Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002775.1 Hibiscus syriacus cultivar Beakdansim tig00005717_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: 86251
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4849 original size:27 final size:27
Alignment explanation
Indices: 4811--4882 Score: 128
Period size: 27 Copynumber: 2.7 Consensus size: 27
4801 CAACATGGTA
*
4811 TCTACCCTGACATGCTTTTATAAAAGT
1 TCTACCCAGACATGCTTTTATAAAAGT
4838 TCTACCCAGACATGCTTTTATAAAAGT
1 TCTACCCAGACATGCTTTTATAAAAGT
4865 TCTACCCAGACATG-TTTT
1 TCTACCCAGACATGCTTTT
4883 GTACCTCCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
26 4 0.09
27 40 0.91
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (27 bp):
TCTACCCAGACATGCTTTTATAAAAGT
Found at i:8402 original size:10 final size:10
Alignment explanation
Indices: 8387--8438 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
8377 GACTTGCAAT
8387 AAAATAATAA
1 AAAATAATAA
8397 AAAATAATAA
1 AAAATAATAA
* *
8407 TAATTAAT-A
1 AAAATAATAA
*
8416 ATAATAATAA
1 AAAATAATAA
* *
8426 TAAATATTAA
1 AAAATAATAA
8436 AAA
1 AAA
8439 TATCCGACGA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
9 6 0.19
10 26 0.81
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAATAATAA
Found at i:8405 original size:3 final size:3
Alignment explanation
Indices: 8384--8428 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
8374 ATGGACTTGC
8384 AAT AA- AAT AAT AA- AA- AAT AAT AAT AATT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
8427 AA
1 AA
8429 ATATTAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 6 0.15
3 30 0.77
4 3 0.08
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:8423 original size:13 final size:12
Alignment explanation
Indices: 8384--8428 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 12
8374 ATGGACTTGC
8384 AATAA-AATAAT
1 AATAATAATAAT
8395 AA-AA-AATAAT
1 AATAATAATAAT
8405 AATAATTAATAAT
1 AATAA-TAATAAT
8418 AATAATAATAA
1 AATAATAATAA
8429 ATATTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.32
11 4 0.13
12 6 0.19
13 11 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAATAATAAT
Found at i:8440 original size:16 final size:16
Alignment explanation
Indices: 8387--8440 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
8377 GACTTGCAAT
*
8387 AAAATAATAAAAAATA
1 AAAATAATAAATAATA
* *
8403 ATAATAATTAATAATA
1 AAAATAATAAATAATA
* *
8419 ATAATAATAAATATTA
1 AAAATAATAAATAATA
8435 AAAATA
1 AAAATA
8441 TCCGACGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATAATAAATAATA
Found at i:10008 original size:22 final size:22
Alignment explanation
Indices: 9983--10032 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
9973 AAAACTAGAG
9983 TTTATATTAATTAA-ATT-AAATT
1 TTTATATTAA--AATATTAAAATT
10005 TTTAATATTAAAATATTAAAATT
1 TTT-ATATTAAAATATTAAAATT
10028 TTTAT
1 TTTAT
10033 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 2 0.08
22 8 0.32
23 15 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTATATTAAAATATTAAAATT
Found at i:24966 original size:36 final size:37
Alignment explanation
Indices: 24728--25124 Score: 253
Period size: 38 Copynumber: 10.5 Consensus size: 37
24718 AAATCATAAA
*
24728 TAAAAACTATATAATATATATATATTTTTTAAAAATATTGTT
1 TAAAAACTATAT-AT-TATATATA-TTTTCAAAAATA-T-TT
* * *
24770 TTAAAACTATATATAATATATATTTCCAAAAAAAATATTT
1 TAAAAACTATATATTATATATATTTTC---AAAAATATTT
** * * *
24810 CCAAAACAATATATTATATA-ATTTTAAAAAATGTTT
1 TAAAAACTATATATTATATATATTTTCAAAAATATTT
** * * *
24846 T-TGAACTATATGTTATATA-GTTTTCAAAAATGTTT
1 TAAAAACTATATATTATATATATTTTCAAAAATATTT
* *
24881 T-AAAAC--TATA-T-TATATGTTTTCAAAAATGTTTTTTTT
1 TAAAAACTATATATTATATATATTTTCAAAAA-----TATTT
*
24918 TCAAAAATTATATATTATATATATTTTC-AAAATATTT
1 T-AAAAACTATATATTATATATATTTTCAAAAATATTT
* * * *
24955 TCAGAACTATATATATTATATATATTTTCTAAAATGTTT
1 TAAAAAC--TATATATTATATATATTTTCAAAAATATTT
* *
24994 TAAAAATCTATATATTATTTA-ATTTTCAAAAATGTTT
1 TAAAAA-CTATATATTATATATATTTTCAAAAATATTT
* *
25031 TAAAAACTATATAATATATACATTTTC-AAAATATTT
1 TAAAAACTATATATTATATATATTTTCAAAAATATTT
* *
25067 TGAAAACTAT-TATTATACCTGTATTTTCAAAAACTA-TT
1 TAAAAACTATATATTATA--TATATTTTCAAAAA-TATTT
** *
25105 TGCAAACTATATAATATATA
1 TAAAAACTATATATTATATA
25125 GATATATATA
Statistics
Matches: 287, Mismatches: 43, Indels: 55
0.75 0.11 0.14
Matches are distributed among these distances:
31 4 0.01
32 12 0.04
33 3 0.01
35 38 0.13
36 41 0.14
37 45 0.16
38 47 0.16
39 31 0.11
40 26 0.09
41 7 0.02
42 23 0.08
43 10 0.03
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (37 bp):
TAAAAACTATATATTATATATATTTTCAAAAATATTT
Found at i:25042 original size:112 final size:107
Alignment explanation
Indices: 24732--25076 Score: 277
Period size: 112 Copynumber: 3.1 Consensus size: 107
24722 CATAAATAAA
* *
24732 AACTATATAATATATATATATTTTTTAAAAATATTGTTTTAAAACTATATATAATATATATTTCC
1 AACTATAT-ATAT-TATATA-ATTTTCAAAA-A-TGTTTTAAAACTATAT-T-ATATAT-TTT-C
** * * * * **
24797 AAAAAAAATATTTCCAAAACAATATATTATATAATTTT-AAAAAATGTTTTTG
57 -AAAAATGTTTTTCAAAAACTATATATTATATAATTTTCAAAATAT-TTTCAG
* * *
24849 AAC--TATATGTTATATAGTTTTCAAAAATGTTTTAAAACTATATTATATGTTTTCAAAAATGTT
1 AACTATATATATTATATAATTTTCAAAAATGTTTTAAAACTATATTATATATTTTCAAAAATG--
*
24912 TTTTTTTCAAAAATTATATATTATATATATTTTCAAAATATTTTCAG
64 --TTTTTCAAAAACTATATATTATATA-ATTTTCAAAATATTTTCAG
* *
24959 AACTATATATATTATATATATTTTCTAAAATGTTTTAAAAATCTATATATTATTTAATTTTCAAA
1 AACTATATATATTATATA-ATTTTCAAAAATGTTTT-AAAA-C--TATATTATAT-ATTTTCAAA
* * *
25024 AATG-TTTT-AAAAACTATATAATATATACATTTTCAAAATATTTTGAA
60 AATGTTTTTCAAAAACTATATATTATATA-ATTTTCAAAATATTTTCAG
25071 AACTAT
1 AACTAT
25077 TATTATACCT
Statistics
Matches: 191, Mismatches: 23, Indels: 33
0.77 0.09 0.13
Matches are distributed among these distances:
105 5 0.03
106 1 0.01
107 3 0.02
108 5 0.03
109 22 0.12
110 28 0.15
111 7 0.04
112 60 0.31
113 25 0.13
114 7 0.04
115 4 0.02
117 12 0.06
118 12 0.06
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.46
Consensus pattern (107 bp):
AACTATATATATTATATAATTTTCAAAAATGTTTTAAAACTATATTATATATTTTCAAAAATGTT
TTTCAAAAACTATATATTATATAATTTTCAAAATATTTTCAG
Found at i:25093 original size:74 final size:72
Alignment explanation
Indices: 24915--25124 Score: 196
Period size: 74 Copynumber: 2.8 Consensus size: 72
24905 AAATGTTTTT
* * *
24915 TTTTCAAAAAT-TATATATTATATATATTTTC-AAAATATTTTCAGAACTATATATATTATATAT
1 TTTT-AAAAATCTATATATTAT-T-TATTTTCAAAAAT-TTTTAAAAACTATATA-A-TATATAC
*
24978 ATTTTCTAAAATG
60 ATTTTCTAAAATA
24991 TTTTAAAAATCTATATATTATTTAATTTTCAAAAATGTTTTAAAAACTATATAATATATACATTT
1 TTTTAAAAATCTATATATTATTT-ATTTTCAAAAAT-TTTTAAAAACTATATAATATATACATTT
25056 TC-AAAATA
64 TCTAAAATA
* * **
25064 TTTTGAAAA-CTAT-TATTATACCTGTATTTTCAAAAACTATTTGCAAACTATATAATATATA
1 TTTTAAAAATCTATATATTAT---T-TATTTTCAAAAA-TTTTTAAAAACTATATAATATATA
25125 GATATATATA
Statistics
Matches: 117, Mismatches: 9, Indels: 18
0.81 0.06 0.12
Matches are distributed among these distances:
71 6 0.05
72 4 0.03
73 13 0.11
74 45 0.38
75 16 0.14
76 33 0.28
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (72 bp):
TTTTAAAAATCTATATATTATTTATTTTCAAAAATTTTTAAAAACTATATAATATATACATTTTC
TAAAATA
Found at i:25891 original size:84 final size:84
Alignment explanation
Indices: 25706--26621 Score: 940
Period size: 84 Copynumber: 11.0 Consensus size: 84
25696 GCTATGTTGT
* * *
25706 AAATGATGTGCCCTAGAGCTGAGCGTAGTCGAACTCGAAGGTC--T--TTGGCAGATAGCCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* * * * * *
25767 TAGCCTTGAGCTATACCGC
66 TCGACTTAAGTTATGCTGC
* ** * *
25786 AAATGACGCACCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
25851 TCGACTTAAGTTATGCTGC
66 TCGACTTAAGTTATGCTGC
* * * *
25870 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAATGTCTTTGG-TGACAGATAACCATTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* * *
25934 TAGCCTTGAA-TTATGCTGT
66 TCGACTT-AAGTTATGCTGC
** * * *
25953 AAATGATGTGCCCTTAAAGCTGAGTGTAATCGAACTC-AAGGGTC--T--TTGGCAGATAGCCCT
1 AAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA-GGTCTTTGGTTGGCAGATAACCCT
* *
26013 TCTCGACTTAAGCTATGCTAC
64 TCTCGACTTAAGTTATGCTGC
* * *
26034 AAATGATGTGCCTTGGAGCTTAGCGTAGTCGAACTCAAAGGTTTTTGGTTGGCAGATAACCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
26099 TCGACTTAAGTTATGCTGC
66 TCGACTTAAGTTATGCTGC
* * * * * *
26118 AAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGATAACCCTT
1 AAATGATG-TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
26179 CTCGACTTAAGTTATGCTGC
65 CTCGACTTAAGTTATGCTGC
*
26199 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
26264 TCGACTTAAGTTATGCTGC
66 TCGACTTAAGTTATGCTGC
* * * * ** * *
26283 AAATGATGTTCCTTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTTGGATGGAAGATAACCCT
1 AAATGATGTGCCTT-GGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCT
* * *
26348 TCTTGATTTAAGCTATGCTGC
64 TCTCGACTTAAGTTATGCTGC
* * * **
26369 AAATGTTGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTGG-TCACAGATAACCCTT
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG-TCTTTGGTTGGCAGATAACCCTT
* *
26433 CT-AACCTTGAGTTATGCTGC
65 CTCGA-CTTAAGTTATGCTGC
* * * * * * *
26453 AAATAATGTGCCCTTGAAGCTGAGTGTAATCGAACACGAGGGTC--T--TTGGCAGATAGCCCTT
1 AAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
* *
26514 TTCGACTTAAGCTATGCTGC
65 CTCGACTTAAGTTATGCTGC
* * * * *
26534 AAATGATATGCCTCGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGACAAATAGCCCTT
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTT
* *
26598 CTTGACTTAAGCTATGCTGC
65 CTCGACTTAAGTTATGCTGC
26618 AAAT
1 AAAT
26622 AGTTTCTTTA
Statistics
Matches: 684, Mismatches: 121, Indels: 58
0.79 0.14 0.07
Matches are distributed among these distances:
80 118 0.17
81 114 0.17
82 6 0.01
83 40 0.06
84 257 0.38
85 100 0.15
86 49 0.07
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (84 bp):
AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
TCGACTTAAGTTATGCTGC
Found at i:26451 original size:335 final size:325
Alignment explanation
Indices: 25691--26621 Score: 1170
Period size: 335 Copynumber: 2.8 Consensus size: 325
25681 CCCTTCTTTC
* * * * *
25691 CTTAGGCTATGTTGTAAATGATGTGCCCTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-C
1 CTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTGGTC
* * * * * * * *
25755 AGATAGCCCTTCTAGCCTTGAGCTATACCGCAAATGACG-CACCTTGGAGCTGAGCGTAATCGAA
66 AGATAACCCTTCTAACCTTGAGTTATGCTGCAAATGATGTC-CCTTGAAGCTGAGTGTAATCGAA
* *
25819 CTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTT
130 CTCGAGGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTT
* * *
25884 GGAGCTGAGCGTAGTCGAACTCGAATGTCTTTGGTGACAGATAACCATTCTAGCCTTGAA-TTAT
191 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTT-AAGTTAT
* * *
25948 GCTGTAAATGATGTGCCCTTAAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCT
255 GCTGCAAATGATGTGCCCTTAAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGAAGATAACCCT
26013 TCTCGA
320 TCTCGA
* * * *
26019 CTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTTAGCGTAGTCGAACTCAAAGGTTTTTGGTT
1 CTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTGG-T
* * *
26084 GGCAGATAACCCTTCTCGA-CTTAAGTTATGCTGCAAATGATGTTCCCTCGAAGCTGAGTGTAAT
65 --CAGATAACCCTTCT-AACCTTGAGTTATGCTGCAAATGATG-TCCCTTGAAGCTGAGTGTAAT
*
26148 CGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
126 CGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTT
* * *
26213 GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
191 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGACTTAAGTTAT
* * **
26278 GCTGCAAATGATGT-TCCTTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTTGGATGGAAGAT
255 GCTGCAAATGATGTGCCCTT-AAAGCTGAGTGTAATCGAACTCAAGGGTC--TT---TGGAAGAT
*
26342 AACCCTTCTTGA
314 AACCCTTCTCGA
* * *
26354 TTTAAGCTATGCTGCAAATGTTGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTGGT
1 CTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGG-TTTTTGGT
*
26419 CACAGATAACCCTTCTAACCTTGAGTTATGCTGCAAATAATGTGCCCTTGAAGCTGAGTGTAATC
65 --CAGATAACCCTTCTAACCTTGAGTTATGCTGCAAATGATGT-CCCTTGAAGCTGAGTGTAATC
* * * * *
26484 GAACACGAGGGTCTTTGGCAGATAGCCCTTTTCGACTTAAGCTATGCTGCAAATGATATGCCTCG
127 GAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTG
* * * *
26549 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAAATAGCCCTTCTTGACTTAAGCTATG
192 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGACTTAAGTTATG
26614 CTGCAAAT
256 CTGCAAAT
26622 AGTTTCTTTA
Statistics
Matches: 523, Mismatches: 61, Indels: 31
0.85 0.10 0.05
Matches are distributed among these distances:
328 54 0.10
329 86 0.16
330 62 0.12
331 1 0.00
332 33 0.06
333 29 0.06
334 3 0.01
335 243 0.46
336 12 0.02
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (325 bp):
CTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTGGTC
AGATAACCCTTCTAACCTTGAGTTATGCTGCAAATGATGTCCCTTGAAGCTGAGTGTAATCGAAC
TCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGC
TGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCA
AATGATGTGCCCTTAAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGAAGATAACCCTTCTCGA
Found at i:26622 original size:165 final size:164
Alignment explanation
Indices: 25691--26621 Score: 1140
Period size: 165 Copynumber: 5.6 Consensus size: 164
25681 CCCTTCTTTC
* * * * *
25691 CTTAGGCTATGTTGTAAATGATGTGCCCTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-G-G
1 CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTG
* * * * * * * * *
25754 -CAGATAGCCCTTCTAGCCTTGAGCTATACCGCAAATGA--CGCACCTTGGAGCTGAGCGTAATC
66 ACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGC-CCTTGAAGCTGAGTGTAATC
* *
25816 GAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTCGA
130 GAACTCGAGGGTC--T--TTGGCAGATAACCCTTCTCGA
* * *
25855 CTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAATGTCTTTGGTG
1 CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTG
* * * *
25920 ACAGATAACCATTCTAGCCTTGAA-TTATGCTGTAAATGATGTGCCCTTAAAGCTGAGTGTAATC
66 ACAGATAACCCTTCTAGACTT-AAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAATC
* *
25984 GAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGA
130 GAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGA
* * * *
26019 CTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTTAGCGTAGTCGAACTCAAAGGTTTTTGGTT
1 CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-T
* * * *
26084 GGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTTCCCTCGAAGCTGAGTGTAATC
65 GACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAATC
26149 GAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGA
130 GAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGA
* *
26184 CTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTT
1 CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-T
* * *
26249 GGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT-TCCTTCGAAGCTGAGTGTAAT
65 GACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTT-GAAGCTGAGTGTAAT
* * *
26313 CGAACTCGGGGGTCTTTTGGATGGAAGATAACCCTTCTTGA
129 CGAACTCGAGGGTC--TT---TGGCAGATAACCCTTCTCGA
* * * *
26354 TTTAAGCTATGCTGCAAATGTTGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTGGT
1 CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG-TCTTTGGT
* * *
26419 CACAGATAACCCTTCTA-ACCTTGAGTTATGCTGCAAATAATGTGCCCTTGAAGCTGAGTGTAAT
65 GACAGATAACCCTTCTAGA-CTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAAT
* * *
26483 CGAACACGAGGGTCTTTGGCAGATAGCCCTTTTCGA
129 CGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGA
* *
26519 CTTAAGCTATGCTGCAAATGATATGCCTCGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGT
1 CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGT
* * * *
26584 GACAAATAGCCCTTCTTGACTTAAGCTATGCTGCAAAT
65 GACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAAT
26622 AGTTTCTTTA
Statistics
Matches: 669, Mismatches: 79, Indels: 37
0.85 0.10 0.05
Matches are distributed among these distances:
164 134 0.20
165 324 0.48
166 3 0.00
167 31 0.05
168 31 0.05
169 3 0.00
170 133 0.20
171 10 0.01
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (164 bp):
CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTG
ACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAATCG
AACTCGAGGGTCTTTGGCAGATAACCCTTCTCGA
Found at i:30200 original size:2 final size:2
Alignment explanation
Indices: 30148--30181 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30138 CTTGTGTAGA
30148 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30182 GATTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30423 original size:14 final size:15
Alignment explanation
Indices: 30395--30554 Score: 55
Period size: 15 Copynumber: 10.2 Consensus size: 15
30385 ATATATATAT
30395 ATATAAAAATAAATA
1 ATATAAAAATAAATA
30410 ATATAAAAAT-AATA
1 ATATAAAAATAAATA
* *
30424 CA-AGTAATAATACAAGA
1 -ATA-TAAAAATA-AATA
* *
30441 ATAATAAAAAGAAAGA
1 AT-ATAAAAATAAATA
*
30457 GAAAGTAAAAAATATAATA
1 -ATA-T-AAAAATA-AATA
30476 ATAATAAAATATAAA-A
1 AT-ATAAAA-ATAAATA
* * *
30492 A-ATATACATATATA
1 ATATAAAAATAAATA
30506 ATATAAATAAGTAAAATA
1 ATATAAA-AA-T-AAATA
* *
30524 AAATGAAAAT--ATA
1 ATATAAAAATAAATA
30537 ATAGTAAAAAT-AATA
1 ATA-TAAAAATAAATA
30552 ATA
1 ATA
30555 AATATAATAG
Statistics
Matches: 108, Mismatches: 18, Indels: 38
0.66 0.11 0.23
Matches are distributed among these distances:
13 9 0.08
14 17 0.16
15 27 0.25
16 10 0.09
17 20 0.19
18 21 0.19
19 4 0.04
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (15 bp):
ATATAAAAATAAATA
Found at i:30434 original size:12 final size:11
Alignment explanation
Indices: 30406--30446 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
30396 TATAAAAATA
* *
30406 AATAATATAAA
1 AATAATACAAG
30417 AATAATACAAG
1 AATAATACAAG
30428 TAATAATACAAG
1 -AATAATACAAG
30440 AATAATA
1 AATAATA
30447 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:30479 original size:6 final size:6
Alignment explanation
Indices: 30470--30573 Score: 50
Period size: 6 Copynumber: 18.2 Consensus size: 6
30460 AGTAAAAAAT
30470 ATAATA ATAATA A-AAT- ATAA-A A-AAT- ATACATA TATAAT- ATAAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATA-ATA -ATAATA AT-AATA
* *
30515 AGTAA-A ATAA-A ATGAA-A AT-ATA ATAGTA AAAATA ATAATA A-ATATA
1 A-TAATA ATAATA AT-AATA ATAATA ATAATA ATAATA ATAATA ATA-ATA
*
30561 ATAGTA ATAATA A
1 ATAATA ATAATA A
30574 AAATGCAAAG
Statistics
Matches: 77, Mismatches: 6, Indels: 30
0.68 0.05 0.27
Matches are distributed among these distances:
4 5 0.06
5 19 0.25
6 43 0.56
7 6 0.08
8 4 0.05
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (6 bp):
ATAATA
Found at i:30562 original size:24 final size:24
Alignment explanation
Indices: 30465--30573 Score: 82
Period size: 24 Copynumber: 4.3 Consensus size: 24
30455 GAGAAAGTAA
*
30465 AAAATATAATAAT-AATAAAATA-T
1 AAAA-ATAATAATAAATATAATAGT
*
30488 AAAAAATATACATATATAATATAAATAAGT
1 -AAAAATA-ATA-ATA-AATAT-AAT-AGT
30518 -AAAATAA-AATGAAAATATAATAGT
1 AAAAATAATAAT--AAATATAATAGT
30542 AAAAATAATAATAAATATAATAGT
1 AAAAATAATAATAAATATAATAGT
*
30566 AATAATAA
1 AAAAATAA
30574 AAATGCAAAG
Statistics
Matches: 71, Mismatches: 3, Indels: 22
0.74 0.03 0.23
Matches are distributed among these distances:
23 3 0.04
24 28 0.39
25 14 0.20
26 9 0.13
27 6 0.08
28 9 0.13
29 1 0.01
30 1 0.01
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (24 bp):
AAAAATAATAATAAATATAATAGT
Found at i:31228 original size:37 final size:37
Alignment explanation
Indices: 31130--31231 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
31120 GTGCTTGTGG
* ** * *
31130 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
*
31167 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
*
31204 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAG
31232 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
Found at i:32026 original size:106 final size:106
Alignment explanation
Indices: 31841--33646 Score: 2790
Period size: 106 Copynumber: 17.0 Consensus size: 106
31831 GCATTGTTTT
* * * *
31841 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * * *
31905 ACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
31947 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
32012 CCAGCGGTCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * *
32054 G-GTCCAAGATCCTTCACTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
32118 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
32159 GAGTCCAATATCCTACGCTATGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
32224 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
32265 GAGTCCAATATCCTTCGTTGTGAAGTTGAATTTGGCTCTAAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
32330 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
32371 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
32436 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
32477 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
32542 CCAGCGGTCCCTT-GATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTG
* * *
32583 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
32648 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
32689 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
32754 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
32795 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
32860 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * * *
32901 AAGTCCAATATCCTACGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
32966 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
33007 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGATGTTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
33072 CCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
33113 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
33178 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
33219 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATAGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
33284 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
33325 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTCGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
33390 TCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
33431 GAGTCCAATATTCTTCGCTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
33496 CCAGTGGTTCCTTCGTCGTGAAGTTAAACTTGCGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
33537 GAGTCCAATATCATTAGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
33602 CCAGCGGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
33643 GAGT
1 GAGT
33647 GGCACGATAT
Statistics
Matches: 1562, Mismatches: 133, Indels: 10
0.92 0.08 0.01
Matches are distributed among these distances:
105 2 0.00
106 1556 1.00
107 4 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:34477 original size:22 final size:22
Alignment explanation
Indices: 34451--34527 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
34441 TTATGTTTGG
34451 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
34473 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
34495 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
34517 TCAACGGTTTG
1 TCAAAGGTTTG
34528 ATGGGGTAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:35178 original size:10 final size:10
Alignment explanation
Indices: 35163--35210 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
35153 TTGTTTCTCT
35163 TTTTTCTTTG
1 TTTTTCTTTG
35173 TTTTTCTTTG
1 TTTTTCTTTG
*
35183 TTTTT-TTGTT
1 TTTTTCTT-TG
35193 TTTTTCTTT-
1 TTTTTCTTTG
35202 TTTGTTCTT
1 TTT-TTCTT
35211 GATTGGATCT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
9 5 0.15
10 27 0.79
11 2 0.06
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.83
Consensus pattern (10 bp):
TTTTTCTTTG
Found at i:35192 original size:18 final size:17
Alignment explanation
Indices: 35153--35207 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
35143 ATTTTTGTTC
*
35153 TTGTTTCTCTTTTTTCT
1 TTGTTTTTCTTTTTTCT
*
35170 TTGTTTTTCTTTGTTTTT
1 TTGTTTTTCTTT-TTTCT
*
35188 TTGTTTTT-TTCTTT-T
1 TTGTTTTTCTTTTTTCT
35203 TTGTT
1 TTGTT
35208 CTTGATTGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.18
16 3 0.09
17 13 0.38
18 12 0.35
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (17 bp):
TTGTTTTTCTTTTTTCT
Found at i:39863 original size:11 final size:12
Alignment explanation
Indices: 39837--39973 Score: 50
Period size: 13 Copynumber: 10.9 Consensus size: 12
39827 GTAAGTAAAA
39837 AAAATAAATAAT
1 AAAATAAATAAT
39849 AAAATATATATAA-
1 AAAATA-A-ATAAT
* *
39862 AAAAGAAA-AAGA
1 AAAATAAATAA-T
*
39874 AAAAGGAAATAAAT
1 AAAA-TAAAT-AAT
* *
39888 AAAACAAATAAAC
1 AAAATAAAT-AAT
39901 AAAAT-AATAAT
1 AAAATAAATAAT
* **
39912 AACA-AAATACG
1 AAAATAAATAAT
*
39923 AATAATATATATAT
1 AA-AATAAATA-AT
39937 AAAATAAATAA-
1 AAAATAAATAAT
39948 AAAAGTAAATATAT
1 AAAA-TAAATA-AT
*
39962 ATAAATTAATAA
1 A-AAATAAATAA
39974 ATTAAATGAC
Statistics
Matches: 95, Mismatches: 15, Indels: 29
0.68 0.11 0.21
Matches are distributed among these distances:
10 2 0.02
11 16 0.17
12 22 0.23
13 34 0.36
14 16 0.17
15 5 0.05
ACGTcount: A:0.71, C:0.03, G:0.04, T:0.22
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:40493 original size:12 final size:11
Alignment explanation
Indices: 40465--40505 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
40455 TAACAAAATA
* *
40465 AATAATATAAA
1 AATAATACAAG
40476 AATAATACAAG
1 AATAATACAAG
40487 TAATAATACAAG
1 -AATAATACAAG
40499 AATAATA
1 AATAATA
40506 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:40611 original size:12 final size:12
Alignment explanation
Indices: 40589--40633 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
40579 GAATAAAAGG
40589 AAAATATAATAGT
1 AAAA-ATAATAGT
*
40602 AAAAATAATAAT
1 AAAAATAATAGT
*
40614 AAATATAATAGT
1 AAAAATAATAGT
*
40626 AATAATAA
1 AAAAATAA
40634 AAATGCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:41284 original size:37 final size:37
Alignment explanation
Indices: 41186--41287 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
41176 GTGCTTGCGG
* ** *
41186 ATCCTATCTTTAGGAGTTTAAATAATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
* *
41223 ATCTTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
*
41260 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAG
41288 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
Found at i:43781 original size:3 final size:3
Alignment explanation
Indices: 43773--43821 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
43763 ATACATCCAA
43773 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
43821 A
1 A
43822 GTGAGTAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:43903 original size:25 final size:24
Alignment explanation
Indices: 43857--43907 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
43847 AGAATAAATC
*
43857 AAAAAGAAAAGAGGGAATAAAATAAA
1 AAAAAGAAAAGA-GGAA-AAAAAAAA
*
43883 AAAAGGAAAA-AGGAAAAAAAAAA
1 AAAAAGAAAAGAGGAAAAAAAAAA
43906 AA
1 AA
43908 TATAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 9 0.39
24 4 0.17
25 1 0.04
26 9 0.39
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (24 bp):
AAAAAGAAAAGAGGAAAAAAAAAA
Found at i:44111 original size:4 final size:4
Alignment explanation
Indices: 44097--44133 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
44087 ATATATATAT
* *
44097 ATAA ATGA ATAA ATAA TTAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
44134 AGGGACCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:44678 original size:24 final size:26
Alignment explanation
Indices: 44627--44678 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
44617 CTCTAAGGCC
*
44627 TTTGGTTGATGCTTCGATTTTGTGTG
1 TTTGGTTGATGCTTCGAATTTGTGTG
44653 TTTGGTTG-TG-TTCGACATTTGT-TG
1 TTTGGTTGATGCTTCGA-ATTTGTGTG
44677 TT
1 TT
44679 GGTCGATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 9 0.38
25 7 0.29
26 8 0.33
ACGTcount: A:0.08, C:0.08, G:0.29, T:0.56
Consensus pattern (26 bp):
TTTGGTTGATGCTTCGAATTTGTGTG
Found at i:45239 original size:37 final size:34
Alignment explanation
Indices: 45198--45570 Score: 181
Period size: 37 Copynumber: 10.4 Consensus size: 34
45188 AACTATATAA
*
45198 TATATATATAAATATTTTAAAAATATTGTTTTAAAAC
1 TATATATATATATATTTTAAAAA-A-T-TTTTAAAAC
* **
45235 TATATATAATATATATTTCAAAAAAAATTTCCAAAAC
1 TATATAT-ATATATATTT--TAAAAAATTTTTAAAAC
* **
45272 AATATAT-TATATAATTTTAAAAAATATTTTCGAAC
1 TATATATATATAT-ATTTTAAAAAAT-TTTTAAAAC
* * **
45307 TGTATGT-TATATAGTTTTCAAAAACGTTTTAAAAC
1 TATATATATATATA-TTTT-AAAAAATTTTTAAAAC
* *
45342 TATAT-TATATGT-TTTTAAAAATATTTTTTCAAAAAT
1 TATATATATATATATTTTAAAAA-A-TTTTT--AAAAC
* *
45378 TATATATTATATATATTTTCAAAATTATTTTCAAAA-
1 TATATA-TATATATATTTT-AAAA-AATTTTTAAAAC
* ** *
45414 T-TATATATAT-T-TTCTAAAATGTTTTAAAAATC
1 TATATATATATATATTTTAAAAAATTTTTAAAA-C
*
45446 TATATAT-TATATAATTTTTAAAAATATTTTAAAAAC
1 TATATATATATAT-A-TTTTAAAAA-ATTTTTAAAAC
* * *
45482 TATATAATATATACATTTTCAAAACTATTTTAAAAAC
1 TATAT-ATATATATATTTT-AAAA-AATTTTTAAAAC
* * *
45519 TATATATTATACCCATATTTTTAAAAACTATTTACAAAC
1 TATATA-TATA--TATA-TTTTAAAAAATTTTTA-AAAC
45558 TATATA-ATATATA
1 TATATATATATATA
45571 GATATATATA
Statistics
Matches: 262, Mismatches: 40, Indels: 70
0.70 0.11 0.19
Matches are distributed among these distances:
30 9 0.03
31 4 0.02
32 12 0.05
33 11 0.04
34 18 0.07
35 45 0.17
36 37 0.14
37 63 0.24
38 24 0.09
39 25 0.10
40 14 0.05
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (34 bp):
TATATATATATATATTTTAAAAAATTTTTAAAAC
Found at i:45408 original size:12 final size:12
Alignment explanation
Indices: 45391--45417 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
45381 ATATTATATA
45391 TATTTTCAAAAT
1 TATTTTCAAAAT
45403 TATTTTCAAAAT
1 TATTTTCAAAAT
45415 TAT
1 TAT
45418 ATATATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (12 bp):
TATTTTCAAAAT
Found at i:45417 original size:68 final size:67
Alignment explanation
Indices: 45277--45487 Score: 187
Period size: 67 Copynumber: 3.1 Consensus size: 67
45267 AAAACAATAT
* ** * * * **
45277 ATTATATA-ATTTTAAAAAATATTTT-CGAA-CTGTATGTTATATAGTTTTCAAAAACGTTTTAA
1 ATTATATATATTTTAAAAAATGTTTTAAAAATCTATATATTATATAATTTTCAAAAATATTTTAA
45339 AA
66 AA
* * * *
45341 CTATATTATATGTTTTTAAAAATATTTTTTCAAAAAT-TATATATTATATATATTTTCAAAATTA
1 AT-TA-TATAT-ATTTTAAAAA-ATGTTTT-AAAAATCTATATATTATATA-ATTTTCAAAAATA
*
45405 TTTTCAAA
60 TTTTAAAA
** *
45413 ATTATATATATTTTCTAAAATGTTTTAAAAATCTATATATTATATAATTTTTAAAAATATTTTAA
1 ATTATATATATTTTAAAAAATGTTTTAAAAATCTATATATTATATAATTTTCAAAAATATTTTAA
45478 AA
66 AA
*
45480 ACTATATA
1 ATTATATA
45488 ATATATACAT
Statistics
Matches: 116, Mismatches: 21, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
64 1 0.01
65 2 0.02
66 4 0.03
67 31 0.27
68 28 0.24
69 13 0.11
70 5 0.04
71 15 0.13
72 17 0.15
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (67 bp):
ATTATATATATTTTAAAAAATGTTTTAAAAATCTATATATTATATAATTTTCAAAAATATTTTAA
AA
Found at i:45419 original size:30 final size:30
Alignment explanation
Indices: 45383--45452 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
45373 AAAATTATAT
*
45383 ATTATATATATTTTC-AAAATTATTTTCAAA
1 ATTATATATATTTTCTAAAA-TATTTTAAAA
*
45413 ATTATATATATTTTCTAAAATGTTTTAAAA
1 ATTATATATATTTTCTAAAATATTTTAAAA
45443 ATCTATATAT
1 AT-TATATAT
45453 TATATAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 25 0.69
31 11 0.31
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (30 bp):
ATTATATATATTTTCTAAAATATTTTAAAA
Found at i:45500 original size:104 final size:102
Alignment explanation
Indices: 45224--45525 Score: 297
Period size: 104 Copynumber: 2.9 Consensus size: 102
45214 TTAAAAATAT
* ** * ** *
45224 TGTTTTAAAACTATATATAATATATATTTCAAAAAAAATTTCCAAAACAATATATTATATAATTT
1 TGTTTTAAAACTATATATTATATA-ATTTTTAAAAATATTTTAAAAACTATATATTATATAATTT
* * *
45289 TAAAAAATATTTTCGAACTGTATGTTATATAGTTTTCAAAAA
65 TCAAAAATATTTTCAAAAT-TA---TATATAGTTTTCAAAAA
* * *
45331 CGTTTTAAAAC--TATATTATAT-GTTTTTAAAAATATTTTTTCAAAAATTATATATTATATATA
1 TGTTTTAAAACTATATATTATATAATTTTTAAAAATA--TTTT-AAAAACTATATATTATATA-A
* *
45393 TTTTCAAAATTATTTTCAAAATTATATATA-TTTTCTAAAA
62 TTTTCAAAAATATTTTCAAAATTATATATAGTTTTCAAAAA
*
45433 TGTTTTAAAAATCTATATATTATATAATTTTTAAAAATATTTTAAAAACTATATAATATATACAT
1 TGTTTT-AAAA-CTATATATTATATAATTTTTAAAAATATTTTAAAAACTATATATTATATA-AT
* * *
45498 TTTCAAAACTATTTTAAAAACTATATAT
63 TTTCAAAAATATTTTCAAAATTATATAT
45526 TATACCCATA
Statistics
Matches: 163, Mismatches: 23, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
102 14 0.09
103 19 0.12
104 45 0.28
105 16 0.10
106 28 0.17
107 41 0.25
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (102 bp):
TGTTTTAAAACTATATATTATATAATTTTTAAAAATATTTTAAAAACTATATATTATATAATTTT
CAAAAATATTTTCAAAATTATATATAGTTTTCAAAAA
Found at i:45517 original size:12 final size:12
Alignment explanation
Indices: 45461--45521 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
45451 ATTATATAAT
45461 TTTTAAAAA-TA
1 TTTTAAAAACTA
45472 TTTTAAAAACTA
1 TTTTAAAAACTA
*
45484 -TATAATATATAC-A
1 TTTTAA-A-A-ACTA
*
45497 TTTTCAAAACTA
1 TTTTAAAAACTA
45509 TTTTAAAAACTA
1 TTTTAAAAACTA
45521 T
1 T
45522 ATATTATACC
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
11 15 0.38
12 17 0.43
13 3 0.08
14 5 0.12
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (12 bp):
TTTTAAAAACTA
Found at i:45563 original size:76 final size:74
Alignment explanation
Indices: 45415--45570 Score: 210
Period size: 76 Copynumber: 2.1 Consensus size: 74
45405 TTTTCAAAAT
* * *
45415 TATATATATTTTCTAAAATGTTTTAAAAATCTATATATTATATAATTTTTAAAAATATTTTAAAA
1 TATATACATTTTCTAAAATATTTTAAAAATCTATATATTATACAATTTTTAAAAATATTTTAAAA
45480 ACTATATAA
66 ACTATATAA
45489 TATATACATTTTC-AAAACTATTTTAAAAA-CTATATATTATACCCATATTTTTAAAAACTA-TT
1 TATATACATTTTCTAAAA-TATTTTAAAAATCTATATATTATA--CA-ATTTTTAAAAA-TATTT
*
45551 TACAAACTATATAA
61 TAAAAACTATATAA
45565 TATATA
1 TATATA
45571 GATATATATA
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
73 16 0.22
74 22 0.30
75 1 0.01
76 32 0.44
77 2 0.03
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (74 bp):
TATATACATTTTCTAAAATATTTTAAAAATCTATATATTATACAATTTTTAAAAATATTTTAAAA
ACTATATAA
Found at i:46019 original size:14 final size:15
Alignment explanation
Indices: 45984--46013 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
45974 TTTATATTTT
45984 ATAATTTTTTTAAAA
1 ATAATTTTTTTAAAA
45999 ATAATTTTTTTAAAA
1 ATAATTTTTTTAAAA
46014 CTATTTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATAATTTTTTTAAAA
Found at i:48230 original size:38 final size:38
Alignment explanation
Indices: 48172--48256 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 38
48162 TCATTGAGAA
* *
48172 TGAGAAACTGCCGAAGAAAGATGACAGACTCAAATTTT
1 TGAGAAACTGCCGAAGAAAGATGACAGACTCAAACTGT
* * *
48210 TGAGAAACTG-TGAAGAAAAGATGATAGACTTAAACTGT
1 TGAGAAACTGCCGAAG-AAAGATGACAGACTCAAACTGT
48248 TGAGAAACT
1 TGAGAAACT
48257 ATCTAATGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
37 4 0.10
38 37 0.90
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (38 bp):
TGAGAAACTGCCGAAGAAAGATGACAGACTCAAACTGT
Found at i:48338 original size:18 final size:20
Alignment explanation
Indices: 48297--48338 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
48287 TTTTTTTTAC
*
48297 TTTTTTATAACATTTAATAT
1 TTTTTTATAACATTTAATAA
*
48317 TTTTTTA-AAC-TTTTATAA
1 TTTTTTATAACATTTAATAA
48335 TTTT
1 TTTT
48339 AAAATAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 10 0.50
19 3 0.15
20 7 0.35
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTTATAACATTTAATAA
Found at i:49191 original size:27 final size:27
Alignment explanation
Indices: 49157--49209 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
49147 TTACAGAAGG
49157 AGAATTGGGAATCGGGGTAAGAGAGGA
1 AGAATTGGGAATCGGGGTAAGAGAGGA
49184 AGAATTGGGAATCGGGGTAAGAGAGG
1 AGAATTGGGAATCGGGGTAAGAGAGG
49210 GGATGGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.04, G:0.45, T:0.15
Consensus pattern (27 bp):
AGAATTGGGAATCGGGGTAAGAGAGGA
Found at i:49548 original size:19 final size:19
Alignment explanation
Indices: 49526--49568 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
49516 CTATTTCATC
* * *
49526 TTCTCGATTCTATTTTTAT
1 TTCTCAATTCTACTTCTAT
*
49545 TTCTAAATTCTACTTCTAT
1 TTCTCAATTCTACTTCTAT
49564 TTCTC
1 TTCTC
49569 TTGACTATAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.19, C:0.21, G:0.02, T:0.58
Consensus pattern (19 bp):
TTCTCAATTCTACTTCTAT
Found at i:53077 original size:3 final size:3
Alignment explanation
Indices: 53071--53128 Score: 89
Period size: 3 Copynumber: 18.7 Consensus size: 3
53061 GTTTTTTTTA
*
53071 TAT TAT TAT TAT TAT TAT TTT TAT TAT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
53117 TAT TAT ATAT TA
1 TAT TAT -TAT TA
53129 CAGGCCCAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
3 45 0.88
4 6 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:53104 original size:22 final size:22
Alignment explanation
Indices: 53066--53128 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
53056 TTTGGGTTTT
53066 TTTTATATTATTA-TTATTATTA
1 TTTT-TATTATTATTTATTATTA
53088 TTTTTATTATTATTTATTATTA
1 TTTTTATTATTATTTATTATTA
* *
53110 TTATTATTATTATATATTA
1 TTTTTATTATTATTTATTA
53129 CAGGCCCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.21
22 30 0.79
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTATTATTATTTATTATTA
Found at i:54546 original size:29 final size:29
Alignment explanation
Indices: 54514--54570 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
54504 TTTTACAAGT
*
54514 TTTATATATA-GTTTTAATTTTATTTATTG
1 TTTATATATATG-TTTAATTTTAATTATTG
* *
54543 TTTATTTATATGTTTACTTTTAATTATT
1 TTTATATATATGTTTAATTTTAATTATT
54571 ATTACTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (29 bp):
TTTATATATATGTTTAATTTTAATTATTG
Found at i:54573 original size:3 final size:3
Alignment explanation
Indices: 54565--54594 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
54555 TTTACTTTTA
*
54565 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
54595 TAACCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:55477 original size:9 final size:8
Alignment explanation
Indices: 55422--55483 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
55412 TTCTTTCAAA
55422 TTTTTTAT
1 TTTTTTAT
55430 TTCTTATTAT
1 TT-TT-TTAT
* *
55440 TTTTATAC
1 TTTTTTAT
55448 TTTTTTAT
1 TTTTTTAT
****
55456 TCAGGTAT
1 TTTTTTAT
55464 TTTTTTAT
1 TTTTTTAT
55472 TTTTTTAT
1 TTTTTTAT
55480 TTTT
1 TTTT
55484 CTGTTAGAGG
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
8 30 0.75
9 4 0.10
10 6 0.15
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (8 bp):
TTTTTTAT
Found at i:57085 original size:14 final size:14
Alignment explanation
Indices: 57047--57100 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
57037 ATTTTAAATA
*
57047 ATTTACATTTACAT
1 ATTTACATTTGCAT
* *
57061 TTTTACATTTGTAT
1 ATTTACATTTGCAT
57075 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
57090 CTTTGCATTTG
1 ATTTACATTTG
57101 TATTTTTATG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
14 21 0.66
15 11 0.34
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.54
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:59017 original size:34 final size:34
Alignment explanation
Indices: 58967--59032 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
58957 CAGCAAAGAA
* *
58967 AGAAAAAAAAAGAAAAAAATGAAAAGGAAAAATG
1 AGAAAAAAAAAGAAAAAAAGGAAAAAGAAAAATG
59001 AGAAAAAAGAAA-AAAAAAAGGAAAAAGAAAAA
1 AGAAAAAA-AAAGAAAAAAAGGAAAAAGAAAAA
59033 GGGGAGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 26 0.90
35 3 0.10
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (34 bp):
AGAAAAAAAAAGAAAAAAAGGAAAAAGAAAAATG
Found at i:63369 original size:54 final size:54
Alignment explanation
Indices: 63287--63426 Score: 219
Period size: 54 Copynumber: 2.6 Consensus size: 54
63277 CATAAAAAAT
* *
63287 GATGAATGTGTTGTCAAACGCTTTACGAACATCTGAGCAGAAACCACAAGAAAG
1 GATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAACCACAAGAAAG
* *
63341 GATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAGCCACAGGAAAG
1 GATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAACCACAAGAAAG
*
63395 GATGAAT-TCGCTGTCAAATGTTTTACGAACAT
1 GATGAATGT-GTTGTCAAATGTTTTACGAACAT
63427 GCTATTCTGA
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 1 0.01
54 79 0.99
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (54 bp):
GATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAACCACAAGAAAG
Found at i:63826 original size:22 final size:22
Alignment explanation
Indices: 63791--63845 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
63781 ATCTACACTC
63791 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGATAGATTCCCTT
* * *
63813 TTTAAATATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCCCTT
63835 TTCAAAGATGA
1 TTCAAAGATGA
63846 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCCCTT
Found at i:64448 original size:113 final size:113
Alignment explanation
Indices: 64281--64805 Score: 865
Period size: 113 Copynumber: 4.6 Consensus size: 113
64271 TTCCAGAGAG
*
64281 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAATAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
64346 AACTTTTCGCTTGAATTCATCATTTGATGGATCATCATTACCAGGTCA
66 AACTTTTCGCTTGAATTCATCATTTGATGGATCATCATTACCAGGTCA
64394 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
64459 AACTTTTCGCTTGAATTCATCATTTGATGGATCAGCATTACCAGGTCA
66 AACTTTTCGCTTGAATTCATCATTTGATGGATCATCATTACCAGGTCA
*
64507 AGTTCATAATGAGAACAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
64572 AACTTTTCGCTTGAATTCATCATTTGATGGATCATCATTACCAGGTCA
66 AACTTTTCGCTTGAATTCATCATTTGATGGATCATCATTACCAGGTCA
* * * *
64620 AGTTCATAATGAGAAGAACTCATTTGAAGAAAGAATAAGAAGTTCATAATGAGAAGAATTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * * * *
64685 AACTTTTTGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAG--A
66 AACTTTTCGCTTGAATTCATCATTTGATGGATCATCATTACCAG-GTCA
* *
64732 GAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 -AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
64797 CAATCTTTT
65 CAA-CTTTT
64806 GCATGATTCT
Statistics
Matches: 388, Mismatches: 21, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
112 1 0.00
113 381 0.98
114 6 0.02
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTCGCTTGAATTCATCATTTGATGGATCATCATTACCAGGTCA
Found at i:65089 original size:3 final size:3
Alignment explanation
Indices: 65083--65151 Score: 93
Period size: 3 Copynumber: 22.0 Consensus size: 3
65073 ATATTTATAT
*
65083 TTA TTA TTA TTA TTT TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
*
65129 ATA TTA TTA TTTA TTA TATA TTA
1 TTA TTA TTA -TTA TTA T-TA TTA
65152 CAGGCCCAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
3 50 0.85
4 9 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:65098 original size:28 final size:29
Alignment explanation
Indices: 65067--65151 Score: 106
Period size: 28 Copynumber: 3.0 Consensus size: 29
65057 ACATTTGGTT
65067 TTTTTTATATTTA-TATTTATTATTATTA
1 TTTTTTATATTTATTATTTATTATTATTA
65095 -TTTTTAT-TATTATTATTTATTATTATTA
1 TTTTTTATAT-TTATTATTTATTATTATTA
* *
65123 TTATTAATA-TTATTATTTATTATATATTA
1 TTTTTTATATTTATTATTTATTAT-TATTA
65152 CAGGCCCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
26 1 0.02
27 10 0.20
28 29 0.58
29 10 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (29 bp):
TTTTTTATATTTATTATTTATTATTATTA
Found at i:66568 original size:29 final size:29
Alignment explanation
Indices: 66536--66592 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
66526 TTTTACAAGT
*
66536 TTTATATATA-GTTTTAATTTTATTTATTG
1 TTTATATATATG-TTTAATTTTAATTATTG
* *
66565 TTTATTTATATGTTTACTTTTAATTATT
1 TTTATATATATGTTTAATTTTAATTATT
66593 ATTACTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (29 bp):
TTTATATATATGTTTAATTTTAATTATTG
Found at i:66595 original size:3 final size:3
Alignment explanation
Indices: 66587--66622 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
66577 TTTACTTTTA
* *
66587 ATT ATT ATT ACT ATT ATT ACT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
66623 TAACCATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:68724 original size:27 final size:27
Alignment explanation
Indices: 68690--68742 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
68680 TTACAGAAGG
68690 AGAATTGGGAATC-GAGGTAAGAGAGGA
1 AGAATTGGGAATCAG-GGTAAGAGAGGA
68717 AGAATTGGGAATCAGGGTAAGAGAGG
1 AGAATTGGGAATCAGGGTAAGAGAGG
68743 GTATGGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.42, T:0.15
Consensus pattern (27 bp):
AGAATTGGGAATCAGGGTAAGAGAGGA
Found at i:69085 original size:6 final size:6
Alignment explanation
Indices: 69074--69114 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
69064 ATCTTCTCGA
* *
69074 TTCTAT TTCTAT TTCTAT TTCTAAA TTCTAC TTCTAT TTCT
1 TTCTAT TTCTAT TTCTAT TTCT-AT TTCTAT TTCTAT TTCT
69115 CTTGACTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.61
Consensus pattern (6 bp):
TTCTAT
Found at i:69095 original size:25 final size:26
Alignment explanation
Indices: 69056--69114 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
69046 CTCTAAATTC
** *
69056 TCTATTTC-ATCTTCTCGATTCTATT
1 TCTATTTCTATCTTCTAAATTCTACT
69081 TCTATTTCTAT-TTCTAAATTCTACT
1 TCTATTTCTATCTTCTAAATTCTACT
69106 TCTATTTCT
1 TCTATTTCT
69115 CTTGACTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 28 0.93
26 2 0.07
ACGTcount: A:0.19, C:0.22, G:0.02, T:0.58
Consensus pattern (26 bp):
TCTATTTCTATCTTCTAAATTCTACT
Found at i:71687 original size:27 final size:27
Alignment explanation
Indices: 71638--71690 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
71628 AAACGACACG
*
71638 TAAAAAAATTAAAATTATAAAAATATA
1 TAAAAAAATTAAAAATATAAAAATATA
* *
71665 TAAAAAAATTAAAAATGTTAAAATAT
1 TAAAAAAATTAAAAATATAAAAATAT
71691 TTTACTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (27 bp):
TAAAAAAATTAAAAATATAAAAATATA
Found at i:73806 original size:12 final size:13
Alignment explanation
Indices: 73760--73803 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
73750 TCATTTCTTC
73760 TTTCCTTCTCATT
1 TTTCCTTCTCATT
73773 TTTCCTTCTCATT
1 TTTCCTTCTCATT
73786 TTTCC-TCTCATT
1 TTTCCTTCTCATT
*
73798 CTTCCT
1 TTTCCT
73804 CTCCAAGTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.07, C:0.34, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTCCTTCTCATT
Found at i:78700 original size:37 final size:38
Alignment explanation
Indices: 78650--78725 Score: 145
Period size: 37 Copynumber: 2.0 Consensus size: 38
78640 AAAGTTTCCT
78650 TACCACCTATAGTAGATGAAGTCAAACCTCCA-CACCC
1 TACCACCTATAGTAGATGAAGTCAAACCTCCACCACCC
78687 TACCACCTATAGTAGATGAAGTCAAACCTCCACCACCC
1 TACCACCTATAGTAGATGAAGTCAAACCTCCACCACCC
78725 T
1 T
78726 TTCCTCAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 32 0.84
38 6 0.16
ACGTcount: A:0.34, C:0.36, G:0.11, T:0.20
Consensus pattern (38 bp):
TACCACCTATAGTAGATGAAGTCAAACCTCCACCACCC
Done.