Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006762.1 Corchorus capsularis cultivar CVL-1 contig06783, 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: 49841
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:386 original size:30 final size:30
Alignment explanation
Indices: 352--412 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
342 ACAAGTTGTG
* *
352 CCATTTGATTCTTAAGGTTTGTGAGTTCTC
1 CCATTTGATTCTTAAGGCTTGTGAGCTCTC
* *
382 CCATTTGATTCTTGATGCTTGTGAGCTCTC
1 CCATTTGATTCTTAAGGCTTGTGAGCTCTC
412 C
1 C
413 ATCATATCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (30 bp):
CCATTTGATTCTTAAGGCTTGTGAGCTCTC
Found at i:1057 original size:36 final size:36
Alignment explanation
Indices: 1000--1194 Score: 141
Period size: 36 Copynumber: 5.4 Consensus size: 36
990 TAAACACAGT
* *
1000 CAAAGTCTTAATT-AAAGGTAATTAAG-AAAAGTAAAG
1 CAAAGACTTAATTCATA-GTAATTAAGTAAAAG-AAAG
* *
1036 CACAGACTTAATTCATAGTAATTAAGTAAAA-ACAG
1 CAAAGACTTAATTCATAGTAATTAAGTAAAAGAAAG
* * * *
1071 TAAAAGGACTTAATTCA-GGAAATTAAGTAAAAG-CAG
1 -CAAA-GACTTAATTCATAGTAATTAAGTAAAAGAAAG
* * * *
1107 TTAAAGGACTTAATTCATGGTAATTAAGTAAAAGCAAT
1 -CAAA-GACTTAATTCATAGTAATTAAGTAAAAGAAAG
* *
1145 TAAAGGACTTAATTCATAGTAATTAAGT-AATGAAAAG
1 CAAA-GACTTAATTCATAGTAATTAAGTAAAAG-AAAG
*
1182 CACAGACTTAATT
1 CAAAGACTTAATT
1195 TCAAGGAAGG
Statistics
Matches: 133, Mismatches: 18, Indels: 16
0.80 0.11 0.10
Matches are distributed among these distances:
35 3 0.02
36 66 0.50
37 63 0.47
38 1 0.01
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.27
Consensus pattern (36 bp):
CAAAGACTTAATTCATAGTAATTAAGTAAAAGAAAG
Found at i:1085 original size:37 final size:37
Alignment explanation
Indices: 1040--1174 Score: 209
Period size: 37 Copynumber: 3.7 Consensus size: 37
1030 GTAAAGCACA
* *
1040 GACTTAATTCATAGTAATTAAGTAAAAACAGTAAAAG
1 GACTTAATTCATAGTAATTAAGTAAAAGCAGTTAAAG
* *
1077 GACTTAATTCA-GGAAATTAAGTAAAAGCAGTTAAAG
1 GACTTAATTCATAGTAATTAAGTAAAAGCAGTTAAAG
* *
1113 GACTTAATTCATGGTAATTAAGTAAAAGCAATTAAAG
1 GACTTAATTCATAGTAATTAAGTAAAAGCAGTTAAAG
1150 GACTTAATTCATAGTAATTAAGTAA
1 GACTTAATTCATAGTAATTAAGTAA
1175 TGAAAAGCAC
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
36 32 0.36
37 58 0.64
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (37 bp):
GACTTAATTCATAGTAATTAAGTAAAAGCAGTTAAAG
Found at i:1190 original size:73 final size:71
Alignment explanation
Indices: 1006--1194 Score: 200
Period size: 73 Copynumber: 2.6 Consensus size: 71
996 CAGTCAAAGT
* * * *
1006 CTTAATTAAAGGTAATTAAGAAAAGTAAAGCACAGACTTAATTCATAGTAATTAAGTAAAAACAG
1 CTTAATTCAA-GTAATTAAG-TAAGAAAAGCACAGACTTAATTCATAGTAATTAAGTAAAAACAA
1071 TAAAAGGA
64 TAAAAGGA
* * * * * * *
1079 CTTAATTCAGGAAATTAAGTAA-AAGCAGTTAAAGGACTTAATTCATGGTAATTAAGTAAAAGCA
1 CTTAATTCAAGTAATTAAGTAAGAA-AAG-CACA-GACTTAATTCATAGTAATTAAGTAAAAACA
*
1143 ATTAAAGGA
63 ATAAAAGGA
1152 CTTAATTCATAGTAATTAAGTAATGAAAAGCACAGACTTAATT
1 CTTAATTCA-AGTAATTAAGTAA-GAAAAGCACAGACTTAATT
1195 TCAAGGAAGG
Statistics
Matches: 93, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
70 1 0.01
71 4 0.04
72 10 0.11
73 61 0.66
74 13 0.14
75 2 0.02
76 2 0.02
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.28
Consensus pattern (71 bp):
CTTAATTCAAGTAATTAAGTAAGAAAAGCACAGACTTAATTCATAGTAATTAAGTAAAAACAATA
AAAGGA
Found at i:1210 original size:41 final size:41
Alignment explanation
Indices: 1178--1402 Score: 346
Period size: 41 Copynumber: 5.4 Consensus size: 41
1168 TAAGTAATGA
1178 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGT
1 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGT
1219 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGT
1 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGT
*
1260 AAAGCACAGATTTAATTTCAAGGAAGGAAATTAGGTAGAGT
1 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGT
* *
1301 AAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGT
1 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGT
* *
1342 AAAGCAATATTGACTTAATTTCAAGGAAGGAAATTAGGTAAAG-
1 AAAGC-ACA--GACTTAATTTCAAGGAAGGAAATTAGGTAGAGT
1385 ACAAGCACATG-CTTAATT
1 A-AAGCACA-GACTTAATT
1403 CAGGGTAATT
Statistics
Matches: 173, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
41 131 0.76
42 4 0.02
43 3 0.02
44 35 0.20
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.24
Consensus pattern (41 bp):
AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGT
Found at i:1485 original size:36 final size:36
Alignment explanation
Indices: 1409--1500 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 36
1399 AATTCAGGGT
*
1409 AATTAAGT-AAATCAACAAAGACTAAATTTCACAAG
1 AATTAAGTAAAATCAACAAAGACTAAATTCCACAAG
* *
1444 AATTAAGTAAAATCATCAAAGACTTAA-TCCA-AAG
1 AATTAAGTAAAATCAACAAAGACTAAATTCCACAAG
*
1478 ATGATTAAGTAAGATCAGACAAA
1 A--ATTAAGTAAAATCA-ACAAA
1501 AACTTAACCC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
34 4 0.08
35 11 0.23
36 29 0.60
37 4 0.08
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.23
Consensus pattern (36 bp):
AATTAAGTAAAATCAACAAAGACTAAATTCCACAAG
Found at i:1673 original size:37 final size:37
Alignment explanation
Indices: 1530--1689 Score: 239
Period size: 37 Copynumber: 4.3 Consensus size: 37
1520 AAGTAAAGAA
* * * **
1530 AAGGGCTTACTTTCAAGGAAGGAAATTAAGTAAAGAA
1 AAGGACTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
*
1567 AAGGACTTAATTTCAAGGAAGGAAATTAAGTAGAGCC
1 AAGGACTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
*
1604 AAGGACTTAATTTCAAGGAAGGAAATTAAGTAGGGTC
1 AAGGACTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
*
1641 AAGGACTTAATTTCAAGGAAGGAAATTAAGTAGAGTT
1 AAGGACTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
*
1678 AGGGACTTAATT
1 AAGGACTTAATT
1690 CGGGGTAATT
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:0.25, T:0.24
Consensus pattern (37 bp):
AAGGACTTAATTTCAAGGAAGGAAATTAAGTAGAGTC
Found at i:1717 original size:32 final size:32
Alignment explanation
Indices: 1664--1850 Score: 133
Period size: 36 Copynumber: 5.5 Consensus size: 32
1654 CAAGGAAGGA
* * *
1664 AATTAAGTAGAGTTAGGGACTTAATTCGGGGT
1 AATTAAGTAGAGTCAGAGACTTAATTCAGGGT
*
1696 AATTAAGTCA-AGTCAGAGACTTAATTTAGGGT
1 AATTAAGT-AGAGTCAGAGACTTAATTCAGGGT
* * *
1728 AATTAAGTAGCGTCAATAAAAGGCTTAATTCAGGGT
1 AATTAAGTAGAGTC----AGAGACTTAATTCAGGGT
* * *
1764 AATTAAGTGGAGTCAATAAGAGTCTTAATTCAAGGT
1 AATTAAGTAGAGTC----AGAGACTTAATTCAGGGT
* *
1800 AATTAAGTGGAGTCAATAAAGAACTTAATTCAGGGT
1 AATTAAGTAGAGTC---AGAG-ACTTAATTCAGGGT
*
1836 AATTAAGTGGAGTCA
1 AATTAAGTAGAGTCA
1851 ATAAAGAACT
Statistics
Matches: 130, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
31 1 0.01
32 37 0.28
33 2 0.02
35 4 0.03
36 86 0.66
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (32 bp):
AATTAAGTAGAGTCAGAGACTTAATTCAGGGT
Found at i:1763 original size:36 final size:36
Alignment explanation
Indices: 1712--1864 Score: 211
Period size: 36 Copynumber: 4.2 Consensus size: 36
1702 GTCAAGTCAG
* * *
1712 AGACTTAATTTAGGGTAATTAAGTAGCGTCAATAAA
1 AGACTTAATTCAGGGTAATTAAGTGGAGTCAATAAA
* *
1748 AGGCTTAATTCAGGGTAATTAAGTGGAGTCAATAAG
1 AGACTTAATTCAGGGTAATTAAGTGGAGTCAATAAA
* *
1784 AGTCTTAATTCAAGGTAATTAAGTGGAGTCAAT-AA
1 AGACTTAATTCAGGGTAATTAAGTGGAGTCAATAAA
1819 AGAACTTAATTCAGGGTAATTAAGTGGAGTCAAT-AA
1 AG-ACTTAATTCAGGGTAATTAAGTGGAGTCAATAAA
1855 AGAACTTAAT
1 AG-ACTTAAT
1865 CTAAAAAGAT
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
35 3 0.03
36 103 0.97
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (36 bp):
AGACTTAATTCAGGGTAATTAAGTGGAGTCAATAAA
Found at i:1817 original size:72 final size:72
Alignment explanation
Indices: 1682--1864 Score: 225
Period size: 72 Copynumber: 2.6 Consensus size: 72
1672 AGAGTTAGGG
* ** * * *
1682 ACTTAATTCGGGGTAATTAAGTCAAGTC----AGAGACTTAATTTAGGGTAATTAAGTAGCGTCA
1 ACTTAATTCAGGGTAATTAAGTGGAGTCAATAAGAGACTTAATTCAAGGTAATTAAGTAGAGTCA
1743 ATAAA-A
66 ATAAAGA
* * *
1749 GGCTTAATTCAGGGTAATTAAGTGGAGTCAATAAGAGTCTTAATTCAAGGTAATTAAGTGGAGTC
1 -ACTTAATTCAGGGTAATTAAGTGGAGTCAATAAGAGACTTAATTCAAGGTAATTAAGTAGAGTC
1814 AATAAAGA
65 AATAAAGA
1822 ACTTAATTCAGGGTAATTAAGTGGAGTCAATAA-AGAACTTAAT
1 ACTTAATTCAGGGTAATTAAGTGGAGTCAATAAGAG-ACTTAAT
1865 CTAAAAAGAT
Statistics
Matches: 98, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
68 24 0.24
71 2 0.02
72 71 0.72
73 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (72 bp):
ACTTAATTCAGGGTAATTAAGTGGAGTCAATAAGAGACTTAATTCAAGGTAATTAAGTAGAGTCA
ATAAAGA
Found at i:1877 original size:36 final size:35
Alignment explanation
Indices: 1764--1879 Score: 119
Period size: 36 Copynumber: 3.2 Consensus size: 35
1754 AATTCAGGGT
* * *
1764 AATTAAGTGGAGTCAAT-AAGAGTCTTAATTCAAGG
1 AATTAAGTGGAGTCAATAAAGA-ACTTAATTAAAAG
* **
1799 TAATTAAGTGGAGTCAATAAAGAACTTAATTCAGGG
1 -AATTAAGTGGAGTCAATAAAGAACTTAATTAAAAG
1835 TAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAA-
1 -AATTAAGTGGAGTCAATAAAGAACTTAAT-TAAAAG
1871 AGATTAAGT
1 A-ATTAAGT
1880 AGAACAATAA
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
35 1 0.01
36 65 0.90
37 6 0.08
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (35 bp):
AATTAAGTGGAGTCAATAAAGAACTTAATTAAAAG
Found at i:1877 original size:72 final size:71
Alignment explanation
Indices: 1681--1891 Score: 195
Period size: 72 Copynumber: 3.0 Consensus size: 71
1671 TAGAGTTAGG
* ** * ** *
1681 GACTTAATTCGGGGTAATTAAGTCAAGTC----AGAGACTTAATTTAGGGTAATTAAGTAGCGTC
1 GACTTAATTCAGGGTAATTAAGTGGAGTCAATAAGAGACTTAATTAAAAG-AATTAAGTAGAGTC
1742 AATAAAA
65 AATAAAA
* * * * *
1749 GGCTTAATTCAGGGTAATTAAGTGGAGTCAATAAGAGTCTTAATTCAAGGTAATTAAGTGGAGTC
1 GACTTAATTCAGGGTAATTAAGTGGAGTCAATAAGAGACTTAATTAAAAG-AATTAAGTAGAGTC
1814 AAT-AAA
65 AATAAAA
1820 GAACTTAATTCAGGGTAATTAAGTGGAGTCAATAA-AGAACTTAATCTAAAA-AGATTAAGTAGA
1 G-ACTTAATTCAGGGTAATTAAGTGGAGTCAATAAGAG-ACTTAAT-TAAAAGA-ATTAAGTAGA
*
1883 -ACAATAAAA
62 GTCAATAAAA
1892 AGGGCTTAAT
Statistics
Matches: 119, Mismatches: 15, Indels: 14
0.80 0.10 0.09
Matches are distributed among these distances:
68 25 0.21
71 11 0.09
72 80 0.67
73 3 0.03
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (71 bp):
GACTTAATTCAGGGTAATTAAGTGGAGTCAATAAGAGACTTAATTAAAAGAATTAAGTAGAGTCA
ATAAAA
Found at i:8576 original size:12 final size:12
Alignment explanation
Indices: 8559--8590 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
8549 ACCGCGCAAC
8559 ACCGGCCACATG
1 ACCGGCCACATG
*
8571 ACCGGCCACTTG
1 ACCGGCCACATG
8583 ACCGGCCA
1 ACCGGCCA
8591 TCGCATGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.22, C:0.44, G:0.25, T:0.09
Consensus pattern (12 bp):
ACCGGCCACATG
Found at i:8620 original size:30 final size:29
Alignment explanation
Indices: 8586--8683 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 29
8576 CCACTTGACC
8586 GGCCATCGCATGGAGCAACCAGCCACAACT
1 GGCCATCGCATGGAGCAACC-GCCACAACT
*
8616 GGCCATCGCATGGGGCATCAACCGGCCACAACT
1 GGCCATCGCAT--GG-AGCAACC-GCCACAACT
* * * *
8649 GGCTATCGCATGGGGCATCCGCGCACAACC
1 GGCCATCGCATGGAGCAACCGC-CACAACT
8679 GGCCA
1 GGCCA
8684 ATGGATCCTT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
29 2 0.04
30 25 0.45
31 2 0.04
32 2 0.04
33 25 0.45
ACGTcount: A:0.24, C:0.37, G:0.28, T:0.11
Consensus pattern (29 bp):
GGCCATCGCATGGAGCAACCGCCACAACT
Found at i:8644 original size:33 final size:33
Alignment explanation
Indices: 8586--8667 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 33
8576 CCACTTGACC
*
8586 GGCCATCGCAT--GG-AGCAACCAGCCACAACT
1 GGCCATCGCATGGGGCATCAACCAGCCACAACT
*
8616 GGCCATCGCATGGGGCATCAACCGGCCACAACT
1 GGCCATCGCATGGGGCATCAACCAGCCACAACT
*
8649 GGCTATCGCATGGGGCATC
1 GGCCATCGCATGGGGCATC
8668 CGCGCACAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 11 0.24
32 2 0.04
33 33 0.72
ACGTcount: A:0.24, C:0.34, G:0.28, T:0.13
Consensus pattern (33 bp):
GGCCATCGCATGGGGCATCAACCAGCCACAACT
Found at i:13690 original size:30 final size:30
Alignment explanation
Indices: 13654--13713 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
13644 AAAGGAGAGG
* * *
13654 ATGGAATCGCAAAGTCTCATGTAGATGCCA
1 ATGGAATCACAAAGCCTCATGGAGATGCCA
13684 ATGGAATCACAAAGCCTCATGGAGATGCCA
1 ATGGAATCACAAAGCCTCATGGAGATGCCA
13714 TTAAGATGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (30 bp):
ATGGAATCACAAAGCCTCATGGAGATGCCA
Found at i:28443 original size:15 final size:16
Alignment explanation
Indices: 28414--28443 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28404 GAATGAAGTC
28414 AAATTGATCTTTTGAA
1 AAATTGATCTTTTGAA
28430 AAATTGAT-TTTTGA
1 AAATTGATCTTTTGA
28444 TTAACTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (16 bp):
AAATTGATCTTTTGAA
Found at i:35389 original size:21 final size:23
Alignment explanation
Indices: 35365--35407 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
35355 TTTTCATTAA
35365 AAATTAA-ATT-TTTGAAAAAAG
1 AAATTAATATTCTTTGAAAAAAG
*
35386 AAATTAATTTTCTTTGAAAAAA
1 AAATTAATATTCTTTGAAAAAA
35408 AACCTTAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 2 0.11
23 10 0.53
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (23 bp):
AAATTAATATTCTTTGAAAAAAG
Found at i:43028 original size:30 final size:29
Alignment explanation
Indices: 42964--43045 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 29
42954 ACTTAATACC
* *
42964 CAAATTAGCCCCTTAACTATTCATTTTTGGA
1 CAAATTGGCCCCTTAACT-TT-TTTTTTGGA
*
42995 CAAATTGGCTCCTTAACTTTTTTTTTCGGA
1 CAAATTGGCCCCTTAACTTTTTTTTT-GGA
*
43025 CAAATTGCCCCCTTAACTTTT
1 CAAATTGGCCCCTTAACTTTT
43046 AAAAACGAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 5 0.11
30 24 0.53
31 16 0.36
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.41
Consensus pattern (29 bp):
CAAATTGGCCCCTTAACTTTTTTTTTGGA
Found at i:43769 original size:29 final size:29
Alignment explanation
Indices: 43736--43806 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
43726 TCTCGTTTTT
43736 AAAAGTTAAGGGGTCAATTTATCTCAAAA-
1 AAAAGTTAAGGGGTCAATTTATC-CAAAAG
* *
43765 AAAAGTTAAAGGGTCAATTTGTCCAAAATG
1 AAAAGTTAAGGGGTCAATTTATCCAAAA-G
*
43795 AATAGTTAAGGG
1 AAAAGTTAAGGG
43807 ACTAATTTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 5 0.14
29 21 0.58
30 10 0.28
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.27
Consensus pattern (29 bp):
AAAAGTTAAGGGGTCAATTTATCCAAAAG
Found at i:43880 original size:6 final size:7
Alignment explanation
Indices: 43864--43890 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
43854 TGGGACATTT
43864 AAAAACA
1 AAAAACA
43871 AAAAACA
1 AAAAACA
43878 AAAAACA
1 AAAAACA
43885 AAAAAC
1 AAAAAC
43891 TGGAACCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:44353 original size:5 final size:5
Alignment explanation
Indices: 44340--44373 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
44330 AAAGATTGAA
* *
44340 AAAAC AAAAT AAAAT AAAAC AAAAC AAAAC AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
44374 AGTAATAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.82, C:0.12, G:0.00, T:0.06
Consensus pattern (5 bp):
AAAAC
Found at i:49735 original size:2 final size:2
Alignment explanation
Indices: 49728--49765 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
49718 GCTAATTTAT
49728 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
49766 TCTCTCTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.