Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006211.1 Corchorus capsularis cultivar CVL-1 contig06230, 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: 26045
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:8 original size:1 final size:1
Alignment explanation
Indices: 3--48 Score: 92
Period size: 1 Copynumber: 46.0 Consensus size: 1
1 AA
3 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
49 CCACAAGGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:6737 original size:2 final size:2
Alignment explanation
Indices: 6730--6758 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6720 TTCTAAACAT
6730 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
6759 GACATAGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:14972 original size:1 final size:1
Alignment explanation
Indices: 14966--14991 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
14956 AGAGCTCCAG
14966 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
14992 CGAGAGAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16952 original size:27 final size:27
Alignment explanation
Indices: 16882--16957 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
16872 AAGTGGACTT
* * *
16882 AAAATGACCAAAATACCCCTAAATGCA
1 AAAATGACCAAAGTGCCCCTGAATGCA
*
16909 AAAATGA-CAAAGATGCCCCTGAATGTA
1 AAAATGACCAAAG-TGCCCCTGAATGCA
16936 AAAATGACCAAAGTGCCCCTGA
1 AAAATGACCAAAGTGCCCCTGA
16958 GTGACCCTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 4 0.09
27 34 0.79
28 5 0.12
ACGTcount: A:0.46, C:0.24, G:0.14, T:0.16
Consensus pattern (27 bp):
AAAATGACCAAAGTGCCCCTGAATGCA
Found at i:18254 original size:41 final size:41
Alignment explanation
Indices: 18208--18342 Score: 180
Period size: 41 Copynumber: 3.3 Consensus size: 41
18198 TAATTAAGAA
* *
18208 AATTAAGAAAAGCAAACACAGTTAAGGTCTTAATTCAGGGT
1 AATTAAGAAAAGTAAACACAGTTAAGGTCTTAATTCAAGGT
** *
18249 AATTAAGAAAAGTAAACACAGTTGGGGTCTTAATTCATGGT
1 AATTAAGAAAAGTAAACACAGTTAAGGTCTTAATTCAAGGT
* * * *
18290 AATTATGAAAAGTAAACACAGTCAAGGACTTAATTCAAGGA
1 AATTAAGAAAAGTAAACACAGTTAAGGTCTTAATTCAAGGT
*
18331 AATTAAGTAAAG
1 AATTAAGAAAAG
18343 GCAGTCAAAG
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 81 1.00
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.25
Consensus pattern (41 bp):
AATTAAGAAAAGTAAACACAGTTAAGGTCTTAATTCAAGGT
Found at i:18433 original size:37 final size:37
Alignment explanation
Indices: 18313--19025 Score: 859
Period size: 37 Copynumber: 19.6 Consensus size: 37
18303 AAACACAGTC
* * *
18313 AAGGACTTAATTCAAGGAAATTAAGTAAAGGCAGTCA
1 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTA
* * *
18350 AA-GACTTAATTCAAGGTAATTAAGTAAACA-TAG-TA
1 AAGGACTTAATTCAGGGAAATTAAGTAAA-AGCAGTTA
* * *
18385 AAGAACTTAATTCAGGGTAATTAAGTAAAAACAGTTA
1 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTA
* *
18422 AAGGGCTTAATTCAGGGAAATTAAGTAAAAGTAGTTA
1 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTA
*
18459 AAGGACTTAATTCAGGGAGATTAAGTAAAAGCAGTTA
1 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTA
* *
18496 AATGACTTAATTCAGGGAAATTAAGTAAAAACAGTTA
1 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTA
18533 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAG-TA
1 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTA
*
18569 AAGGACTTAA-TCTAGGGTAATTAAGTAAAAGCAG-TA
1 AAGGACTTAATTC-AGGGAAATTAAGTAAAAGCAGTTA
* **
18605 AAGGGCTTAATTCAGGGAAATTAAACAAAAGCAGTTA
1 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTA
*
18642 AAGGACTTAATTCAGGGAAATTAAGTAAAAGTAGTTA
1 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTA
* *
18679 AAGAACTTAATTCAGGGTAATTAAGTAAAAGCAG-TA
1 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTA
* *
18715 AAGGGCTTAGTTCAGGGAAA-T---T--AAGCAG-TA
1 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTA
* *
18745 AAAGACTTAATTCAGGGTAATTAAGTAAAAGCAGTTA
1 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTA
* *
18782 AAGGGCTTAATTCAGGGAAATTAAGTAGAAGCAGTTA
1 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTA
** * *
18819 AAGGTTTTAATTCAAGGAAAATTAAGTAAAAGCAGTAA
1 AAGGACTTAATTC-AGGGAAATTAAGTAAAAGCAGTTA
* * * *
18857 AATGA-TCTAATCCAGGGTAATTAAGTAAAAACAGTTA
1 AAGGACT-TAATTCAGGGAAATTAAGTAAAAGCAGTTA
* * *
18894 AAGGACTTAATTCATGGTAATTAAGTAAAAGTAG-TA
1 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTA
*
18930 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAG-TC
1 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTA
* * * *
18966 AAGGACTTAATTCAGGGTAATTAAGTGAAAGTAG-TC
1 AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTA
*
19002 AAGGACTTAATTTCAAGGAAATTA
1 AAGGACTTAA-TTCAGGGAAATTA
19026 GCTAAAGATA
Statistics
Matches: 588, Mismatches: 70, Indels: 36
0.85 0.10 0.05
Matches are distributed among these distances:
30 24 0.04
31 1 0.00
32 1 0.00
34 1 0.00
35 7 0.01
36 215 0.37
37 309 0.53
38 30 0.05
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.26
Consensus pattern (37 bp):
AAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTA
Found at i:18695 original size:220 final size:217
Alignment explanation
Indices: 18299--19013 Score: 901
Period size: 220 Copynumber: 3.3 Consensus size: 217
18289 TAATTATGAA
* * * *
18299 AAGTAAACACAGTCAAGGACTTAATTCAAGGAAATTAAGTAAAGGCAGTCAAA-GACTTAATTCA
1 AAGTAAAAACAGTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGT-AAAGGACTTAATTCA
* * * * * *
18363 AGGTAATTAAGTAAACA-TAGTAAAGAACTTAATTCAGGGTAATTAAGTAAAAACAGTTAAAGGG
65 GGGTAATTAAGTAAA-AGCAGTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTAAAGGA
18427 CTTAATTCAGGGAAATTAAGTAAAAGTAGTTAAAGGACTTAATTCAGGGAGATTAAGTAAAAGCA
129 CTTAATTCAGGGAAATTAAGTAAAAGTAGTTAAAGGACTTAATTCAGGGA-ATTAAGTAAAAGCA
*
18492 GTTAAATGACTTAATTCAGGGAAATT
193 G-TAAAGGACTTAATTCAGGGAAATT
18518 AAGTAAAAACAGTTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTAAAGGACTTAA-TCT
1 AAGTAAAAACAG-TAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTAAAGGACTTAATTC-
* **
18582 AGGGTAATTAAGTAAAAGCAGTAAAGGGCTTAATTCAGGGAAATTAAACAAAAGCAGTTAAAGGA
64 AGGGTAATTAAGTAAAAGCAGTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTAAAGGA
*
18647 CTTAATTCAGGGAAATTAAGTAAAAGTAGTTAAAGAACTTAATTCAGGGTAATTAAGTAAAAGCA
129 CTTAATTCAGGGAAATTAAGTAAAAGTAGTTAAAGGACTTAATTCAGGG-AATTAAGTAAAAGCA
* *
18712 GTAAAGGGCTTAGTTCAGGGAAATT
193 GTAAAGGACTTAATTCAGGGAAATT
* * *
18737 AAG------CAGTAAAAGACTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAAGGGCTTAATTCA
1 AAGTAAAAACAGTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAG-TAAAGGACTTAATTCA
* * ** * * *
18796 GGGAAATTAAGTAGAAGCAGTTAAAGGTTTTAATTCAAGGAAAATTAAGTAAAAGCAGTAAAATG
65 GGGTAATTAAGTAAAAGCAG-TAAAGGACTTAATTC-AGGGAAATTAAGTAAAAGCAGTTAAAGG
* * ** *
18861 A-TCTAATCCAGGGTAATTAAGTAAAAACAGTTAAAGGACTTAATTCATGGTAATTAAGTAAAAG
128 ACT-TAATTCAGGGAAATTAAGTAAAAGTAGTTAAAGGACTTAATTCA-GGGAATTAAGTAAAAG
*
18925 TAGTAAAGGACTTAATTCAGGGAAATT
191 CAGTAAAGGACTTAATTCAGGGAAATT
* * * * * *
18952 AAGTAAAAGCAGTCAAGGACTTAATTCAGGGTAATTAAGTGAAAGTAGTCAAGGACTTAATT
1 AAGTAAAAACAGTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTAAAGGACTTAATT
19014 TCAAGGAAAT
Statistics
Matches: 435, Mismatches: 44, Indels: 33
0.85 0.09 0.06
Matches are distributed among these distances:
212 34 0.08
213 33 0.08
214 16 0.04
215 103 0.24
216 2 0.00
219 41 0.09
220 170 0.39
221 36 0.08
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (217 bp):
AAGTAAAAACAGTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTAAAGGACTTAATTCAG
GGTAATTAAGTAAAAGCAGTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTTAAAGGACT
TAATTCAGGGAAATTAAGTAAAAGTAGTTAAAGGACTTAATTCAGGGAATTAAGTAAAAGCAGTA
AAGGACTTAATTCAGGGAAATT
Found at i:18743 original size:30 final size:30
Alignment explanation
Indices: 18707--18806 Score: 101
Period size: 30 Copynumber: 3.1 Consensus size: 30
18697 AATTAAGTAA
*
18707 AAGCAGTAAAGGGCTTAGTTCAGGGAAATT
1 AAGCAGTAAAGGGCTTAATTCAGGGAAATT
* * *
18737 AAGCAGTAAAAGACTTAATTCAGGGTAATTAAGTAA
1 AAGCAGTAAAGGGCTTAATTCAGGG--A--AA-T-T
18773 AAGCAGTTAAAGGGCTTAATTCAGGGAAATT
1 AAGCAG-TAAAGGGCTTAATTCAGGGAAATT
18804 AAG
1 AAG
18807 TAGAAGCAGT
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
30 22 0.39
31 3 0.05
32 2 0.04
33 2 0.04
34 2 0.04
35 2 0.04
36 6 0.11
37 17 0.30
ACGTcount: A:0.42, C:0.09, G:0.25, T:0.24
Consensus pattern (30 bp):
AAGCAGTAAAGGGCTTAATTCAGGGAAATT
Found at i:19047 original size:37 final size:38
Alignment explanation
Indices: 19005--19282 Score: 304
Period size: 41 Copynumber: 7.3 Consensus size: 38
18995 AGTAGTCAAG
* *
19005 GACTTAATTTC-AAGGAAATTAGCTAAAGATAAGCACA
1 GACTTAATTTCAAAGGAAATTAGGTAAAGACAAGCACA
* *
19042 TACTTAATTTCAAGGAAGGAAATTAGGTAAAGATAAGCACA
1 GACTTAATTTC-A--AAGGAAATTAGGTAAAGACAAGCACA
*
19083 GACTTAATTTC-AAGGAAATTAGGTAAAGATAAGCACA
1 GACTTAATTTCAAAGGAAATTAGGTAAAGACAAGCACA
*
19120 GACTTAATTTCAAGGAAGGAAATTAGGT-AA-ACAAGCATA
1 GACTTAATTTC-A--AAGGAAATTAGGTAAAGACAAGCACA
19159 GACTTAATTTC-AAGGAAATTAGGTAAAGACAAGCACA
1 GACTTAATTTCAAAGGAAATTAGGTAAAGACAAGCACA
19196 GACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACA
1 GACTTAATTTC-A--AAGGAAATTAGGTAAAGACAAGCACA
* * * * * *
19237 AACTTAA-TTC-AGGGTAATTAAGTAAA-TC-AGCAAA
1 GACTTAATTTCAAAGGAAATTAGGTAAAGACAAGCACA
19271 GACTTAATTTCA
1 GACTTAATTTCA
19283 CAAGAATTAA
Statistics
Matches: 212, Mismatches: 13, Indels: 33
0.82 0.05 0.13
Matches are distributed among these distances:
34 11 0.05
35 17 0.08
36 15 0.07
37 66 0.31
39 18 0.08
40 5 0.02
41 80 0.38
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (38 bp):
GACTTAATTTCAAAGGAAATTAGGTAAAGACAAGCACA
Found at i:19073 original size:41 final size:41
Alignment explanation
Indices: 19016--19245 Score: 327
Period size: 41 Copynumber: 5.9 Consensus size: 41
19006 ACTTAATTTC
* * *
19016 AAGGAAATTAGCTAAAGATAAGCACATACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
*
19057 AAGGAAATTAGGTAAAGATAAGCACAGACTTAATTTC----
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
*
19094 AAGGAAATTAGGTAAAGATAAGCACAGACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
*
19135 AAGGAAATTAGGT-AA-ACAAGCATAGACTTAATTTC----
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
19170 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
*
19211 AAGGAAATTAGGTAAAGACAAGCACAAACTTAATT
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATT
19246 CAGGGTAATT
Statistics
Matches: 173, Mismatches: 6, Indels: 20
0.87 0.03 0.10
Matches are distributed among these distances:
35 13 0.08
36 2 0.01
37 56 0.32
39 18 0.10
40 2 0.01
41 82 0.47
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (41 bp):
AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
Found at i:19180 original size:154 final size:151
Alignment explanation
Indices: 19005--19282 Score: 439
Period size: 154 Copynumber: 1.8 Consensus size: 151
18995 AGTAGTCAAG
* *
19005 GACTTAATTTCAAGGAAATTAGCTAAAGATAAGCACATACTTAATTTCAAGGAAGGAAATTAGGT
1 GACTTAATTTCAAGGAAATTAGCTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGT
* * * *
19070 AAAGATAAGCACAGACTTAATTTCAAGGAAATTAGGTAAAGATAAGCACAGACTTAATTTCAAGG
66 AAAGACAAGCACAAACTTAA-TTCAAGGAAATTAAGT-AA-ATAAGCAAAGACTTAATTTCAAGG
19135 AAGGAAATTAGGTAAACAAGCATA
128 AAGGAAATTAGGTAAACAAGCATA
*
19159 GACTTAATTTCAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGT
1 GACTTAATTTCAAGGAAATTAGCTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGT
* * *
19224 AAAGACAAGCACAAACTTAATTCAGGGTAATTAAGTAAATCAGCAAAGACTTAATTTCA
66 AAAGACAAGCACAAACTTAATTCAAGGAAATTAAGTAAATAAGCAAAGACTTAATTTCA
19283 CAAGAATTAA
Statistics
Matches: 114, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
151 19 0.17
152 2 0.02
153 13 0.11
154 80 0.70
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (151 bp):
GACTTAATTTCAAGGAAATTAGCTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGT
AAAGACAAGCACAAACTTAATTCAAGGAAATTAAGTAAATAAGCAAAGACTTAATTTCAAGGAAG
GAAATTAGGTAAACAAGCATA
Found at i:19328 original size:36 final size:35
Alignment explanation
Indices: 19252--19343 Score: 107
Period size: 36 Copynumber: 2.5 Consensus size: 35
19242 AATTCAGGGT
* *
19252 AATTAAGTAAATCAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAATCAGCAAAGACTTAAGTCCACAAG
19287 AATTAAGTGAAATCAGCAAAGACTT-AGTCCA-AAG
1 AATTAAGT-AAATCAGCAAAGACTTAAGTCCACAAG
19321 ATGATTAAGTAAAATCAGACAAA
1 A--ATTAAGT-AAATCAG-CAAA
19344 AACCTAACCC
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
34 4 0.08
35 12 0.24
36 30 0.60
37 4 0.08
ACGTcount: A:0.50, C:0.13, G:0.14, T:0.23
Consensus pattern (35 bp):
AATTAAGTAAATCAGCAAAGACTTAAGTCCACAAG
Found at i:19403 original size:37 final size:37
Alignment explanation
Indices: 19373--19532 Score: 266
Period size: 37 Copynumber: 4.3 Consensus size: 37
19363 AAGTAGGGAA
19373 AAGGACTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
1 AAGGACTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
*
19410 AAGGATTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
1 AAGGACTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
* * *
19447 AATGACCTAATTTCAAGGAAGGAGATTAAGTAGAGTC
1 AAGGACTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
* *
19484 AAGGACTTAATTTCAGGGAAGGAAATTAAATAGAGTC
1 AAGGACTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
19521 AAGGACTTAATT
1 AAGGACTTAATT
19533 CAGGGTAGTT
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 113 1.00
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (37 bp):
AAGGACTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
Found at i:19598 original size:37 final size:37
Alignment explanation
Indices: 19555--19651 Score: 144
Period size: 37 Copynumber: 2.6 Consensus size: 37
19545 GTCAAGTTAG
*
19555 GGACTTAATTCAGGGTAATTAAGTAGCGTCAAT-AAA
1 GGACTTAATTCAGGGTAATTAAGTAGCGCCAATAAAA
**
19591 GGAACTTAATTCAGGGCCATTAAGTAGCGCCAATAAAA
1 GG-ACTTAATTCAGGGTAATTAAGTAGCGCCAATAAAA
19629 GG-CTTAATTCAGGGTAATTAAGT
1 GGACTTAATTCAGGGTAATTAAGT
19652 GGAATAAATA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
36 21 0.39
37 28 0.52
38 5 0.09
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (37 bp):
GGACTTAATTCAGGGTAATTAAGTAGCGCCAATAAAA
Found at i:19670 original size:36 final size:36
Alignment explanation
Indices: 19558--19672 Score: 133
Period size: 36 Copynumber: 3.2 Consensus size: 36
19548 AAGTTAGGGA
*
19558 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAGGAA
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAA-GAG
** *
19595 CTTAATTCAGGGCCATTAAGTAGCGCCAATAAA-AGG
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAGA-G
* ** *
19631 CTTAATTCAGGGTAATTAAGTGGAATAAATAAAGAG
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAGAG
19667 CTTAAT
1 CTTAAT
19673 CTAAAAAGAG
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
35 1 0.02
36 33 0.51
37 31 0.48
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (36 bp):
CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAGAG
Found at i:21871 original size:6 final size:6
Alignment explanation
Indices: 21862--21900 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
21852 CACTAAAACG
*
21862 AAAAAT AAAAAT AAAAAT -AAAAC AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
21901 TAACGAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.13
Consensus pattern (6 bp):
AAAAAT
Found at i:21883 original size:11 final size:11
Alignment explanation
Indices: 21863--21903 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
21853 ACTAAAACGA
21863 AAAATAAAAAT
1 AAAATAAAAAT
21874 AAAAATAAAACA-
1 -AAAATAAAA-AT
21886 AAAATAAAAAT
1 AAAATAAAAAT
21897 AAAATAA
1 AAAATAA
21904 CGAAAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 1 0.04
11 16 0.59
12 9 0.33
13 1 0.04
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:21888 original size:17 final size:17
Alignment explanation
Indices: 21863--21900 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
21853 ACTAAAACGA
*
21863 AAAATAAAAATAAAAAT
1 AAAACAAAAATAAAAAT
21880 AAAACAAAAATAAAAAT
1 AAAACAAAAATAAAAAT
21897 AAAA
1 AAAA
21901 TAACGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (17 bp):
AAAACAAAAATAAAAAT
Found at i:21921 original size:23 final size:22
Alignment explanation
Indices: 21858--21921 Score: 53
Period size: 23 Copynumber: 2.9 Consensus size: 22
21848 TTAGCACTAA
*
21858 AACG-AAAAATAAAAATAAAAAT
1 AACGAAAAAAAAAAAAT-AAAAT
21880 AA--AACAAAAATAAAAATAAAAT
1 AACGAA-AAAAA-AAAAATAAAAT
*
21902 AACGAAAAAGAAAAAGATAA
1 AACGAAAAA-AAAAAAATAA
21922 GGGTAAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
21 1 0.03
22 13 0.38
23 16 0.47
24 4 0.12
ACGTcount: A:0.78, C:0.05, G:0.06, T:0.11
Consensus pattern (22 bp):
AACGAAAAAAAAAAAATAAAAT
Found at i:22938 original size:11 final size:10
Alignment explanation
Indices: 22914--22939 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
22904 AAAATCACCA
22914 TTTTTGTACC
1 TTTTTGTACC
22924 TTTTTGTACC
1 TTTTTGTACC
22934 TTTTTG
1 TTTTTG
22940 GATGATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.15, G:0.12, T:0.65
Consensus pattern (10 bp):
TTTTTGTACC
Done.