Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016071.1 Corchorus capsularis cultivar CVL-1 contig16092, 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: 27749
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:131 original size:35 final size:34
Alignment explanation
Indices: 87--309 Score: 133
Period size: 35 Copynumber: 6.5 Consensus size: 34
77 GTAATTGGAT
87 AATAGTAATCAGTAAAA-AGTAATCGGTAAGAGTAA
1 AATAGTAATCAGTAAAAGA-TAAT-GGTAAGAGTAA
* * *
122 AATAATAATCAGTAAGAGCA-AAGTGGTAATAGTAA
1 AATAGTAATCAGTAAAAG-ATAA-TGGTAAGAGTAA
*
157 AATAGTAATCAGTAAAAGATAATTAGTAAGAGTAA
1 AATAGTAATCAGTAAAAGATAA-TGGTAAGAGTAA
** *
192 AATAGTAAAGAGTAAGATGATAA----AA-AGT-A
1 AATAGTAATCAGTAA-AAGATAATGGTAAGAGTAA
* * * *
221 AAGACTAATCAGTAAAGAGTAAAATGGTAAAAAGT-A
1 AATAGTAATCAGTAAA-AG-ATAATGGT-AAGAGTAA
* *
257 AAGAGTAATCAGTAAAAGAGTAAAATGGTAAAAGGT-A
1 AATAGTAATCAGTAAAAGA-T--AATGGTAAGA-GTAA
*
294 AAGAGTAATCAGTAAA
1 AATAGTAATCAGTAAA
310 GAGAAAAATG
Statistics
Matches: 152, Mismatches: 19, Indels: 32
0.75 0.09 0.16
Matches are distributed among these distances:
28 1 0.01
29 13 0.09
30 6 0.04
31 2 0.01
34 2 0.01
35 72 0.47
36 30 0.20
37 26 0.17
ACGTcount: A:0.54, C:0.04, G:0.20, T:0.22
Consensus pattern (34 bp):
AATAGTAATCAGTAAAAGATAATGGTAAGAGTAA
Found at i:221 original size:36 final size:37
Alignment explanation
Indices: 147--319 Score: 148
Period size: 36 Copynumber: 4.8 Consensus size: 37
137 GAGCAAAGTG
* ** **
147 GTAATAGTAAAAT-AGTAATCAGTAAAA-GATAATTA
1 GTAAGAGTAAAATCAGTAAAGAGTAAAATGATAAAAA
*
182 GTAAGAGTAAAAT-AGTAAAGAGTAAGATGATAAAAA
1 GTAAGAGTAAAATCAGTAAAGAGTAAAATGATAAAAA
* *
218 GTAA-AG-ACTAATCAGTAAAGAGTAAAATGGTAAAAA
1 GTAAGAGTA-AAATCAGTAAAGAGTAAAATGATAAAAA
* *
254 GTAAAGAGT--AATCAGTAAAAGAGTAAAATGGTAAAAG
1 GT-AAGAGTAAAATCAGT-AAAGAGTAAAATGATAAAAA
*
291 GTAAAGAGT--AATCAGTAAAGAGAAAAATG
1 GT-AAGAGTAAAATCAGTAAAGAGTAAAATG
320 GCAAAATATA
Statistics
Matches: 120, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
34 1 0.01
35 28 0.23
36 52 0.43
37 37 0.31
38 2 0.02
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (37 bp):
GTAAGAGTAAAATCAGTAAAGAGTAAAATGATAAAAA
Found at i:222 original size:7 final size:7
Alignment explanation
Indices: 187--301 Score: 50
Period size: 7 Copynumber: 15.7 Consensus size: 7
177 AATTAGTAAG
187 AGTAAAA
1 AGTAAAA
*
194 TAGTAAAG
1 -AGTAAAA
*
202 AGTAAGA
1 AGTAAAA
*
209 TGATAAAA
1 AG-TAAAA
*
217 AGTAAAG
1 AGTAAAA
* **
224 ACTAATC
1 AGTAAAA
*
231 AGTAAAG
1 AGTAAAA
238 AGTAAAA
1 AGTAAAA
*
245 TGGTAAAA
1 -AGTAAAA
*
253 AGTAAAG
1 AGTAAAA
**
260 AGTAATC
1 AGTAAAA
267 AGTAAAA
1 AGTAAAA
274 GAGTAAAA
1 -AGTAAAA
*
282 TGGTAAAA
1 -AGTAAAA
* *
290 GGTAAAG
1 AGTAAAA
297 AGTAA
1 AGTAA
302 TCAGTAAAGA
Statistics
Matches: 79, Mismatches: 25, Indels: 7
0.71 0.23 0.06
Matches are distributed among these distances:
7 49 0.62
8 30 0.38
ACGTcount: A:0.57, C:0.03, G:0.22, T:0.19
Consensus pattern (7 bp):
AGTAAAA
Found at i:320 original size:36 final size:36
Alignment explanation
Indices: 195--325 Score: 199
Period size: 36 Copynumber: 3.6 Consensus size: 36
185 AGAGTAAAAT
* * *
195 AGTAAAGAGTAAGATGATAAAAAGTAAAGACTAATC
1 AGTAAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
231 AGTAAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
1 AGTAAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
*
267 AGTAAAAGAGTAAAATGGTAAAAGGTAAAGAGTAATC
1 AGT-AAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
* *
304 AGTAAAGAGAAAAATGGCAAAA
1 AGTAAAGAGTAAAATGGTAAAA
326 TATATATATA
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
36 53 0.60
37 35 0.40
ACGTcount: A:0.56, C:0.04, G:0.22, T:0.18
Consensus pattern (36 bp):
AGTAAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
Found at i:8014 original size:20 final size:20
Alignment explanation
Indices: 7989--8036 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
7979 AACTGGCGCT
*
7989 GGGCGCCCATGTGGTAAGTC
1 GGGCGCCCATGTGATAAGTC
8009 GGGCGCCCATGTGATAAGTC
1 GGGCGCCCATGTGATAAGTC
*
8029 TGGCGCCC
1 GGGCGCCC
8037 CACCAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.29, G:0.38, T:0.19
Consensus pattern (20 bp):
GGGCGCCCATGTGATAAGTC
Found at i:9783 original size:42 final size:42
Alignment explanation
Indices: 9715--9932 Score: 242
Period size: 42 Copynumber: 5.2 Consensus size: 42
9705 AATCCAGGGT
* * * * * *
9715 AATTGAGAAAGTCAAGTACAGTTAAAATTCTTAATTCAGGGA
1 AATTAAGAAGGTCAAATACAGTTAAAAGTCTTAATGCAAGGA
* *
9757 AATTAAGAAGGTTAAATACAATTAAAAGTCTTAATGCAAGGA
1 AATTAAGAAGGTCAAATACAGTTAAAAGTCTTAATGCAAGGA
* *
9799 AATTAAGAAGGTCAAATACAGTTAAAGGTCCTAATGCAAGGA
1 AATTAAGAAGGTCAAATACAGTTAAAAGTCTTAATGCAAGGA
* * *
9841 AATTAAGAAAGTCAAATACAGTTAAAAGTCTTAATGCAATGT
1 AATTAAGAAGGTCAAATACAGTTAAAAGTCTTAATGCAAGGA
* * * * * *
9883 AATTAAG-AGAGTCAAACACAATT-AAGGTCTTAATTCAGGGT
1 AATTAAGAAG-GTCAAATACAGTTAAAAGTCTTAATGCAAGGA
9924 AATTAAGAA
1 AATTAAGAA
9933 AAGTAAGCAT
Statistics
Matches: 150, Mismatches: 24, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
41 22 0.15
42 128 0.85
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (42 bp):
AATTAAGAAGGTCAAATACAGTTAAAAGTCTTAATGCAAGGA
Found at i:9823 original size:84 final size:84
Alignment explanation
Indices: 9715--9933 Score: 271
Period size: 84 Copynumber: 2.6 Consensus size: 84
9705 AATCCAGGGT
* * * ** * *
9715 AATTGAGAAAGTCAAGTACAGTTAAAATTCTTAATTCAGGGAAATTAAGAAGGTTAAATACAATT
1 AATTAAGAAGGTCAAATACAGTTAAAGGTCTTAATTCAGGGAAATTAAGAAAGTCAAATACAATT
9780 AAAAGTCTTAATGCAAGGA
66 AAAAGTCTTAATGCAAGGA
* * * *
9799 AATTAAGAAGGTCAAATACAGTTAAAGGTCCTAATGCAAGGAAATTAAGAAAGTCAAATACAGTT
1 AATTAAGAAGGTCAAATACAGTTAAAGGTCTTAATTCAGGGAAATTAAGAAAGTCAAATACAATT
* *
9864 AAAAGTCTTAATGCAATGT
66 AAAAGTCTTAATGCAAGGA
* * *
9883 AATTAAG-AGAGTCAAACACAATT-AAGGTCTTAATTCAGGGTAATTAAGAAA
1 AATTAAGAAG-GTCAAATACAGTTAAAGGTCTTAATTCAGGGAAATTAAGAAA
9934 AGTAAGCATA
Statistics
Matches: 115, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
83 26 0.23
84 89 0.77
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.26
Consensus pattern (84 bp):
AATTAAGAAGGTCAAATACAGTTAAAGGTCTTAATTCAGGGAAATTAAGAAAGTCAAATACAATT
AAAAGTCTTAATGCAAGGA
Found at i:10195 original size:30 final size:30
Alignment explanation
Indices: 10161--10356 Score: 90
Period size: 32 Copynumber: 5.7 Consensus size: 30
10151 CACAGTCAAG
*
10161 GTCTTAATTTGGTAATTAAGAATAGTTAGA
1 GTCTTAATTTGGTAATTAAGAACAGTTAGA
* *
10191 GTCTTAATTCAGGGTAATTAAGAGA-AGTAAGCACAGTCAA
1 GTCTTAATT--TGGTAATTAAGA-ACAGT-----TAG---A
*
10231 GGTCTTAATTTGGTAATTAAGAACAGCTAGA
1 G-TCTTAATTTGGTAATTAAGAACAGTTAGA
* *
10262 GTCTTAATTCAGGGTAATTAAGAGA-AGTAAGCACA
1 GTCTTAATT--TGGTAATTAAGA-ACAGTTAG---A
10297 GTCAAGGTGTTAATTTGGTAATTAAGAACAGTTAGA
1 GTC------TTAATTTGGTAATTAAGAACAGTTAGA
10333 GTCTTAATTTAGGGTAATTAAGAA
1 GTCTTAATTT--GGTAATTAAGAA
10357 AAGAGAGTAC
Statistics
Matches: 128, Mismatches: 10, Indels: 54
0.67 0.05 0.28
Matches are distributed among these distances:
30 24 0.19
31 2 0.02
32 41 0.32
33 2 0.02
34 2 0.02
35 4 0.03
36 4 0.03
37 2 0.02
38 2 0.02
39 29 0.23
40 2 0.02
41 14 0.11
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (30 bp):
GTCTTAATTTGGTAATTAAGAACAGTTAGA
Found at i:10364 original size:30 final size:29
Alignment explanation
Indices: 10306--10364 Score: 75
Period size: 32 Copynumber: 2.0 Consensus size: 29
10296 AGTCAAGGTG
*
10306 TTAATTTGGTAATTAAGAACAGTTAGAGTC
1 TTAATTTGGTAATTAAGAAAAG-TAGAGTC
10336 TTAATTTAGGGTAATTAAGAAAAG-AGAGT
1 TTAATTT--GGTAATTAAGAAAAGTAGAGT
10365 ACAGTCAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 12 0.46
32 14 0.54
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (29 bp):
TTAATTTGGTAATTAAGAAAAGTAGAGTC
Found at i:10531 original size:70 final size:70
Alignment explanation
Indices: 9909--10593 Score: 843
Period size: 71 Copynumber: 9.7 Consensus size: 70
9899 CACAATTAAG
* * * * * * *
9909 GTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCCTAATCTGGTAATCAGGAGAA
1 GTCTTAATTCAGGGTAATTAAGAGAAGTAAGCACAGTCAAGGTCTTAATTTGGTAATTAAGAAAA
* *
9974 TTAAA
66 GTAGA
** * * * *
9979 GTCCCAACTCAGGGTAATTAAGAAAAGTAAGCATAGTTAAGGTCTTAATTTGGTAATTAAGAAAA
1 GTCTTAATTCAGGGTAATTAAGAGAAGTAAGCACAGTCAAGGTCTTAATTTGGTAATTAAGAAAA
* *
10044 GCAAA
66 GTAGA
*
10049 GTCTTAATTCAAGGTAATTAAGAGAAGTAAGCACAGTCAAGGTCTTAATTTGGTAATTAAGAACA
1 GTCTTAATTCAGGGTAATTAAGAGAAGTAAGCACAGTCAAGGTCTTAATTTGGTAATTAAGAA-A
**
10114 TTTAGA
65 AGTAGA
* *
10120 GTCTTAATTCAGGGTAATTAAGAGAAGTATGCACAGTCAAGGTCTTAATTTGGTAATTAAGAATA
1 GTCTTAATTCAGGGTAATTAAGAGAAGTAAGCACAGTCAAGGTCTTAATTTGGTAATTAAGAAAA
10185 GTTAGA
66 G-TAGA
*
10191 GTCTTAATTCAGGGTAATTAAGAGAAGTAAGCACAGTCAAGGTCTTAATTTGGTAATTAAGAACA
1 GTCTTAATTCAGGGTAATTAAGAGAAGTAAGCACAGTCAAGGTCTTAATTTGGTAATTAAGAAAA
10256 GCTAGA
66 G-TAGA
* *
10262 GTCTTAATTCAGGGTAATTAAGAGAAGTAAGCACAGTCAAGGTGTTAATTTGGTAATTAAGAACA
1 GTCTTAATTCAGGGTAATTAAGAGAAGTAAGCACAGTCAAGGTCTTAATTTGGTAATTAAGAAAA
10327 GTTAGA
66 G-TAGA
* * * **
10333 GTCTTAATTTAGGGTAATTAAGAAAAG-AGAGTACAGTCAAGGTCTTAATCCGGTAATTAAGTAA
1 GTCTTAATTCAGGGTAATTAAGAGAAGTA-AGCACAGTCAAGGTCTTAATTTGGTAATTAAG-AA
* *
10397 AAATAAA
64 AAGTAGA
* * **
10404 GTCTTAGTTCAGGGTAATTTAGAGAAGTAAGCACAGTCAAGGTCTTAATCCGGTAATTAAGAAAA
1 GTCTTAATTCAGGGTAATTAAGAGAAGTAAGCACAGTCAAGGTCTTAATTTGGTAATTAAGAAAA
*
10469 GCAGA
66 GTAGA
* ** *
10474 GTTTTAATTCAGGGTAATTAAGAGAAGTAAGCACAGTCAAGGTCTTAATCCGGTAATTAAGAGAA
1 GTCTTAATTCAGGGTAATTAAGAGAAGTAAGCACAGTCAAGGTCTTAATTTGGTAATTAAGAAAA
* *
10539 GCAAA
66 GTAGA
* * * * * * *
10544 GTATTAATCCAGGATAATTGAGCAG-AGTAAACACAGTCAGGGGCTTAATT
1 GTCTTAATTCAGGGTAATTAAG-AGAAGTAAGCACAGTCAAGGTCTTAATT
10594 CATAGAAATT
Statistics
Matches: 547, Mismatches: 62, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
70 226 0.41
71 317 0.58
72 4 0.01
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (70 bp):
GTCTTAATTCAGGGTAATTAAGAGAAGTAAGCACAGTCAAGGTCTTAATTTGGTAATTAAGAAAA
GTAGA
Found at i:11119 original size:41 final size:40
Alignment explanation
Indices: 10924--11137 Score: 320
Period size: 40 Copynumber: 5.3 Consensus size: 40
10914 AATTCATGGT
* * *
10924 AATTAAGTAAAAGATAAGCACAAACTTAATTTCAAGGAAGCA
1 AATTAGGT-AAAG-TAAGCACAGACTTAATTTCAAGGAAGGA
* *
10966 AATTAGGTAAAGTACGCACAAACTTAATTTCAAGGAAGGA
1 AATTAGGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGA
* *
11006 AATTAGGTAAGGTAAGCACCGACTTAATTTCAAGGAAGGA
1 AATTAGGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGA
*
11046 AATTAGGTAAAGTAAACACAGACTTAATTTCAAGGAAGGA
1 AATTAGGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGA
*
11086 AATTAGGTAAGGTAAAGCACAGACTTAATTTCAAGGAAGGA
1 AATTAGGTAAAGT-AAGCACAGACTTAATTTCAAGGAAGGA
11127 AATTAGGTAAA
1 AATTAGGTAAA
11138 AGGGCTTAAT
Statistics
Matches: 158, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
40 111 0.70
41 40 0.25
42 7 0.04
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.22
Consensus pattern (40 bp):
AATTAGGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGA
Found at i:11180 original size:32 final size:34
Alignment explanation
Indices: 11142--11226 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 34
11132 GGTAAAAGGG
*
11142 CTTAATTCAGGGTAATTAAGT-AG-AATAAAGAA-
1 CTTAATTTAGGGTAATTAAGTGAGCAATAAA-AAT
*
11174 CTTAATTTAGGGAAATTAAGTGGAGCCAATAAAAAT
1 CTTAATTTAGGGTAATTAAGT-GAG-CAATAAAAAT
11210 CTTAATTTAGGGTAATT
1 CTTAATTTAGGGTAATT
11227 GGGCAAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
32 19 0.42
34 2 0.04
35 2 0.04
36 22 0.49
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (34 bp):
CTTAATTTAGGGTAATTAAGTGAGCAATAAAAAT
Found at i:13139 original size:5 final size:5
Alignment explanation
Indices: 13129--13163 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
13119 CCTAAAGAAA
*
13129 AAAAG AAAAG AAAAG AATAG AAAAG AAAAGG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA-G AAAA
13164 TTACAGACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:13152 original size:15 final size:14
Alignment explanation
Indices: 13122--13158 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
13112 TTGATTTCCT
13122 AAAGAAAA-AAAGA
1 AAAGAAAAGAAAGA
13135 AAAGAAAAGAATAGA
1 AAAGAAAAGAA-AGA
13150 AAAGAAAAG
1 AAAGAAAAG
13159 GAAAATTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.36
14 2 0.09
15 12 0.55
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (14 bp):
AAAGAAAAGAAAGA
Found at i:13348 original size:53 final size:52
Alignment explanation
Indices: 13249--13351 Score: 134
Period size: 53 Copynumber: 2.0 Consensus size: 52
13239 GGTGATCTTT
* * * * *
13249 GATCACCTGTGGTGATCTTGGGTGGTTATCTCAAATCACTCTATTTGGTTGG
1 GATCACCCGTGGTAATCTTGGGTGGTGATCTCAAATCACCCCATTTGGTTGG
**
13301 GATCACCCGTTGGTAATCTTGGGTGGTGATCTCAGGTCACCCCATTTGGTT
1 GATCACCCG-TGGTAATCTTGGGTGGTGATCTCAAATCACCCCATTTGGTT
13352 ACACTTTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
52 8 0.19
53 35 0.81
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (52 bp):
GATCACCCGTGGTAATCTTGGGTGGTGATCTCAAATCACCCCATTTGGTTGG
Found at i:15267 original size:16 final size:17
Alignment explanation
Indices: 15246--15278 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
15236 AAATCCGATC
15246 GAACCCGAACCC-AAAA
1 GAACCCGAACCCGAAAA
15262 GAACCCGAACCCGAAAA
1 GAACCCGAACCCGAAAA
15279 AATCAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.48, C:0.36, G:0.15, T:0.00
Consensus pattern (17 bp):
GAACCCGAACCCGAAAA
Found at i:15320 original size:16 final size:16
Alignment explanation
Indices: 15301--15344 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
15291 CCCAAACTCG
*
15301 AAAATACCCGATCCCA
1 AAAATACCCGAACCCA
* *
15317 AAAATACCTGAACCGA
1 AAAATACCCGAACCCA
*
15333 AAAATATCCGAA
1 AAAATACCCGAA
15345 TTCAATACTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.50, C:0.27, G:0.09, T:0.14
Consensus pattern (16 bp):
AAAATACCCGAACCCA
Found at i:16089 original size:32 final size:32
Alignment explanation
Indices: 16029--16089 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
16019 AACCGAATTA
* * *
16029 ACCTGACCTGGAATTGACTTGAATCCGAAAAC
1 ACCTGACCTGAAATTGACTCGAACCCGAAAAC
16061 ACCTGACCTGAAATTGA-TCCGAACCCGAA
1 ACCTGACCTGAAATTGACT-CGAACCCGAA
16090 TTAATCTGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 1 0.04
32 24 0.96
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (32 bp):
ACCTGACCTGAAATTGACTCGAACCCGAAAAC
Found at i:16822 original size:16 final size:16
Alignment explanation
Indices: 16803--16928 Score: 62
Period size: 16 Copynumber: 7.9 Consensus size: 16
16793 CGAATCCGAG
16803 ACCCGAATGACCCGTA
1 ACCCGAATGACCCGTA
*
16819 ACCC-AGATGACTCG-A
1 ACCCGA-ATGACCCGTA
* *
16834 GACCCAAATGACTCGTA
1 -ACCCGAATGACCCGTA
* * **
16851 ACCC-ATATAATCCAAA
1 ACCCGA-ATGACCCGTA
* **
16867 ACTCGAATGACAGGTA
1 ACCCGAATGACCCGTA
*
16883 ACCCGAGTGACCCG-A
1 ACCCGAATGACCCGTA
* * *
16898 TATCCGAATGAACCGTG
1 -ACCCGAATGACCCGTA
16915 ACCCGAATGACCCG
1 ACCCGAATGACCCG
16929 AGAATATTAC
Statistics
Matches: 79, Mismatches: 23, Indels: 16
0.67 0.19 0.14
Matches are distributed among these distances:
15 4 0.05
16 72 0.91
17 3 0.04
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (16 bp):
ACCCGAATGACCCGTA
Found at i:18951 original size:13 final size:14
Alignment explanation
Indices: 18933--18962 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
18923 ACTTTTGACC
18933 ATATATTATG-ATA
1 ATATATTATGTATA
18946 ATATATTATGTATA
1 ATATATTATGTATA
18960 ATA
1 ATA
18963 ATTTTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
ATATATTATGTATA
Found at i:19723 original size:31 final size:31
Alignment explanation
Indices: 19679--19739 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
19669 CTCAAATAGG
**
19679 TACTAAATGTTTCAAAATTGGATCAATTTAA
1 TACTAAACATTTCAAAATTGGATCAATTTAA
19710 TACTAAACATTTCAAAATTGGATCAATTTA
1 TACTAAACATTTCAAAATTGGATCAATTTA
19740 GATTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (31 bp):
TACTAAACATTTCAAAATTGGATCAATTTAA
Found at i:24150 original size:30 final size:30
Alignment explanation
Indices: 24094--24152 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
24084 TGTCTTCAAG
* * *
24094 TCCATGATAAGTTCTTTGCGCTTCATTCCT
1 TCCATGATAAGTCCTTGGCGCATCATTCCT
24124 TCCATGATAAG-CCTTGGGCGCATCATTCC
1 TCCATGATAAGTCCTT-GGCGCATCATTCC
24153 CTCCCCATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.36
Consensus pattern (30 bp):
TCCATGATAAGTCCTTGGCGCATCATTCCT
Found at i:26028 original size:30 final size:30
Alignment explanation
Indices: 25994--26052 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
25984 TGTCTTCAAG
* *
25994 TCCATGATAAGTTCTT-GGCGCTTCATTCCT
1 TCCATGATAAG-CCTTGGGCGCATCATTCCT
26024 TCCATGATAAGCCTTGGGCGCATCATTCC
1 TCCATGATAAGCCTTGGGCGCATCATTCC
26053 CTCCCCCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.34
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCT
Done.