGATAG-
1 AAGAGATATAGA-AGA
31194054 AAGAGATATAGAAGA
1 AAGAGATATAGAAGA
31194069 AAGAGA
1 AAGAGA
31194075 GAGAGGGGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 2 0.07
14 5 0.17
15 17 0.57
16 4 0.13
17 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.27, T:0.12
Consensus pattern (15 bp):
AAGAGATATAGAAGA
Found at i:31202246 original size:18 final size:17
Alignment explanation
Indices: 31202223--31202261 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
31202213 AATGACAAAA
*
31202223 AAAATTCTAAAAATATAT
1 AAAATTCCAAAAATAT-T
31202241 AAAATTCCAAAAATATT
1 AAAATTCCAAAAATATT
31202258 AAAA
1 AAAA
31202262 GTTGATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATTCCAAAAATATT
Found at i:31204927 original size:41 final size:41
Alignment explanation
Indices: 31204864--31205092 Score: 219
Period size: 41 Copynumber: 5.6 Consensus size: 41
31204854 CGACGTTTTT
* * *
31204864 GTCGCTAATACCATT-ACCTTTAGTGGCACTTTTGAGAAAGC
1 GTCGCTAATGCC-TTGACCTTTAGCGGCACTTATGAGAAAGC
* * * *
31204905 GTCGCTAATGCCCTGACTTTTAGCGGCGCTTATGGGAAAGC
1 GTCGCTAATGCCTTGACCTTTAGCGGCACTTATGAGAAAGC
* * * * * *
31204946 GCCACTGACGCCTTGACCTTTAGCGGCGCTTATGGGAAAGC
1 GTCGCTAATGCCTTGACCTTTAGCGGCACTTATGAGAAAGC
* * * * *
31204987 GCCACTGACGCCTTGACCTTTAGCGGCACTTATGAAAAAGC
1 GTCGCTAATGCCTTGACCTTTAGCGGCACTTATGAGAAAGC
* * * *
31205028 GTCGCTAATGCC-TAACCTTTAGCGGGATTTATGAGAAAGT
1 GTCGCTAATGCCTTGACCTTTAGCGGCACTTATGAGAAAGC
* *
31205068 GCCGCTAATGTCTTGACCTTTAGCG
1 GTCGCTAATGCCTTGACCTTTAGCG
31205093 ATGCTTATAG
Statistics
Matches: 158, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
40 34 0.22
41 124 0.78
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (41 bp):
GTCGCTAATGCCTTGACCTTTAGCGGCACTTATGAGAAAGC
Found at i:31205099 original size:122 final size:123
Alignment explanation
Indices: 31204879--31205111 Score: 308
Period size: 122 Copynumber: 1.9 Consensus size: 123
31204869 TAATACCATT
* * * * * *
31204879 ACCTTTAGTGGCACTTTTGAGAAAGCGTCGCTAATGCCCTGACTTTTAGCGGCGCTTATGGGAAA
1 ACCTTTAGCGGCACTTATGAAAAAGCGTCGCTAATGCCCTAACCTTTAGCGGCGCTTATGAGAAA
* * *
31204944 GCGCCACTGACGCCTTGACCTTTAGCGGCGCTTATGGGAAAGCGCCACTGACGCCTTG
66 GCGCCACTAACGCCTTGACCTTTAGCGACGCTTATAGGAAAGCGCCACTGACGCCTTG
*
31205002 ACCTTTAGCGGCACTTATGAAAAAGCGTCGCTAATG-CCTAACCTTTAGCGG-GATTTATGAGAA
1 ACCTTTAGCGGCACTTATGAAAAAGCGTCGCTAATGCCCTAACCTTTAGCGGCG-CTTATGAGAA
* * * * *
31205065 AGTGCCGCTAATGTCTTGACCTTTAGCGATGCTTATAGGAAAGCGCC
65 AGCGCCACTAACGCCTTGACCTTTAGCGACGCTTATAGGAAAGCGCC
31205112 GCGAATACTG
Statistics
Matches: 94, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
121 1 0.01
122 60 0.64
123 33 0.35
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (123 bp):
ACCTTTAGCGGCACTTATGAAAAAGCGTCGCTAATGCCCTAACCTTTAGCGGCGCTTATGAGAAA
GCGCCACTAACGCCTTGACCTTTAGCGACGCTTATAGGAAAGCGCCACTGACGCCTTG
Found at i:31215123 original size:15 final size:15
Alignment explanation
Indices: 31215068--31215124 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
31215058 TTTATATTAC
*
31215068 AAAATATTTATCATT
1 AAAATATTTATAATT
*
31215083 AATATATTTATAATTGT
1 AAAATATTTATAA-T-T
*
31215100 AATAAATATTTATTATT
1 -A-AAATATTTATAATT
31215117 AAAATATT
1 AAAATATT
31215125 AATTTTGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 18 0.53
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.29
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
AAAATATTTATAATT
Found at i:31218654 original size:68 final size:68
Alignment explanation
Indices: 31218545--31218675 Score: 235
Period size: 68 Copynumber: 1.9 Consensus size: 68
31218535 GCTACATGTC
*
31218545 CTAAGATTATAGATATTGGAAATTTTACGTTAACAGGGAAAAATAGAATTTTGCATGTCTAATGT
1 CTAAGATTATAGATATTGGAAATTCTACGTTAACAGGGAAAAATAGAATTTTGCATGTCTAATGT
31218610 GTG
66 GTG
* *
31218613 CTAAGATTATAGATATTGGTAATTCTACGTTAACAGGGAAAAATAGAGTTTTGCATGTCTAAT
1 CTAAGATTATAGATATTGGAAATTCTACGTTAACAGGGAAAAATAGAATTTTGCATGTCTAAT
31218676 ACTTTGCATG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (68 bp):
CTAAGATTATAGATATTGGAAATTCTACGTTAACAGGGAAAAATAGAATTTTGCATGTCTAATGT
GTG
Found at i:31222999 original size:66 final size:65
Alignment explanation
Indices: 31222923--31223164 Score: 173
Period size: 66 Copynumber: 3.7 Consensus size: 65
31222913 AGCTGTCACG
* * * *
31222923 TCCTTCGCTTCCTTCGCTTTTTCAGCTGCATAGTCTTTATACTCGGTCGCTTTTTCAACTGTGGT
1 TCCTTTGCTTCCTTAGCTTTTTCAGCTGCATAGTCTTTATACTCGGTCGCTTTTGC-ACTGTCGT
31222988 A
65 A
* * * * * ** * *
31222989 TCTTTTGCTTCCCTAGCTTTCTGC-GCTGCATAGTCTGTAAACTCGGAAGCCTTCTGCGCTGTCG
1 TCCTTTGCTTCCTTAGCTTT-TTCAGCTGCATAGTCTTTATACTCGGTCG-CTTTTGCACTGTCG
31223053 TA
64 TA
* * * * * * * *
31223055 TCCTTTGCTCCCTTGGCTTTCTCAGCTGCATAGTCCTTATATTCAGTCGCTTTTCCCATTG-CAG
1 TCCTTTGCTTCCTTAGCTTTTTCAGCTGCATAGTCTTTATACTCGGTCGCTTTT-GCACTGTC-G
*
31223119 CA
64 TA
* * ** * *
31223121 TCCTTTGCATCCTTAGCTTTCTGTGCTGCATAATCTGTATACTC
1 TCCTTTGCTTCCTTAGCTTTTTCAGCTGCATAGTCTTTATACTC
31223165 AGAAGCCTTT
Statistics
Matches: 131, Mismatches: 40, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
65 6 0.05
66 118 0.90
67 7 0.05
ACGTcount: A:0.14, C:0.29, G:0.17, T:0.40
Consensus pattern (65 bp):
TCCTTTGCTTCCTTAGCTTTTTCAGCTGCATAGTCTTTATACTCGGTCGCTTTTGCACTGTCGTA
Found at i:31223074 original size:132 final size:132
Alignment explanation
Indices: 31222923--31223340 Score: 464
Period size: 132 Copynumber: 3.2 Consensus size: 132
31222913 AGCTGTCACG
* * * * * * * * * * * *
31222923 TCCTTCGCTTCCTTCGCTTTTTCAGCTGCATAGTCTTTATACTCGGTCGCTTTTTCAACTGTGGT
1 TCCTTTGCTCCCTTGGCTTTCTCAGCTGCATAGTCCTTATATTCAGTCGCTTTTCCCATTGTAGC
* * * * * * *
31222988 ATCTTTTGCTTCCCTAGCTTTCTGCGCTGCATAGTCTGTAAACTCGGAAGCCTTCTGCGCTGTCG
66 ATCCTTTGCATCCTTAGCTTTCTGTGCTGCATAGTCTGTATACTCAGAAGCCTTTTGCGCTGTCG
31223053 TA
131 TA
*
31223055 TCCTTTGCTCCCTTGGCTTTCTCAGCTGCATAGTCCTTATATTCAGTCGCTTTTCCCATTGCAGC
1 TCCTTTGCTCCCTTGGCTTTCTCAGCTGCATAGTCCTTATATTCAGTCGCTTTTCCCATTGTAGC
* * *
31223120 ATCCTTTGCATCCTTAGCTTTCTGTGCTGCATAATCTGTATACTCAGAAGCCTTTTGGGCTGTGG
66 ATCCTTTGCATCCTTAGCTTTCTGTGCTGCATAGTCTGTATACTCAGAAGCCTTTTGCGCTGTCG
31223185 TA
131 TA
** * * *
31223187 T-CTCTTGC-CTCCTTGGCTTTCTGGGCTGTATAATCCTTATATTCAGTCGCTTTCCCCATTGTA
1 TCCT-TTGCTC-CCTTGGCTTTCTCAGCTGCATAGTCCTTATATTCAGTCGCTTTTCCCATTGTA
* * * *
31223250 GCATCCTTTGCATCCTTAGTTTTCTGTGCTGCATAGTCTGTATACTCTGATGCCTTTTGTGCTGT
64 GCATCCTTTGCATCCTTAGCTTTCTGTGCTGCATAGTCTGTATACTCAGAAGCCTTTTGCGCTGT
* *
31223315 GGTG
129 CGTA
* *
31223319 TCTTTTGCGT-CCTTAGCTTTCT
1 TCCTTTGC-TCCCTTGGCTTTCT
31223341 GGGCAGCATA
Statistics
Matches: 244, Mismatches: 37, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
131 3 0.01
132 240 0.98
133 1 0.00
ACGTcount: A:0.13, C:0.27, G:0.19, T:0.42
Consensus pattern (132 bp):
TCCTTTGCTCCCTTGGCTTTCTCAGCTGCATAGTCCTTATATTCAGTCGCTTTTCCCATTGTAGC
ATCCTTTGCATCCTTAGCTTTCTGTGCTGCATAGTCTGTATACTCAGAAGCCTTTTGCGCTGTCG
TA
Found at i:31223200 original size:66 final size:66
Alignment explanation
Indices: 31222981--31223368 Score: 231
Period size: 66 Copynumber: 5.9 Consensus size: 66
31222971 GCTTTTTCAA
* * * * * * * *
31222981 CTGTGGTATCTTTTGCTTCCCTAGCTTTCTGCGCTGCATAGTCTGTAAACTCGGAAGCCTTCTGC
1 CTGTGGTATCTCTTGCATCCTTAGCTTTCTGGGCTGCATAATCTGTATACTCAGAAGCCTTTTGC
31223046 G
66 G
* * ** * * **
31223047 CTGTCGTATC-CTTTGC-TCCCTTGGCTTTCTCAGCTGCATAGTCCT-TATATTCAGTCG-CTTT
1 CTGTGGTATCTC-TTGCAT-CCTTAGCTTTCTGGGCTGCATAAT-CTGTATACTCAGAAGCCTTT
*
31223108 T-CC
63 TGCG
* *
31223111 CAT-TGCAGCATC-CTTTGCATCCTTAGCTTTCTGTGCTGCATAATCTGTATACTCAGAAGCCTT
1 C-TGTG--GTATCTC-TTGCATCCTTAGCTTTCTGGGCTGCATAATCTGTATACTCAGAAGCCTT
*
31223174 TTGGG
62 TTGCG
* * * * ** *
31223179 CTGTGGTATCTCTTGCCTCCTTGGCTTTCTGGGCTGTATAATCCT-TATATTCAGTCG-C-TTTC
1 CTGTGGTATCTCTTGCATCCTTAGCTTTCTGGGCTGCATAAT-CTGTATACTCAGAAGCCTTTTG
*
31223241 CC
65 CG
* * * * * * *
31223243 CATTGTAGCATC-CTTTGCATCCTTAGTTTTCTGTGCTGCATAGTCTGTATACTCTGATGCCTTT
1 C--TGTGGTATCTC-TTGCATCCTTAGCTTTCTGGGCTGCATAATCTGTATACTCAGAAGCCTTT
*
31223307 TGTG
63 TGCG
* * * * *
31223311 CTGTGGTGTCTTTTGCGTCCTTAGCTTTCTGGGCAGCATAACCTGTATACTCAGAAGC
1 CTGTGGTATCTCTTGCATCCTTAGCTTTCTGGGCTGCATAATCTGTATACTCAGAAGC
31223369 TTTACCTGTT
Statistics
Matches: 240, Mismatches: 62, Indels: 40
0.70 0.18 0.12
Matches are distributed among these distances:
64 7 0.03
65 12 0.05
66 201 0.84
67 13 0.05
68 7 0.03
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.39
Consensus pattern (66 bp):
CTGTGGTATCTCTTGCATCCTTAGCTTTCTGGGCTGCATAATCTGTATACTCAGAAGCCTTTTGC
G
Found at i:31223341 original size:132 final size:131
Alignment explanation
Indices: 31222992--31223364 Score: 478
Period size: 132 Copynumber: 2.8 Consensus size: 131
31222982 TGTGGTATCT
* * * * * * *
31222992 TTTGCTTCCCTAGCTTTCTGCGCTGCATAGTCTGTAAACTCGGAAGCCTTCTGCGCTGTCGTATC
1 TTTGCATCCTTAGCTTTCTGTGCTGCATAGTCTGTATACTCAGAAGCCTTTTGCGCTGTGGTATC
* ** * *
31223057 CTTTGCTCCCTTGGCTTTCTCAGCTGCATAGTCCTTATATTCAGTCGCTTTTCCCATTGCAGCAT
66 TTTTGCT-CCTTGGCTTTCTGGGCTGCATAATCCTTATATTCAGTCGCTTTCCCCATTGCAGCAT
31223122 CC
130 CC
* *
31223124 TTTGCATCCTTAGCTTTCTGTGCTGCATAATCTGTATACTCAGAAGCCTTTTGGGCTGTGGTATC
1 TTTGCATCCTTAGCTTTCTGTGCTGCATAGTCTGTATACTCAGAAGCCTTTTGCGCTGTGGTATC
* * *
31223189 TCTTGCCTCCTTGGCTTTCTGGGCTGTATAATCCTTATATTCAGTCGCTTTCCCCATTGTAGCAT
66 TTTTG-CTCCTTGGCTTTCTGGGCTGCATAATCCTTATATTCAGTCGCTTTCCCCATTGCAGCAT
31223254 CC
130 CC
* * * * *
31223256 TTTGCATCCTTAGTTTTCTGTGCTGCATAGTCTGTATACTCTGATGCCTTTTGTGCTGTGGTGTC
1 TTTGCATCCTTAGCTTTCTGTGCTGCATAGTCTGTATACTCAGAAGCCTTTTGCGCTGTGGTATC
* * *
31223321 TTTTGCGTCCTTAGCTTTCTGGGCAGCATAA-CCTGTATACTCAG
66 TTTTGC-TCCTTGGCTTTCTGGGCTGCATAATCCT-TATATTCAG
31223365 AAGCTTTACC
Statistics
Matches: 210, Mismatches: 28, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
131 4 0.02
132 204 0.97
133 2 0.01
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.40
Consensus pattern (131 bp):
TTTGCATCCTTAGCTTTCTGTGCTGCATAGTCTGTATACTCAGAAGCCTTTTGCGCTGTGGTATC
TTTTGCTCCTTGGCTTTCTGGGCTGCATAATCCTTATATTCAGTCGCTTTCCCCATTGCAGCATC
C
Found at i:31224877 original size:27 final size:26
Alignment explanation
Indices: 31224831--31224884 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
31224821 TAATTTTCAT
* *
31224831 AATTTTATAATATTTTATAATTATAA
1 AATTTTATAATATTTAATAATGATAA
31224857 AATTTT-TAATATTTAGAATAATGATAA
1 AATTTTATAATATTT--AATAATGATAA
31224884 A
1 A
31224885 TTGATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.33
26 6 0.25
27 10 0.42
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (26 bp):
AATTTTATAATATTTAATAATGATAA
Found at i:31225170 original size:14 final size:12
Alignment explanation
Indices: 31225149--31225200 Score: 61
Period size: 14 Copynumber: 4.1 Consensus size: 12
31225139 ATTATTCTAA
31225149 ATATTAAAAAATT
1 ATATTAAAAAA-T
31225162 ATAATTAAAAAAT
1 AT-ATTAAAAAAT
31225175 AT-TTAAAAAAT
1 ATATTAAAAAAT
31225186 ATTATTATAAAAAT
1 A-TATTA-AAAAAT
31225200 A
1 A
31225201 AAACAACTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
11 10 0.29
12 1 0.03
13 8 0.23
14 16 0.46
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATATTAAAAAAT
Found at i:31225174 original size:24 final size:25
Alignment explanation
Indices: 31225147--31225200 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
31225137 TCATTATTCT
31225147 AAATA-TTAAAAAATTATAATTA-AA
1 AAATATTTAAAAAA-TATAATTATAA
*
31225171 AAATATTTAAAAAATATTATTATAA
1 AAATATTTAAAAAATATAATTATAA
31225196 AAATA
1 AAATA
31225201 AAACAACTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AAATATTTAAAAAATATAATTATAA
Found at i:31225182 original size:11 final size:11
Alignment explanation
Indices: 31225147--31225188 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
31225137 TCATTATTCT
31225147 AAATA-TTAAA
1 AAATATTTAAA
31225157 AAATTATAATTAAA
1 AAA-TAT--TTAAA
31225171 AAATATTTAAA
1 AAATATTTAAA
31225182 AAATATT
1 AAATATT
31225189 ATTATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 3 0.11
11 14 0.50
13 3 0.11
14 8 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AAATATTTAAA
Found at i:31226057 original size:151 final size:154
Alignment explanation
Indices: 31225874--31226171 Score: 449
Period size: 151 Copynumber: 2.0 Consensus size: 154
31225864 TATTGTTAAC
* *
31225874 TATTTCAATCAAAATATTGACCTTAATTTTTTCTCAAAAACACTATTCCAACAGAAATAAATTAC
1 TATTTCAATCAAAATATTGACCTCAATTTTTTCTCAAAAACACTATTCCAACAGAAAAAAATTAC
**
31225939 TTTATCGTAACGGTTTTGAATGGATGTACTTAAGAAAAAAACATAATAAATATTTTTAACGAT-G
66 TTTATCACAACGGTTTTGAATGGATGTACTTAAGAAAAAAACATAATAAATATTTTTAACGATAG
31226003 TTTTTATTGTTATATAACTACAAA
131 TTTTTATTGTTATATAACTACAAA
* *
31226027 TATTTCAATC-AAA-ATTGACCTCAATTTTTTCTCAAAAACACTATTTCAAGAGAAAAAAATTAC
1 TATTTCAATCAAAATATTGACCTCAATTTTTTCTCAAAAACACTATTCCAACAGAAAAAAATTAC
* * * * * * * *
31226090 TTTATCACAATGGTTTTGAATGGCTGTTCTTAATAAAAAATCATAATAAGTATTTTTAATGATAT
66 TTTATCACAACGGTTTTGAATGGATGTACTTAAGAAAAAAACATAATAAATATTTTTAACGATAG
31226155 TTTTTATTGTTATATAA
131 TTTTTATTGTTATATAA
31226172 TTATCAAGTA
Statistics
Matches: 130, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
151 100 0.77
152 20 0.15
153 10 0.08
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (154 bp):
TATTTCAATCAAAATATTGACCTCAATTTTTTCTCAAAAACACTATTCCAACAGAAAAAAATTAC
TTTATCACAACGGTTTTGAATGGATGTACTTAAGAAAAAAACATAATAAATATTTTTAACGATAG
TTTTTATTGTTATATAACTACAAA
Found at i:31230039 original size:13 final size:13
Alignment explanation
Indices: 31230017--31230080 Score: 69
Period size: 13 Copynumber: 4.9 Consensus size: 13
31230007 TTTAGTTTTG
*
31230017 TTTTTGAAAAATA
1 TTTTTAAAAAATA
31230030 TTTTTAAAAAATA
1 TTTTTAAAAAATA
*
31230043 -CTTTAGAAAAAT-
1 TTTTTA-AAAAATA
*
31230055 TATTTTAAAAAGTA
1 T-TTTTAAAAAATA
31230069 TTTTTAAAAAAT
1 TTTTTAAAAAAT
31230081 TTAGTTTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
12 4 0.10
13 33 0.79
14 5 0.12
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (13 bp):
TTTTTAAAAAATA
Found at i:31230078 original size:26 final size:26
Alignment explanation
Indices: 31230017--31230091 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 26
31230007 TTTAGTTTTG
*
31230017 TTTTTGAAAAA-TATTTTTAAAAAATA
1 TTTTTAAAAAATTA-TTTTAAAAAATA
* *
31230043 -CTTTAGAAAAATTATTTTAAAAAGTA
1 TTTTTA-AAAAATTATTTTAAAAAATA
*
31230069 TTTTTAAAAAATTTAGTTTAAAA
1 TTTTTAAAAAA-TTATTTTAAAA
31230092 TTTAAGTGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
25 3 0.08
26 21 0.52
27 16 0.40
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.44
Consensus pattern (26 bp):
TTTTTAAAAAATTATTTTAAAAAATA
Found at i:31230495 original size:18 final size:17
Alignment explanation
Indices: 31230464--31230507 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
31230454 TATTTAATAT
31230464 TACTTTTAATTTAAAAG
1 TACTTTTAATTTAAAAG
*
31230481 TACTTTTTATGTTAAAAG
1 TACTTTTAAT-TTAAAAG
*
31230499 TAATTTTAA
1 TACTTTTAA
31230508 AAAGCAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (17 bp):
TACTTTTAATTTAAAAG
Found at i:31234368 original size:20 final size:20
Alignment explanation
Indices: 31234331--31234374 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
31234321 TTAATACTAC
* *
31234331 TTATTAAGAAGTTCAATTAA
1 TTATTAAAAACTTCAATTAA
* *
31234351 TTATTAAAAACTTGAATTAT
1 TTATTAAAAACTTCAATTAA
31234371 TTAT
1 TTAT
31234375 ACTTTTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (20 bp):
TTATTAAAAACTTCAATTAA
Found at i:31241222 original size:62 final size:61
Alignment explanation
Indices: 31241126--31241311 Score: 225
Period size: 62 Copynumber: 3.0 Consensus size: 61
31241116 CGGCTATGCC
* * * * *
31241126 CTTTTCTCAAGAAAAAAATTCAAAATTTTTTGGTGTAGGCCATCAAATGGCCGACACCCCT
1 CTTTTTTCGAGAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCT
*
31241187 CTTTTCCTT-GAGAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGTCGACACCTCC-
1 CTTTT--TTCGAGAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACC-CCT
* *
31241249 CTTTTTTCGAGAAAAAAATTTTAAAATTTTTTT-GTGTTGGCCATCAAATTGCCGACACTCCCT
1 CTTTTTTCGAG-AAAAAA-TTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACAC-CCCT
31241312 ATTTAAAAAA
Statistics
Matches: 108, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
60 2 0.02
61 8 0.07
62 81 0.75
63 17 0.16
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (61 bp):
CTTTTTTCGAGAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCT
Found at i:31241608 original size:31 final size:31
Alignment explanation
Indices: 31241573--31241632 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
31241563 TACAATCGAA
* *
31241573 TTTCGGGGTTGAGCTATATACTGTCATGTAT
1 TTTCGGAGTTGAACTATATACTGTCATGTAT
* *
31241604 TTTCGGAGTTGAATTATATACTGTTATGT
1 TTTCGGAGTTGAACTATATACTGTCATGT
31241633 GAAGCGGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.22, C:0.10, G:0.23, T:0.45
Consensus pattern (31 bp):
TTTCGGAGTTGAACTATATACTGTCATGTAT
Found at i:31244500 original size:17 final size:17
Alignment explanation
Indices: 31244468--31244551 Score: 80
Period size: 17 Copynumber: 4.9 Consensus size: 17
31244458 AAAACTTTAG
*
31244468 ATTTTAAATCTT-AATTC
1 ATTTTAAAT-TTAAATTT
*
31244485 ATTTTAATTTTAAATTT
1 ATTTTAAATTTAAATTT
* **
31244502 ATTATAAATTTAAGCTT
1 ATTTTAAATTTAAATTT
** *
31244519 ATTTGGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
31244536 ATTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
31244552 GAAATAAAAA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
16 2 0.04
17 49 0.96
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:31244547 original size:6 final size:6
Alignment explanation
Indices: 31244527--31244573 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
31244517 TTATTTGGAG
* * **
31244527 TTTAAA TTT-AT TTTAAA TTTAAA TTGAAA TAAAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
31244574 AGTTTAATTG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:31244716 original size:26 final size:27
Alignment explanation
Indices: 31244687--31244747 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
31244677 GCCTAAGCCA
* *
31244687 CCACATCAACTACCACGTCATCACGT-
1 CCACATCAACTACCACATCATCACATG
* * *
31244713 CCACGTCAGCTGCCACATCATCACATG
1 CCACATCAACTACCACATCATCACATG
31244740 CCACATCA
1 CCACATCA
31244748 TTGCGTCCAC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 21 0.75
27 7 0.25
ACGTcount: A:0.30, C:0.43, G:0.10, T:0.18
Consensus pattern (27 bp):
CCACATCAACTACCACATCATCACATG
Found at i:31247656 original size:11 final size:12
Alignment explanation
Indices: 31247616--31247664 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
31247606 TATTTGTGTA
31247616 AAAATTAATTTG
1 AAAATTAATTTG
31247628 AAAATTAATTTAAG
1 AAAATTAATTT--G
*
31247642 TTGAAATTAATTTG
1 --AAAATTAATTTG
31247656 AAAATTAAT
1 AAAATTAAT
31247665 GAACATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:31247774 original size:22 final size:22
Alignment explanation
Indices: 31247746--31247787 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
31247736 TTGAAGTTGA
31247746 AATTTAA-ATTACATTTAAAATT
1 AATTTAACATTA-ATTTAAAATT
*
31247768 AATTTAACATTATTTTAAAA
1 AATTTAACATTAATTTAAAA
31247788 AAAGATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTTAACATTAATTTAAAATT
Found at i:31247940 original size:45 final size:46
Alignment explanation
Indices: 31247881--31248036 Score: 125
Period size: 45 Copynumber: 3.5 Consensus size: 46
31247871 TACAAATTAT
31247881 TATTATATTA-CAATTTT-TATCAAATAATGTGTTGATTTGACAATA
1 TATTATATTATCAATTTTATATCAAATAATGTGTT-ATTTGACAATA
*** **
31247926 TATTAT-TTATCAATTTTATATCTTTAAATAA-AAATTA-TT-ATTAT-
1 TATTATATTATCAATTTTATATC---AAATAATGTGTTATTTGACAATA
*
31247970 TATTATATTAT-AATTTT-TATCATATAATGTGTTAATTTGACAATA
1 TATTATATTATCAATTTTATATCAAATAATGTGTT-ATTTGACAATA
* *
31248015 CATTAT-TTATTAATTTTATATC
1 TATTATATTATCAATTTTATATC
31248037 TTTAAATAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
40 5 0.06
41 2 0.02
42 1 0.01
43 6 0.07
44 22 0.26
45 31 0.36
46 10 0.12
47 1 0.01
48 2 0.02
49 6 0.07
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (46 bp):
TATTATATTATCAATTTTATATCAAATAATGTGTTATTTGACAATA
Found at i:31248000 original size:89 final size:89
Alignment explanation
Indices: 31247796--31248168 Score: 452
Period size: 89 Copynumber: 4.3 Consensus size: 89
31247786 AAAAAGATAG
* * *
31247796 TTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAATACATTATTTATCAAATTTTC
1 TTATTATATTACAATTTTTATCATATAATGTGTTAATTTGACAATACATTATTTATC-AATTTT-
*
31247861 ATA--TTTAAAGT--ACA--A--ATTA
64 ATATCTTTAAA-TAAAAATTATTATTA
* * *
31247880 TTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATATATTATTTATCAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTAATTTGACAATACATTATTTATCAATTTTAT
31247945 ATCTTTAAATAAAAATTATTATTA
66 ATCTTTAAATAAAAATTATTATTA
* *
31247969 TTATTATATTATAATTTTTATCATATAATGTGTTAATTTGACAATACATTATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTAATTTGACAATACATTATTTATCAATTTTAT
31248034 ATCTTTAAAT--AAA--A--ATTA
66 ATCTTTAAATAAAAATTATTATTA
* * * * *
31248052 TTATTATATTACAATTTTTATTATATTTTAA-ATGTTGATTTGATAATACATTATTTATTAATTT
1 TTATTATATTACAATTTTTATCATA---TAATGTGTTAATTTGACAATACATTATTTATCAATTT
31248116 TATATCTTTAAATAAAAATTATTATTA
63 TATATCTTTAAATAAAAATTATTATTA
*
31248143 TCATTATATTACAATTTTTATCATAT
1 TTATTATATTACAATTTTTATCATAT
31248169 TTTAAATTTA
Statistics
Matches: 255, Mismatches: 17, Indels: 30
0.84 0.06 0.10
Matches are distributed among these distances:
82 3 0.01
83 34 0.13
84 59 0.23
85 46 0.18
86 3 0.01
87 7 0.03
88 1 0.00
89 75 0.29
91 27 0.11
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (89 bp):
TTATTATATTACAATTTTTATCATATAATGTGTTAATTTGACAATACATTATTTATCAATTTTAT
ATCTTTAAATAAAAATTATTATTA
Found at i:31248129 original size:174 final size:173
Alignment explanation
Indices: 31247796--31248168 Score: 556
Period size: 174 Copynumber: 2.2 Consensus size: 173
31247786 AAAAAGATAG
* * *
31247796 TTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAATACATTATTTATCAAATTTTC
1 TTATTATATTACAATTTTTATCATATAATGTGTTAATTTGACAATACATTATTTATCAAATTTTC
* *
31247861 ATATTTAAAGTACAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATA
66 ATATTTAAAGTAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTGACAATA
*
31247926 TATTATTTATCAATTTTATATCTTTAAATAAAAATTATTATTA
131 CATTATTTATCAATTTTATATCTTTAAATAAAAATTATTATTA
* *
31247969 TTATTATATTATAATTTTTATCATATAATGTGTTAATTTGACAATACATTATTTAT-TAATTTT-
1 TTATTATATTACAATTTTTATCATATAATGTGTTAATTTGACAATACATTATTTATCAAATTTTC
* *
31248032 ATATCTTTAAA-TAAAAATTATTATTATATTACAATTTTTATTATATTTTAA-ATGTTGATTTGA
66 ATA--TTTAAAGTAAAAATTATTATTATATTACAATTTTTATCA-A--ATAATATGTTGATTTGA
* *
31248095 TAATACATTATTTATTAATTTTATATCTTTAAATAAAAATTATTATTA
126 CAATACATTATTTATCAATTTTATATCTTTAAATAAAAATTATTATTA
*
31248143 TCATTATATTACAATTTTTATCATAT
1 TTATTATATTACAATTTTTATCATAT
31248169 TTTAAATTTA
Statistics
Matches: 181, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
171 3 0.02
172 36 0.20
173 59 0.33
174 80 0.44
175 3 0.02
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (173 bp):
TTATTATATTACAATTTTTATCATATAATGTGTTAATTTGACAATACATTATTTATCAAATTTTC
ATATTTAAAGTAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTGACAATA
CATTATTTATCAATTTTATATCTTTAAATAAAAATTATTATTA
Found at i:31248295 original size:22 final size:22
Alignment explanation
Indices: 31248270--31248321 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
31248260 CACTTTCCAC
*
31248270 CTCACTTAAACC-AATATTTCAG
1 CTCACTAAAACCGAA-ATTTCAG
31248292 CTCAAC-AAAACCGAAATTTCAG
1 CTC-ACTAAAACCGAAATTTCAG
31248314 CTCACTAA
1 CTCACTAA
31248322 CGTCTCGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 2 0.08
22 20 0.77
23 4 0.15
ACGTcount: A:0.40, C:0.29, G:0.06, T:0.25
Consensus pattern (22 bp):
CTCACTAAAACCGAAATTTCAG
Found at i:31248364 original size:10 final size:10
Alignment explanation
Indices: 31248330--31248364 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
31248320 AACGTCTCGA
31248330 GACCGTCGTT
1 GACCGTCGTT
**
31248340 GACCACCGTT
1 GACCGTCGTT
31248350 GACCGTCGTT
1 GACCGTCGTT
31248360 GACCG
1 GACCG
31248365 AGTTTCGTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.14, C:0.34, G:0.29, T:0.23
Consensus pattern (10 bp):
GACCGTCGTT
Found at i:31248726 original size:61 final size:60
Alignment explanation
Indices: 31248526--31248725 Score: 265
Period size: 61 Copynumber: 3.3 Consensus size: 60
31248516 AAGGGGTGTC
31248526 GGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAAAGGGGGTGTCGGCCATCAAAT
1 GGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAAAGGGGGTGTCGGCCATC-AAT
** * **
31248587 GGCCAACACCAAAAAAATTTGATTTTTTTTTCTTGAGAAAAGGGGGGTGTCGGCCATTTGAT
1 GGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAAA-GGGGGTGTCGGCCA-TCAAT
* * * *
31248649 GGCCAACACTAAAAAATTTTGAAACTTTTTTCTCGAGAAAAGGGGGTGTCAGCCATGCAAT
1 GGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAAAGGGGGTGTCGGCCAT-CAAT
* *
31248710 GGCCAATACCCAAAAA
1 GGCCAACACCAAAAAA
31248726 TGTAATTTTT
Statistics
Matches: 119, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
60 1 0.01
61 66 0.55
62 51 0.43
63 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (60 bp):
GGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAAAGGGGGTGTCGGCCATCAAT
Found at i:31248811 original size:101 final size:102
Alignment explanation
Indices: 31248634--31248837 Score: 275
Period size: 101 Copynumber: 2.0 Consensus size: 102
31248624 AAAAGGGGGG
* * **
31248634 TGTCGGCCATTTGATGGCCAACACTAAAAAATTTTGAAACTTTTTTCTCGAGAAAAGGGGGTGTC
1 TGTCGGCCATTTGATGACCAACACAAAAAAAAATTGAAACTTTTTTCTCGAGAAAAGGGGGTGTC
* * *
31248699 AGCCATGCAATGGCCAATACCCAAAAATGTAATTTTT
66 AGCCATACAATGGCCAACACCCAAAAATGCAATTTTT
* * *
31248736 TGTCGGTCATTTGATGACCAATACAAAAAAAAATTG-AATTTTTTTCTCGAGAAAAGGGGGTGTC
1 TGTCGGCCATTTGATGACCAACACAAAAAAAAATTGAAACTTTTTTCTCGAGAAAAGGGGGTGTC
* * * *
31248800 GGTCATACAATGGTCAACACTCAAAAATGCAATTTTT
66 AGCCATACAATGGCCAACACCCAAAAATGCAATTTTT
31248837 T
1 T
31248838 TTAAATAGGA
Statistics
Matches: 88, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
101 58 0.66
102 30 0.34
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (102 bp):
TGTCGGCCATTTGATGACCAACACAAAAAAAAATTGAAACTTTTTTCTCGAGAAAAGGGGGTGTC
AGCCATACAATGGCCAACACCCAAAAATGCAATTTTT
Found at i:31249224 original size:30 final size:31
Alignment explanation
Indices: 31249183--31249242 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
31249173 ATTTTTGAAC
*
31249183 TTGGGTCATTTTCA-TAAATAATCAAAATTT
1 TTGGGTCATTTTCATTAAATAACCAAAATTT
* * *
31249213 TTGGGTTATTTTGATTAATTAACCAAAATT
1 TTGGGTCATTTTCATTAAATAACCAAAATT
31249243 GGGATGTCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (31 bp):
TTGGGTCATTTTCATTAAATAACCAAAATTT
Found at i:31253019 original size:13 final size:13
Alignment explanation
Indices: 31253001--31253039 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
31252991 ATACTGACTT
31253001 GAGACGCACGGGC
1 GAGACGCACGGGC
31253014 GAGACGCACGGGC
1 GAGACGCACGGGC
*
31253027 GAGACACACGGGC
1 GAGACGCACGGGC
31253040 CTGTGTTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.26, C:0.31, G:0.44, T:0.00
Consensus pattern (13 bp):
GAGACGCACGGGC
Found at i:31253106 original size:13 final size:13
Alignment explanation
Indices: 31253088--31253112 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31253078 ACTGACTTGA
31253088 GACACATGGGCGG
1 GACACATGGGCGG
31253101 GACACATGGGCG
1 GACACATGGGCG
31253113 TGTCCCAGAC
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:0.24, C:0.24, G:0.44, T:0.08
Consensus pattern (13 bp):
GACACATGGGCGG
Found at i:31255323 original size:131 final size:132
Alignment explanation
Indices: 31255078--31255329 Score: 323
Period size: 131 Copynumber: 1.9 Consensus size: 132
31255068 TATTTTTTAG
* *
31255078 CCATTAGAATAAATAGGGTTATAAATGTCATTTTAATTTAATCTTATATTTTCATTTTTAATATT
1 CCATTAAAATAAATAGGGTTATAAATGTCATTTTAATTTAATCTTATATTTTCA-TTTTAAGATT
* *
31255143 TTTAAAGGAAGTAAATAGAGTTAGTTTAGTCTTTAAAATAGAGAGAAAATATTAAATATAATATA
65 TTTAAAGAAAGTAAATAGAGTTAGTTTAGTCTTTAAAATACAGAGAAAATATTAAATATAATATA
31255208 AAA
130 AAA
* * *
31255211 CCATTAAAATAAATAGGG-TATAAATGTTATTTTAGTTTAATTTTATATTTATC-TTTTAAGATT
1 CCATTAAAATAAATAGGGTTATAAATGTCATTTTAATTTAATCTTATATTT-TCATTTTAAGATT
* * * * * *
31255274 TTTGAAGAAAGTATAT-GTGATTAGTTT-GTTTTCTTAAATACAGATAAAATATTAAA
65 TTTAAAGAAAGTAAATAGAG-TTAGTTTAGTCTT-TAAAATACAGAGAAAATATTAAA
31255330 AACTTAATTA
Statistics
Matches: 103, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
130 6 0.06
131 49 0.48
132 29 0.28
133 19 0.18
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (132 bp):
CCATTAAAATAAATAGGGTTATAAATGTCATTTTAATTTAATCTTATATTTTCATTTTAAGATTT
TTAAAGAAAGTAAATAGAGTTAGTTTAGTCTTTAAAATACAGAGAAAATATTAAATATAATATAA
AA
Found at i:31259744 original size:25 final size:26
Alignment explanation
Indices: 31259704--31259754 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
31259694 TAAGAAAAAA
* *
31259704 TAAAAAAATCTATA-TTTATTAATTT
1 TAAAAAAATATATATTTTAATAATTT
*
31259729 TAAAAAAATATTTATTTTAATAATTT
1 TAAAAAAATATATATTTTAATAATTT
31259755 CCTTAATTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
TAAAAAAATATATATTTTAATAATTT
Found at i:31263946 original size:4 final size:4
Alignment explanation
Indices: 31263937--31263965 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
31263927 CATATTTCAT
31263937 ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
31263966 ATAACATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:31265123 original size:21 final size:22
Alignment explanation
Indices: 31265099--31265141 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
31265089 ACCATTACTT
*
31265099 ATATTAATTATAAA-AATTAAA
1 ATATTAATTAAAAATAATTAAA
*
31265120 ATATTTATTAAAAATAATTAAA
1 ATATTAATTAAAAATAATTAAA
31265142 TGTATTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATTAATTAAAAATAATTAAA
Found at i:31271854 original size:22 final size:22
Alignment explanation
Indices: 31271823--31271946 Score: 133
Period size: 22 Copynumber: 5.4 Consensus size: 22
31271813 ACGTTAGCGC
*
31271823 GCTTACTGTTCAGCATTGTGTGT
1 GCTT-CTGTTCAGCACTGTGTGT
*
31271846 GCTTTTGTTCAGCACTGTGTG-
1 GCTTCTGTTCAGCACTGTGTGT
*
31271867 GCTTCTGTTTCCCCAGCACTATGTGT
1 GCTTCTG-TT---CAGCACTGTGTGT
* *
31271893 GCTTCTGATCAGCACTATGTGT
1 GCTTCTGTTCAGCACTGTGTGT
*
31271915 GCTTATTGTTCAGCACTGTGTGT
1 GCTT-CTGTTCAGCACTGTGTGT
31271938 GCTTCTGTT
1 GCTTCTGTT
31271947 TCCCCAGCAG
Statistics
Matches: 86, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
21 6 0.07
22 38 0.44
23 23 0.27
25 12 0.14
26 7 0.08
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.42
Consensus pattern (22 bp):
GCTTCTGTTCAGCACTGTGTGT
Found at i:31274222 original size:35 final size:35
Alignment explanation
Indices: 31274173--31274251 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 35
31274163 GTGACCCTTT
** * *
31274173 CGAGAATTGGAGCTAGTGATATGTATTCAACTCTC
1 CGAGAATTAAAGCTAGTGAAATGTATTCAACCCTC
31274208 CGAGAATTAAAGCTAGTGAAATGTATTCAACCCTC
1 CGAGAATTAAAGCTAGTGAAATGTATTCAACCCTC
*
31274243 TGAGAATTA
1 CGAGAATTA
31274252 GAGTACGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (35 bp):
CGAGAATTAAAGCTAGTGAAATGTATTCAACCCTC
Found at i:31277549 original size:27 final size:26
Alignment explanation
Indices: 31277498--31277549 Score: 61
Period size: 27 Copynumber: 1.9 Consensus size: 26
31277488 AGTTTTAAAT
*
31277498 TTTTTGATTTAGTCCTTGCTTTTATTA
1 TTTTTGATTTAGT-CTTGCTCTTATTA
31277525 TTTTTGAATTTAGT-TTGCATCTTAT
1 TTTTTG-ATTTAGTCTTGC-TCTTAT
31277550 ATGTCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 4 0.18
27 11 0.50
28 7 0.32
ACGTcount: A:0.17, C:0.10, G:0.12, T:0.62
Consensus pattern (26 bp):
TTTTTGATTTAGTCTTGCTCTTATTA
Found at i:31285419 original size:2 final size:2
Alignment explanation
Indices: 31285412--31285437 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31285402 TTAAATGATA
31285412 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
31285438 TGCGAATTGG
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:31289055 original size:23 final size:23
Alignment explanation
Indices: 31289029--31289072 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
31289019 AACAGAGAAG
*
31289029 AAGAGATTAAATCAAAAGAAAAA
1 AAGAGATAAAATCAAAAGAAAAA
*
31289052 AAGAGATAAAATCAAATGAAA
1 AAGAGATAAAATCAAAAGAAA
31289073 TTTATTCGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.68, C:0.05, G:0.14, T:0.14
Consensus pattern (23 bp):
AAGAGATAAAATCAAAAGAAAAA
Found at i:31293535 original size:32 final size:33
Alignment explanation
Indices: 31293473--31293537 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
31293463 TAATTTATAA
*
31293473 AATTTTAAAATAATAATAATAAATTTACATTTT
1 AATTTTAAAATAATAATAATAAATTGACATTTT
*
31293506 AATTTTCAAAA-AATGATAA-AAATTGACATTTT
1 AATTTT-AAAATAATAATAATAAATTGACATTTT
31293538 TTTAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 12 0.41
33 13 0.45
34 4 0.14
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (33 bp):
AATTTTAAAATAATAATAATAAATTGACATTTT
Found at i:31304258 original size:18 final size:20
Alignment explanation
Indices: 31304234--31304286 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 20
31304224 AAAGTAGCAC
*
31304234 CAAAACAACAAAAAAAA-CT
1 CAAAACAACAAAAAAAATAT
*
31304253 -AAAACAGCAAAAAAAATAT
1 CAAAACAACAAAAAAAATAT
31304272 CAAAACAACAAAAAA
1 CAAAACAACAAAAAA
31304287 TAACACCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 15 0.52
19 1 0.03
20 13 0.45
ACGTcount: A:0.75, C:0.17, G:0.02, T:0.06
Consensus pattern (20 bp):
CAAAACAACAAAAAAAATAT
Found at i:31304267 original size:21 final size:20
Alignment explanation
Indices: 31304243--31304303 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
31304233 CCAAAACAAC
31304243 AAAAAAAACTAAAACAGCAAA
1 AAAAAAAAC-AAAACAGCAAA
* * *
31304264 AAAAATATCAAAACAACAAA
1 AAAAAAAACAAAACAGCAAA
* *
31304284 AAATAACACCAAAACAGCAA
1 AAA-AAAAACAAAACAGCAA
31304304 TATAATTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 13 0.39
21 20 0.61
ACGTcount: A:0.72, C:0.18, G:0.03, T:0.07
Consensus pattern (20 bp):
AAAAAAAACAAAACAGCAAA
Found at i:31314333 original size:3 final size:3
Alignment explanation
Indices: 31314325--31314367 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
31314315 GGACTACACT
31314325 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
31314368 AGTTGTTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:31319232 original size:30 final size:30
Alignment explanation
Indices: 31319198--31319281 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
31319188 AAATTGGAGT
*
31319198 TTTAGATCCATTAAAAGTTGAAAAAAAAAA
1 TTTAGATCCTTTAAAAGTTGAAAAAAAAAA
**
31319228 TTTAGGCCCTTTCAAAA-TTGGTAAAAAAAAAA
1 TTTAGATCCTTT-AAAAGTT-G-AAAAAAAAAA
*
31319260 TTT-GATCCTTTAAAAGCTGAAA
1 TTTAGATCCTTTAAAAGTTGAAA
31319282 TTTTTTTACC
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
29 3 0.07
30 16 0.36
31 12 0.27
32 13 0.30
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.30
Consensus pattern (30 bp):
TTTAGATCCTTTAAAAGTTGAAAAAAAAAA
Found at i:31319577 original size:10 final size:10
Alignment explanation
Indices: 31319558--31319586 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
31319548 GGATGAGCAT
31319558 TCGA-TCGAA
1 TCGAGTCGAA
31319567 TCGAGTCGAA
1 TCGAGTCGAA
31319577 TCGAGTCGAA
1 TCGAGTCGAA
31319587 AAAATTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.21
Consensus pattern (10 bp):
TCGAGTCGAA
Found at i:31332837 original size:41 final size:41
Alignment explanation
Indices: 31332792--31332926 Score: 198
Period size: 41 Copynumber: 3.3 Consensus size: 41
31332782 GTATGATGCG
* * * *
31332792 GTCATATTTGTTGCCTATTACCTCAACCGATATTGTGATGA
1 GTCATATTTATTGTCTATTATCTCAACCGATGTTGTGATGA
31332833 GTCATATTTATTGTCTATTATCTCAACCGATGTTGTGATGA
1 GTCATATTTATTGTCTATTATCTCAACCGATGTTGTGATGA
* *
31332874 GTCATATTTATTGTCTATTATCTCAACGGGTGTTGTGATGA
1 GTCATATTTATTGTCTATTATCTCAACCGATGTTGTGATGA
**
31332915 GTTGTATTTATT
1 GTCATATTTATT
31332927 ACCTCTTTTC
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 86 1.00
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (41 bp):
GTCATATTTATTGTCTATTATCTCAACCGATGTTGTGATGA
Found at i:31345804 original size:23 final size:25
Alignment explanation
Indices: 31345765--31345810 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
31345755 AATGCAATAT
31345765 TGTTGAAAAATCAAATAA-AAAAGG
1 TGTTGAAAAATCAAATAACAAAAGG
31345789 TGTTG-AAAA-CACAATAACAAAA
1 TGTTGAAAAATCA-AATAACAAAA
31345811 AAACATAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 2 0.10
23 9 0.45
24 9 0.45
ACGTcount: A:0.59, C:0.09, G:0.13, T:0.20
Consensus pattern (25 bp):
TGTTGAAAAATCAAATAACAAAAGG
Found at i:31347028 original size:30 final size:30
Alignment explanation
Indices: 31346974--31347030 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
31346964 TTATTTTAGA
*
31346974 ATATTTTTAAAATTTTAATTTTTTTTATAT
1 ATATTTTTAAAATTTTAATATTTTTTATAT
* **
31347004 ATATTTTTAGAATTTTTCTATTTTTTA
1 ATATTTTTAAAATTTTAATATTTTTTA
31347031 AAATATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (30 bp):
ATATTTTTAAAATTTTAATATTTTTTATAT
Found at i:31356209 original size:23 final size:23
Alignment explanation
Indices: 31356182--31356299 Score: 150
Period size: 23 Copynumber: 5.0 Consensus size: 23
31356172 CTAGCGCGCG
31356182 CTCTGATTAGCACTGTGTGTGCT
1 CTCTGATTAGCACTGTGTGTGCT
* *
31356205 CTCTGTTTAGCAC-GTCTCGTGCT
1 CTCTGATTAGCACTGTGT-GTGCT
31356228 CTCTGTTATTAGCACTGTGTGTGCT
1 CTCTG--ATTAGCACTGTGTGTGCT
*
31356253 CTCCGATTAGCACT-TCGTGTGCT
1 CTCTGATTAGCACTGT-GTGTGCT
*
31356276 CTCTGATTAGCACTTTGTGTGCT
1 CTCTGATTAGCACTGTGTGTGCT
31356299 C
1 C
31356300 AGTACTTTGT
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
22 4 0.05
23 59 0.71
24 1 0.01
25 16 0.19
26 3 0.04
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (23 bp):
CTCTGATTAGCACTGTGTGTGCT
Found at i:31356248 original size:48 final size:46
Alignment explanation
Indices: 31356182--31356299 Score: 166
Period size: 48 Copynumber: 2.5 Consensus size: 46
31356172 CTAGCGCGCG
* *
31356182 CTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGTGCT
1 CTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGT-GTGCT
*
31356228 CTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCT
1 CTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGTGCT
*
31356276 CTCTGATTAGCACTTTGTGTGCTC
1 CTCTGATTAGCACTGTGTGTGCTC
31356300 AGTACTTTGT
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 23 0.35
48 41 0.63
49 1 0.02
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (46 bp):
CTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGTGCT
Found at i:31356328 original size:39 final size:39
Alignment explanation
Indices: 31356264--31356338 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
31356254 TCCGATTAGC
*
31356264 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
31356303 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
31356339 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:31356333 original size:23 final size:23
Alignment explanation
Indices: 31356298--31356391 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
31356288 CTTTGTGTGC
*
31356298 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
31356321 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
31356344 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
31356369 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
31356391 T
1 T
31356392 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:31359746 original size:41 final size:38
Alignment explanation
Indices: 31359646--31359749 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
31359636 TTCGAAGCAA
* *
31359646 TAAAGTGACACCCAGTGTCTCATC-AGCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
31359683 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
31359721 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
31359750 CTCGAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 20 0.39
38 11 0.22
40 2 0.04
41 18 0.35
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:31359877 original size:12 final size:13
Alignment explanation
Indices: 31359854--31359891 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
31359844 AATTCATATC
*
31359854 ACTTTCAATTTCA
1 ACTTTCACTTTCA
31359867 AC-TTCACTTTC-
1 ACTTTCACTTTCA
31359878 ACTTTCACTTTCA
1 ACTTTCACTTTCA
31359891 A
1 A
31359892 TTTTGATCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 2 0.09
12 17 0.77
13 3 0.14
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (13 bp):
ACTTTCACTTTCA
Found at i:31360067 original size:22 final size:22
Alignment explanation
Indices: 31360041--31360086 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
31360031 TAAACGTATA
*
31360041 ATATTTCATATATACATTGTTC
1 ATATTTCACATATACATTGTTC
31360063 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTGTTC
31360085 AT
1 AT
31360087 CACATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.48
Consensus pattern (22 bp):
ATATTTCACATATACATTGTTC
Found at i:31360097 original size:22 final size:22
Alignment explanation
Indices: 31360046--31360097 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
31360036 GTATAATATT
**
31360046 TCATATATACATTGTTCATATT
1 TCATATATACATTGTTCATACA
*
31360068 TCACATATACATTGTTCATCACA
1 TCATATATACATTGTTCAT-ACA
31360091 T-ATATAT
1 TCATATAT
31360098 CATCATATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.44
Consensus pattern (22 bp):
TCATATATACATTGTTCATACA
Found at i:31362622 original size:741 final size:741
Alignment explanation
Indices: 31361201--31367869 Score: 13313
Period size: 741 Copynumber: 9.0 Consensus size: 741
31361191 TTAAAAATGG
31361201 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
1 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
31361266 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
66 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
31361331 TCCACTAAAATATCTCTC-TAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
131 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
31361395 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
196 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
31361460 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
261 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
31361525 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
326 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
*
31361590 TTCTAATTCTCAATTCTATTTTATCACTGTTCTAGATCCGATTTGAGCACGCGGATGTTACATGT
391 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
31361655 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
456 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
31361720 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
521 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
31361785 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
586 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
31361850 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
651 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
31361915 TTAAAAAGTAAAAGGACCGACATTCT
716 TTAAAAAGTAAAAGGACCGACATTCT
31361941 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
1 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
31362006 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
66 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
31362071 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
131 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
31362136 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
196 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
31362201 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
261 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
31362266 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
326 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
31362331 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
391 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
31362396 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
456 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
31362461 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
521 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
31362526 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
586 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
31362591 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
651 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
31362656 TTAAAAAGTAAAAGGACCGACATTCT
716 TTAAAAAGTAAAAGGACCGACATTCT
31362682 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
1 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
31362747 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
66 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
31362812 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
131 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
31362877 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
196 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
31362942 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
261 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
31363007 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
326 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
31363072 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
391 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
31363137 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
456 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
31363202 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
521 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
31363267 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
586 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
31363332 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
651 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
31363397 TTAAAAAGTAAAAGGACCGACATTCT
716 TTAAAAAGTAAAAGGACCGACATTCT
31363423 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
1 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
31363488 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
66 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
31363553 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
131 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
31363618 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
196 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
31363683 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
261 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
31363748 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
326 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
31363813 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
391 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
31363878 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
456 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
31363943 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
521 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
31364008 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
586 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
31364073 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
651 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
31364138 TTAAAAAGTAAAAGGACCGACATTCT
716 TTAAAAAGTAAAAGGACCGACATTCT
31364164 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
1 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
31364229 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
66 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
31364294 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
131 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
31364359 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
196 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
31364424 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
261 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
31364489 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
326 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
31364554 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
391 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
31364619 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
456 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
31364684 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
521 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
31364749 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
586 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
31364814 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
651 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
31364879 TTAAAAAGTAAAAGGACCGACATTCT
716 TTAAAAAGTAAAAGGACCGACATTCT
31364905 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
1 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
31364970 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
66 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
31365035 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
131 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
31365100 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
196 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
31365165 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
261 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
31365230 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
326 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
31365295 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
391 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
31365360 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
456 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
31365425 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
521 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
31365490 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
586 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
31365555 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
651 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
31365620 TTAAAAAGTAAAAGGACCGACATTCT
716 TTAAAAAGTAAAAGGACCGACATTCT
31365646 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
1 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
31365711 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
66 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
31365776 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
131 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
31365841 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
196 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
31365906 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
261 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
31365971 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
326 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
31366036 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
391 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
31366101 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
456 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
31366166 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
521 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
31366231 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
586 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
31366296 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
651 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
31366361 TTAAAAAGTAAAAGGACCGACATTCT
716 TTAAAAAGTAAAAGGACCGACATTCT
31366387 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
1 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
31366452 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
66 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
31366517 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
131 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
31366582 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
196 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
31366647 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
261 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
31366712 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
326 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
31366777 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
391 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
31366842 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
456 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
31366907 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
521 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
31366972 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
586 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
31367037 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
651 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
31367102 TTAAAAAGTAAAAGGACCGACATTCT
716 TTAAAAAGTAAAAGGACCGACATTCT
31367128 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
1 TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
31367193 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
66 TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
31367258 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
131 TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
31367323 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
196 TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
31367388 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
261 CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
31367453 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
326 ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
31367518 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
391 TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
*
31367583 CCTAACAGGGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
456 CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
31367648 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
521 TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
31367713 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
586 CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
31367778 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
651 CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
31367843 TTAAAAAGTAAAAGGACCGACATTCT
716 TTAAAAAGTAAAAGGACCGACATTCT
31367869 T
1 T
31367870 TATGTTTTGG
Statistics
Matches: 5926, Mismatches: 2, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
740 148 0.02
741 5778 0.98
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (741 bp):
TGGAAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGATATGCATGTGACGTTGGAAA
TGAATGAAAAAGATGATATTTTCATCTTTTATCTAATTTTATTTCTCTCAAATTCTCTAGATTTC
TCCACTAAAATATCTCTCTTAATAAAAATGGTAAAATTGTACTTTTAGTCCTTGGGCCTTCCAAC
TTTACACTTTGACGCAAAACTTTGCCTCCAAAAATATCTTCCACCAAATTACTCTTTTGCCCCTC
CTTAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTATTTAGTCCTTC
ATATTTTCTCTCATTTACTATTTAATCCTTAAATTTTTCTAACCTTCATCACTTCAACTAAACAT
TTCTAATTCTCAATTCTATTTTATCACTGTTCCAGATCCGATTTGAGCACGCGGATGTTACATGT
CCTAACAGAGAATAGTTCTCCACATACAATTCAGTTGAATGTAGAGTTGTGTGCATGGAAAATGA
TTCATCTAGTAAGGTAATCAGTATTGGTACTATTAAAATTAGGATGCATGATGAGACGATTATGA
CACTCTCAGATGTCAGGTATGTACCTAATTTACGAAGAATCTCGTCTCCTTAAGTATTTTAGACT
CCAAAGGTTGCAAGATCAACATCGAGTCTAGCAGCATTCAGGTATCTTTTGAGGTTCTTGTTTTG
TTAAAAAGTAAAAGGACCGACATTCT
Found at i:31373510 original size:12 final size:12
Alignment explanation
Indices: 31373493--31373522 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
31373483 TTATTTTATT
31373493 TGTGTGCGTGTG
1 TGTGTGCGTGTG
*
31373505 TGTGTGCGTGTT
1 TGTGTGCGTGTG
31373517 TGTGTG
1 TGTGTG
31373523 TCATATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.47, T:0.47
Consensus pattern (12 bp):
TGTGTGCGTGTG
Found at i:31379448 original size:21 final size:20
Alignment explanation
Indices: 31379400--31379448 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
31379390 ATTAAAGTGT
* *
31379400 AATAATTTATTTTTAAAACA
1 AATAATTTATGTTAAAAACA
*
31379420 AATAAATTTAATGTTAAAAATA
1 AAT-AATTT-ATGTTAAAAACA
31379442 AATAATT
1 AATAATT
31379449 ATAACAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 9 0.38
22 12 0.50
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
AATAATTTATGTTAAAAACA
Found at i:31385463 original size:17 final size:15
Alignment explanation
Indices: 31385424--31385467 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
31385414 CAAATTTTAT
31385424 TTACTTTCCCTGGAG
1 TTACTTTCCCTGGAG
31385439 TCTAACTTTCCCTTGGGAG
1 T-T-ACTTTCCC-T-GGAG
31385458 TTACTTTCCC
1 TTACTTTCCC
31385468 ATGAACATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 1 0.04
17 16 0.64
18 2 0.08
19 5 0.20
ACGTcount: A:0.14, C:0.30, G:0.16, T:0.41
Consensus pattern (15 bp):
TTACTTTCCCTGGAG
Found at i:31396406 original size:113 final size:113
Alignment explanation
Indices: 31396232--31396450 Score: 411
Period size: 113 Copynumber: 1.9 Consensus size: 113
31396222 ATTTTCCTAT
31396232 GGATATTAGTGGATGATGATGAAAAATTTCACTAAATATGATTAATGAATTATTTAAGTTAAATA
1 GGATATTAGTGGATGATGATGAAAAATTTCACTAAATATGATTAATGAATTATTTAAGTTAAATA
31396297 AATTATGATTAGTTTAATTAATCCATAGTTGGATTATAATGGGAGAAA
66 AATTATGATTAGTTTAATTAATCCATAGTTGGATTATAATGGGAGAAA
*
31396345 GGATATTAGTGGATGATGATGAAAAATTTCACTAAGTATGATTAATGAATTATTTAAGTTAAATA
1 GGATATTAGTGGATGATGATGAAAAATTTCACTAAATATGATTAATGAATTATTTAAGTTAAATA
* *
31396410 ATTTATGATTAGTTTAATTAATCTATAGTTGGATTATAATG
66 AATTATGATTAGTTTAATTAATCCATAGTTGGATTATAATG
31396451 CAAGAAAATG
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 103 1.00
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.39
Consensus pattern (113 bp):
GGATATTAGTGGATGATGATGAAAAATTTCACTAAATATGATTAATGAATTATTTAAGTTAAATA
AATTATGATTAGTTTAATTAATCCATAGTTGGATTATAATGGGAGAAA
Found at i:31400894 original size:84 final size:83
Alignment explanation
Indices: 31400743--31400902 Score: 189
Period size: 84 Copynumber: 1.9 Consensus size: 83
31400733 TATGGATTTG
* * * * *
31400743 TAATTTTATTATTTTAATAATTTATAATTTATAATTTTTAAAAAATTAAATTAAATTATTATTAT
1 TAATTTTATTA-TTTAATAATTTAAAATTTATAAATTATAAAAAATTAAATTAAAATATTATCAT
31400808 TTTAGGAAGGTTAAAAGTA
65 TTTAGGAAGGTTAAAAGTA
* **
31400827 TAATTTTATTA-TTATTAATTTAAAATTTTATAAATTATAAAGAGTTTAAATTAAAA-ATTTATC
1 TAATTTTATTATTTAATAATTTAAAA-TTTATAAATTATAAA-AAATTAAATTAAAATA-TTATC
*
31400890 ATTTTAGGGAGGT
63 ATTTTAGGAAGGT
31400903 CATGGATCTC
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
82 12 0.19
83 14 0.22
84 38 0.59
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (83 bp):
TAATTTTATTATTTAATAATTTAAAATTTATAAATTATAAAAAATTAAATTAAAATATTATCATT
TTAGGAAGGTTAAAAGTA
Found at i:31401293 original size:3 final size:3
Alignment explanation
Indices: 31401285--31401314 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
31401275 CGTATTCCAC
31401285 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31401315 ATAAGCAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:31401678 original size:19 final size:19
Alignment explanation
Indices: 31401646--31401685 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
31401636 ATTTGGTTCT
31401646 TTTACTTTTAATTTCAAAAA
1 TTTACTTTTAATTT-AAAAA
*
31401666 TTTA-TTTTTATTTAAAAA
1 TTTACTTTTAATTTAAAAA
31401684 TT
1 TT
31401686 AAAATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 8 0.42
20 4 0.21
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTACTTTTAATTTAAAAA
Found at i:31416865 original size:19 final size:20
Alignment explanation
Indices: 31416841--31416889 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
31416831 ATTTACTCTA
31416841 ATTTTATTTTTTA-TTTCAT
1 ATTTTATTTTTTATTTTCAT
31416860 ATTTTATTTTTTATTTTCAT
1 ATTTTATTTTTTATTTTCAT
31416880 ATTTTTATTT
1 A-TTTTATTT
31416890 GAAAATAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 13 0.46
20 7 0.25
21 8 0.29
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (20 bp):
ATTTTATTTTTTATTTTCAT
Found at i:31417260 original size:24 final size:24
Alignment explanation
Indices: 31417206--31417262 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
31417196 AACCAGAATC
* *
31417206 AGAAGAAGATTCCGAAGAAACCGA
1 AGAACAAGATTCCGAAGAAAACGA
* *
31417230 AGGACAAGATTCCGATGAAGAAC-A
1 AGAACAAGATTCCGAAGAA-AACGA
31417254 AGAACAAGA
1 AGAACAAGA
31417263 AGGGCTTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.51, C:0.16, G:0.25, T:0.09
Consensus pattern (24 bp):
AGAACAAGATTCCGAAGAAAACGA
Found at i:31418356 original size:21 final size:21
Alignment explanation
Indices: 31418307--31418357 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
31418297 TCTGATTAAA
* *
31418307 AAAGAAGATGCATGGAAAAAG
1 AAAGAAGCTGAATGGAAAAAG
31418328 AAAGAAGCTGAATGGAAAAAG
1 AAAGAAGCTGAATGGAAAAAG
*
31418349 AGAGAAGCT
1 AAAGAAGCT
31418358 TTGTTGCAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.55, C:0.06, G:0.29, T:0.10
Consensus pattern (21 bp):
AAAGAAGCTGAATGGAAAAAG
Found at i:31423060 original size:16 final size:15
Alignment explanation
Indices: 31423018--31423061 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
31423008 TTTAAAATTC
31423018 AAAATTCAAAATTAAA
1 AAAATT-AAAATTAAA
31423034 AAAACTGTAAAATATAAA
1 AAAA-T-TAAAAT-TAAA
31423052 AAAATTAAAA
1 AAAATTAAAA
31423062 GCTCATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 9 0.36
17 7 0.28
18 9 0.36
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (15 bp):
AAAATTAAAATTAAA
Found at i:31425107 original size:31 final size:30
Alignment explanation
Indices: 31425072--31425130 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 30
31425062 AAATTTTGTA
*
31425072 GTAAATTTATATGTTTTATATATATTTTTTT
1 GTAAATTTATATATTTTATATAT-TTTTTTT
31425103 GTAAATTTATATATTTTATATATTTTTT
1 GTAAATTTATATATTTTATATATTTTTT
31425131 ATTTTTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (30 bp):
GTAAATTTATATATTTTATATATTTTTTTT
Found at i:31425122 original size:9 final size:9
Alignment explanation
Indices: 31425108--31425145 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
31425098 TTTTTGTAAA
31425108 TTTATATAT
1 TTTATATAT
31425117 TTTATATAT
1 TTTATATAT
* *
31425126 TTTTTATTT
1 TTTATATAT
31425135 TTTA-ATAT
1 TTTATATAT
31425143 TTT
1 TTT
31425146 TCATTGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
8 6 0.24
9 19 0.76
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTATATAT
Found at i:31425274 original size:43 final size:43
Alignment explanation
Indices: 31425213--31425299 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
31425203 TGATGTGTGA
31425213 TAACATATGATTGGGTTGAATATTACAACCATTAGATTTTAAT
1 TAACATATGATTGGGTTGAATATTACAACCATTAGATTTTAAT
*
31425256 TAACATATGATTGGGTTGAATATTATAACCATTAGATTTTAAT
1 TAACATATGATTGGGTTGAATATTACAACCATTAGATTTTAAT
31425299 T
1 T
31425300 TCCAAAAGAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (43 bp):
TAACATATGATTGGGTTGAATATTACAACCATTAGATTTTAAT
Found at i:31432932 original size:5 final size:5
Alignment explanation
Indices: 31432922--31432947 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31432912 TGAGCTCTAA
31432922 GTGAT GTGAT GTGAT GTGAT GTGAT G
1 GTGAT GTGAT GTGAT GTGAT GTGAT G
31432948 AAAGGTCCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.38
Consensus pattern (5 bp):
GTGAT
Found at i:31433321 original size:23 final size:23
Alignment explanation
Indices: 31433295--31433348 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
31433285 TAGCGCAAAT
* **
31433295 CAGTAGGCACACGAGGTGCGAAA
1 CAGTAAGCACACGAACTGCGAAA
31433318 CAGTAAGCACACGAACTGCGAAA
1 CAGTAAGCACACGAACTGCGAAA
31433341 CAGTAAGC
1 CAGTAAGC
31433349 GTGCTAGCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.39, C:0.24, G:0.28, T:0.09
Consensus pattern (23 bp):
CAGTAAGCACACGAACTGCGAAA
Found at i:31434303 original size:7 final size:7
Alignment explanation
Indices: 31434291--31434316 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31434281 CATAAACACA
31434291 TATAAGC
1 TATAAGC
31434298 TATAAGC
1 TATAAGC
31434305 TATAAGC
1 TATAAGC
31434312 TATAA
1 TATAA
31434317 TTCAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (7 bp):
TATAAGC
Found at i:31435112 original size:10 final size:11
Alignment explanation
Indices: 31435088--31435135 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
31435078 CCCTTTATTT
*
31435088 TTTCACACAAA
1 TTTCACTCAAA
31435099 TTTCACTC-AA
1 TTTCACTCAAA
*
31435109 TTTCTCTCTAAA
1 TTTCACTC-AAA
*
31435121 TTTCACACAAA
1 TTTCACTCAAA
31435132 TTTC
1 TTTC
31435136 TCTCTAAAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 9 0.29
11 14 0.45
12 8 0.26
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (11 bp):
TTTCACTCAAA
Found at i:31435121 original size:22 final size:23
Alignment explanation
Indices: 31435096--31435143 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
31435086 TTTTTCACAC
*
31435096 AAATTTCACTC-AATTTCTCTCT
1 AAATTTCACACAAATTTCTCTCT
31435118 AAATTTCACACAAATTTCTCTCT
1 AAATTTCACACAAATTTCTCTCT
31435141 AAA
1 AAA
31435144 GCTCTCTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATTTCACACAAATTTCTCTCT
Found at i:31435124 original size:12 final size:12
Alignment explanation
Indices: 31435107--31435158 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
31435097 AATTTCACTC
31435107 AATTTCTCTCTA
1 AATTTCTCTCTA
* *
31435119 AATTTCACAC-A
1 AATTTCTCTCTA
31435130 AATTTCTCTCTA
1 AATTTCTCTCTA
**
31435142 AAGCTCTCTCTA
1 AATTTCTCTCTA
31435154 AATTT
1 AATTT
31435159 TTTATTTTTC
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
11 9 0.29
12 22 0.71
ACGTcount: A:0.31, C:0.25, G:0.02, T:0.42
Consensus pattern (12 bp):
AATTTCTCTCTA
Found at i:31435130 original size:33 final size:34
Alignment explanation
Indices: 31435088--31435158 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
31435078 CCCTTTATTT
**
31435088 TTTCACACAAATTTCACTC-AATTTCTCTCTAAA
1 TTTCACACAAATTTCACTCAAAGCTCTCTCTAAA
*
31435121 TTTCACACAAATTTCTCTCTAAAGCTCTCTCTAAA
1 TTTCACACAAATTTCACTC-AAAGCTCTCTCTAAA
31435156 TTT
1 TTT
31435159 TTTATTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 18 0.55
35 15 0.45
ACGTcount: A:0.31, C:0.27, G:0.01, T:0.41
Consensus pattern (34 bp):
TTTCACACAAATTTCACTCAAAGCTCTCTCTAAA
Found at i:31435337 original size:10 final size:11
Alignment explanation
Indices: 31435321--31435365 Score: 51
Period size: 10 Copynumber: 4.2 Consensus size: 11
31435311 AGAGTTACTT
31435321 TTATTTTTTAA
1 TTATTTTTTAA
31435332 -TATTTTTTAA
1 TTATTTTTTAA
31435342 TTATTTTATT--
1 TTATTTT-TTAA
31435352 TTATTTTTATAA
1 TTATTTTT-TAA
31435364 TT
1 TT
31435366 TTTATGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
9 1 0.03
10 18 0.62
11 6 0.21
12 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTTTTTAA
Found at i:31435347 original size:21 final size:22
Alignment explanation
Indices: 31435321--31435365 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
31435311 AGAGTTACTT
31435321 TTATTTT-TTAATATTTTT-TAA
1 TTATTTTATT-ATATTTTTATAA
*
31435342 TTATTTTATTTTATTTTTATAA
1 TTATTTTATTATATTTTTATAA
31435364 TT
1 TT
31435366 TTTATGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (22 bp):
TTATTTTATTATATTTTTATAA
Found at i:31437512 original size:20 final size:19
Alignment explanation
Indices: 31437466--31437513 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
31437456 AAACCTTAAA
*
31437466 TAATTAAAAACCTAAACTT
1 TAATTAAAAACATAAACTT
31437485 TAATTTAAAAATCATAAA-TCT
1 TAA-TTAAAAA-CATAAACT-T
31437506 TAATTAAA
1 TAATTAAA
31437514 CAAAAAACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 13 0.52
21 9 0.36
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.35
Consensus pattern (19 bp):
TAATTAAAAACATAAACTT
Found at i:31445268 original size:29 final size:29
Alignment explanation
Indices: 31445189--31445269 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
31445179 ACAAAATAAC
*
31445189 AACATAAATGACTAAAACATAATATTTTA
1 AACATAAATGACTAAAACGTAATATTTTA
* * *
31445218 AATATAAATGGCTAAAAGGTAATATTTTA
1 AACATAAATGACTAAAACGTAATATTTTA
* *
31445247 AACATAAGTGACTAAAATGTAAT
1 AACATAAATGACTAAAACGTAAT
31445270 CTGAGGTAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (29 bp):
AACATAAATGACTAAAACGTAATATTTTA
Found at i:31455582 original size:29 final size:29
Alignment explanation
Indices: 31455445--31455583 Score: 76
Period size: 29 Copynumber: 4.8 Consensus size: 29
31455435 CTTTGAATGC
*
31455445 TCGGGGGTAAAATGATAATTTTTGGTGAAA
1 TCGGGGGTAAAATGGTAA-TTTTGGTGAAA
* *
31455475 TCGGGGTTAAAAATTG-AATTTT-G-GAAA
1 TCGGGGGT-AAAATGGTAATTTTGGTGAAA
* ** *
31455502 GTTTGAAGGTAAAACGGTAATTTTGGTGAAA
1 --TCGGGGGTAAAATGGTAATTTTGGTGAAA
* *
31455533 TCAGGGTTAAAAAT-G-AGATTTT-G-GAAA
1 TCGGGGGT-AAAATGGTA-ATTTTGGTGAAA
31455560 GTTCGGGGGTAAAATGGTAATTTT
1 --TCGGGGGTAAAATGGTAATTTT
31455584 TGGTAGTTTC
Statistics
Matches: 80, Mismatches: 17, Indels: 25
0.66 0.14 0.20
Matches are distributed among these distances:
27 8 0.10
28 13 0.16
29 35 0.44
30 15 0.19
31 9 0.11
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.33
Consensus pattern (29 bp):
TCGGGGGTAAAATGGTAATTTTGGTGAAA
Found at i:31455604 original size:58 final size:58
Alignment explanation
Indices: 31455445--31455587 Score: 207
Period size: 58 Copynumber: 2.4 Consensus size: 58
31455435 CTTTGAATGC
*
31455445 TCGGGGGTAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATTGAATTTTGGAAAGT
1 TCGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAA-TGAATTTTGGAAAGT
* ** * *
31455504 TTGAAGGTAAAACGGTAA-TTTTGGTGAAATCAGGGTTAAAAATGAGATTTTGGAAAGT
1 TCGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGA-ATTTTGGAAAGT
31455562 TCGGGGGTAAAATGGTAATTTTTGGT
1 TCGGGGGTAAAATGGTAATTTTTGGT
31455588 AGTTTCGGGG
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
57 3 0.04
58 49 0.68
59 20 0.28
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (58 bp):
TCGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAATTTTGGAAAGT
Found at i:31455688 original size:30 final size:30
Alignment explanation
Indices: 31455551--31455711 Score: 120
Period size: 30 Copynumber: 5.4 Consensus size: 30
31455541 AAAAATGAGA
* *
31455551 TTTTGGAAAG-TTCGGGGGTAAAATGGTAAT
1 TTTTAGAAAGTTTCGGGGTTAAAAT-GTAAT
** *
31455581 TTTT-GGTAGTTTCGGGGTTAAAATAT-AT
1 TTTTAGAAAGTTTCGGGGTTAAAATGTAAT
* * *
31455609 TTTTCAG-AAGTTTTGAGGTCAAAATGTAA-
1 TTTT-AGAAAGTTTCGGGGTTAAAATGTAAT
* *
31455638 TTTTA-AAGGAATTCGAGGGTTAAAATGTAAT
1 TTTTAGAAAG-TTTCG-GGGTTAAAATGTAAT
* *
31455669 TTTTAGAAAGTTTTGGGGTTAAAATATAAT
1 TTTTAGAAAGTTTCGGGGTTAAAATGTAAT
31455699 TTTT-GAATAGTTT
1 TTTTAGAA-AGTTT
31455712 AGGGACCTAT
Statistics
Matches: 103, Mismatches: 18, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
28 9 0.09
29 29 0.28
30 54 0.52
31 8 0.08
32 3 0.03
ACGTcount: A:0.32, C:0.03, G:0.24, T:0.41
Consensus pattern (30 bp):
TTTTAGAAAGTTTCGGGGTTAAAATGTAAT
Found at i:31457581 original size:33 final size:32
Alignment explanation
Indices: 31457544--31457614 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
31457534 TTCAAATTAT
** *
31457544 TTTAAATGTATTTAAATTTAAAACAAATCTAAA
1 TTTAAATAAATTTAAAATTAAAACAAA-CTAAA
** *
31457577 TTTAAATAAATTTAAAATTAATTCAAACTTAA
1 TTTAAATAAATTTAAAATTAAAACAAACTAAA
31457609 TTTAAA
1 TTTAAA
31457615 ATCTAAGTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (32 bp):
TTTAAATAAATTTAAAATTAAAACAAACTAAA
Done.