Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003035.1 Hibiscus syriacus cultivar Beakdansim tig00006316_pilon, whole genome shotgun sequence
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: 96096
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2915 original size:130 final size:129
Alignment explanation
Indices: 2669--2935 Score: 493
Period size: 130 Copynumber: 2.1 Consensus size: 129
2659 TAAACAAAGG
2669 AGTTGCTAGGAACCCTTGTTCCATGTTCAATTGAGGTATTGTGTTCCTATTTTTAGAGTTCTGGA
1 AGTTGCTAGGAACCCTTGTTCCATGTTCAATTGAGGTATTGTGTTCCTATTTTTAGAGTTCTGGA
2734 AAATAGAGTTGGCATGTAACGAATATCTTCTTGTGTCACTTTCACCTGAAACTGATTGTCATTTG
66 AAATAGAGTTGGCATGTAACGAATATCTTCTTGTGTCACTTTCACCTGAAACTGA---TCATTTG
2799 TC
128 TC
2801 AGTTGCTA-GAACCCTTGTTCCATGTTCAATTGAGGTATTGTGTTCCTATTTTTAGAGTTCT-GA
1 AGTTGCTAGGAACCCTTGTTCCATGTTCAATTGAGGTATTGTGTTCCTATTTTTAGAGTTCTGGA
2864 AAATAGAGTTGGCATGTAACGAATATCTTCTTGTGTCACTTTCACCTGAAACTGATCATTTGTC
66 AAATAGAGTTGGCATGTAACGAATATCTTCTTGTGTCACTTTCACCTGAAACTGATCATTTGTC
2928 AGTTGCTA
1 AGTTGCTA
2936 TTTATGTTGA
Statistics
Matches: 135, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
127 17 0.13
130 57 0.42
131 53 0.39
132 8 0.06
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (129 bp):
AGTTGCTAGGAACCCTTGTTCCATGTTCAATTGAGGTATTGTGTTCCTATTTTTAGAGTTCTGGA
AAATAGAGTTGGCATGTAACGAATATCTTCTTGTGTCACTTTCACCTGAAACTGATCATTTGTC
Found at i:13198 original size:15 final size:15
Alignment explanation
Indices: 13171--13213 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
13161 TAAAAATATT
13171 TAAAAAT-AAACAAG
1 TAAAAATAAAACAAG
*
13185 TAAAATTAAAACAA-
1 TAAAAATAAAACAAG
*
13199 TAAAAATACAACAAG
1 TAAAAATAAAACAAG
13214 AACGATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.70, C:0.09, G:0.05, T:0.16
Consensus pattern (15 bp):
TAAAAATAAAACAAG
Found at i:14557 original size:11 final size:10
Alignment explanation
Indices: 14527--14567 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
14517 GGGCTTTGTA
14527 ATTTAATATT
1 ATTTAATATT
14537 ATTTATATATGT
1 ATTTA-ATAT-T
14549 ATTTAATATAT
1 ATTTAATAT-T
14560 ATTTAATA
1 ATTTAATA
14568 ATAATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:14571 original size:3 final size:3
Alignment explanation
Indices: 14563--14647 Score: 118
Period size: 3 Copynumber: 28.7 Consensus size: 3
14553 AATATATATT
*
14563 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
14611 TTA TAG T-A TAA TAA TAA TTA TAA TAA CAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
14648 TTTATAATAT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
2 1 0.01
3 70 0.99
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:15239 original size:226 final size:225
Alignment explanation
Indices: 14977--15867 Score: 1425
Period size: 226 Copynumber: 4.0 Consensus size: 225
14967 GAATTATGCA
*
14977 AAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
15042 ATGAAC-TTCTCTGGAAAAGCTG-CCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTC
66 ATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAATTC
* * *
15105 TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CT
131 TTCTCATTACGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCT
* * * *
15169 GGCAATGTTGATCCATCAAATGATGAATTCAAAC
192 GGAAAAGATAATCCATCAAATGATGAATTCAAAC
15203 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
15268 ATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAATTC
66 ATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAATTC
15333 TTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
131 TTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
*
15398 AAGATAAT-CATCAATTGATGAATTC-AAC
196 AAGATAATCCATCAAATGATGAATTCAAAC
15426 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 -AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
15491 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGAGTAAAAGGTTGAACAAATT
65 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAATT
*
15556 CTTCCCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
130 CTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
* ***
15621 AAAGATAATCCATCAATTGATGAATTCAGGT
195 AAAGATAATCCATCAAATGATGAATTCAAAC
* *
15652 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * ** *
15717 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATT
65 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAATT
15782 CTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
130 CTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
*
15847 AATG-TCAATCCATCAAATGAT
195 AAAGAT-AATCCATCAAATGAT
15868 AGATTTGAAT
Statistics
Matches: 629, Mismatches: 28, Indels: 16
0.93 0.04 0.02
Matches are distributed among these distances:
223 3 0.00
224 219 0.35
225 53 0.08
226 267 0.42
227 16 0.03
228 71 0.11
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (225 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAATTC
TTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
AAGATAATCCATCAAATGATGAATTCAAAC
Found at i:15359 original size:113 final size:113
Alignment explanation
Indices: 14974--15875 Score: 1264
Period size: 113 Copynumber: 8.0 Consensus size: 113
14964 ATAGAATTAT
* * *
14974 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
15039 ATTATGAAC-TTCTCTGGAAAAGCTG-CCCATCAAGTGATAGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATAGATTTGA
*
15085 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
* * * * **
15150 CTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGAT-GAATTCAA
63 CTCATTATGAACT-TTCTCTGGAAAAGATGATCCATCAAATGATAG-ATTTGA
* *
15201 ACAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
15265 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATAGATTTGA
*
15313 GCAAAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
15378 ATTATGAACTTTCTCTGGAAAAGATAAT-CATCAATTGAT-GAATTCA
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATAGATTTGA
* * *
15424 ACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
15489 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATAGATTTGA
* * *
15537 GTAAAAGGTTGAACAAATTCTTCCCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
15602 ATTATGAACTTTCTCTGGAAAAGATAATCCATCAATTGAT-GAATTCA
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATAGATTTGA
* *
15649 GGTAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 -GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * **
15714 CATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAA
65 CATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATAGATTTGA
* *
15763 GTAAAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
15828 ATTATGAACTTTCTCTGGAAATG-TCAATCCATCAAATGATAGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGAT-GATCCATCAAATGATAGATTTGA
15876 ATCTTTGCTA
Statistics
Matches: 707, Mismatches: 69, Indels: 28
0.88 0.09 0.03
Matches are distributed among these distances:
111 144 0.20
112 75 0.11
113 387 0.55
114 24 0.03
115 55 0.08
116 22 0.03
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATAGATTTGA
Found at i:15663 original size:450 final size:448
Alignment explanation
Indices: 14975--15848 Score: 1446
Period size: 450 Copynumber: 1.9 Consensus size: 448
14965 TAGAATTATG
*
14975 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
15040 TTATGAACTTCTCTGGAAAAGCTGCCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTC
66 TTATGAACTTCTCTGGAAAAGCTGCCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAATTC
* * *
15105 TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTG
131 TTCCCATTACGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTACCTG
* * * * *
15170 GCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGTTGAACAAGTTCTTCTCATTATGAACT
194 GAAAAGATAATCCATCAAATGATGAATTCAAACAAAAGTTGAACAAATTCTTCTCATTATGAACT
*
15235 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAA
259 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAA
* **
15300 GTAATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAG
324 ATAATAGATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAG
15365 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCATCAATTGATGAATTCAA
389 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCATCAATTGATGAATTCAA
15425 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
15490 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGAGTAAAAGGTTGAACAAAT
66 TTATGAAC-TTCTCTGGAAAAGCTG-CCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAAT
*
15555 TCTTCCCATTACGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAACT-TTCTCT
129 TCTTCCCATTACGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTAC-CT
* ***
15618 GGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAA
193 GGAAAAGATAATCCATCAAATGATGAATTCAAACAAAA-GTTGAACAAATTCTTCTCATTATGAA
* *
15683 TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATC
257 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATC
* * *
15748 AAATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTC
322 AAATAATAGATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTC
15813 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
387 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
15849 TGTCAATCCA
Statistics
Matches: 394, Mismatches: 26, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
448 2 0.01
449 53 0.13
450 254 0.64
451 16 0.04
452 69 0.18
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (448 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTCTCTGGAAAAGCTGCCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAATTC
TTCCCATTACGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACCTGGA
AAAGATAATCCATCAAATGATGAATTCAAACAAAAGTTGAACAAATTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAAT
AATAGATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGAT
GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCATCAATTGATGAATTCAA
Found at i:16907 original size:83 final size:83
Alignment explanation
Indices: 16659--17024 Score: 596
Period size: 83 Copynumber: 4.4 Consensus size: 83
16649 CTTATTTCTA
* * *
16659 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAATTCAAA
1 CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
* *
16724 GACCACTTTCAGAA-ATG
66 GAACACTTCCAGAAGATG
* * *
16741 CTATGAACACA-TTATTCTTCTC-AATTCAATGATTGGTTTTATC-AACCAGATCGGATAACTCA
1 CTATGAGCACATTTA-TCTTC-CAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCA
16803 AAGAACACTTCCAGAAGATG
64 AAGAACACTTCCAGAAGATG
16823 CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
*
16888 GAACATTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
16906 CTATGAGCACATTTATCTTCCCAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
16971 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
16989 CTATGAGCACATTTATCTTCCAAATTCAATGATTGG
1 CTATGAGCACATTTATCTTCCAAATTCAATGATTGG
17025 ACTAGGATAT
Statistics
Matches: 263, Mismatches: 15, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
81 34 0.13
82 72 0.27
83 157 0.60
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (83 bp):
CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:17798 original size:16 final size:18
Alignment explanation
Indices: 17757--17804 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
17747 ATTCAATAGA
*
17757 AAAATAAATTGAATTTCC
1 AAAATAAATTGAATCTCC
17775 AAAAATAAATTGAATCT-C
1 -AAAATAAATTGAATCTCC
17793 -AAATAAATTGAA
1 AAAATAAATTGAA
17805 CTTGAAATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 12 0.43
18 1 0.04
19 15 0.54
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.29
Consensus pattern (18 bp):
AAAATAAATTGAATCTCC
Found at i:18157 original size:11 final size:11
Alignment explanation
Indices: 18134--18200 Score: 75
Period size: 11 Copynumber: 6.0 Consensus size: 11
18124 TTGACCCCCC
18134 TTTTTTTTC--
1 TTTTTTTTCTT
*
18143 TTTTTTCTCTT
1 TTTTTTTTCTT
18154 TTTTTTTTCTT
1 TTTTTTTTCTT
18165 TTTTTTTTCTT
1 TTTTTTTTCTT
18176 TTCTTTTTTCCTT
1 TT-TTTTTT-CTT
*
18189 CATTTTTTTCTT
1 -TTTTTTTTCTT
18201 CAAGCATAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
9 8 0.16
11 23 0.46
12 9 0.18
13 9 0.18
14 1 0.02
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:18161 original size:13 final size:13
Alignment explanation
Indices: 18138--18199 Score: 60
Period size: 12 Copynumber: 4.9 Consensus size: 13
18128 CCCCCCTTTT
18138 TTTTCTTTTTTCTC
1 TTTT-TTTTTTCTC
18152 -TTTTTTTTT-TC
1 TTTTTTTTTTCTC
18163 TTTTTTTTTTCT-
1 TTTTTTTTTTCTC
*
18175 TTTCTTTTTTC-C
1 TTTTTTTTTTCTC
*
18187 TTCATTTTTTTCT
1 TT-TTTTTTTTCT
18200 TCAAGCATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
11 2 0.05
12 27 0.68
13 11 0.28
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTTCTC
Found at i:30970 original size:11 final size:10
Alignment explanation
Indices: 30940--30980 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
30930 GGGCTTTGTA
30940 ATTTAATATT
1 ATTTAATATT
30950 ATTTATATATGT
1 ATTTA-ATAT-T
30962 ATTTAATATAT
1 ATTTAATAT-T
30973 ATTTAATA
1 ATTTAATA
30981 ATAATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:30984 original size:3 final size:3
Alignment explanation
Indices: 30976--31058 Score: 121
Period size: 3 Copynumber: 27.7 Consensus size: 3
30966 AATATATATT
* * *
30976 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TTA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
31024 TAA TAA TAA TAA TTA TAA TAA CAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
31059 TTTATAATAT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:40317 original size:50 final size:53
Alignment explanation
Indices: 40249--40386 Score: 147
Period size: 59 Copynumber: 2.5 Consensus size: 53
40239 CACACTCCAA
* * *
40249 TTTGCATTTTCATCGCGACTAGGAGGGTT-T-G-TTAGAGCCATATTATCGAG
1 TTTGCCTTTTCATTGCGACTAGGAGGGTTATAGATTAGAGCAATATTATCGAG
*
40299 TTTGTCTTTTCATTGCGACTAGGAGGGTTCGATAGGACACTTAGAGCAATATTATCGAG
1 TTTGCCTTTTCATTGCGACTAGGAGGGTT--ATA-G--A-TTAGAGCAATATTATCGAG
* *
40358 TTTGCCTTTTCATTACGATTAGGAGGGTT
1 TTTGCCTTTTCATTGCGACTAGGAGGGTT
40387 CGATAGGACA
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
50 26 0.36
53 1 0.01
55 1 0.01
59 44 0.61
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.37
Consensus pattern (53 bp):
TTTGCCTTTTCATTGCGACTAGGAGGGTTATAGATTAGAGCAATATTATCGAG
Found at i:40381 original size:59 final size:59
Alignment explanation
Indices: 40280--40400 Score: 206
Period size: 59 Copynumber: 2.1 Consensus size: 59
40270 GGAGGGTTTG
* * *
40280 TTAGAGCCATATTATCGAGTTTGTCTTTTCATTGCGACTAGGAGGGTTCGATAGGACAC
1 TTAGAGCAATATTATCGAGTTTGCCTTTTCATTACGACTAGGAGGGTTCGATAGGACAC
*
40339 TTAGAGCAATATTATCGAGTTTGCCTTTTCATTACGATTAGGAGGGTTCGATAGGACAC
1 TTAGAGCAATATTATCGAGTTTGCCTTTTCATTACGACTAGGAGGGTTCGATAGGACAC
40398 TTA
1 TTA
40401 TCCATCTATT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.35
Consensus pattern (59 bp):
TTAGAGCAATATTATCGAGTTTGCCTTTTCATTACGACTAGGAGGGTTCGATAGGACAC
Found at i:44781 original size:23 final size:22
Alignment explanation
Indices: 44733--44803 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 22
44723 AACACTTTAG
44733 ATTTT-ATTATT-TTATTTAGGA
1 ATTTTAATTATTATTA-TTAGGA
*
44754 TTTTTAATTATTTATTATTAGGA
1 ATTTTAATTA-TTATTATTAGGA
*
44777 ATTTTAACTTACTATTAATTAGGA
1 ATTTTAA-TTATTATT-ATTAGGA
44801 ATT
1 ATT
44804 AAAAGTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
21 4 0.10
22 4 0.10
23 18 0.43
24 16 0.38
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.56
Consensus pattern (22 bp):
ATTTTAATTATTATTATTAGGA
Found at i:45428 original size:30 final size:31
Alignment explanation
Indices: 45392--45449 Score: 109
Period size: 30 Copynumber: 1.9 Consensus size: 31
45382 ATCCAAACAA
45392 GGGCTAAATTCCAAGG-TTGACTTTGGATTT
1 GGGCTAAATTCCAAGGATTGACTTTGGATTT
45422 GGGCTAAATTCCAAGGATTGACTTTGGA
1 GGGCTAAATTCCAAGGATTGACTTTGGA
45450 AAATTAGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.33
Consensus pattern (31 bp):
GGGCTAAATTCCAAGGATTGACTTTGGATTT
Found at i:45851 original size:36 final size:36
Alignment explanation
Indices: 45811--45885 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
45801 AAAAAAGAAT
45811 TATTTATTTGACAATTACGACGCTTGTCAATCACAA
1 TATTTATTTGACAATTACGACGCTTGTCAATCACAA
*
45847 TATTTATTTGACAATTACGGCGCTTGTCAATCACAA
1 TATTTATTTGACAATTACGACGCTTGTCAATCACAA
45883 TAT
1 TAT
45886 GTGTAATACG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (36 bp):
TATTTATTTGACAATTACGACGCTTGTCAATCACAA
Found at i:48169 original size:22 final size:22
Alignment explanation
Indices: 48144--48206 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
48134 TGACCCGTTA
*
48144 ACTGGTCTGACCGTTGAGTTTG
1 ACTGGTCTGACCGTTGACTTTG
*
48166 ACTGGTTTGACCGTTGACTTTG
1 ACTGGTCTGACCGTTGACTTTG
* *
48188 ACCGGTCTGGCCGTTGACT
1 ACTGGTCTGACCGTTGACT
48207 CCGACTTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.13, C:0.22, G:0.30, T:0.35
Consensus pattern (22 bp):
ACTGGTCTGACCGTTGACTTTG
Found at i:49869 original size:19 final size:19
Alignment explanation
Indices: 49821--49862 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
49811 ATATCTATTT
* * *
49821 TGATCTCTAATTTCTGTTC
1 TGATCTCTTATCTCTGCTC
49840 TGATCTCTTATCTCTGCTC
1 TGATCTCTTATCTCTGCTC
49859 TGAT
1 TGAT
49863 TTTTTATATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.24, G:0.12, T:0.50
Consensus pattern (19 bp):
TGATCTCTTATCTCTGCTC
Found at i:50333 original size:16 final size:15
Alignment explanation
Indices: 50297--50344 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
50287 TTTTACTATG
* **
50297 GTTTTAAAAAAATAC
1 GTTTTAAAAAGATTT
*
50312 GTTTTAAACAGATATT
1 GTTTTAAAAAGAT-TT
50328 GTTTTAAAAAGATTT
1 GTTTTAAAAAGATTT
50343 GT
1 GT
50345 ACATTTTCAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (15 bp):
GTTTTAAAAAGATTT
Found at i:50791 original size:14 final size:14
Alignment explanation
Indices: 50772--50803 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
50762 TAAAAATATT
50772 AAATTTATAATTGA
1 AAATTTATAATTGA
50786 AAATTTATAATTGA
1 AAATTTATAATTGA
50800 AAAT
1 AAAT
50804 GTTTTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (14 bp):
AAATTTATAATTGA
Found at i:52203 original size:372 final size:359
Alignment explanation
Indices: 51527--52339 Score: 1049
Period size: 372 Copynumber: 2.2 Consensus size: 359
51517 GAGATTATAT
* * *
51527 ACATCGGGGCGAATTTGTTTCTAAGACAGTGGTTTTCACCACGACATGGTTTCGGATGTTTATTT
1 ACATCGGGGCGAATTTGTTTCTAAGACAGTGGTTTTCACCACGACATGATTTCAGTTGTTTATTT
* * * *
51592 GTCCAATATTTTTATTTGTGCCAGTTTCAGACAAAGTTTTAATTCGAAAATTAATGAGGTTTATA
66 GTTCAATATTTTTATTTGTGCCAGTTTCAAACAAAATTTTAATTCGAAAATTAATCAGGTTTATA
* * * * *
51657 TTTGGTTTTTTACCCCTGAACGAAGTCTATAAATAAGAGGTTTTTCAAGCTTCTCAGCACACTCT
131 TTTGGTCTTTTACCCCTGAACGAAGCCTATAAATAAGACGCTTTTCAAGCTTCTCAACACACTCT
* * *
51722 CAACTCTCACAAATCCTCTCATTCTAAAGCATTCCAAGTTTCTTTTCTCTGATGCTATCAGAAGA
196 CAACTCTCACAAATCCTCTCATGCTAAAGCATTCCAAGCTTCTTTTCTCTGATCCTATCAGAAGA
* * * * * *
51787 GCAGTACCACCGATAATCCACTCTAGTTTTGGGTTTATGAATTCTCAGAGCGACCTTGTTAACCT
261 GCAGTACCACCGACAATCCACTCTAGTTTTGGGTATACGAATTCTCAGAGCAACCATGTTAACAT
*
51852 -AGGGGGACGATTCATCAATTGCAGCGATTACAC
326 CAGGGGGACGATCCATCAATTGCAGCGATTACAC
* * * *
51885 ACTTCGGGGCGAATTTGTTTCTAAGGCAGTGATTTTCACCATGACATGATTTCAGTTGTTTATTT
1 ACATCGGGGCGAATTTGTTTCTAAGACAGTGGTTTTCACCACGACATGATTTCAGTTGTTTATTT
* *
51950 GTTTAATATTTTTATTTGTGCCAGTTTCAAACAAAATTTTAATTC-AGAAATTAATCATGTTTAT
66 GTTCAATATTTTTATTTGTGCCAGTTTCAAACAAAATTTTAATTCGA-AAATTAATCAGGTTTA-
*
52014 CTATGGTTTTGTTGTGGACACTTTTACCCCTGAATGAAGCCTATAAATAGAGACGCTTTTCAAGC
129 -TA----TTTG--GT-----CTTTTACCCCTGAACGAAGCCTATAAATA-AGACGCTTTTCAAGC
*
52079 TTCTCAATACACTCTCAACTCTCACAAATCCTCTCATGCTAAAGCATTCCAAGCTTCTTTTCTCT
181 TTCTCAACACACTCTCAACTCTCACAAATCCTCTCATGCTAAAGCATTCCAAGCTTCTTTTCTCT
* * * *
52144 GCTCCTATCAGAAGAGCAGTACCACCGGCAATCCACT-TCGGTTTTGGGTATACGAATTCTCGGA
246 GATCCTATCAGAAGAGCAGTACCACCGACAATCCACTCT-AGTTTTGGGTATACGAATTCTCAGA
* * *
52208 GTAACCATGTTAACATCGGGGGGACGATCCATCAATTGCAGCGATTATAC
310 GCAACCATGTTAACATCAGGGGGACGATCCATCAATTGCAGCGATTACAC
* * * * * *
52258 ACATCAGGACGAATTTATTTCTAAGACCGTGGTTTTTACCACGACA-CAGTTTCAGTTGTTTATT
1 ACATCGGGGCGAATTTGTTTCTAAGACAGTGGTTTTCACCACGACATGA-TTTCAGTTGTTTATT
*
52322 TGTTCAATGTTTTTATTT
65 TGTTCAATATTTTTATTT
52340 TTCCTGTTAG
Statistics
Matches: 388, Mismatches: 49, Indels: 21
0.85 0.11 0.05
Matches are distributed among these distances:
357 1 0.00
358 113 0.29
360 2 0.01
364 4 0.01
366 2 0.01
371 27 0.07
372 141 0.36
373 98 0.25
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (359 bp):
ACATCGGGGCGAATTTGTTTCTAAGACAGTGGTTTTCACCACGACATGATTTCAGTTGTTTATTT
GTTCAATATTTTTATTTGTGCCAGTTTCAAACAAAATTTTAATTCGAAAATTAATCAGGTTTATA
TTTGGTCTTTTACCCCTGAACGAAGCCTATAAATAAGACGCTTTTCAAGCTTCTCAACACACTCT
CAACTCTCACAAATCCTCTCATGCTAAAGCATTCCAAGCTTCTTTTCTCTGATCCTATCAGAAGA
GCAGTACCACCGACAATCCACTCTAGTTTTGGGTATACGAATTCTCAGAGCAACCATGTTAACAT
CAGGGGGACGATCCATCAATTGCAGCGATTACAC
Found at i:57699 original size:12 final size:12
Alignment explanation
Indices: 57682--57706 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57672 GTTCTTAAGA
57682 GAAGATAATGAG
1 GAAGATAATGAG
57694 GAAGATAATGAG
1 GAAGATAATGAG
57706 G
1 G
57707 GTGACAGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (12 bp):
GAAGATAATGAG
Found at i:60503 original size:9 final size:9
Alignment explanation
Indices: 60489--60513 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
60479 CCCCTCTCTC
60489 TCTCTCTTT
1 TCTCTCTTT
60498 TCTCTCTTT
1 TCTCTCTTT
60507 TCTCTCT
1 TCTCTCT
60514 CTTTTTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (9 bp):
TCTCTCTTT
Found at i:60503 original size:11 final size:11
Alignment explanation
Indices: 60485--60518 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
60475 CCCCCCCCTC
60485 TCTCTCTCTCTT
1 TCTCTCTCT-TT
60497 T-TCTCTCTTT
1 TCTCTCTCTTT
60507 TCTCTCTCTTT
1 TCTCTCTCTTT
60518 T
1 T
60519 TATCTTCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 17 0.81
12 1 0.05
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (11 bp):
TCTCTCTCTTT
Found at i:61604 original size:34 final size:34
Alignment explanation
Indices: 61566--61795 Score: 142
Period size: 34 Copynumber: 6.6 Consensus size: 34
61556 CAGAAAACCG
*
61566 TCTCAAGTGAGATAAAATTTTTCAAGACAAAATA
1 TCTCAAGTGAGATAAAATTTTTCAAGAGAAAATA
* * * * * *
61600 TCTCAAGAGAGAT-GATTTTTTCTAA-ATAAATTG
1 TCTCAAGTGAGATAAAATTTTTC-AAGAGAAAATA
* *
61633 TCTCAAGTGAGACAAAAATTTTCAAGAGAAAATA
1 TCTCAAGTGAGATAAAATTTTTCAAGAGAAAATA
* * * ** *
61667 TTTCAAGTGAGATGAAATTTTGTTTCAAGTGAAGTTG
1 TCTCAAGTGAGAT-AAA-ATT-TTTCAAGAGAAAATA
* * ** *
61704 TCTTAAGTGAGACAAAAAATTTCAAGGGAAAATA
1 TCTCAAGTGAGATAAAATTTTTCAAGAGAAAATA
** * * *
61738 TCTCAAGTGAGATGCAATTTTTGTTTCAAG-GAGATTG
1 TCTCAAGTGAGAT--AA-AATT-TTTCAAGAGAAAATA
61775 TCTCAAGTGAGATAAAATTTT
1 TCTCAAGTGAGATAAAATTTT
61796 GTTTCGAGTG
Statistics
Matches: 143, Mismatches: 43, Indels: 21
0.69 0.21 0.10
Matches are distributed among these distances:
33 27 0.19
34 60 0.42
35 5 0.03
36 6 0.04
37 38 0.27
38 7 0.05
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.33
Consensus pattern (34 bp):
TCTCAAGTGAGATAAAATTTTTCAAGAGAAAATA
Found at i:61678 original size:17 final size:19
Alignment explanation
Indices: 61635--61678 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
61625 ATAAATTGTC
61635 TCAAGTGAGACAAAAATTT
1 TCAAGTGAGACAAAAATTT
*
61654 TCAA--GAGA-AAATA-TT
1 TCAAGTGAGACAAAAATTT
61669 TCAAGTGAGA
1 TCAAGTGAGA
61679 TGAAATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
15 6 0.27
16 4 0.18
17 8 0.36
19 4 0.18
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (19 bp):
TCAAGTGAGACAAAAATTT
Found at i:61695 original size:37 final size:36
Alignment explanation
Indices: 61652--61888 Score: 122
Period size: 37 Copynumber: 6.4 Consensus size: 36
61642 AGACAAAAAT
*
61652 TTTCAAGAGAAAATATTTCAAGTGAGATGAAATTTTG
1 TTTCAAG-GAAAATATCTCAAGTGAGATGAAATTTTG
** * * * ***
61689 TTTCAAGTGAAGTTGTCTTAAGTGAGA-CAAA--AAA
1 TTTCAAG-GAAAATATCTCAAGTGAGATGAAATTTTG
*
61723 TTTCAAGGGAAAATATCTCAAGTGAGATGCAATTTTTG
1 TTTCAA-GGAAAATATCTCAAGTGAGATG-AAATTTTG
* * * *
61761 TTTCAAGGAGATTGTCTCAAGTGAGATAAAATTTTG
1 TTTCAAGGAAAATATCTCAAGTGAGATGAAATTTTG
* * * ** *
61797 TTTCGAGTGAAACTGTCTCGAA-TGAGACAAAAATTGATTT
1 TTTCAAG-GAAAATATCTC-AAGTGAGA-TGAAATT--TTG
** * *
61837 TTTGGAGGAAAACTATCTCAAGTGAGATAAATATTTTC
1 TTTCAAGGAAAA-TATCTCAAGTGAGATGAA-ATTTTG
61875 TTTCAAGGGAAAAT
1 TTTCAA-GGAAAAT
61889 TGTCTCATAT
Statistics
Matches: 150, Mismatches: 36, Indels: 27
0.70 0.17 0.13
Matches are distributed among these distances:
34 21 0.14
35 1 0.01
36 18 0.12
37 53 0.35
38 21 0.14
39 15 0.10
40 21 0.14
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.33
Consensus pattern (36 bp):
TTTCAAGGAAAATATCTCAAGTGAGATGAAATTTTG
Found at i:61727 original size:71 final size:71
Alignment explanation
Indices: 61565--61795 Score: 271
Period size: 71 Copynumber: 3.3 Consensus size: 71
61555 TCAGAAAACC
* * * * *
61565 GTCTCAAGTGAGATAAAATTTTTCAAGACAAAATATCTCAAGAGAGATG--A-TTT-TTTCTAAA
1 GTCTCAAGTGAGACAAAAATTTTCAAGAGAAAATATCTCAAGTGAGATGAAATTTTGTTTC-AAG
*
61626 T-AAATT
65 TGAAGTT
*
61632 GTCTCAAGTGAGACAAAAATTTTCAAGAGAAAATATTTCAAGTGAGATGAAATTTTGTTTCAAGT
1 GTCTCAAGTGAGACAAAAATTTTCAAGAGAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGT
61697 GAAGTT
66 GAAGTT
* * * *
61703 GTCTTAAGTGAGACAAAAAATTTCAAGGGAAAATATCTCAAGTGAGATGCAATTTTTGTTTCAAG
1 GTCTCAAGTGAGACAAAAATTTTCAAGAGAAAATATCTCAAGTGAGATG-AAATTTTGTTTCAAG
61768 -G-AGATT
65 TGAAG-TT
*
61774 GTCTCAAGTGAGA-TAAAATTTT
1 GTCTCAAGTGAGACAAAAATTTT
61796 GTTTCGAGTG
Statistics
Matches: 142, Mismatches: 15, Indels: 11
0.85 0.09 0.07
Matches are distributed among these distances:
67 44 0.31
69 1 0.01
70 15 0.11
71 68 0.48
72 14 0.10
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (71 bp):
GTCTCAAGTGAGACAAAAATTTTCAAGAGAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGT
GAAGTT
Found at i:70383 original size:4 final size:4
Alignment explanation
Indices: 70374--70398 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
70364 GTTTTACCTT
70374 ATAG ATAG ATAG ATAG ATAG ATAG A
1 ATAG ATAG ATAG ATAG ATAG ATAG A
70399 CATATACTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
ATAG
Found at i:71716 original size:23 final size:22
Alignment explanation
Indices: 71690--71747 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
71680 TCAACAAATA
* *
71690 CAAAACATGACACCAAGCAAACT
1 CAAAACATAACACCAA-AAAACT
* *
71713 CAAATCATAACATCAAAAAACT
1 CAAAACATAACACCAAAAAACT
71735 CAAAACATAACAC
1 CAAAACATAACAC
71748 TTATAATAGC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.57, C:0.28, G:0.03, T:0.12
Consensus pattern (22 bp):
CAAAACATAACACCAAAAAACT
Found at i:72618 original size:38 final size:38
Alignment explanation
Indices: 72567--72643 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
72557 ACTATATCAC
72567 TAATCCTAAACGATAATCCATATGAAGTGTAAAAACTA
1 TAATCCTAAACGATAATCCATATGAAGTGTAAAAACTA
72605 TAATCCTAAACGATAATCCATATGAAGTGTAAAAACTA
1 TAATCCTAAACGATAATCCATATGAAGTGTAAAAACTA
72643 T
1 T
72644 CTCAAGCGAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (38 bp):
TAATCCTAAACGATAATCCATATGAAGTGTAAAAACTA
Found at i:80792 original size:21 final size:22
Alignment explanation
Indices: 80768--80825 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
80758 AGACCCTGTG
*
80768 GGGGGTATCGATTCCCCT-AAA
1 GGGGGAATCGATTCCCCTCAAA
*
80789 GGGGGAATCGGTTCCCCTGCAAA
1 GGGGGAATCGATTCCCCT-CAAA
*
80812 -GGGGAATCAATTCC
1 GGGGGAATCGATTCC
80826 TCTTTAAGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 16 0.52
22 12 0.39
23 3 0.10
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.21
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTCAAA
Found at i:93524 original size:26 final size:23
Alignment explanation
Indices: 93487--93547 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 23
93477 AATATATATG
*
93487 TTTA-ATTATATTTCCATTATTATTT
1 TTTATATTATATTT-CA-T-TTATTC
*
93512 TTTATATTTTATTTCATTTATTC
1 TTTATATTATATTTCATTTATTC
93535 TTTATATATATAT
1 TTTATAT-TATAT
93548 ATATATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 12 0.39
24 5 0.16
25 6 0.19
26 8 0.26
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATATTATATTTCATTTATTC
Found at i:93544 original size:2 final size:2
Alignment explanation
Indices: 93537--93614 Score: 135
Period size: 2 Copynumber: 40.5 Consensus size: 2
93527 ATTTATTCTT
93537 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
93578 TA TA TA TA TA TA TA TA T- TA TA TA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
93615 TTTTTTATTG
Statistics
Matches: 73, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.04
2 70 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:93634 original size:32 final size:30
Alignment explanation
Indices: 93536--93622 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 30
93526 CATTTATTCT
* * *
93536 TTATATA-TATATATATATATATATATATA
1 TTATATATTATATATATATATTTTTTTATA
* * *
93565 -TATATATTATATATATATATATATATATA
1 TTATATATTATATATATATATTTTTTTATA
93594 TTATATATTATATATATATATTTTTTTAT
1 TTATATATTATATATATATATTTTTTTAT
93623 TGTTTTTATA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
28 6 0.11
29 22 0.42
30 25 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TTATATATTATATATATATATTTTTTTATA
Found at i:93694 original size:15 final size:16
Alignment explanation
Indices: 93502--93754 Score: 64
Period size: 17 Copynumber: 15.6 Consensus size: 16
93492 TTATATTTCC
93502 ATTATTAT-TTTTTAT
1 ATTATTATATTTTTAT
93517 ATT-TTAT-TTCATTTAT
1 ATTATTATATT--TTTAT
* *
93533 -TCT-TTATATATATAT
1 AT-TATTATATTTTTAT
* *
93548 ATATATATATATATATAT
1 AT-TAT-TATATTTTTAT
* *
93566 ATATATTATATATATAT
1 AT-TATTATATTTTTAT
*
93583 A-TATATATATATTATAT
1 ATTAT-TATAT-TTTTAT
* *
93600 ATTA-TATATATATAT
1 ATTATTATATTTTTAT
* * *
93615 TTTTTTATTGTTTTTAT
1 ATTATTA-TATTTTTAT
*
93632 ATTTTTATA-TTTTAT
1 ATTATTATATTTTTAT
* * *
93647 ATT-TTTTCTGTTTCTTT
1 ATTATTATAT-TTT-TAT
* *
93664 TTTATTATATTCTTAT
1 ATTATTATATTTTTAT
93680 ATTATTAT-TTTTTAT
1 ATTATTATATTTTTAT
* * *
93695 TTTAATACTATTATTACT
1 ATTATTA-TATTTTTA-T
93713 A-TATT-T-TTTTTAT
1 ATTATTATATTTTTAT
* *
93726 ACCTTGTTATAATTTTAT
1 A--TTATTATATTTTTAT
93744 ATTATATATAT
1 ATTAT-TATAT
93755 GACTATTATT
Statistics
Matches: 181, Mismatches: 32, Indels: 48
0.69 0.12 0.18
Matches are distributed among these distances:
13 2 0.01
14 14 0.08
15 39 0.22
16 44 0.24
17 51 0.28
18 31 0.17
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (16 bp):
ATTATTATATTTTTAT
Found at i:93695 original size:13 final size:12
Alignment explanation
Indices: 93592--93695 Score: 52
Period size: 13 Copynumber: 8.3 Consensus size: 12
93582 TATATATATA
* *
93592 TATTATATATTA
1 TATTATATTTTT
*
93604 TATATATATATTT
1 TAT-TATATTTTT
*
93617 T-TT-TATTGTT
1 TATTATATTTTT
93627 T-TTATATTTTT
1 TATTATATTTTT
93638 ATATTTTATATTTTT
1 -TA--TTATATTTTT
* * *
93653 TCTGTTTCTTTTT
1 TAT-TATATTTTT
*
93666 TATTATATTCTTA
1 TATTATATT-TTT
93679 TATTATTATTTTT
1 TATTA-TATTTTT
93692 TATT
1 TATT
93696 TTAATACTAT
Statistics
Matches: 71, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
10 8 0.11
11 7 0.10
12 10 0.14
13 31 0.44
14 5 0.07
15 10 0.14
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (12 bp):
TATTATATTTTT
Found at i:93827 original size:36 final size:35
Alignment explanation
Indices: 93732--93827 Score: 81
Period size: 39 Copynumber: 2.7 Consensus size: 35
93722 TTATACCTTG
*
93732 TTATAATT-TTATATTATATATATGACTATTATTA
1 TTATTATTATTATATTATATATATGACTATTATTA
* * * *
93766 TT-TTAGTATTTTACTATAGCGTATAT-ACATATATATTT
1 TTATTATTATTATATTATA---TATATGAC-TAT-TATTA
93804 TTATTATTATTATATTATATATAT
1 TTATTATTATTATATTATATATAT
93828 CTTTTTATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
33 3 0.06
34 10 0.21
36 7 0.15
37 8 0.17
38 6 0.13
39 13 0.28
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.56
Consensus pattern (35 bp):
TTATTATTATTATATTATATATATGACTATTATTA
Done.