Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000484.1 Hibiscus syriacus cultivar Beakdansim tig00000922_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: 146073
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1819 original size:8 final size:8
Alignment explanation
Indices: 1807--1841 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
1797 TTTAATCTCC
*
1807 CTTGTTTC
1 CTTGTTTA
1815 CTTGTTTA
1 CTTGTTTA
1823 CTTGTTTA
1 CTTGTTTA
1831 CTTGTTTA
1 CTTGTTTA
1839 CTT
1 CTT
1842 AGGTCCTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.63
Consensus pattern (8 bp):
CTTGTTTA
Found at i:3944 original size:21 final size:21
Alignment explanation
Indices: 3918--3962 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3908 GATTTCTGGG
* *
3918 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3939 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3960 CAA
1 CAA
3963 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4659 original size:21 final size:22
Alignment explanation
Indices: 4630--4673 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4620 GTTGTATGAT
4630 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
4651 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
4673 A
1 A
4674 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:5789 original size:149 final size:149
Alignment explanation
Indices: 5435--5882 Score: 834
Period size: 146 Copynumber: 3.0 Consensus size: 149
5425 GAGTCGAGGG
* *
5435 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCCGGAAAGACATAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
5500 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
5565 TATGG--C-ACGGTGCAAT
131 TATGGCACTACGGTGCAAT
5581 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
5646 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
5711 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
5730 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
5795 ACTTGATCCCTAGCATATG--TATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
5858 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
5877 TCTACG
1 TCTACG
5883 GGGCACTTCG
Statistics
Matches: 296, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
146 133 0.45
147 68 0.23
148 1 0.00
149 94 0.32
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:5905 original size:23 final size:23
Alignment explanation
Indices: 5861--5905 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5851 ATCATTATAT
*
5861 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
5884 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
5906 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:13209 original size:21 final size:20
Alignment explanation
Indices: 13185--13224 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
13175 GAACTACTTG
*
13185 ATCAATGAAAGAAAAAAAATA
1 ATCAAAGAAA-AAAAAAAATA
*
13206 ATCAAAGAAAAAAAGAAAT
1 ATCAAAGAAAAAAAAAAAT
13225 CTTTGGTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.72, C:0.05, G:0.10, T:0.12
Consensus pattern (20 bp):
ATCAAAGAAAAAAAAAAATA
Found at i:14129 original size:2 final size:2
Alignment explanation
Indices: 14122--14190 Score: 78
Period size: 2 Copynumber: 37.5 Consensus size: 2
14112 CCGCCTCGAT
*
14122 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
14163 TA T- TT TA TA T- TA -A T- TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14191 TTTTGGGTTC
Statistics
Matches: 59, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
1 6 0.10
2 53 0.90
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:17914 original size:16 final size:17
Alignment explanation
Indices: 17895--17926 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
17885 TAATTCGACC
17895 CGAAAATTGA-CTTACT
1 CGAAAATTGACCTTACT
17911 CGAAAATTGACCTTAC
1 CGAAAATTGACCTTAC
17927 ATGTTACCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (17 bp):
CGAAAATTGACCTTACT
Found at i:18034 original size:15 final size:15
Alignment explanation
Indices: 18005--18047 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
17995 ATCGAATATA
*
18005 ATCTAGACCCTAAATG
1 ATCTA-ACCCAAAATG
18021 AT-TCAACCCAAAATG
1 ATCT-AACCCAAAATG
18036 ATCTAACCCAAA
1 ATCTAACCCAAA
18048 CTCAATCCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.44, C:0.28, G:0.07, T:0.21
Consensus pattern (15 bp):
ATCTAACCCAAAATG
Found at i:21027 original size:18 final size:18
Alignment explanation
Indices: 20983--21027 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
20973 CAGTTTAAGG
* *
20983 AAAGAAACCTGATAAAAC
1 AAAGAAACTTGACAAAAC
21001 AAAGAAACTTGACAAAAC
1 AAAGAAACTTGACAAAAC
21019 AAAGAAACT
1 AAAGAAACT
21028 AGGCAACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.62, C:0.16, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAGAAACTTGACAAAAC
Found at i:21705 original size:2 final size:2
Alignment explanation
Indices: 21698--21722 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21688 GTTGTTTTAT
21698 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
21723 TAGGTTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25963 original size:20 final size:21
Alignment explanation
Indices: 25938--25981 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
25928 TAGAAGTTCT
*
25938 TTCAGTTTTGC-TTATCTTTC
1 TTCAGTTTTACGTTATCTTTC
*
25958 TTCAGTTTTACGTTCTCTTTC
1 TTCAGTTTTACGTTATCTTTC
25979 TTC
1 TTC
25982 TTTCTCCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.09, C:0.23, G:0.09, T:0.59
Consensus pattern (21 bp):
TTCAGTTTTACGTTATCTTTC
Found at i:26350 original size:10 final size:11
Alignment explanation
Indices: 26335--26375 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 11
26325 TATAATTCAA
26335 ATTTTAT-TTT
1 ATTTTATATTT
26345 ATTTTATATTT
1 ATTTTATATTT
*
26356 ATTTT-TAATT
1 ATTTTATATTT
26366 A-TTTATATTT
1 ATTTTATATTT
26376 TTATGATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 3 0.11
10 16 0.59
11 8 0.30
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTTATATTT
Found at i:26686 original size:19 final size:20
Alignment explanation
Indices: 26651--26688 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
26641 ATTTATTAAC
26651 AAAATAATAATAATAATTTT
1 AAAATAATAATAATAATTTT
*
26671 AAAATATTAA-AATAATTT
1 AAAATAATAATAATAATTT
26689 ATTTAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATAATAATAATAATTTT
Found at i:26817 original size:42 final size:43
Alignment explanation
Indices: 26748--26829 Score: 114
Period size: 42 Copynumber: 1.9 Consensus size: 43
26738 AAAATAAAAT
*
26748 TATTATTAAATTATATTAAGTATTTATTACAATAAGAATAGTA
1 TATTATTAAATTATATTAAGTATTTATTAAAATAAGAATAGTA
* *
26791 TATTATT-AATTATATTAA-TTTCTTATTAAAATAATAATA
1 TATTATTAAATTATATTAAGTAT-TTATTAAAATAAGAATA
26830 TTATTAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 2 0.06
42 26 0.74
43 7 0.20
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (43 bp):
TATTATTAAATTATATTAAGTATTTATTAAAATAAGAATAGTA
Found at i:26835 original size:17 final size:17
Alignment explanation
Indices: 26813--26873 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 17
26803 TATTAATTTC
*
26813 TTATTAAAATAATAATA
1 TTATTAAAATAAAAATA
26830 TTATTAAAATACTAAAATTA
1 TTATTAAAATA--AAAA-TA
26850 TAGTATTAAAATAAAAATA
1 T--TATTAAAATAAAAATA
26869 TTATT
1 TTATT
26874 TTATATTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 15 0.39
19 6 0.16
20 7 0.18
22 10 0.26
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
TTATTAAAATAAAAATA
Found at i:26871 original size:22 final size:22
Alignment explanation
Indices: 26831--26872 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
26821 ATAATAATAT
*
26831 TATTAAAATACTAAAATTATAG
1 TATTAAAATACAAAAATTATAG
26853 TATTAAAATA-AAAATATTAT
1 TATTAAAATACAAAA-ATTAT
26873 TTTATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
TATTAAAATACAAAAATTATAG
Found at i:27058 original size:24 final size:22
Alignment explanation
Indices: 27029--27090 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
27019 AATATTGTAT
27029 ATTATAATAATATAGTTATAAAAA
1 ATTATAATAATATA-TTAT-AAAA
* * *
27053 ATTATATTATTATATTATTAAA
1 ATTATAATAATATATTATAAAA
27075 ATTATTAATAAATATA
1 ATTA-TAAT-AATATA
27091 ATTTTATAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 7 0.23
23 7 0.23
24 17 0.55
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTATAATAATATATTATAAAA
Found at i:27158 original size:19 final size:19
Alignment explanation
Indices: 27112--27158 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
27102 AATTTTTTAT
27112 TAAAATAATACTAAAATAA
1 TAAAATAATACTAAAATAA
* * *
27131 TATATTAATA-TTAAATATA
1 TAAAATAATACTAAAATA-A
27150 TAAAATAAT
1 TAAAATAAT
27159 TGTTTATGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAATAATACTAAAATAA
Found at i:28445 original size:9 final size:9
Alignment explanation
Indices: 28431--28520 Score: 63
Period size: 9 Copynumber: 10.7 Consensus size: 9
28421 ACATTAACAG
28431 ATAATGCAC
1 ATAATGCAC
28440 ATAATG-AC
1 ATAATGCAC
*
28448 ATTAA--CAG
1 A-TAATGCAC
28456 ATAATGCAC
1 ATAATGCAC
28465 ATAATG-AC
1 ATAATGCAC
*
28473 ATTAA--CAG
1 A-TAATGCAC
28481 ATAATGCAC
1 ATAATGCAC
28490 ATAATG-AC
1 ATAATGCAC
*
28498 ATTAA--CAG
1 A-TAATGCAC
28506 ATAATGCAC
1 ATAATGCAC
28515 ATAATG
1 ATAATG
28521 ACAGACGAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 24
0.68 0.06 0.26
Matches are distributed among these distances:
7 9 0.14
8 15 0.24
9 39 0.62
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (9 bp):
ATAATGCAC
Found at i:28449 original size:25 final size:25
Alignment explanation
Indices: 28420--28523 Score: 208
Period size: 25 Copynumber: 4.2 Consensus size: 25
28410 ATATTTACTA
28420 GACATTAACAGATAATGCACATAAT
1 GACATTAACAGATAATGCACATAAT
28445 GACATTAACAGATAATGCACATAAT
1 GACATTAACAGATAATGCACATAAT
28470 GACATTAACAGATAATGCACATAAT
1 GACATTAACAGATAATGCACATAAT
28495 GACATTAACAGATAATGCACATAAT
1 GACATTAACAGATAATGCACATAAT
28520 GACA
1 GACA
28524 GACGAAGTGG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 79 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.23
Consensus pattern (25 bp):
GACATTAACAGATAATGCACATAAT
Found at i:45460 original size:20 final size:20
Alignment explanation
Indices: 45430--45475 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
45420 ATTAAACGGG
*
45430 AATTAACGACTGAGGGACTAA
1 AATT-ACGACTGAGAGACTAA
45451 AATTACGACTGAGAGACTAA
1 AATTACGACTGAGAGACTAA
45471 AATTA
1 AATTA
45476 GACAGGGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.22
Consensus pattern (20 bp):
AATTACGACTGAGAGACTAA
Found at i:48403 original size:20 final size:21
Alignment explanation
Indices: 48378--48427 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
48368 TTTTCCCAAT
48378 TCGCAATGCAAATAAGT-AAA
1 TCGCAATGCAAATAAGTAAAA
* * **
48398 TCGCAACGCGAATTGGTAAAA
1 TCGCAATGCAAATAAGTAAAA
48419 TCGCAATGC
1 TCGCAATGC
48428 GATACTGACT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (21 bp):
TCGCAATGCAAATAAGTAAAA
Found at i:48443 original size:20 final size:20
Alignment explanation
Indices: 48419--48511 Score: 141
Period size: 20 Copynumber: 4.7 Consensus size: 20
48409 ATTGGTAAAA
* *
48419 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTGACTT
48439 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
48459 TCGCAACGCGATATTGACTT
1 TCGCAACGCGATACTGACTT
*
48479 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
*
48499 TCGCAACGAGATA
1 TCGCAACGCGATA
48512 ATACAGAATC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:48872 original size:20 final size:20
Alignment explanation
Indices: 48847--48924 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
48837 ATTCATTTGA
48847 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
48867 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
48887 CTATCGCAACACGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
48907 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
48925 CGCATTGCGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:48966 original size:19 final size:19
Alignment explanation
Indices: 48944--49007 Score: 128
Period size: 19 Copynumber: 3.4 Consensus size: 19
48934 ATTTTCTCGG
48944 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
48963 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
48982 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
49001 TGCGATT
1 TGCGATT
49008 CTCTTGTTGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.16, C:0.20, G:0.17, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCAT
Found at i:48966 original size:33 final size:35
Alignment explanation
Indices: 48924--49012 Score: 119
Period size: 38 Copynumber: 2.5 Consensus size: 35
48914 AACGAGAAAA
48924 TCGCATTGCGATTTTC-TCG-GTGCGATTTTCATT
1 TCGCATTGCGATTTTCTTCGAGTGCGATTTTCATT
*
48957 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC--TTCG-AGTGCGATTTTCATT
*
48995 TCGCATTGCGATTCTCTT
1 TCGCATTGCGATTTTCTT
49013 GTTGCGATAG
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.33
36 5 0.10
38 28 0.57
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (35 bp):
TCGCATTGCGATTTTCTTCGAGTGCGATTTTCATT
Found at i:49037 original size:20 final size:20
Alignment explanation
Indices: 49012--49049 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
49002 GCGATTCTCT
49012 TGTTGCGATAGTCAGTTTCG
1 TGTTGCGATAGTCAGTTTCG
*
49032 TGTTGCGATAGTCTGTTT
1 TGTTGCGATAGTCAGTTT
49050 TGCCTTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.29, T:0.45
Consensus pattern (20 bp):
TGTTGCGATAGTCAGTTTCG
Found at i:49166 original size:14 final size:15
Alignment explanation
Indices: 49147--49184 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
49137 CATCAATTAA
49147 ACAAATCAAT-ATTT
1 ACAAATCAATCATTT
*
49161 ACAAATC-ATCTTTT
1 ACAAATCAATCATTT
49175 ACAAATCAAT
1 ACAAATCAAT
49185 TAAACAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (15 bp):
ACAAATCAATCATTT
Found at i:50813 original size:20 final size:19
Alignment explanation
Indices: 50790--50857 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
50780 GAAACTTAAA
50790 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
* *
50810 ATCGCAATGCTGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
50830 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
50849 ATCGCAACG
1 ATCGCAACG
50858 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:50887 original size:32 final size:32
Alignment explanation
Indices: 50830--50919 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
50820 TGAAATGGCT
50830 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAAT-AAAATCGCAACGACAAA
50863 ATCGCAATGCGAAATAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAATCGCAACGACAAA
* *
50895 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAATGCGAAATA-AAATCGCA
50920 TTGTGATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.11
Consensus pattern (32 bp):
ATCGCAATGCGAAATAAAATCGCAACGACAAA
Found at i:50915 original size:19 final size:17
Alignment explanation
Indices: 50830--50919 Score: 75
Period size: 14 Copynumber: 5.4 Consensus size: 17
50820 TGAAATGGCT
*
50830 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAA-CAAA
50849 ATCGCAA-CG--ACAAA
1 ATCGCAAGCGAAACAAA
*
50863 ATCGCAATGCGAAATAAA
1 ATCGCAA-GCGAAACAAA
50881 ATCGCAA-CG--ACAAA
1 ATCGCAAGCGAAACAAA
50895 ATCGCAACGCGAAACACAA
1 ATCGCAA-GCGAAACA-AA
50914 ATCGCA
1 ATCGCA
50920 TTGTGATTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
14 21 0.36
15 1 0.02
16 6 0.10
17 2 0.03
18 14 0.24
19 15 0.25
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.11
Consensus pattern (17 bp):
ATCGCAAGCGAAACAAA
Found at i:50972 original size:20 final size:19
Alignment explanation
Indices: 50915--50973 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
50905 GAAACACAAA
* **
50915 TCGCATTGTGATTTTCATT
1 TCGCATTGCGATAGTCATT
*
50934 TCGCATTGCGATAGCCATT
1 TCGCATTGCGATAGTCATT
* *
50953 TCCGCGTTGTGATAGTCATT
1 T-CGCATTGCGATAGTCATT
50973 T
1 T
50974 TCGTGTTGCG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGCATTGCGATAGTCATT
Found at i:50981 original size:20 final size:20
Alignment explanation
Indices: 50930--50973 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
50920 TTGTGATTTT
* *
50930 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGTGATAGC
*
50949 CATTTCCGCGTTGTGATAGT
1 CATTTCCGCGTTGTGATAGC
50969 CATTT
1 CATTT
50974 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
CATTTCCGCGTTGTGATAGC
Found at i:51491 original size:18 final size:18
Alignment explanation
Indices: 51465--51504 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
51455 GTCGATCAGA
* *
51465 TGATGGCTCTGGGTGAGG
1 TGATAGCTCTGGGCGAGG
51483 TGATAGCTCTGGGCGAGG
1 TGATAGCTCTGGGCGAGG
51501 TGAT
1 TGAT
51505 GACTCCCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.45, T:0.28
Consensus pattern (18 bp):
TGATAGCTCTGGGCGAGG
Found at i:52854 original size:20 final size:20
Alignment explanation
Indices: 52829--52902 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
52819 AATAGCTTCT
*
52829 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
52849 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
52869 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
52889 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
52903 GTTGCGATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:53435 original size:20 final size:20
Alignment explanation
Indices: 53329--53463 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
53319 CGCTTAGAAA
*
53329 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
53350 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
53370 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
53390 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
53411 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
53431 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
53451 ATCGCATTGCGAT
1 ATCGCATTGCGAT
53464 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:53435 original size:61 final size:61
Alignment explanation
Indices: 53329--53466 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
53319 CGCTTAGAAA
* * * *
53329 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
53390 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
53451 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
53467 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:53482 original size:61 final size:61
Alignment explanation
Indices: 53329--53484 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 61
53319 CGCTTAGAAA
* ** * * * *
53329 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * *
53390 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
53451 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
53485 TTACTTATTC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
61 77 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:53574 original size:21 final size:21
Alignment explanation
Indices: 53534--53574 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
53524 ACTGTAGACC
** *
53534 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
53555 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
53575 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:61547 original size:15 final size:15
Alignment explanation
Indices: 61538--61570 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
61528 CATTTTTTTT
61538 ATAAATATTTTCTGA
1 ATAAATATTTTCTGA
61553 ATAAATATTTTCTGA
1 ATAAATATTTTCTGA
61568 ATA
1 ATA
61571 GTCTGAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAAATATTTTCTGA
Found at i:69586 original size:30 final size:30
Alignment explanation
Indices: 69552--69611 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
69542 AGTACTCCAT
* * *
69552 AGGTCGCCGTGTGCTCTTGGAGACCTATGG
1 AGGTCGCCATGTCCTCCTGGAGACCTATGG
*
69582 AGGTCGTCATGTCCTCCTGGAGACCTATGG
1 AGGTCGCCATGTCCTCCTGGAGACCTATGG
69612 TGATAACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.15, C:0.25, G:0.33, T:0.27
Consensus pattern (30 bp):
AGGTCGCCATGTCCTCCTGGAGACCTATGG
Found at i:75742 original size:27 final size:27
Alignment explanation
Indices: 75712--75779 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
75702 TTTATTTTAT
*
75712 TTTATTTCGTTTTTCTTTTTACCTTAA
1 TTTATTTTGTTTTTCTTTTTACCTTAA
75739 TTTATTTTGTTTTTCTTTTTACCTTAA
1 TTTATTTTGTTTTTCTTTTTACCTTAA
75766 TTTATTTTGTTTTT
1 TTTATTTTGTTTTT
75780 TATTCGATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.13, C:0.10, G:0.04, T:0.72
Consensus pattern (27 bp):
TTTATTTTGTTTTTCTTTTTACCTTAA
Found at i:75994 original size:36 final size:36
Alignment explanation
Indices: 75945--76014 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
75935 CTCCTCTACT
*
75945 CGGTGCGCGTTAGTGTTTCCCTTTTGAGATTAGAAA
1 CGGTGCGCATTAGTGTTTCCCTTTTGAGATTAGAAA
75981 CGGTGCGCATTAGTGTTTCCCTTTTGAGATTAGA
1 CGGTGCGCATTAGTGTTTCCCTTTTGAGATTAGA
76015 GCATGTTAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (36 bp):
CGGTGCGCATTAGTGTTTCCCTTTTGAGATTAGAAA
Found at i:79738 original size:17 final size:17
Alignment explanation
Indices: 79691--79732 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
79681 GAAGCAGAAA
79691 CGTTCAAGAAAAAAACT
1 CGTTCAAGAAAAAAACT
*
79708 CATTCAAGAAAAAAAACT
1 CGTTCAAG-AAAAAAACT
79726 CGTTCAA
1 CGTTCAA
79733 ACAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (17 bp):
CGTTCAAGAAAAAAACT
Found at i:81980 original size:18 final size:18
Alignment explanation
Indices: 81957--81991 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
81947 ATTAAAATGA
81957 TATATTT-TGTAATAATTT
1 TATATTTCT-TAATAATTT
81975 TATATTTCTTAATAATT
1 TATATTTCTTAATAATT
81992 AAATAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
TATATTTCTTAATAATTT
Found at i:88621 original size:31 final size:31
Alignment explanation
Indices: 88586--88672 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 31
88576 GTACTTTTCA
88586 TTTGATAAAATGTCCAATATGGTACAC-ATAC
1 TTTGATAAAATGTCCAATATGGTAC-CTATAC
** *
88617 TTTGATAAAATGTCCAACGTGGTGCCTATAC
1 TTTGATAAAATGTCCAATATGGTACCTATAC
*
88648 TTTG-TCAAAATGTCTAATATGGTAC
1 TTTGAT-AAAATGTCCAATATGGTAC
88673 TTGAATTATT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 2 0.04
31 45 0.96
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (31 bp):
TTTGATAAAATGTCCAATATGGTACCTATAC
Found at i:91716 original size:30 final size:30
Alignment explanation
Indices: 91682--91746 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
91672 GTTAACGTCG
*
91682 AGTGATCATTTTGTAACAAACAATAATATT
1 AGTGATCATTTTGTAACAAACAATAACATT
*
91712 AGTGATCATTTTGTAACAAACGATAACATT
1 AGTGATCATTTTGTAACAAACAATAACATT
91742 AGTGA
1 AGTGA
91747 CTAGTTTGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (30 bp):
AGTGATCATTTTGTAACAAACAATAACATT
Found at i:91755 original size:30 final size:30
Alignment explanation
Indices: 91682--91755 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
91672 GTTAACGTCG
* *
91682 AGTGATCATTTTGTAACAAACAATAATATT
1 AGTGATCAGTTTGTAACAAACAATAACATT
* *
91712 AGTGATCATTTTGTAACAAACGATAACATT
1 AGTGATCAGTTTGTAACAAACAATAACATT
91742 AGTGA-CTAGTTTGT
1 AGTGATC-AGTTTGT
91756 GTCTTTTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 1 0.03
30 39 0.98
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (30 bp):
AGTGATCAGTTTGTAACAAACAATAACATT
Found at i:93491 original size:36 final size:35
Alignment explanation
Indices: 93369--93508 Score: 246
Period size: 35 Copynumber: 4.0 Consensus size: 35
93359 TGGCAACCAA
*
93369 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
93404 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
93439 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
93474 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
93509 GATAGATGTT
Statistics
Matches: 102, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
35 78 0.76
36 24 0.24
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.46
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:110767 original size:16 final size:15
Alignment explanation
Indices: 110727--110783 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
110717 AAAATTAATG
110727 AAAATAAATAAAT-AA
1 AAAATAAAT-AATGAA
*
110742 AAAATAAATACTGAA
1 AAAATAAATAATGAA
*
110757 AAAATATAATAATGAG
1 AAAATA-AATAATGAA
110773 AAAATAAATAA
1 AAAATAAATAA
110784 AGTAAAAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 2 0.05
15 22 0.59
16 13 0.35
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (15 bp):
AAAATAAATAATGAA
Found at i:115735 original size:30 final size:30
Alignment explanation
Indices: 115699--115766 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
115689 ACTGCAAGTC
115699 CCATCAACGTGCGTTCCACCA-GTGCCTGCT
1 CCATCAACGTGCGTTCCACCATGTG-CTGCT
* *
115729 CCATCAACGTGTGTTCCACCATGTGCTTCT
1 CCATCAACGTGCGTTCCACCATGTGCTGCT
115759 CCATCAAC
1 CCATCAAC
115767 ACATGACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 32 0.91
31 3 0.09
ACGTcount: A:0.19, C:0.38, G:0.16, T:0.26
Consensus pattern (30 bp):
CCATCAACGTGCGTTCCACCATGTGCTGCT
Found at i:120398 original size:41 final size:41
Alignment explanation
Indices: 120318--120399 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
120308 ATGGCCTGGT
* * *
120318 CTATTTAACTAAACAGGCCAGGCCCAGGCCTTTTTAAAAGC
1 CTATTTAACTAAACAGGCCAGGCCCAGGCATATTAAAAAGC
** *
120359 CTATTTAACTAAACAGGCCAGGCTTAGGTATATTAAAAAGC
1 CTATTTAACTAAACAGGCCAGGCCCAGGCATATTAAAAAGC
120400 TTTATAAGCC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (41 bp):
CTATTTAACTAAACAGGCCAGGCCCAGGCATATTAAAAAGC
Found at i:123409 original size:4 final size:4
Alignment explanation
Indices: 123400--123426 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
123390 CCAGCTTGAT
123400 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
123427 TGATGCTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:128591 original size:23 final size:22
Alignment explanation
Indices: 128565--128607 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
128555 TATAAAAAAT
128565 TATTTTTTATTAAATATTTTTGG
1 TATTTTTTATTAAAT-TTTTTGG
*
128588 TATTTTTTATTTAATTTTTT
1 TATTTTTTATTAAATTTTTT
128608 AAATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (22 bp):
TATTTTTTATTAAATTTTTTGG
Found at i:145016 original size:29 final size:29
Alignment explanation
Indices: 144974--145032 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
144964 ATTTTCACCT
*
144974 AACTAAATTGATGTAAGCAATGACTTCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
145003 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
145032 A
1 A
145033 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Done.