Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007152.1 Corchorus capsularis cultivar CVL-1 contig07173, 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: 33434
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:1634 original size:6 final size:6
Alignment explanation
Indices: 1623--1654 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1613 ATTAATTTGC
1623 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
1655 GCTTTGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:3833 original size:16 final size:16
Alignment explanation
Indices: 3808--3839 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3798 CATCAATATA
*
3808 ACTAATATGATTAATG
1 ACTAACATGATTAATG
3824 ACTAACATGATTAATG
1 ACTAACATGATTAATG
3840 GGAAGATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (16 bp):
ACTAACATGATTAATG
Found at i:6368 original size:3 final size:3
Alignment explanation
Indices: 6360--6408 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
6350 TTTCCAAGTT
6360 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6408 T
1 T
6409 ATATAACTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:8361 original size:29 final size:31
Alignment explanation
Indices: 8327--8390 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
8317 TGGCAATTTA
* *
8327 GAAATAT-TTTTAAAAA-AGGGGTACAATTG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
*
8356 GAAATATATTTTAAAAATAAGGGTATAATCG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
8387 GAAA
1 GAAA
8391 ACATAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 7 0.23
30 9 0.30
31 14 0.47
ACGTcount: A:0.48, C:0.03, G:0.19, T:0.30
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATCG
Found at i:8745 original size:17 final size:17
Alignment explanation
Indices: 8682--8747 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 17
8672 TTTATTTTTA
*
8682 TTTTATTAAATTCAATAT
1 TTTTA-TAAATTTAATAT
* * *
8700 TTTTATCAATTATATTTT
1 TTTTATAAATT-TAATAT
8718 TATTTAAATAAATTTAATAT
1 T-TTT--ATAAATTTAATAT
8738 TTTTATAAAT
1 TTTTATAAAT
8748 ATTTTAATGT
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
17 11 0.30
18 9 0.24
19 6 0.16
20 5 0.14
21 6 0.16
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTATAAATTTAATAT
Found at i:9993 original size:30 final size:30
Alignment explanation
Indices: 9954--10011 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
9944 GTGTTCTTAC
9954 CCTTATTTGTAAAACACGAAAACATTTTGT
1 CCTTATTTGTAAAACACGAAAACATTTTGT
* *
9984 CCTTGTTTGTAAAACATGAAAACATTTT
1 CCTTATTTGTAAAACACGAAAACATTTT
10012 ACCTTTATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (30 bp):
CCTTATTTGTAAAACACGAAAACATTTTGT
Found at i:10785 original size:18 final size:18
Alignment explanation
Indices: 10762--10797 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
10752 GTAAATAACC
10762 GTAGGAAATTACAAAAAA
1 GTAGGAAATTACAAAAAA
* *
10780 GTAGGAAGTTATAAAAAA
1 GTAGGAAATTACAAAAAA
10798 AAGGATGATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.19, T:0.19
Consensus pattern (18 bp):
GTAGGAAATTACAAAAAA
Found at i:14857 original size:284 final size:273
Alignment explanation
Indices: 14387--14943 Score: 927
Period size: 284 Copynumber: 2.0 Consensus size: 273
14377 CATAGAAAAT
14387 CATTTAACATGTGTTAATTTGAATCTTAATTTATTCTTCTTTTTTATGCGAAATCCTTCGGTAGC
1 CATTTAACATGTGTTAATTTGAATCTTAATTTATTCTTCTTTTTTATGCGAAATCCTTCGGTAGC
* *
14452 CACATTCGACCCCGATTAATCCGAAGACAAGACTCTATAATATGTTCAACAATAGTTTTTTTTTT
66 CACATTCGACCCCGACTAATCCGAAGACAAGACTCCATAATATGTTCAACAATAGTTTTTTTTTT
*
14517 TGTATGGACTTTGAAACTCATAGAAAATCATTTAACATGTGTTAATTTGAATCTAAATTTATTCT
131 TGTATGGACTTTGAAACTCATAGAAAATCATTTAACATCTGTTAATTTGAATCTAAATTTATTCT
14582 TCTTTTTTATGTGAAATCCTTCGGTATAAGGTAGCCACATTCGACCCCGACTAATCTGAAGACAA
196 TC-TTTTTATGTGAAATCCTTCGGTATAAGGTAGCCACATTCGACCCCGACTAATCTGAAGACAA
14647 GACTCCATAATATG
260 GACTCCATAATATG
14661 CATTTAACATGTGTTAATTTGAATCTTAATTTATTCTTCTTTTTTATGCGAAATCCTTGGGTATA
1 CATTTAACATGTGTTAATTTGAATCTTAATTTATTCTTCTTTTTTATGCGAAATCC---------
* * *
14726 TATATGGTAGCCACATTCGACCCCGACTAATCCGAAGACAAGACTCCATAATATGTTTAATAATA
57 T-T-CGGTAGCCACATTCGACCCCGACTAATCCGAAGACAAGACTCCATAATATGTTCAACAATA
14791 G-TTTTTTTTTTGTATGGACTTTGAAACTCATAGAAAATCATTTAACATCTGTTAATTTGAATCT
120 GTTTTTTTTTTTGTATGGACTTTGAAACTCATAGAAAATCATTTAACATCTGTTAATTTGAATCT
* *
14855 AAATTTATTCTTCTTTTTATGTGAAATCCTTCGGTATAAGGTAGCTACATTTGACCCCGACTAAT
185 AAATTTATTCTTCTTTTTATGTGAAATCCTTCGGTATAAGGTAGCCACATTCGACCCCGACTAAT
14920 CTGAAGACAAGACTCCATAATATG
250 CTGAAGACAAGACTCCATAATATG
14944 AGTTGGAATG
Statistics
Matches: 264, Mismatches: 8, Indels: 13
0.93 0.03 0.05
Matches are distributed among these distances:
274 56 0.21
283 75 0.28
284 76 0.29
285 57 0.22
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (273 bp):
CATTTAACATGTGTTAATTTGAATCTTAATTTATTCTTCTTTTTTATGCGAAATCCTTCGGTAGC
CACATTCGACCCCGACTAATCCGAAGACAAGACTCCATAATATGTTCAACAATAGTTTTTTTTTT
TGTATGGACTTTGAAACTCATAGAAAATCATTTAACATCTGTTAATTTGAATCTAAATTTATTCT
TCTTTTTATGTGAAATCCTTCGGTATAAGGTAGCCACATTCGACCCCGACTAATCTGAAGACAAG
ACTCCATAATATG
Found at i:20983 original size:37 final size:37
Alignment explanation
Indices: 20917--21221 Score: 270
Period size: 38 Copynumber: 7.8 Consensus size: 37
20907 TACCCCAATA
* *
20917 AATTAAGAGTCAAA-AAATAGTAATTAGTAAATCGAT
1 AATTAAGAGTCAAAGTAATAGTAATCAGTAAATCGAT
* * *
20953 AATTAAGAGCCAAAGTAATAGTAACCAGTAAAATTGAT
1 AATTAAGAGTCAAAGTAATAGTAATCAGT-AAATCGAT
* * **
20991 AAAATTAAGAGTCAAAATAATAGTAATCAGTGAATTAAGT
1 --AATTAAGAGTCAAAGTAATAGTAATCAGTAAATCGA-T
* *
21031 AATTAAGAGTCAAAGTAATAGTAATTAGTAAAATTGAT
1 AATTAAGAGTCAAAGTAATAGTAATCAGT-AAATCGAT
* **
21069 AATTAAGAGTAAAAAAAATAGTAATCAGTAAATCGAT
1 AATTAAGAGTCAAAGTAATAGTAATCAGTAAATCGAT
*
21106 AATTAAGAGTCAAAGTGATAGTAATCAGTAAATCAGTAAATCAGT
1 AATTAAGAGTCAAAGTAATAGTAATCAGTAAATC-G------A-T
* * * *
21151 AATTGAGAGTCAAAATAATAGTAATCAGCAAATTGAT
1 AATTAAGAGTCAAAGTAATAGTAATCAGTAAATCGAT
**
21188 AATTAAGAGAAAAAGTAGAATTAGTAATCAGTAA
1 AATTAAGAGTCAAAGT--AA-TAGTAATCAGTAA
21222 TTAAGAAATG
Statistics
Matches: 219, Mismatches: 33, Indels: 30
0.78 0.12 0.11
Matches are distributed among these distances:
36 13 0.06
37 61 0.28
38 62 0.28
39 12 0.05
40 39 0.18
44 2 0.01
45 30 0.14
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (37 bp):
AATTAAGAGTCAAAGTAATAGTAATCAGTAAATCGAT
Found at i:21104 original size:153 final size:155
Alignment explanation
Indices: 20917--21196 Score: 397
Period size: 153 Copynumber: 1.8 Consensus size: 155
20907 TACCCCAATA
* *
20917 AATTAAGAGTCAAAAAATAGTAATTAGTAAATCGATAATTAAGAGCCAAAGTAATAGTAACCAGT
1 AATTAAGAGTAAAAAAATAGTAATCAGTAAATCGATAATTAAGAGCCAAAGTAATAGTAACCAGT
** **
20982 AAA-A-TTGAT-A-AAATTAAGAGTCAAAATAATAGTAATCAGTGAATTAAGTAATTAAGAGTCA
66 AAACAGTAAATCAGAAATTAAGAGTCAAAATAATAGTAATCAGCAAATTAA-TAATTAAGAGTCA
21043 AAGTAATAGTAATTAGTAAAATTGAT
130 AAGTAATAGTAATTAGTAAAATTGAT
* * *
21069 AATTAAGAGTAAAAAAAATAGTAATCAGTAAATCGATAATTAAGAGTCAAAGTGATAGTAATCAG
1 AATTAAGAGT-AAAAAAATAGTAATCAGTAAATCGATAATTAAGAGCCAAAGTAATAGTAACCAG
* * *
21134 TAAATCAGTAAATCAGTAATTGAGAGTCAAAATAATAGTAATCAGCAAATTGATAATTAAGAG
65 TAAA-CAGTAAATCAGAAATTAAGAGTCAAAATAATAGTAATCAGCAAATTAATAATTAAGAG
21197 AAAAAGTAGA
Statistics
Matches: 110, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
152 10 0.09
153 53 0.48
155 1 0.01
156 3 0.03
157 11 0.10
158 32 0.29
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (155 bp):
AATTAAGAGTAAAAAAATAGTAATCAGTAAATCGATAATTAAGAGCCAAAGTAATAGTAACCAGT
AAACAGTAAATCAGAAATTAAGAGTCAAAATAATAGTAATCAGCAAATTAATAATTAAGAGTCAA
AGTAATAGTAATTAGTAAAATTGAT
Found at i:21140 original size:45 final size:45
Alignment explanation
Indices: 21091--21183 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
21081 AAAAAATAGT
* * *
21091 AATCAGTAAATC-GATAATTAAGAGTCAAAGTGATAGTAATCAGTA
1 AATCAGTAAATCAG-TAATTAAGAGTCAAAATAATAGTAATCAGCA
*
21136 AATCAGTAAATCAGTAATTGAGAGTCAAAATAATAGTAATCAGCA
1 AATCAGTAAATCAGTAATTAAGAGTCAAAATAATAGTAATCAGCA
21181 AAT
1 AAT
21184 TGATAATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 42 0.98
46 1 0.02
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (45 bp):
AATCAGTAAATCAGTAATTAAGAGTCAAAATAATAGTAATCAGCA
Found at i:21141 original size:8 final size:8
Alignment explanation
Indices: 21128--21152 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
21118 AAGTGATAGT
21128 AATCAGTA
1 AATCAGTA
21136 AATCAGTA
1 AATCAGTA
21144 AATCAGTA
1 AATCAGTA
21152 A
1 A
21153 TTGAGAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (8 bp):
AATCAGTA
Found at i:21171 original size:82 final size:85
Alignment explanation
Indices: 21068--21221 Score: 224
Period size: 82 Copynumber: 1.8 Consensus size: 85
21058 GTAAAATTGA
* **
21068 TAATTAAGAGTAAAAAAAATAGTAATCAGTAAATCGATAATTAAGAGTCAAAGT-G-A-TAGTAA
1 TAATTAAGAGTAAAAAAAATAGTAATCAGCAAATCGATAATTAAGAGAAAAAGTAGAATTAGTAA
21130 TCAGTAAATCAGTAAATCAG
66 TCAGTAAATCAGTAAATCAG
* * * *
21150 TAATTGAGAGTCAAAATAATAGTAATCAGCAAATTGATAATTAAGAGAAAAAGTAGAATTAGTAA
1 TAATTAAGAGTAAAAAAAATAGTAATCAGCAAATCGATAATTAAGAGAAAAAGTAGAATTAGTAA
21215 TCAGTAA
66 TCAGTAA
21222 TTAAGAAATG
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
82 47 0.76
83 1 0.02
84 1 0.02
85 13 0.21
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.26
Consensus pattern (85 bp):
TAATTAAGAGTAAAAAAAATAGTAATCAGCAAATCGATAATTAAGAGAAAAAGTAGAATTAGTAA
TCAGTAAATCAGTAAATCAG
Found at i:21236 original size:32 final size:31
Alignment explanation
Indices: 21187--21294 Score: 117
Period size: 32 Copynumber: 3.3 Consensus size: 31
21177 AGCAAATTGA
* *
21187 TAATTAAGAGAAAAAGTAGAATTAGTAATCAG
1 TAATTAAGA-AAGAAGTAAAATTAGTAATCAG
21219 TAATTAAGAAATGAAGTAAAATTAGTAATCAG
1 TAATTAAGAAA-GAAGTAAAATTAGTAATCAG
* ** *
21251 TAGTTAAGAAAGGAAGTAAAAAGGACTAATCAG
1 TAATTAAGAAA-GAAGT-AAAATTAGTAATCAG
21284 TAAATTAAGAA
1 T-AATTAAGAA
21295 GAGATTAATA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
31 2 0.03
32 42 0.65
33 13 0.20
34 8 0.12
ACGTcount: A:0.54, C:0.04, G:0.19, T:0.24
Consensus pattern (31 bp):
TAATTAAGAAAGAAGTAAAATTAGTAATCAG
Found at i:21240 original size:153 final size:150
Alignment explanation
Indices: 20928--21252 Score: 356
Period size: 153 Copynumber: 2.1 Consensus size: 150
20918 ATTAAGAGTC
* **
20928 AAAAAATAGTAATTAGTAAATCGATAATTAAGAGCCAAAGTAATAGTAACCAGTAAAATTGATAA
1 AAAAAATAGTAATCAGTAAATCGATAATTAAGAGCCAAAGTAATAGTAACCAGTAAAATAAATAA
**
20993 AATTAAGAGTCAAAATAATAGTAATCAGTGAATTAAGTAATTAAGAGTCAAAGTAATAGTAATTA
66 AATTAAGAGTCAAAATAATAGTAATCAGCAAATTAAGTAATTAAGAG-CAAAG-AATAGTAATTA
* *
21058 GTAAAATTGATAATTAAGAGTAA
129 GT-AAATAGATAATTAAGAATAA
* * *
21081 AAAAAATAGTAATCAGTAAATCGATAATTAAGAGTCAAAGTGATAGTAATCAGTAAATCAGTAAA
1 AAAAAATAGTAATCAGTAAATCGATAATTAAGAGCCAAAGTAATAGTAACCAGTAAA--A-TAAA
* * *
21146 TCAGTAATTGAGAGTCAAAATAATAGTAATCAGCAAATTGA-TAATTAAGAG-AAA-AAGTAG-A
63 T-A-AAATTAAGAGTCAAAATAATAGTAATCAGCAAATTAAGTAATTAAGAGCAAAGAA-TAGTA
21207 ATTAGT-AATCAG-TAATTAAGAAATGAA
125 ATTAGTAAAT-AGATAATTAAG-AAT-AA
* *
21234 GTAAAATTAGTAATCAGTA
1 -AAAAAATAGTAATCAGTA
21253 GTTAAGAAAG
Statistics
Matches: 147, Mismatches: 15, Indels: 19
0.81 0.08 0.10
Matches are distributed among these distances:
151 11 0.07
152 3 0.02
153 64 0.44
154 19 0.13
155 4 0.03
156 3 0.02
157 11 0.07
158 32 0.22
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.27
Consensus pattern (150 bp):
AAAAAATAGTAATCAGTAAATCGATAATTAAGAGCCAAAGTAATAGTAACCAGTAAAATAAATAA
AATTAAGAGTCAAAATAATAGTAATCAGCAAATTAAGTAATTAAGAGCAAAGAATAGTAATTAGT
AAATAGATAATTAAGAATAA
Found at i:21708 original size:22 final size:22
Alignment explanation
Indices: 21681--21770 Score: 130
Period size: 22 Copynumber: 4.2 Consensus size: 22
21671 AGCAGAGTAA
*
21681 AGTAAAAGTAAAAGAAGCAATC
1 AGTAAAAGTAAAAGAAGTAATC
* *
21703 AGTAAAAG--GAAGAAGTTATC
1 AGTAAAAGTAAAAGAAGTAATC
21723 AGTAAAAGTAAAAGAAGTAATC
1 AGTAAAAGTAAAAGAAGTAATC
*
21745 AGTAAAAGTAAAAGAAATAATC
1 AGTAAAAGTAAAAGAAGTAATC
21767 AGTA
1 AGTA
21771 GAAAAGAGTA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
20 17 0.28
22 43 0.72
ACGTcount: A:0.58, C:0.06, G:0.19, T:0.18
Consensus pattern (22 bp):
AGTAAAAGTAAAAGAAGTAATC
Found at i:21717 original size:20 final size:21
Alignment explanation
Indices: 21681--21792 Score: 110
Period size: 22 Copynumber: 5.5 Consensus size: 21
21671 AGCAGAGTAA
*
21681 AGTAAAAGTAAAAGAAGCAATC
1 AGTAAAAG-AAAAGAAGTAATC
* *
21703 AGTAAAAG-GAAGAAGTTATC
1 AGTAAAAGAAAAGAAGTAATC
21723 AGTAAAAGTAAAAGAAGTAATC
1 AGTAAAAG-AAAAGAAGTAATC
*
21745 AGTAAAAGTAAAAGAAATAATC
1 AGTAAAAG-AAAAGAAGTAATC
*
21767 AGT---AGAAAAG-AGTAA-A
1 AGTAAAAGAAAAGAAGTAATC
21783 AGTAAAAGAA
1 AGTAAAAGAA
21793 GTAATTAAGA
Statistics
Matches: 77, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
16 3 0.04
17 4 0.05
18 5 0.06
19 6 0.08
20 17 0.22
22 42 0.55
ACGTcount: A:0.60, C:0.04, G:0.20, T:0.16
Consensus pattern (21 bp):
AGTAAAAGAAAAGAAGTAATC
Found at i:21802 original size:25 final size:25
Alignment explanation
Indices: 21723--21821 Score: 83
Period size: 25 Copynumber: 3.8 Consensus size: 25
21713 AGAAGTTATC
*
21723 AGTAAAAGTAAAAGAAGTAATCAGTAAA
1 AGTAAAAGTAAAAGAAGTAAT---TAAG
* ** *
21751 AGTAAAAGAAATAATCAGTAGA-AAAG
1 AGTAAAAGTAA-AAGAAGTA-ATTAAG
21777 AGTAAAAGTAAAAGAAGTAATTAAG
1 AGTAAAAGTAAAAGAAGTAATTAAG
* *
21802 ATTAAAAGTAAGAGAAGTAA
1 AGTAAAAGTAAAAGAAGTAA
21822 GAGAAGTAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
24 1 0.02
25 27 0.47
26 12 0.21
28 10 0.18
29 6 0.11
30 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.19, T:0.18
Consensus pattern (25 bp):
AGTAAAAGTAAAAGAAGTAATTAAG
Found at i:23130 original size:58 final size:59
Alignment explanation
Indices: 23054--23165 Score: 181
Period size: 58 Copynumber: 1.9 Consensus size: 59
23044 CCACTTTCAT
* *
23054 GAGAGAAAGTATTCGGGTTAAATTTTCTTAAACTTTCTTACCCT-ACTTTCTCATTTTG
1 GAGAAAAAGTATTCGGGTTAAATTTTCTTAAAATTTCTTACCCTAACTTTCTCATTTTG
*
23112 GAGAAAAAGTATTTGGGTTAAATTTTCTTAAAATTTCTTACCCTAAACTTTCTC
1 GAGAAAAAGTATTCGGGTTAAATTTTCTTAAAATTTCTTACCCT-AACTTTCTC
23166 TTAAAAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
58 41 0.84
60 8 0.16
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.42
Consensus pattern (59 bp):
GAGAAAAAGTATTCGGGTTAAATTTTCTTAAAATTTCTTACCCTAACTTTCTCATTTTG
Found at i:29748 original size:1 final size:1
Alignment explanation
Indices: 29742--29772 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
29732 CTGCCAAGAG
29742 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29773 GAATTAGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:30294 original size:31 final size:31
Alignment explanation
Indices: 30251--30329 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
30241 TTTTTCTGTT
*
30251 TTTATACTCAAATTGGTCAAATTTTGAAAGG
1 TTTAAACTCAAATTGGTCAAATTTTGAAAGG
* * *
30282 TTTAAATTCAAATTGAG-CAACTTTTGAATGG
1 TTTAAACTCAAATTG-GTCAAATTTTGAAAGG
*
30313 TTTAGACTCAAATTGGT
1 TTTAAACTCAAATTGGT
30330 GGCTAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 1 0.03
31 38 0.95
32 1 0.03
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTAAACTCAAATTGGTCAAATTTTGAAAGG
Found at i:32014 original size:2 final size:2
Alignment explanation
Indices: 32007--32034 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31997 CCTTATCGCA
32007 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32035 CAAATTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.