Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 116 of 135
Found at i:39022500 original size:41 final size:40
Alignment explanation
Indices: 39022452--39022562 Score: 143
Period size: 41 Copynumber: 2.8 Consensus size: 40
39022442 TAACTAGAAG
* *
39022452 GCAGATTGAAGACCATTCAATCTTTTACCCCGGCCATGAGA
1 GCAGATTGAAGACCATCCAATCTTTTACCCCGACCATG-GA
* * * *
39022493 GTAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGG
1 GCAGATTGAAGACCATCCAATCTTTTACCCCGACCATGGA
*
39022533 GCAGATTGAAG-CAATCCAATCTTTTACCCC
1 GCAGATTGAAGACCATCCAATCTTTTACCCC
39022563 TAAAGTTATA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 16 0.27
40 11 0.18
41 33 0.55
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (40 bp):
GCAGATTGAAGACCATCCAATCTTTTACCCCGACCATGGA
Found at i:39023305 original size:4 final size:4
Alignment explanation
Indices: 39023296--39023338 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
39023286 AAAGGCTTAA
*
39023296 ATTT ATTT ATTT ATTC ATTT AATTT AATTT ATTT A-TT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT -ATTT -ATTT ATTT ATTT ATTT AT
39023339 AAATAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 23 0.66
5 9 0.26
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (4 bp):
ATTT
Found at i:39023317 original size:22 final size:22
Alignment explanation
Indices: 39023292--39023337 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
39023282 TTGCAAAGGC
39023292 TTAAATTT-ATTTATTTATTCAT
1 TTAAATTTAATTTATTTATT-AT
39023314 TT-AATTTAATTTATTTATTAT
1 TTAAATTTAATTTATTTATTAT
39023335 TTA
1 TTA
39023338 TAAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TTAAATTTAATTTATTTATTAT
Found at i:39023511 original size:4 final size:4
Alignment explanation
Indices: 39023502--39023540 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
39023492 AACCTAAGTC
39023502 CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
39023541 TTGTATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:39024094 original size:30 final size:30
Alignment explanation
Indices: 39024060--39024116 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
39024050 TTTGTTTTGA
*
39024060 CCCCAAATTTCTCAAAAATTCAAATTTATC
1 CCCCAAACTTCTCAAAAATTCAAATTTATC
39024090 CCCCAAACTTCTCAAAAATTCAAATTT
1 CCCCAAACTTCTCAAAAATTCAAATTT
39024117 GACCTCTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (30 bp):
CCCCAAACTTCTCAAAAATTCAAATTTATC
Found at i:39024129 original size:30 final size:28
Alignment explanation
Indices: 39024071--39024301 Score: 140
Period size: 30 Copynumber: 7.8 Consensus size: 28
39024061 CCCAAATTTC
**
39024071 TCAAAAATTCAAATTT-ATCCCCCAAACTT
1 TCAAAAATTCAAATTTGA--CCCTGAACTT
39024100 CTCAAAAATTCAAATTTGACCTCTGAACTT
1 -TCAAAAATTCAAATTTGACC-CTGAACTT
** *
39024130 TCTAAAAATTTGAATTTGACCCTTGAATTTT
1 TC-AAAAATTCAAATTTGACCC-TGAA-CTT
** *
39024161 TCAAAAATTTGAACTTGACCCTCGAACTT
1 TCAAAAATTCAAATTTGACCCT-GAACTT
* ** * * *
39024190 TCTAGAAATTTGAATTTAACCCTTAAATTT
1 TC-AAAAATTCAAATTTGACCC-TGAACTT
* * *
39024220 TCTAAAAAATCCAATTTGACCCCTGAAGTT
1 TC-AAAAATTCAAATTTGA-CCCTGAACTT
* *
39024250 TCCAAAAATTCTAATTTGACCCCTGAAGTT
1 T-CAAAAATTCAAATTTGA-CCCTGAACTT
*
39024280 TCCAAAAATTCAAAATTGACCC
1 T-CAAAAATTCAAATTTGACCC
39024302 GGTTTTAATG
Statistics
Matches: 168, Mismatches: 23, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
29 13 0.08
30 145 0.86
31 10 0.06
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (28 bp):
TCAAAAATTCAAATTTGACCCTGAACTT
Found at i:39024146 original size:60 final size:57
Alignment explanation
Indices: 39024101--39024301 Score: 188
Period size: 60 Copynumber: 3.4 Consensus size: 57
39024091 CCCAAACTTC
*
39024101 TCAAAAATTCAAATTTGACCTCTGAACTTTCTAAAAATTTGAATTTGACCCTTGAATTTT
1 TCAAAAATTCAAATTTGACC-CTGAACTTTCTAAAAATTTGAATTT-ACCCTT-AAATTT
** * *
39024161 TCAAAAATTTGAACTTGACCCTCGAACTTTCTAGAAATTTGAATTTAACCCTTAAATTT
1 TCAAAAATTCAAATTTGACCCT-GAACTTTCTAAAAATTTGAATTT-ACCCTTAAATTT
* * * * * *
39024220 TCTAAAAAATCCAATTTGACCCCTGAAGTTTCCAAAAATTCT-AATTTGACCCCTGAAGTTT
1 TC-AAAAATTCAAATTTGA-CCCTGAACTTTCTAAAAATT-TGAATTT-A-CCCTTAAATTT
* *
39024281 CCAAAAATTCAAAATTGACCC
1 TCAAAAATTCAAATTTGACCC
39024302 GGTTTTAATG
Statistics
Matches: 116, Mismatches: 20, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
59 12 0.10
60 89 0.77
61 15 0.13
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.35
Consensus pattern (57 bp):
TCAAAAATTCAAATTTGACCCTGAACTTTCTAAAAATTTGAATTTACCCTTAAATTT
Found at i:39024199 original size:90 final size:90
Alignment explanation
Indices: 39024102--39024301 Score: 208
Period size: 90 Copynumber: 2.2 Consensus size: 90
39024092 CCAAACTTCT
* * ** * * *
39024102 CAAAAATTCAAATTTGA-CCTCTGAACTTTCTAAAAATTTGAATTTGACCCTTGAATTTTTCAAA
1 CAAAAATTCAAATTTGACCCT-TAAACTTTCTAAAAAATCCAATTTGACCCCTGAAGTTTCCAAA
39024166 AATT-TGAACTTGA-CCCTCGAACTTTC
65 AATTCT-AACTTGACCCCT-GAACTTTC
* * ** * *
39024192 TAGAAATTTGAATTTAACCCTTAAATTTTCTAAAAAATCCAATTTGACCCCTGAAGTTTCCAAAA
1 CAAAAATTCAAATTTGACCCTTAAACTTTCTAAAAAATCCAATTTGACCCCTGAAGTTTCCAAAA
* *
39024257 ATTCTAATTTGACCCCTGAAGTTTC
66 ATTCTAACTTGACCCCTGAACTTTC
*
39024282 CAAAAATTCAAAATTGACCC
1 CAAAAATTCAAATTTGACCC
39024302 GGTTTTAATG
Statistics
Matches: 86, Mismatches: 21, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
90 78 0.91
91 8 0.09
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.34
Consensus pattern (90 bp):
CAAAAATTCAAATTTGACCCTTAAACTTTCTAAAAAATCCAATTTGACCCCTGAAGTTTCCAAAA
ATTCTAACTTGACCCCTGAACTTTC
Found at i:39026941 original size:23 final size:23
Alignment explanation
Indices: 39026908--39026963 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
39026898 AAGGTAGAAG
* *
39026908 CGTGCCACAAGACAGAGGAAAAT
1 CGTGCCGCAAGACAGAGGAAAAA
39026931 CGTGCCGCAAGACAGAGGAAAAA
1 CGTGCCGCAAGACAGAGGAAAAA
39026954 CGTGCCGCAA
1 CGTGCCGCAA
39026964 AAGTAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.39, C:0.25, G:0.29, T:0.07
Consensus pattern (23 bp):
CGTGCCGCAAGACAGAGGAAAAA
Found at i:39027957 original size:3 final size:3
Alignment explanation
Indices: 39027949--39027980 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
39027939 AGTTTGTCTT
39027949 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
39027981 TAGTTGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:39028170 original size:11 final size:11
Alignment explanation
Indices: 39028154--39028197 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
39028144 TTTCATATAT
*
39028154 TTATTTTTTTA
1 TTATTTATTTA
*
39028165 TTATTTACTTA
1 TTATTTATTTA
*
39028176 TTTATTTATTTG
1 -TTATTTATTTA
39028188 TTATTTATTT
1 TTATTTATTT
39028198 TCTTTGTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:39028178 original size:23 final size:23
Alignment explanation
Indices: 39028151--39028194 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
39028141 GCATTTCATA
*
39028151 TATTTATTTTTTTATTATTTACT
1 TATTTATTTATTTATTATTTACT
*
39028174 TATTTATTTATTTGTTATTTA
1 TATTTATTTATTTATTATTTA
39028195 TTTTCTTTGT
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:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (23 bp):
TATTTATTTATTTATTATTTACT
Found at i:39028182 original size:4 final size:4
Alignment explanation
Indices: 39028151--39028197 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
39028141 GCATTTCATA
* * *
39028151 TATT TATT TTTT TA-T TATT TACT TATT TATT TATT T-GT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
39028197 T
1 T
39028198 TCTTTGTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
3 5 0.14
4 30 0.86
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:39028195 original size:27 final size:27
Alignment explanation
Indices: 39028151--39028210 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
39028141 GCATTTCATA
*
39028151 TATTTATTTTTTTATTATTTACTTAT-T
1 TATTTATTTTTATATTATTTACTT-TGT
*
39028178 TATTTATTTGTTAT-TTATTTTCTTTGT
1 TATTTATTT-TTATATTATTTACTTTGT
39028205 TATTTA
1 TATTTA
39028211 CGTTATTGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 1 0.03
27 25 0.86
28 3 0.10
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (27 bp):
TATTTATTTTTATATTATTTACTTTGT
Found at i:39028203 original size:16 final size:15
Alignment explanation
Indices: 39028173--39028257 Score: 66
Period size: 16 Copynumber: 5.4 Consensus size: 15
39028163 TATTATTTAC
39028173 TTATTTATTTATTTG
1 TTATTTATTTATTTG
*
39028188 TTATTTATTTTCTTTG
1 TTATTTA-TTTATTTG
*
39028204 TTATTTACGTTA-TTG
1 TTATTTA-TTTATTTG
* *
39028219 CT-TTTATTTAATTTTA
1 TTATTTATTT-A-TTTG
39028235 TGTATTTTATTTATTTG
1 T-TA-TTTATTTATTTG
39028252 TTATTT
1 TTATTT
39028258 TTATGCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
13 2 0.04
14 5 0.09
15 14 0.26
16 20 0.37
17 5 0.09
18 1 0.02
19 7 0.13
ACGTcount: A:0.19, C:0.04, G:0.07, T:0.71
Consensus pattern (15 bp):
TTATTTATTTATTTG
Found at i:39028532 original size:26 final size:24
Alignment explanation
Indices: 39028479--39028529 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
39028469 TTTTATTTAC
* *
39028479 TATTATTGTTTTATTTTATTGTGT
1 TATTATTGTTTTATTATATTATGT
39028503 TATTAATTGTGTTTATTATATTCATGT
1 TATT-ATTGT-TTTATTATATT-ATGT
39028530 ATTTTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 4 0.18
25 5 0.23
26 10 0.45
27 3 0.14
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.65
Consensus pattern (24 bp):
TATTATTGTTTTATTATATTATGT
Found at i:39031556 original size:32 final size:32
Alignment explanation
Indices: 39031520--39031584 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
39031510 CTTTCAGAGT
* *
39031520 TAGCATCTGCCAACTTCACTTTATTGTTCTGA
1 TAGCATCTACCAACTTCACTTTATCGTTCTGA
*
39031552 TAGCATCTATCAACTTCACTTTATCGTTCTGA
1 TAGCATCTACCAACTTCACTTTATCGTTCTGA
39031584 T
1 T
39031585 TAGTATTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.42
Consensus pattern (32 bp):
TAGCATCTACCAACTTCACTTTATCGTTCTGA
Found at i:39043121 original size:71 final size:71
Alignment explanation
Indices: 39043041--39043265 Score: 371
Period size: 71 Copynumber: 3.2 Consensus size: 71
39043031 AGCCTTCTAG
39043041 GTATCGGTAGAAGCCTCAGGCCACAACTTCTTTGCTCTCTGGAGTTTGTTCTACCGATAGAACTC
1 GTATCGGTAGAAGCCTCAGGCCACAACTTCTTTGCTCTCTGGAGTTTGTTCTACCGATAGAACTC
39043106 TTGGTT
66 TTGGTT
* * * *
39043112 GTATTGGTAGAAGTCTCAGGCCACAACTTCTTTGCTTTCTGGAGTTTGTTCTATCGATAGAACTC
1 GTATCGGTAGAAGCCTCAGGCCACAACTTCTTTGCTCTCTGGAGTTTGTTCTACCGATAGAACTC
39043177 TTGGTT
66 TTGGTT
* *
39043183 GTATCGGTAGAAGTCC-CAGGCCACAACTTCTTTGCTCTCTAGAGTTTGTTCTACCGATAGAAGT
1 GTATCGGTAGAAG-CCTCAGGCCACAACTTCTTTGCTCTCTGGAGTTTGTTCTACCGATAGAACT
39043247 CTTGGTT
65 CTTGGTT
*
39043254 GAATCGGTAGAA
1 GTATCGGTAGAA
39043266 CCAAGATATG
Statistics
Matches: 142, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
71 141 0.99
72 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (71 bp):
GTATCGGTAGAAGCCTCAGGCCACAACTTCTTTGCTCTCTGGAGTTTGTTCTACCGATAGAACTC
TTGGTT
Found at i:39044079 original size:3 final size:3
Alignment explanation
Indices: 39044071--39044109 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
39044061 TACATCCCAA
39044071 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
39044110 GAATAGAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39045180 original size:20 final size:20
Alignment explanation
Indices: 39045155--39045196 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
39045145 GTTTTTCGAA
39045155 AAAGTCAACGGTCAACGATC
1 AAAGTCAACGGTCAACGATC
* *
39045175 AAAGTCAACGGTTAACGGTC
1 AAAGTCAACGGTCAACGATC
39045195 AA
1 AA
39045197 CGATCAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (20 bp):
AAAGTCAACGGTCAACGATC
Found at i:39045228 original size:21 final size:21
Alignment explanation
Indices: 39045190--39045258 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
39045180 CAACGGTTAA
* * *
39045190 CGGTCAACGATCAATCAACAC
1 CGGTCAACGGTCAGTCAACAT
* *
39045211 CGGTCAACGGTCGGTCAACGT
1 CGGTCAACGGTCAGTCAACAT
*
39045232 CGGTCAAC-GCCAGTCAACAT
1 CGGTCAACGGTCAGTCAACAT
39045252 CGGTCAA
1 CGGTCAA
39045259 TGGTTTGACT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.29, C:0.32, G:0.23, T:0.16
Consensus pattern (21 bp):
CGGTCAACGGTCAGTCAACAT
Found at i:39045233 original size:10 final size:10
Alignment explanation
Indices: 39045211--39045258 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
39045201 CAATCAACAC
39045211 CGGTCAACGGT
1 CGGTCAAC-GT
39045222 CGGTCAACGT
1 CGGTCAACGT
*
39045232 CGGTCAACGC
1 CGGTCAACGT
* *
39045242 CAGTCAACAT
1 CGGTCAACGT
39045252 CGGTCAA
1 CGGTCAA
39045259 TGGTTTGACT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 24 0.75
11 8 0.25
ACGTcount: A:0.25, C:0.31, G:0.27, T:0.17
Consensus pattern (10 bp):
CGGTCAACGT
Found at i:39045315 original size:15 final size:15
Alignment explanation
Indices: 39045295--39045324 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39045285 TGGTTCATTT
39045295 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
39045310 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
39045325 AATTTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:39045334 original size:21 final size:21
Alignment explanation
Indices: 39045308--39045417 Score: 184
Period size: 21 Copynumber: 5.2 Consensus size: 21
39045298 TTGGTTCAAA
39045308 TGGGTTTGGTTTAAATGAATT
1 TGGGTTTGGTTTAAATGAATT
*
39045329 TGGGTTTGGTTTAAATGAATG
1 TGGGTTTGGTTTAAATGAATT
39045350 TGGGTTTGGTTTAAATGAATT
1 TGGGTTTGGTTTAAATGAATT
*
39045371 TGGGTTTGGTTTAAATGAATG
1 TGGGTTTGGTTTAAATGAATT
*
39045392 TGGGTTTGGTTTAAATAGGATT
1 TGGGTTTGGTTTAAAT-GAATT
39045414 TGGG
1 TGGG
39045418 CTTAATGGGT
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
21 76 0.92
22 7 0.08
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.45
Consensus pattern (21 bp):
TGGGTTTGGTTTAAATGAATT
Found at i:39045820 original size:11 final size:11
Alignment explanation
Indices: 39045787--39045861 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
39045777 AAGTGTGATT
*
39045787 AAAAGAGGAAG
1 AAAAGAGAAAG
*
39045798 AAAATAGAAAAG
1 AAAAGAG-AAAG
39045810 AAAAGAGAAAG
1 AAAAGAGAAAG
39045821 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* *
39045833 AATGAGAAAAAG
1 AA-AAGAGAAAG
39045845 AAAAGAGAAAG
1 AAAAGAGAAAG
*
39045856 GAAAGA
1 AAAAGA
39045862 TGAGAGGCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 30 0.59
12 17 0.33
13 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.05
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:39045829 original size:23 final size:23
Alignment explanation
Indices: 39045787--39045859 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
39045777 AAGTGTGATT
*
39045787 AAAAGAGGAAGAAAATAGAAAAG
1 AAAAGAGAAAGAAAATAGAAAAG
*
39045810 AAAAGAGAAAG-AAATAAGAAATG
1 AAAAGAGAAAGAAAAT-AGAAAAG
* * * *
39045833 AATGAGAAAAAGAAAAGAGAAAGG
1 AA-AAGAGAAAGAAAATAGAAAAG
39045857 AAA
1 AAA
39045860 GATGAGAGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
22 4 0.10
23 18 0.45
24 15 0.38
25 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAAGAGAAAGAAAATAGAAAAG
Found at i:39051253 original size:3 final size:3
Alignment explanation
Indices: 39051245--39051274 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
39051235 TACATCCCAA
39051245 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
39051275 GAATAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:39052345 original size:20 final size:20
Alignment explanation
Indices: 39052320--39052375 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
39052310 GTTTTTCGAA
39052320 AAAGTCAACGGTCAACGATC
1 AAAGTCAACGGTCAACGATC
*
39052340 AAAGTCAACGGTCAACGGTC
1 AAAGTCAACGGTCAACGATC
* *
39052360 AACGGTCAACGATCAA
1 AA-AGTCAACGGTCAA
39052376 TCAACACCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.14
Consensus pattern (20 bp):
AAAGTCAACGGTCAACGATC
Found at i:39052394 original size:7 final size:7
Alignment explanation
Indices: 39052323--39052375 Score: 72
Period size: 7 Copynumber: 7.7 Consensus size: 7
39052313 TTTCGAAAAA
39052323 GTCAACG
1 GTCAACG
39052330 GTCAACG
1 GTCAACG
* *
39052337 ATCAA-A
1 GTCAACG
39052343 GTCAACG
1 GTCAACG
39052350 GTCAACG
1 GTCAACG
39052357 GTCAACG
1 GTCAACG
39052364 GTCAACG
1 GTCAACG
*
39052371 ATCAA
1 GTCAA
39052376 TCAACACCGG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
6 4 0.10
7 36 0.90
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:39052400 original size:21 final size:21
Alignment explanation
Indices: 39052362--39052430 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
39052352 CAACGGTCAA
* * *
39052362 CGGTCAACGATCAATCAACAC
1 CGGTCAACGGTCAGTCAACAT
* *
39052383 CGGTCAACGGTCGGTCAACGT
1 CGGTCAACGGTCAGTCAACAT
*
39052404 CGGTCAAC-GCCAGTCAACAT
1 CGGTCAACGGTCAGTCAACAT
39052424 CGGTCAA
1 CGGTCAA
39052431 TGGTTTGACT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.29, C:0.32, G:0.23, T:0.16
Consensus pattern (21 bp):
CGGTCAACGGTCAGTCAACAT
Found at i:39052405 original size:10 final size:10
Alignment explanation
Indices: 39052383--39052430 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
39052373 CAATCAACAC
39052383 CGGTCAACGGT
1 CGGTCAAC-GT
39052394 CGGTCAACGT
1 CGGTCAACGT
*
39052404 CGGTCAACGC
1 CGGTCAACGT
* *
39052414 CAGTCAACAT
1 CGGTCAACGT
39052424 CGGTCAA
1 CGGTCAA
39052431 TGGTTTGACT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 24 0.75
11 8 0.25
ACGTcount: A:0.25, C:0.31, G:0.27, T:0.17
Consensus pattern (10 bp):
CGGTCAACGT
Found at i:39052487 original size:15 final size:15
Alignment explanation
Indices: 39052467--39052496 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39052457 TGGTTCATTT
39052467 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
39052482 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
39052497 AATTTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:39052506 original size:21 final size:21
Alignment explanation
Indices: 39052480--39052589 Score: 184
Period size: 21 Copynumber: 5.2 Consensus size: 21
39052470 TTGGTTCAAA
39052480 TGGGTTTGGTTTAAATGAATT
1 TGGGTTTGGTTTAAATGAATT
*
39052501 TGGGTTTGGTTTAAATGAATG
1 TGGGTTTGGTTTAAATGAATT
39052522 TGGGTTTGGTTTAAATGAATT
1 TGGGTTTGGTTTAAATGAATT
*
39052543 TGGGTTTGGTTTAAATGAATG
1 TGGGTTTGGTTTAAATGAATT
*
39052564 TGGGTTTGGTTTAAATAGGATT
1 TGGGTTTGGTTTAAAT-GAATT
39052586 TGGG
1 TGGG
39052590 CTTAATGGGT
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
21 76 0.92
22 7 0.08
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.45
Consensus pattern (21 bp):
TGGGTTTGGTTTAAATGAATT
Found at i:39052992 original size:11 final size:11
Alignment explanation
Indices: 39052959--39053033 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
39052949 AAGTGTGATT
*
39052959 AAAAGAGGAAG
1 AAAAGAGAAAG
*
39052970 AAAATAGAAAAG
1 AAAAGAG-AAAG
39052982 AAAAGAGAAAG
1 AAAAGAGAAAG
39052993 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* *
39053005 AATGAGAAAAAG
1 AA-AAGAGAAAG
39053017 AAAAGAGAAAG
1 AAAAGAGAAAG
*
39053028 GAAAGA
1 AAAAGA
39053034 TGAGAGGCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 30 0.59
12 17 0.33
13 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.05
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:39053001 original size:23 final size:23
Alignment explanation
Indices: 39052959--39053031 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
39052949 AAGTGTGATT
*
39052959 AAAAGAGGAAGAAAATAGAAAAG
1 AAAAGAGAAAGAAAATAGAAAAG
*
39052982 AAAAGAGAAAG-AAATAAGAAATG
1 AAAAGAGAAAGAAAAT-AGAAAAG
* * * *
39053005 AATGAGAAAAAGAAAAGAGAAAGG
1 AA-AAGAGAAAGAAAATAGAAAAG
39053029 AAA
1 AAA
39053032 GATGAGAGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
22 4 0.10
23 18 0.45
24 15 0.38
25 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAAGAGAAAGAAAATAGAAAAG
Found at i:39058808 original size:59 final size:59
Alignment explanation
Indices: 39058740--39058858 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
39058730 GAAGTAAGAG
* *
39058740 AGAAAAACAAATGTTAAAATACTTGGGAGGTCTTTATATTATAGGGATTAGACTAAATT
1 AGAAAAACAAAGGTTAAAATACTTGGGAGGTCTCTATATTATAGGGATTAGACTAAATT
39058799 AGAAAAACAAAGGTTAAAATACTTGGGAGGTCTCTATATTATAGGGATTAGACTAAATT
1 AGAAAAACAAAGGTTAAAATACTTGGGAGGTCTCTATATTATAGGGATTAGACTAAATT
39058858 A
1 A
39058859 ATCCCTCTAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.43, C:0.08, G:0.19, T:0.30
Consensus pattern (59 bp):
AGAAAAACAAAGGTTAAAATACTTGGGAGGTCTCTATATTATAGGGATTAGACTAAATT
Found at i:39060844 original size:19 final size:20
Alignment explanation
Indices: 39060808--39060846 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39060798 TTTAATTTTG
* *
39060808 AGCTTTTTTTATTATTTAAA
1 AGCTTTTATAATTATTTAAA
39060828 AGCTTTTATAATT-TTTAAA
1 AGCTTTTATAATTATTTAAA
39060847 TTATTTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (20 bp):
AGCTTTTATAATTATTTAAA
Found at i:39062738 original size:21 final size:22
Alignment explanation
Indices: 39062693--39062740 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
39062683 ACATAATAAT
* *
39062693 AAAATGACAGCAAAACATCATC
1 AAAATGACAGCAAAACAACAAC
*
39062715 AAAATGGCAGC-AAACAACAAC
1 AAAATGACAGCAAAACAACAAC
39062736 AAAAT
1 AAAAT
39062741 AGTAGTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.58, C:0.21, G:0.10, T:0.10
Consensus pattern (22 bp):
AAAATGACAGCAAAACAACAAC
Found at i:39063462 original size:21 final size:22
Alignment explanation
Indices: 39063414--39063473 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
39063404 CCAATATAAT
39063414 AACAAAATGACAGCAAAGCAAC
1 AACAAAATGACAGCAAAGCAAC
* *
39063436 ATCAAAATGGCAGCAAA-CAAC
1 AACAAAATGACAGCAAAGCAAC
* *
39063457 AACAAAATAACAACAAA
1 AACAAAATGACAGCAAA
39063474 ATAGTAGTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.62, C:0.22, G:0.10, T:0.07
Consensus pattern (22 bp):
AACAAAATGACAGCAAAGCAAC
Found at i:39066437 original size:2 final size:2
Alignment explanation
Indices: 39066430--39066455 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39066420 TATTCGAGAC
39066430 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
39066456 ATGCTTTTTA
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):
TA
Found at i:39069799 original size:24 final size:24
Alignment explanation
Indices: 39069767--39069813 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
39069757 TGACTCAAAA
*
39069767 AAATAAACAGAATTTAATTGAAAC
1 AAATAAACAGAATTTAACTGAAAC
*
39069791 AAATAAACAGAGTTTAACTGAAA
1 AAATAAACAGAATTTAACTGAAA
39069814 GATTATTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.23
Consensus pattern (24 bp):
AAATAAACAGAATTTAACTGAAAC
Found at i:39071952 original size:23 final size:21
Alignment explanation
Indices: 39071911--39071953 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39071901 TAAAAGTTTA
*
39071911 CAAATATAAATATAATATAAT
1 CAAATATAAATACAATATAAT
39071932 CAAATATATAATACAATTATAA
1 CAAATATA-AATACAA-TATAA
39071954 ACACACATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 6 0.32
23 5 0.26
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
CAAATATAAATACAATATAAT
Found at i:39075157 original size:18 final size:18
Alignment explanation
Indices: 39075128--39075197 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 18
39075118 GATTCCAAAA
39075128 TTATTATTTTATAAAATTT
1 TTATT-TTTTATAAAATTT
** *
39075147 TTATTTTTTATGTATTTT
1 TTATTTTTTATAAAATTT
* *
39075165 TTATTTATTAAAAAATTT
1 TTATTTTTTATAAAATTT
*
39075183 ATATTTTTTA-AAAAT
1 TTATTTTTTATAAAAT
39075198 AAAAATTTTA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
17 5 0.12
18 31 0.76
19 5 0.12
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (18 bp):
TTATTTTTTATAAAATTT
Found at i:39075200 original size:24 final size:24
Alignment explanation
Indices: 39075173--39075222 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
39075163 TTTTATTTAT
* *
39075173 TAAAAAATTTATATTTTTTAAAAA
1 TAAAAAATTTAGAGTTTTTAAAAA
* *
39075197 TAAAAATTTTAGAGTTTTTATAAA
1 TAAAAAATTTAGAGTTTTTAAAAA
39075221 TA
1 TA
39075223 TTTTGAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
TAAAAAATTTAGAGTTTTTAAAAA
Found at i:39075245 original size:19 final size:20
Alignment explanation
Indices: 39075221--39075265 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
39075211 TTTTTATAAA
*
39075221 TATTTTGAA-ATTTAAAAAT
1 TATTTTCAATATTTAAAAAT
* *
39075240 TATTTTCAATTTTTGAAAAT
1 TATTTTCAATATTTAAAAAT
39075260 TATTTT
1 TATTTT
39075266 AATTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTCAATATTTAAAAAT
Found at i:39075273 original size:20 final size:20
Alignment explanation
Indices: 39075235--39075272 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39075225 TTGAAATTTA
39075235 AAAATTATTTTCAATTTTTG
1 AAAATTATTTTCAATTTTTG
39075255 AAAATTATTTT-AATTTTT
1 AAAATTATTTTCAATTTTT
39075273 TTTGTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (20 bp):
AAAATTATTTTCAATTTTTG
Found at i:39077668 original size:22 final size:24
Alignment explanation
Indices: 39077623--39077695 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 24
39077613 AATCCAAATT
* *
39077623 AAATTGTAT-TTTTTATGATATTAA
1 AAATT-TATATTTTTATAATTTTAA
*
39077647 AAATTTA-A-TTTTATTATTTTAA
1 AAATTTATATTTTTATAATTTTAA
** *
39077669 TGATTTATATTTTTATAATTTTTA
1 AAATTTATATTTTTATAATTTTAA
39077693 AAA
1 AAA
39077696 GATAAAATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
22 17 0.45
23 3 0.08
24 18 0.47
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (24 bp):
AAATTTATATTTTTATAATTTTAA
Found at i:39077743 original size:30 final size:29
Alignment explanation
Indices: 39077674--39077753 Score: 74
Period size: 30 Copynumber: 2.7 Consensus size: 29
39077664 TTTAATGATT
* *
39077674 TATATTTTTATAATTTTTAAAAGATAAAA
1 TATAATTTTATTATTTTTAAAAGATAAAA
* *
39077703 T-TAAATTTTTATTATTTTTAAAGGGTTAAAA
1 TAT-AA-TTTTATTATTTTTAAA-AGATAAAA
39077734 TATAATTTTATT-TTTATTAA
1 TATAATTTTATTATTT-TTAA
39077754 TTTAAAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
28 1 0.02
29 5 0.12
30 26 0.62
31 9 0.21
32 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (29 bp):
TATAATTTTATTATTTTTAAAAGATAAAA
Found at i:39083012 original size:46 final size:46
Alignment explanation
Indices: 39082943--39083045 Score: 156
Period size: 46 Copynumber: 2.2 Consensus size: 46
39082933 TCCAGAGTGT
*
39082943 ATATAAATTGAATTGAACGTTATAAGGAAATGGG-TGTTTGTTTGCC
1 ATATAAATTGAATTAAACGTTATAAGGAAATGGGAT-TTTGTTTGCC
*
39082989 ATATAAATTGAATTAAATC-TTATAAGGAAATGGGATTTTGTTTGCT
1 ATATAAATTGAATTAAA-CGTTATAAGGAAATGGGATTTTGTTTGCC
39083035 ATATAAATTGA
1 ATATAAATTGA
39083046 TTTGATTTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
46 51 0.96
47 2 0.04
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (46 bp):
ATATAAATTGAATTAAACGTTATAAGGAAATGGGATTTTGTTTGCC
Found at i:39087920 original size:227 final size:227
Alignment explanation
Indices: 39087525--39087986 Score: 924
Period size: 227 Copynumber: 2.0 Consensus size: 227
39087515 GTTGTTTAAT
39087525 ATATGAATTTTGATTTGATATAAAAATACATCTTTTGGCGTATAGAGTGGGCGGATACAATTATG
1 ATATGAATTTTGATTTGATATAAAAATACATCTTTTGGCGTATAGAGTGGGCGGATACAATTATG
39087590 TATTTAAGTCAATGAAGATTCCATGTCAAATTGCAAGGTTAGTTAGAATAAAATTTGGGCCAAAT
66 TATTTAAGTCAATGAAGATTCCATGTCAAATTGCAAGGTTAGTTAGAATAAAATTTGGGCCAAAT
39087655 AAATTGATATAGGGGGTATGAGTTCACATAAAAGAATACTTTAACTGTGCTACTCTACAAGTTAA
131 AAATTGATATAGGGGGTATGAGTTCACATAAAAGAATACTTTAACTGTGCTACTCTACAAGTTAA
39087720 ATCGCAAGGTAAACTGATTAGGGAACTATTGA
196 ATCGCAAGGTAAACTGATTAGGGAACTATTGA
39087752 ATATGAATTTTGATTTGATATAAAAATACATCTTTTGGCGTATAGAGTGGGCGGATACAATTATG
1 ATATGAATTTTGATTTGATATAAAAATACATCTTTTGGCGTATAGAGTGGGCGGATACAATTATG
39087817 TATTTAAGTCAATGAAGATTCCATGTCAAATTGCAAGGTTAGTTAGAATAAAATTTGGGCCAAAT
66 TATTTAAGTCAATGAAGATTCCATGTCAAATTGCAAGGTTAGTTAGAATAAAATTTGGGCCAAAT
39087882 AAATTGATATAGGGGGTATGAGTTCACATAAAAGAATACTTTAACTGTGCTACTCTACAAGTTAA
131 AAATTGATATAGGGGGTATGAGTTCACATAAAAGAATACTTTAACTGTGCTACTCTACAAGTTAA
39087947 ATCGCAAGGTAAACTGATTAGGGAACTATTGA
196 ATCGCAAGGTAAACTGATTAGGGAACTATTGA
39087979 ATATGAAT
1 ATATGAAT
39087987 CAGAATAGTT
Statistics
Matches: 235, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
227 235 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (227 bp):
ATATGAATTTTGATTTGATATAAAAATACATCTTTTGGCGTATAGAGTGGGCGGATACAATTATG
TATTTAAGTCAATGAAGATTCCATGTCAAATTGCAAGGTTAGTTAGAATAAAATTTGGGCCAAAT
AAATTGATATAGGGGGTATGAGTTCACATAAAAGAATACTTTAACTGTGCTACTCTACAAGTTAA
ATCGCAAGGTAAACTGATTAGGGAACTATTGA
Found at i:39100156 original size:15 final size:16
Alignment explanation
Indices: 39100130--39100159 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39100120 GAAAGGGAAG
39100130 AAAAGCAATATATATC
1 AAAAGCAATATATATC
39100146 AAAAG-AATATATAT
1 AAAAGCAATATATAT
39100160 AATAATGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (16 bp):
AAAAGCAATATATATC
Found at i:39112661 original size:20 final size:20
Alignment explanation
Indices: 39112628--39112699 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 20
39112618 AAAAATATCA
* *
39112628 ATTTACCAATATTTATAAG-
1 ATTTATCAAAATTTATAAGC
*
39112647 ATTTTATCAAAATTTCTAAGC
1 A-TTTATCAAAATTTATAAGC
* * * *
39112668 ATTTATCAATATATCTAAGG
1 ATTTATCAAAATTTATAAGC
*
39112688 ATTTACCAAAAT
1 ATTTATCAAAAT
39112700 CTTTATCGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (20 bp):
ATTTATCAAAATTTATAAGC
Found at i:39112678 original size:40 final size:40
Alignment explanation
Indices: 39112628--39112722 Score: 97
Period size: 40 Copynumber: 2.4 Consensus size: 40
39112618 AAAAATATCA
* *
39112628 ATTTACCAATATTTATAA-GATTTTATCAAAAT-TTCTAAGC-
1 ATTTATCAATATTTATAAGGA-TTTACCAAAATCTT-T-AGCG
* * *
39112668 ATTTATCAATATATCTAAGGATTTACCAAAATCTTTATCG
1 ATTTATCAATATTTATAAGGATTTACCAAAATCTTTAGCG
39112708 ATTTATCAATATTTA
1 ATTTATCAATATTTA
39112723 CGGAGACTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
39 2 0.04
40 39 0.87
41 4 0.09
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.43
Consensus pattern (40 bp):
ATTTATCAATATTTATAAGGATTTACCAAAATCTTTAGCG
Found at i:39112879 original size:20 final size:20
Alignment explanation
Indices: 39112856--39112909 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
39112846 ATTTCTATCG
* *
39112856 TTTTATTAATATTTATGAGA
1 TTTTATCAATATTTATAAGA
* *
39112876 TTTTACCAAAATTTATAAGA
1 TTTTATCAATATTTATAAGA
39112896 TTTTATCAATATTT
1 TTTTATCAATATTT
39112910 TCAAAATTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTATCAATATTTATAAGA
Found at i:39112969 original size:147 final size:148
Alignment explanation
Indices: 39112694--39112970 Score: 328
Period size: 147 Copynumber: 1.9 Consensus size: 148
39112684 AAGGATTTAC
* * * *
39112694 CAAAATCTTTATCGATTTATCAATATTTACGGAGACTTTACTAAATTTTTTATGATTTTACCAAT
1 CAAAATCTTTATCGATTTATCAATATTTACGGAGACTTTACCAAAATTTATAAGATTTTACCAAT
* * * * *
39112759 ATTTTCAAATTTTCTAAGCCCCATACAAAGTCTTGACAATTACCAAAATTTCTATCGTCTTACCA
66 ATTTTCAAAATTTCCAAGCCCCATACAAAGTCTTAACAATTACAAAAATTTCTATCGACTTACCA
39112824 AAATGTATAATGAGTTAA
131 AAATGTATAATGAGTTAA
* * * * *
39112842 CAAAAT-TTCTATCGTTTTATTAATATTTA-TGAGATTTTACCAAAATTTATAAGATTTTATCAA
1 CAAAATCTT-TATCGATTTATCAATATTTACGGAGACTTTACCAAAATTTATAAGATTTTACCAA
* * * * *
39112905 TATTTTCAAAATTTCCAATCCCTATGCCAAGTCTTAATAATTATCAAAAATTT-TAT-GACTTTA
65 TATTTTCAAAATTTCCAAGCCCCATACAAAGTCTTAACAATTA-CAAAAATTTCTATCGAC-TTA
39112968 CCA
128 CCA
39112971 TAATATTTAA
Statistics
Matches: 107, Mismatches: 19, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
146 2 0.02
147 73 0.68
148 32 0.30
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (148 bp):
CAAAATCTTTATCGATTTATCAATATTTACGGAGACTTTACCAAAATTTATAAGATTTTACCAAT
ATTTTCAAAATTTCCAAGCCCCATACAAAGTCTTAACAATTACAAAAATTTCTATCGACTTACCA
AAATGTATAATGAGTTAA
Found at i:39112983 original size:21 final size:21
Alignment explanation
Indices: 39112954--39113020 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 21
39112944 ATTATCAAAA
*
39112954 ATTTTATGACTTTACC-ATAAT
1 ATTTAATGACTTTACCAAT-AT
*
39112975 ATTTAATGA-TTTACTAATAT
1 ATTTAATGACTTTACCAATAT
* *
39112995 ATTTAACGAC-TTACTAATAT
1 ATTTAATGACTTTACCAATAT
*
39113015 TTTTAA
1 ATTTAA
39113021 GGATTTATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 30 0.75
21 10 0.25
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.48
Consensus pattern (21 bp):
ATTTAATGACTTTACCAATAT
Found at i:39112996 original size:20 final size:20
Alignment explanation
Indices: 39112973--39113128 Score: 75
Period size: 20 Copynumber: 7.8 Consensus size: 20
39112963 CTTTACCATA
*
39112973 ATATTTAATGATTTACTAAT
1 ATATTTAACGATTTACTAAT
*
39112993 ATATTTAACGACTTACTAAT
1 ATATTTAACGATTTACTAAT
* * *
39113013 ATTTTTAAGGATTTA-TCAAA
1 ATATTTAACGATTTACT-AAT
* *
39113033 ATATCTATCGATTT-CTGAAT
1 ATATTTAACGATTTACT-AAT
* * * * * *
39113053 AAATCTACCGGTTTACCAAA
1 ATATTTAACGATTTACTAAT
* * *
39113073 ATATCTAACGATTTACCAAA
1 ATATTTAACGATTTACTAAT
* * *
39113093 AT-TTTAAAGGATTTACCAAA
1 ATATTT-AACGATTTACTAAT
* *
39113113 ATATCTAACAATTTAC
1 ATATTTAACGATTTAC
39113129 CAAAATTTTT
Statistics
Matches: 106, Mismatches: 25, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
19 3 0.03
20 100 0.94
21 3 0.03
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.38
Consensus pattern (20 bp):
ATATTTAACGATTTACTAAT
Found at i:39113108 original size:40 final size:40
Alignment explanation
Indices: 39112964--39113191 Score: 183
Period size: 40 Copynumber: 5.7 Consensus size: 40
39112954 ATTTTATGAC
* * * * * *
39112964 TTTACCATAATATTTAATGATTTACTAATATATTTAACGA
1 TTTACCAAAATTTTTAAGGATTTACCAAAATATCTAACGA
* * * * *
39113004 CTTACTAATATTTTTAAGGATTTATCAAAATATCTATCGA
1 TTTACCAAAATTTTTAAGGATTTACCAAAATATCTAACGA
* * * *
39113044 TTT-CTGAATAA-ATCTACCGG-TTTACCAAAATATCTAACGA
1 TTTAC-CAA-AATTTTTA-AGGATTTACCAAAATATCTAACGA
* *
39113084 TTTACCAAAATTTTAAAGGATTTACCAAAATATCTAACAA
1 TTTACCAAAATTTTTAAGGATTTACCAAAATATCTAACGA
* * * * *
39113124 TTTACCAAAATTTTTAATGTTTTACCAAAATTTCTAATGT
1 TTTACCAAAATTTTTAAGGATTTACCAAAATATCTAACGA
* **
39113164 TTTACTAAAATTTTTATCGATTTACCAA
1 TTTACCAAAATTTTTAAGGATTTACCAA
39113192 TATTTATGAG
Statistics
Matches: 146, Mismatches: 36, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
39 5 0.03
40 137 0.94
41 4 0.03
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (40 bp):
TTTACCAAAATTTTTAAGGATTTACCAAAATATCTAACGA
Found at i:39113147 original size:20 final size:20
Alignment explanation
Indices: 39113064--39113196 Score: 133
Period size: 20 Copynumber: 6.7 Consensus size: 20
39113054 AATCTACCGG
*
39113064 TTTACCAAAATATCTAACGA
1 TTTACCAAAATTTCTAACGA
*
39113084 TTTACCAAAATTT-TAAAGGA
1 TTTACCAAAATTTCT-AACGA
* *
39113104 TTTACCAAAATATCTAACAA
1 TTTACCAAAATTTCTAACGA
* * *
39113124 TTTACCAAAATTTTTAATGT
1 TTTACCAAAATTTCTAACGA
* *
39113144 TTTACCAAAATTTCTAATGT
1 TTTACCAAAATTTCTAACGA
* * *
39113164 TTTACTAAAATTTTTATCGA
1 TTTACCAAAATTTCTAACGA
*
39113184 TTTACCAATATTT
1 TTTACCAAAATTT
39113197 ATGAGACTTT
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
19 1 0.01
20 91 0.98
21 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.41
Consensus pattern (20 bp):
TTTACCAAAATTTCTAACGA
Found at i:39113245 original size:20 final size:20
Alignment explanation
Indices: 39113204--39113245 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
39113194 TTTATGAGAC
* *
39113204 TTTATCAAAATTTTCAAGTT
1 TTTATCAAAATTTCCAAATT
39113224 TTTA-CAAATATTTCCAAATT
1 TTTATCAAA-ATTTCCAAATT
39113244 TT
1 TT
39113246 CTAAGCCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTATCAAAATTTCCAAATT
Found at i:39113373 original size:20 final size:20
Alignment explanation
Indices: 39113323--39113381 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
39113313 TTTCAATATT
* *
39113323 TCTAAGAATTTATCAATATA
1 TCTAACAATTTATCAAAATA
* *
39113343 TCTTATC-ATTTGTCAAAATA
1 TC-TAACAATTTATCAAAATA
*
39113363 TCTAACAATTTACCAAAAT
1 TCTAACAATTTATCAAAAT
39113382 TTCCATCCAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 3 0.10
20 25 0.83
21 2 0.07
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (20 bp):
TCTAACAATTTATCAAAATA
Found at i:39124746 original size:24 final size:24
Alignment explanation
Indices: 39124685--39124749 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
39124675 TGAGAAATAA
39124685 TATTTCAGTTAAACTCTATTTATT
1 TATTTCAGTTAAACTCTATTTATT
* *
39124709 TGTTTCAATTAAACTCTATTTATT
1 TATTTCAGTTAAACTCTATTTATT
* *
39124733 TATTTGAGTCAAACTCT
1 TATTTCAGTTAAACTCT
39124750 TATTAGTCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (24 bp):
TATTTCAGTTAAACTCTATTTATT
Found at i:39126700 original size:24 final size:24
Alignment explanation
Indices: 39126672--39126734 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
39126662 AGAAATAATC
*
39126672 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
*
39126696 TTTCAATTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
39126720 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
39126735 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTG
Found at i:39128965 original size:12 final size:12
Alignment explanation
Indices: 39128948--39129000 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
39128938 AATAAAATAC
39128948 TATTAAAATAAA
1 TATTAAAATAAA
*
39128960 TATTAAATTAAA
1 TATTAAAATAAA
*
39128972 T-TTAATATTAAA
1 TATTAA-AATAAA
39128984 TAATTAAAAT-AA
1 T-ATTAAAATAAA
39128996 TATTA
1 TATTA
39129001 TTTTTGAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
11 8 0.22
12 22 0.61
13 2 0.06
14 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TATTAAAATAAA
Found at i:39128971 original size:17 final size:17
Alignment explanation
Indices: 39128949--39128984 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39128939 ATAAAATACT
39128949 ATTAAAATAAATATTAA
1 ATTAAAATAAATATTAA
* *
39128966 ATTAAATTTAATATTAA
1 ATTAAAATAAATATTAA
39128983 AT
1 AT
39128985 AATTAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTAAAATAAATATTAA
Found at i:39138786 original size:2 final size:2
Alignment explanation
Indices: 39138781--39138816 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
39138771 CATACATATA
*
39138781 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
39138817 CATTCCTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:39146853 original size:22 final size:21
Alignment explanation
Indices: 39146796--39146854 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
39146786 TACGCTAAAT
*
39146796 TAAAAAAAATAACTCTTAATT
1 TAAAAAAAATAACTCTTAATG
* *
39146817 TAAAGAAAATAAACT-TAGTTATG
1 TAAAAAAAAT-AACTCT--TAATG
39146840 TAAAAAAAATAACTC
1 TAAAAAAAATAACTC
39146855 AATAAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 10 0.33
22 8 0.27
23 12 0.40
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (21 bp):
TAAAAAAAATAACTCTTAATG
Found at i:39147314 original size:19 final size:19
Alignment explanation
Indices: 39147273--39147312 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
39147263 ATAAAAACAT
39147273 AATTTTTAAAAATATATAA
1 AATTTTTAAAAATATATAA
* *
39147292 AATTATTTAAATATGTATAA
1 AATT-TTTAAAAATATATAA
39147312 A
1 A
39147313 TTTAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
AATTTTTAAAAATATATAA
Found at i:39156017 original size:17 final size:18
Alignment explanation
Indices: 39155971--39156017 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
39155961 CAAAGGTTTA
39155971 AAAGAATTTAAAAGGTAACT
1 AAAG-ATTTAAAA-GTAACT
*
39155991 -AAGTTTTAAAA-TAACT
1 AAAGATTTAAAAGTAACT
39156007 AAAGATTTAAA
1 AAAGATTTAAA
39156018 GACAGATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 5 0.21
17 9 0.38
18 7 0.29
19 3 0.12
ACGTcount: A:0.55, C:0.04, G:0.11, T:0.30
Consensus pattern (18 bp):
AAAGATTTAAAAGTAACT
Found at i:39158580 original size:6 final size:6
Alignment explanation
Indices: 39158569--39158607 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
39158559 TGATCAAAAT
* * *
39158569 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
39158608 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:39159754 original size:13 final size:13
Alignment explanation
Indices: 39159689--39159754 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 13
39159679 ATCATGCTTC
*
39159689 TTTGTTTTTTTCCA
1 TTTGTTTTTTT-CT
39159703 TTTGTTTTTTTCT
1 TTTGTTTTTTTCT
* * *
39159716 CTTGTCGTCTTCTGCT
1 -TT-T-GTTTTTTTCT
39159732 TTTGTCTTTTTTCT
1 TTTGT-TTTTTTCT
39159746 TTTGTTTTT
1 TTTGTTTTT
39159755 ACAGGCACCT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
13 7 0.17
14 24 0.59
15 3 0.07
16 7 0.17
ACGTcount: A:0.02, C:0.15, G:0.11, T:0.73
Consensus pattern (13 bp):
TTTGTTTTTTTCT
Found at i:39165067 original size:26 final size:26
Alignment explanation
Indices: 39165038--39165116 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
39165028 AATAAAAAGT
39165038 TTGGTATA-CTGTTAAAAATATTGGTA
1 TTGGTATATC-GTTAAAAATATTGGTA
* * * **
39165064 TTGGTATGTCGTTAGAAATTTTAATA
1 TTGGTATATCGTTAAAAATATTGGTA
*
39165090 TTGGTATATCGCTAAAAATATTGGTA
1 TTGGTATATCGTTAAAAATATTGGTA
39165116 T
1 T
39165117 AGCATTAGAA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 40 0.98
27 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (26 bp):
TTGGTATATCGTTAAAAATATTGGTA
Found at i:39165128 original size:20 final size:20
Alignment explanation
Indices: 39165086--39165156 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 20
39165076 TAGAAATTTT
* *
39165086 AATATTGGTATATCGCTAAA
1 AATATTGGTATAGCACTAAA
* *
39165106 AATATTGGTATAGCATTAGA
1 AATATTGGTATAGCACTAAA
* * *
39165126 AATTTTGATATAAC-CGTAAA
1 AATATTGGTATAGCAC-TAAA
39165146 AAT-TTGGTATA
1 AATATTGGTATA
39165157 ACATTTTTTT
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
19 7 0.17
20 33 0.82
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (20 bp):
AATATTGGTATAGCACTAAA
Found at i:39165372 original size:11 final size:11
Alignment explanation
Indices: 39165349--39165411 Score: 81
Period size: 11 Copynumber: 5.5 Consensus size: 11
39165339 TCAAATTTAT
39165349 TTTAATCTTAAA
1 TTTAAT-TTAAA
*
39165361 TTTATTTTAAA
1 TTTAATTTAAA
*
39165372 TTCAATTTAAA
1 TTTAATTTAAA
*
39165383 TTTAAATTTGAA
1 TTT-AATTTAAA
39165395 TTTAATTTAAA
1 TTTAATTTAAA
39165406 TTTAAT
1 TTTAAT
39165412 GTTATTATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
11 29 0.66
12 15 0.34
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:39165408 original size:17 final size:16
Alignment explanation
Indices: 39165359--39165427 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 16
39165349 TTTAATCTTA
* *
39165359 AATTTATTTTAAATTC
1 AATTTAATTTAAATTT
39165375 AATTTAAATTTAAATTT
1 AATTT-AATTTAAATTT
39165392 GAATTTAATTTAAATTT
1 -AATTTAATTTAAATTT
39165409 AATGTT-ATTATAAATTT
1 AAT-TTAATT-TAAATTT
39165426 AA
1 AA
39165428 AAAGAAAGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
16 11 0.23
17 31 0.66
18 5 0.11
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (16 bp):
AATTTAATTTAAATTT
Found at i:39165428 original size:6 final size:6
Alignment explanation
Indices: 39165356--39165410 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
39165346 TATTTTAATC
* * *
39165356 TTAAAT TT-ATT TTAAA- TTCAAT TTAAAT TTAAAT TTGAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
39165401 TTAAAT TTAA
1 TTAAAT TTAA
39165411 TGTTATTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
5 13 0.32
6 28 0.68
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:39165473 original size:14 final size:14
Alignment explanation
Indices: 39165454--39165514 Score: 90
Period size: 14 Copynumber: 4.5 Consensus size: 14
39165444 CATGGCCCAG
39165454 GGCCCAATTACAAT
1 GGCCCAATTACAAT
*
39165468 GGCCCAATTACAAA
1 GGCCCAATTACAAT
*
39165482 GGCCCAATT--AAG
1 GGCCCAATTACAAT
39165494 GGCCCAATTACAAT
1 GGCCCAATTACAAT
39165508 GGCCCAA
1 GGCCCAA
39165515 ATAGGTCCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
12 11 0.26
14 31 0.74
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.16
Consensus pattern (14 bp):
GGCCCAATTACAAT
Found at i:39165503 original size:26 final size:27
Alignment explanation
Indices: 39165454--39165514 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
39165444 CATGGCCCAG
*
39165454 GGCCCAATTACAATGGCCCAATTACAAA
1 GGCCCAATTA-AAGGGCCCAATTACAAA
*
39165482 GGCCCAATT-AAGGGCCCAATTACAAT
1 GGCCCAATTAAAGGGCCCAATTACAAA
39165508 GGCCCAA
1 GGCCCAA
39165515 ATAGGTCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 22 0.71
28 9 0.29
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.16
Consensus pattern (27 bp):
GGCCCAATTAAAGGGCCCAATTACAAA
Found at i:39166136 original size:9 final size:9
Alignment explanation
Indices: 39166110--39166144 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
39166100 TAGCAGAAGC
*
39166110 ATTAATAAC
1 ATTAATAAT
39166119 ATTAATAAT
1 ATTAATAAT
39166128 ATTAATAAT
1 ATTAATAAT
*
39166137 AATAATAA
1 ATTAATAA
39166145 ATATATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (9 bp):
ATTAATAAT
Found at i:39166461 original size:14 final size:14
Alignment explanation
Indices: 39166442--39166469 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39166432 TATGTTGAAA
39166442 ATTTCCAGATCTGG
1 ATTTCCAGATCTGG
39166456 ATTTCCAGATCTGG
1 ATTTCCAGATCTGG
39166470 TTTTGGCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
ATTTCCAGATCTGG
Found at i:39167183 original size:161 final size:163
Alignment explanation
Indices: 39166985--39167297 Score: 506
Period size: 162 Copynumber: 1.9 Consensus size: 163
39166975 TTTTCAATTC
* *
39166985 AGTCCTTTGACTATTTGACTGTACCATAGGCTGCCACGTGTCA-CTTTTTGGATTATTTATGCAT
1 AGTCCTTTGACTATTTGACTGCACCAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTATGCAT
* *
39167049 TTAGTCCTTTTTATTTTTTATTTGTTTTAATTTAATCC-TAAATCAAC-TTTATTTTAATTACGA
66 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTA-TTTAATTACAA
*
39167112 AATTGGCCCAATAATTTTTCAAGGTTTATAAACT
130 AATTGGCCCAAAAATTTTTCAAGGTTTATAAACT
* * *
39167146 AGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATCTTTTTGGATTATTTCTGCAT
1 AGTCCTTTGACTATTTGACTGCACCAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTATGCAT
*
39167211 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACAAA
66 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTATTTAATTACAAA
*
39167276 ATTGGTCCAAAAATTTTTCAAG
131 ATTGGCCCAAAAATTTTTCAAG
39167298 ATTTTCAAAT
Statistics
Matches: 139, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
161 39 0.28
162 57 0.41
163 39 0.28
164 4 0.03
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (163 bp):
AGTCCTTTGACTATTTGACTGCACCAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTATGCAT
TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTATTTAATTACAAA
ATTGGCCCAAAAATTTTTCAAGGTTTATAAACT
Found at i:39167430 original size:30 final size:30
Alignment explanation
Indices: 39167394--39167800 Score: 589
Period size: 30 Copynumber: 13.4 Consensus size: 30
39167384 AAATTATCCA
* **
39167394 AAAATTACATTTTGACCCTAAAACTTCCCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
39167424 AAAATTATATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * *
39167454 AAAATTATATTTTCGACCCCGAAACTTTACC
1 AAAATTACATTTT-GACCCCAAAACTTTTCC
* *
39167485 AAAATTACATTTTGACCCCGAAACTTTACC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
39167515 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
39167545 AAAATTACATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
39167575 AAAATTATATTTTTGACCCCAAAACATTTCC
1 AAAATTACA-TTTTGACCCCAAAACTTTTCC
39167606 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * *
39167636 AAAATTATATTTTTGACCCCGAAACTTTACC
1 AAAATTACA-TTTTGACCCCAAAACTTTTCC
* *
39167667 AAAATTACATTTTAACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
39167697 AAAATTACATTTTGACCCCAAAACTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * *
39167727 AAAATTATATTTTTGACCCCGAAACTTTACC
1 AAAATTACA-TTTTGACCCCAAAACTTTTCC
39167758 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
39167788 AAAATTACATTTT
1 AAAATTACATTTT
39167801 AACCTCGATT
Statistics
Matches: 340, Mismatches: 33, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
30 233 0.69
31 107 0.31
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:39167487 original size:61 final size:60
Alignment explanation
Indices: 39167394--39167800 Score: 589
Period size: 61 Copynumber: 6.7 Consensus size: 60
39167384 AAATTATCCA
* ** *
39167394 AAAATTACATTTTGACCCTAAAACTTCCCCAAAATTATATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
* * * * *
39167454 AAAATTATATTTTCGACCCCGAAACTTTACCAAAATTACATTTTGACCCCGAAACTTTACC
1 AAAATTACATTTT-GACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
*
39167515 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
* *
39167575 AAAATTATATTTTTGACCCCAAAACATTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACA-TTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
* * * * *
39167636 AAAATTATATTTTTGACCCCGAAACTTTACCAAAATTACATTTTAACCCTAAAACTTTTCC
1 AAAATTACA-TTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
* * * *
39167697 AAAATTACATTTTGACCCCAAAACTTTTCTAAAATTATATTTTTGACCCCGAAACTTTACC
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACA-TTTTGACCCCAAAACTTTTCC
39167758 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTT
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTT
39167801 AACCTCGATT
Statistics
Matches: 311, Mismatches: 33, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
60 92 0.30
61 219 0.70
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (60 bp):
AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:39167549 original size:91 final size:91
Alignment explanation
Indices: 39167394--39167800 Score: 654
Period size: 91 Copynumber: 4.5 Consensus size: 91
39167384 AAATTATCCA
* ** *
39167394 AAAATTACATTTTGACCCTAAAACTTCCCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAAT
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAAT
*
39167459 TATATTTTCGACCCCGAAACTTTACC
66 TATATTTTTGACCCCGAAACTTTACC
* *
39167485 AAAATTACATTTTGACCCCGAAACTTTACCAAAATTACATTTTGACCCCAAAACTTTTCCAAAAT
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAAT
* * * *
39167550 TACA-TTTTAACCCCAAAACTTTTCC
66 TATATTTTTGACCCCGAAACTTTACC
* *
39167575 AAAATTATATTTTTGACCCCAAAACATTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAA
1 AAAATTACA-TTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAA
39167640 TTATATTTTTGACCCCGAAACTTTACC
65 TTATATTTTTGACCCCGAAACTTTACC
* * *
39167667 AAAATTACATTTTAACCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCTAAAAT
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAAT
39167732 TATATTTTTGACCCCGAAACTTTACC
66 TATATTTTTGACCCCGAAACTTTACC
39167758 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTT
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTT
39167801 AACCTCGATT
Statistics
Matches: 289, Mismatches: 25, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
90 25 0.09
91 238 0.82
92 26 0.09
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (91 bp):
AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAAT
TATATTTTTGACCCCGAAACTTTACC
Found at i:39167906 original size:58 final size:59
Alignment explanation
Indices: 39167758--39168012 Score: 367
Period size: 58 Copynumber: 4.4 Consensus size: 59
39167748 AAACTTTACC
* * * *
39167758 AAAATTA-CATTTTGA-CCCCAAAACTTTTCCAAAATTACA-TTTTAACCTCGATTTCACCG
1 AAAATTACCATTTT-ACCCCCGAATCTTTT--AAAATTCCATTTTTAACCCCGATTTCACCG
*
39167817 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCATCG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
* * *
39167876 AAAATTACCATTTTACCCCCGAATC-TTTAAAATTCCATTTTTAATCCTGATTTCACCA
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
39167934 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACC-
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
*
39167992 AAAATTACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
39168013 GGTATCCATA
Statistics
Matches: 180, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
58 82 0.46
59 81 0.45
60 17 0.09
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
Found at i:39167944 original size:117 final size:115
Alignment explanation
Indices: 39167788--39168012 Score: 380
Period size: 117 Copynumber: 1.9 Consensus size: 115
39167778 AAACTTTTCC
*
39167788 AAAATTACATTTTAACCTCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTC
1 AAAATTACATTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTC
*
39167853 CATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCCGAATCTTT
66 CATTTTTAACCCCGATTTCA-CCAAAATTACCATTTTACCCCCGAATCTTT
*
39167904 AAAATTCCATTTTTAATCCT-GATTTCACCAAAAATTACCATTTTACCCCCGAATCTTTTAAAAT
1 AAAATTACA-TTTTAA-CCTCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTTTTAAAAT
*
39167968 TCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTGCCCCCG
64 TCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCG
39168013 GGTATCCATA
Statistics
Matches: 103, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
116 29 0.28
117 71 0.69
118 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.36
Consensus pattern (115 bp):
AAAATTACATTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTC
CATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCGAATCTTT
Found at i:39168034 original size:117 final size:117
Alignment explanation
Indices: 39167797--39168047 Score: 355
Period size: 117 Copynumber: 2.1 Consensus size: 117
39167787 CAAAATTACA
*
39167797 TTTTAACCTCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAA
1 TTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAA
* ** *
39167862 CCCCGATTTCATCGAAAATTACCATTTTACCCCCGAATCTTTAAAATTCCAT
66 CCCCGATTTCATCCAAAATTACCATTTTACCCCCGAATCCATAAAATCCCAT
39167914 TTTTAATCCT-GATTTCACCAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTA
1 TTTTAA-CCTCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTA
* * * *
39167978 ACCCCGATTTCA-CCAAAATTACCATTTTGCCCCCGGGTATCCAT-AAGTCCCGT
65 ACCCCGATTTCATCCAAAATTACCATTTTACCCCC--GAATCCATAAAATCCCAT
* *
39168031 TTTTCACCCCGATTTCA
1 TTTTAACCTCGATTTCA
39168048 TCATATATCA
Statistics
Matches: 119, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
116 22 0.18
117 89 0.75
118 8 0.07
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.36
Consensus pattern (117 bp):
TTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAA
CCCCGATTTCATCCAAAATTACCATTTTACCCCCGAATCCATAAAATCCCAT
Found at i:39180175 original size:31 final size:31
Alignment explanation
Indices: 39180071--39180385 Score: 136
Period size: 37 Copynumber: 9.4 Consensus size: 31
39180061 TCTTCATCTC
*
39180071 TGAAATTGAAGTAAGAGCAACATCGTCCCCTT
1 TGAAATTGAAGTAAGAGCAACATCGT-CCCAT
* * *
39180103 TGAAATTGAAGTAGAGTGGATAACAT-GTCTTCATCT
1 TGAAATTGAAGTA-AG-AG-CAACATCGTC-CCA--T
*
39180139 CTGAAATTGAAGTAAGAGCAACATCATCCCAT
1 -TGAAATTGAAGTAAGAGCAACATCGTCCCAT
* * * *
39180171 TGAAATTGGAGTAGAGTGGATAACA-CGTCTTCATCT
1 TGAAATTGAAGTA-AG-AG-CAACATCGTC-CCA--T
*
39180207 CTGAAATTGAAGTAAGAGCAACATCGTCCCCT
1 -TGAAATTGAAGTAAGAGCAACATCGTCCCAT
* * * *
39180239 TGAAATTGGAGTAGAGTGGATAACAT-GTCTTCATCT
1 TGAAATTGAAGTA-AG-AG-CAACATCGTC-CCA--T
* *
39180275 CTGAAATTGAAGTAAGAGCAACATCATCCCCT
1 -TGAAATTGAAGTAAGAGCAACATCGTCCCAT
* * *
39180307 TGAAATTGGAGT-AGAATGGATAACAT-GTCTTCATCT
1 TGAAATTGAAGTAAG-A--G-CAACATCGTC-CCA--T
*
39180343 CTGAAATTGAAGTAAGAGCAACATCGTCCCCT
1 -TGAAATTGAAGTAAGAGCAACATCGTCCCAT
*
39180375 TGAAATGGAAG
1 TGAAATTGAAG
39180386 CAGAGTGGAT
Statistics
Matches: 210, Mismatches: 39, Indels: 69
0.66 0.12 0.22
Matches are distributed among these distances:
30 2 0.01
31 46 0.22
32 21 0.10
33 14 0.07
34 46 0.22
35 20 0.10
36 10 0.05
37 49 0.23
38 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (31 bp):
TGAAATTGAAGTAAGAGCAACATCGTCCCAT
Found at i:39180206 original size:68 final size:68
Alignment explanation
Indices: 39180015--39180449 Score: 728
Period size: 68 Copynumber: 6.4 Consensus size: 68
39180005 TAAGAGCAAC
* * *
39180015 AAGAGCAACGTCGTCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGA
1 AAGAGCAACATCGTCCCCTTGAAATTGGAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGA
39180080 AGT
66 AGT
*
39180083 AAGAGCAACATCGTCCCCTTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTG
1 AAGAGCAACATCGTCCCC-TTGAAATTGGAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTG
39180148 AAGT
65 AAGT
* * *
39180152 AAGAGCAACATCATCCCATTGAAATTGGAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGA
1 AAGAGCAACATCGTCCCCTTGAAATTGGAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGA
39180217 AGT
66 AGT
39180220 AAGAGCAACATCGTCCCCTTGAAATTGGAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGA
1 AAGAGCAACATCGTCCCCTTGAAATTGGAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGA
39180285 AGT
66 AGT
* *
39180288 AAGAGCAACATCATCCCCTTGAAATTGGAGTAGAATGGATAACATGTCTTCATCTCTGAAATTGA
1 AAGAGCAACATCGTCCCCTTGAAATTGGAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGA
39180353 AGT
66 AGT
*
39180356 AAGAGCAACATCGTCCCCTTGAAA-TGGAAGCAGAGTGGATAACATGTCTTCATCTCTGAAATTG
1 AAGAGCAACATCGTCCCCTTGAAATTGG-AGTAGAGTGGATAACATGTCTTCATCTCTGAAATTG
39180420 AAGT
65 AAGT
* * *
39180424 AAGAGCAACGTCATCCTCTTGAAATT
1 AAGAGCAACATCGTCCCCTTGAAATT
39180450 AAAGTAAAGT
Statistics
Matches: 347, Mismatches: 17, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
67 3 0.01
68 278 0.80
69 66 0.19
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (68 bp):
AAGAGCAACATCGTCCCCTTGAAATTGGAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGA
AGT
Found at i:39180410 original size:204 final size:205
Alignment explanation
Indices: 39179943--39180465 Score: 798
Period size: 204 Copynumber: 2.5 Consensus size: 205
39179933 TTGCAGATCT
*
39179943 CAACATCGTCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
1 CAACATCGTCCCCTTGAAATGGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
39180008 GAGCAACAAGAGCAACGTCGTCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTG
66 GAG---C-A-A-C-A--TCGTCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTG
* *
39180073 AAATTGAAGTAAGAGCAACATCGTCCCCTTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATC
122 AAATTGAAGTAAGAGCAACATCATCCCCTTTGAAATTGAAGTAGAATGGATAACATGTCTTCATC
39180138 TCTGAAATTGAAGTAAGAG
187 TCTGAAATTGAAGTAAGAG
* * *
39180157 CAACATCATCCCATTGAAATTGG-AGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTA
1 CAACATCGTCCCCTTGAAA-TGGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTA
* *
39180221 AGAGCAACATCGTCCCCTTGAAATTGGAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAA
65 AGAGCAACATCGTCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAA
*
39180286 GTAAGAGCAACATCATCCCC-TTGAAATTGGAGTAGAATGGATAACATGTCTTCATCTCTGAAAT
130 GTAAGAGCAACATCATCCCCTTTGAAATTGAAGTAGAATGGATAACATGTCTTCATCTCTGAAAT
39180350 TGAAGTAAGAG
195 TGAAGTAAGAG
*
39180361 CAACATCGTCCCCTTGAAATGGAAGCAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
1 CAACATCGTCCCCTTGAAATGGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
* * * * *
39180426 GAGCAACGTCATCCTCTTGAAATTAAAGTAAAGTTGGATA
66 GAGCAACATCGTCCCCTTGAAATTGAAGTAGAG-TGGATA
39180466 GCAAAGTCTT
Statistics
Matches: 287, Mismatches: 19, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
203 3 0.01
204 137 0.48
205 79 0.28
207 1 0.00
208 1 0.00
209 1 0.00
210 1 0.00
211 1 0.00
214 61 0.21
215 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (205 bp):
CAACATCGTCCCCTTGAAATGGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
GAGCAACATCGTCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAG
TAAGAGCAACATCATCCCCTTTGAAATTGAAGTAGAATGGATAACATGTCTTCATCTCTGAAATT
GAAGTAAGAG
Found at i:39180791 original size:11 final size:11
Alignment explanation
Indices: 39180768--39180830 Score: 81
Period size: 11 Copynumber: 5.5 Consensus size: 11
39180758 TAAAATTTAT
39180768 TTTAATCTTAAA
1 TTTAAT-TTAAA
*
39180780 TTTATTTTAAA
1 TTTAATTTAAA
*
39180791 TTCAATTTAAA
1 TTTAATTTAAA
*
39180802 TTTAAATTTGAA
1 TTT-AATTTAAA
39180814 TTTAATTTAAA
1 TTTAATTTAAA
39180825 TTTAAT
1 TTTAAT
39180831 GTTATTATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
11 29 0.66
12 15 0.34
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:39180827 original size:17 final size:16
Alignment explanation
Indices: 39180778--39180846 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 16
39180768 TTTAATCTTA
* *
39180778 AATTTATTTTAAATTC
1 AATTTAATTTAAATTT
39180794 AATTTAAATTTAAATTT
1 AATTT-AATTTAAATTT
39180811 GAATTTAATTTAAATTT
1 -AATTTAATTTAAATTT
39180828 AATGTT-ATTATAAATTT
1 AAT-TTAATT-TAAATTT
39180845 AA
1 AA
39180847 AAAGAAAGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
16 11 0.23
17 31 0.66
18 5 0.11
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (16 bp):
AATTTAATTTAAATTT
Found at i:39180847 original size:6 final size:6
Alignment explanation
Indices: 39180775--39180829 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
39180765 TATTTTAATC
* * *
39180775 TTAAAT TT-ATT TTAAA- TTCAAT TTAAAT TTAAAT TTGAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
39180820 TTAAAT TTAA
1 TTAAAT TTAA
39180830 TGTTATTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
5 13 0.32
6 28 0.68
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:39180892 original size:14 final size:14
Alignment explanation
Indices: 39180873--39180933 Score: 90
Period size: 14 Copynumber: 4.5 Consensus size: 14
39180863 CATGGCCTAG
39180873 GGCCCAATTACAAT
1 GGCCCAATTACAAT
*
39180887 GGCCCAATTACAAA
1 GGCCCAATTACAAT
*
39180901 GGCCCAATT--AAG
1 GGCCCAATTACAAT
39180913 GGCCCAATTACAAT
1 GGCCCAATTACAAT
39180927 GGCCCAA
1 GGCCCAA
39180934 ATAGGCCCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
12 11 0.26
14 31 0.74
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.16
Consensus pattern (14 bp):
GGCCCAATTACAAT
Found at i:39180922 original size:26 final size:27
Alignment explanation
Indices: 39180873--39180933 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
39180863 CATGGCCTAG
*
39180873 GGCCCAATTACAATGGCCCAATTACAAA
1 GGCCCAATTA-AAGGGCCCAATTACAAA
*
39180901 GGCCCAATT-AAGGGCCCAATTACAAT
1 GGCCCAATTAAAGGGCCCAATTACAAA
39180927 GGCCCAA
1 GGCCCAA
39180934 ATAGGCCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 22 0.71
28 9 0.29
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.16
Consensus pattern (27 bp):
GGCCCAATTAAAGGGCCCAATTACAAA
Found at i:39181556 original size:9 final size:9
Alignment explanation
Indices: 39181530--39181564 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
39181520 TAGCAGAAGC
*
39181530 ATTAATAAC
1 ATTAATAAT
39181539 ATTAATAAT
1 ATTAATAAT
39181548 ATTAATAAT
1 ATTAATAAT
*
39181557 AATAATAA
1 ATTAATAA
39181565 ATATATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (9 bp):
ATTAATAAT
Found at i:39181881 original size:14 final size:14
Alignment explanation
Indices: 39181862--39181889 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39181852 TATGTTGAAA
39181862 ATTTCCAGATCTGG
1 ATTTCCAGATCTGG
39181876 ATTTCCAGATCTGG
1 ATTTCCAGATCTGG
39181890 TTTTGGCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
ATTTCCAGATCTGG
Found at i:39182581 original size:162 final size:164
Alignment explanation
Indices: 39182402--39182716 Score: 492
Period size: 163 Copynumber: 1.9 Consensus size: 164
39182392 CTTTTCAATT
* * *
39182402 TAGTCCTTTGACTGTTTGACTGTACCATAGGCTGCCACGTGTCA-CTTTTTGGATTATTTGTGCA
1 TAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTCTGCA
* *
39182466 TTTAGTCCTTTTTATTTTTTATTTGTTTTAATTTAATC-CCAAATCAAC-TTTATTTTAATTACG
66 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCACCAAATCAACTTTTA-TTTAATTACA
*
39182529 AAATTGGCCCAATAATTTTTCAAGGTTTATAAAAC
130 AAATTGGCCCAAAAATTTTTCAAGGTTTATAAAAC
* *
39182564 TAGTCCTTTGACTGTTTGACTGCACTAGAGGTTGCCACGTGTCATCTTTTTGGATTATTTCTGCA
1 TAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTCTGCA
** *
39182629 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCATTAAATCGACTTTTATTTAATTACAA
66 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCACCAAATCAACTTTTATTTAATTACAA
*
39182694 AATTGGTCCAAAAATTTTTCAAG
131 AATTGGCCCAAAAATTTTTCAAG
39182717 ATTTTCAAAT
Statistics
Matches: 138, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
162 40 0.29
163 56 0.41
164 38 0.28
165 4 0.03
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.46
Consensus pattern (164 bp):
TAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTCTGCA
TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCACCAAATCAACTTTTATTTAATTACAA
AATTGGCCCAAAAATTTTTCAAGGTTTATAAAAC
Found at i:39182855 original size:30 final size:30
Alignment explanation
Indices: 39182809--39183188 Score: 553
Period size: 30 Copynumber: 12.5 Consensus size: 30
39182799 CCCTAAATTG
* *
39182809 TCCAGAAATTACATTTTGACCCTAAAACTTC
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
* *
39182840 CCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
39182870 TCCAAAATTATATTTTCGACCCCGAAACTTT
1 TCCAAAATTACATTTT-GACCCCAAAACTTT
*
39182901 ACCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
39182931 ACCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
39182961 TCCAAAATTATATTTTTGACCCCAAAACTTT
1 TCCAAAATTACA-TTTTGACCCCAAAACTTT
* *
39182992 ACCAAAATTACATTTTGACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
**
39183022 TTGAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
39183052 TCCAAAATTATATTTTTGACCCCGAAACTTT
1 TCCAAAATTACA-TTTTGACCCCAAAACTTT
* *
39183083 ACCAAAATTACATTTTGATCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
39183113 TCCAAAATTACATTTTGACCCCGAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
39183143 ACCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
39183173 TCCAAAATTACATTTT
1 TCCAAAATTACATTTT
39183189 AACCTCGATT
Statistics
Matches: 314, Mismatches: 32, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
30 229 0.73
31 85 0.27
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.34
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:39182908 original size:61 final size:60
Alignment explanation
Indices: 39182809--39183188 Score: 562
Period size: 61 Copynumber: 6.3 Consensus size: 60
39182799 CCCTAAATTG
* ** *
39182809 TCCAGAAATTACATTTTGACCCTAAAACTTCCCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTTACCAAAATTACATTTTGACCCCAAAACTTT
* *
39182870 TCCAAAATTATATTTTCGACCCCGAAACTTTACCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTT-GACCCCAAAACTTTACCAAAATTACATTTTGACCCCAAAACTTT
* * *
39182931 ACCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTTACCAAAATTACA-TTTTGACCCCAAAACTTT
* * ***
39182992 ACCAAAATTACATTTTGACCCTAAAACTTTTTGAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTTACCAAAATTACATTTTGACCCCAAAACTTT
* * *
39183052 TCCAAAATTATATTTTTGACCCCGAAACTTTACCAAAATTACATTTTGATCCCAAAACTTT
1 TCCAAAATTACA-TTTTGACCCCAAAACTTTACCAAAATTACATTTTGACCCCAAAACTTT
*
39183113 TCCAAAATTACATTTTGACCCCGAAACTTTACCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTTACCAAAATTACATTTTGACCCCAAAACTTT
39183173 TCCAAAATTACATTTT
1 TCCAAAATTACATTTT
39183189 AACCTCGATT
Statistics
Matches: 291, Mismatches: 25, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
60 125 0.43
61 166 0.57
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.34
Consensus pattern (60 bp):
TCCAAAATTACATTTTGACCCCAAAACTTTACCAAAATTACATTTTGACCCCAAAACTTT
Found at i:39182926 original size:19 final size:19
Alignment explanation
Indices: 39182902--39182956 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
39182892 CGAAACTTTA
39182902 CCAAAATTACATTTTGACC
1 CCAAAATTACATTTTGACC
39182921 CC-AAA--AC--TTT-A--
1 CCAAAATTACATTTTGACC
39182932 CCAAAATTACATTTTGACC
1 CCAAAATTACATTTTGACC
39182951 CCAAAA
1 CCAAAA
39182957 CTTTTCCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 2 0.07
12 3 0.11
13 1 0.04
14 5 0.18
16 5 0.18
17 1 0.04
18 3 0.11
19 8 0.29
ACGTcount: A:0.42, C:0.27, G:0.04, T:0.27
Consensus pattern (19 bp):
CCAAAATTACATTTTGACC
Found at i:39182969 original size:91 final size:91
Alignment explanation
Indices: 39182814--39183188 Score: 599
Period size: 91 Copynumber: 4.1 Consensus size: 91
39182804 AATTGTCCAG
* ** *
39182814 AAATTACATTTTGACCCTAAAACTTCCCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATT
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATT
* *
39182879 ATATTTTCGACCCCGAAACTTTACCA
66 ATATTTTTGACCCCAAAACTTTACCA
*
39182905 AAATTACATTTTGACCCCAAAACTTTACCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATT
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATT
39182970 ATATTTTTGACCCCAAAACTTTACCA
66 ATATTTTTGACCCCAAAACTTTACCA
* **
39182996 AAATTACATTTTGACCCTAAAACTTTTTGAAAATTACATTTTGACCCCAAAACTTTTCCAAAATT
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATT
*
39183061 ATATTTTTGACCCCGAAACTTTACCA
66 ATATTTTTGACCCCAAAACTTTACCA
* * *
39183087 AAATTACATTTTGATCCCAAAACTTTTCCAAAATTACATTTTGACCCCGAAACTTTACCAAAATT
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATT
* *
39183152 ACA-TTTTGACCCCAAAACTTTTCCA
66 ATATTTTTGACCCCAAAACTTTACCA
39183177 AAATTACATTTT
1 AAATTACATTTT
39183189 AACCTCGATT
Statistics
Matches: 264, Mismatches: 20, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
90 32 0.12
91 232 0.88
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.34
Consensus pattern (91 bp):
AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATT
ATATTTTTGACCCCAAAACTTTACCA
Found at i:39183217 original size:60 final size:58
Alignment explanation
Indices: 39182841--39183399 Score: 464
Period size: 61 Copynumber: 9.4 Consensus size: 58
39182831 TAAAACTTCC
* * *
39182841 CCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTATATTTTCGACCCCGAAACTTTA
1 CCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTT-AACCCCG--ACTTTA
* * * *
39182902 CCAAAATTACATTTTGACCCCAAAACTTTACCAAAATTACATTTTGACCCCAAAACTTTT
1 CCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCC--GACTTTA
* * * ** *
39182962 CCAAAATTATATTTTTGACCCCAAAACTTTACCAAAATTACATTTTGACCCTAAAACTTTT
1 CCAAAATTACA-TTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCC--CGACTTTA
** * *
39183023 TGAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTTGACCCCGAAACTTTA
1 CCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACA-TTTTAACCCCG--ACTTTA
* *
39183084 CCAAAATTACATTTTGATCCCAAAACTTTTCCAAAATTACATTTTGACCCCGAAACTTTA
1 CCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCG--ACTTTA
*
39183144 CCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCTCGA-TTTCA
1 CCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCGACTTT-A
* *
39183202 CCAAAAATTACCATTTT-ACCCCCAAATCTTTT--AAAATTCCATTTTTAACCCCGA-TTTCA
1 CC-AAAATTA-CATTTTGA-CCCCAAAACTTTTCCAAAATTACA-TTTTAACCCCGACTTT-A
* * * *
39183261 TCGAAAATTACCATTTT-ACCCTCGAATC-TTT--AAAATT-CTTTTTTTAACCCCGA-TTTCA
1 -CCAAAATTA-CATTTTGACCC-CAAAACTTTTCCAAAATTAC--ATTTTAACCCCGACTTT-A
* * *
39183319 CCGAAAATTACCATTTT-ACCCCCGAATCTTTT--AAAATTCCATTTTTAACCCCGA-TTTCA
1 CC-AAAATTA-CATTTTGA-CCCCAAAACTTTTCCAAAATTACA-TTTTAACCCCGACTTT-A
*
39183378 CCAAAATTACCATTTTGCCCCC
1 CCAAAATTA-CATTTTGACCCC
39183400 GGGTATCCAT
Statistics
Matches: 444, Mismatches: 31, Indels: 49
0.85 0.06 0.09
Matches are distributed among these distances:
57 5 0.01
58 80 0.18
59 75 0.17
60 137 0.31
61 147 0.33
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (58 bp):
CCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCGACTTTA
Found at i:39183249 original size:59 final size:59
Alignment explanation
Indices: 39183024--39183399 Score: 348
Period size: 60 Copynumber: 6.4 Consensus size: 59
39183014 AAAACTTTTT
* ** *
39183024 GAAAATTA-CATTTTGA-CCCCAAAACTTTTCCAAAATTATATTTTTGACCCCGAAACTTT-ACC
1 GAAAATTACCATTTT-ACCCCCAAATCTTTT--AAAATTCCATTTTTAACCCCG--A-TTTCACC
* * * *
39183086 -AAAATTA-CATTTTGA-TCCCAAAACTTTTCCAAAATTACA-TTTTGACCCCGAAACTTT-ACC
1 GAAAATTACCATTTT-ACCCCCAAATCTTTT--AAAATTCCATTTTTAACCCCG--A-TTTCACC
* * *
39183146 -AAAATTA-CATTTTGA-CCCCAAAACTTTTCCAAAATTACA-TTTTAACCTCGATTTCACC
1 GAAAATTACCATTTT-ACCCCCAAATCTTTT--AAAATTCCATTTTTAACCCCGATTTCACC
* *
39183204 AAAAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAACCCCGATTTCATC
1 GAAAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACC
* * **
39183263 GAAAATTACCATTTTACCCTCGAATC-TTTAAAATTCTTTTTTTAACCCCGATTTCACC
1 GAAAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACC
*
39183321 GAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACC
1 GAAAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACC
*
39183380 -AAAATTACCATTTTGCCCCC
1 GAAAATTACCATTTTACCCCC
39183400 GGGTATCCAT
Statistics
Matches: 289, Mismatches: 19, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
57 3 0.01
58 85 0.29
59 78 0.27
60 86 0.30
61 37 0.13
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.35
Consensus pattern (59 bp):
GAAAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:39183399 original size:29 final size:29
Alignment explanation
Indices: 39183174--39183400 Score: 130
Period size: 29 Copynumber: 7.8 Consensus size: 29
39183164 CAAAACTTTT
* *
39183174 CCAAAATTA-CATTTTAACCTCGATTTCA
1 CCAAAATTACCATTTTACCCCCGATTTCA
*
39183202 CCAAAAATTACCATTTTACCCCCAAATCTT--
1 CC-AAAATTACCATTTTACCCCC-GAT-TTCA
** *
39183232 TTAAAATT-CCATTTTTAACCCCGATTTCA
1 CCAAAATTACCA-TTTTACCCCCGATTTCA
* * * *
39183261 TCGAAAATTACCATTTTACCCTCGA-ATCT
1 -CCAAAATTACCATTTTACCCCCGATTTCA
** ** *
39183290 TTAAAATT-CTTTTTTTAACCCCGATTTCA
1 CCAAAATTAC-CATTTTACCCCCGATTTCA
39183319 CCGAAAATTACCATTTTACCCCCGAATCTT--
1 CC-AAAATTACCATTTTACCCCCG-AT-TTCA
** *
39183349 TTAAAATT-CCATTTTTAACCCCGATTTCA
1 CCAAAATTACCA-TTTTACCCCCGATTTCA
*
39183378 CCAAAATTACCATTTTGCCCCCG
1 CCAAAATTACCATTTTACCCCCG
39183401 GGTATCCATA
Statistics
Matches: 147, Mismatches: 33, Indels: 37
0.68 0.15 0.17
Matches are distributed among these distances:
27 5 0.03
28 28 0.19
29 57 0.39
30 45 0.31
31 8 0.05
32 4 0.03
ACGTcount: A:0.31, C:0.28, G:0.04, T:0.36
Consensus pattern (29 bp):
CCAAAATTACCATTTTACCCCCGATTTCA
Found at i:39183422 original size:58 final size:59
Alignment explanation
Indices: 39183185--39183435 Score: 276
Period size: 58 Copynumber: 4.3 Consensus size: 59
39183175 CAAAATTACA
* * * ** *
39183185 TTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCAAATCTTTTAAAATTCCAT
1 TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTCATAAAATCCCAT
* * * * **
39183244 TTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCTCGAATCT-TTAAAATTCTTT
1 TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTCATAAAATCCCAT
** *
39183302 TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCAT
1 TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTCATAAAATCCCAT
* * * *
39183361 TTTTAACCCCGATTTCACC-AAAATTACCATTTTGCCCCCGGGTATC-CAT-AAGTCCCGT
1 TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCC--GAATCTCATAAAATCCCAT
*
39183419 TTTTCACCCCGATTTCA
1 TTTTAACCCCGATTTCA
39183436 TCATTTATCA
Statistics
Matches: 170, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
58 95 0.56
59 71 0.42
60 4 0.02
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.37
Consensus pattern (59 bp):
TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTCATAAAATCCCAT
Found at i:39183422 original size:117 final size:117
Alignment explanation
Indices: 39183185--39183435 Score: 344
Period size: 117 Copynumber: 2.1 Consensus size: 117
39183175 CAAAATTACA
*
39183185 TTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAA
1 TTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAA
* * ** * **
39183250 CCCCGATTTCATCGAAAATTACCATTTTACCCTCGAATCTTTAAAATTCTTT
66 CCCCGATTTCATCCAAAATTACCATTTTACCCCCGAATCCATAAAATCCCGT
* *
39183302 TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAA
1 TTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAA
* * *
39183367 CCCCGATTTCA-CCAAAATTACCATTTTGCCCCCGGGTATCCAT-AAGTCCCGT
66 CCCCGATTTCATCCAAAATTACCATTTTACCCCC--GAATCCATAAAATCCCGT
*
39183419 TTTTCACCCCGATTTCA
1 TTTTAACCCCGATTTCA
39183436 TCATTTATCA
Statistics
Matches: 118, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
116 19 0.16
117 94 0.80
118 5 0.04
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.37
Consensus pattern (117 bp):
TTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAA
CCCCGATTTCATCCAAAATTACCATTTTACCCCCGAATCCATAAAATCCCGT
Found at i:39184888 original size:17 final size:18
Alignment explanation
Indices: 39184856--39184889 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39184846 GAGTTAAACG
*
39184856 AATCGAGTTGTTCGAGTT
1 AATCGAGTTATTCGAGTT
39184874 AATCGAG-TATTCGAGT
1 AATCGAGTTATTCGAGT
39184890 CAACTCGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:39185721 original size:18 final size:19
Alignment explanation
Indices: 39185699--39185741 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
39185689 AAAAAATCAC
39185699 ATTTTTACATTT-AAAATAT
1 ATTTTTA-ATTTCAAAATAT
39185718 -TTTTTAATTTCAAAATAT
1 ATTTTTAATTTCAAAATAT
39185736 ATTTTT
1 ATTTTT
39185742 TAATCATGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.18
18 13 0.59
19 5 0.23
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTTAATTTCAAAATAT
Found at i:39194306 original size:23 final size:22
Alignment explanation
Indices: 39194280--39194332 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
39194270 AATGTATAAT
*
39194280 AAAATTATATTTTAA-TTATTCAA
1 AAAATAATA-TTTAATTTATT-AA
*
39194303 AAAAAAATATTTAATTTATTAA
1 AAAATAATATTTAATTTATTAA
39194325 AAAATAAT
1 AAAATAAT
39194333 TAAATTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAATAATATTTAATTTATTAA
Found at i:39194328 original size:19 final size:19
Alignment explanation
Indices: 39194304--39194340 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39194294 ATTATTCAAA
* *
39194304 AAAAAATATTTAATTTATT
1 AAAAAATAATTAAATTATT
39194323 AAAAAATAATTAAATTAT
1 AAAAAATAATTAAATTAT
39194341 AAATTAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAAAATAATTAAATTATT
Found at i:39194346 original size:23 final size:24
Alignment explanation
Indices: 39194319--39194377 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
39194309 ATATTTAATT
*
39194319 TATTAAAAAATAATTAAATTATAA
1 TATTAAAAAATAATAAAATTATAA
** *
39194343 -ATTAATCAATGATAAAATTATAA
1 TATTAAAAAATAATAAAATTATAA
39194366 TATTTAAAAAAT
1 TA-TTAAAAAAT
39194378 TTATAATTCA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
23 19 0.70
24 1 0.04
25 7 0.26
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
TATTAAAAAATAATAAAATTATAA
Found at i:39195492 original size:29 final size:28
Alignment explanation
Indices: 39195436--39195503 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
39195426 ATTTTAATAT
* *
39195436 ATTTGAAATTTATCTTTTTTATTTTTAA
1 ATTTAAAATTTATCTTTTTAATTTTTAA
* *
39195464 TTTTAGAATTTAGTC-TTTTAATTTATTAA
1 ATTTAAAATTTA-TCTTTTTAATTT-TTAA
39195493 ATTTAAAATTT
1 ATTTAAAATTT
39195504 CAAGGTTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 17 0.53
29 15 0.47
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.60
Consensus pattern (28 bp):
ATTTAAAATTTATCTTTTTAATTTTTAA
Found at i:39197268 original size:30 final size:31
Alignment explanation
Indices: 39197232--39197297 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
39197222 AATAGTCTAT
* *
39197232 ATTTTTATAATTTTTA-AAAGATTAAATTA-A
1 ATTTTTATAA-TTTTAGAAAGACTAAAGTATA
*
39197262 ATTTTTATCATTTTAGAAAGACTAAAGTATA
1 ATTTTTATAATTTTAGAAAGACTAAAGTATA
39197293 ATTTT
1 ATTTT
39197298 ATTTTTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.16
30 20 0.65
31 6 0.19
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (31 bp):
ATTTTTATAATTTTAGAAAGACTAAAGTATA
Found at i:39200509 original size:51 final size:51
Alignment explanation
Indices: 39200427--39200717 Score: 388
Period size: 51 Copynumber: 5.6 Consensus size: 51
39200417 GCTATAAACG
* *
39200427 AAAGAGTCCGATGACTAAGTGTCATCATGAGTAAATGAATTCCTTACGTATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATTCCTTACGGATT
39200479 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATTCCTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATTCCTTACGGATT
* *
39200530 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACAGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATTCC-TTACGGATT
* * * *
39200581 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATTCC-TTACGGATT
* * * *
39200633 AAAGGTTCGATGACTCAGTGTCATCGTGAGTATATGAATTCCTATACGGAAT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATTCCT-TACGGATT
* *
39200685 AAGGGGTTCGATGACTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
39200718 TTAAATGAAA
Statistics
Matches: 214, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
50 3 0.01
51 127 0.59
52 57 0.27
53 26 0.12
54 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATTCCTTACGGATT
Found at i:39204315 original size:28 final size:28
Alignment explanation
Indices: 39204283--39204386 Score: 113
Period size: 28 Copynumber: 3.8 Consensus size: 28
39204273 TTTGGATGTC
*
39204283 CGAGGGTAAAATGATAATTTTAGACTCT
1 CGAGGGTAAAATGATAATTTTAGACACT
* * * *
39204311 CGAGGGCAAAATGGTAATTTTAAAAACT
1 CGAGGGTAAAATGATAATTTTAGACACT
* *
39204339 TG-GGGTTAAAATGA-CATTTTAGACACT
1 CGAGGG-TAAAATGATAATTTTAGACACT
*
39204366 TGAGGGTAAAATGATAATTTT
1 CGAGGGTAAAATGATAATTTT
39204387 TGGAAAAAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
27 23 0.38
28 38 0.62
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.32
Consensus pattern (28 bp):
CGAGGGTAAAATGATAATTTTAGACACT
Found at i:39204366 original size:27 final size:27
Alignment explanation
Indices: 39204327--39204379 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
39204317 CAAAATGGTA
39204327 ATTTTAAAAACTTG-GGGTTAAAATGAC
1 ATTTTAAAAACTTGAGGG-TAAAATGAC
* *
39204354 ATTTTAGACACTTGAGGGTAAAATGA
1 ATTTTAAAAACTTGAGGGTAAAATGA
39204380 TAATTTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.32
Consensus pattern (27 bp):
ATTTTAAAAACTTGAGGGTAAAATGAC
Found at i:39204444 original size:143 final size:145
Alignment explanation
Indices: 39204173--39204446 Score: 360
Period size: 143 Copynumber: 1.9 Consensus size: 145
39204163 GCCCGGGGGA
* * *
39204173 AAAATGGTAATTTTAGAAAATTTTGGGGTTAAAAATGATATTTTAGACACTTAAGAGTAAAATGG
1 AAAATGGTAATTTTAGAAAATCTTGGGGTTAAAAATGACATTTTAGACACTTAAGAGTAAAATGA
* * *
39204238 TAATTTTCAGAAGAATCGAGATCAAAACGGGACTTTTTGGATGTCCGAGGGTAAAATGATAATTT
66 TAATTTTCAGAAAAATCGAGATAAAAACGGGACTTTTTGGATATCCGAGGGTAAAATGATAATTT
39204303 TAGACTCTCGAGGGC
131 TAGACTCTCGAGGGC
* *
39204318 AAAATGGTAATTTTA-AAAA-CTTGGGGTT-AAAATGACATTTTAGACACTTGAGGGTAAAATGA
1 AAAATGGTAATTTTAGAAAATCTTGGGGTTAAAAATGACATTTTAGACACTTAAGAGTAAAATGA
** * * * *
39204380 TAATTTTTGGAAAAAATC-ACGATAAAAAATGGGA-TTTTTGGATATTCGGGGGTAAAATGGTAA
66 TAATTTTCAG-AAAAATCGA-GAT-AAAAACGGGACTTTTTGGATATCCGAGGGTAAAATGATAA
39204443 TTTT
128 TTTT
39204447 GAGAGTTTCG
Statistics
Matches: 112, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
142 39 0.35
143 46 0.41
144 12 0.11
145 15 0.13
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.32
Consensus pattern (145 bp):
AAAATGGTAATTTTAGAAAATCTTGGGGTTAAAAATGACATTTTAGACACTTAAGAGTAAAATGA
TAATTTTCAGAAAAATCGAGATAAAAACGGGACTTTTTGGATATCCGAGGGTAAAATGATAATTT
TAGACTCTCGAGGGC
Found at i:39204499 original size:30 final size:30
Alignment explanation
Indices: 39204440--39204519 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
39204430 GGTAAAATGG
*
39204440 TAATTTTGAG-AGTTTCGGGGTCAAAAATA
1 TAATTTTGAGAAGTTTAGGGGTCAAAAATA
39204469 TAATTTTAGAGAAGTTTAGGGGTC-AAAATA
1 TAATTTT-GAGAAGTTTAGGGGTCAAAAATA
39204499 TAATTTTTG-GATAGTTTAGGG
1 TAA-TTTTGAGA-AGTTTAGGG
39204520 ACCTCCAAGG
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
29 9 0.20
30 22 0.48
31 15 0.33
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.38
Consensus pattern (30 bp):
TAATTTTGAGAAGTTTAGGGGTCAAAAATA
Found at i:39205857 original size:12 final size:12
Alignment explanation
Indices: 39205828--39205876 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
39205818 AATTACTGCA
* *
39205828 AATATTATCACT
1 AATATTATTAAT
* *
39205840 ATTATTATTATT
1 AATATTATTAAT
39205852 AATATTATTAAT
1 AATATTATTAAT
*
39205864 AATATAATTAAT
1 AATATTATTAAT
39205876 A
1 A
39205877 TTCACATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (12 bp):
AATATTATTAAT
Done.