Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016720.1 Corchorus olitorius cultivar O-4 contig16753, 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: 72889
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2827 original size:36 final size:36
Alignment explanation
Indices: 2780--2849 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
2770 TTCAATAACC
* * *
2780 TTACATCTTTTGTGATTTTGGTTATTATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
2816 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
2850 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.61
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:3713 original size:25 final size:24
Alignment explanation
Indices: 3679--3725 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
3669 ACGTTTGCAC
3679 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
3704 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
3726 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:3770 original size:39 final size:40
Alignment explanation
Indices: 3716--3796 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
3706 ATACCTAAGA
*
3716 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
3755 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
3795 AT
1 AT
3797 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:19265 original size:22 final size:24
Alignment explanation
Indices: 19230--19288 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
19220 ATAAATGTTG
* *
19230 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
19252 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
19275 CTTGATAATATCTT
1 C-TGATAAT-TCTT
19289 GCCAGATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 10 0.33
23 10 0.33
24 7 0.23
25 2 0.07
26 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Found at i:22718 original size:62 final size:62
Alignment explanation
Indices: 22601--22964 Score: 550
Period size: 62 Copynumber: 5.8 Consensus size: 62
22591 AATCTTAGGG
* *
22601 TGACAACTTCTAGTGTCAATAATTTCCTCAGCATGACAACTTCTGGTGTCAAGATAATAATTTGC
1 TGACAACTTCTGGTGTCAATAATTT--T---CATGACAACTTCTGGTGTCAAGATAATAATTTGA
22666 TA
61 TA
* *
22668 TGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTTAAGATAATAATTTGCTA
1 TGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGATA
22730 TGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGATA
1 TGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGATA
* *
22792 TGACAACTTCTGGTGTCAAAAATTTTTATGACAACTTCTGGTGTCAAGATAATAATTTGATA
1 TGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGATA
* * *
22854 TGACAACTTCTGGTGTCAAAAATTTTCATGACAACTTCTGGTGTCAAGATAATAATATAATA
1 TGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGATA
**
22916 TGACAACTTCTGGTGTCAATTGCAA-CATCATGACAACTTCTGGTGTCAA
1 TGACAACTTCTGGTGTCAA-T--AATTTTCATGACAACTTCTGGTGTCAA
22965 TTGCAACATC
Statistics
Matches: 282, Mismatches: 12, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
62 233 0.83
64 22 0.08
65 3 0.01
67 24 0.09
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (62 bp):
TGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGATA
Found at i:23007 original size:124 final size:121
Alignment explanation
Indices: 22632--23143 Score: 456
Period size: 124 Copynumber: 4.2 Consensus size: 121
22622 ATTTCCTCAG
* ** *
22632 CATGACAACTTCTGGTGTCAAGATAATAATTTGCTATGACAACTTCTGGTGTCAAT-AATTTTCA
1 CATGACAACTTCTGGTGTCAAGATAATAATATAATATGACAACTTCTGGTGTCAATCAATTATCA
* ** **
22696 TGACAACTTCTGGTGTTAAGATAATAATTTGCTATGACAACTTCTGGTGTCAATAATTTT
66 TGACAACTTCTGGTG-TCAGATAATAAGAT-C-ATGACAACTTCTGGTGTCAATAA-AAT
* * * * *
22756 CATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAA-AAATTTTTA
1 CATGACAACTTCTGGTGTCAAGATAATAATATAATATGACAACTTCTGGTGTCAATCAATTATCA
*
22820 TGACAACTTCTGGTGTCAAGATAATAATTTGAT-ATGACAACTTCTGGTGTCAA-AAATTTT
66 TGACAACTTCTGGTGTC-AGATAATAA---GATCATGACAACTTCTGGTGTCAATAAA--AT
*
22880 CATGACAACTTCTGGTGTCAAGATAATAATATAATATGACAACTTCTGGTGTCAATTGCAA-CAT
1 CATGACAACTTCTGGTGTCAAGATAATAATATAATATGACAACTTCTGGTGTCAA-T-CAATTAT
*** *
22944 CATGACAACTTCTGGTGTCA-ATTGCAACATCATGACAACTTCTGGTGTCAATTGCAAAAT
64 CATGACAACTTCTGGTGTCAGATAATAAGATCATGACAACTTCTGGTGTCAA-T--AAAAT
* * ** *
23004 CATGACAACTTCTGGTGTC-A-AT--TGCA-AGAGCATGACAACTTCTGGTGTCAATTGCAA-GA
1 CATGACAACTTCTGGTGTCAAGATAAT-AATATAATATGACAACTTCTGGTGTCAA-T-CAATTA
* * ** * * *
23063 TTATGACAACTTCTGGTGTCA-TTTGTAAGACCATGACAACTTCTGGTGTCAATTGTAAGAC
63 TCATGACAACTTCTGGTGTCAGATAATAAGATCATGACAACTTCTGGTGTCAA---TAAAAT
23124 CATGACAACTTCTGGTGTCA
1 CATGACAACTTCTGGTGTCA
23144 TTTGTAAGTA
Statistics
Matches: 339, Mismatches: 30, Indels: 41
0.83 0.07 0.10
Matches are distributed among these distances:
120 99 0.29
121 3 0.01
122 23 0.07
123 4 0.01
124 184 0.54
125 1 0.00
126 22 0.06
127 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (121 bp):
CATGACAACTTCTGGTGTCAAGATAATAATATAATATGACAACTTCTGGTGTCAATCAATTATCA
TGACAACTTCTGGTGTCAGATAATAAGATCATGACAACTTCTGGTGTCAATAAAAT
Found at i:23011 original size:186 final size:183
Alignment explanation
Indices: 22632--23024 Score: 526
Period size: 186 Copynumber: 2.1 Consensus size: 183
22622 ATTTCCTCAG
* *
22632 CATGACAACTTCTGGTGTCAAGATAATAATTTGCTATGACAACTTCTGGTGTCAATAATTTTCAT
1 CATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTTCAT
* * ** **
22697 GACAACTTCTGGTGTTAAGATAATAATTTGCTATGACAACTTCTGGTGTCAATAATTTTCATGAC
66 GACAACTTCTGGTGTCAAGATAATAATATAATATGACAACTTCTGGTGTCAATAATCATCATGAC
* * *
22762 AACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTT
131 AACTTCTGGTGTCAAGATAACAA--TCATATGACAACTTCTGGTGTCAAAAA-TAT
*
22818 TATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTTCAT
1 CATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTTCAT
22883 GACAACTTCTGGTGTCAAGATAATAATATAATATGACAACTTCTGGTGTCAATTGCAA-CATCAT
66 GACAACTTCTGGTGTCAAGATAATAATATAATATGACAACTTCTGGTGTCAA-T--AATCATCAT
**
22947 GACAACTTCTGGTGTC-A-ATTGCAA-CATCATGACAACTTCTGGTGTCAATTGCAAA-AT
128 GACAACTTCTGGTGTCAAGATAACAATCAT-ATGACAACTTCTGGTGTCAA----AAATAT
23004 CATGACAACTTCTGGTGTCAA
1 CATGACAACTTCTGGTGTCAA
23025 TTGCAAGAGC
Statistics
Matches: 184, Mismatches: 15, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
183 2 0.01
184 20 0.11
186 135 0.73
187 2 0.01
188 23 0.12
189 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Consensus pattern (183 bp):
CATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTTCAT
GACAACTTCTGGTGTCAAGATAATAATATAATATGACAACTTCTGGTGTCAATAATCATCATGAC
AACTTCTGGTGTCAAGATAACAATCATATGACAACTTCTGGTGTCAAAAATAT
Found at i:23151 original size:30 final size:30
Alignment explanation
Indices: 22915--23143 Score: 368
Period size: 30 Copynumber: 7.6 Consensus size: 30
22905 ATAATATAAT
*
22915 ATGACAACTTCTGGTGTCAATTGCAACATC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
*
22945 ATGACAACTTCTGGTGTCAATTGCAACATC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
*
22975 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
*
23005 ATGACAACTTCTGGTGTCAATTGCAAGAGC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
*
23035 ATGACAACTTCTGGTGTCAATTGCAAGATT
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
* * *
23065 ATGACAACTTCTGGTGTCATTTGTAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
* *
23095 ATGACAACTTCTGGTGTCAATTGTAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
23125 ATGACAACTTCTGGTGTCA
1 ATGACAACTTCTGGTGTCA
23144 TTTGTAAGTA
Statistics
Matches: 189, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 189 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGCAAGATC
Found at i:24328 original size:22 final size:24
Alignment explanation
Indices: 24293--24351 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
24283 ATAAATGTTG
* *
24293 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
24315 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
24338 CTTGATAATATCTT
1 C-TGATAAT-TCTT
24352 GCCAGATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 10 0.33
23 10 0.33
24 7 0.23
25 2 0.07
26 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Found at i:28266 original size:12 final size:12
Alignment explanation
Indices: 28225--28268 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
28215 TTTAATACAG
*
28225 ATATCCACGGAT
1 ATATCGACGGAT
*
28237 ATATCGAATGGAT
1 ATATCG-ACGGAT
*
28250 TTATCGACGGAT
1 ATATCGACGGAT
28262 ATATCGA
1 ATATCGA
28269 GGTATCGATG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (12 bp):
ATATCGACGGAT
Found at i:29043 original size:21 final size:21
Alignment explanation
Indices: 29018--29100 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 21
29008 TATCTTAGAT
29018 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
29039 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* *
29060 ATAAATAATGA-GTTTAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
29082 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
29101 TTACTAAACG
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
21 19 0.37
22 21 0.41
23 11 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:29051 original size:25 final size:25
Alignment explanation
Indices: 29020--29068 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
29010 TCTTAGATAT
*
29020 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
29045 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
29069 GAGTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:30575 original size:10 final size:10
Alignment explanation
Indices: 30560--30605 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
30550 TAAAAAAAAT
30560 GGATATTTAC
1 GGATATTTAC
*
30570 GGATATTTAT
1 GGATATTTAC
* *
30580 GGATATCTAT
1 GGATATTTAC
30590 GGATATTTAC
1 GGATATTTAC
30600 GGATAT
1 GGATAT
30606 ATCGAGATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (10 bp):
GGATATTTAC
Found at i:30634 original size:20 final size:19
Alignment explanation
Indices: 30599--30656 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
30589 TGGATATTTA
30599 CGGATATATCGA--GATAT
1 CGGATATATCGACGGATAT
*
30616 C-GATAAATATCGACGGATACA
1 CGGAT--ATATCGACGGATA-T
30637 CGGATATATCGACGGATAT
1 CGGATATATCGACGGATAT
30656 C
1 C
30657 CGGTGACATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
16 3 0.09
17 1 0.03
18 7 0.21
19 1 0.03
20 17 0.52
21 1 0.03
22 3 0.09
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.24
Consensus pattern (19 bp):
CGGATATATCGACGGATAT
Found at i:35531 original size:10 final size:10
Alignment explanation
Indices: 35516--35545 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
35506 AAAGGAAATA
35516 AAAAAAAAAC
1 AAAAAAAAAC
35526 AAAAAAAAAC
1 AAAAAAAAAC
35536 AAAAGAAAAA
1 AAAA-AAAAA
35546 ATCAAACTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:36652 original size:17 final size:18
Alignment explanation
Indices: 36630--36664 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
36620 ATTGACACGA
*
36630 TTCAATTT-CTCAAATAT
1 TTCAATTTACTAAAATAT
36647 TTCAATTTACTAAAATAT
1 TTCAATTTACTAAAATAT
36665 ATATAATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (18 bp):
TTCAATTTACTAAAATAT
Found at i:38364 original size:13 final size:13
Alignment explanation
Indices: 38346--38370 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38336 TAAGGCCTTG
38346 GTAGTTAATTAAA
1 GTAGTTAATTAAA
38359 GTAGTTAATTAA
1 GTAGTTAATTAA
38371 GGAGGTTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
GTAGTTAATTAAA
Found at i:39843 original size:23 final size:23
Alignment explanation
Indices: 39817--39881 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
39807 AACTTAGAAT
39817 GTTTGGCAATACTCTCACTCTAA
1 GTTTGGCAATACTCTCACTCTAA
39840 GTTTGGCAATACTCTCACTCTAA
1 GTTTGGCAATACTCTCACTCTAA
*
39863 GTTTGACAATACTCTCACT
1 GTTTGGCAATACTCTCACT
39882 AGTGTGGCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.35
Consensus pattern (23 bp):
GTTTGGCAATACTCTCACTCTAA
Found at i:46769 original size:35 final size:34
Alignment explanation
Indices: 46723--46788 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
46713 TATTGCCTTC
46723 ACCTTTATCTTGTAATTAGTGGCCAAAAAAAAAAA
1 ACCTTTATCTTGTAATT-GTGGCCAAAAAAAAAAA
**
46758 ACCTTTATCTTGTAATTGTGTTCAAAAAAAA
1 ACCTTTATCTTGTAATTGTGGCCAAAAAAAA
46789 TATTTTGGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 12 0.41
35 17 0.59
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (34 bp):
ACCTTTATCTTGTAATTGTGGCCAAAAAAAAAAA
Found at i:51765 original size:18 final size:19
Alignment explanation
Indices: 51733--51769 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
51723 TTGGCTGACT
*
51733 TTTAATTAATTTAATTTAA
1 TTTAATTAATGTAATTTAA
51752 TTTAA-TAATGTAATTTAA
1 TTTAATTAATGTAATTTAA
51770 AATATTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TTTAATTAATGTAATTTAA
Found at i:52719 original size:178 final size:178
Alignment explanation
Indices: 52450--52788 Score: 495
Period size: 178 Copynumber: 1.9 Consensus size: 178
52440 TCGATTAAGG
* * * *
52450 TGATTTAAGTGTCTATTTAAAGATTGTTCCATGATCTACAACTTTCATGAAGGTCTAGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTAGAAAACAA
* * **
52515 AATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAA-AATTTGTTGTTTCGATTAACGGGAATAG
66 AATTTAATGTTTCAAGTATAAAAAATGCTTCC-AAAGAATTAGTTGTTTCGATTAACGAAAATAG
*
52579 ACGGTCCACTTAATATTATATAACTTT-TGCTTCAGATGTATGATTGAGA
130 ACGGTCCACTTAATATTACATAA-TTTGTGCTTCAGATGTATGATTGAGA
* * *
52628 TGATTCAAGTGTCTCTTAAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACAA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTAGAAAACAA
*
52693 AATTTAATG-TTCAAGGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACGAAAATAG
66 AATTTAATGTTTCAA-GTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGATTAACGAAAATAG
**
52757 ACGGTCTGCTTAATATTACATAATTTGTGCTT
130 ACGGTCCACTTAATATTACATAATTTGTGCTT
52789 ATGGTAAAAA
Statistics
Matches: 143, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
177 11 0.08
178 132 0.92
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTAGAAAACAA
AATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGATTAACGAAAATAGA
CGGTCCACTTAATATTACATAATTTGTGCTTCAGATGTATGATTGAGA
Found at i:55764 original size:14 final size:14
Alignment explanation
Indices: 55742--55778 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
55732 ATGCAGCATT
*
55742 ATTTCAAGAACTTA
1 ATTTGAAGAACTTA
55756 ATTTGAAGAACTTA
1 ATTTGAAGAACTTA
55770 ATTTGAAGA
1 ATTTGAAGA
55779 CATGTAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (14 bp):
ATTTGAAGAACTTA
Found at i:56180 original size:159 final size:159
Alignment explanation
Indices: 55917--56207 Score: 408
Period size: 159 Copynumber: 1.8 Consensus size: 159
55907 GTGCAGTAAG
* * *
55917 GGAATTAGTTCTTCAAGTGTAGCGATTATATCATACTGCGCGTAAAGACATAAAATGCAATATGG
1 GGAATTAATTCTTCAAGTGCAGCGATTATATCATACTGCGCGCAAAGACATAAAATGCAATATGG
* * *
55982 ACTTAGTATATACGGCATGCTTACATTATTCACATTCTAATATCTTGGTTAAGCCGCCCATACCC
66 ACTTAGTATATACGGCATGCTTACATTATTCACACTCTAATATCATGGTTAAGCCACCCATACCC
56047 TGCGCTGCGTGGTTTTCAAGTGTTGCAAA
131 TGCGCTGCGTGGTTTTCAAGTGTTGCAAA
* * * *
56076 GGAATTAATTCTTCAAGTGCAGCGATTATATCATACTGTGCGCAGAGACATGAGATGCAATATGG
1 GGAATTAATTCTTCAAGTGCAGCGATTATATCATACTGCGCGCAAAGACATAAAATGCAATATGG
* * * *
56141 ACTCTA-TATATGA-TGCGTG-TCTACATTATTGACACTCTAATATCATGGTTAAGCCACCCGTA
66 ACT-TAGTATAT-ACGGCATGCT-TACATTATTCACACTCTAATATCATGGTTAAGCCACCCATA
56203 CCCTG
128 CCCTG
56208 TGTTGTGCTG
Statistics
Matches: 115, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
158 1 0.01
159 111 0.97
160 3 0.03
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (159 bp):
GGAATTAATTCTTCAAGTGCAGCGATTATATCATACTGCGCGCAAAGACATAAAATGCAATATGG
ACTTAGTATATACGGCATGCTTACATTATTCACACTCTAATATCATGGTTAAGCCACCCATACCC
TGCGCTGCGTGGTTTTCAAGTGTTGCAAA
Found at i:64954 original size:18 final size:18
Alignment explanation
Indices: 64911--64946 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
64901 ATCATCATCA
*
64911 GAAAGGAATTTAGATTCT
1 GAAAAGAATTTAGATTCT
64929 GAAAAGAATTTAGATTCT
1 GAAAAGAATTTAGATTCT
64947 TGCAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (18 bp):
GAAAAGAATTTAGATTCT
Found at i:69841 original size:21 final size:21
Alignment explanation
Indices: 69817--69861 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
69807 ATGACATTGC
* *
69817 CCACCTAGGTGATCAGACAAA
1 CCACATAGGTCATCAGACAAA
* *
69838 CCACATGGGTCTTCAGACAAA
1 CCACATAGGTCATCAGACAAA
69859 CCA
1 CCA
69862 TGTGGGCGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.31, G:0.18, T:0.16
Consensus pattern (21 bp):
CCACATAGGTCATCAGACAAA
Done.