Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006155.1 Corchorus capsularis cultivar CVL-1 contig06173, 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: 20817
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2285 original size:19 final size:18
Alignment explanation
Indices: 2261--2300 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2251 TTGAAGATTT
*
2261 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
2280 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
2298 ATT
1 ATT
2301 ATCTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:2911 original size:18 final size:17
Alignment explanation
Indices: 2884--2919 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
2874 TTTCTCTTCA
*
2884 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTATAGT
2901 TCTAGTTTTTCTTATAGT
1 TCTA-TTTTTCTTATAGT
2919 T
1 T
2920 TTAGGTTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.14, C:0.14, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTATAGT
Found at i:6773 original size:12 final size:13
Alignment explanation
Indices: 6749--6781 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
6739 AACCTAAAAA
6749 TAAAAATTGAAAT
1 TAAAAATTGAAAT
*
6762 TGAAAATT-AAAT
1 TAAAAATTGAAAT
6774 TAAAAATT
1 TAAAAATT
6782 TGGTTGCCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (13 bp):
TAAAAATTGAAAT
Found at i:15754 original size:52 final size:52
Alignment explanation
Indices: 15566--15896 Score: 280
Period size: 52 Copynumber: 6.4 Consensus size: 52
15556 TATTTTTCCT
* * * **
15566 CTTTTTAGTTTAATTGCTCTGAATTAAACTAATCTACTGCTTACTCTTTCTTTTA
1 CTTTTTAGTTTAATTACTCTGAATTAAACCAATTTACTAATTACTC---CTTTTA
* * * ** * * * *
15621 CTCTTTTTAGTTTAATTACTTTAAACT-AACC--TCCAGCTTACTCCTTCTTTTA
1 --CTTTTTAGTTTAATTACTCTGAATTAAACCAATTTA-CTAATTACTCCTTTTA
** ** *
15673 C-TTTTAACTTAATTACTCAAAATTAAACCAATTCACTAATTACTCCTTTTA
1 CTTTTTAGTTTAATTACTCTGAATTAAACCAATTTACTAATTACTCCTTTTA
* * *
15724 CTTTTTAGTTTAACTACTGTGAATTAAACCAATTTACTAATTACTCCATTTA
1 CTTTTTAGTTTAATTACTCTGAATTAAACCAATTTACTAATTACTCCTTTTA
* * *
15776 CTTTTTAGTTTAATTACTTTGAATTAAACCAATTTATTGAA-TACTCTTTTTA
1 CTTTTTAGTTTAATTACTCTGAATTAAACCAATTTACT-AATTACTCCTTTTA
* * * *
15828 C-TTTTAGCTTAATTACTCTGAATTAAAGCAATTTACTGATTACTCCTTCTA
1 CTTTTTAGTTTAATTACTCTGAATTAAACCAATTTACTAATTACTCCTTTTA
*
15879 C-TTTTAGCTTAATTACTC
1 CTTTTTAGTTTAATTACTC
15897 ATTACTGCTT
Statistics
Matches: 226, Mismatches: 41, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
49 18 0.08
50 6 0.03
51 72 0.32
52 96 0.42
53 2 0.01
54 3 0.01
55 5 0.02
56 3 0.01
57 21 0.09
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.47
Consensus pattern (52 bp):
CTTTTTAGTTTAATTACTCTGAATTAAACCAATTTACTAATTACTCCTTTTA
Found at i:15854 original size:51 final size:51
Alignment explanation
Indices: 15667--15896 Score: 291
Period size: 52 Copynumber: 4.5 Consensus size: 51
15657 CTTACTCCTT
* ** *
15667 CTTTTACTTTTAACTTAATTACTCAAAATTAAACCAATTCACTAATTACTC
1 CTTTTACTTTTAGCTTAATTACTCTGAATTAAACCAATTTACTAATTACTC
* * *
15718 CTTTTACTTTTTAGTTTAACTACTGTGAATTAAACCAATTTACTAATTACTC
1 CTTTTAC-TTTTAGCTTAATTACTCTGAATTAAACCAATTTACTAATTACTC
* * * *
15770 CATTTACTTTTTAGTTTAATTACTTTGAATTAAACCAATTTATTGAA-TACTC
1 CTTTTAC-TTTTAGCTTAATTACTCTGAATTAAACCAATTTACT-AATTACTC
* * *
15822 TTTTTACTTTTAGCTTAATTACTCTGAATTAAAGCAATTTACTGATTACTC
1 CTTTTACTTTTAGCTTAATTACTCTGAATTAAACCAATTTACTAATTACTC
*
15873 CTTCTACTTTTAGCTTAATTACTC
1 CTTTTACTTTTAGCTTAATTACTC
15897 ATTACTGCTT
Statistics
Matches: 156, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
50 1 0.01
51 66 0.42
52 87 0.56
53 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (51 bp):
CTTTTACTTTTAGCTTAATTACTCTGAATTAAACCAATTTACTAATTACTC
Found at i:15870 original size:103 final size:103
Alignment explanation
Indices: 15671--15895 Score: 285
Period size: 103 Copynumber: 2.2 Consensus size: 103
15661 CTCCTTCTTT
* *** *
15671 TACTTTTAACTTAATTACTCAAAATTAAACCAATTCACTAATTACTCCTTTTACTTTTTAGTTTA
1 TACTTTTAGCTTAATTACTTTGAATTAAACCAATTCACTAATTACTCCTTTTACTTTTTAGCTTA
*
15736 ACTACTGTGAATTAAACCAATTTACTAATTACTCCATT-
66 ACTACTCTGAATTAAACCAATTTACTAATTACTCC-TTC
* * * *
15774 TACTTTTTAGTTTAATTACTTTGAATTAAACCAATTTATTGAA-TACTCTTTTTAC-TTTTAGCT
1 TAC-TTTTAGCTTAATTACTTTGAATTAAACCAATTCACT-AATTACTCCTTTTACTTTTTAGCT
* * *
15837 TAATTACTCTGAATTAAAGCAATTTACTGATTACTCCTTC
64 TAACTACTCTGAATTAAACCAATTTACTAATTACTCCTTC
15877 TACTTTTAGCTTAATTACT
1 TACTTTTAGCTTAATTACT
15896 CATTACTGCT
Statistics
Matches: 105, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
102 17 0.16
103 46 0.44
104 40 0.38
105 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.46
Consensus pattern (103 bp):
TACTTTTAGCTTAATTACTTTGAATTAAACCAATTCACTAATTACTCCTTTTACTTTTTAGCTTA
ACTACTCTGAATTAAACCAATTTACTAATTACTCCTTC
Found at i:15949 original size:40 final size:40
Alignment explanation
Indices: 15856--16166 Score: 311
Period size: 40 Copynumber: 7.8 Consensus size: 40
15846 TGAATTAAAG
* * *
15856 CAATTTACTGATTACTCCTTCTACTTTTA-GCTTAATTAC
1 CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTAC
* *
15895 TC-A-TTACTGCTTACTTCTTTTACTTTTGCTCTTAATTAC
1 -CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTAC
* *
15934 CGATTTACTGATTACTTCTTTTACTTTTACTCTTAGTTAC
1 CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTAC
* *
15974 AAATTTACTGATTACTCCTTTTACTTTTACTTTTACTCATAATTAC
1 CAATTTACTGATTA---C--TT-CTTTTACTTTTACTCTTAATTAC
* *
16020 CAATTTACTGATTAATCCTTTTACTTTTAC-CATTAATTAC
1 CAATTTACTGATTACTTCTTTTACTTTTACTC-TTAATTAC
** *
16060 GGATTCACTGATTACTTCTTTTACTTTTACTCTTAATTAC
1 CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTAC
* *
16100 C-ATTTTCTG---A--T-TTTTACTTTTACACTTAATTAC
1 CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTAC
* *
16133 CAACTTACTGATTACCTCTTTTACTTTTACTCTT
1 CAATTTACTGATTACTTCTTTTACTTTTACTCTT
16167 TACTGATTAC
Statistics
Matches: 225, Mismatches: 28, Indels: 36
0.78 0.10 0.12
Matches are distributed among these distances:
33 22 0.10
34 7 0.03
36 1 0.00
37 1 0.00
38 22 0.10
39 19 0.08
40 114 0.51
41 2 0.01
43 1 0.00
45 2 0.01
46 34 0.15
ACGTcount: A:0.24, C:0.21, G:0.05, T:0.50
Consensus pattern (40 bp):
CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTAC
Found at i:15989 original size:80 final size:80
Alignment explanation
Indices: 15856--16166 Score: 311
Period size: 86 Copynumber: 3.9 Consensus size: 80
15846 TGAATTAAAG
* * * *
15856 CAATTTACTGATTACTCCTTCTACTTTTA-GCTTAATTACTC-A-TTACTGCTTACTTCTTTTAC
1 CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTAC-CAATTTACTGATTACTTCTTTTAC
*
15918 TTTTGCTCTTAATTAC
65 TTTTACTCTTAATTAC
* * *
15934 CGATTTACTGATTACTTCTTTTACTTTTACTCTTAGTTACAAATTTACTGATTACTCCTTTTACT
1 CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTACTGATTA---C--TT-CT
*
15999 TTTACTTTTACTCATAATTAC
60 TTTACTTTTACTCTTAATTAC
* * ** *
16020 CAATTTACTGATTAATCCTTTTACTTTTAC-CATTAATTACGGATTCACTGATTACTTCTTTTAC
1 CAATTTACTGATTACTTCTTTTACTTTTACTC-TTAATTACCAATTTACTGATTACTTCTTTTAC
16084 TTTTACTCTTAATTAC
65 TTTTACTCTTAATTAC
* * * *
16100 C-ATTTTCTG---A--T-TTTTACTTTTACACTTAATTACCAACTTACTGATTACCTCTTTTACT
1 CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTACTGATTACTTCTTTTACT
16158 TTTACTCTT
66 TTTACTCTT
16167 TACTGATTAC
Statistics
Matches: 198, Mismatches: 24, Indels: 27
0.80 0.10 0.11
Matches are distributed among these distances:
73 49 0.25
74 1 0.01
76 1 0.01
78 26 0.13
79 16 0.08
80 32 0.16
81 2 0.01
83 2 0.01
85 3 0.02
86 66 0.33
ACGTcount: A:0.24, C:0.21, G:0.05, T:0.50
Consensus pattern (80 bp):
CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTACTGATTACTTCTTTTACT
TTTACTCTTAATTAC
Found at i:16001 original size:46 final size:45
Alignment explanation
Indices: 15911--16683 Score: 302
Period size: 40 Copynumber: 18.2 Consensus size: 45
15901 CTGCTTACTT
* *
15911 CTTTTACTTTTGCTCTTAATTACCGATTTACTGATTA--C--TT-
1 CTTTTACTTTTACTCTTAATTACCAATTTACTGATTATCCTTTTA
* *
15951 CTTTTACTTTTACTCTTAGTTACAAATTTACTGATTACTCCTTTTA
1 CTTTTACTTTTACTCTTAATTACCAATTTACTGATTA-TCCTTTTA
*
15997 CTTTTACTTTTACTCATAATTACCAATTTACTGATTAATCCTTTTA
1 CTTTTACTTTTACTCTTAATTACCAATTTACTGATT-ATCCTTTTA
* ** *
16043 CTTTTAC-----C-ATTAATTACGGATTCACTGATTA--C--TT-
1 CTTTTACTTTTACTCTTAATTACCAATTTACTGATTATCCTTTTA
*
16077 CTTTTACTTTTACTCTTAATTACC-ATTTTCTG---AT--TTTTA
1 CTTTTACTTTTACTCTTAATTACCAATTTACTGATTATCCTTTTA
* *
16116 CTTTTAC----A--CTTAATTACCAACTTACTGATTACCTCTTTTA
1 CTTTTACTTTTACTCTTAATTACCAATTTACTGATTATC-CTTTTA
* * * * *
16156 CTTTTACTCTTTACTGATTACTT-CTTTTAGTTTTACT-CTTAATTACCAATTTT-
1 CTTTTACT-TTTACT-CTTAATTAC---CA-ATTTACTGATT-A-T-CC--TTTTA
* * ** *
16209 CTGATTACTTTT--T-TTACTTTGACTCTTAA-TTACCAATTTTCCGATTACTT-
1 CT-TTTACTTTTACTCTTA-ATT-AC-C--AATTTACTGATTATCC--TT--TTA
* *
16259 CTTTTACTTTAACTCTTAATTACCAATTTTCTGATTA--C--TT-
1 CTTTTACTTTTACTCTTAATTACCAATTTACTGATTATCCTTTTA
* * *
16299 CTTATACTTTTACTCTTAATTATCAATTTACT-ACTTA--C---TC
1 CTTTTACTTTTACTCTTAATTACCAATTTACTGA-TTATCCTTTTA
*
16339 CTTTTACTTTTACTCTTAATTACCAATTTACTGCTTACTCC-TTTA
1 CTTTTACTTTTACTCTTAATTACCAATTTACTGATTA-TCCTTTTA
*
16384 CTTTTA-----A-TCTTAATTACCAATTTTCTGATTA--C--TT-
1 CTTTTACTTTTACTCTTAATTACCAATTTACTGATTATCCTTTTA
16418 CTTTTACTTTTACTCTTAATTACCAATTTACTGATTA--C--TT-
1 CTTTTACTTTTACTCTTAATTACCAATTTACTGATTATCCTTTTA
*
16458 CTTTTACTTTTACTCTTAATTACCAATTTTCTGATTA--C--TT-
1 CTTTTACTTTTACTCTTAATTACCAATTTACTGATTATCCTTTTA
* *
16498 CTTTTACTTTTACTCTTAATTACAAATTTACTGCTTACTCCTTTTA
1 CTTTTACTTTTACTCTTAATTACCAATTTACTGATTA-TCCTTTTA
* *
16544 CTTTTA-----A-GCTTAATTACCAATTTTCTGATTA--C--TT-
1 CTTTTACTTTTACTCTTAATTACCAATTTACTGATTATCCTTTTA
* *
16578 CTTTTACATTTACTCTTAATTACCAATTTACTGATTACTTCTTTTA
1 CTTTTACTTTTACTCTTAATTACCAATTTACTGATTA-TCCTTTTA
* * * *
16624 CTTTTTAGTTTAATTACTCTGAATTAAACATATTTACTGATTACTCCTTTTTT
1 C-TTTTA-CTT--TTACTCTTAATT-ACCA-ATTTACTGATTA-TCC-TTTTA
16677 CTTTTAC
1 CTTTTAC
16684 CTATTTTAGC
Statistics
Matches: 571, Mismatches: 69, Indels: 175
0.70 0.08 0.21
Matches are distributed among these distances:
33 10 0.02
34 25 0.04
35 7 0.01
36 2 0.00
37 3 0.01
38 2 0.00
39 41 0.07
40 279 0.49
41 2 0.00
43 4 0.01
45 14 0.02
46 56 0.10
47 9 0.02
48 17 0.03
49 12 0.02
50 27 0.05
51 15 0.03
52 26 0.05
53 11 0.02
54 9 0.02
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.52
Consensus pattern (45 bp):
CTTTTACTTTTACTCTTAATTACCAATTTACTGATTATCCTTTTA
Found at i:16146 original size:199 final size:198
Alignment explanation
Indices: 15856--16628 Score: 837
Period size: 199 Copynumber: 3.9 Consensus size: 198
15846 TGAATTAAAG
* * * *
15856 CAATTTACTGATTACTCCTTCTACTTTTA-GCTTAATTACTC-A-TTACTGCTTACTTCTTTTAC
1 CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTAC-CAATTTTCTG--TAC-T-TTTTAC
* * * * *
15918 TTTTGCTCTTAATTACCGATTTACTGATTACTTCTTTTACTTTTACTCTTAGTTACAAATTTACT
61 TTTTACTCTTAATTACCAATTTACTGATTACTCCTTTTACTTTTACTCTTAATTACCAATTTACT
* * *
15983 GATTACTCCTTTTACTTTTACTTTTACTCATAATTACCAATTTACTGATTAATCCTTTTACTTTT
126 GATTACTCC-TTTACTTTTAC---TACTCTTAATTACCAATTTACTGATTACTTCTTTTACTTTT
16048 AC-CATTAATTAC
187 ACTC-TTAATTAC
** *
16060 GGATTCACTGATTACTTCTTTTACTTTTACTCTTAATTACC-ATTTTCTG-A-TTTTTACTTTTA
1 CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTTCTGTACTTTTTACTTTTA
* * **
16122 CACTTAATTACCAACTTACTGATTAC-CTCTTTTACTTTTACTC-T--TTACTGA-TTAC---TT
66 CTCTTAATTACCAATTTACTGATTACTC-CTTTTACTTTTACTCTTAATTACCAATTTACTGATT
* * * *
16179 -CT--TTTA-GTTT--TACTCTTAATTACCAATTTTCTGATTACTTTTTTTACTTTGACTCTTAA
130 ACTCCTTTACTTTTACTACTCTTAATTACCAATTTACTGATTACTTCTTTTACTTTTACTCTTAA
16238 TTAC
195 TTAC
* * *
16242 CAATTTTCCGATTACTTCTTTTACTTTAACTCTTAATTACCAATTTTCTGATTACTTCTTATACT
1 CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTTCTG--TACTT-TT-TACT
*
16307 TTTACTCTTAATTATCAATTTACT-ACTTACTCCTTTTACTTTTACTCTTAATTACCAATTTACT
62 TTTACTCTTAATTACCAATTTACTGA-TTACTCCTTTTACTTTTACTCTTAATTACCAATTTACT
* *
16371 GCTTACTCCTTTACTTTTA--A-TCTTAATTACCAATTTTCTGATTACTTCTTTTACTTTTACTC
126 GATTACTCCTTTACTTTTACTACTCTTAATTACCAATTTACTGATTACTTCTTTTACTTTTACTC
16433 TTAATTAC
191 TTAATTAC
16441 CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTTCTGATTACTTCTTTTACT
1 CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTTCTG--TAC-T-TTTTACT
* * ** *
16506 TTTACTCTTAATTACAAATTTACTGCTTACTCCTTTTACTTTTAAGCTTAATTACCAATTTTCTG
62 TTTACTCTTAATTACCAATTTACTGATTACTCCTTTTACTTTTACTCTTAATTACCAATTTACTG
* *
16571 ATTACTTCTTTTAC-ATT--TACTCTTAATTACCAATTTACTGATTACTTCTTTTACTTTT
127 ATTAC-TCCTTTACTTTTACTACTCTTAATTACCAATTTACTGATTACTTCTTTTACTTTT
16629 TAGTTTAATT
Statistics
Matches: 490, Mismatches: 48, Indels: 66
0.81 0.08 0.11
Matches are distributed among these distances:
182 80 0.16
183 9 0.02
186 1 0.00
187 5 0.01
188 7 0.01
189 44 0.09
190 2 0.00
191 2 0.00
192 7 0.01
193 4 0.01
195 4 0.01
196 7 0.01
197 2 0.00
198 1 0.00
199 221 0.45
200 52 0.11
201 1 0.00
202 1 0.00
204 26 0.05
205 14 0.03
ACGTcount: A:0.24, C:0.21, G:0.04, T:0.52
Consensus pattern (198 bp):
CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTTCTGTACTTTTTACTTTTA
CTCTTAATTACCAATTTACTGATTACTCCTTTTACTTTTACTCTTAATTACCAATTTACTGATTA
CTCCTTTACTTTTACTACTCTTAATTACCAATTTACTGATTACTTCTTTTACTTTTACTCTTAAT
TAC
Found at i:16167 original size:14 final size:14
Alignment explanation
Indices: 16148--16195 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
16138 TACTGATTAC
16148 CTCTTTTACTTTTA
1 CTCTTTTACTTTTA
*
16162 CTC-TTTACTGATTA
1 CTCTTTTACT-TTTA
*
16176 CTTCTTTTAGTTTTA
1 C-TCTTTTACTTTTA
16191 CTCTT
1 CTCTT
16196 AATTACCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 6 0.21
14 11 0.39
15 6 0.21
16 5 0.18
ACGTcount: A:0.15, C:0.21, G:0.04, T:0.60
Consensus pattern (14 bp):
CTCTTTTACTTTTA
Found at i:16169 original size:80 final size:80
Alignment explanation
Indices: 15909--16628 Score: 654
Period size: 80 Copynumber: 9.2 Consensus size: 80
15899 TACTGCTTAC
* * * *
15909 TTCTTTTACTTTTGCTCTTAATTACCGATTTACTGATTACTTCTTTTACTTTTACTCTTAGTTAC
1 TTCTTTTACTTTTACTCTTAATTACCAATTTTCTG--TAC-TCTTTTACTTTTACTCTTAATTAC
*
15974 AAATTTACTGATTACTCCTT
63 CAATTTACTGATTACT-C-T
* * *
15994 TTACTTTTACTTTTACTCATAATTACCAATTTACTGATTAATCCTTTTACTTTTAC-CATTAATT
1 TT-CTTTTACTTTTACTCTTAATTACCAATTTTCTG--TACT-CTTTTACTTTTACTC-TTAATT
** *
16058 ACGGATTCACTGATTA--C-
61 ACCAATTTACTGATTACTCT
*
16075 TTCTTTTACTTTTACTCTTAATTACC-ATTTTCTG-A-T-TTTTACTTTTACACTTAATTACCAA
1 TTCTTTTACTTTTACTCTTAATTACCAATTTTCTGTACTCTTTTACTTTTACTCTTAATTACCAA
*
16136 CTTACTGATTAC-C-
66 TTTACTGATTACTCT
** * *
16149 -TCTTTTACTTTTACTC-T--TTACTGA-TTAC--T--TCTTTTAGTTTTACTCTTAATTACCAA
1 TTCTTTTACTTTTACTCTTAATTACCAATTTTCTGTACTCTTTTACTTTTACTCTTAATTACCAA
*
16205 TTTTCTGATTA--CT
66 TTTACTGATTACTCT
* * *
16218 TT-TTTTACTTTGACTCTTAATTACCAATTTTCCGATTACTTCTTTTACTTTAACTCTTAATTAC
1 TTCTTTTACTTTTACTCTTAATTACCAATTTTCTG--TAC-TCTTTTACTTTTACTCTTAATTAC
*
16282 CAATTTTCTGATTA--C-
63 CAATTTACTGATTACTCT
* *
16297 TTCTTATACTTTTACTCTTAATTATCAATTTACTACT-TACTCCTTTTACTTTTACTCTTAATTA
1 TTCTTTTACTTTTACTCTTAATTACCAATTT--T-CTGTACT-CTTTTACTTTTACTCTTAATTA
*
16361 CCAATTTACTGCTTACTC-
62 CCAATTTACTGATTACTCT
*
16379 --C-TTTACTTTTAATCTTAATTACCAATTTTCTGATTACTTCTTTTACTTTTACTCTTAATTAC
1 TTCTTTTACTTTTACTCTTAATTACCAATTTTCTG--TAC-TCTTTTACTTTTACTCTTAATTAC
16441 CAATTTACTGATTA--C-
63 CAATTTACTGATTACTCT
16456 TTCTTTTACTTTTACTCTTAATTACCAATTTTCTGATTACTTCTTTTACTTTTACTCTTAATTAC
1 TTCTTTTACTTTTACTCTTAATTACCAATTTTCTG--TAC-TCTTTTACTTTTACTCTTAATTAC
* *
16521 AAATTTACTGCTTACTC-
63 CAATTTACTGATTACTCT
** *
16538 --CTTTTACTTTTAAGCTTAATTACCAATTTTCTGATTACTTCTTTTACATTTACTCTTAATTAC
1 TTCTTTTACTTTTACTCTTAATTACCAATTTTCTG--TAC-TCTTTTACTTTTACTCTTAATTAC
16601 CAATTTACTGATTA--C-
63 CAATTTACTGATTACTCT
16616 TTCTTTTACTTTT
1 TTCTTTTACTTTT
16629 TAGTTTAATT
Statistics
Matches: 551, Mismatches: 45, Indels: 83
0.81 0.07 0.12
Matches are distributed among these distances:
68 2 0.00
69 45 0.08
70 9 0.02
71 1 0.00
72 6 0.01
73 49 0.09
74 2 0.00
75 1 0.00
76 3 0.01
77 3 0.01
78 1 0.00
79 74 0.13
80 279 0.51
81 2 0.00
82 3 0.01
83 2 0.00
85 4 0.01
86 65 0.12
ACGTcount: A:0.24, C:0.20, G:0.03, T:0.52
Consensus pattern (80 bp):
TTCTTTTACTTTTACTCTTAATTACCAATTTTCTGTACTCTTTTACTTTTACTCTTAATTACCAA
TTTACTGATTACTCT
Found at i:16181 original size:29 final size:29
Alignment explanation
Indices: 16137--16195 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
16127 AATTACCAAC
16137 TTACTGATTACCTCTTTTACTTTTACTCT
1 TTACTGATTACCTCTTTTACTTTTACTCT
* *
16166 TTACTGATTACTTCTTTTAGTTTTACTCT
1 TTACTGATTACCTCTTTTACTTTTACTCT
16195 T
1 T
16196 AATTACCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.17, C:0.20, G:0.05, T:0.58
Consensus pattern (29 bp):
TTACTGATTACCTCTTTTACTTTTACTCT
Found at i:16213 original size:40 final size:40
Alignment explanation
Indices: 16169--16628 Score: 699
Period size: 40 Copynumber: 11.5 Consensus size: 40
16159 TTACTCTTTA
*
16169 CTGATTACTTCTTTTAGTTTTACTCTTAATTACCAATTTT
1 CTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTT
* *
16209 CTGATTACTTTTTTTACTTTGACTCTTAATTACCAATTTT
1 CTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTT
* *
16249 CCGATTACTTCTTTTACTTTAACTCTTAATTACCAATTTT
1 CTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTT
* * *
16289 CTGATTACTTCTTATACTTTTACTCTTAATTATCAATTTA
1 CTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTT
* *
16329 CT-ACTTACTCCTTTTACTTTTACTCTTAATTACCAATTTA
1 CTGA-TTACTTCTTTTACTTTTACTCTTAATTACCAATTTT
* * *
16369 CTGCTTAC-TCCTTTACTTTTAATCTTAATTACCAATTTT
1 CTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTT
*
16408 CTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTA
1 CTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTT
16448 CTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTT
1 CTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTT
* *
16488 CTGATTACTTCTTTTACTTTTACTCTTAATTACAAATTTA
1 CTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTT
* * **
16528 CTGCTTACTCCTTTTACTTTTAAGCTTAATTACCAATTTT
1 CTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTT
* *
16568 CTGATTACTTCTTTTACATTTACTCTTAATTACCAATTTA
1 CTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTT
16608 CTGATTACTTCTTTTACTTTT
1 CTGATTACTTCTTTTACTTTT
16629 TAGTTTAATT
Statistics
Matches: 378, Mismatches: 39, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
39 35 0.09
40 343 0.91
ACGTcount: A:0.24, C:0.20, G:0.03, T:0.53
Consensus pattern (40 bp):
CTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTT
Done.