Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013053.1 Corchorus capsularis cultivar CVL-1 contig13074, 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: 30949
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:37 original size:22 final size:21
Alignment explanation
Indices: 3--361 Score: 147
Period size: 22 Copynumber: 16.9 Consensus size: 21
1 CN
*
3 GTAAAGAGTAAAATAGTAATCA
1 GTAAA-AGCAAAATAGTAATCA
* *
25 GATAAAAGCAAAATGGGAATCA
1 G-TAAAAGCAAAATAGTAATCA
*
47 GTAAAGAGTAAAATAGTAATCA
1 GTAAA-AGCAAAATAGTAATCA
*
69 GTAAAAGCAAAATGGTAAAAT-A
1 GTAAAAGCAAAATAGT--AATCA
** *
91 GTAAAA--AGTGAT-GATAATCC
1 GTAAAAGCA-AAATAG-TAATCA
* *
111 GTAAAAGGTAAAATGGTAATCA
1 GTAAAA-GCAAAATAGTAATCA
*
133 GTAAGAGCAAAATAGTAATCA
1 GTAAAAGCAAAATAGTAATCA
* *
154 GTAAAAAGTAAGAA-GGTAATCA
1 GT-AAAAGCAA-AATAGTAATCA
*
176 GTAAAGAGTAAAATAGTAA--A
1 GTAAA-AGCAAAATAGTAATCA
** *
196 --AAAAG--TGAT-GACAATCA
1 GTAAAAGCAAAATAG-TAATCA
* *
213 GTAAAAGGTAAAATGGTAATCA
1 GTAAAA-GCAAAATAGTAATCA
* *
235 GTAAGAGCGAAATAGTAATCA
1 GTAAAAGCAAAATAGTAATCA
*
256 ATAAAGAGCAAAA-AGGTAATCA
1 GTAAA-AGCAAAATA-GTAATCA
*
278 GTAAGAA-CAAAATGGTAATCA
1 GTAA-AAGCAAAATAGTAATCA
* * *
299 ATAAAGAG-TAAATAAGTAATTA
1 GTAAA-AGCAAAAT-AGTAATCA
* * *
321 GTAAAAAGTAAGA-AGATGATCA
1 GT-AAAAGCAAAATAG-TAATCA
*
343 GTAAAGAGTAAAATAGTAA
1 GTAAA-AGCAAAATAGTAA
362 AAACTAATCA
Statistics
Matches: 254, Mismatches: 47, Indels: 72
0.68 0.13 0.19
Matches are distributed among these distances:
14 1 0.00
15 4 0.02
17 3 0.01
18 3 0.01
19 7 0.03
20 11 0.04
21 77 0.30
22 128 0.50
23 20 0.08
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (21 bp):
GTAAAAGCAAAATAGTAATCA
Found at i:122 original size:64 final size:64
Alignment explanation
Indices: 42--406 Score: 195
Period size: 64 Copynumber: 5.6 Consensus size: 64
32 GCAAAATGGG
* *
42 AATCAGTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAAAAT-AGTAAAAAGT-GATGA
1 AATCAGTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATAGT--AATCAGTAAAAAGTAGAAGA
105 T
64 T
* * * *
106 AATCCGTAAA-AGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAAAGTAAGAAGG
1 AATCAGTAAAGA-GTAAAATAGTAATCAGTAAAAGCAAAATAGTAATCAGTAAAAAGT-AGAAGA
170 T
64 T
** * * * *
171 AATCAGTAAAGAGTAAAATAGTAA--A--AAAAG--TGAT-GACAATCAGTAAAAGGTAAAATGG
1 AATCAGTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATAG-TAATCAGTAAAAAGTAGAA-GA
229 T
64 T
** * * * *
230 AATCAGT-AAGAGCGAAATAGTAATCAATAAAGAGCAAAA-AGGTAATCAGTAAGAA-CAAAATG
1 AATCAGTAAAGAGTAAAATAGTAATCAGTAAA-AGCAAAATA-GTAATCAGTAAAAAGTAGAA-G
*
292 GT
63 AT
* * * **
294 AATCAATAAAGAGT-AAATAAGTAATTAGTAAAAAGTAAGAAGATGATCAGTAAAGAGTAAAATA
1 AATCAGTAAAGAGTAAAAT-AGTAATCAGT-AAAAG---CAA-A--AT-AGTAATCAGTAAAA-A
*
358 GTA-AAAACT
56 GTAGAAGA-T
*
367 AATCAGTAAA-AGGTAAAATAGTAATCAGTAAGAGCAAAAT
1 AATCAGTAAAGA-GTAAAATAGTAATCAGTAAAAGCAAAAT
407 GGTTATTAGA
Statistics
Matches: 232, Mismatches: 37, Indels: 62
0.70 0.11 0.19
Matches are distributed among these distances:
58 18 0.08
59 25 0.11
60 1 0.00
61 4 0.02
62 6 0.03
63 14 0.06
64 55 0.24
65 50 0.22
66 7 0.03
68 3 0.01
69 3 0.01
71 1 0.00
72 15 0.06
73 25 0.11
74 5 0.02
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.20
Consensus pattern (64 bp):
AATCAGTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATAGTAATCAGTAAAAAGTAGAAGAT
Found at i:152 original size:43 final size:43
Alignment explanation
Indices: 3--361 Score: 284
Period size: 43 Copynumber: 8.4 Consensus size: 43
1 CN
*
3 GTAAAGAGTAAAATAGTAATCAGATAAAAGCAAAATGGGAATCA
1 GTAAAGAGTAAAATAGTAATCAG-TAAAAGCAAAATGGTAATCA
47 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAAAAT-A
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGT--AATCA
* * * *
91 GTAAAAAGT--GAT-GATAATCCGTAAAAGGTAAAATGGTAATCA
1 GTAAAGAGTAAAATAG-TAATCAGTAAAA-GCAAAATGGTAATCA
* *
133 GT-AAGAGCAAAATAGTAATCAGTAAAAAGTAAGAA-GGTAATCA
1 GTAAAGAGTAAAATAGTAATCAGT-AAAAGCAA-AATGGTAATCA
** **
176 GTAAAGAGTAAAATAGTAA--A--AAAAG--TGATGACAATCA
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAATCA
* * * *
213 GTAAA-AGGTAAAATGGTAATCAGTAAGAGCGAAATAGTAATCA
1 GTAAAGA-GTAAAATAGTAATCAGTAAAAGCAAAATGGTAATCA
* *
256 ATAAAGAGCAAAA-AGGTAATCAGTAAGAA-CAAAATGGTAATCA
1 GTAAAGAGTAAAATA-GTAATCAGTAA-AAGCAAAATGGTAATCA
* * * * *
299 ATAAAGAGT-AAATAAGTAATTAGTAAAAAGTAAGAA-GATGATCA
1 GTAAAGAGTAAAAT-AGTAATCAGT-AAAAGCAA-AATGGTAATCA
343 GTAAAGAGTAAAATAGTAA
1 GTAAAGAGTAAAATAGTAA
362 AAACTAATCA
Statistics
Matches: 254, Mismatches: 33, Indels: 56
0.74 0.10 0.16
Matches are distributed among these distances:
36 2 0.01
37 22 0.09
39 6 0.02
41 12 0.05
42 20 0.08
43 103 0.41
44 80 0.31
45 9 0.04
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (43 bp):
GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAATCA
Found at i:235 original size:102 final size:101
Alignment explanation
Indices: 5--281 Score: 333
Period size: 102 Copynumber: 2.6 Consensus size: 101
1 CNGT
* * * * *
5 AAAGAGTAAAATAGTAATCAGATAAAAGCAAAATGGGAATCAGTAAAGAGTAAAATAGTAATCAG
1 AAAG-GTAAAATGGTAATCAG-TAAGAGCAAAATAGTAATCAGTAAAGAGTAAAA-GGTAATCAG
* *
70 TAAAAGCAAAATGGTAAAATAGTAAAAAGTGATGATAATCCGTA
63 T-AAAG---AA-GGTAAAATAGTAAAAAGTGATGACAATCAGTA
*
114 AAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAGTA
1 AAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAGAGTAA-AAGGTAATCAGTA
179 AAG-A-GTAAAATAGTAAAAAAAGTGATGACAATCAGTA
65 AAGAAGGTAAAATAGT--AAAAAGTGATGACAATCAGTA
* * *
216 AAAGGTAAAATGGTAATCAGTAAGAGCGAAATAGTAATCAATAAAGAGCAAAAAGGTAATCAGTA
1 AAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAGAG-TAAAAGGTAATCAGTA
281 A
65 A
282 GAACAAAATG
Statistics
Matches: 152, Mismatches: 12, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
100 10 0.07
102 79 0.52
103 2 0.01
106 4 0.03
107 36 0.24
108 17 0.11
109 4 0.03
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.19
Consensus pattern (101 bp):
AAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAGAGTAAAAGGTAATCAGTAA
AGAAGGTAAAATAGTAAAAAGTGATGACAATCAGTA
Found at i:311 original size:21 final size:21
Alignment explanation
Indices: 222--302 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
212 AGTAAAAGGT
*
222 AAAATGGTAATCAGTAAGAGC
1 AAAATGGTAATCAATAAGAGC
* *
243 GAAATAGTAATCAATAAAGAGC
1 AAAATGGTAATCAAT-AAGAGC
* * *
265 AAAAAGGTAATCAGTAAGAAC
1 AAAATGGTAATCAATAAGAGC
286 AAAATGGTAATCAATAA
1 AAAATGGTAATCAATAA
303 AGAGTAAATA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
21 32 0.65
22 17 0.35
ACGTcount: A:0.54, C:0.09, G:0.19, T:0.19
Consensus pattern (21 bp):
AAAATGGTAATCAATAAGAGC
Found at i:374 original size:22 final size:22
Alignment explanation
Indices: 349--397 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
339 ATCAGTAAAG
349 AGTAAAATAGTAAAA-ACTAATC
1 AGTAAAA-AGTAAAATACTAATC
* *
371 AGTAAAAGGTAAAATAGTAATC
1 AGTAAAAAGTAAAATACTAATC
393 AGTAA
1 AGTAA
398 GAGCAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.57, C:0.06, G:0.14, T:0.22
Consensus pattern (22 bp):
AGTAAAAAGTAAAATACTAATC
Found at i:1285 original size:4 final size:4
Alignment explanation
Indices: 1276--1313 Score: 67
Period size: 4 Copynumber: 9.2 Consensus size: 4
1266 TGGCTTTTAT
1276 ATAA ATAA ATAA ATAA ATAA ATAA TATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA -ATAA ATAA ATAA A
1314 AATATAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 29 0.88
5 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:1308 original size:25 final size:25
Alignment explanation
Indices: 1274--1321 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
1264 CTTGGCTTTT
1274 ATATAAATAAATAAATAA-ATAAATA
1 ATATAAATAAATAAA-AATATAAATA
1299 ATATAAATAAATAAAAATATAAA
1 ATATAAATAAATAAAAATATAAA
1322 ATTCAATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (25 bp):
ATATAAATAAATAAAAATATAAATA
Found at i:1323 original size:17 final size:17
Alignment explanation
Indices: 1276--1321 Score: 78
Period size: 16 Copynumber: 2.8 Consensus size: 17
1266 TGGCTTTTAT
1276 ATAAATAA-ATAAATAA
1 ATAAATAATATAAATAA
1292 ATAAATAATATAAATAA
1 ATAAATAATATAAATAA
1309 ATAAA-AATATAAA
1 ATAAATAATATAAA
1322 ATTCAATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAATAATATAAATAA
Found at i:1921 original size:14 final size:13
Alignment explanation
Indices: 1894--1941 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
1884 ACTTATGAGA
*
1894 TTCAGTATTAAATT
1 TTCAGCATT-AATT
1908 TTCAGCATTCAATTT
1 TTCAGCATT-AA-TT
1923 TTCAGCACTTAATT
1 TTCAGCA-TTAATT
1937 TTCAG
1 TTCAG
1942 TTTATCAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 17 0.57
15 11 0.37
16 2 0.07
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (13 bp):
TTCAGCATTAATT
Found at i:1926 original size:15 final size:15
Alignment explanation
Indices: 1901--1938 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1891 AGATTCAGTA
*
1901 TTAAATTTTCAGCA-
1 TTAATTTTTCAGCAC
1915 TTCAATTTTTCAGCAC
1 TT-AATTTTTCAGCAC
1931 TTAATTTT
1 TTAATTTT
1939 CAGTTTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 17 0.81
16 2 0.10
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (15 bp):
TTAATTTTTCAGCAC
Found at i:2076 original size:37 final size:37
Alignment explanation
Indices: 1988--2345 Score: 470
Period size: 37 Copynumber: 9.6 Consensus size: 37
1978 CCGTTGTTGG
* * * *
1988 TTTTACTTAATTACCATGAATTAATTCCTTTAATTGTTT
1 TTTTACTTAATTTCCCTGAATTAAGTCCTTTAACTG--T
*
2027 TTTTACTTAATTAT-CCTGAATTAAGTCCTTTAACTAT
1 TTTTACTTAATT-TCCCTGAATTAAGTCCTTTAACTGT
* *
2064 TTTTACTTAATTACCTTGAATTAAGTCCTTTAACTGT
1 TTTTACTTAATTTCCCTGAATTAAGTCCTTTAACTGT
* *
2101 TTTTACTTAATTACCCTGAATTAAGTCATTTAACTGT
1 TTTTACTTAATTTCCCTGAATTAAGTCCTTTAACTGT
* *
2138 TTTTACTTAATTTCCCTGAATTAAGTACTTTAACTGC
1 TTTTACTTAATTTCCCTGAATTAAGTCCTTTAACTGT
* * * *
2175 TCTTACTTAATTTCCCTGAGTTAAGTCCTTT-ATTGC
1 TTTTACTTAATTTCCCTGAATTAAGTCCTTTAACTGT
*
2211 TTTTACTTAATTTCCCAT-AATTAAGTCCTTTAACTGC
1 TTTTACTTAATTTCCC-TGAATTAAGTCCTTTAACTGT
* *
2248 TTTTACTTAATTTCCCTGAATTAAGTCTTTTAACTGC
1 TTTTACTTAATTTCCCTGAATTAAGTCCTTTAACTGT
*
2285 TTTTACTTAATTTCCCTGAATTAAGTCATTTAACTGT
1 TTTTACTTAATTTCCCTGAATTAAGTCCTTTAACTGT
* *
2322 TTTTATTTAATCTCCCTGAATTAA
1 TTTTACTTAATTTCCCTGAATTAA
2346 AACCTTAACT
Statistics
Matches: 288, Mismatches: 26, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
36 32 0.11
37 226 0.78
39 30 0.10
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (37 bp):
TTTTACTTAATTTCCCTGAATTAAGTCCTTTAACTGT
Found at i:2270 original size:184 final size:186
Alignment explanation
Indices: 1990--2345 Score: 531
Period size: 184 Copynumber: 1.9 Consensus size: 186
1980 GTTGTTGGTT
* *
1990 TTACTTAATTACCATGAATTAATTCCTTTAATTGTTTTTTTACTTAATTATCCTGAATTAAGTCC
1 TTACTTAATTACCATGAATTAAGTCCTTTAATTG-TCTTTTACTTAATTATCCTGAATTAAGTCC
* * *
2055 TTTAACTATTTTTACTTAATTACCTTGAATTAAGTCCTTTAACTGTTTTTACTTAATTACCCTGA
65 TTTAACTACTTTTACTTAATTACCCTGAATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTGA
*
2120 ATTAAGTCATTTAACTGTTTTTACTTAATTTCCCTGAATTAAGTACTTTAACTGCTC
130 ATTAAGTCATTTAACTGTTTTTACTTAATCTCCCTGAATTAAGTACTTTAACTGCTC
* * *
2177 TTACTTAATTTCCCTGAGTTAAGTCCTTT-ATTG-CTTTTACTTAATT-TCCCAT-AATTAAGTC
1 TTACTTAATTACCATGAATTAAGTCCTTTAATTGTCTTTTACTTAATTAT-CC-TGAATTAAGTC
* * * *
2238 CTTTAACTGCTTTTACTTAATTTCCCTGAATTAAGTCTTTTAACTGCTTTTACTTAATTTCCCTG
64 CTTTAACTACTTTTACTTAATTACCCTGAATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTG
*
2303 AATTAAGTCATTTAACTGTTTTTATTTAATCTCCCTGAATTAA
129 AATTAAGTCATTTAACTGTTTTTACTTAATCTCCCTGAATTAA
2346 AACCTTAACT
Statistics
Matches: 153, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
183 1 0.01
184 122 0.80
185 1 0.01
186 4 0.03
187 25 0.16
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (186 bp):
TTACTTAATTACCATGAATTAAGTCCTTTAATTGTCTTTTACTTAATTATCCTGAATTAAGTCCT
TTAACTACTTTTACTTAATTACCCTGAATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTGAA
TTAAGTCATTTAACTGTTTTTACTTAATCTCCCTGAATTAAGTACTTTAACTGCTC
Found at i:2382 original size:41 final size:41
Alignment explanation
Indices: 2335--2422 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 41
2325 TATTTAATCT
2335 CCCTGAATTAAAACCTTAACTGTGTTTGA-CTTTCTTAATTA
1 CCCTGAATTAAAACCTTAACTGTGTTT-ATCTTTCTTAATTA
* * * *
2376 CTCTGAATTAAGACTTTAACTGTGTTTATTTTTCTTAATTA
1 CCCTGAATTAAAACCTTAACTGTGTTTATCTTTCTTAATTA
2417 CCCTGA
1 CCCTGA
2423 GACTTTGACT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 1 0.02
41 40 0.98
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.44
Consensus pattern (41 bp):
CCCTGAATTAAAACCTTAACTGTGTTTATCTTTCTTAATTA
Found at i:2438 original size:36 final size:36
Alignment explanation
Indices: 2386--2454 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
2376 CTCTGAATTA
* *
2386 AGACTTTAACTGTGTTTATTTTTCTTAATTACCCTG
1 AGACTTTAACTATGTTTACTTTTCTTAATTACCCTG
* *
2422 AGACTTTGACTATGTTTGCTTTTCTTAATTACC
1 AGACTTTAACTATGTTTACTTTTCTTAATTACC
2455 ATAATTAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.22, C:0.17, G:0.12, T:0.49
Consensus pattern (36 bp):
AGACTTTAACTATGTTTACTTTTCTTAATTACCCTG
Found at i:3717 original size:38 final size:38
Alignment explanation
Indices: 3633--3780 Score: 239
Period size: 38 Copynumber: 4.0 Consensus size: 38
3623 GATTAAGTTC
* * *
3633 TTTATTGACTCCACTTAGTTACCCTGAATTAAG--CCT
1 TTTATTGACGCTACTTAATTACCCTGAATTAAGTCCCT
3669 TTTATTGACGCTACTTAATTACCCTGAATTAAGTCCCT
1 TTTATTGACGCTACTTAATTACCCTGAATTAAGTCCCT
3707 TTTATTGACGCTACTTAATTACCCTGAATTAAGTCCC-
1 TTTATTGACGCTACTTAATTACCCTGAATTAAGTCCCT
*
3744 TTTATTGACGCTACTTAATTGCCCTGAATTAAGTCCC
1 TTTATTGACGCTACTTAATTACCCTGAATTAAGTCCC
3781 CAACTTGACT
Statistics
Matches: 106, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
36 30 0.28
37 36 0.34
38 40 0.38
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (38 bp):
TTTATTGACGCTACTTAATTACCCTGAATTAAGTCCCT
Found at i:3773 original size:75 final size:74
Alignment explanation
Indices: 3633--3780 Score: 242
Period size: 75 Copynumber: 2.0 Consensus size: 74
3623 GATTAAGTTC
* * *
3633 TTTATTGACTCCACTTAGTTACCCTGAATTAAGCCTTTTATTGACGCTACTTAATTACCCTGAAT
1 TTTATTGACGCCACTTAATTACCCTGAATTAAGCCCTTTATTGACGCTACTTAATTACCCTGAAT
3698 TAAGTCCCT
66 TAAGTCCCT
* *
3707 TTTATTGACGCTACTTAATTACCCTGAATTAAGTCCCTTTATTGACGCTACTTAATTGCCCTGAA
1 TTTATTGACGCCACTTAATTACCCTGAATTAAG-CCCTTTATTGACGCTACTTAATTACCCTGAA
3772 TTAAGTCCC
65 TTAAGTCCC
3781 CAACTTGACT
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
74 30 0.44
75 38 0.56
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (74 bp):
TTTATTGACGCCACTTAATTACCCTGAATTAAGCCCTTTATTGACGCTACTTAATTACCCTGAAT
TAAGTCCCT
Found at i:3789 original size:37 final size:37
Alignment explanation
Indices: 3624--3780 Score: 237
Period size: 37 Copynumber: 4.3 Consensus size: 37
3614 CTCTTTTTAG
* * * *
3624 ATTAAGT-TCTTTATTGACTCCACTTAGTTACCCTGA
1 ATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
*
3660 ATTAAG-CCTTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
3696 ATTAAGTCCCTTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGTCCC-TTTATTGACGCTACTTAATTACCCTGA
*
3734 ATTAAGTCCCTTTATTGACGCTACTTAATTGCCCTGA
1 ATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
3771 ATTAAGTCCC
1 ATTAAGTCCC
3781 CAACTTGACT
Statistics
Matches: 111, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
36 36 0.32
37 38 0.34
38 37 0.33
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (37 bp):
ATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
Found at i:3815 original size:37 final size:37
Alignment explanation
Indices: 3769--4026 Score: 326
Period size: 37 Copynumber: 7.0 Consensus size: 37
3759 TAATTGCCCT
* *
3769 GAATTAAGTCCCCAACT-TGACTTAATTCCCTTCCTTG
1 GAATCAAGTCCCTAACTCT-ACTTAATTCCCTTCCTTG
*
3806 GAATCAAGTCCCTAACTCCACTTAATTCCCTTCCTTG
1 GAATCAAGTCCCTAACTCTACTTAATTCCCTTCCTTG
* *
3843 GAATCAAGTCCTTAACTCCACTTAATTCCCTTCCTTG
1 GAATCAAGTCCCTAACTCTACTTAATTCCCTTCCTTG
* *
3880 GAATCAAGT-CTTGTACTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCCT-AACTCTACTTAATTCCCTTCCTTG
* *
3917 GAATCAAG-CCCTTTACTCTACTTAATTCCCTTCCTTA
1 GAATCAAGTCCC-TAACTCTACTTAATTCCCTTCCTTG
*
3954 GAATCAAG-CCCTTTACTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCC-TAACTCTACTTAATTCCCTTCCTTG
** * *
3991 GAATTTAGTCCTTAACTCTACTTAATTACCTTCCTT
1 GAATCAAGTCCCTAACTCTACTTAATTCCCTTCCTT
4027 AAAATTAAGT
Statistics
Matches: 202, Mismatches: 14, Indels: 10
0.89 0.06 0.04
Matches are distributed among these distances:
36 3 0.01
37 196 0.97
38 3 0.01
ACGTcount: A:0.24, C:0.31, G:0.08, T:0.38
Consensus pattern (37 bp):
GAATCAAGTCCCTAACTCTACTTAATTCCCTTCCTTG
Found at i:4128 original size:35 final size:35
Alignment explanation
Indices: 4071--4198 Score: 163
Period size: 35 Copynumber: 3.7 Consensus size: 35
4061 TCTTTGGATC
* * *
4071 AAGTCTATGCTGACTTTACTTAATTCTTGTGAAATG
1 AAGTCTTTGCT-AATTTACTTAATTCTTGTGAAATT
*
4107 AGGTCTTTGCTAATTTACTTAATTCTTGTGAAATT
1 AAGTCTTTGCTAATTTACTTAATTCTTGTGAAATT
* *
4142 AAGTCTCTGCTAATTTTACCTAATTC---TGAAATT
1 AAGTCTTTGCTAA-TTTACTTAATTCTTGTGAAATT
4175 AAGTCTTTGCTAATTTACTTAATT
1 AAGTCTTTGCTAATTTACTTAATT
4199 ACCCTGAATT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
32 10 0.12
33 19 0.23
35 33 0.40
36 20 0.24
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.45
Consensus pattern (35 bp):
AAGTCTTTGCTAATTTACTTAATTCTTGTGAAATT
Found at i:4263 original size:41 final size:41
Alignment explanation
Indices: 4205--4369 Score: 209
Period size: 41 Copynumber: 4.1 Consensus size: 41
4195 AATTACCCTG
*
4205 AATTAA-TTCTGTACTTGTCTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTT-TGTGCTTGTCTTTACCTAATTTCCTTCCTTGA
4246 AATTAAGTTTGTGCTTGTCTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTTTGTGCTTGTCTTTACCTAATTTCCTTCCTTGA
* *
4287 AATTAAGTTTGTGCTT-TACTTTACTTAA-TTAC--CC-TG-
1 AATTAAGTTTGTGCTTGT-CTTTACCTAATTTCCTTCCTTGA
* * *
4323 AATTAAGTCTGTGCTTGTCTTTACCTAGTTTCCTTCCTTGG
1 AATTAAGTTTGTGCTTGTCTTTACCTAATTTCCTTCCTTGA
4364 AATTAA
1 AATTAA
4370 TCCTTTAACT
Statistics
Matches: 109, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
36 23 0.21
37 6 0.06
38 2 0.02
39 2 0.02
40 6 0.06
41 68 0.62
42 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (41 bp):
AATTAAGTTTGTGCTTGTCTTTACCTAATTTCCTTCCTTGA
Found at i:4304 original size:77 final size:76
Alignment explanation
Indices: 4219--4369 Score: 196
Period size: 77 Copynumber: 2.0 Consensus size: 76
4209 AATTCTGTAC
* ** * *
4219 TTGTCTTTACCTAATTTCCTT-CCTTGAAATTAAGTTTGTGCTTGTCTTTACCTAATTTCCTTCC
1 TTGTCTTTACCTAACTTAATTACCCTG-AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCC
4283 TTGAAATTAAGT
65 TTGAAATTAAGT
* * *
4295 TTGTGCTTTACTTTACTTAATTACCCTGAATTAAGTCTGTGCTTGTCTTTACCTAGTTTCCTTCC
1 TTGT-CTTTACCTAACTTAATTACCCTGAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCC
*
4360 TTGGAATTAA
65 TTGAAATTAA
4370 TCCTTTAACT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
76 4 0.06
77 56 0.88
78 4 0.06
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.48
Consensus pattern (76 bp):
TTGTCTTTACCTAACTTAATTACCCTGAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCCT
TGAAATTAAGT
Found at i:4424 original size:37 final size:37
Alignment explanation
Indices: 4383--4922 Score: 848
Period size: 37 Copynumber: 14.6 Consensus size: 37
4373 TTTAACTACT
* * *
4383 TTTACTTAATTTCCCTGGATTAAGCTCTTTAACTGTG
1 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
*
4420 TTTACTTAATTACCCGGAATTAAGTTCTTTAACTGTG
1 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
* * *
4457 TTTACTTAATTACCCAGAATTAAGTCCTTTGACTGTG
1 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
* *
4494 TTTACTTAATTACCCAGAATTAAGTT-TTCTGACTGTG
1 TTTACTTAATTACCCTGAATTAAGTTCTT-TAACTGTG
4531 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
1 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
*
4568 TTTACTTAATTACCCTGAATTAAGTTCTCTAACTGTG
1 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
* * * *
4605 TTAACTTAATTACCCTGAAATAAGTTCTCTGACTGTG
1 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
4642 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
1 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
*
4679 TTTACTTAATTACCCTGAATTAAGTTCTTTGACTGTG
1 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
*
4716 TTTACTTAATTACCCTGAATTAAGTTCTTTGACTGTG
1 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
4753 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
1 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
*
4790 TTTACTTAATTACCCTGAATTAAGTTCTTTGACTGTG
1 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
*
4827 TTTACTTAATTACCCCGAATTAAGTTCTTTAACTGTG
1 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
* * ** *
4864 TTTACTTAATTTCCCAGAATTAAGCCCTTTAACTGTC
1 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
*
4901 TTTACTTAATTGCCCTGAATTA
1 TTTACTTAATTACCCTGAATTA
4923 CTTAATTACT
Statistics
Matches: 471, Mismatches: 30, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
36 2 0.00
37 467 0.99
38 2 0.00
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (37 bp):
TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGTG
Found at i:4938 original size:18 final size:18
Alignment explanation
Indices: 4902--4940 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4892 TTAACTGTCT
* *
4902 TTACTTAATTGCCCTGAA
1 TTACTTAATTACCCAGAA
*
4920 TTACTTAATTACTCAGAA
1 TTACTTAATTACCCAGAA
4938 TTA
1 TTA
4941 AGTCCTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (18 bp):
TTACTTAATTACCCAGAA
Found at i:5044 original size:41 final size:41
Alignment explanation
Indices: 4998--5171 Score: 222
Period size: 41 Copynumber: 4.2 Consensus size: 41
4988 CTATTTTTTC
* * **
4998 CTTTCTTAATCACCTTGGATTAAAACTTTAACTACGTTTTC
1 CTTTCTTAATCACCCTGGATTAAAACTTTAACTATGTTTGA
* * *
5039 CTTTCTTAATCACCCTGTATTGAAACTTTAACTATGGTTGA
1 CTTTCTTAATCACCCTGGATTAAAACTTTAACTATGTTTGA
* *
5080 CTTTCTTAATCGCCCTGGATTAAAACTTCAACTATGTTTGA
1 CTTTCTTAATCACCCTGGATTAAAACTTTAACTATGTTTGA
* * * *
5121 CTTCCTTAATCGCCCTGGATTAAAACTTTAACTATGCTTGT
1 CTTTCTTAATCACCCTGGATTAAAACTTTAACTATGTTTGA
*
5162 TTTTCTTAAT
1 CTTTCTTAAT
5172 TGCCTTGAAT
Statistics
Matches: 115, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 115 1.00
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (41 bp):
CTTTCTTAATCACCCTGGATTAAAACTTTAACTATGTTTGA
Found at i:7052 original size:29 final size:29
Alignment explanation
Indices: 7010--7070 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
7000 GGTTGGTCAT
*
7010 CAACGCCTCTTGCATTTTGTCATGTGCTC
1 CAACGCCTCTTGCATCTTGTCATGTGCTC
7039 CAACGCCTCTTGCATCTTGTCATGTGCTC
1 CAACGCCTCTTGCATCTTGTCATGTGCTC
7068 CAA
1 CAA
7071 GCCCTTTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.16, C:0.33, G:0.16, T:0.34
Consensus pattern (29 bp):
CAACGCCTCTTGCATCTTGTCATGTGCTC
Found at i:8398 original size:25 final size:25
Alignment explanation
Indices: 8370--8423 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
8360 TTAGTTAATT
8370 AAATTAGATTGGAACTACATGAATG
1 AAATTAGATTGGAACTACATGAATG
* * *
8395 AAATTAGATTTGAGCTACATGACTG
1 AAATTAGATTGGAACTACATGAATG
8420 AAAT
1 AAAT
8424 GCAAACTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.30
Consensus pattern (25 bp):
AAATTAGATTGGAACTACATGAATG
Found at i:8847 original size:22 final size:22
Alignment explanation
Indices: 8820--8978 Score: 165
Period size: 22 Copynumber: 7.2 Consensus size: 22
8810 GAGTCCGTCT
* * *
8820 TGAGACGCTTAAAAGTCTACCC
1 TGAGACACTTGAAAGTCTGCCC
* * *
8842 TAAGACGCTTGGAAGTCTGCCC
1 TGAGACACTTGAAAGTCTGCCC
*
8864 TGAGACACTTGAAAGTCTTCCC
1 TGAGACACTTGAAAGTCTGCCC
8886 TGAGACACTTGAAAGTCTGCCC
1 TGAGACACTTGAAAGTCTGCCC
* * *
8908 TGAGACATTTGACAGTCTGGCC
1 TGAGACACTTGAAAGTCTGCCC
* *** *
8930 TGAGACGCTTGATTTTCTACCC
1 TGAGACACTTGAAAGTCTGCCC
* *
8952 TGAAACACTTGAAGGTCTGCCC
1 TGAGACACTTGAAAGTCTGCCC
8974 TGAGA
1 TGAGA
8979 TGCTGAAGAA
Statistics
Matches: 111, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 111 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (22 bp):
TGAGACACTTGAAAGTCTGCCC
Found at i:10764 original size:12 final size:12
Alignment explanation
Indices: 10747--10783 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
10737 ACCCTCACCT
10747 AAAACTAGAAGA
1 AAAACTAGAAGA
10759 AAAACTA-AAGA
1 AAAACTAGAAGA
*
10770 AAAA-TTGAAGA
1 AAAACTAGAAGA
10781 AAA
1 AAA
10784 GAATTGTGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
10 1 0.04
11 15 0.65
12 7 0.30
ACGTcount: A:0.70, C:0.05, G:0.14, T:0.11
Consensus pattern (12 bp):
AAAACTAGAAGA
Found at i:14649 original size:35 final size:35
Alignment explanation
Indices: 14600--14668 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
14590 GCCTATGATA
*
14600 ACTACATTAGGTCTTGATTAATCCAAAATCGACTC
1 ACTACATTAAGTCTTGATTAATCCAAAATCGACTC
*
14635 ACTACATTAAGTCTTGATTAATCCAAAGTCGACT
1 ACTACATTAAGTCTTGATTAATCCAAAATCGACT
14669 AACATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.32
Consensus pattern (35 bp):
ACTACATTAAGTCTTGATTAATCCAAAATCGACTC
Found at i:15345 original size:20 final size:20
Alignment explanation
Indices: 15320--15361 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
15310 AGTAATTACT
*
15320 CAAACTTAATAATACCATTA
1 CAAACTTAATAAAACCATTA
15340 CAAACTTAATAAAACCATTA
1 CAAACTTAATAAAACCATTA
15360 CA
1 CA
15362 GAATATAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.26
Consensus pattern (20 bp):
CAAACTTAATAAAACCATTA
Found at i:17951 original size:40 final size:40
Alignment explanation
Indices: 17892--17986 Score: 181
Period size: 40 Copynumber: 2.4 Consensus size: 40
17882 AACTAGCCCA
*
17892 CAGCTAAAATATGGGTTCCAACATTGCATGTTGGTTCATG
1 CAGCTAAAATATGGATTCCAACATTGCATGTTGGTTCATG
17932 CAGCTAAAATATGGATTCCAACATTGCATGTTGGTTCATG
1 CAGCTAAAATATGGATTCCAACATTGCATGTTGGTTCATG
17972 CAGCTAAAATATGGA
1 CAGCTAAAATATGGA
17987 GGGTTAAAGA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (40 bp):
CAGCTAAAATATGGATTCCAACATTGCATGTTGGTTCATG
Found at i:18532 original size:48 final size:48
Alignment explanation
Indices: 18452--18632 Score: 211
Period size: 48 Copynumber: 3.8 Consensus size: 48
18442 TTGAAGAAAT
***
18452 TGGAGCTACAAGTTGGGTCATGAGTTTTAGAACGAGTGTAAAAGTAAA
1 TGGAGCTACAAGTTGGGTCATGAGTTTTAGAACGAGCACAAAAGTAAA
* * *
18500 TGGAACTATAAGTTGGGTCATGGGTTTTAGAACGAGCACAAAAGTAAA
1 TGGAGCTACAAGTTGGGTCATGAGTTTTAGAACGAGCACAAAAGTAAA
* * * * * * * *
18548 TGGGGCTGCAAGTTGGGTGATGGGCTTTAGAACAAGCCCAAAAGTAAT
1 TGGAGCTACAAGTTGGGTCATGAGTTTTAGAACGAGCACAAAAGTAAA
*
18596 TAGG-GCTACAAGTTGGGTCATTAGTTTTAGAACGAGC
1 T-GGAGCTACAAGTTGGGTCATGAGTTTTAGAACGAGC
18633 CCAGAAGTTT
Statistics
Matches: 111, Mismatches: 21, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
48 109 0.98
49 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.26
Consensus pattern (48 bp):
TGGAGCTACAAGTTGGGTCATGAGTTTTAGAACGAGCACAAAAGTAAA
Found at i:22785 original size:13 final size:13
Alignment explanation
Indices: 22764--22793 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
22754 GTTTTCACTA
*
22764 ACAGTAGGTTGAG
1 ACAGCAGGTTGAG
22777 ACAGCAGGTTGAG
1 ACAGCAGGTTGAG
22790 ACAG
1 ACAG
22794 GAAAATTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.37, T:0.17
Consensus pattern (13 bp):
ACAGCAGGTTGAG
Found at i:24521 original size:11 final size:11
Alignment explanation
Indices: 24478--24515 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
24468 CTCCTATATA
*
24478 AAATAAATTAT
1 AAATTAATTAT
24489 CAAA-TAATTAT
1 -AAATTAATTAT
24500 AAATTAATTAT
1 AAATTAATTAT
24511 AAATT
1 AAATT
24516 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Done.