Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002333.1 Hibiscus syriacus cultivar Beakdansim tig00004769_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: 68776
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:910 original size:16 final size:17
Alignment explanation
Indices: 870--923 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 17
860 TTTATATATA
870 TTATAATATTACAT-ATT
1 TTAT-ATATTACATAATT
*
887 TAAT-TATTA-ATAATT
1 TTATATATTACATAATT
*
902 TTATATATTATATAAGTT
1 TTATATATTACATAA-TT
920 TTAT
1 TTAT
924 TTTTAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.35
16 5 0.16
17 7 0.23
18 6 0.19
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TTATATATTACATAATT
Found at i:7042 original size:45 final size:47
Alignment explanation
Indices: 6982--7073 Score: 161
Period size: 45 Copynumber: 2.0 Consensus size: 47
6972 TTCTCCCATT
*
6982 TTTTTCGTTAAAAACTGGCATGGTCTAATCA-AAGCTGACATGTGTA
1 TTTTTCGTTAAAAACTGGCATGGTCTAATCAGAAGATGACATGTGTA
7028 TTTTT-GTTAAAAACTGGCATGGTCTAATCAGAAGATGACATGTGTA
1 TTTTTCGTTAAAAACTGGCATGGTCTAATCAGAAGATGACATGTGTA
7074 ATAGATAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 25 0.57
46 19 0.43
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.35
Consensus pattern (47 bp):
TTTTTCGTTAAAAACTGGCATGGTCTAATCAGAAGATGACATGTGTA
Found at i:8579 original size:203 final size:199
Alignment explanation
Indices: 8217--8594 Score: 684
Period size: 203 Copynumber: 1.9 Consensus size: 199
8207 GAATAATAGG
8217 TGACAAAGTTATAACTTTAATAATTCATGGACTCAACAAAACAACTCTATAGTCTAAGAACTATT
1 TGACAAAGTTATAACTTTAATAATTCATGGACTCAACAAAACAACTCTATAGTCTAAGAACTATT
8282 TTGTAACTTTTAACAGTCGAAAGACTTAATAAAATATCATATAGTCGGGACTGTTCTACTTTATA
66 TTGTAACTTTTAACAGTCGAAAGACTTAATAAAATATCATATAGTCGGGACTGTTCTACTTTATA
8347 ACCAAGTATTTTTTTACATTATTATTTGTAAATTAAAATAATAATTTTTAAGTTTTAACTTTTAA
131 ACCAAGTATTTTTTTACATTATTATTTGTAAATTAAAAT-ATAATTTTTAAGTTTTAACTTTTAA
8412 TTAGA
195 TTAGA
* * *
8417 TGACAAAGTTATAGCTTTTAATAATTCATGGACTCAACAAAACAACACTTTATAGTTTAAGAACT
1 TGACAAAGTTATAAC-TTTAATAATTCATGGACTCAACAAAAC-A-ACTCTATAGTCTAAGAACT
*
8482 ATTTTGTAACTTTTAACGGTCGAAAGACTTAATAAAATATCATATAGTCGGGACTGTTCTACTTT
63 ATTTTGTAACTTTTAACAGTCGAAAGACTTAATAAAATATCATATAGTCGGGACTGTTCTACTTT
8547 ATAACCAAGTATTTTTTTACATTATTATTTGTAAATTAAAATATAATT
128 ATAACCAAGTATTTTTTTACATTATTATTTGTAAATTAAAATATAATT
8595 AATCTATAGC
Statistics
Matches: 171, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
200 14 0.08
201 27 0.16
202 7 0.04
203 123 0.72
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (199 bp):
TGACAAAGTTATAACTTTAATAATTCATGGACTCAACAAAACAACTCTATAGTCTAAGAACTATT
TTGTAACTTTTAACAGTCGAAAGACTTAATAAAATATCATATAGTCGGGACTGTTCTACTTTATA
ACCAAGTATTTTTTTACATTATTATTTGTAAATTAAAATATAATTTTTAAGTTTTAACTTTTAAT
TAGA
Found at i:9075 original size:24 final size:24
Alignment explanation
Indices: 9048--9103 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
9038 AGGAGATCAC
* *
9048 CAGAACCGGACGAGAGAAACCATA
1 CAGAACCAGACGAGAGAAACCACA
9072 CAGAACCAGACGAGAGAAACCACA
1 CAGAACCAGACGAGAGAAACCACA
9096 CAGAACCA
1 CAGAACCA
9104 TCACCGAGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.48, C:0.29, G:0.21, T:0.02
Consensus pattern (24 bp):
CAGAACCAGACGAGAGAAACCACA
Found at i:9112 original size:24 final size:24
Alignment explanation
Indices: 9048--9112 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
9038 AGGAGATCAC
** *
9048 CAGAACCGGACGAGAGAAACCATA
1 CAGAACCACACGAGAGAAACCACA
*
9072 CAGAACCAGACGAGAGAAACCACA
1 CAGAACCACACGAGAGAAACCACA
9096 CAGAACCATCACCGAGA
1 CAGAACCA-CA-CGAGA
9113 CAAAGGAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 30 0.83
25 1 0.03
26 5 0.14
ACGTcount: A:0.46, C:0.29, G:0.22, T:0.03
Consensus pattern (24 bp):
CAGAACCACACGAGAGAAACCACA
Found at i:13816 original size:179 final size:181
Alignment explanation
Indices: 13515--13862 Score: 612
Period size: 179 Copynumber: 1.9 Consensus size: 181
13505 ATTAAATCCG
13515 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
**
13580 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
13645 TTGTCAGGCC-A-ACTTTGTGATGAGACGAACCCTTCAGAGATTTGTCCCTC
131 TTGTCA-GCCAAGACTTTGTGATGAGACGAACCCTTCAGAGATTTGTCCCTC
*
13695 TAAAGCTGAGCTATTCCACTAAGGC-ATTGGTTATAGAGGAAACTCGAAAGCCCTGGTTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
13759 ATAGATTACATTCAAACTATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
13824 TTGTCAGCCAAAGACTTTGTGATGAGATGAACCCTTCAG
131 TTGTCAGCC-AAGACTTTGTGATGAGACGAACCCTTCAG
13863 TTAAACCTGA
Statistics
Matches: 160, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
178 3 0.02
179 106 0.66
180 26 0.16
181 25 0.16
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (181 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTACATTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGCCAAGACTTTGTGATGAGACGAACCCTTCAGAGATTTGTCCCTC
Found at i:15106 original size:72 final size:76
Alignment explanation
Indices: 15023--15181 Score: 229
Period size: 72 Copynumber: 2.1 Consensus size: 76
15013 ATCTCACTTG
* *
15023 AGATTGCTTTTCTTAAAAC-AGACTTTGTCTCACTTGAGACTGTTTT-ACTCGAAAGAA-G-ATT
1 AGATTGTTTTTCTTAAAACAAGA-TTTGTCTCACTTGAGACCGTTTTCACTCGAAAGAAGGCATT
15084 T-ATTTCACTCA
65 TCATTTCACTCA
*
15095 AGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTT
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGAAAGAAGGCATTT
15160 CATTTCACTCA
66 CATTTCACTCA
**
15171 AGGCTGTTTTT
1 AGATTGTTTTT
15182 AAAGAATATT
Statistics
Matches: 77, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
72 39 0.51
73 14 0.18
74 1 0.01
75 4 0.05
76 19 0.25
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (76 bp):
AGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGAAAGAAGGCATTT
CATTTCACTCA
Found at i:15140 original size:36 final size:36
Alignment explanation
Indices: 15014--15140 Score: 121
Period size: 36 Copynumber: 3.5 Consensus size: 36
15004 CAGATGATTA
* *
15014 TCTCACTTGAGATTGCTTTTCTTAAAAC-AGACTTTG
1 TCTCACTTGAGACTGTTTTTCTTAAAACAAGA-TTTG
* ** * *
15050 TCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTA
1 TCTCACTTGAGACTGTTTTTCTTAAAACAAGATTTG
* ** *
15086 TTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTG
1 TCTCACTTGAGACTGTTTTTCTTAAAACAAGATTTG
* *
15122 TCTCGCTTGAGACCGTTTT
1 TCTCACTTGAGACTGTTTT
15141 CACTCGAAAG
Statistics
Matches: 68, Mismatches: 22, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
36 65 0.96
37 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (36 bp):
TCTCACTTGAGACTGTTTTTCTTAAAACAAGATTTG
Found at i:15332 original size:105 final size:104
Alignment explanation
Indices: 15189--15483 Score: 461
Period size: 105 Copynumber: 2.9 Consensus size: 104
15179 TTTAAAGAAT
* * *
15189 ATTTTATCTTGCTTGAGATAGTTTCCCTCTAAATAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
1 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
* *
15254 TTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
66 CTTGAAACATAAACATTGAAAACATTTCCATTGAAATGA
* *
15293 ATTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTC
1 A-TTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTC
15358 TCTTGAAACATAAACATTGAAAACATTTCCATTGAAATGA
65 TCTTGAAACATAAACATTGAAAACATTTCCATTGAAATGA
*
15398 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AATTTTGTCTCCCTTGAGACAGTTTCT
1 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
** *
15460 CTCCAAACATAAACTTTGAAAACA
66 CTTGAAACATAAACATTGAAAACA
15484 ATTTAACGAA
Statistics
Matches: 177, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
101 48 0.27
103 1 0.01
104 31 0.18
105 97 0.55
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (104 bp):
ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
CTTGAAACATAAACATTGAAAACATTTCCATTGAAATGA
Found at i:15430 original size:36 final size:36
Alignment explanation
Indices: 15383--15458 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
15373 ATTGAAAACA
* * *
15383 TTTCCATTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCATTGAAACGAATTTTATCTCCCTTGAGACAG
* *
15419 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCATTGAAACGAATTTTATCTCCCTTGAGACAG
15455 TTTC
1 TTTC
15459 TCTCCAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCATTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:15537 original size:88 final size:88
Alignment explanation
Indices: 15418--15643 Score: 380
Period size: 88 Copynumber: 2.6 Consensus size: 88
15408 GCTTGAGATA
* * * *
15418 GTTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACTTTGAAAAC
1 GTTTTCCTTCAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTCGAAACATAAACTTTGAAAAC
15483 AATTTAACGAAATCTTTAAATAT
66 AATTTAACGAAATCTTTAAATAT
*
15506 GTTTTCCTTCAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAAC
1 GTTTTCCTTCAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTCGAAACATAAACTTTGAAAAC
*
15571 AATTTAACGAAATCTTTGAATAT
66 AATTTAACGAAATCTTTAAATAT
* *
15594 GTTTTCCTTCAAACAAATTTTGTCTCCTTTGAGACAATTTCTCTCGAAAC
1 GTTTTCCTTCAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTCGAAAC
15644 GACACAATTT
Statistics
Matches: 129, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 129 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.37
Consensus pattern (88 bp):
GTTTTCCTTCAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTCGAAACATAAACTTTGAAAAC
AATTTAACGAAATCTTTAAATAT
Found at i:21912 original size:23 final size:21
Alignment explanation
Indices: 21863--21925 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
21853 TTTTTGTGCA
* *
21863 GAGGGAATCGATCCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
21884 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
21905 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
21926 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 19 0.53
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:21933 original size:21 final size:21
Alignment explanation
Indices: 21907--21946 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21897 CCCCCTTTGA
*
21907 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
21928 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
21947 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:24214 original size:21 final size:21
Alignment explanation
Indices: 24190--24232 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
24180 GAGAAGAATA
24190 AGTGTTAAAGTAAGGGGGAGT
1 AGTGTTAAAGTAAGGGGGAGT
24211 AGTGTTAAAGTAAGGGGGAGT
1 AGTGTTAAAGTAAGGGGGAGT
24232 A
1 A
24233 ATTTAGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.42, T:0.23
Consensus pattern (21 bp):
AGTGTTAAAGTAAGGGGGAGT
Found at i:25641 original size:106 final size:105
Alignment explanation
Indices: 25518--25728 Score: 341
Period size: 106 Copynumber: 2.0 Consensus size: 105
25508 ATATCGTGCC
*
25518 ACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAATTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAAATTCCC
25583 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTC-CAGCGAAGGATATTGG
* * *
25624 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTTCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAAATTCCC
* ** *
25689 AGTTTCAGAGTTAGTTTCAACTTCCAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCCAGCGAAGGATATTGG
25729 CCTCGAAACA
Statistics
Matches: 97, Mismatches: 8, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
105 16 0.16
106 81 0.84
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (105 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAAATTCCC
AATTTCAGAGCCAATTTCAACTTCCAGCGAAGGATATTGG
Found at i:26584 original size:24 final size:24
Alignment explanation
Indices: 26557--26609 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
26547 AGATCACCAT
* *
26557 AACCGGACGAGAGAAACCATACAG
1 AACCAGACGAGAGAAACCACACAG
26581 AACCAGACGAGAGAAACCACACAG
1 AACCAGACGAGAGAAACCACACAG
26605 AACCA
1 AACCA
26610 TCACCGAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.49, C:0.28, G:0.21, T:0.02
Consensus pattern (24 bp):
AACCAGACGAGAGAAACCACACAG
Found at i:26618 original size:24 final size:24
Alignment explanation
Indices: 26563--26620 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 24
26553 CCATAACCGG
* *
26563 ACGAGAGAAACCATACAGAACCAG
1 ACGAGAGAAACCACACAGAACCAC
26587 ACGAGAGAAACCACACAGAACCATC
1 ACGAGAGAAACCACACAGAACCA-C
26612 ACCGAGAGA
1 A-CGAGAGA
26621 CAAAGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 22 0.73
25 1 0.03
26 7 0.23
ACGTcount: A:0.48, C:0.28, G:0.21, T:0.03
Consensus pattern (24 bp):
ACGAGAGAAACCACACAGAACCAC
Found at i:28652 original size:22 final size:22
Alignment explanation
Indices: 28624--28708 Score: 125
Period size: 22 Copynumber: 3.9 Consensus size: 22
28614 TGTCCTGCGC
** *
28624 CCTGCTCCCTGCTGCATGCTAG
1 CCTGCTCCCCACTGCATGCTCG
*
28646 CCTGCTCCTCACTGCATGCTCG
1 CCTGCTCCCCACTGCATGCTCG
*
28668 CCTGCTCCCCACTACATGCTCG
1 CCTGCTCCCCACTGCATGCTCG
28690 CCTGCTCCCCACTGCATGC
1 CCTGCTCCCCACTGCATGC
28709 AGGCGACCTC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.11, C:0.47, G:0.18, T:0.25
Consensus pattern (22 bp):
CCTGCTCCCCACTGCATGCTCG
Found at i:28774 original size:31 final size:31
Alignment explanation
Indices: 28739--28797 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
28729 CATGGCGCAT
28739 GCAAAGCTTCATCCTCT-GACCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCG-CCACAGCTCGTA
28770 GCAAAGCTTCATCCTCTCGCCACAGCTC
1 GCAAAGCTTCATCCTCTCGCCACAGCTC
28798 ATATAGAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.22
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
Found at i:40135 original size:32 final size:32
Alignment explanation
Indices: 40099--40264 Score: 314
Period size: 32 Copynumber: 5.2 Consensus size: 32
40089 TATAATATTT
*
40099 CATTAACAAAGGAAGCACAACAATAGGGGCAA
1 CATTAAAAAAGGAAGCACAACAATAGGGGCAA
40131 CATTAAAAAAGGAAGCACAACAATAGGGGCAA
1 CATTAAAAAAGGAAGCACAACAATAGGGGCAA
40163 CATTAAAAAAGGAAGCACAACAATAGGGGCAA
1 CATTAAAAAAGGAAGCACAACAATAGGGGCAA
*
40195 CATTAACAAAGGAAGCACAACAATAGGGGCAA
1 CATTAAAAAAGGAAGCACAACAATAGGGGCAA
40227 CATTAAAAAAGGAAGCACAACAATAGGGGCAA
1 CATTAAAAAAGGAAGCACAACAATAGGGGCAA
40259 CATTAA
1 CATTAA
40265 GGACGACAAT
Statistics
Matches: 131, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 131 1.00
ACGTcount: A:0.52, C:0.17, G:0.21, T:0.10
Consensus pattern (32 bp):
CATTAAAAAAGGAAGCACAACAATAGGGGCAA
Found at i:43390 original size:55 final size:54
Alignment explanation
Indices: 43241--43390 Score: 160
Period size: 55 Copynumber: 2.7 Consensus size: 54
43231 CATGAACTTG
*
43241 GACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGATCAATTCATGAAGAAA
1 GACATCCGATGAATGAAGAAATTTGAAACAGATTGAAGA-CAATTCATGAAGAAA
* * * * *
43296 AACATTCGATGATTGAAGAAATCTT-AAACAGATTGAAGACAGA-TCTGTGAAGAAT
1 GACATCCGATGAATGAAGAAAT-TTGAAACAGATTGAAGACA-ATTC-ATGAAGAAA
* * * *
43351 GACATCCAATGAAGGAAGAAATTTGAAGCCGATTGAAGAC
1 GACATCCGATGAATGAAGAAATTTGAAACAGATTGAAGAC
43391 TTCCTTTAAA
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
54 6 0.08
55 70 0.90
56 2 0.03
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (54 bp):
GACATCCGATGAATGAAGAAATTTGAAACAGATTGAAGACAATTCATGAAGAAA
Found at i:46140 original size:27 final size:27
Alignment explanation
Indices: 46108--46211 Score: 190
Period size: 27 Copynumber: 3.8 Consensus size: 27
46098 GGATCAACAT
*
46108 TTTTGCATATGCATTTGCATCTTTGCA
1 TTTTGCATCTGCATTTGCATCTTTGCA
46135 TTTTGCATCTGCATTTGCATCTTTGCA
1 TTTTGCATCTGCATTTGCATCTTTGCA
46162 TTTTGCATCTGCATTTGCATCTTTGCA
1 TTTTGCATCTGCATTTGCATCTTTGCA
46189 TTTTGCATCTGCATTTTGCATCT
1 TTTTGCATCTGCA-TTTGCATCT
46212 GTATTTACAT
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
27 66 0.88
28 9 0.12
ACGTcount: A:0.15, C:0.21, G:0.14, T:0.49
Consensus pattern (27 bp):
TTTTGCATCTGCATTTGCATCTTTGCA
Found at i:46223 original size:67 final size:67
Alignment explanation
Indices: 46117--46271 Score: 258
Period size: 67 Copynumber: 2.3 Consensus size: 67
46107 TTTTTGCATA
* *
46117 TGCA-TTTGCATCTTTGCATTTTGCATCTGCATTTGCATCTTTGCATTTTGCATCTGCATTTGCA
1 TGCATTTTGCATC--TGCATTTTGCATCTGCATTTACATCTTTGCATTTTGCATCTGCATTTACA
46181 TCTT
64 TCTT
*
46185 TGCATTTTGCATCTGCATTTTGCATCTGTATTTACATCTTTGCATTTTGCATCTGCATTTACATC
1 TGCATTTTGCATCTGCATTTTGCATCTGCATTTACATCTTTGCATTTTGCATCTGCATTTACATC
46250 TT
66 TT
46252 TGCATTTTGCATCTGCATTT
1 TGCATTTTGCATCTGCATTT
46272 ACATCTTTGC
Statistics
Matches: 83, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
67 71 0.86
68 4 0.05
69 8 0.10
ACGTcount: A:0.16, C:0.21, G:0.14, T:0.49
Consensus pattern (67 bp):
TGCATTTTGCATCTGCATTTTGCATCTGCATTTACATCTTTGCATTTTGCATCTGCATTTACATC
TT
Found at i:46228 original size:27 final size:27
Alignment explanation
Indices: 46198--46298 Score: 184
Period size: 27 Copynumber: 3.7 Consensus size: 27
46188 ATTTTGCATC
*
46198 TGCATTTTGCATCTGTATTTACATCTT
1 TGCATTTTGCATCTGCATTTACATCTT
46225 TGCATTTTGCATCTGCATTTACATCTT
1 TGCATTTTGCATCTGCATTTACATCTT
46252 TGCATTTTGCATCTGCATTTACATCTT
1 TGCATTTTGCATCTGCATTTACATCTT
*
46279 TGCATTTTGCATTTGCATTT
1 TGCATTTTGCATCTGCATTT
46299 GCATTTCATT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 72 1.00
ACGTcount: A:0.18, C:0.20, G:0.12, T:0.50
Consensus pattern (27 bp):
TGCATTTTGCATCTGCATTTACATCTT
Found at i:46229 original size:54 final size:54
Alignment explanation
Indices: 46117--46302 Score: 140
Period size: 54 Copynumber: 3.4 Consensus size: 54
46107 TTTTTGCATA
*
46117 TGCATTTGCATCTTTGCATTTTGCATCTGCATTTGCATCTTTGCATTTTGCATC--
1 TGCATTTGCATC--TGCATTTTGCATCTGCATTTACATCTTTGCATTTTGCATCTT
* * *
46171 TGCATTTGCATCTTTGCATTTTGCATCTGCATTTTGCATC--TGTA-TTTACATCTT
1 TGCATTTGCATC--TGCATTTTGCATCTGCA-TTTACATCTTTGCATTTTGCATCTT
* * *
46225 TGCATTTTGCATCTGCA-TTTACATCTTTGCATTTTGCATC--TGCA-TTTACATCTT
1 TGCA-TTTGCATCTGCATTTTGCATC--TGCA-TTTACATCTTTGCATTTTGCATCTT
*
46279 TGCATTTTGCATTTGCA-TTTGCAT
1 TGCA-TTTGCATCTGCATTTTGCAT
46303 TTCATTTTTA
Statistics
Matches: 120, Mismatches: 6, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
52 14 0.12
53 7 0.06
54 83 0.69
55 16 0.13
ACGTcount: A:0.17, C:0.21, G:0.13, T:0.49
Consensus pattern (54 bp):
TGCATTTGCATCTGCATTTTGCATCTGCATTTACATCTTTGCATTTTGCATCTT
Found at i:46265 original size:94 final size:94
Alignment explanation
Indices: 46108--46302 Score: 329
Period size: 94 Copynumber: 2.1 Consensus size: 94
46098 GGATCAACAT
* *
46108 TTTTGCATATGCATTTGCATCTTTGCATTTTGCATCTGCATTTGCATCTTTGCATTTTGCATCTG
1 TTTTGCATATGCATTTACATCTTTGCATTTTGCATCTGCATTTACATCTTTGCATTTTGCATCTG
*
46173 CATTTGCATCTTTGCATTTTGCATCTGCA
66 CATTTACATCTTTGCATTTTGCATCTGCA
* *
46202 TTTTGCATCTGTATTTACATCTTTGCATTTTGCATCTGCATTTACATCTTTGCATTTTGCATCTG
1 TTTTGCATATGCATTTACATCTTTGCATTTTGCATCTGCATTTACATCTTTGCATTTTGCATCTG
*
46267 CATTTACATCTTTGCATTTTGCATTTGCA
66 CATTTACATCTTTGCATTTTGCATCTGCA
46296 -TTTGCAT
1 TTTTGCAT
46303 TTCATTTTTA
Statistics
Matches: 95, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
93 7 0.07
94 88 0.93
ACGTcount: A:0.17, C:0.21, G:0.13, T:0.49
Consensus pattern (94 bp):
TTTTGCATATGCATTTACATCTTTGCATTTTGCATCTGCATTTACATCTTTGCATTTTGCATCTG
CATTTACATCTTTGCATTTTGCATCTGCA
Found at i:46294 original size:67 final size:66
Alignment explanation
Indices: 46117--46302 Score: 227
Period size: 67 Copynumber: 2.8 Consensus size: 66
46107 TTTTTGCATA
* * *
46117 TGCA-TTTGCATCTTTGCATTTTGCATCTGCATTTGCATCTTTGCATTTTGCATCTGCATTTGCA
1 TGCATTTTGCATC--TGCATTTTACATCTGCATTTACA-CTTTGCATTTTGCATCTGCATTTACA
46181 TCTT
63 TCTT
* *
46185 TGCATTTTGCATCTGCATTTTGCATCTGTATTTACATCTTTGCATTTTGCATCTGCATTTACATC
1 TGCATTTTGCATCTGCATTTTACATCTGCATTTACA-CTTTGCATTTTGCATCTGCATTTACATC
46250 TT
65 TT
*
46252 TGCATTTTGCATCTGCA-TTTACATCTTTGCATTTTGCA-TTTGCA-TTTGCAT
1 TGCATTTTGCATCTGCATTTTACATC--TGCA-TTTACACTTTGCATTTTGCAT
46303 TTCATTTTTA
Statistics
Matches: 108, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
66 14 0.13
67 74 0.69
68 7 0.06
69 13 0.12
ACGTcount: A:0.17, C:0.21, G:0.13, T:0.49
Consensus pattern (66 bp):
TGCATTTTGCATCTGCATTTTACATCTGCATTTACACTTTGCATTTTGCATCTGCATTTACATCT
T
Found at i:47473 original size:5 final size:5
Alignment explanation
Indices: 47463--47612 Score: 55
Period size: 5 Copynumber: 29.4 Consensus size: 5
47453 TCAAACAAAT
* * *
47463 AAGAA AAGAA AAGAAA AAGAAA CAGAGAA AAGAG AA-AA GAGAA AAGAG
1 AAGAA AAGAA AAG-AA AAG-AA -A-AGAA AAGAA AAGAA AAGAA AAGAA
* * *
47511 AA-AA GAGAA AAGAA AAGAA AA-ATTA AAGCA AATAA AA-AA AGAGCAAA
1 AAGAA AAGAA AAGAA AAGAA AAGA--A AAGAA AAGAA AAGAA A-AG--AA
* * * *
47558 AATGAA AAGAA AA-AGA AA-CA AAGAA AAAAA AAGAA AA-AA GA-AA AAGTA
1 AA-GAA AAGAA AAGA-A AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
47606 AAGAA AA
1 AAGAA AA
47613 AGGGACGATA
Statistics
Matches: 110, Mismatches: 19, Indels: 32
0.68 0.12 0.20
Matches are distributed among these distances:
4 18 0.16
5 66 0.60
6 16 0.15
7 4 0.04
8 6 0.05
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (5 bp):
AAGAA
Found at i:47493 original size:14 final size:13
Alignment explanation
Indices: 47466--47601 Score: 96
Period size: 14 Copynumber: 10.7 Consensus size: 13
47456 AACAAATAAG
47466 AAAAG-AAA-AGA
1 AAAAGAAAAGAGA
47477 AAAAGAAACAGAGA
1 AAAAGAAA-AGAGA
47491 AAAGAGAAAAGAGA
1 AAA-AGAAAAGAGA
47505 AAAGAGAAAAGAG-
1 AAA-AGAAAAGAGA
47518 AAAAG-AAA-AGA
1 AAAAGAAAAGAGA
**
47529 AAAATTAAAGCA-A
1 AAAAGAAAAG-AGA
47542 ATAAA-AAAAGAGCA
1 A-AAAGAAAAGAG-A
47556 AAAATG-AAA-AGA
1 AAAA-GAAAAGAGA
*
47568 AAAAGAAACAAAGA
1 AAAAGAAA-AGAGA
47582 AAAA-AAAAGA-A
1 AAAAGAAAAGAGA
47593 AAAAGAAAA
1 AAAAGAAAA
47602 AGTAAAGAAA
Statistics
Matches: 105, Mismatches: 3, Indels: 33
0.74 0.02 0.23
Matches are distributed among these distances:
10 2 0.02
11 18 0.17
12 21 0.20
13 19 0.18
14 40 0.38
15 5 0.05
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (13 bp):
AAAAGAAAAGAGA
Found at i:47498 original size:7 final size:7
Alignment explanation
Indices: 47469--47523 Score: 87
Period size: 7 Copynumber: 8.1 Consensus size: 7
47459 AAATAAGAAA
47469 AGAAAAG
1 AGAAAAG
47476 A-AAAAG
1 AGAAAAG
*
47482 A-AACAG
1 AGAAAAG
47488 AGAAAAG
1 AGAAAAG
47495 AGAAAAG
1 AGAAAAG
47502 AGAAAAG
1 AGAAAAG
47509 AGAAAAG
1 AGAAAAG
47516 AGAAAAG
1 AGAAAAG
47523 A
1 A
47524 AAAGAAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
6 11 0.24
7 34 0.76
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (7 bp):
AGAAAAG
Found at i:47500 original size:21 final size:20
Alignment explanation
Indices: 47474--47614 Score: 100
Period size: 19 Copynumber: 7.0 Consensus size: 20
47464 AGAAAAGAAA
47474 AGAAAAAGAAACAGAGAAAAG
1 AGAAAAAGAAA-AGAGAAAAG
47495 AGAAAAGAGAAAAGAGAAAAG
1 AGAAAA-AGAAAAGAGAAAAG
* *
47516 AG-AAAAGAAAAGAAAAATTAA
1 AGAAAAAGAAAAGAGAAA--AG
*
47537 AGCAAATAAAAAAAGAGCAAAA-
1 AG-AAA-AAGAAAAGAG-AAAAG
*
47559 ATG-AAAAGAAAA-AGAAACAA
1 A-GAAAAAGAAAAGAGAAA-AG
47579 AGAAAAA-AAAAGA-AAAA-
1 AGAAAAAGAAAAGAGAAAAG
*
47596 AGAAAAAGTAAAGA-AAAAG
1 AGAAAAAGAAAAGAGAAAAG
47615 GGACGATAAT
Statistics
Matches: 100, Mismatches: 6, Indels: 30
0.74 0.04 0.22
Matches are distributed among these distances:
17 7 0.07
18 13 0.13
19 22 0.22
20 15 0.15
21 22 0.22
22 6 0.06
23 4 0.04
24 8 0.08
25 3 0.03
ACGTcount: A:0.75, C:0.03, G:0.18, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAAAAGAGAAAAG
Found at i:47596 original size:7 final size:7
Alignment explanation
Indices: 47471--47602 Score: 60
Period size: 7 Copynumber: 18.4 Consensus size: 7
47461 ATAAGAAAAG
47471 AAAAG-A
1 AAAAGAA
47477 AAAAG-A
1 AAAAGAA
* *
47483 AACAGAG
1 AAAAGAA
*
47490 AAAAGAG
1 AAAAGAA
*
47497 AAAAGAG
1 AAAAGAA
*
47504 AAAAGAG
1 AAAAGAA
*
47511 AAAAGAG
1 AAAAGAA
47518 AAAAGAA
1 AAAAGAA
47525 AAGAA-AA
1 AA-AAGAA
47532 ATTAAAGCAA
1 A--AAAG-AA
47542 ATAAA-AA
1 A-AAAGAA
*
47549 AAGAGCAA
1 AAAAG-AA
*
47557 AAATGAA
1 AAAAGAA
47564 AAGAA-AA
1 AA-AAGAA
*
47571 AGAAACAA
1 A-AAAGAA
47579 AGAAA-AA
1 A-AAAGAA
47586 AAAAGAA
1 AAAAGAA
47593 AAAAGAA
1 AAAAGAA
47600 AAA
1 AAA
47603 GTAAAGAAAA
Statistics
Matches: 106, Mismatches: 8, Indels: 23
0.77 0.06 0.17
Matches are distributed among these distances:
6 15 0.14
7 65 0.61
8 18 0.17
9 5 0.05
10 3 0.03
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (7 bp):
AAAAGAA
Found at i:47608 original size:18 final size:17
Alignment explanation
Indices: 47463--47613 Score: 97
Period size: 18 Copynumber: 8.1 Consensus size: 17
47453 TCAAACAAAT
*
47463 AAGAAAAGAAAAG-AAA
1 AAGAAAAAAAAAGAAAA
47479 AAGAAACAGAGAAAAGAGAAA
1 AAGAAA-A-A-AAAAGA-AAA
*
47500 AGAGAAAAGAGAAAAGAGAA
1 A-AGAAAA-A-AAAAGAAAA
*
47520 AAGAAAAGAAAAATTAAAGCA
1 AAGAAAA-AAAAA-GAAA--A
* *
47541 AATAAAAAAAGAGCAAAA
1 AAGAAAAAAAAAG-AAAA
*
47559 ATGAAAAGAAAAAGAAACA
1 AAGAAAA-AAAAAGAAA-A
47578 AAGAAAAAAAAAGAAAA
1 AAGAAAAAAAAAGAAAA
*
47595 AAGAAAAAGTAAAGAAAA
1 AAGAAAAA-AAAAGAAAA
47613 A
1 A
47614 GGGACGATAA
Statistics
Matches: 110, Mismatches: 12, Indels: 24
0.75 0.08 0.16
Matches are distributed among these distances:
16 6 0.05
17 10 0.09
18 31 0.28
19 27 0.25
20 10 0.09
21 21 0.19
22 5 0.05
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (17 bp):
AAGAAAAAAAAAGAAAA
Found at i:48752 original size:33 final size:32
Alignment explanation
Indices: 48655--48788 Score: 205
Period size: 32 Copynumber: 4.2 Consensus size: 32
48645 AGCAATAGAA
*
48655 GGCATCTTTGAAGATTCAACATCAAATGTTGG
1 GGCATCTTTGGAGATTCAACATCAAATGTTGG
*
48687 GGCATCTTTGGAAATTCAACATCAAATGTTGG
1 GGCATCTTTGGAGATTCAACATCAAATGTTGG
48719 GGCATCTTTGGAGATTCAACATCAAAATGTTGG
1 GGCATCTTTGGAGATTCAACATC-AAATGTTGG
* * * *
48752 GGCATCCTTGGAGATTCAAGATCGAATATTGG
1 GGCATCTTTGGAGATTCAACATCAAATGTTGG
48784 GGCAT
1 GGCAT
48789 TCAATATCTT
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
32 64 0.68
33 30 0.32
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (32 bp):
GGCATCTTTGGAGATTCAACATCAAATGTTGG
Found at i:48769 original size:65 final size:64
Alignment explanation
Indices: 48655--48788 Score: 205
Period size: 65 Copynumber: 2.1 Consensus size: 64
48645 AGCAATAGAA
* *
48655 GGCATCTTTGAAGATTCAACATCAAATGTTGGGGCATCTTTGGAAATTCAACATCAAATGTTGG
1 GGCATCTTTGAAGATTCAACATCAAATGTTGGGGCATCCTTGGAAATTCAACATCAAATATTGG
* * * *
48719 GGCATCTTTGGAGATTCAACATCAAAATGTTGGGGCATCCTTGGAGATTCAAGATCGAATATTGG
1 GGCATCTTTGAAGATTCAACATC-AAATGTTGGGGCATCCTTGGAAATTCAACATCAAATATTGG
48784 GGCAT
1 GGCAT
48789 TCAATATCTT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
64 22 0.35
65 41 0.65
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (64 bp):
GGCATCTTTGAAGATTCAACATCAAATGTTGGGGCATCCTTGGAAATTCAACATCAAATATTGG
Found at i:49032 original size:39 final size:34
Alignment explanation
Indices: 48893--49012 Score: 168
Period size: 34 Copynumber: 3.5 Consensus size: 34
48883 TTAAAAAAAT
* * *
48893 TCTCACTTGAGATAATTTCTCAAAACAAATTTTG
1 TCTCGCTTGAGACAATTTCTCAAAACAAATTTCG
* * * *
48927 TCTCACTTGAGACAATTTATCAAAGCAAATTCCG
1 TCTCGCTTGAGACAATTTCTCAAAACAAATTTCG
48961 TCTCGCTTGAGACAATTTCTCAAAACAAATTTCG
1 TCTCGCTTGAGACAATTTCTCAAAACAAATTTCG
*
48995 TCTCGTTTGAGACAATTT
1 TCTCGCTTGAGACAATTT
49013 TTCTCTGAGA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 76 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35
Consensus pattern (34 bp):
TCTCGCTTGAGACAATTTCTCAAAACAAATTTCG
Found at i:49360 original size:40 final size:40
Alignment explanation
Indices: 49311--49590 Score: 407
Period size: 40 Copynumber: 7.0 Consensus size: 40
49301 TTTCATTTTA
* * * **
49311 CAAGATTGTTTTTCCTTGAAACATAATATTTTATTTTGCT
1 CAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACT
* *
49351 CAAGATTGTTTTTCCTTGAAACAGAAGATTTAATCTCATT
1 CAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACT
* * *
49391 CATGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCATT
1 CAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACT
* *
49431 CAAGATTGTTTTTCTTTGAAACAGAAGATTTAATCTCACT
1 CAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACT
* *
49471 CAAGATTGTTTTTTCTTGAAACATAAGATTTTATCTCACT
1 CAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACT
*
49511 CAATATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACT
1 CAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACT
* *
49551 CAAGATTGTTTTTTCTTGAAACAAAAGATTTTATCTCACT
1 CAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACT
49591 TGAGATAATT
Statistics
Matches: 215, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 215 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (40 bp):
CAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACT
Found at i:49620 original size:26 final size:26
Alignment explanation
Indices: 49584--49634 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
49574 AAAGATTTTA
*
49584 TCTCACTTGAGATAATTTCCCTTGAG
1 TCTCACTTGAGACAATTTCCCTTGAG
* *
49610 TCTCCCTTGAGACAGTTTCCCTTGA
1 TCTCACTTGAGACAATTTCCCTTGA
49635 AACAAAAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.37
Consensus pattern (26 bp):
TCTCACTTGAGACAATTTCCCTTGAG
Found at i:49692 original size:21 final size:21
Alignment explanation
Indices: 49666--49730 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
49656 TGAGATAGTT
49666 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
* *
49687 TCCCTTGAGAC--A----GTT
1 TCCCTTGAAACAAATTTTGTC
49702 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
49723 TCCCTTGA
1 TCCCTTGA
49731 GATTGTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 12 0.35
17 1 0.03
19 1 0.03
21 20 0.59
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.37
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:49694 original size:36 final size:36
Alignment explanation
Indices: 49609--49893 Score: 408
Period size: 36 Copynumber: 7.8 Consensus size: 36
49599 TTTCCCTTGA
49609 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAAAGATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAAC--AA-ATTTT
* * *
49648 ATCTCACTTGAGATAGTTTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
49684 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
** *
49720 GTCTCCCTTGAGATTGTTTCCCATGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
**
49756 GTCTTTCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
* * *
49792 ATCTCTCTTGAGACAGTTTCCGTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
*
49828 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
* * *
49864 GTCTCCCTTGAGATAATTTCTCTTGAAACA
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACA
49894 CAAAATTTTG
Statistics
Matches: 223, Mismatches: 23, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
36 195 0.87
37 2 0.01
39 26 0.12
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (36 bp):
GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
Found at i:49786 original size:108 final size:108
Alignment explanation
Indices: 49609--50060 Score: 438
Period size: 108 Copynumber: 4.3 Consensus size: 108
49599 TTTCCCTTGA
*
49609 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAAAGATTTTATCTCACTTGAGATAGTTTCCCTTGA
1 GTCTCCCTTGAGACAGTTTCCCTTGAAAC--AA-ATTTTGTCTCACTTGAGATAGTTTCCCTTGA
*
49674 AACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
63 AACAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
** * ** *
49720 GTCTCCCTTGAGATTGTTTCCCATGAAACAAATTTTGTCTTTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGATAGTTTCCCTTGAAAC
* *
49785 AAATTTTATCTCTCTTGAGACAGTTTCCGTTGAAACAAATTTT
66 AAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
* * * *
49828 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAATTTCTCTTGAAAC
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGATAGTTTCCCTTGAAAC
* ** *
49893 ACAA---AAT-T---TTGAGA-ACGTTTCCCTTGAAATGATTTTT
66 A-AATTTTATCTCCCTTGAGACA-GTTTCCCTTGAAACAAATTTT
** * *
49930 GTCTCCCTT--GACAGTTTCTTTTGAAAC-AA----GT-T--TTTGAGATAGTTTCTCTTGAAA-
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGATAGTTTCCCTTGAAAC
* * * ** **
49984 AAATGTTTTGTCTCTCTTAAGATGGTTTTTCTTGAAACAAATTTT
66 AAA--TTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
50029 GTCTCCCTTGAGACAGATTTCCCTTGAAACAA
1 GTCTCCCTTGAGACAG-TTTCCCTTGAAACAA
50061 GAAATTGAAT
Statistics
Matches: 285, Mismatches: 40, Indels: 40
0.78 0.11 0.11
Matches are distributed among these distances:
90 2 0.01
91 1 0.00
92 20 0.07
94 1 0.00
95 3 0.01
96 1 0.00
99 32 0.11
100 16 0.06
101 6 0.02
102 42 0.15
103 1 0.00
105 1 0.00
106 2 0.01
108 127 0.45
109 4 0.01
111 26 0.09
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (108 bp):
GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGATAGTTTCCCTTGAAAC
AAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
Found at i:50032 original size:36 final size:36
Alignment explanation
Indices: 49966--50097 Score: 95
Period size: 37 Copynumber: 3.5 Consensus size: 36
49956 CAAGTTTTTG
* *
49966 AGATAGTTTCTCTTGAAA-AAATGTTTTGTCTCTCTTA
1 AGATGGTTTCTCTTGAAACAAA--TTTTGTCTCACTTA
* * *
50003 AGATGGTTTTTCTTGAAACAAATTTTGTCTCCCTTG
1 AGATGGTTTCTCTTGAAACAAATTTTGTCTCACTTA
* * * **
50039 AGACAGATTTCCCTTGAAACAAGAAATTGAATCTCACTTA
1 AGA-TGGTTTCTCTTGAAACAA-ATTTTG--TCTCACTTA
* *
50079 AGATGGTTTTTCTTAAAAC
1 AGATGGTTTCTCTTGAAAC
50098 TTACTTCGTC
Statistics
Matches: 73, Mismatches: 17, Indels: 8
0.74 0.17 0.08
Matches are distributed among these distances:
36 15 0.21
37 30 0.41
38 7 0.10
39 11 0.15
40 10 0.14
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (36 bp):
AGATGGTTTCTCTTGAAACAAATTTTGTCTCACTTA
Found at i:50126 original size:76 final size:76
Alignment explanation
Indices: 49994--50173 Score: 183
Period size: 76 Copynumber: 2.4 Consensus size: 76
49984 AAATGTTTTG
* * * *
49994 TCTCTCTTAAGATGGTTTTTCTTGAAACAAATTTTGTCTCCCTTGAGACAGATTTCCCTT-GAAA
1 TCTCACTTAAGATGGTTTTTCTTAAAACAAACTTCGTCTCCCTTGAGACAGATTT-CCTTCGAAA
50058 CAAGAAATTGAA
65 CAAGAAATTGAA
** **
50070 TCTCACTTAAGATGGTTTTTCTTAAAACTTACTTCGTCTTGCTTGAGACA-ATTTTCCTTCGAAA
1 TCTCACTTAAGATGGTTTTTCTTAAAACAAACTTCGTCTCCCTTGAGACAGA-TTTCCTTCGAAA
*
50134 C-A-AAATT-TA
65 CAAGAAATTGAA
* *
50143 TCTCACTCGAGAGA-GCTTTTTCTTAAAACAA
1 TCTCACT-TA-AGATGGTTTTTCTTAAAACAA
50174 GTTTCTTATT
Statistics
Matches: 87, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
73 8 0.09
74 20 0.23
75 9 0.10
76 50 0.57
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (76 bp):
TCTCACTTAAGATGGTTTTTCTTAAAACAAACTTCGTCTCCCTTGAGACAGATTTCCTTCGAAAC
AAGAAATTGAA
Found at i:50888 original size:19 final size:17
Alignment explanation
Indices: 50865--50918 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
50855 TCCAGAAGAG
50865 TTCATAATGAGAAGAAC
1 TTCATAATGAGAAGAAC
* * *
50882 TCGTCATAAAG-GAAAAAG
1 T--TCATAATGAGAAGAAC
50900 TTCATAATGAGAAGAAC
1 TTCATAATGAGAAGAAC
50917 TT
1 TT
50919 GTTCCTTTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
16 7 0.25
17 8 0.29
18 6 0.21
19 7 0.25
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.24
Consensus pattern (17 bp):
TTCATAATGAGAAGAAC
Done.