Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012687.1 Corchorus capsularis cultivar CVL-1 contig12708, 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: 27024
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:325 original size:24 final size:23
Alignment explanation
Indices: 298--344 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
288 AGTTATTTAA
298 TTTATGCTT-TATCTTTAATTTTTC
1 TTTAT-CTTATATCTTT-ATTTTTC
*
322 TTTATCTTATGTCTTTATTTTTC
1 TTTATCTTATATCTTTATTTTTC
345 CAGTTTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.15, C:0.13, G:0.04, T:0.68
Consensus pattern (23 bp):
TTTATCTTATATCTTTATTTTTC
Found at i:326 original size:17 final size:18
Alignment explanation
Indices: 293--329 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
283 GGTTTAGTTA
293 TTTAATTTATGCTTTATC
1 TTTAATTTATGCTTTATC
*
311 TTTAATTT-TTCTTTATC
1 TTTAATTTATGCTTTATC
328 TT
1 TT
330 ATGTCTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.19, C:0.11, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTAATTTATGCTTTATC
Found at i:9429 original size:41 final size:41
Alignment explanation
Indices: 9281--9879 Score: 568
Period size: 41 Copynumber: 14.0 Consensus size: 41
9271 ATCAGTAAAT
* * * *
9281 ACAGTCAAAGTCTTAATTCAAGGTAATTATGAAAAGCAAGC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
* *
9322 ACAGTTAAAGTCAAAATCTTAATTCAGGGTAATTAAGAGAAG-AAGC
1 ACAGTTAAAG------TCTTAATTCAGGGTAATTAAGAAAAGCAAAC
9368 ACAGTTAAAGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGCAAAC
1 ACAGTTAAAG------TCTTAATTCAGGGTAATTAAGAAAAGCAAAC
*
9415 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAGAAG--AAC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
* * *
9454 ACA-TTCAAAGTCTTAATTCAGGATAATTAAGAGAAG-AAGC
1 ACAGTT-AAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
*
9494 ACAGTTAAAGTCAAAATCTTAATTCAGTGTAATTAAGAAAAGCAAAC
1 ACAGTTAAAG------TCTTAATTCAGGGTAATTAAGAAAAGCAAAC
*
9541 ACAGTTAAAGTCTTAATTCAGGGTAATTGAGAAAAGCAAAC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
* *
9582 GCAGTTAAAGT-TTAATT-ATGGGTAATTAAGAAAAGAAGAAC
1 ACAGTTAAAGTCTTAATTCA-GGGTAATTAAGAAAAGCA-AAC
* * * *
9623 ACAGTCAAAGTTTTAATTCTGGGTAATTAAGAAAAGCAAGC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
*
9664 ACAGTTAAAGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGTAAAC
1 ACAGTTAAAG------TCTTAATTCAGGGTAATTAAGAAAAGCAAAC
*
9711 ACAGTGAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
* ** * * *
9752 ATAGTCGAAGTTTTAATTCAGGGTAATTAAGAAAAGCTAGC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
*
9793 ACAGTTAAGGTCAAAGTCTTAATTCAGGGTAATTAATAAAAGCAAAC
1 ACAG-T----T-AAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
* * *
9840 ACAGTTAAAGTCTCAA--CATGGTAATTAAGAAAAGTAAAC
1 ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
9879 A
1 A
9880 TAGTCAAGGG
Statistics
Matches: 478, Mismatches: 47, Indels: 68
0.81 0.08 0.11
Matches are distributed among these distances:
38 2 0.00
39 57 0.12
40 31 0.06
41 175 0.37
42 25 0.05
46 69 0.14
47 119 0.25
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.25
Consensus pattern (41 bp):
ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAAC
Found at i:9764 original size:129 final size:127
Alignment explanation
Indices: 9283--9886 Score: 592
Period size: 129 Copynumber: 4.7 Consensus size: 127
9273 CAGTAAATAC
* * * *
9283 AGTCAAAGTCTTAATTCAAGGTAATTATGAAAAGCAAGCACAGTTAAAGTCAAAATCTTAATTCA
1 AGTCAAA-TCTTAATTCAGGGTAATTAAGAAAAGCAAACACAG-T---G--AAAGTCTTAATTCA
*
9348 GGGTAATTAAGAGAAGAAGCACAGTTAAAGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGCAA
59 GGGTAATTAAGAAAAGAA--ACA--T--AGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGCAA
9413 ACACAGTTAA
118 ACACAGTTAA
* * * *
9423 AG-----TCTTAATTCAGGGTAATTAAGAGAAG--AACACATTCAAAGTCTTAATTCAGGATAAT
1 AGTCAAATCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTGAAAGTCTTAATTCAGGGTAAT
* *
9481 TAAGAGAAGAAGCACAGTTAAAGTCAAAATCTTAATTCAGTGTAATTAAGAAAAGCAAACACAGT
66 TAAGAAAAGAA--ACA--T--AGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGT
9546 TAA
125 TAA
* * *
9549 AG-----TCTTAATTCAGGGTAATTGAGAAAAGCAAACGCAGTTAAAGT-TTAATT-ATGGGTAA
1 AGTCAAATCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTGAAAGTCTTAATTCA-GGGTAA
* * * * *
9607 TTAAGAAAAGAAGAACACAGTCAAAGTTTTAATTCTGGGTAATTAAGAAAAGCAAGCACAGTTAA
65 TTAAGAAAAG-A-AACATAGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTTAA
*
9672 AGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTGAAAGTCTTAATTCAGGGTAA
1 AGTC-AAATCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTGAAAGTCTTAATTCAGGGTAA
* * * * *
9737 TTAAGAAAAGCAAACATAGTCGAAGTTTTAATTCAGGGTAATTAAGAAAAGCTAGCACAGTTAA
65 TTAAGAAAAG-AAACATAGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTTAA
* * * * *
9801 GGTCAAAGTCTTAATTCAGGGTAATTAATAAAAGCAAACACAGTTAAAGTCTCAA--CATGGTAA
1 AGTCAAA-TCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTGAAAGTCTTAATTCAGGGTAA
9864 TTAAGAAAAGTAAACATAGTCAA
65 TTAAGAAAAG-AAACATAGTCAA
9887 GGGCTTAGTT
Statistics
Matches: 411, Mismatches: 39, Indels: 41
0.84 0.08 0.08
Matches are distributed among these distances:
123 44 0.11
126 113 0.27
127 51 0.12
128 15 0.04
129 133 0.32
130 23 0.06
131 2 0.00
132 5 0.01
134 23 0.06
140 2 0.00
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (127 bp):
AGTCAAATCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTGAAAGTCTTAATTCAGGGTAAT
TAAGAAAAGAAACATAGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTTAA
Found at i:9912 original size:36 final size:36
Alignment explanation
Indices: 9871--10055 Score: 201
Period size: 36 Copynumber: 5.1 Consensus size: 36
9861 TAATTAAGAA
* * *
9871 AAGTAAACATAGTCAAGGGCTTAGTTCAAGGAAATT
1 AAGTAAACATAGTCAAGGACTTAATTCAAGGTAATT
*** * *
9907 AAGTAAAGGCAGTCAAAGACTTAATTCAAGGTATTT
1 AAGTAAACATAGTCAAGGACTTAATTCAAGGTAATT
* * *
9943 AAGTAAACATAGTAAAGAACTTAATTCAGGGTAATT
1 AAGTAAACATAGTCAAGGACTTAATTCAAGGTAATT
* *
9979 AAGTAAA-AGTAGTTAAAGGACTTAATTCAGGGTAATT
1 AAGTAAACA-TAG-TCAAGGACTTAATTCAAGGTAATT
* * *
10016 AAGTAAAAACAGTCAAGGACTTAATTCTAGGTAATT
1 AAGTAAACATAGTCAAGGACTTAATTCAAGGTAATT
10052 AAGT
1 AAGT
10056 GAAAGCAAGA
Statistics
Matches: 125, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
35 1 0.01
36 91 0.73
37 32 0.26
38 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (36 bp):
AAGTAAACATAGTCAAGGACTTAATTCAAGGTAATT
Found at i:10038 original size:73 final size:71
Alignment explanation
Indices: 9871--10062 Score: 231
Period size: 73 Copynumber: 2.6 Consensus size: 71
9861 TAATTAAGAA
* * * *
9871 AAGTAAACATAGTCAAGGGCTTAGTTCAAGGAAATTAAGTAAAGGCAGTCAAAGACTTAATTCAA
1 AAGTAAACATAGTCAAGGACTTAATTC-AGGTAATTAAGTAAAAGCAGTCAAAGACTTAATTCAA
*
9936 GGTATTT
65 GGTAATT
* * * *
9943 AAGTAAACATAGTAAAGAACTTAATTCAGGGTAATTAAGTAAAAGTAGTTAAAGGACTTAATTCA
1 AAGTAAACATAGTCAAGGACTTAATTCA-GGTAATTAAGTAAAAGCAGTCAAA-GACTTAATTCA
*
10008 GGGTAATT
64 AGGTAATT
* * *
10016 AAGTAAAAACAGTCAAGGACTTAATTCTAGGTAATTAAGTGAAAGCA
1 AAGTAAACATAGTCAAGGACTTAATTC-AGGTAATTAAGTAAAAGCA
10063 AGAACAAACT
Statistics
Matches: 101, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
71 1 0.01
72 43 0.43
73 56 0.55
74 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (71 bp):
AAGTAAACATAGTCAAGGACTTAATTCAGGTAATTAAGTAAAAGCAGTCAAAGACTTAATTCAAG
GTAATT
Found at i:10116 original size:39 final size:39
Alignment explanation
Indices: 10061--10274 Score: 347
Period size: 39 Copynumber: 5.4 Consensus size: 39
10051 TAAGTGAAAG
* * *
10061 CAAGAACAAACTTAATTTCAAGGAAGGAAACTAGGTAAA
1 CAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA
10100 CAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA
1 CAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA
*
10139 CAAGCACAGACTTAATTTCAAGGAAGGAAACTAGGTAAA
1 CAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA
*
10178 CAAGCACAGACTTAATTTTAAGGAAGGAAATTAGGTAAA
1 CAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA
* *
10217 CAAGCACAAACTTAATTTCAAGGAAGAAAATTAGGTAAA
1 CAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA
10256 GGCAAGCACAGACTTAATT
1 --CAAGCACAGACTTAATT
10275 CAGGGTAATT
Statistics
Matches: 163, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 147 0.90
41 16 0.10
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (39 bp):
CAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA
Found at i:10356 original size:36 final size:35
Alignment explanation
Indices: 10282--10362 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 35
10272 ATTCAGGGTA
*
10282 ATTAAGTAAATCAGCGAAGACTTAATCCAAAGATG
1 ATTAAGTAAATCAGCGAAGACTTAATCCAAAGAGG
* *
10317 ATTAAGTAAGATCAGTC-AAGGACTTAA-CCTAAGGGG
1 ATTAAGTAA-ATCAG-CGAA-GACTTAATCCAAAGAGG
10353 ATTAAGTAAA
1 ATTAAGTAAA
10363 GAAAATGACT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
35 10 0.25
36 22 0.55
37 8 0.20
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.23
Consensus pattern (35 bp):
ATTAAGTAAATCAGCGAAGACTTAATCCAAAGAGG
Found at i:10389 original size:31 final size:31
Alignment explanation
Indices: 10334--10444 Score: 89
Period size: 37 Copynumber: 3.4 Consensus size: 31
10324 AAGATCAGTC
*
10334 AAGGACTTAACCT-AAGGGGATTAAGTAAAGAA
1 AAGGACTTAA--TGAAGGAGATTAAGTAAAGAA
* * *
10366 AATGACTTAATGAAGGAGATTAAGTAGAGTA
1 AAGGACTTAATGAAGGAGATTAAGTAAAGAA
* *
10397 AAGGACTTAATTTCAAGAAAGGAGATTAAGTAGAGTA
1 AAGGACTTAA--T---G-AAGGAGATTAAGTAAAGAA
10434 AAGGACTTAAT
1 AAGGACTTAAT
10445 TTCAAGGAAG
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
30 1 0.01
31 25 0.37
32 9 0.13
33 1 0.01
35 1 0.01
36 1 0.01
37 29 0.43
ACGTcount: A:0.46, C:0.06, G:0.24, T:0.23
Consensus pattern (31 bp):
AAGGACTTAATGAAGGAGATTAAGTAAAGAA
Found at i:10417 original size:18 final size:18
Alignment explanation
Indices: 10396--10456 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
10386 TAAGTAGAGT
10396 AAAGGACTTAATTTCAAG
1 AAAGGACTTAATTTCAAG
* *
10414 AAAGGAGATTAA-GT-AGAG
1 AAAGGA-CTTAATTTCA-AG
10432 TAAAGGACTTAATTTCAAG
1 -AAAGGACTTAATTTCAAG
*
10451 GAAGGA
1 AAAGGA
10457 AATTAAGTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 1 0.03
18 18 0.55
19 13 0.39
20 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.25, T:0.23
Consensus pattern (18 bp):
AAAGGACTTAATTTCAAG
Found at i:10421 original size:37 final size:37
Alignment explanation
Indices: 10377--10593 Score: 371
Period size: 37 Copynumber: 5.9 Consensus size: 37
10367 ATGACTTAAT
* *
10377 GAAGGAGATTAAGTAGAGTAAAGGACTTAATTTCAAG
1 GAAGGAAATTAAGTAGAGTCAAGGACTTAATTTCAAG
* * *
10414 AAAGGAGATTAAGTAGAGTAAAGGACTTAATTTCAAG
1 GAAGGAAATTAAGTAGAGTCAAGGACTTAATTTCAAG
10451 GAAGGAAATTAAGTAGAGTCAAGGACTTAATTTCAAG
1 GAAGGAAATTAAGTAGAGTCAAGGACTTAATTTCAAG
* *
10488 GAAGGAAATTAAGTGGAGTCAAGGACTTAATTTTAAG
1 GAAGGAAATTAAGTAGAGTCAAGGACTTAATTTCAAG
10525 GAAGGAAATTAAGTAGAGTCAAGGACTTAATTTCAAG
1 GAAGGAAATTAAGTAGAGTCAAGGACTTAATTTCAAG
10562 GAAGGAAATTAAGTAGAGTCAAGGACTTAATT
1 GAAGGAAATTAAGTAGAGTCAAGGACTTAATT
10594 CAGGGCAATT
Statistics
Matches: 172, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 172 1.00
ACGTcount: A:0.43, C:0.06, G:0.25, T:0.25
Consensus pattern (37 bp):
GAAGGAAATTAAGTAGAGTCAAGGACTTAATTTCAAG
Found at i:10436 original size:19 final size:19
Alignment explanation
Indices: 10378--10438 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
10368 TGACTTAATG
10378 AAGGAGATTAAGTAGAGTA
1 AAGGAGATTAAGTAGAGTA
* *
10397 AAGGA-CTTAATTTCA-AG-A
1 AAGGAGATTAA-GT-AGAGTA
10415 AAGGAGATTAAGTAGAGTA
1 AAGGAGATTAAGTAGAGTA
10434 AAGGA
1 AAGGA
10439 CTTAATTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
17 1 0.03
18 13 0.39
19 18 0.55
20 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.28, T:0.21
Consensus pattern (19 bp):
AAGGAGATTAAGTAGAGTA
Found at i:10630 original size:36 final size:36
Alignment explanation
Indices: 10586--10736 Score: 214
Period size: 36 Copynumber: 4.2 Consensus size: 36
10576 AGAGTCAAGG
* * *
10586 ACTTAATTCAGGGCAATTAAGTAGCGTCTATAAA-A
1 ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
*
10621 GACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGA
1 -ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
* *
10658 ACTTAATTCAGGATAATTAAGTCGAGTCAATAAAGA
1 ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
* *
10694 ACTTAATTCAGGGTAATTAAGTGGAATCAATAAAGA
1 ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
10730 ACTTAAT
1 ACTTAAT
10737 CTAAAAAGAG
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
36 104 0.99
37 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (36 bp):
ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
Found at i:12583 original size:33 final size:32
Alignment explanation
Indices: 12500--12591 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 32
12490 CGCCAAGCGA
* * *
12500 TGGCCGGT-TGTGGCCGGACATGTCCATGTTACG
1 TGGCCGGTGT-TGGCCGGGCATCTCCA-GTCACG
12533 TGGCCGGTGTTGGCCGGGCATCTCCGAGTCACG
1 TGGCCGGTGTTGGCCGGGCATCTCC-AGTCACG
*
12566 TGGCCGGTGTTGGCCGGGCTTCTCCA
1 TGGCCGGTGTTGGCCGGGCATCTCCA
12592 AGTCGCTTGG
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
32 1 0.02
33 50 0.94
34 2 0.04
ACGTcount: A:0.09, C:0.28, G:0.38, T:0.25
Consensus pattern (32 bp):
TGGCCGGTGTTGGCCGGGCATCTCCAGTCACG
Found at i:17958 original size:11 final size:10
Alignment explanation
Indices: 17939--17974 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 10
17929 GGTCGGAAAA
17939 TTTTTTTTAT
1 TTTTTTTTAT
17949 TTTATTTTTAT
1 TTT-TTTTTAT
17960 TTTTTTTATAT
1 TTTTTTT-TAT
17971 TTTT
1 TTTT
17975 CGATATAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 7 0.29
11 17 0.71
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:17971 original size:17 final size:18
Alignment explanation
Indices: 17941--17974 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17931 TCGGAAAATT
*
17941 TTTTTTATTTTATTTTTA
1 TTTTTTATTATATTTTTA
17959 TTTTTT-TTATATTTTT
1 TTTTTTATTATATTTTT
17975 CGATATAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTTATTATATTTTTA
Found at i:19079 original size:23 final size:23
Alignment explanation
Indices: 19049--19102 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
19039 ATGGCCGTTT
* *
19049 GTGGCCGGACATGTCC-ATGTCGC
1 GTGGCCGGACATCTCCGA-GTCAC
*
19072 GTGGCCGGGCATCTCCGAGTCAC
1 GTGGCCGGACATCTCCGAGTCAC
19095 GTGGCCGG
1 GTGGCCGG
19103 TGTTGGCCGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.11, C:0.31, G:0.39, T:0.19
Consensus pattern (23 bp):
GTGGCCGGACATCTCCGAGTCAC
Found at i:19110 original size:33 final size:33
Alignment explanation
Indices: 19073--19136 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
19063 CCATGTCGCG
* *
19073 TGGCCGGGCATCTCCGAGTCACGTGGCCGGTGT
1 TGGCCGGGCATCTCCAAGTCACATGGCCGGTGT
* *
19106 TGGCCGGGCTTCTCCAAGTCGCATGGCCGGT
1 TGGCCGGGCATCTCCAAGTCACATGGCCGGT
19137 CACTAGTGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.09, C:0.31, G:0.38, T:0.22
Consensus pattern (33 bp):
TGGCCGGGCATCTCCAAGTCACATGGCCGGTGT
Found at i:21006 original size:14 final size:15
Alignment explanation
Indices: 20989--21017 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20979 TGTAAGTTAA
20989 TCAAAA-ATCAATTT
1 TCAAAAGATCAATTT
21003 TCAAAAGATCAATTT
1 TCAAAAGATCAATTT
21018 GAATTCACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.34
Consensus pattern (15 bp):
TCAAAAGATCAATTT
Found at i:22229 original size:33 final size:33
Alignment explanation
Indices: 22190--22296 Score: 128
Period size: 33 Copynumber: 3.2 Consensus size: 33
22180 GGTGCGAGTA
* *
22190 ACCGGCCATGCGACATGGAGAAGACCGGCCAAC
1 ACCGGCCACGCGACATGGAGATGACCGGCCAAC
* *
22223 ACCGGCCACGCGAC-TCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACAT-GGAGATGACCGGCCAAC
* *
22256 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
1 ACCGGCCACGCGACATGGAGATGACCGGCCAAC
22288 AACCGGCCA
1 -ACCGGCCA
22297 TCGCTTGGCG
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 2 0.03
33 61 0.95
34 1 0.02
ACGTcount: A:0.24, C:0.39, G:0.29, T:0.07
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGAGATGACCGGCCAAC
Found at i:23251 original size:8 final size:8
Alignment explanation
Indices: 23238--23271 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
23228 CACCTTCTTG
23238 AAAAATTC
1 AAAAATTC
23246 AAAAATTC
1 AAAAATTC
*
23254 AGAAACTTC
1 A-AAAATTC
23263 AAAAATTC
1 AAAAATTC
23271 A
1 A
23272 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Done.