Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011332.1 Corchorus capsularis cultivar CVL-1 contig11353, 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: 45007
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:167 original size:40 final size:40
Alignment explanation
Indices: 107--196 Score: 162
Period size: 40 Copynumber: 2.2 Consensus size: 40
97 TCTTTGTTCA
*
107 TGAGTTTTGATGTTGTTTTACTTAAATGATTTTGAATGAT
1 TGAGATTTGATGTTGTTTTACTTAAATGATTTTGAATGAT
147 TGAGATTTGATGTTGTTTTACTTAAATGATTTTGAATGAT
1 TGAGATTTGATGTTGTTTTACTTAAATGATTTTGAATGAT
*
187 TGAGGTTTGA
1 TGAGATTTGA
197 AAGTTTGAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.26, C:0.02, G:0.22, T:0.50
Consensus pattern (40 bp):
TGAGATTTGATGTTGTTTTACTTAAATGATTTTGAATGAT
Found at i:5170 original size:19 final size:18
Alignment explanation
Indices: 5146--5184 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
5136 AACCAGCTTA
5146 TTTAAAAAGTGCCTTCAGT
1 TTTAAAAA-TGCCTTCAGT
*
5165 TTTAAATATGCCTTCAGT
1 TTTAAAAATGCCTTCAGT
5183 TT
1 TT
5185 AGTGGCTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (18 bp):
TTTAAAAATGCCTTCAGT
Found at i:14479 original size:25 final size:25
Alignment explanation
Indices: 14447--14494 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
14437 TCGCTATTAA
14447 ATATATAATAATAATCAATATATAT
1 ATATATAATAATAATCAATATATAT
*
14472 ATATATAATAATAATCAGTATAT
1 ATATATAATAATAATCAATATAT
14495 TTCTTAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (25 bp):
ATATATAATAATAATCAATATATAT
Found at i:14791 original size:13 final size:13
Alignment explanation
Indices: 14755--14824 Score: 65
Period size: 13 Copynumber: 5.6 Consensus size: 13
14745 CTTATGGCAA
* *
14755 AATACCTTTTGAT
1 AATACCTTATGGT
*
14768 AATA-CTCATGGT
1 AATACCTTATGGT
*
14780 AATACCTTATGGA
1 AATACCTTATGGT
*
14793 AATA-C-TATGGA
1 AATACCTTATGGT
*
14804 AATACCTTATGAT
1 AATACCTTATGGT
14817 AATACCTT
1 AATACCTT
14825 GTGACAATGG
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
11 10 0.21
12 11 0.23
13 26 0.55
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (13 bp):
AATACCTTATGGT
Found at i:14807 original size:24 final size:26
Alignment explanation
Indices: 14754--14821 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 26
14744 CCTTATGGCA
*
14754 AAATACCTT-TTGATAATACTCATGG
1 AAATACCTTATGGATAATACTCATGG
*
14779 TAATACCTTATGGA-AATACT-ATGG
1 AAATACCTTATGGATAATACTCATGG
14803 AAATACCTTAT-GATAATAC
1 AAATACCTTATGGATAATAC
14822 CTTGTGACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 2 0.05
24 19 0.50
25 14 0.37
26 3 0.08
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (26 bp):
AAATACCTTATGGATAATACTCATGG
Found at i:15427 original size:21 final size:20
Alignment explanation
Indices: 15399--15439 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
15389 AGCAAAGTAT
15399 TCATTTTTACACACAAAAAA
1 TCATTTTTACACACAAAAAA
* *
15419 TCATATTTTACCCATAAAAAA
1 TCAT-TTTTACACACAAAAAA
15440 AACAGAGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.32
Consensus pattern (20 bp):
TCATTTTTACACACAAAAAA
Found at i:19460 original size:16 final size:17
Alignment explanation
Indices: 19441--19475 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
19431 AGAACATGAA
19441 AAAGAAAAAGAA-AGAG
1 AAAGAAAAAGAAGAGAG
*
19457 AAAGAAGAAGAAGAGAG
1 AAAGAAAAAGAAGAGAG
19474 AA
1 AA
19476 GGGTTTGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAGAGAG
Found at i:21608 original size:19 final size:19
Alignment explanation
Indices: 21566--21608 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
21556 TAGGGTAGTT
*
21566 AAGAAAGTGAGTAGGAGGA
1 AAGAGAGTGAGTAGGAGGA
* * *
21585 GAGAGAGTGAGTGGGGGGA
1 AAGAGAGTGAGTAGGAGGA
21604 AAGAG
1 AAGAG
21609 TACAGGGGTA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.51, T:0.09
Consensus pattern (19 bp):
AAGAGAGTGAGTAGGAGGA
Found at i:22645 original size:80 final size:80
Alignment explanation
Indices: 22506--22752 Score: 449
Period size: 80 Copynumber: 3.1 Consensus size: 80
22496 CAGCATCTAG
*
22506 CTTATGGCGTTGGAGAGGAATATATATGGTGTTGACGACACCCTGTTGGAAGTATGGTGTTGGAA
1 CTTAT-GCGTTGGAGAGAAATATATATGGTGTTGACGACACCCTGTTGGAAGTATGGTGTTGGAA
22571 ACGCCGCCTTCCATTT
65 ACGCCGCCTTCCATTT
*
22587 CATATGCGTTGGAGAGAAATATATATGGTGTTGACGACACCCTGTTGGAAGTATGGTGTTGGAAA
1 CTTATGCGTTGGAGAGAAATATATATGGTGTTGACGACACCCTGTTGGAAGTATGGTGTTGGAAA
*
22652 CACCGCCTTCCATTT
66 CGCCGCCTTCCATTT
*
22667 CTTATGCGTTGGAGAGAAATATATATGGTGTTGACGACACCCTGTTGGAAGTATGGTGCTGGAAA
1 CTTATGCGTTGGAGAGAAATATATATGGTGTTGACGACACCCTGTTGGAAGTATGGTGTTGGAAA
22732 CGCCGCCTTCCATTT
66 CGCCGCCTTCCATTT
22747 CTTATG
1 CTTATG
22753 TGAAAGAGGA
Statistics
Matches: 160, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
80 156 0.98
81 4 0.03
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (80 bp):
CTTATGCGTTGGAGAGAAATATATATGGTGTTGACGACACCCTGTTGGAAGTATGGTGTTGGAAA
CGCCGCCTTCCATTT
Found at i:23159 original size:46 final size:46
Alignment explanation
Indices: 23089--23231 Score: 178
Period size: 46 Copynumber: 3.1 Consensus size: 46
23079 AATGCGTTGC
* * *
23089 AAGAGGCTACCGTATAGAGAATTCTTTCTGGAGATGGGTGCTCACAT
1 AAGA-GCTACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACAT
* * *
23136 AAGAGCTACCATGTAGAGTATTCTTTCTGAAGAAGTGTGCTCACAT
1 AAGAGCTACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACAT
** * * *
23182 AAGAGCTATTGTATAGAGTAATCTTTCTGAAGAAAGATGCTCACAT
1 AAGAGCTACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACAT
23228 AAGA
1 AAGA
23232 TGCATCTCCT
Statistics
Matches: 82, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
46 78 0.95
47 4 0.05
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (46 bp):
AAGAGCTACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACAT
Found at i:23486 original size:36 final size:36
Alignment explanation
Indices: 23391--23507 Score: 146
Period size: 36 Copynumber: 3.2 Consensus size: 36
23381 GTCAGTGGCG
* *
23391 TTATAGCCAAATATTGGGCGAC-TATGGCCAGCGGCT
1 TTATAGCCAAATATTGGGCGACTTA-GGCCATCGGCA
** * *
23427 TTATAGCCATTTTTTGGGTGACTTAGGCCATCGGCA
1 TTATAGCCAAATATTGGGCGACTTAGGCCATCGGCA
* *
23463 TTATAGCCAAAGATTAGGCGACTTAGGCCATCGGCA
1 TTATAGCCAAATATTGGGCGACTTAGGCCATCGGCA
23499 TTATAGCCA
1 TTATAGCCA
23508 GAAACAAAGC
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
36 66 0.97
37 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (36 bp):
TTATAGCCAAATATTGGGCGACTTAGGCCATCGGCA
Found at i:24015 original size:20 final size:20
Alignment explanation
Indices: 23986--24069 Score: 99
Period size: 17 Copynumber: 4.5 Consensus size: 20
23976 ATTTCTCTCC
23986 GTTGGAAGCGTCAGCATCAT
1 GTTGGAAGCGTCAGCATCAT
* *
24006 GTTAGAAGCG-CA--ACCAT
1 GTTGGAAGCGTCAGCATCAT
24023 GTTGGAAGCGTCAGCATCAT
1 GTTGGAAGCGTCAGCATCAT
*
24043 GTTGGAAGCG-CA--ACCAT
1 GTTGGAAGCGTCAGCATCAT
24060 GTTGGAAGCG
1 GTTGGAAGCG
24070 CATATAAATT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
17 27 0.48
18 2 0.04
19 4 0.07
20 23 0.41
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.21
Consensus pattern (20 bp):
GTTGGAAGCGTCAGCATCAT
Found at i:24036 original size:37 final size:37
Alignment explanation
Indices: 23986--24069 Score: 159
Period size: 37 Copynumber: 2.3 Consensus size: 37
23976 ATTTCTCTCC
23986 GTTGGAAGCGTCAGCATCATGTTAGAAGCGCAACCAT
1 GTTGGAAGCGTCAGCATCATGTTAGAAGCGCAACCAT
*
24023 GTTGGAAGCGTCAGCATCATGTTGGAAGCGCAACCAT
1 GTTGGAAGCGTCAGCATCATGTTAGAAGCGCAACCAT
24060 GTTGGAAGCG
1 GTTGGAAGCG
24070 CATATAAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.21
Consensus pattern (37 bp):
GTTGGAAGCGTCAGCATCATGTTAGAAGCGCAACCAT
Found at i:24110 original size:45 final size:45
Alignment explanation
Indices: 24042--24372 Score: 260
Period size: 45 Copynumber: 7.2 Consensus size: 45
24032 GTCAGCATCA
*
24042 TGTTGGAAGCG-CA--ACCATGTTGGAAGCGCATATAAATTTTAT
1 TGTTGGAAGCGCCACCATCATGTTGGAAGCGCATATAAATTTTAT
* * * * ** *
24084 CGCTGGAAGCGCCACCCTCATGTTGGAAGAGTGTATAAATTTT-G
1 TGTTGGAAGCGCCACCATCATGTTGGAAGCGCATATAAATTTTAT
* *
24128 TGATTGGAGGCGCCACAATCATGTTGGAAGCGCATATAAA-TTTAT
1 TG-TTGGAAGCGCCACCATCATGTTGGAAGCGCATATAAATTTTAT
* * * *
24173 TGTTGGAAGCGCCACCATCATGTTGGAAAGAGCGTATAATTTTTTTTTTTT
1 TGTTGGAAGCGCCACCATCATGTTGG-AAGCGCATATAA-----ATTTTAT
* * * * ** *
24224 GTGATTGGAGGCGTCACCATCATTTTGGAAGTG-AGTATAGGTTTTGT
1 -TG-TTGGAAGCGCCACCATCATGTTGGAAGCGCA-TATAAATTTTAT
* *
24271 CTGTTGGAAGCGCCACCCCACCGTGTTGGAAGCGCATATAAATTTTAT
1 -TGTTGGAAGCGCCA--CCATCATGTTGGAAGCGCATATAAATTTTAT
* *
24319 TGTTGGAAGCGCCACCATCATGTTGGAAAGGGCGTATAAATTTTCAT
1 TGTTGGAAGCGCCACCATCATGTTGG-AAGCGCATATAAATTTT-AT
24366 TGTTGGA
1 TGTTGGA
24373 GGAAGGTGAT
Statistics
Matches: 224, Mismatches: 45, Indels: 35
0.74 0.15 0.12
Matches are distributed among these distances:
42 9 0.04
43 2 0.01
44 26 0.12
45 74 0.33
46 25 0.11
47 30 0.13
48 22 0.10
49 1 0.00
51 4 0.02
52 10 0.04
53 21 0.09
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (45 bp):
TGTTGGAAGCGCCACCATCATGTTGGAAGCGCATATAAATTTTAT
Found at i:24160 original size:20 final size:20
Alignment explanation
Indices: 24131--24200 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
24121 AATTTTGTGA
*
24131 TTGGAGGCGCCACAATCATG
1 TTGGAAGCGCCACAATCATG
* * *
24151 TTGGAAGCGCATATAAATTTATTG
1 TTGGAAGCGC-CA-CAA-TCA-TG
*
24175 TTGGAAGCGCCACCATCATG
1 TTGGAAGCGCCACAATCATG
24195 TTGGAA
1 TTGGAA
24201 AGAGCGTATA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 17 0.45
21 3 0.08
22 3 0.08
23 3 0.08
24 12 0.32
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.27
Consensus pattern (20 bp):
TTGGAAGCGCCACAATCATG
Found at i:24325 original size:47 final size:47
Alignment explanation
Indices: 24272--24372 Score: 134
Period size: 47 Copynumber: 2.1 Consensus size: 47
24262 AGGTTTTGTC
*
24272 TGTTGGAAGCGCCACCCCACCGTGTTGG-AAGCGCATATAAATTTT-AT
1 TGTTGGAAGCGCCA--CCACCATGTTGGAAAGCGCATATAAATTTTCAT
* * *
24319 TGTTGGAAGCGCCACCATCATGTTGGAAAGGGCGTATAAATTTTCAT
1 TGTTGGAAGCGCCACCACCATGTTGGAAAGCGCATATAAATTTTCAT
24366 TGTTGGA
1 TGTTGGA
24373 GGAAGGTGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
45 10 0.21
46 15 0.31
47 23 0.48
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (47 bp):
TGTTGGAAGCGCCACCACCATGTTGGAAAGCGCATATAAATTTTCAT
Found at i:25061 original size:75 final size:77
Alignment explanation
Indices: 24970--25110 Score: 232
Period size: 75 Copynumber: 1.9 Consensus size: 77
24960 ATTTTTTTTT
* *
24970 AAGCTACATAGGCTATAGGCATTGTAAGCC-ATT-TTTTTAAGCTGCATAGGCTATAGGCGTTGT
1 AAGCTACATAGGCTATAGGCATTGTAAGCCTATTCTTTTTAAGCTACATAGGCTATAGGCATTGT
25033 ACGCCCTCTTTC
66 ACGCCCTCTTTC
* *
25045 AAGCTACATTGGCTATAGGCATTGTAAGCCTTTTCTTTTTAAGCTACATAGGCTATAGGCATTGT
1 AAGCTACATAGGCTATAGGCATTGTAAGCCTATTCTTTTTAAGCTACATAGGCTATAGGCATTGT
25110 A
66 A
25111 AGCCTTTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
75 29 0.48
76 2 0.03
77 29 0.48
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (77 bp):
AAGCTACATAGGCTATAGGCATTGTAAGCCTATTCTTTTTAAGCTACATAGGCTATAGGCATTGT
ACGCCCTCTTTC
Found at i:25100 original size:40 final size:40
Alignment explanation
Indices: 24929--25140 Score: 238
Period size: 40 Copynumber: 5.4 Consensus size: 40
24919 AGGCGTTGCA
* * * *
24929 AAGCTGCATAGACTGTAGGC-TTAGTAAGCCTATTTTTTTTT
1 AAGCTACATAGGCTATAGGCATT-GTAAGCCT-TTTCTTTTT
*
24970 AAGCTACATAGGCTATAGGCATTGTAAGCC-ATT-TTTTT
1 AAGCTACATAGGCTATAGGCATTGTAAGCCTTTTCTTTTT
* * * * *
25008 AAGCTGCATAGGCTATAGGCGTTGTACGCC--CTC-TTTC
1 AAGCTACATAGGCTATAGGCATTGTAAGCCTTTTCTTTTT
*
25045 AAGCTACATTGGCTATAGGCATTGTAAGCCTTTTCTTTTT
1 AAGCTACATAGGCTATAGGCATTGTAAGCCTTTTCTTTTT
*
25085 AAGCTACATAGGCTATAGGCATTGTAAGCCTTTTTTTTTT
1 AAGCTACATAGGCTATAGGCATTGTAAGCCTTTTCTTTTT
*
25125 AAAGCTGCATAGGCTA
1 -AAGCTACATAGGCTA
25141 GAAGTGTCAA
Statistics
Matches: 147, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
37 30 0.20
38 32 0.22
39 4 0.03
40 41 0.28
41 38 0.26
42 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (40 bp):
AAGCTACATAGGCTATAGGCATTGTAAGCCTTTTCTTTTT
Found at i:25246 original size:110 final size:110
Alignment explanation
Indices: 25147--25376 Score: 320
Period size: 110 Copynumber: 2.1 Consensus size: 110
25137 GCTAGAAGTG
* * * *
25147 TCAACAAGGAGGGGCACTCCTAGAGGTGCAATCAGTGCAACACTCCTAAGGGTGCAC-CTGCTCC
1 TCAACAAGGAAGGGCACTCCCAGAGGTGCAACCAGTGCAACACTCCTAAGGGTGCACTC-ACTCC
25211 AAGTCAAAAAAAATTTTTTTTTAATGGGCTACATAGGCCAGAATCA
65 AAGTCAAAAAAAATTTTTTTTTAATGGGCTACATAGGCCAGAATCA
* * *
25257 TCAACAAGGAAGGGCACTCCCGGAGGTGCAACCAGTGCAGCACTCCTATGGGTGCACTCACTCCA
1 TCAACAAGGAAGGGCACTCCCAGAGGTGCAACCAGTGCAACACTCCTAAGGGTGCACTCACTCCA
* * ** *
25322 AGTCAAAATATAGATTTTTTTAATGGGCTACATAAGCCAGAATCA
66 AGTCAAAAAAAATTTTTTTTTAATGGGCTACATAGGCCAGAATCA
*
25367 ACAA-AAGGAA
1 TCAACAAGGAA
25377 ATGCACTTTT
Statistics
Matches: 106, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
109 6 0.06
110 99 0.93
111 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (110 bp):
TCAACAAGGAAGGGCACTCCCAGAGGTGCAACCAGTGCAACACTCCTAAGGGTGCACTCACTCCA
AGTCAAAAAAAATTTTTTTTTAATGGGCTACATAGGCCAGAATCA
Found at i:25426 original size:68 final size:68
Alignment explanation
Indices: 25341--25471 Score: 201
Period size: 68 Copynumber: 1.9 Consensus size: 68
25331 ATAGATTTTT
* *
25341 TTAATGGGCTACATAAGCCAGAATCAACA-AAAGGAAATGCACTTTTGGCTACGATCCTTGCTGG
1 TTAATGGGCTACATAAGCCAGAAGCAACACAAAGGAAA-GCACTTATGGCTACGATCCTTGCTGG
25405 AATC
65 AATC
* **
25409 TTAATTGGCTACATAAGCCAGAAGCAACACAAAGGAAAGCACTTATGGCTGTGATCCTTGCTG
1 TTAATGGGCTACATAAGCCAGAAGCAACACAAAGGAAAGCACTTATGGCTACGATCCTTGCTG
25472 AATATGGAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 49 0.86
69 8 0.14
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (68 bp):
TTAATGGGCTACATAAGCCAGAAGCAACACAAAGGAAAGCACTTATGGCTACGATCCTTGCTGGA
ATC
Found at i:29720 original size:30 final size:30
Alignment explanation
Indices: 29686--29746 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
29676 TCCACATGAA
*
29686 AATGAAAATGAAAACCCTTATATTACATGC
1 AATGAAAATGAAAACCCTTAAATTACATGC
29716 AATGAAAATGAAAACCCTTAAATTACATGC
1 AATGAAAATGAAAACCCTTAAATTACATGC
29746 A
1 A
29747 CACACTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.25
Consensus pattern (30 bp):
AATGAAAATGAAAACCCTTAAATTACATGC
Found at i:38282 original size:15 final size:16
Alignment explanation
Indices: 38254--38285 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
38244 AATATGCGCC
38254 TTTAGCATTTTTTACA
1 TTTAGCATTTTTTACA
38270 TTTAGCA-TTTTTACA
1 TTTAGCATTTTTTACA
38285 T
1 T
38286 ATTTTATGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.56
Consensus pattern (16 bp):
TTTAGCATTTTTTACA
Found at i:39776 original size:19 final size:19
Alignment explanation
Indices: 39752--39792 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
39742 CACTCTCTTT
39752 TCTCTCACTCTTCAATCTC
1 TCTCTCACTCTTCAATCTC
* * *
39771 TCTCTCTCTCTTGATTCTC
1 TCTCTCACTCTTCAATCTC
39790 TCT
1 TCT
39793 GGGAATACAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.10, C:0.39, G:0.02, T:0.49
Consensus pattern (19 bp):
TCTCTCACTCTTCAATCTC
Found at i:44657 original size:2 final size:2
Alignment explanation
Indices: 44650--44684 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
44640 AATTATGATA
44650 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44685 GGCATAATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.