Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002388.1 Hibiscus syriacus cultivar Beakdansim tig00004886_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: 100207
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:1504 original size:27 final size:27
Alignment explanation
Indices: 1433--1509 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 27
1423 AAATTTTAAA
* * * *
1433 ATTAAATGTTTA-TTTTGTCTTAATTT
1 ATTAAATATTTATTTTTATTTTAATCT
1459 ATTAAATATATTGATTTTTATTTTAATCT
1 ATTAAATAT-TT-ATTTTTATTTTAATCT
1488 ATTAAATATTTATTTTTATTTT
1 ATTAAATATTTATTTTTATTTT
1510 TATGTAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
26 8 0.18
27 13 0.30
28 3 0.07
29 20 0.45
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (27 bp):
ATTAAATATTTATTTTTATTTTAATCT
Found at i:1523 original size:27 final size:28
Alignment explanation
Indices: 1452--1523 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
1442 TTATTTTGTC
*
1452 TTAATTTATTAAATATATTGATTTTTATT
1 TTAATCTA-TAAATATATTGATTTTTATT
1481 TTAATCTATTAAATAT-TT-ATTTTTATT
1 TTAATCTA-TAAATATATTGATTTTTATT
* *
1508 TTTATGTA-AAATATAT
1 TTAATCTATAAATATAT
1524 ATTTATCTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
25 6 0.15
26 1 0.03
27 15 0.38
28 2 0.05
29 15 0.38
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (28 bp):
TTAATCTATAAATATATTGATTTTTATT
Found at i:2777 original size:18 final size:18
Alignment explanation
Indices: 2754--2790 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2744 CATTTTTGGT
2754 TGACAACCGAAAATGTTA
1 TGACAACCGAAAATGTTA
2772 TGACAACCGAAAATGTTA
1 TGACAACCGAAAATGTTA
2790 T
1 T
2791 ATTTTATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (18 bp):
TGACAACCGAAAATGTTA
Found at i:6480 original size:5 final size:5
Alignment explanation
Indices: 6470--6495 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
6460 CTCTAATTAC
6470 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
6496 GTCCCCCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:15215 original size:42 final size:43
Alignment explanation
Indices: 15169--15275 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 43
15159 GGTGATTCAT
* *
15169 CGAGAATAGAAAGTGA-TATGCTTCCTTTCATTATACTTTAGA
1 CGAGAATAGAAAGTGACGATGCCTCCTTTCATTATACTTTAGA
* *
15211 CGAGAATCA-AAAGT-ACGATGCCTCCTTTCGTTCTACTTTAGA
1 CGAGAAT-AGAAAGTGACGATGCCTCCTTTCATTATACTTTAGA
* *
15253 CAAGAATCGAAAGTG-CGATGCCT
1 CGAGAATAGAAAGTGACGATGCCT
15276 TTTTTGGTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
41 1 0.02
42 53 0.96
43 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (43 bp):
CGAGAATAGAAAGTGACGATGCCTCCTTTCATTATACTTTAGA
Found at i:15286 original size:42 final size:42
Alignment explanation
Indices: 15186--15292 Score: 133
Period size: 42 Copynumber: 2.5 Consensus size: 42
15176 AGAAAGTGAT
* * * *
15186 ATGCTTCCTTTCATTATACTTTAGACGAGAATCAAAAGTACG
1 ATGCCTCCTTTCGTTCTACTTTAGACAAGAATCAAAAGTACG
* *
15228 ATGCCTCCTTTCGTTCTACTTTAGACAAGAATCGAAAGTGCG
1 ATGCCTCCTTTCGTTCTACTTTAGACAAGAATCAAAAGTACG
** *
15270 ATGCCTTTTTTGGTTCTACTTTA
1 ATGCCTCCTTTCGTTCTACTTTA
15293 TTCACCTTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (42 bp):
ATGCCTCCTTTCGTTCTACTTTAGACAAGAATCAAAAGTACG
Found at i:20837 original size:20 final size:20
Alignment explanation
Indices: 20814--20851 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20804 GGTACTGACA
* *
20814 TCTGGATTTCGATACTATCC
1 TCTGGATATCAATACTATCC
20834 TCTGGATATCAATACTAT
1 TCTGGATATCAATACTAT
20852 TGACTTATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (20 bp):
TCTGGATATCAATACTATCC
Found at i:29911 original size:21 final size:21
Alignment explanation
Indices: 29887--29953 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
29877 GAAGTAGTGG
*
29887 AAGTAGATGAATTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
29908 AAGTAGATGAAGTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
* * *
29929 AAATAGGTAAAGTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
29950 AAGT
1 AAGT
29954 GTCTCTGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.30
Consensus pattern (21 bp):
AAGTAGATGAAGTACCTTGGT
Found at i:31414 original size:16 final size:17
Alignment explanation
Indices: 31385--31417 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31375 TTTTTGTTCC
31385 TTTTTATTTGTCTTTTT
1 TTTTTATTTGTCTTTTT
*
31402 TTTTTCTTT-TCTTTTT
1 TTTTTATTTGTCTTTTT
31418 GATGAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.03, C:0.09, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTTATTTGTCTTTTT
Found at i:50955 original size:23 final size:22
Alignment explanation
Indices: 50873--50954 Score: 112
Period size: 23 Copynumber: 3.7 Consensus size: 22
50863 TTAGTACAGA
50873 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
*
50895 GGGAATCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC-TTGAAG
* * *
50918 GGGAACCGATTCCCCC-TGTAG
1 GGGAATCGATACCCCCTTGAAG
50939 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
50955 CTGGGGTTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
21 18 0.33
22 15 0.28
23 21 0.39
ACGTcount: A:0.23, C:0.30, G:0.27, T:0.20
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:50957 original size:22 final size:22
Alignment explanation
Indices: 50873--50957 Score: 100
Period size: 22 Copynumber: 3.9 Consensus size: 22
50863 TTAGTACAGA
*
50873 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCCTGAAG
* *
50895 GGGAATCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC-CTGAAG
* * *
50918 GGGAACCGAT-TCCCCCTGTAG
1 GGGAATCGATACCCCCCTGAAG
50939 GGGAATCGATACCCCCCTG
1 GGGAATCGATACCCCCCTG
50958 GGGTTCTGGT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 13 0.24
22 26 0.48
23 15 0.28
ACGTcount: A:0.22, C:0.31, G:0.27, T:0.20
Consensus pattern (22 bp):
GGGAATCGATACCCCCCTGAAG
Found at i:52539 original size:18 final size:18
Alignment explanation
Indices: 52518--52558 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
52508 AGAACAGCAC
52518 GAGGAACAAGAACGAA-CA
1 GAGGAACAAGAAC-AACCA
*
52536 GAGGAACAAGCACAACCA
1 GAGGAACAAGAACAACCA
52554 GAGGA
1 GAGGA
52559 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.51, C:0.20, G:0.29, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGAACAACCA
Found at i:54836 original size:12 final size:12
Alignment explanation
Indices: 54799--54852 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
54789 AATCATGCTT
54799 GAATCAAGTTGA
1 GAATCAAGTTGA
*
54811 -AATCATGCTT--
1 GAATCAAG-TTGA
54821 GAATCAAGTTGA
1 GAATCAAGTTGA
54833 GAATCAAGTTGA
1 GAATCAAGTTGA
*
54845 AAATCAAG
1 GAATCAAG
54853 CATAAAATAC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 2 0.06
11 12 0.34
12 21 0.60
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (12 bp):
GAATCAAGTTGA
Found at i:54845 original size:22 final size:22
Alignment explanation
Indices: 54784--54838 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
54774 ATGTTTATAG
54784 GTTGAAATCATGCTTGAATCAA
1 GTTGAAATCATGCTTGAATCAA
54806 GTTGAAATCATGCTTGAATCAA
1 GTTGAAATCATGCTTGAATCAA
54828 GTTGAGAATCA
1 GTTGA-AATCA
54839 AGTTGAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 27 0.84
23 5 0.16
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (22 bp):
GTTGAAATCATGCTTGAATCAA
Found at i:63714 original size:284 final size:284
Alignment explanation
Indices: 63201--63773 Score: 1056
Period size: 284 Copynumber: 2.0 Consensus size: 284
63191 TATTGTTCTC
*
63201 GCATAAAGTAAGGATTGGTCCGATCAAATTAGTTGGAAACCCATTCTAACTATTTATTGCCTCGA
1 GCATAAAGTAAGGATTGGTCCGATCAAATTAGTTGGAAACCCATTCTAAATATTTATTGCCTCGA
* *
63266 AACCCACTCAGCATCACTTTGGTTAAGCATTATTGTATAAATATCACCATGAGGTACCCTTATTA
66 AACCCACTAAGCACCACTTTGGTTAAGCATTATTGTATAAATATCACCATGAGGTACCCTTATTA
* *
63331 ACCATAAGGCAAGCGTCTCGGCAAACCTTAAAGACAAGTGCCCATGCACGCAAATCACCATTAAG
131 ACCATAAGGCAAGCATCTCGGCAAACCTTAAAGACAAGTACCCATGCACGCAAATCACCATTAAG
* *
63396 AACCTCAATGCAATGGTAAACAAACTATTGCCTCTTACGCAAAAACAAAATGCACACCTCTGTTC
196 AACCTCAATGCAATGGTAAACAAACTAGTGCCTCTTACGCAAAAACAAAATGCACACCTCTGTGC
* *
63461 TTTCGCAGAGTAAGCACCCCTTAT
261 TTTCGCAGAGCAAGAACCCCTTAT
63485 GCATAAAGTAAGGATTGGTCCGATCAAATTAGTTGGAAACCCATTCTAAATATTTATTGCCTCGA
1 GCATAAAGTAAGGATTGGTCCGATCAAATTAGTTGGAAACCCATTCTAAATATTTATTGCCTCGA
63550 AACCCACTAAGCACCACTTTGGTTAAGCATTATTGTATAAATATCACCATGAGGTACCCTTATTA
66 AACCCACTAAGCACCACTTTGGTTAAGCATTATTGTATAAATATCACCATGAGGTACCCTTATTA
*
63615 ACCATAAGGCAAGCATCTCGGCAAACCTTAAAGACAAGTACCCATGCACGTAAATCACCATTAAG
131 ACCATAAGGCAAGCATCTCGGCAAACCTTAAAGACAAGTACCCATGCACGCAAATCACCATTAAG
63680 AACCTCAATGCAATGGTAAACAAACTAGTGCCTCTTACGCAAAAACAAAATGCACACCTCTGTGC
196 AACCTCAATGCAATGGTAAACAAACTAGTGCCTCTTACGCAAAAACAAAATGCACACCTCTGTGC
63745 TTTCGCAGAGCAAGAACCCCTTAT
261 TTTCGCAGAGCAAGAACCCCTTAT
63769 GCATA
1 GCATA
63774 TATCTGCAGT
Statistics
Matches: 279, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
284 279 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (284 bp):
GCATAAAGTAAGGATTGGTCCGATCAAATTAGTTGGAAACCCATTCTAAATATTTATTGCCTCGA
AACCCACTAAGCACCACTTTGGTTAAGCATTATTGTATAAATATCACCATGAGGTACCCTTATTA
ACCATAAGGCAAGCATCTCGGCAAACCTTAAAGACAAGTACCCATGCACGCAAATCACCATTAAG
AACCTCAATGCAATGGTAAACAAACTAGTGCCTCTTACGCAAAAACAAAATGCACACCTCTGTGC
TTTCGCAGAGCAAGAACCCCTTAT
Found at i:65667 original size:23 final size:23
Alignment explanation
Indices: 65637--65737 Score: 195
Period size: 23 Copynumber: 4.4 Consensus size: 23
65627 GCTGTAGACA
65637 TTCA-TTTTCGTCCGAAAATCAT
1 TTCACTTTTCGTCCGAAAATCAT
65659 TTCACTTTTCGTCCGAAAATCAT
1 TTCACTTTTCGTCCGAAAATCAT
65682 TTCACTTTTCGTCCGAAAATCAT
1 TTCACTTTTCGTCCGAAAATCAT
65705 TTCACTTTTCGTCCGAAAATCAT
1 TTCACTTTTCGTCCGAAAATCAT
65728 TTCACTTTTC
1 TTCACTTTTC
65738 CTTTATATAT
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
22 4 0.05
23 74 0.95
ACGTcount: A:0.25, C:0.26, G:0.08, T:0.42
Consensus pattern (23 bp):
TTCACTTTTCGTCCGAAAATCAT
Found at i:65844 original size:7 final size:7
Alignment explanation
Indices: 65818--65882 Score: 60
Period size: 7 Copynumber: 8.7 Consensus size: 7
65808 CATTATCTAA
*
65818 ATATAGT
1 ATATATT
65825 ATAGTATTT
1 ATA-TA-TT
65834 ATATATT
1 ATATATT
*
65841 ATATAGT
1 ATATATT
65848 ATAT-TT
1 ATATATT
65854 ATATATTAT
1 ATATA-T-T
65863 AGTATATT
1 A-TATATT
65871 ATATATT
1 ATATATT
65878 ATATA
1 ATATA
65883 GTACATATAG
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
6 5 0.10
7 26 0.53
8 7 0.14
9 7 0.14
10 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (7 bp):
ATATATT
Found at i:65845 original size:18 final size:19
Alignment explanation
Indices: 65824--65885 Score: 94
Period size: 18 Copynumber: 3.4 Consensus size: 19
65814 CTAAATATAG
65824 TATAGTAT-TTATATATTA
1 TATAGTATATTATATATTA
65842 TATAGTATATT-TATA-TA
1 TATAGTATATTATATATTA
65859 TTATAGTATATTATATATTA
1 -TATAGTATATTATATATTA
65879 TATAGTA
1 TATAGTA
65886 CATATAGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.05
18 23 0.57
19 13 0.32
20 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
TATAGTATATTATATATTA
Found at i:66036 original size:14 final size:14
Alignment explanation
Indices: 65977--66074 Score: 67
Period size: 14 Copynumber: 6.9 Consensus size: 14
65967 CAAGAAATAA
65977 TATATATATATATAT
1 TATATATAT-TATAT
*
65992 TATAAAGTA-TATAT
1 TATATA-TATTATAT
** *
66006 TAGGTATTTTATAT
1 TATATATATTATAT
66020 TATATATATTATAT
1 TATATATATTATAT
*
66034 TAT-TATTATTGTAT
1 TATATA-TATTATAT
* *
66048 TATCTTTATTAATAT
1 TATATATATT-ATAT
66063 TAT-TATTATTAT
1 TATATA-TATTAT
66075 TGCAGGTCCA
Statistics
Matches: 65, Mismatches: 12, Indels: 13
0.72 0.13 0.14
Matches are distributed among these distances:
13 3 0.05
14 44 0.68
15 16 0.25
16 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (14 bp):
TATATATATTATAT
Found at i:66039 original size:3 final size:3
Alignment explanation
Indices: 66017--66075 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
66007 AGGTATTTTA
* *
66017 TAT TA- TAT ATAT TA- TAT TAT TAT TAT T-G TAT TAT CT-T TAT TAA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
66060 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
66076 GCAGGTCCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
2 6 0.13
3 36 0.78
4 4 0.09
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:66043 original size:23 final size:23
Alignment explanation
Indices: 65999--66068 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 23
65989 TATTATAAAG
65999 TATATATTAGGTATT-TTA-TATTA
1 TATATATTA--TATTATTATTATTA
*
66022 TATATATTATATTATTATTATTG
1 TATATATTATATTATTATTATTA
* *
66045 TAT-TATCTTTATTAATATTATTA
1 TATATAT-TATATTATTATTATTA
66068 T
1 T
66069 TATTATTGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 4 0.10
22 6 0.15
23 30 0.75
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (23 bp):
TATATATTATATTATTATTATTA
Found at i:71266 original size:3 final size:3
Alignment explanation
Indices: 71258--71355 Score: 169
Period size: 3 Copynumber: 32.7 Consensus size: 3
71248 TTTTTATCCA
* *
71258 TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
71306 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
71354 TA
1 TA
71356 AATATATATT
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:72755 original size:19 final size:19
Alignment explanation
Indices: 72717--72752 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
72707 TAATTTAGTC
72717 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
72736 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
72753 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:80531 original size:9 final size:8
Alignment explanation
Indices: 80508--80537 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
80498 AGATGGCAAT
80508 CATTCTTTA
1 CATT-TTTA
80517 CATTTTTA
1 CATTTTTA
80525 CATTTTTA
1 CATTTTTA
80533 CATTT
1 CATTT
80538 CATAAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (8 bp):
CATTTTTA
Found at i:84049 original size:1 final size:1
Alignment explanation
Indices: 84043--84099 Score: 69
Period size: 1 Copynumber: 57.0 Consensus size: 1
84033 GAAGAGAAAG
* * ** *
84043 AAAAAAAAGAAAAAAAAAAAAAAAAAAAAGAAAATGAAAAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
84100 GAAAGGGGTC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.91, C:0.00, G:0.07, T:0.02
Consensus pattern (1 bp):
A
Found at i:84059 original size:13 final size:13
Alignment explanation
Indices: 84037--84104 Score: 93
Period size: 13 Copynumber: 5.2 Consensus size: 13
84027 ATGCTTGAAG
*
84037 AGAAAGAAAAAAA
1 AGAAAAAAAAAAA
84050 AGAAAAAAAAAAA
1 AGAAAAAAAAAAA
84063 A-AAAAAAAAGAAA
1 AGAAAAAAAA-AAA
84076 ATGAAAAAAAAAAA
1 A-GAAAAAAAAAAA
*
84090 AGAAAAAAAAGAA
1 AGAAAAAAAAAAA
84103 AG
1 AG
84105 GGGTCAAGGT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
12 8 0.16
13 30 0.60
14 4 0.08
15 8 0.16
ACGTcount: A:0.87, C:0.00, G:0.12, T:0.01
Consensus pattern (13 bp):
AGAAAAAAAAAAA
Found at i:85260 original size:84 final size:84
Alignment explanation
Indices: 85113--85598 Score: 877
Period size: 84 Copynumber: 5.8 Consensus size: 84
85103 TAGTCCAAAC
*
85113 ATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
1 ATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
85178 TGGCAGAACCAATCATTGA
66 TGGCAGAACCAATCATTGA
* *
85197 ATTTGAAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATT
1 ATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
85262 TGGCAGAACCAATCATTGA
66 TGGCAGAACCAATCATTGA
* * *
85281 ATTTGAAAGATGAGTTTGCTCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATT
1 ATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
85346 TGGCAGAACCAATCATTGA
66 TGGCAGAACCAATCATTGA
*
85365 ATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATT
1 ATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
85430 TGGCAGAACCAATCATTGA
66 TGGCAGAACCAATCATTGA
85449 ATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
1 ATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
85514 TGGCAGAACCAATCATTGA
66 TGGCAGAACCAATCATTGA
* *
85533 ATTTGGAAGATGAATTTGC-CAATAGCATCTT-TGGAAGTGTTCTTTGAGTTATCTAATCTGGTT
1 ATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
85596 TGG
66 TGG
85599 TAAAAACAGA
Statistics
Matches: 391, Mismatches: 11, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
82 33 0.08
83 12 0.03
84 346 0.88
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (84 bp):
ATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
TGGCAGAACCAATCATTGA
Found at i:86622 original size:113 final size:113
Alignment explanation
Indices: 86316--87097 Score: 1319
Period size: 112 Copynumber: 7.0 Consensus size: 113
86306 CAAAGATTCA
* * * * * *
86316 AATCTATCATTTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAATTCATCTTAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
86381 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTA-CTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
86428 AATCCATCATTTGATGGATCAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
86492 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
86540 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
86605 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
86653 AAT-CATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
86717 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
86765 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
86830 AGGAAGAAGAAGTTCATAATGAAAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
86878 AAT-CATCATTTGATGGATCAGC-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
86941 A-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * *
86988 AATTCATCATTTGATGGATCAAC-TTGCCAG-GTTAGAGTTCATAATGAGAAGAATCGTCATCTG
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAG--AAAGTTCATAATGAGAAGAA-C-TCATCTG
* * * *
87051 AAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
62 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
87098 GCATAATTCT
Statistics
Matches: 644, Mismatches: 17, Indels: 15
0.95 0.03 0.02
Matches are distributed among these distances:
110 47 0.07
111 138 0.21
112 216 0.34
113 194 0.30
114 12 0.02
115 37 0.06
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:86788 original size:225 final size:225
Alignment explanation
Indices: 86316--87097 Score: 1324
Period size: 225 Copynumber: 3.5 Consensus size: 225
86306 CAAAGATTCA
* * * * * *
86316 AATCTATCATTTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAATTCATCTTAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
86381 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTA-CTGAATCCATCATTTGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT-CATCATTTGATGG
86445 ATCAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
130 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
86509 AATGAGAAGAATTTGTTCAACCTTTTACCTG
195 AATGAGAAGAATTTGTTCAACCTTTTACCTG
86540 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
86605 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCATCATTTGATGGA
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCATCATTTGATGGA
86670 TCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
131 TCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
86735 ATGAGAAGAATTTGTTCAACCTTTTACCTG
196 ATGAGAAGAATTTGTTCAACCTTTTACCTG
86765 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
86830 AGGAAGAAGAAGTTCATAATGAAAAGAATTTGTTCAACCTTTTACCTGAATCATCATTTGATGGA
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCATCATTTGATGGA
86895 TCAGC-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATA
131 TCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
* *
86958 ATGAGAAGAATTTGTTCAACCTTTTGCTTG
196 ATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * *
86988 AATTCATCATTTGATGGATCAAC-TTGCCAG-GTTAGAGTTCATAATGAGAAGAATCGTCATCTG
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAG--AAAGTTCATAATGAGAAGAA-C-TCATCTG
* * * *
87051 AAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
62 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
87098 GCATAATTCT
Statistics
Matches: 534, Mismatches: 18, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
221 1 0.00
222 6 0.01
223 84 0.16
224 175 0.33
225 268 0.50
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (225 bp):
AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCATCATTTGATGGA
TCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
ATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:87407 original size:3 final size:3
Alignment explanation
Indices: 87401--87481 Score: 121
Period size: 3 Copynumber: 27.7 Consensus size: 3
87391 TTTTTATCCA
* *
87401 TAT TAT T-T TAT TAG TAT TAT TAT TAT TAT TAT TA- TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
87447 TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
87482 AATATATATT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
2 4 0.06
3 67 0.94
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:89674 original size:287 final size:281
Alignment explanation
Indices: 89169--89738 Score: 947
Period size: 287 Copynumber: 2.0 Consensus size: 281
89159 ATAGAGACAA
89169 TTATAATTAAAAATACCAATTTGGGCGTTGTAGGGGTGCTAATCCTTCCCTAAACGTAAACCGAC
1 TTATAATTAAAAATACCAATTTGGGCGTTGTAGGGGTGCTAATCCTTCCCTAAACGTAAACCGAC
89234 CACGAATTTTTTTTTAAAAAGAACGAATTTTTGGTTATAAACGCAGATCAGTTCATCTTTTAATT
66 CACGAATTTTTTTTTAAAAAGAACGAATTTTTGGTTATAAACGCAGATCAGTTCATCTTTTAATT
*
89299 GATGTTTTCTTAAAACTCTTTAAAGATATTTTTAGGTATTCGACCTACCTGATCCAAAAGGCCGA
131 GATGTTTTCTTAAAACTCTTTAAAGATATTTTTAGGTATTCGACCTACCTGACCCAAAAGGCCGA
89364 TGGCGACTCCCAAATTATTTTCAAAACTATTTATTCACATC-ACTTTCCCC-CAAAA-TAATA-T
196 TGGCGACTCCCAAATTATTTTCAAAACTATTTATTCACATCAAC-TTCCCCGCAAAATTAATATT
89425 TCGTGCCC-GACG-AAACCGGT
260 TCGTGCCCGGACGAAAACCGGT
89445 TTATAATTAAAAAATACCAATTTTGGGCGTTGTAGGGGTGCTAATCCTTCCCTAAACGT-AACCG
1 TTATAATT-AAAAATACCAA-TTTGGGCGTTGTAGGGGTGCTAATCCTTCCCTAAACGTAAACCG
*
89509 ACCACGAATTTTTTTTTTTGTTAAAAAGAACGAATTTTTGGTTATAAAACGCAGATCAGTTTATC
64 ACCACGAA----TTTTTTT-TTAAAAAGAACGAATTTTTGGTTAT-AAACGCAGATCAGTTCATC
89574 TTTTAATTGATGTTTTCTTAAAAACTCTTTTAAAAGATATTTTTTAGGTATTCGACCTACCTGAC
123 TTTTAATTGATGTTTTCTT-AAAACTC-TTT-AAAGATA-TTTTTAGGTATTCGACCTACCTGAC
89639 CCAAAAGGCCGATGGCGACTCCCAAATTATTTTCAAAACTATTTATTCACATCAACTTCCCCGCA
184 CCAAAAGGCCGATGGCGACTCCCAAATTATTTTCAAAACTATTTATTCACATCAACTTCCCCGCA
89704 AAATTTAATATTTCGTGCCCGGACGAAAACCGGT
249 AAA-TTAATATTTCGTGCCCGGACGAAAACCGGT
89738 T
1 T
89739 ACGACAGAAC
Statistics
Matches: 273, Mismatches: 2, Indels: 21
0.92 0.01 0.07
Matches are distributed among these distances:
276 8 0.03
277 24 0.09
278 38 0.14
281 7 0.03
282 25 0.09
283 37 0.14
284 7 0.03
285 3 0.01
286 7 0.03
287 83 0.30
288 7 0.03
290 5 0.02
291 9 0.03
292 4 0.01
293 9 0.03
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (281 bp):
TTATAATTAAAAATACCAATTTGGGCGTTGTAGGGGTGCTAATCCTTCCCTAAACGTAAACCGAC
CACGAATTTTTTTTTAAAAAGAACGAATTTTTGGTTATAAACGCAGATCAGTTCATCTTTTAATT
GATGTTTTCTTAAAACTCTTTAAAGATATTTTTAGGTATTCGACCTACCTGACCCAAAAGGCCGA
TGGCGACTCCCAAATTATTTTCAAAACTATTTATTCACATCAACTTCCCCGCAAAATTAATATTT
CGTGCCCGGACGAAAACCGGT
Found at i:92433 original size:39 final size:39
Alignment explanation
Indices: 92351--92431 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
92341 AACAAGTTGG
* *
92351 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAATATTTATATATTTTCTTTAAAAAATTGAAAATCAT
* *
92390 AAAAT-TTATATATATTTTTTTTACAAAATTGAAAAT-AT
1 AAAATATT-TATATATTTTCTTTAAAAAATTGAAAATCAT
92428 AAAA
1 AAAA
92432 ATGTTTAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 8 0.22
39 29 0.78
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (39 bp):
AAAATATTTATATATTTTCTTTAAAAAATTGAAAATCAT
Found at i:93325 original size:3 final size:3
Alignment explanation
Indices: 93317--93366 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
93307 ACTATTTTTA
93317 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
93365 TA
1 TA
93367 AGTTTACAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:96247 original size:42 final size:42
Alignment explanation
Indices: 96188--96280 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
96178 TTGTTAAAGT
* *** *
96188 CCTTTTGTGGCGTTTGTTCCAAAACGCCGCTATATATATTGA
1 CCTTTTGCGGCGTTTGTTCCAAAAAAACACTATATATATTGA
* *
96230 CCTTTTGCGGCGTTTGTTCTAAAAAAACACTATATATCTTGA
1 CCTTTTGCGGCGTTTGTTCCAAAAAAACACTATATATATTGA
*
96272 CCTATTGCG
1 CCTTTTGCG
96281 ACTTTTTTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (42 bp):
CCTTTTGCGGCGTTTGTTCCAAAAAAACACTATATATATTGA
Found at i:97201 original size:16 final size:17
Alignment explanation
Indices: 97175--97206 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
97165 AAAATCTGAA
97175 TTTATTTTTATTAATTC
1 TTTATTTTTATTAATTC
97192 TTTA-TTTTATTAATT
1 TTTATTTTTATTAATT
97207 ATATTTCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTTTTATTAATTC
Found at i:97270 original size:25 final size:24
Alignment explanation
Indices: 97240--97288 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
97230 ACATTCATTT
97240 TATATAAAAAATATTATGTTATATA
1 TATATAAAAAATATT-TGTTATATA
* * *
97265 TATATATATAATATTTTTTATATA
1 TATATAAAAAATATTTGTTATATA
97289 AAATGAATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TATATAAAAAATATTTGTTATATA
Done.