Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013990.1 Corchorus olitorius cultivar O-4 contig14023, 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: 42133
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:3574 original size:27 final size:28
Alignment explanation
Indices: 3529--3584 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
3519 AGAAAAGAAA
*
3529 TTTTTTTTTTTAAATAAAAACGCAAAAAC
1 TTTTTTTTTTT-AAGAAAAACGCAAAAAC
3558 TTTTTTTTTTT-AGAAAAACGCAAAAAC
1 TTTTTTTTTTTAAGAAAAACGCAAAAAC
3585 ACAAAACAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 15 0.58
29 11 0.42
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (28 bp):
TTTTTTTTTTTAAGAAAAACGCAAAAAC
Found at i:3675 original size:63 final size:63
Alignment explanation
Indices: 3559--3677 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 63
3549 CGCAAAAACT
* * *
3559 TTTTTTTTTTAGAAAAACGCAAAAACACAAAACAAATTTTTTTTATGACGAAAAAAAACATAA
1 TTTTTTTTTTACAAAAACGCAAAAACACAAAACAAATTTTTTTTATAAAGAAAAAAAACATAA
* * * *
3622 TTTTTTTTTT-CAAAAACGCAAGACACACAACACAATTTTTTTTTTTAAAGAAAAAA
1 TTTTTTTTTTACAAAAACGCAA-AAACACAAAACAAATTTTTTTTATAAAGAAAAAA
3678 TTAAAGACGC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
62 10 0.21
63 38 0.79
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (63 bp):
TTTTTTTTTTACAAAAACGCAAAAACACAAAACAAATTTTTTTTATAAAGAAAAAAAACATAA
Found at i:4038 original size:15 final size:16
Alignment explanation
Indices: 4014--4053 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
4004 AGAGGTTGAA
*
4014 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
4029 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
4045 AGAAAACAA
1 AGAAAACAA
4054 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:9297 original size:21 final size:22
Alignment explanation
Indices: 9259--9303 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
9249 ATAGTTTAGA
*
9259 TTTAGTTTACTTTGCTTTA-AT
1 TTTAGTTTACATTGCTTTATAT
9280 TTTAGTTTA-ATTGCCTTTATAT
1 TTTAGTTTACATTG-CTTTATAT
9302 TT
1 TT
9304 AATTGTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 3 0.14
21 14 0.67
22 4 0.19
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (22 bp):
TTTAGTTTACATTGCTTTATAT
Found at i:9304 original size:21 final size:20
Alignment explanation
Indices: 9253--9304 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
9243 ATTGCCATAG
*
9253 TTTAGATTTAGTTTACTTTGC
1 TTTA-ATTTAGTTTACATTGC
9274 TTTAATTTTAGTTTA-ATTGCC
1 TTTAA-TTTAGTTTACATTG-C
9295 TTTATATTTA
1 TTTA-ATTTA
9305 ATTGTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.15
21 22 0.81
22 1 0.04
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.60
Consensus pattern (20 bp):
TTTAATTTAGTTTACATTGC
Found at i:12067 original size:16 final size:16
Alignment explanation
Indices: 12048--12078 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12038 TTTATTGCAG
12048 TTGCTTTAATTGATTA
1 TTGCTTTAATTGATTA
*
12064 TTGCTTTTATTGATT
1 TTGCTTTAATTGATT
12079 GCCTATTCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (16 bp):
TTGCTTTAATTGATTA
Found at i:18808 original size:45 final size:42
Alignment explanation
Indices: 18759--18852 Score: 136
Period size: 45 Copynumber: 2.2 Consensus size: 42
18749 AGCAAAAATT
*
18759 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGAT--A-GAGTAG
*
18804 AATATCAGCTTTATTTTGATGAATTACCTAGAGATAGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATAGAGTAG
18846 AAT-TTAG
1 AATATTAG
18853 ATAATGCACT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 3 0.07
42 9 0.20
43 1 0.02
45 33 0.72
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.37
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATAGAGTAG
Found at i:24129 original size:9 final size:8
Alignment explanation
Indices: 24107--24140 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
24097 ATCTCATTAG
*
24107 AAAATACA
1 AAAAAACA
24115 AAAAAACA
1 AAAAAACA
24123 AATAAAACA
1 AA-AAAACA
24132 AAAAAACA
1 AAAAAACA
24140 A
1 A
24141 TCAACTTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.82, C:0.12, G:0.00, T:0.06
Consensus pattern (8 bp):
AAAAAACA
Found at i:24510 original size:8 final size:8
Alignment explanation
Indices: 24492--24525 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
24482 AAAACGAAAC
24492 AAAAACA-
1 AAAAACAG
24499 AAAAACAG
1 AAAAACAG
24507 AAAAACAG
1 AAAAACAG
24515 AAAAAC-G
1 AAAAACAG
24522 AAAA
1 AAAA
24526 CGATGCCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 12 0.46
8 14 0.54
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (8 bp):
AAAAACAG
Found at i:24512 original size:15 final size:15
Alignment explanation
Indices: 24488--24525 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
24478 AACGAAAACG
24488 AAAC-AAAAACA-AA
1 AAACGAAAAACAGAA
24501 AAACAGAAAAACAGAA
1 AAAC-GAAAAACAGAA
24517 AAACGAAAA
1 AAACGAAAA
24526 CGATGCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.18
15 12 0.55
16 6 0.27
ACGTcount: A:0.79, C:0.13, G:0.08, T:0.00
Consensus pattern (15 bp):
AAACGAAAAACAGAA
Found at i:28673 original size:46 final size:46
Alignment explanation
Indices: 28622--29222 Score: 593
Period size: 47 Copynumber: 12.6 Consensus size: 46
28612 AATTAGAAGA
* *
28622 GTAATTAAAGTAAACAGTAAAAAAGAAGAGGTTAGTTTAATTCTGG
1 GTAATTAAACTAAATAGTAAAAAAGAAGAGGTTAGTTTAATTCTGG
* * *
28668 GTAATTAAACTAAATAGTAAAAGGAGAAGAGATTAGTTTAATTCAGG
1 GTAATTAAACTAAATAGTAAAA-AAGAAGAGGTTAGTTTAATTCTGG
*
28715 GTAATTAAACTAAATAGTAAAAAAGAAGAGATTAGTTTAATTCTGG
1 GTAATTAAACTAAATAGTAAAAAAGAAGAGGTTAGTTTAATTCTGG
*
28761 GTAATTAAACTAAATAGTAAAAAAGAAGAGGTTAGTTTATTTCTGG
1 GTAATTAAACTAAATAGTAAAAAAGAAGAGGTTAGTTTAATTCTGG
* ** * *
28807 GTGATTAAACTAAATAGTAAAAAAAGAAGAAATTAGTTTAATTCAGC
1 GTAATTAAACTAAATAGT-AAAAAAGAAGAGGTTAGTTTAATTCTGG
** * *
28854 GTAATTAAACTAAATAGTAAATGGAGAAGAGATTAGTTTAATTCAGG
1 GTAATTAAACTAAATAGTAAA-AAAGAAGAGGTTAGTTTAATTCTGG
* * ** *
28901 GTAATTAAACTAAACAGTAAAAGAAGAATAAATTAGTTTAATTCAGG
1 GTAATTAAACTAAATAGTAAAA-AAGAAGAGGTTAGTTTAATTCTGG
* * * *
28948 CTAATTAAACTAAATAGTAAAAAGGAAGATGTTAGTTTAATTCTAG
1 GTAATTAAACTAAATAGTAAAAAAGAAGAGGTTAGTTTAATTCTGG
28994 GTAATTAAACTAAATAGTAAAGGAAGAAGTAAACAGAGGTTAG-TTAATTCTGG
1 GTAATTAAACTAAATAGT-AA--AA-AAG---A-AGAGGTTAGTTTAATTCTGG
* * *
29047 GTAATTAAAATAAAGAGTAAAGTAAACTGTA-A--TTAGTTTAATTCTGG
1 GTAATTAAACTAAATAGTAAA--AAA--GAAGAGGTTAGTTTAATTCTGG
* *
29094 GTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGCTAGTTTAATTCT-G
1 GTAATTAAACTAAATAGT--AA-AA-AAG---A-AGAGGTTAGTTTAATTCTGG
* * * *
29147 GTAATTAAACTAAAGAGTAAAGTAAA-CAGAGGTTACTTTAATTCAGG
1 GTAATTAAACTAAATAGTAAA--AAAGAAGAGGTTAGTTTAATTCTGG
* *
29194 GTAATTAAACTAAAGAATAAAAGAAGAAG
1 GTAATTAAACTAAATAGTAAAA-AAGAAG
29223 TAAACAGTAA
Statistics
Matches: 473, Mismatches: 49, Indels: 65
0.81 0.08 0.11
Matches are distributed among these distances:
45 1 0.00
46 162 0.34
47 218 0.46
48 2 0.00
49 7 0.01
50 5 0.01
51 7 0.01
52 5 0.01
53 46 0.10
54 20 0.04
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.28
Consensus pattern (46 bp):
GTAATTAAACTAAATAGTAAAAAAGAAGAGGTTAGTTTAATTCTGG
Found at i:29259 original size:30 final size:30
Alignment explanation
Indices: 29223--29287 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
29213 AAAGAAGAAG
29223 TAAACAGTA-ATTAGTTTAATTCTGGGTAAT
1 TAAACAG-AGATTAGTTTAATTCTGGGTAAT
*
29253 TAAACAGAGGTTAGTTTAATTCTGGGTAAT
1 TAAACAGAGATTAGTTTAATTCTGGGTAAT
29283 TAAAC
1 TAAAC
29288 TAAAAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 32 0.97
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (30 bp):
TAAACAGAGATTAGTTTAATTCTGGGTAAT
Found at i:29422 original size:47 final size:47
Alignment explanation
Indices: 29263--29786 Score: 533
Period size: 47 Copynumber: 10.9 Consensus size: 47
29253 TAAACAGAGG
* * * *
29263 TTAGTTTAATTCTGGGTAATTAAACTAAAAAATATAA-AAGAAGAGA
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGAAA
* * **
29309 TTAGTTTAATTCTAGGTAATTCAACTAAATAGTAAAA-AAGAAGAGG
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGAAA
29355 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGAAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGAAA
* ** * *
29402 TTAGTTTAATTCAGCATAATTAAACTAAATAGTAAAAGGAGAAGAGA
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGAAA
* * *
29449 TTAGTTTTATTCAGGGTAATTAAACTAAATAGTAAAAGAATAAGAAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGAAA
* * * **
29496 TTAGTTTAATTCAGGCTAATTAAACTAAATAGTAAAA-AGGAAGATG
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGAAA
29542 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGTAAACAAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAG-----AAA
* *
29594 GGTTAG-TTAATTCTGGGTAATTAAACTAAAGAGT-AAAGTAA-ACAGTAA
1 --TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAG-AAGA-AGAAA
* *
29642 TTAGTTTAATTCTGGGTAATTAAATTAAAGAGTAAAAGAAGAAGTAAACAGA
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAG---A-A-A
* * ** *
29694 GGCTAGTTTAATTCTGGGTAATTAAACTAAAGAGT-AAAGTAA-ACTAAGG
1 --TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAG-AAGAAGAA-A
* * *
29743 TTAGTTTAATTCAGGGTAATTAAACTAAAGAATAAAAGAAGAAG
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAG
29787 TAAACAATAA
Statistics
Matches: 408, Mismatches: 46, Indels: 46
0.82 0.09 0.09
Matches are distributed among these distances:
46 119 0.29
47 193 0.47
48 12 0.03
49 2 0.00
50 1 0.00
51 1 0.00
52 7 0.02
53 36 0.09
54 37 0.09
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (47 bp):
TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGAAA
Found at i:29463 original size:563 final size:564
Alignment explanation
Indices: 28695--29863 Score: 2063
Period size: 563 Copynumber: 2.1 Consensus size: 564
28685 TAAAAGGAGA
* * * * *
28695 AGAGATTAGTTTAATTCAGGGTAATTAAACTAAATAGTAAAAAAGAAGAGATTAGTTTAATTCTG
1 AGAGGTTAGTTTAATTCTGGGTAATTAAACTAAAAAATAAAAAAGAAGAGATTAGTTTAATTCTA
* *
28760 GGTAATTAAACTAAATAGTAAAAAAGAAGAGGTTAGTTTATTTCTGGGTGATTAAACTAAATAGT
66 GGTAATTAAACTAAATAGTAAAAAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAATAGT
* *
28825 AAAAAAAGAAGAAATTAGTTTAATTCAGCGTAATTAAACTAAATAGTAAATGGAGAAGAGATTAG
131 AAAAAAAGAAGAAATTAGTTTAATTCAGCATAATTAAACTAAATAGTAAAAGGAGAAGAGATTAG
*
28890 TTTAATTCAGGGTAATTAAACTAAACAGTAAAAGAAGAATAAATTAGTTTAATTCAGGCTAATTA
196 TTTAATTCAGGGTAATTAAACTAAACAGTAAAAGAAGAAGAAATTAGTTTAATTCAGGCTAATTA
*
28955 AACTAAATAGTAAAAAGGAAGATGTTAGTTTAATTCTAGGTAATTAAACTAAATAGTAAAGGAAG
261 AACTAAATAGTAAAAAGGAAGATGTTAGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAG
* *
29020 AAGTAAACAGAGGTTAGTTAATTCTGGGTAATTAAAATAAAGAGTAAAGTAAACTGTAATTAGTT
326 AAGTAAACAAAGGTTAGTTAATTCTGGGTAATTAAAATAAAGAGTAAAGTAAACAGTAATTAGTT
29085 TAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGCTAGTTTAATTCT-GGT
391 TAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGCTAGTTTAATTCTGGGT
29149 AATTAAACTAAAGAGTAAAGTAAAC-AGAGGTTACTTTAATTCAGGGTAATTAAACTAAAGAATA
456 AATTAAACTAAAGAGTAAAGTAAACTA-AGGTTACTTTAATTCAGGGTAATTAAACTAAAGAATA
* *
29213 AAAGAAGAAGTAAACAGTAATTAGTTTAATTCTGGGTAATTAAAC
520 AAAGAAGAAGTAAACAATAATTAGTTGAATTCTGGGTAATTAAAC
*
29258 AGAGGTTAGTTTAATTCTGGGTAATTAAACTAAAAAATATAAAAGAAGAGATTAGTTTAATTCTA
1 AGAGGTTAGTTTAATTCTGGGTAATTAAACTAAAAAATAAAAAAGAAGAGATTAGTTTAATTCTA
*
29323 GGTAATTCAACTAAATAGTAAAAAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAATAGT
66 GGTAATTAAACTAAATAGTAAAAAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAATAGT
*
29388 AAAAGAAGAAGAAATTAGTTTAATTCAGCATAATTAAACTAAATAGTAAAAGGAGAAGAGATTAG
131 AAAAAAAGAAGAAATTAGTTTAATTCAGCATAATTAAACTAAATAGTAAAAGGAGAAGAGATTAG
* * *
29453 TTTTATTCAGGGTAATTAAACTAAATAGTAAAAGAATAAGAAATTAGTTTAATTCAGGCTAATTA
196 TTTAATTCAGGGTAATTAAACTAAACAGTAAAAGAAGAAGAAATTAGTTTAATTCAGGCTAATTA
*
29518 AACTAAATAGTAAAAAGGAAGATGTTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAG
261 AACTAAATAGTAAAAAGGAAGATGTTAGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAG
*
29583 AAGTAAACAAAGGTTAGTTAATTCTGGGTAATTAAACTAAAGAGTAAAGTAAACAGTAATTAGTT
326 AAGTAAACAAAGGTTAGTTAATTCTGGGTAATTAAAATAAAGAGTAAAGTAAACAGTAATTAGTT
*
29648 TAATTCTGGGTAATTAAATTAAAGAGTAAAAGAAGAAGTAAACAGAGGCTAGTTTAATTCTGGGT
391 TAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGCTAGTTTAATTCTGGGT
*
29713 AATTAAACTAAAGAGTAAAGTAAACTAAGGTTAGTTTAATTCAGGGTAATTAAACTAAAGAATAA
456 AATTAAACTAAAGAGTAAAGTAAACTAAGGTTACTTTAATTCAGGGTAATTAAACTAAAGAATAA
29778 AAGAAGAAGTAAACAATAATTAGTTGAATTCTGGGTAATTAAAC
521 AAGAAGAAGTAAACAATAATTAGTTGAATTCTGGGTAATTAAAC
* * *
29822 AGAGGTTTGTTTAATTCTAGGTAATTAAACTAAAAAGTAAAA
1 AGAGGTTAGTTTAATTCTGGGTAATTAAACTAAAAAATAAAA
29864 GAAAGAGTAA
Statistics
Matches: 575, Mismatches: 29, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
563 429 0.75
564 145 0.25
565 1 0.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.30
Consensus pattern (564 bp):
AGAGGTTAGTTTAATTCTGGGTAATTAAACTAAAAAATAAAAAAGAAGAGATTAGTTTAATTCTA
GGTAATTAAACTAAATAGTAAAAAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAATAGT
AAAAAAAGAAGAAATTAGTTTAATTCAGCATAATTAAACTAAATAGTAAAAGGAGAAGAGATTAG
TTTAATTCAGGGTAATTAAACTAAACAGTAAAAGAAGAAGAAATTAGTTTAATTCAGGCTAATTA
AACTAAATAGTAAAAAGGAAGATGTTAGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAG
AAGTAAACAAAGGTTAGTTAATTCTGGGTAATTAAAATAAAGAGTAAAGTAAACAGTAATTAGTT
TAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGCTAGTTTAATTCTGGGT
AATTAAACTAAAGAGTAAAGTAAACTAAGGTTACTTTAATTCAGGGTAATTAAACTAAAGAATAA
AAGAAGAAGTAAACAATAATTAGTTGAATTCTGGGTAATTAAAC
Found at i:29719 original size:101 final size:96
Alignment explanation
Indices: 28653--29821 Score: 1020
Period size: 100 Copynumber: 12.3 Consensus size: 96
28643 AAAGAAGAGG
* *
28653 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGGAGAAGAGATTAGTTTAATTCAGGGTA
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGT-AAA-GAAAAGAGATTAGTTTAATTCTGGGTA
*
28718 ATTAAACTAAATAGTAAAA-AAGAAG---A-GA
64 ATTAAACTAAATAGTAAAAGAAGAAGTAAACAA
* * * *
28746 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAAAGAAGAGGTTAGTTTATTTCTGGGTGA
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAGAA-AAGAGATTAGTTTAATTCTGGGTAA
*
28811 TTAAACTAAATAGTAAAAAAAGAAG---A-AA
65 TTAAACTAAATAGTAAAAGAAGAAGTAAACAA
* * * *
28839 TTAGTTTAATTCAGCGTAATTAAACTAAATAGTAAATGGAGAAGAGATTAGTTTAATTCAGGGTA
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAA--GAAAAGAGATTAGTTTAATTCTGGGTA
*
28904 ATTAAACTAAACAGTAAAAGAAGAA-T--A-AA
64 ATTAAACTAAATAGTAAAAGAAGAAGTAAACAA
* * *
28933 TTAGTTTAATTCAGGCTAATTAAACTAAATAGTAAA-AAGGAAGATG-TTAGTTTAATTCTAGGT
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAGAA--AAGA-GATTAGTTTAATTCTGGGT
*
28996 AATTAAACTAAATAGTAAAGGAAGAAGTAAACAGA
63 AATTAAACTAAATAGTAAAAGAAGAAGTAAACA-A
* * *
29031 GGTTAG-TTAATTCTGGGTAATTAAAATAAAGAGTAAAGTAAACTGTA-ATTAGTTTAATTCTGG
1 --TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAG-AAA-AG-AGATTAGTTTAATTCTGG
*
29094 GTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGA
61 GTAATTAAACTAAATAGTAAAAGAAGAAGTAAACA-A
* * * * *
29131 GGCTAGTTTAATTCT-GGTAATTAAACTAAAGAGTAAAGTAAACAGAGGTTACTTTAATTCAGGG
1 --TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAG-AAA-AGAGATTAGTTTAATTCTGGG
* *
29195 TAATTAAACTAAAGAATAAAAGAAGAAGTAAACAGTAA
62 TAATTAAACTAAATAGTAAAAGAAGAAGTAAAC---AA
* * * *** * ** *
29233 TTAGTTTAATTCTGGGTAATTAAAC-AGA-GGT-TAG--TTTA-ATTCTGGGTAA-T-T---AAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAGAAAAGAGATT-AGTTTAATTCTGGGTAA
*
29287 CTAAA--AAATA-TAAAAGAAG-AG------A
65 TTAAACTAAATAGTAAAAGAAGAAGTAAACAA
* * * *
29309 TTAGTTTAATTCTAGGTAATTCAACTAAATAGTAAAAAAGAAGAGGTTAGTTTAATTCTGGGTAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAGAA-AAGAGATTAGTTTAATTCTGGGTAA
29374 TTAAACTAAATAGTAAAAGAAGAAG---A-AA
65 TTAAACTAAATAGTAAAAGAAGAAGTAAACAA
* ** * * *
29402 TTAGTTTAATTCAGCATAATTAAACTAAATAGTAAAAGGAGAAGAGATTAGTTTTATTCAGGGTA
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGT-AAA-GAAAAGAGATTAGTTTAATTCTGGGTA
*
29467 ATTAAACTAAATAGTAAAAGAATAAG---A-AA
64 ATTAAACTAAATAGTAAAAGAAGAAGTAAACAA
* *
29496 TTAGTTTAATTCAGGCTAATTAAACTAAATAGTAAA-AAGGAAGATG-TTAGTTTAATTCTGGGT
1 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAGAA--AAGA-GATTAGTTTAATTCTGGGT
29559 AATTAAACTAAATAGTAAAAGAAGAAGTAAACAAA
63 AATTAAACTAAATAGTAAAAGAAGAAGTAAAC-AA
*
29594 GGTTAG-TTAATTCTGGGTAATTAAACTAAAGAGTAAAGTAAACAGTA-ATTAGTTTAATTCTGG
1 --TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAG-AAA-AG-AGATTAGTTTAATTCTGG
* *
29657 GTAATTAAATTAAAGAGTAAAAGAAGAAGTAAACAGA
61 GTAATTAAACTAAATAGTAAAAGAAGAAGTAAACA-A
* * * *
29694 GGCTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAGTAAACTA-AGGTTAGTTTAATTCAGG
1 --TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAG-AAA--AGAGATTAGTTTAATTCTGG
* *
29758 GTAATTAAACTAAAGAATAAAAGAAGAAGTAAACAATAA
61 GTAATTAAACTAAATAGTAAAAGAAGAAGTAAAC---AA
*
29797 TTAGTTGAATTCTGGGTAATTAAAC
1 TTAGTTTAATTCTGGGTAATTAAAC
29822 AGAGGTTTGT
Statistics
Matches: 907, Mismatches: 100, Indels: 130
0.80 0.09 0.11
Matches are distributed among these distances:
76 24 0.03
77 2 0.00
78 2 0.00
79 1 0.00
82 5 0.01
83 3 0.00
84 1 0.00
85 2 0.00
86 9 0.01
87 10 0.01
89 11 0.01
90 9 0.01
91 5 0.01
92 42 0.05
93 198 0.22
94 170 0.19
95 2 0.00
96 2 0.00
97 1 0.00
98 5 0.01
99 61 0.07
100 207 0.23
101 130 0.14
102 2 0.00
103 2 0.00
104 1 0.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.30
Consensus pattern (96 bp):
TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAGAAAAGAGATTAGTTTAATTCTGGGTAAT
TAAACTAAATAGTAAAAGAAGAAGTAAACAA
Found at i:33975 original size:36 final size:36
Alignment explanation
Indices: 33933--34020 Score: 167
Period size: 36 Copynumber: 2.4 Consensus size: 36
33923 TGTGAATGCA
33933 ATGCCTAATTACTAATAATTACTAATGTGAACGATG
1 ATGCCTAATTACTAATAATTACTAATGTGAACGATG
*
33969 ATGCCTAATTACTAATAATTACTAATGTGAATGATG
1 ATGCCTAATTACTAATAATTACTAATGTGAACGATG
34005 ATGCCTAATTACTAAT
1 ATGCCTAATTACTAAT
34021 GTGGATACTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (36 bp):
ATGCCTAATTACTAATAATTACTAATGTGAACGATG
Found at i:38930 original size:64 final size:63
Alignment explanation
Indices: 38810--38930 Score: 145
Period size: 65 Copynumber: 1.9 Consensus size: 63
38800 AACTGTTACT
* ** *
38810 ACCCATGCATGGGGTACCCTGGCCTCCCCACGCCTGCGCTATTGCAAAAAGTTTGAATCGTCCA
1 ACCCATGCATGGGGTACCCTGGCCTACCCACGCAAGCGCTAGTGCAAAAAG-TTGAATCGTCCA
* * *
38874 ACCCATGCATGGGGTATCCTTGGCCTACCCATGCAAGGGCTAGTGCAGAAAA-TTGAA
1 ACCCATGCATGGGGTA-CCCTGGCCTACCCACGCAAGCGCTAGTGCA-AAAAGTTGAA
38931 ATCAATAGCA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
64 21 0.44
65 23 0.48
66 4 0.08
ACGTcount: A:0.25, C:0.30, G:0.24, T:0.21
Consensus pattern (63 bp):
ACCCATGCATGGGGTACCCTGGCCTACCCACGCAAGCGCTAGTGCAAAAAGTTGAATCGTCCA
Done.