Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014800.1 Corchorus olitorius cultivar O-4 contig14833, 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: 76464
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:3238 original size:21 final size:20
Alignment explanation
Indices: 3210--3249 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3200 TTTCCACAAC
*
3210 AATCTCATTCGAATGATCTG
1 AATCTCATTCGAATAATCTG
*
3230 AATCATCATTTGAATAATCT
1 AATC-TCATTCGAATAATCT
3250 AACTCTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (20 bp):
AATCTCATTCGAATAATCTG
Found at i:6764 original size:16 final size:16
Alignment explanation
Indices: 6719--6768 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
6709 TCGTTTGGCA
*
6719 TCGTTTTCGTTTT-TC
1 TCGTTTTCGTTTTGTT
6734 T-GTTTTTCTGTTTTTGTT
1 TCG-TTTTC-G-TTTTGTT
6752 TCGTTTTCGTTTTGTT
1 TCGTTTTCGTTTTGTT
6768 T
1 T
6769 TTGTTGCGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.03
15 6 0.21
16 9 0.31
17 5 0.17
18 7 0.24
19 1 0.03
ACGTcount: A:0.00, C:0.12, G:0.16, T:0.72
Consensus pattern (16 bp):
TCGTTTTCGTTTTGTT
Found at i:12396 original size:19 final size:20
Alignment explanation
Indices: 12366--12429 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
12356 TTGACACTAT
12366 TTAGCAACTGTACATATGAGA
1 TTAGC-ACTGTACATATGAGA
*
12387 TTA-CACTGTACATATTAGA
1 TTAGCACTGTACATATGAGA
* *
12406 TTATGTACTGTACAGATGAGA
1 TTA-GCACTGTACATATGAGA
12427 TTA
1 TTA
12430 TTAGAGCAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.46
20 1 0.03
21 19 0.51
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (20 bp):
TTAGCACTGTACATATGAGA
Found at i:12417 original size:21 final size:20
Alignment explanation
Indices: 12372--12430 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
12362 CTATTTAGCA
12372 ACTGTACATATGAGATTA-C
1 ACTGTACATATGAGATTATC
* *
12391 ACTGTACATATTAGATTATGT
1 ACTGTACATATGAGATTAT-C
*
12412 ACTGTACAGATGAGATTAT
1 ACTGTACATATGAGATTAT
12431 TAGAGCAGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (20 bp):
ACTGTACATATGAGATTATC
Found at i:13841 original size:39 final size:40
Alignment explanation
Indices: 13787--13865 Score: 142
Period size: 39 Copynumber: 2.0 Consensus size: 40
13777 AGAGTGAATC
13787 CTAGGAGGGCTTGTAGGGTAA-GGATATGAGTATAGAGAT
1 CTAGGAGGGCTTGTAGGGTAAGGGATATGAGTATAGAGAT
*
13826 CTAGGAGGGCTTGTAGGGTAAGGGATATGGGTATAGAGAT
1 CTAGGAGGGCTTGTAGGGTAAGGGATATGAGTATAGAGAT
13866 ACTAAATTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 21 0.55
40 17 0.45
ACGTcount: A:0.29, C:0.05, G:0.41, T:0.25
Consensus pattern (40 bp):
CTAGGAGGGCTTGTAGGGTAAGGGATATGAGTATAGAGAT
Found at i:15506 original size:5 final size:5
Alignment explanation
Indices: 15496--15521 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
15486 ATTGGCAGCC
15496 CCTAG CCTAG CCTAG CCTAG CCTAG C
1 CCTAG CCTAG CCTAG CCTAG CCTAG C
15522 GCCTAGCCAA
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:0.19, C:0.42, G:0.19, T:0.19
Consensus pattern (5 bp):
CCTAG
Found at i:17271 original size:6 final size:6
Alignment explanation
Indices: 17260--17287 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
17250 ATTCAGATAC
17260 AAAATT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAA
17288 AAATAAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:20505 original size:4 final size:4
Alignment explanation
Indices: 20496--20520 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
20486 CAGCAGCAGC
20496 AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA A
20521 GAAGCTAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:22870 original size:9 final size:9
Alignment explanation
Indices: 22856--22881 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
22846 GAAACAGAGA
22856 GAAAAGAAG
1 GAAAAGAAG
22865 GAAAAGAAG
1 GAAAAGAAG
22874 GAAAAGAA
1 GAAAAGAA
22882 ACAGAAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (9 bp):
GAAAAGAAG
Found at i:24313 original size:164 final size:165
Alignment explanation
Indices: 24031--24360 Score: 536
Period size: 164 Copynumber: 2.0 Consensus size: 165
24021 CGTTATTGTT
*
24031 AGTTAAAACGGTTTTTAAACCGCTCTTTAGGACAAAAAAAATCGAATTTACAATATTGGATAACC
1 AGTTAAAACGGTTTTTAAACCGCTCTTTAGGAC-AAAAAAATCGAATTTACAAGATTGGATAACC
* * ***
24096 CTAGGAAGATTACAGAAACTGTTACATGAAGACTTGATTGGGGTGGTGTGGCCTAGGGCCGTTAT
65 CTAGAAAGATTACAGAAACTGTTACATGAAGACTTGATTGAGGTAACGTGGCCTAGGGCCGTTAT
*
24161 TGTTAGTTAAAACAATGAAGATTTGATTGGGGTGGC
130 TGTTAGTTAAAACAATGAAAATTTGATTGGGGTGGC
24197 AGTTAAAACGGTTTTTAAACCGCTCTTTAGGAC-AAAAAATCGAATTTACAAGATTGGATAACCC
1 AGTTAAAACGGTTTTTAAACCGCTCTTTAGGACAAAAAAATCGAATTTACAAGATTGGATAACCC
* * *
24261 TTGAAAGATTACATAAGCTGTTACATGAAGACTTGATTGAGGTAACGTGGCCTAGGGCCGTTATT
66 TAGAAAGATTACAGAAACTGTTACATGAAGACTTGATTGAGGTAACGTGGCCTAGGGCCGTTATT
**
24326 GTTAGTTAAAATGATGAAAATTTGATTGGGGTGGC
131 GTTAGTTAAAACAATGAAAATTTGATTGGGGTGGC
24361 GTGGCCTAAG
Statistics
Matches: 152, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
164 119 0.78
166 33 0.22
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (165 bp):
AGTTAAAACGGTTTTTAAACCGCTCTTTAGGACAAAAAAATCGAATTTACAAGATTGGATAACCC
TAGAAAGATTACAGAAACTGTTACATGAAGACTTGATTGAGGTAACGTGGCCTAGGGCCGTTATT
GTTAGTTAAAACAATGAAAATTTGATTGGGGTGGC
Found at i:31045 original size:21 final size:20
Alignment explanation
Indices: 30999--31046 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
30989 TTGCCCTTCT
*
30999 TCTCTCTCCCCCACTAACTC
1 TCTCTCTCCCCCACTAACTA
* *
31019 TTTCTCTCCTCCCACTCACTA
1 TCTCTCTCC-CCCACTAACTA
31040 TCTCTCT
1 TCTCTCT
31047 TCATAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.12, C:0.50, G:0.00, T:0.38
Consensus pattern (20 bp):
TCTCTCTCCCCCACTAACTA
Found at i:40332 original size:25 final size:24
Alignment explanation
Indices: 40299--40355 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
40289 GTGGATTGTA
*
40299 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
40324 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
40348 AAA-AAATT
1 AAATAAATT
40356 CAAGGCTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:41126 original size:14 final size:15
Alignment explanation
Indices: 41107--41140 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
41097 ATTAAATTAG
41107 TAAAAT-GGTAAAAA
1 TAAAATAGGTAAAAA
*
41121 TAAAATAGGTATAAA
1 TAAAATAGGTAAAAA
41136 TAAAA
1 TAAAA
41141 AATAGAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (15 bp):
TAAAATAGGTAAAAA
Found at i:44494 original size:18 final size:19
Alignment explanation
Indices: 44471--44509 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
44461 ATTCACATAA
44471 TTCTCTT-TAGATT-TATTT
1 TTCTCTTCTAG-TTCTATTT
44489 TTCTCTTCTAGTTCTATTT
1 TTCTCTTCTAGTTCTATTT
44508 TT
1 TT
44510 TAGCCAAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.13, C:0.15, G:0.05, T:0.67
Consensus pattern (19 bp):
TTCTCTTCTAGTTCTATTT
Found at i:45284 original size:20 final size:20
Alignment explanation
Indices: 45259--45297 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
45249 TAAATCTAGA
*
45259 TTTAATTACTTTGTTTTTAG
1 TTTAATTACTTTCTTTTTAG
*
45279 TTTAATTGCTTTCTTTTTA
1 TTTAATTACTTTCTTTTTA
45298 ATGGTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTAATTACTTTCTTTTTAG
Found at i:50641 original size:9 final size:10
Alignment explanation
Indices: 50618--50645 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
50608 TTCATAAAGA
50618 AAAAAATAGC
1 AAAAAATAGC
50628 AAAAAATAGC
1 AAAAAATAGC
50638 AAAAAATA
1 AAAAAATA
50646 AGAAGATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.75, C:0.07, G:0.07, T:0.11
Consensus pattern (10 bp):
AAAAAATAGC
Found at i:54133 original size:15 final size:15
Alignment explanation
Indices: 54113--54156 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 15
54103 TTGACAACGT
54113 AACAAAAAAAACGAA
1 AACAAAAAAAACGAA
*
54128 AAC-AAAATAA--AA
1 AACAAAAAAAACGAA
54140 AA-AAAAAAAACGAA
1 AACAAAAAAAACGAA
54154 AAC
1 AAC
54157 GATATCAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 8
0.70 0.06 0.24
Matches are distributed among these distances:
12 10 0.43
14 10 0.43
15 3 0.13
ACGTcount: A:0.82, C:0.11, G:0.05, T:0.02
Consensus pattern (15 bp):
AACAAAAAAAACGAA
Found at i:54149 original size:20 final size:21
Alignment explanation
Indices: 54116--54155 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
54106 ACAACGTAAC
**
54116 AAAAAAAACGAAAAC-AAAAT
1 AAAAAAAAAAAAAACGAAAAT
54136 AAAAAAAAAAAAAACGAAAA
1 AAAAAAAAAAAAAACGAAAA
54156 CGATATCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.85, C:0.07, G:0.05, T:0.03
Consensus pattern (21 bp):
AAAAAAAAAAAAAACGAAAAT
Found at i:58170 original size:54 final size:58
Alignment explanation
Indices: 58059--58175 Score: 170
Period size: 60 Copynumber: 2.1 Consensus size: 58
58049 TTAATTTTGA
*
58059 TTTAGTAGTATTAGCACTAATTAAGTTTATATATAAGTTTGATACACTTAGCTTTGTAAT
1 TTTAGTAGTATTAGCACTAATTAAG-TTATATATAAGTTTGATA-ACTTAGCCTTGTAAT
*
58119 TTTAGTAGTATTAGCACTAATTAAG-T-T-TGTAAGTTTGAT-ACTTAGCCTTGTAAT
1 TTTAGTAGTATTAGCACTAATTAAGTTATATATAAGTTTGATAACTTAGCCTTGTAAT
58173 TTT
1 TTT
58176 TTGTGCAAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
54 17 0.31
56 11 0.20
57 1 0.02
58 1 0.02
60 25 0.45
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.46
Consensus pattern (58 bp):
TTTAGTAGTATTAGCACTAATTAAGTTATATATAAGTTTGATAACTTAGCCTTGTAAT
Found at i:59451 original size:13 final size:14
Alignment explanation
Indices: 59433--59463 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
59423 TTTGCAAACT
59433 TTTTTTTTTTAAA-
1 TTTTTTTTTTAAAG
59446 TTTTTTTTTTAAAG
1 TTTTTTTTTTAAAG
59460 TTTT
1 TTTT
59464 ATATACAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTTTTTTTAAAG
Found at i:59765 original size:7 final size:7
Alignment explanation
Indices: 59753--59777 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
59743 ATATTGCTTG
59753 CAACTTT
1 CAACTTT
59760 CAACTTT
1 CAACTTT
59767 CAACTTT
1 CAACTTT
59774 CAAC
1 CAAC
59778 CAATTATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (7 bp):
CAACTTT
Found at i:67828 original size:37 final size:37
Alignment explanation
Indices: 67778--68601 Score: 1171
Period size: 37 Copynumber: 22.1 Consensus size: 37
67768 GTCGAAGTTA
67778 AAACTGAGGAAAGATGACCTGTTTCCAGTCAACTTTGAT
1 AAACTGA--AAAGATGACCTGTTTCCAGTCAACTTTGAT
67817 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
67854 AAATGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
1 AAA--CTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
67893 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
*
67930 AAATGCTGAAAAGATGACCTGTTTCCAGTCAACTTTAAT
1 AAA--CTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
*
67969 AAACTGAAAAGATGACCTGTTTCCAGTCAA-TTCTAAT
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTT-TGAT
* * *
68006 AAACTGGAGAGATGACCTGTTTCCAGTCAACTCTGAT
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
*
68043 AAATGCTGAAAAGATGACCTGTTTCCAGTCAACTTTAAT
1 AAA--CTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
*
68082 AAACTGAAAAGATGACCTGTTTCCAGTCAA-TTCTAAT
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTT-TGAT
* * *
68119 AAACTGGAGAGATGACCTGTTTCCAGTCAACTCTGAT
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
*
68156 AAA-TGAAAAGATGACCTGTTTCCAGTCAA-TTTTAT
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
*
68191 AAACTGAAAAGATGACCTGTCTCCAGTCAACTTTGAT
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
* *
68228 AAATGCTGAAAAGATGACCTGTTTCCAGTCAACTCTGAC
1 AAA--CTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
*
68267 AAA-TGAAAAGATGACCTGTTTCCAGTCAATTTTGAT
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
* *
68303 AAACTGAAGAGATGACCTGTTTCCAGTCAATTTTGAT
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
* *
68340 AAACTGAAGAGATGACCTGTTTCCAGTCAACTCTGAT
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
**
68377 AAA-TGAAAAGATGACCTGTTTCCAACCAACTTTGAT
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
* *
68413 AAACTGAAGAGATGACCTGTTTCCAGTCAACTCTGAT
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
**
68450 AAA-TGAAAAGATGACCTGTTTCCAACCAACTTTGAT
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
* *
68486 AAACTGAAGAGATGACCTGTTTCCAGTCAACTCTGAT
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
68523 AAA-TGAAAAGATGACCTGTTTCCAGTCAA-TTCTGAT
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTT-TGAT
* * **
68559 AAACGCTGAAAAGATGGCCTATTTCCAACCAACTTTGAT
1 AAA--CTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
68598 AAAC
1 AAAC
68602 GCTGAAAAAA
Statistics
Matches: 713, Mismatches: 50, Indels: 46
0.88 0.06 0.06
Matches are distributed among these distances:
35 8 0.01
36 182 0.26
37 343 0.48
38 2 0.00
39 176 0.25
40 2 0.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (37 bp):
AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
Found at i:67909 original size:113 final size:110
Alignment explanation
Indices: 67778--68601 Score: 1165
Period size: 113 Copynumber: 7.4 Consensus size: 110
67768 GTCGAAGTTA
*
67778 AAACTGAGGAAAGATGACCTGTTTCCAGTCAACTTTGATAAACTGAAAAGATGACCTGTTTCCAG
1 AAACTGA--AAAGATGACCTGTTTCCAGTCAACTCTGATAAACTGAAAAGATGACCTGTTTCCAG
67843 TCAACTTTGATAAATGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT
64 TCAACTTTGATAAA--CTGAAAAGATGACCTGTTTCCAGTCAA-TTTGAT
*
67893 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGATGACCTGTTTCCAG
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTCTGATAAA--CTGAAAAGATGACCTGTTTCCAG
* *
67958 TCAACTTTAATAAACTGAAAAGATGACCTGTTTCCAGTCAATTCTAAT
64 TCAACTTTGATAAACTGAAAAGATGACCTGTTTCCAGTCAATT-TGAT
* *
68006 AAACTGGAGAGATGACCTGTTTCCAGTCAACTCTGATAAATGCTGAAAAGATGACCTGTTTCCAG
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTCTGATAAA--CTGAAAAGATGACCTGTTTCCAG
* *
68071 TCAACTTTAATAAACTGAAAAGATGACCTGTTTCCAGTCAATTCTAAT
64 TCAACTTTGATAAACTGAAAAGATGACCTGTTTCCAGTCAATT-TGAT
* *
68119 AAACTGGAGAGATGACCTGTTTCCAGTCAACTCTGATAAA-TGAAAAGATGACCTGTTTCCAGTC
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTCTGATAAACTGAAAAGATGACCTGTTTCCAGTC
* *
68183 AA-TTTTATAAACTGAAAAGATGACCTGTCTCCAGTCAACTTTGAT
66 AACTTTGATAAACTGAAAAGATGACCTGTTTCCAGTCAA-TTTGAT
*
68228 AAATGCTGAAAAGATGACCTGTTTCCAGTCAACTCTGACAAA-TGAAAAGATGACCTGTTTCCAG
1 AAA--CTGAAAAGATGACCTGTTTCCAGTCAACTCTGATAAACTGAAAAGATGACCTGTTTCCAG
* *
68292 TCAATTTTGATAAACTGAAGAGATGACCTGTTTCCAGTCAATTTTGAT
64 TCAACTTTGATAAACTGAAAAGATGACCTGTTTCCAGTCAA-TTTGAT
* **
68340 AAACTGAAGAGATGACCTGTTTCCAGTCAACTCTGATAAA-TGAAAAGATGACCTGTTTCCAACC
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTCTGATAAACTGAAAAGATGACCTGTTTCCAGTC
* *
68404 AACTTTGATAAACTGAAGAGATGACCTGTTTCCAGTCAACTCTGAT
66 AACTTTGATAAACTGAAAAGATGACCTGTTTCCAGTCAA-TTTGAT
** * *
68450 AAA-TGAAAAGATGACCTGTTTCCAACCAACTTTGATAAACTGAAGAGATGACCTGTTTCCAGTC
1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTCTGATAAACTGAAAAGATGACCTGTTTCCAGTC
*
68514 AACTCTGATAAA-TGAAAAGATGACCTGTTTCCAGTCAATTCTGAT
66 AACTTTGATAAACTGAAAAGATGACCTGTTTCCAGTCAATT-TGAT
* * ** *
68559 AAACGCTGAAAAGATGGCCTATTTCCAACCAACTTTGATAAAC
1 AAA--CTGAAAAGATGACCTGTTTCCAGTCAACTCTGATAAAC
68602 GCTGAAAAAA
Statistics
Matches: 663, Mismatches: 34, Indels: 27
0.92 0.05 0.04
Matches are distributed among these distances:
108 1 0.00
109 104 0.16
110 163 0.25
111 60 0.09
112 79 0.12
113 213 0.32
115 43 0.06
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (110 bp):
AAACTGAAAAGATGACCTGTTTCCAGTCAACTCTGATAAACTGAAAAGATGACCTGTTTCCAGTC
AACTTTGATAAACTGAAAAGATGACCTGTTTCCAGTCAATTTGAT
Found at i:68186 original size:73 final size:73
Alignment explanation
Indices: 67778--68601 Score: 1118
Period size: 73 Copynumber: 11.1 Consensus size: 73
67768 GTCGAAGTTA
67778 AAACTGAGGAAAGATGACCTGTTTCCAGTCAACTTTGATAAACTGAAAAGATGACCTGTTTCCAG
1 AAACTGA--AAAGATGACCTGTTTCCAGTCAA-TTTGATAAACTGAAAAGATGACCTGTTTCCAG
*
67843 TCAACTTTGAT
63 TCAACTCTGAT
67854 AAATGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAACTGAAAAGATGACCTGTTTCCAG
1 AAA--CTGAAAAGATGACCTGTTTCCAGTCAA-TTTGATAAACTGAAAAGATGACCTGTTTCCAG
*
67919 TCAACTTTGAT
63 TCAACTCTGAT
*
67930 AAATGCTGAAAAGATGACCTGTTTCCAGTCAACTTTAATAAACTGAAAAGATGACCTGTTTCCAG
1 AAA--CTGAAAAGATGACCTGTTTCCAGTCAA-TTTGATAAACTGAAAAGATGACCTGTTTCCAG
* *
67995 TCAATTCTAAT
63 TCAACTCTGAT
* * *
68006 AAACTGGAGAGATGACCTGTTTCCAGTCAACTCTGATAAATGCTGAAAAGATGACCTGTTTCCAG
1 AAACTGAAAAGATGACCTGTTTCCAGTCAA-TTTGATAAA--CTGAAAAGATGACCTGTTTCCAG
* *
68071 TCAACTTTAAT
63 TCAACTCTGAT
* * *
68082 AAACTGAAAAGATGACCTGTTTCCAGTCAATTCTAATAAACTGGAGAGATGACCTGTTTCCAGTC
1 AAACTGAAAAGATGACCTGTTTCCAGTCAATT-TGATAAACTGAAAAGATGACCTGTTTCCAGTC
68147 AACTCTGAT
65 AACTCTGAT
* *
68156 AAA-TGAAAAGATGACCTGTTTCCAGTCAATTTTATAAACTGAAAAGATGACCTGTCTCCAGTCA
1 AAACTGAAAAGATGACCTGTTTCCAGTCAATTTGATAAACTGAAAAGATGACCTGTTTCCAGTCA
*
68220 ACTTTGAT
66 ACTCTGAT
* *
68228 AAATGCTGAAAAGATGACCTGTTTCCAGTCAACTCTGACAAA-TGAAAAGATGACCTGTTTCCAG
1 AAA--CTGAAAAGATGACCTGTTTCCAGTCAA-TTTGATAAACTGAAAAGATGACCTGTTTCCAG
* *
68292 TCAATTTTGAT
63 TCAACTCTGAT
* *
68303 AAACTGAAGAGATGACCTGTTTCCAGTCAATTTTGATAAACTGAAGAGATGACCTGTTTCCAGTC
1 AAACTGAAAAGATGACCTGTTTCCAGTCAA-TTTGATAAACTGAAAAGATGACCTGTTTCCAGTC
68368 AACTCTGAT
65 AACTCTGAT
** *
68377 AAA-TGAAAAGATGACCTGTTTCCAACCAACTTTGATAAACTGAAGAGATGACCTGTTTCCAGTC
1 AAACTGAAAAGATGACCTGTTTCCAGTCAA-TTTGATAAACTGAAAAGATGACCTGTTTCCAGTC
68441 AACTCTGAT
65 AACTCTGAT
** *
68450 AAA-TGAAAAGATGACCTGTTTCCAACCAACTTTGATAAACTGAAGAGATGACCTGTTTCCAGTC
1 AAACTGAAAAGATGACCTGTTTCCAGTCAA-TTTGATAAACTGAAAAGATGACCTGTTTCCAGTC
68514 AACTCTGAT
65 AACTCTGAT
* * *
68523 AAA-TGAAAAGATGACCTGTTTCCAGTCAATTCTGATAAACGCTGAAAAGATGGCCTATTTCCAA
1 AAACTGAAAAGATGACCTGTTTCCAGTCAATT-TGATAAA--CTGAAAAGATGACCTGTTTCCAG
* *
68587 CCAACTTTGAT
63 TCAACTCTGAT
68598 AAAC
1 AAAC
68602 GCTGAAAAAA
Statistics
Matches: 687, Mismatches: 47, Indels: 28
0.90 0.06 0.04
Matches are distributed among these distances:
72 41 0.06
73 234 0.34
74 99 0.14
75 92 0.13
76 217 0.32
78 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (73 bp):
AAACTGAAAAGATGACCTGTTTCCAGTCAATTTGATAAACTGAAAAGATGACCTGTTTCCAGTCA
ACTCTGAT
Done.