Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014533.1 Corchorus olitorius cultivar O-4 contig14566, 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: 7874
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Found at i:2048 original size:6 final size:6
Alignment explanation
Indices: 2037--2068 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
2027 CAGGCTGCAC
2037 CACAAT CACAAT CACAAT CACAAT CACAAT CA
1 CACAAT CACAAT CACAAT CACAAT CACAAT CA
2069 TCCGTTAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:2224 original size:39 final size:38
Alignment explanation
Indices: 2098--2246 Score: 228
Period size: 38 Copynumber: 3.9 Consensus size: 38
2088 TCGAGTCTAG
2098 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
2135 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * *
2173 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTA
* *
2212 CCATCAGTTTAACCCCCTGACGGTACGGGTCCACT
1 CCAACAGTTTAACCCCCTGA-GGCACGGGTCCACT
2247 ATCGCACAGC
Statistics
Matches: 103, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
37 7 0.07
38 62 0.60
39 21 0.20
40 13 0.13
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:5380 original size:14 final size:14
Alignment explanation
Indices: 5361--5395 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
5351 GAAGAGTAGG
5361 TGATTTTATGATTT
1 TGATTTTATGATTT
5375 TGATTTTATGATTT
1 TGATTTTATGATTT
5389 TGATTTT
1 TGATTTT
5396 CTTGACTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (14 bp):
TGATTTTATGATTT
Found at i:5465 original size:22 final size:21
Alignment explanation
Indices: 5409--5662 Score: 157
Period size: 22 Copynumber: 11.5 Consensus size: 21
5399 GACTCTGTGT
* * *
5409 GGTTGTCAAATTTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* *
5430 TGGTTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
5453 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* **
5475 GGTTACCAAAATTTCATAATAA
1 GGTTATCAAAATTTCAT-AGGA
* * *
5497 AGTCATCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCATAGG-A
*
5519 GGTTATCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCATAGG-A
*
5541 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
5563 GGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGG---A
* *
5587 GGTTATTAAAATTTCTTAGGAA
1 GGTTATCAAAATTTCATAGG-A
** * * *
5609 GGTTATTGAACTTTTATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* * *
5631 GGTTATCACAATTTTATAGAAA
1 GGTTATCAAAATTTCATAG-GA
5653 GGTTATCAAA
1 GGTTATCAAA
5663 GAGATTATCA
Statistics
Matches: 180, Mismatches: 43, Indels: 18
0.75 0.18 0.07
Matches are distributed among these distances:
21 3 0.02
22 154 0.86
23 6 0.03
24 17 0.09
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:5478 original size:44 final size:44
Alignment explanation
Indices: 5430--6835 Score: 199
Period size: 44 Copynumber: 31.9 Consensus size: 44
5420 TTTCATAAGA
* * *
5430 TGGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCATAGTG
1 TGGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCATAGTG
* * ** * * *
5474 TGGTTACCAAAATTTCATAATAAAGTCATCAAAATTTCAT-GGG
1 TGGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCATAGTG
*
5517 AAGGTTATCAAAATTTCATG-GGAAGGTTATCAAAATTTCATAGTG
1 -TGGTTATCAAAATTTCATGAGG-AGGTTATCAAAATTTCATAGTG
* * *
5562 TGGTTACCAAAATTTCAT-AGGATCAGGTTATTAAAATTTCTTAG-G
1 TGGTTATCAAAATTTCATGAGG---AGGTTATCAAAATTTCATAGTG
* ** * * * * * **
5607 AAGGTTATTGAACTTTTAT-AGTGTGGTTATCACAATTTTATAGAA
1 -TGGTTATCAAAATTTCATGAG-GAGGTTATCAAAATTTCATAGTG
* *
5652 AGGTTATC--AA----A-GA-GA--TTATCAAAATGTCATAGTG
1 TGGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCATAGTG
* * * * * *
5686 AGGTTAT-AAGAATTTCAT-AGTGTGGTTGGAGGTTACTAATATTTTATGGGG
1 TGGTTATCAA-AATTTCATGAG-GAGGTT--A---T-C-AAAATTTCATAGTG
* * * **
5737 AGGCTATCAAAATTTCAT-AGTGTGGTTAT-AAAATTTTTTTAGTG
1 TGGTTATCAAAATTTCATGAG-GAGGTTATCAAAA-TTTCATAGTG
* * *
5781 TGGTTATCAAAATTCCAT-ATGAAGGTTAT-AAAAGTCTCAATTTCA-TG
1 TGGTTATCAAAATTTCATGA-GGAGGTTATCAAAA-TTTC-A--T-AGTG
* * * * *
5828 AGGAGTACCAAGATTTGATAGAAAGTTGCGAGGTTAT-AAGAATTTCATAGTG
1 TGG-TTATCAAAATTTCAT-G--A---G-GAGGTTATCAA-AATTTCATAGTG
* * *
5880 TGGTTGGAGGTTACTAATATTTTATGGGGAGGTTATCAAAATTTCATAGTG
1 TGGTT--A---T-C-AAAATTTCATGAGGAGGTTATCAAAATTTCATAGTG
* * * *
5931 TGGTTATCAAAATTT-TTTAGTGTGGTTATCAAAATTCCATA-TG
1 TGGTTATCAAAATTTCATGAG-GAGGTTATCAAAATTTCATAGTG
* * * * * *
5974 AAGGTTATAAAAGTCTCAATTTCATGAGGA-G-TACCAAGATTTGATAG-A
1 -TGGTTAT-CAA-----AATTTCATGAGGAGGTTATCAAAATTTCATAGTG
** * * *
6022 AAGTTATC-AAATCTCAT-AGAGTGGTTATCGAAATTTCAT-GTAG
1 TGGTTATCAAAATTTCATGAG-GAGGTTATCAAAATTTCATAGT-G
* *
6065 ATCGGATATCAAAATTT-AT-AGGAAGATTATCAAAATTTCATAGTG
1 -T-GGTTATCAAAATTTCATGAGG-AGGTTATCAAAATTTCATAGTG
* * ** * * *
6110 TTGTTATCAAAATTTGAAAACGAGGTTATCAAAATTACATAATG
1 TGGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCATAGTG
* * * * * **
6154 TGATTATCAAAATTTCATAAAGG-GGTCAACAAAATTTTATAAAG
1 TGGTTATCAAAATTTCAT-GAGGAGGTTATCAAAATTTCATAGTG
* * * * * * * * *
6198 AGCTTATCAAAATTTCATAAAGAGTTTATCAAATTTTGAAAATG
1 TGGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCATAGTG
* * * * *
6242 TGATTTACCAAAATTTCAT-A-GTGG-TAT-----TTT--TGGGG
1 TG-GTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCATAGTG
* * * *
6277 AGGTTATCAAAATTTCAT-CGTATGGTTA-CCAAA-TT--T-G-G
1 TGGTTATCAAAATTTCATGAGGA-GGTTATCAAAATTTCATAGTG
* * * * * * * *
6315 AAGGTAATTAAAGTTTTATTATGGA-GTAATCAAAATTTC--AGGG
1 -TGGTTATCAAAATTTCATGA-GGAGGTTATCAAAATTTCATAGTG
* * * * * *
6358 AGGATATCAAAGTTTCAT-ACGAAGGTTATCAATATTTCATAGTT
1 TGGTTATCAAAATTTCATGA-GGAGGTTATCAAAATTTCATAGTG
* * * *
6402 TAGTTTTCAAAATTTCAT-AAGAGGGTTATCAAAATTTCATAGTA
1 TGGTTATCAAAATTTCATGAGGA-GGTTATCAAAATTTCATAGTG
* * * *
6446 T-GTAGATCAAAATTTCAT-AGGGAGATTAACAAAATTTCATAATG
1 TGGT-TATCAAAATTTCATGA-GGAGGTTATCAAAATTTCATAGTG
* * **
6490 AGGTTATAAAAAAATCAT-AGGGAGGTTATCAAAA--T--T--TG
1 TGGTTATCAAAATTTCATGA-GGAGGTTATCAAAATTTCATAGTG
* * * * *
6528 TAGTTATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGAG
1 TGGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCATAGTG
* * * * *
6572 AGGTTTATCAAAATTTTAT-AGGATGATTTATTAAAATTTCATAGCG
1 TGG-TTATCAAAATTTCATGAGGA-G-GTTATCAAAATTTCATAGTG
* * * * **
6618 AGGTTATCACAATTTCAT-AGTGTGATTATCAAAATTTCAGGGTG
1 TGGTTATCAAAATTTCATGAG-GAGGTTATCAAAATTTCATAGTG
* * * * * **
6662 TGATTA-CTAACAA-TTCAT-ATGAAGGTTTTTAAATTTTCATAACG
1 TGGTTATC-AA-AATTTCATGA-GGAGGTTATCAAAATTTCATAGTG
* * *
6706 TGGTTATCAATATATT-AT-ATGGAGGTTATCAACATCTCATAGTG
1 TGGTTATCAAAAT-TTCATGA-GGAGGTTATCAAAATTTCATAGTG
* *
6750 TTGGTTACCAAAATTTCATTG-GGAAGTTATCAAAATTTCATAGTG
1 -TGGTTATCAAAATTTCA-TGAGGAGGTTATCAAAATTTCATAGTG
* * * * *
6795 AGGTCT-TCAAAA-TTCCTTAGGAAGATTAACAAAATTTCATA
1 TGGT-TATCAAAATTTCATGAGG-AGGTTATCAAAATTTCATA
6836 AGAAGGTTAA
Statistics
Matches: 986, Mismatches: 250, Indels: 252
0.66 0.17 0.17
Matches are distributed among these distances:
34 35 0.04
35 2 0.00
36 5 0.01
37 5 0.01
38 31 0.03
39 21 0.02
40 19 0.02
41 9 0.01
42 45 0.05
43 37 0.04
44 442 0.45
45 126 0.13
46 63 0.06
47 12 0.01
48 22 0.02
49 4 0.00
50 7 0.01
51 62 0.06
52 11 0.01
53 1 0.00
54 3 0.00
55 12 0.01
56 2 0.00
57 2 0.00
58 8 0.01
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (44 bp):
TGGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCATAGTG
Found at i:5573 original size:66 final size:66
Alignment explanation
Indices: 5430--5662 Score: 209
Period size: 66 Copynumber: 3.5 Consensus size: 66
5420 TTTCATAAGA
* * * * * *
5430 TGGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCATAGTG-TGGTTACCAAAATTTCATA
1 TGGTTATCAAAATTTCAT-AGGAAGGTTATCAAAATTTCAT-GGGAAGGTTATCAAAATTTCATA
* *
5493 ATA
64 GTG
** * *
5496 AAGTCATCAAAATTTCATGGGAAGGTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCATAGT
1 TGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCATAGT
5561 G
66 G
* * * * ** * *
5562 TGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTAGGAAGGTTATTGAACTTTTATA
1 TGGTTATCAAAATTTCATAGGA--AGGTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCATA
5627 GTG
64 GTG
* * *
5630 TGGTTATCACAATTTTATAGAAAGGTTATCAAA
1 TGGTTATCAAAATTTCATAGGAAGGTTATCAAA
5663 GAGATTATCA
Statistics
Matches: 134, Mismatches: 29, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
65 4 0.03
66 75 0.56
68 55 0.41
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (66 bp):
TGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCATAGT
G
Found at i:5882 original size:172 final size:172
Alignment explanation
Indices: 5685--6026 Score: 659
Period size: 172 Copynumber: 2.0 Consensus size: 172
5675 ATGTCATAGT
5685 GAGGTTATAAGAATTTCATAGTGTGGTTGGAGGTTACTAATATTTTATGGGGAGGCTATCAAAAT
1 GAGGTTATAAGAATTTCATAGTGTGGTTGGAGGTTACTAATATTTTATGGGGAGGCTATCAAAAT
5750 TTCATAGTGTGGTTAT-AAAATTTTTTTAGTGTGGTTATCAAAATTCCATATGAAGGTTATAAAA
66 TTCATAGTGTGGTTATCAAAA-TTTTTTAGTGTGGTTATCAAAATTCCATATGAAGGTTATAAAA
5814 GTCTCAATTTCATGAGGAGTACCAAGATTTGATAGAAAGTTGC
130 GTCTCAATTTCATGAGGAGTACCAAGATTTGATAGAAAGTTGC
*
5857 GAGGTTATAAGAATTTCATAGTGTGGTTGGAGGTTACTAATATTTTATGGGGAGGTTATCAAAAT
1 GAGGTTATAAGAATTTCATAGTGTGGTTGGAGGTTACTAATATTTTATGGGGAGGCTATCAAAAT
5922 TTCATAGTGTGGTTATCAAAATTTTTTAGTGTGGTTATCAAAATTCCATATGAAGGTTATAAAAG
66 TTCATAGTGTGGTTATCAAAATTTTTTAGTGTGGTTATCAAAATTCCATATGAAGGTTATAAAAG
5987 TCTCAATTTCATGAGGAGTACCAAGATTTGATAGAAAGTT
131 TCTCAATTTCATGAGGAGTACCAAGATTTGATAGAAAGTT
6027 ATCAAATCTC
Statistics
Matches: 168, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
172 164 0.98
173 4 0.02
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.37
Consensus pattern (172 bp):
GAGGTTATAAGAATTTCATAGTGTGGTTGGAGGTTACTAATATTTTATGGGGAGGCTATCAAAAT
TTCATAGTGTGGTTATCAAAATTTTTTAGTGTGGTTATCAAAATTCCATATGAAGGTTATAAAAG
TCTCAATTTCATGAGGAGTACCAAGATTTGATAGAAAGTTGC
Found at i:5923 original size:22 final size:22
Alignment explanation
Indices: 5885--5966 Score: 76
Period size: 22 Copynumber: 3.7 Consensus size: 22
5875 TAGTGTGGTT
* *
5885 GGAGGTTA-CTAATATTTTATGG
1 GGAGGTTATC-AAAATTTTATAG
*
5907 GGAGGTTATCAAAATTTCATAG
1 GGAGGTTATCAAAATTTTATAG
* * *
5929 TGTGGTTATCAAAATTTTTTAG
1 GGAGGTTATCAAAATTTTATAG
* *
5951 TGTGGTTATCAAAATT
1 GGAGGTTATCAAAATT
5967 CCATATGAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
22 51 0.98
23 1 0.02
ACGTcount: A:0.30, C:0.06, G:0.22, T:0.41
Consensus pattern (22 bp):
GGAGGTTATCAAAATTTTATAG
Found at i:5979 original size:22 final size:22
Alignment explanation
Indices: 5908--6230 Score: 131
Period size: 22 Copynumber: 14.5 Consensus size: 22
5898 ATTTTATGGG
5908 GAGGTTATCAAAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
* **
5930 GTGGTTATCAAAATTTTTTAGT
1 GAGGTTATCAAAATTTCATAGT
* *
5952 GTGGTTATCAAAATTCCATA-T
1 GAGGTTATCAAAATTTCATAGT
*
5973 GAAGGTTAT-AAAAGTCTCAATTTCA-T
1 G-AGGTTATCAAAA-TTTC-A--T-AGT
* * * *
5999 GAGGAGTACCAAGATTTGATAG-
1 GAGG-TTATCAAAATTTCATAGT
* * * *
6021 AAAGTTATC-AAATCTCATAGA
1 GAGGTTATCAAAATTTCATAGT
* *
6042 GTGGTTATCGAAATTTCAT-GT
1 GAGGTTATCAAAATTTCATAGT
*
6063 AGATCGGATATCAAAATTT-ATAG-
1 -GA--GGTTATCAAAATTTCATAGT
*
6086 GAAGATTATCAAAATTTCATAGT
1 G-AGGTTATCAAAATTTCATAGT
** * * **
6109 GTTGTTATCAAAATTTGAAAAC
1 GAGGTTATCAAAATTTCATAGT
* *
6131 GAGGTTATCAAAATTACATAAT
1 GAGGTTATCAAAATTTCATAGT
* * **
6153 GTGATTATCAAAATTTCATAAA
1 GAGGTTATCAAAATTTCATAGT
* * * * **
6175 GGGGTCAACAAAATTTTATAAA
1 GAGGTTATCAAAATTTCATAGT
* **
6197 GAGCTTATCAAAATTTCATAAA
1 GAGGTTATCAAAATTTCATAGT
*
6219 GAGTTTATCAAA
1 GAGGTTATCAAA
6231 TTTTGAAAAT
Statistics
Matches: 224, Mismatches: 59, Indels: 36
0.70 0.18 0.11
Matches are distributed among these distances:
20 8 0.04
21 28 0.12
22 154 0.69
23 6 0.03
24 13 0.06
25 5 0.02
26 7 0.03
27 3 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGT
Found at i:6187 original size:66 final size:66
Alignment explanation
Indices: 6089--6217 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 66
6079 TTTATAGGAA
** ** * * *
6089 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTGA-AAACGAGGTTATCAAAATTACATAAT
1 GATTATCAAAATTTCATAAAGGGGTCAACAAAATTTGATAAA-GAGCTTATCAAAATTACATAAT
6153 GT
65 GT
* *
6155 GATTATCAAAATTTCATAAAGGGGTCAACAAAATTTTATAAAGAGCTTATCAAAATTTCATAA
1 GATTATCAAAATTTCATAAAGGGGTCAACAAAATTTGATAAAGAGCTTATCAAAATTACATAA
6218 AGAGTTTATC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 50 0.94
67 3 0.06
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.34
Consensus pattern (66 bp):
GATTATCAAAATTTCATAAAGGGGTCAACAAAATTTGATAAAGAGCTTATCAAAATTACATAATG
T
Found at i:6583 original size:23 final size:22
Alignment explanation
Indices: 6343--6938 Score: 213
Period size: 22 Copynumber: 27.3 Consensus size: 22
6333 TTATGGAGTA
* *
6343 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGAGAGGTT
*
6363 ATCAAAGTTTCATACGA-AGGTT
1 ATCAAAATTTCATA-GAGAGGTT
* **
6385 ATCAATATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-AGAGGTT
*
6407 TTCAAAATTTCATA-AGAGGGTT
1 ATCAAAATTTCATAGAGA-GGTT
* * *
6429 ATCAAAATTTCATAG-TATGTAG
1 ATCAAAATTTCATAGAGAGGT-T
* *
6451 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGAGAGGTT
*
6473 AACAAAATTTCATA-ATGAGGTT
1 ATCAAAATTTCATAGA-GAGGTT
* ** *
6495 ATAAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGAGAGGTT
*
6517 ATCAAAA-TT--T-G-TA-GTT
1 ATCAAAATTTCATAGAGAGGTT
*
6533 ATCAAGATTTCATA-AGGAGGTT
1 ATCAAAATTTCATAGA-GAGGTT
*
6555 ATCAAAATTTTATAGAGAGGTTT
1 ATCAAAATTTCATAGAGAGG-TT
* *
6578 ATCAAAATTTTATAG-GATGATTT
1 ATCAAAATTTCATAGAGA-G-GTT
* *
6601 ATTAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGAGAGGTT
* * * *
6623 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGAGAGGTT
** * * *
6645 ATCAAAATTTCAGGGTGTGATT
1 ATCAAAATTTCATAGAGAGGTT
6667 A-CTAACAA-TTCATATGA-AGGTT
1 ATC-AA-AATTTCATA-GAGAGGTT
* * * *
6689 TTTAAATTTTCATA-ACGTGGTT
1 ATCAAAATTTCATAGA-GAGGTT
*
6711 ATCAATATATT-ATATG-GAGGTT
1 ATCAAAAT-TTCATA-GAGAGGTT
* * * *
6733 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGAG-AGGTT
* * * *
6756 ACCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGAGAGGTT
*
6778 ATCAAAATTTCATAGTGAGGTCT
1 ATCAAAATTTCATAGAGAGGT-T
* * *
6801 -TCAAAATTCCTTAG-GAAGATT
1 ATCAAAATTTCATAGAG-AGGTT
*
6822 AACAAAATTTCATA-AGAAGGTT
1 ATCAAAATTTCATAGAG-AGGTT
** * * *
6844 AAAAAAAATTT-AAAAAAAGGTT
1 -ATCAAAATTTCATAGAGAGGTT
* * * **
6866 CTCGAAATTCCATAGTA-TCGTT
1 ATCAAAATTTCATAG-AGAGGTT
*
6888 ATTAAAATTTCATA-AGAAGGTT
1 ATCAAAATTTCATAGAG-AGGTT
*
6910 ATCAAAATTTGATA-AGGAGGTT
1 ATCAAAATTTCATAGA-GAGGTT
*
6932 ATAAAAA
1 ATCAAAA
6939 ATAGTGTAAT
Statistics
Matches: 427, Mismatches: 101, Indels: 94
0.69 0.16 0.15
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 1 0.00
19 2 0.00
20 13 0.03
21 16 0.04
22 308 0.72
23 73 0.17
24 2 0.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGAGAGGTT
Found at i:6625 original size:45 final size:45
Alignment explanation
Indices: 6531--6656 Score: 132
Period size: 45 Copynumber: 2.8 Consensus size: 45
6521 AAATTTGTAG
* * * *
6531 TTATCAAGATTTCATAAG-GAGGTTATCAAAATTTTATAGAGAGGT
1 TTATCAAAATTTCAT-AGTGTGATTATCAAAATTTCATAGAGAGGT
* * *
6576 TTATCAAAATTTTATAG-GATGATTTATTAAAATTTCATAGCGAGG-
1 TTATCAAAATTTCATAGTG-TGA-TTATCAAAATTTCATAGAGAGGT
*
6621 TTATCACAATTTCATAGTGTGATTATCAAAATTTCA
1 TTATCAAAATTTCATAGTGTGATTATCAAAATTTCA
6657 GGGTGTGATT
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
44 16 0.24
45 32 0.47
46 20 0.29
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (45 bp):
TTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAGAGAGGT
Found at i:6975 original size:12 final size:12
Alignment explanation
Indices: 6958--6984 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6948 TTATCATAAT
6958 TTAATAGGGAGA
1 TTAATAGGGAGA
6970 TTAATAGGGAGA
1 TTAATAGGGAGA
6982 TTA
1 TTA
6985 CCATATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (12 bp):
TTAATAGGGAGA
Found at i:7169 original size:148 final size:143
Alignment explanation
Indices: 7012--7306 Score: 509
Period size: 148 Copynumber: 2.0 Consensus size: 143
7002 ATATATATAT
7012 AATTTCATATAAATATTTCATTTAAACACGTTGGGCCACGTGCAACGCACGTGAAAGCTAAAACT
1 AATTTCATATAAATATTTCATTTAAACACGTTGGGCCACGTGCAACGCACGTGAAAGCTAAAACT
* * *
7077 AGTAACTTAAAAAATATCAAAATTAAAAATATATATATATATATGATAAATGGCATATTAATTTG
66 AGTAACTTAAAAAATATAAAAATT--AAA-AT-GATATATATATGATAAATCGCATATTAATTTG
*
7142 TAATATATACCTTGATAA
127 TAATATATAACTTGA-AA
7160 AATTTCATATAAATATTTCATTTAAACACGTTGGGCCACGTGCAACGCACGTGAAAGCTAAAACT
1 AATTTCATATAAATATTTCATTTAAACACGTTGGGCCACGTGCAACGCACGTGAAAGCTAAAACT
7225 AGTAACTTAAAAAATATAAAAATTAAAATGATATATATATGATAAATCGCATATTAATTTGTAAT
66 AGTAACTTAAAAAATATAAAAATTAAAATGATATATATATGATAAATCGCATATTAATTTGTAAT
7290 ATATAACTTGAAA
131 ATATAACTTGAAA
7303 AATT
1 AATT
7307 AATTTTTATA
Statistics
Matches: 143, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
143 6 0.04
144 44 0.31
145 2 0.01
146 3 0.02
148 88 0.62
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (143 bp):
AATTTCATATAAATATTTCATTTAAACACGTTGGGCCACGTGCAACGCACGTGAAAGCTAAAACT
AGTAACTTAAAAAATATAAAAATTAAAATGATATATATATGATAAATCGCATATTAATTTGTAAT
ATATAACTTGAAA
Done.