Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007490.1 Corchorus capsularis cultivar CVL-1 contig07511, 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: 34707
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Found at i:516 original size:12 final size:13
Alignment explanation
Indices: 475--519 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
465 AATTATTGTT
475 TGCTTTATTAATC
1 TGCTTTATTAATC
*
488 TGCTTTATTAATT
1 TGCTTTATTAATC
501 TGCTTTA-TAATC
1 TGCTTTATTAATC
513 TGCTTTA
1 TGCTTTA
520 GATTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:7658 original size:12 final size:13
Alignment explanation
Indices: 7617--7661 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
7607 AATTATTGTT
7617 TGCTTTATTAATC
1 TGCTTTATTAATC
*
7630 TGCTTTATTAATT
1 TGCTTTATTAATC
7643 TGCTTTA-TAATC
1 TGCTTTATTAATC
7655 TGCTTTA
1 TGCTTTA
7662 GATTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:7690 original size:5 final size:6
Alignment explanation
Indices: 7658--7689 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
7648 TATAATCTGC
7658 TTTAGA TTTAGA TTTAGA TTTAGA TTT-GA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
7690 GCTTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:15124 original size:31 final size:31
Alignment explanation
Indices: 15088--15189 Score: 83
Period size: 30 Copynumber: 3.5 Consensus size: 31
15078 GGGCATTCAT
15088 AAGTCCCTAAACACAGAGGCATCTATACTAA
1 AAGTCCCTAAACACAGAGGCATCTATACTAA
* * *
15119 AAGTCCTTAAAAACA-AGG-A-CGT-T-C-AT
1 AAGTCCCTAAACACAGAGGCATC-TATACTAA
* * *
15145 AAGTCTCTAAACATAGAGGCATCTATA-TCA
1 AAGTCCCTAAACACAGAGGCATCTATACTAA
*
15175 AAGTCCCCAAACACA
1 AAGTCCCTAAACACA
15190 TATAACGCAA
Statistics
Matches: 52, Mismatches: 12, Indels: 15
0.66 0.15 0.19
Matches are distributed among these distances:
26 12 0.23
27 4 0.08
28 4 0.08
29 4 0.08
30 15 0.29
31 13 0.25
ACGTcount: A:0.42, C:0.25, G:0.13, T:0.21
Consensus pattern (31 bp):
AAGTCCCTAAACACAGAGGCATCTATACTAA
Found at i:15149 original size:57 final size:56
Alignment explanation
Indices: 15061--15189 Score: 170
Period size: 57 Copynumber: 2.3 Consensus size: 56
15051 CCCAACACCC
*
15061 AAAGTCCTAAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
1 AAAGTCCTAAAACACAAGGACATTCATAAGTCCCTAAACACAGAGGCATCTATA-TA
* * * *
15118 AAAGTCCTTAAAA-ACAAGGACGTTCATAAGTCTCTAAACATAGAGGCATCTATATC
1 AAAGTCC-TAAAACACAAGGACATTCATAAGTCCCTAAACACAGAGGCATCTATATA
**
15174 AAAGTCCCCAAACACA
1 AAAGTCCTAAAACACA
15190 TATAACGCAA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
55 3 0.05
56 11 0.17
57 44 0.70
58 5 0.08
ACGTcount: A:0.43, C:0.24, G:0.13, T:0.20
Consensus pattern (56 bp):
AAAGTCCTAAAACACAAGGACATTCATAAGTCCCTAAACACAGAGGCATCTATATA
Found at i:16138 original size:16 final size:16
Alignment explanation
Indices: 16119--16208 Score: 81
Period size: 16 Copynumber: 5.6 Consensus size: 16
16109 CCTGAACCTA
*
16119 AACCCGAAAAAATCCG
1 AACCCGAAAAAACCCG
* * *
16135 AACCCGAAAAAGCTCA
1 AACCCGAAAAAACCCG
**
16151 AACCCGAAAACCCCCG
1 AACCCGAAAAAACCCG
* * * *
16167 AACCCGTAAAAGCTCA
1 AACCCGAAAAAACCCG
16183 AACCCGAAAAAACCCG
1 AACCCGAAAAAACCCG
*
16199 AATCCGAAAA
1 AACCCGAAAA
16209 TTTATGAAAA
Statistics
Matches: 56, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 56 1.00
ACGTcount: A:0.48, C:0.34, G:0.12, T:0.06
Consensus pattern (16 bp):
AACCCGAAAAAACCCG
Found at i:16154 original size:32 final size:32
Alignment explanation
Indices: 16118--16208 Score: 137
Period size: 32 Copynumber: 2.8 Consensus size: 32
16108 ACCTGAACCT
*
16118 AAACCCGAAAAAATCCGAACCCGAAAAAGCTC
1 AAACCCGAAAAAACCCGAACCCGAAAAAGCTC
** *
16150 AAACCCGAAAACCCCCGAACCCGTAAAAGCTC
1 AAACCCGAAAAAACCCGAACCCGAAAAAGCTC
*
16182 AAACCCGAAAAAACCCGAATCCGAAAA
1 AAACCCGAAAAAACCCGAACCCGAAAA
16209 TTTATGAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.48, C:0.34, G:0.12, T:0.05
Consensus pattern (32 bp):
AAACCCGAAAAAACCCGAACCCGAAAAAGCTC
Found at i:16386 original size:15 final size:16
Alignment explanation
Indices: 16363--16423 Score: 81
Period size: 15 Copynumber: 3.9 Consensus size: 16
16353 CTGAACCCGA
*
16363 ACCCGAATT-AACCTG
1 ACCCAAATTCAACCTG
*
16378 ACCCAAATTCAACCCG
1 ACCCAAATTCAACCTG
16394 AACCCAAATT-AACCTG
1 -ACCCAAATTCAACCTG
16410 ACCCAAATTCAACC
1 ACCCAAATTCAACC
16424 CGAACACGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
15 17 0.43
16 14 0.35
17 9 0.22
ACGTcount: A:0.39, C:0.38, G:0.07, T:0.16
Consensus pattern (16 bp):
ACCCAAATTCAACCTG
Found at i:16392 original size:32 final size:32
Alignment explanation
Indices: 16346--16428 Score: 139
Period size: 32 Copynumber: 2.6 Consensus size: 32
16336 TCTGGCCAAA
* * *
16346 ACCCAAACTGAACCCGAACCCGAATTAACCTG
1 ACCCAAATTCAACCCGAACCCAAATTAACCTG
16378 ACCCAAATTCAACCCGAACCCAAATTAACCTG
1 ACCCAAATTCAACCCGAACCCAAATTAACCTG
16410 ACCCAAATTCAACCCGAAC
1 ACCCAAATTCAACCCGAAC
16429 ACGATTCAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.40, C:0.39, G:0.08, T:0.13
Consensus pattern (32 bp):
ACCCAAATTCAACCCGAACCCAAATTAACCTG
Found at i:23358 original size:16 final size:15
Alignment explanation
Indices: 23329--23362 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
23319 TCTTACATAC
23329 CCAAATACCAAATAT
1 CCAAATACCAAATAT
23344 CCAAATACTCAAATAT
1 CCAAATAC-CAAATAT
23360 CCA
1 CCA
23363 TCAAGCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (15 bp):
CCAAATACCAAATAT
Found at i:28200 original size:57 final size:56
Alignment explanation
Indices: 28112--28240 Score: 195
Period size: 57 Copynumber: 2.3 Consensus size: 56
28102 CCCAACACCC
* *
28112 AAAGTCCTCAAACACAAGGGCATCCATAAGTCCCTAAACACAGATGCATCTATACTA
1 AAAGTCCTCAAACACAAGGGCATCCATAAGTCCCTAAACACAGAGGCATATATA-TA
* * *
28169 AAAGTCCTCAAACACAAGGGCATTCATAAGTCTCTAAACACAGAGGCATATATATC
1 AAAGTCCTCAAACACAAGGGCATCCATAAGTCCCTAAACACAGAGGCATATATATA
*
28225 AAAGTCCCCAAACACA
1 AAAGTCCTCAAACACA
28241 TATAACACAT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
56 16 0.24
57 50 0.76
ACGTcount: A:0.42, C:0.27, G:0.12, T:0.19
Consensus pattern (56 bp):
AAAGTCCTCAAACACAAGGGCATCCATAAGTCCCTAAACACAGAGGCATATATATA
Found at i:28217 original size:26 final size:26
Alignment explanation
Indices: 28113--28210 Score: 76
Period size: 26 Copynumber: 3.6 Consensus size: 26
28103 CCAACACCCA
*
28113 AAGTCCTCAAACACAAGGGCATCCAT
1 AAGTCCTCAAACACAAGGGCATTCAT
* *
28139 AAGTCC-CTAAACAC-AGATGCATCTATACTAA
1 AAGTCCTC-AAACACAAG-GGCA--T-T-C-AT
28170 AAGTCCTCAAACACAAGGGCATTCAT
1 AAGTCCTCAAACACAAGGGCATTCAT
28196 AAGT-CTCTAAACACA
1 AAGTCCTC-AAACACA
28211 GAGGCATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
25 6 0.11
26 27 0.47
27 1 0.02
28 2 0.04
29 1 0.02
30 1 0.02
31 16 0.28
32 3 0.05
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.19
Consensus pattern (26 bp):
AAGTCCTCAAACACAAGGGCATTCAT
Found at i:28343 original size:101 final size:97
Alignment explanation
Indices: 28172--28357 Score: 248
Period size: 101 Copynumber: 1.9 Consensus size: 97
28162 TATACTAAAA
* * *
28172 GTCCTCAAACACAAGGGCATTCATAAGTCTCTAAACACAGAGGCATATATATCAAAGTCCCCAAA
1 GTCCTCAAACACAAGGGCATCCATAAGTCCCTAAACACAGAGGCACATATATCAAAGTCCCCAAA
*
28237 CACATATAACACATGGGCAACTCTCTTTCAAT
66 CACATATAACACAAGGGCAACTCTCTTTCAAT
* *
28269 GTCCTCAAGCACAAGGGCATCCATGCGAAAGTCCCTAAACATAGAGGCACATATA-CTAAAGTCC
1 GTCCTCAAACACAAGGGCATCCAT----AAGTCCCTAAACACAGAGGCACATATATC-AAAGTCC
**
28333 TTAAACACATATAACACAAGGGCAA
61 CCAAACACATATAACACAAGGGCAA
28358 TTTTCTTCGT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
97 22 0.29
100 1 0.01
101 53 0.70
ACGTcount: A:0.39, C:0.26, G:0.15, T:0.20
Consensus pattern (97 bp):
GTCCTCAAACACAAGGGCATCCATAAGTCCCTAAACACAGAGGCACATATATCAAAGTCCCCAAA
CACATATAACACAAGGGCAACTCTCTTTCAAT
Found at i:29708 original size:36 final size:35
Alignment explanation
Indices: 29667--29884 Score: 182
Period size: 32 Copynumber: 6.3 Consensus size: 35
29657 TCTTTTTTAG
29667 ATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
1 ATTAAG-TCTTTATTGACTCCACTTAATTACCCTGA
* ** ** *
29703 ATTAAGTCTTTTATTG-TTTTACTTAATCT-CTTTTTA
1 ATTAAGTC-TTTATTGACTCCACTTAAT-TAC-CCTGA
29739 GATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
1 -ATTAAG-TCTTTATTGACTCCACTTAATTACCCTGA
* *
29776 ATTAAGTCTTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGTC-TTTATTGACTCCACTTAATTACCCTGA
* ** *
29812 ATTAAGTCTCTA---ACTTGACTTAATTACCCTAA
1 ATTAAGTCTTTATTGACTCCACTTAATTACCCTGA
* **
29844 ATTAAGTCTCTA---ACTTGACTTAATTACCCTGA
1 ATTAAGTCTTTATTGACTCCACTTAATTACCCTGA
29876 ATTAAGTCT
1 ATTAAGTCT
29885 CTGACTTGAC
Statistics
Matches: 154, Mismatches: 20, Indels: 20
0.79 0.10 0.10
Matches are distributed among these distances:
32 56 0.36
35 16 0.10
36 55 0.36
37 16 0.10
38 11 0.07
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (35 bp):
ATTAAGTCTTTATTGACTCCACTTAATTACCCTGA
Found at i:29754 original size:73 final size:74
Alignment explanation
Indices: 29636--29791 Score: 287
Period size: 73 Copynumber: 2.1 Consensus size: 74
29626 AAATCAAGCC
* *
29636 CTTTTATTATTTTGCTTAATCTCTTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCT
1 CTTTTATTGTTTTACTTAATCTCTTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCT
29701 GAATTAAGT
66 GAATTAAGT
29710 CTTTTATTGTTTTACTTAATCTC-TTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCT
1 CTTTTATTGTTTTACTTAATCTCTTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCT
29774 GAATTAAGT
66 GAATTAAGT
29783 CTTTTATTG
1 CTTTTATTG
29792 ACGCTACTTA
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
73 59 0.74
74 21 0.26
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (74 bp):
CTTTTATTGTTTTACTTAATCTCTTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCT
GAATTAAGT
Found at i:29830 original size:73 final size:72
Alignment explanation
Indices: 29680--29895 Score: 204
Period size: 73 Copynumber: 3.1 Consensus size: 72
29670 AAGTTCTTTA
** ** *
29680 TTGACTCCACTTAATTACCCTGAATTAAGTCTTTTATTGTTTTACTTAATCT-CTTTTTAGATTA
1 TTGACTCCACTTAATTACCCTGAATTAAGTCTTTTATTGACTTACTTAAT-TAC-CCTGA-ATTA
*
29744 AGT-TCTTTA-
63 AGTCTC-TAAC
*
29753 TTGACTCCACTTAATTACCCTGAATTAAGTCTTTTATTGACGCTACTTAATTACCCTGAATTAAG
1 TTGACTCCACTTAATTACCCTGAATTAAGTCTTTTATTGAC-TTACTTAATTACCCTGAATTAAG
29818 TCTCTAAC
65 TCTCTAAC
* *
29826 TTG-----ACTTAATTACCCTAAATTAAGTC-TCTA---ACTTGACTTAATTACCCTGAATTAAG
1 TTGACTCCACTTAATTACCCTGAATTAAGTCTTTTATTGACTT-ACTTAATTACCCTGAATTAAG
*
29882 TCTCTGAC
65 TCTCTAAC
29890 TTGACT
1 TTGACT
29896 TAATTTCCTT
Statistics
Matches: 124, Mismatches: 11, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
63 1 0.01
64 33 0.27
67 3 0.02
68 22 0.18
72 9 0.07
73 47 0.38
74 9 0.07
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (72 bp):
TTGACTCCACTTAATTACCCTGAATTAAGTCTTTTATTGACTTACTTAATTACCCTGAATTAAGT
CTCTAAC
Found at i:29838 original size:32 final size:32
Alignment explanation
Indices: 29761--29900 Score: 192
Period size: 32 Copynumber: 4.2 Consensus size: 32
29751 TATTGACTCC
* *
29761 ACTTAATTACCCTGAATTAAGTCTTTTA-TTGACG
1 ACTTAATTACCCTGAATTAAGTCTCTAACTT---G
29795 CTACTTAATTACCCTGAATTAAGTCTCTAACTTG
1 --ACTTAATTACCCTGAATTAAGTCTCTAACTTG
*
29829 ACTTAATTACCCTAAATTAAGTCTCTAACTTG
1 ACTTAATTACCCTGAATTAAGTCTCTAACTTG
*
29861 ACTTAATTACCCTGAATTAAGTCTCTGACTTG
1 ACTTAATTACCCTGAATTAAGTCTCTAACTTG
29893 ACTTAATT
1 ACTTAATT
29901 TCCTTCCTTG
Statistics
Matches: 98, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
32 69 0.70
34 1 0.01
36 26 0.27
37 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (32 bp):
ACTTAATTACCCTGAATTAAGTCTCTAACTTG
Found at i:29934 original size:37 final size:37
Alignment explanation
Indices: 29893--30067 Score: 225
Period size: 37 Copynumber: 4.9 Consensus size: 37
29883 CTCTGACTTG
*
29893 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCT
1 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTTACTCT
* * *
29930 ACTTAATTCCCTTCCTTGGAATCAAGT-C----CTCT
1 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTTACTCT
*
29962 ACTTAATTTCCTTCCTTGAAATTAAGCCCTTTACTCT
1 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTTACTCT
* * *
29999 ACTTAATTCCCTTCCTTGGAATCAAGTCCTTTACTCT
1 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTTACTCT
* *
30036 ACTTAATTTCCCTCCTTGAAATTAAGTTCTTT
1 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTT
30068 GCCTGATCTT
Statistics
Matches: 117, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
32 27 0.23
33 1 0.01
36 1 0.01
37 88 0.75
ACGTcount: A:0.24, C:0.27, G:0.07, T:0.42
Consensus pattern (37 bp):
ACTTAATTTCCTTCCTTGAAATTAAGTCCTTTACTCT
Found at i:29966 original size:69 final size:71
Alignment explanation
Indices: 29893--30062 Score: 272
Period size: 69 Copynumber: 2.4 Consensus size: 71
29883 CTCTGACTTG
29893 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATCAAGT-
1 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATCAAGTC
29957 C-CTCT
66 CTCTCT
* *
29962 ACTTAATTTCCTTCCTTGAAATTAAGCCCTTTACTCTACTTAATTCCCTTCCTTGGAATCAAGTC
1 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATCAAGTC
30027 CTTTACTCT
66 C--T-CTCT
*
30036 ACTTAATTTCCCTCCTTGAAATTAAGT
1 ACTTAATTTCCTTCCTTGAAATTAAGT
30063 TCTTTGCCTG
Statistics
Matches: 92, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
69 62 0.67
70 1 0.01
74 29 0.32
ACGTcount: A:0.25, C:0.27, G:0.07, T:0.41
Consensus pattern (71 bp):
ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATCAAGTC
CTCTCT
Found at i:29967 original size:32 final size:32
Alignment explanation
Indices: 29926--30033 Score: 126
Period size: 32 Copynumber: 3.2 Consensus size: 32
29916 AAGTCCTTAA
29926 CTCTACTTAATTCCCTTCCTTGGAATCAAGTC
1 CTCTACTTAATTCCCTTCCTTGGAATCAAGTC
* * * *
29958 CTCTACTTAATTTCCTTCCTTGAAATTAAGCCCTTTA
1 CTCTACTTAATTCCCTTCCTTGGAATCAAG-----TC
29995 CTCTACTTAATTCCCTTCCTTGGAATCAAGTC
1 CTCTACTTAATTCCCTTCCTTGGAATCAAGTC
*
30027 CTTTACT
1 CTCTACT
30034 CTACTTAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
32 34 0.55
37 28 0.45
ACGTcount: A:0.22, C:0.30, G:0.07, T:0.41
Consensus pattern (32 bp):
CTCTACTTAATTCCCTTCCTTGGAATCAAGTC
Found at i:30227 original size:76 final size:76
Alignment explanation
Indices: 30147--30413 Score: 444
Period size: 76 Copynumber: 3.5 Consensus size: 76
30137 CTTTGCTAAT
* * * * * *
30147 TTTACTTGATTACCCTGAATTAAGTCTGCGCTTGCCTTTACCTAATTTTCTTCCTTGAAATTAAG
1 TTTACTTAATTACCCTGAATTAAGTCTGTGCTTGTCTTCACCTAATTTCCTTTCTTGAAATTAAG
30212 CATGTGCTTAC
66 CATGTGCTTAC
*
30223 TTTACTTAATTACCCTGAATTAAGTCTGTGCTTGTCTTCACTTAATTTCCTTTCTTGAAATTAAG
1 TTTACTTAATTACCCTGAATTAAGTCTGTGCTTGTCTTCACCTAATTTCCTTTCTTGAAATTAAG
*
30288 CTTGTGCTTAC
66 CATGTGCTTAC
*
30299 TTTACTTAATTACCCTGAATTAAGTTTGTGCTTGTCTTCACCTAATTTCCTTTCTTGAAATTAAG
1 TTTACTTAATTACCCTGAATTAAGTCTGTGCTTGTCTTCACCTAATTTCCTTTCTTGAAATTAAG
30364 CATGTGCTTAC
66 CATGTGCTTAC
*
30375 TTTACTTAATTACCCTGAATTAAGTATGTGCTTGTCTTC
1 TTTACTTAATTACCCTGAATTAAGTCTGTGCTTGTCTTC
30414 TTAATTGTCC
Statistics
Matches: 179, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 179 1.00
ACGTcount: A:0.23, C:0.20, G:0.12, T:0.45
Consensus pattern (76 bp):
TTTACTTAATTACCCTGAATTAAGTCTGTGCTTGTCTTCACCTAATTTCCTTTCTTGAAATTAAG
CATGTGCTTAC
Found at i:30253 original size:35 final size:35
Alignment explanation
Indices: 30076--30407 Score: 195
Period size: 36 Copynumber: 8.9 Consensus size: 35
30066 TTGCCTGATC
* * * * * *
30076 TTACTTAATCATCCTTGGATTAACTCTTTGCTGACT
1 TTACTTAATTA-CCCTGAATTAAGTCTGTGCTTACT
** * * *
30112 TTACTTAATT-CTTGTGAAATTAAGTCTTTGCTAATT
1 TTACTTAATTAC-CCTG-AATTAAGTCTGTGCTTACT
* * *
30148 TTACTTGATTACCCTGAATTAAGTCTGCGCTTGCCT
1 TTACTTAATTACCCTGAATTAAGTCTGTGCTT-ACT
* *
30184 TTACCTAATTTTCTTCCTTGAAATTAAG-CATGTGCTTACT
1 TTACTTAA-TTAC--CC-TG-AATTAAGTC-TGTGCTTACT
*
30224 TTACTTAATTACCCTGAATTAAGTCTGTGCTTGTCT
1 TTACTTAATTACCCTGAATTAAGTCTGTGCTT-ACT
* *
30260 TCACTTAATTTCCTTTCTTGAAATTAAG-CTTGTGCTTACT
1 TTACTTAATTACC---C-TG-AATTAAGTC-TGTGCTTACT
* *
30300 TTACTTAATTACCCTGAATTAAGTTTGTGCTTGTCT
1 TTACTTAATTACCCTGAATTAAGTCTGTGCTT-ACT
* * *
30336 TCACCTAATTTCCTTTCTTGAAATTAAG-CATGTGCTTACT
1 TTACTTAATTACC---C-TG-AATTAAGTC-TGTGCTTACT
*
30376 TTACTTAATTACCCTGAATTAAGTATGTGCTT
1 TTACTTAATTACCCTGAATTAAGTCTGTGCTT
30408 GTCTTCTTAA
Statistics
Matches: 230, Mismatches: 39, Indels: 55
0.71 0.12 0.17
Matches are distributed among these distances:
34 1 0.00
35 57 0.25
36 74 0.32
37 8 0.03
39 7 0.03
40 42 0.18
41 41 0.18
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.45
Consensus pattern (35 bp):
TTACTTAATTACCCTGAATTAAGTCTGTGCTTACT
Found at i:30529 original size:40 final size:40
Alignment explanation
Indices: 30476--30601 Score: 121
Period size: 40 Copynumber: 3.4 Consensus size: 40
30466 AATTAAGACT
*
30476 TTTCTTCTCTTAATTGCCCAACTTAGGACCTTGATTGTAC
1 TTTCTTTTCTTAATTGCCCAACTTAGGACCTTGATTGTAC
* *
30516 TTTCTTTTCTTAATTACCCTGAA-TTAAGA-C----TT-TA-
1 TTTCTTTTCTTAATTGCCC--AACTTAGGACCTTGATTGTAC
*
30550 -GTC--TTCTTAATTGCCCAACTTAGGACCTTGATTGTAC
1 TTTCTTTTCTTAATTGCCCAACTTAGGACCTTGATTGTAC
30587 TTTCTTTTCTTAATT
1 TTTCTTTTCTTAATT
30602 ACCCTGAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 26
0.67 0.07 0.26
Matches are distributed among these distances:
29 2 0.03
30 5 0.08
31 13 0.20
33 2 0.03
35 4 0.06
36 4 0.06
38 2 0.03
40 27 0.41
41 5 0.08
42 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.47
Consensus pattern (40 bp):
TTTCTTTTCTTAATTGCCCAACTTAGGACCTTGATTGTAC
Found at i:30620 original size:71 final size:71
Alignment explanation
Indices: 30374--30620 Score: 383
Period size: 71 Copynumber: 3.4 Consensus size: 71
30364 CATGTGCTTA
* * *
30374 CTTTACTTAATTACCCTGAATTAAGTA-TGTGCTTGTCTTCTTAATTGTCCAACTTAGGACCTTG
1 CTTTTCTTAATTACCCTGAATTAAG-ACT-T--TAGTCTTCTTAATTGCCCAACTTAGGACCTTG
30438 ATTGTACTTT
62 ATTGTACTTT
*
30448 CTTTCCTTAATTACCCTGAATTAAGACTTT--TCTTCTCTTAATTGCCCAACTTAGGACCTTGAT
1 CTTTTCTTAATTACCCTGAATTAAGACTTTAGTC-T-TCTTAATTGCCCAACTTAGGACCTTGAT
30511 TGTACTTT
64 TGTACTTT
30519 CTTTTCTTAATTACCCTGAATTAAGACTTTAGTCTTCTTAATTGCCCAACTTAGGACCTTGATTG
1 CTTTTCTTAATTACCCTGAATTAAGACTTTAGTCTTCTTAATTGCCCAACTTAGGACCTTGATTG
30584 TACTTT
66 TACTTT
30590 CTTTTCTTAATTACCCTGAATTAAGACTTTA
1 CTTTTCTTAATTACCCTGAATTAAGACTTTA
30621 ATTGTGCATA
Statistics
Matches: 165, Mismatches: 3, Indels: 13
0.91 0.02 0.07
Matches are distributed among these distances:
69 2 0.01
70 1 0.01
71 132 0.80
72 1 0.01
73 4 0.02
74 25 0.15
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.44
Consensus pattern (71 bp):
CTTTTCTTAATTACCCTGAATTAAGACTTTAGTCTTCTTAATTGCCCAACTTAGGACCTTGATTG
TACTTT
Done.