Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024279.1 Corchorus olitorius cultivar O-4 contig24312, 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: 71508
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:10206 original size:2 final size:2
Alignment explanation
Indices: 10199--10225 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10189 CTCTAACTAG
10199 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
10226 TTCAATTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10324 original size:15 final size:17
Alignment explanation
Indices: 10306--10344 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
10296 GAAAAGAGCA
10306 AAAAGGAAAG-AAAG-C
1 AAAAGGAAAGAAAAGCC
*
10321 AAAAGGAGAGAAAAGCC
1 AAAAGGAAAGAAAAGCC
10338 AAAAGGA
1 AAAAGGA
10345 TTCATTGCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
16 4 0.19
17 8 0.38
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (17 bp):
AAAAGGAAAGAAAAGCC
Found at i:15902 original size:32 final size:31
Alignment explanation
Indices: 15832--15914 Score: 107
Period size: 32 Copynumber: 2.7 Consensus size: 31
15822 ATTCTATTAA
* *
15832 TTTCCAAAATCTTCTTTTGG-GTTTCTTTAT
1 TTTCCAAAATCTTCTTTTGGAATTCCTTTAT
15862 TTTCCAAAATCTTCTTTTGGAATTACCTTCT-T
1 TTTCCAAAATCTTCTTTTGGAATT-CCTT-TAT
*
15894 TTTCCAAAACCTTCTTTTGGA
1 TTTCCAAAATCTTCTTTTGGA
15915 TTTGCTTAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
30 20 0.43
31 2 0.04
32 24 0.51
33 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.08, T:0.51
Consensus pattern (31 bp):
TTTCCAAAATCTTCTTTTGGAATTCCTTTAT
Found at i:20193 original size:3 final size:3
Alignment explanation
Indices: 20185--20222 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
20175 TAAAGAGCAT
*
20185 TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
20223 TTTTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:20203 original size:9 final size:9
Alignment explanation
Indices: 20185--20246 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 9
20175 TAAAGAGCAT
*
20185 TTCTTCTTC
1 TTCTTTTTC
20194 TTCTTTTTC
1 TTCTTTTTC
*
20203 TTCTTCTTC
1 TTCTTTTTC
*
20212 TTCTTCTTC
1 TTCTTTTTC
20221 TT-TTTTT-
1 TTCTTTTTC
* *
20228 TTTTTTTTT
1 TTCTTTTTC
20237 TTGCTTTTTC
1 TT-CTTTTTC
20247 CTTATGATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
7 2 0.04
8 9 0.20
9 29 0.64
10 5 0.11
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:20515 original size:27 final size:27
Alignment explanation
Indices: 20485--20560 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
20475 AATGTACTTG
*
20485 AAATGACTAAAATGCCCCTGGACATGC
1 AAATGACCAAAATGCCCCTGGACATGC
* * * *
20512 AAATGACCAAAATGGCACTAGACGTGC
1 AAATGACCAAAATGCCCCTGGACATGC
20539 AAATGACCAAAATGCCCCTGGA
1 AAATGACCAAAATGCCCCTGGA
20561 TGACCCTAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGACATGC
Found at i:25364 original size:14 final size:13
Alignment explanation
Indices: 25347--25403 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
25337 TCATGCACCC
*
25347 AAAATCATTTAAT
1 AAAAACATTTAAT
25360 AAAAACCATTT-AT
1 AAAAA-CATTTAAT
25373 -AAAACATATTAAT
1 AAAAACAT-TTAAT
*
25386 -AAAACA-GTAAT
1 AAAAACATTTAAT
25397 AAAAACA
1 AAAAACA
25404 ATTCCTCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 7 0.18
12 12 0.32
13 14 0.37
14 5 0.13
ACGTcount: A:0.61, C:0.11, G:0.02, T:0.26
Consensus pattern (13 bp):
AAAAACATTTAAT
Found at i:29679 original size:21 final size:20
Alignment explanation
Indices: 29647--29685 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
29637 ATTTCTCTAA
29647 TATTGTTCTTGTTTTATATT
1 TATTGTTCTTGTTTTATATT
*
29667 TATTAGTTTTTGTTTTATA
1 TATT-GTTCTTGTTTTATA
29686 ATTTCCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.18, C:0.03, G:0.10, T:0.69
Consensus pattern (20 bp):
TATTGTTCTTGTTTTATATT
Found at i:35911 original size:62 final size:62
Alignment explanation
Indices: 35833--35957 Score: 207
Period size: 62 Copynumber: 2.0 Consensus size: 62
35823 AGTATCAGAG
** *
35833 TCGTCATTTTTAAGATAATGAAAGAAATATCACTAATCTTTAATTCATTTCTCTAATATTGT
1 TCGTCATTTTTAAGATAATGAAAGAAATATCACTAATAGTTAATTCATTTCCCTAATATTGT
35895 TCGTCATGTTTT-AGATAATGAAAGAAATATCACTAATAGTTAATTCATTTCCCTAATATTGT
1 TCGTCAT-TTTTAAGATAATGAAAGAAATATCACTAATAGTTAATTCATTTCCCTAATATTGT
35957 T
1 T
35958 ATTGTTTTAT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 55 0.93
63 4 0.07
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (62 bp):
TCGTCATTTTTAAGATAATGAAAGAAATATCACTAATAGTTAATTCATTTCCCTAATATTGT
Found at i:37058 original size:62 final size:62
Alignment explanation
Indices: 36936--37061 Score: 182
Period size: 62 Copynumber: 2.0 Consensus size: 62
36926 AGTATAATAG
** *
36936 TCGTCATTTTTAAGATAATGAAAGAAATATCACTAATCATCAATTCATTTCTTTAGTATTGT
1 TCGTCATTTTTAAGATAATGAAAGAAATATCACTAATCATCAATTCATTTCCCTAATATTGT
** *
36998 TCGTCATTTTTTGGATAATGAAAGAAATATCACTAAT-AGTTAATTCATTTCCCTAATATTGT
1 TCGTCATTTTTAAGATAATGAAAGAAATATCACTAATCA-TCAATTCATTTCCCTAATATTGT
37060 TC
1 TC
37062 TTGTTTTATA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 1 0.02
62 56 0.98
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (62 bp):
TCGTCATTTTTAAGATAATGAAAGAAATATCACTAATCATCAATTCATTTCCCTAATATTGT
Found at i:38119 original size:62 final size:62
Alignment explanation
Indices: 38042--38163 Score: 208
Period size: 62 Copynumber: 2.0 Consensus size: 62
38032 TCAGAGTCGC
* * *
38042 CATTTTTAAGATAATGAAAGAAATATCACTAATCGTTAATTCATTTCTCTAATATTGTTCGT
1 CATTTTTAAGATAATGAAAGAAATATCACTAATAGTTAATTCAGTTCCCTAATATTGTTCGT
*
38104 CATTTTTTAGATAATGAAAGAAATATCACTAATAGTTAATTCAGTTCCCTAATATTGTTC
1 CATTTTTAAGATAATGAAAGAAATATCACTAATAGTTAATTCAGTTCCCTAATATTGTTC
38164 TTGTTTTATA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (62 bp):
CATTTTTAAGATAATGAAAGAAATATCACTAATAGTTAATTCAGTTCCCTAATATTGTTCGT
Found at i:40727 original size:61 final size:62
Alignment explanation
Indices: 40643--40767 Score: 218
Period size: 61 Copynumber: 2.0 Consensus size: 62
40633 AGTATCAGAG
*
40643 TCGTCATTTTTAAGATAATGAAAGAAATATCACTAATCA-TTAATTCATTTCTCTAATATTTT
1 TCGTCATTTTTAAGATAATGAAAGAAATATCACTAAT-AGTTAATTCATTTCCCTAATATTTT
40705 TCGTCATTTTT-AGATAATGAAAGAAATATCACTAATAGTTAATTCATTTCCCTAATATTTT
1 TCGTCATTTTTAAGATAATGAAAGAAATATCACTAATAGTTAATTCATTTCCCTAATATTTT
40766 TC
1 TC
40768 TTGTTTTATA
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
60 1 0.02
61 49 0.80
62 11 0.18
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (62 bp):
TCGTCATTTTTAAGATAATGAAAGAAATATCACTAATAGTTAATTCATTTCCCTAATATTTT
Found at i:46400 original size:47 final size:47
Alignment explanation
Indices: 46344--47345 Score: 1560
Period size: 47 Copynumber: 22.1 Consensus size: 47
46334 TTGACTACTC
* **
46344 TTTACTACTTAGTTTAATTACCTATAATTAAAAGAATTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
*
46391 TTTACTACTTAGTTTAATTACCTGGAATTAAACTAATTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
46438 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAA--T-TTCTTC-
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
46481 --T--T-CTTAGTTTAATTACCTAGAATTAAACTAA--T-TTCTTC-
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
*
46519 --T--T-CTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTTT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
46561 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
46608 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
*
46655 TTTACTACTTAGTTTGATTACCTAGAATTAAACTAATTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
* * *
46702 TTTACTACTTTGTTTGATTACCCAGAATTAAACTAATCTTC-TCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAAT-TTCTTCTTCT
*
46749 TTTACTACTTAGTTTAGTTACCTAGAATTAAACTAATCTTC-TCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAAT-TTCTTCTTCT
46796 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
46843 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
* *
46890 TTTACTACTTAGTTTGATTACCCAGAATTAAACTAATTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
46937 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAA--T-TTCTTC-
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
46980 --T--T-CTTAGTTTAATTACCTAGAATTAAACTAA--T-TTCTTC-
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
*
47018 --T--T-CTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTTT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
47060 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
47107 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
* *
47154 TTTACTACTTAGTTTGATTACCCAGAATTAAACTAATTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
47201 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
*
47248 TTTACTACTTAGTTTAAGTACCTAGAATTAAACTAATTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
47295 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTC-TCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAAT-TTCTTCTTCT
47342 TTTA
1 TTTA
47346 GTTTAAAATT
Statistics
Matches: 907, Mismatches: 27, Indels: 42
0.93 0.03 0.04
Matches are distributed among these distances:
38 134 0.15
39 2 0.00
40 2 0.00
41 12 0.01
44 14 0.02
45 2 0.00
46 5 0.01
47 730 0.80
48 6 0.01
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.48
Consensus pattern (47 bp):
TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
Found at i:47282 original size:499 final size:499
Alignment explanation
Indices: 46344--47345 Score: 1850
Period size: 499 Copynumber: 2.0 Consensus size: 499
46334 TTGACTACTC
*
46344 TTTACTACTTAGTTTAATTACCTATAATTAAAAGAATTTCTTCTTCTTTTACTACTTAGTTTAAT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAAAGAATTTCTTCTTCTTTTACTACTTAGTTTAAT
**
46409 TACCTGGAATTAAACTAATTTCTTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAA
66 TACCCAGAATTAAACTAATTTCTTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAA
46474 TTTCTTCTTCTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTAGTTTAATTACCTAG
131 TTTCTTCTTCTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTAGTTTAATTACCTAG
46539 AATTAAACTAATTTCTTCTTTTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTC
196 AATTAAACTAATTTCTTCTTTTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTC
46604 TTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTACTTAGTT
261 TTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTACTTAGTT
* * *
46669 TGATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTACTTTGTTTGATTACCCAGAATTAAA
326 TGATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTACTTAGTTTAATTACCCAGAATTAAA
46734 CTAATCTTCTCTTCTTTTACTACTTAGTTTAGTTACCTAGAATTAAACTAATCTTC-TCTTCTTT
391 CTAATCTTCTCTTCTTTTACTACTTAGTTTAGTTACCTAGAATTAAACTAAT-TTCTTCTTCTTT
46798 TACTACTTAGTTTAATTACCTAGAATTAAACTAAT-TTCTTCTTCT
455 TACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTC-TCTTCT
** *
46843 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTACTTAGTTTGAT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAAAGAATTTCTTCTTCTTTTACTACTTAGTTTAAT
46908 TACCCAGAATTAAACTAATTTCTTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAA
66 TACCCAGAATTAAACTAATTTCTTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAA
46973 TTTCTTCTTCTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTAGTTTAATTACCTAG
131 TTTCTTCTTCTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTAGTTTAATTACCTAG
47038 AATTAAACTAATTTCTTCTTTTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTC
196 AATTAAACTAATTTCTTCTTTTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTC
47103 TTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTACTTAGTT
261 TTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTACTTAGTT
*
47168 TGATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAA
326 TGATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTACTTAGTTTAATTACCCAGAATTAAA
47233 CTAAT-TTCTTCTTCTTTTACTACTTAGTTTAAG-TACCTAGAATTAAACTAATTTCTTCTTCTT
391 CTAATCTTC-TCTTCTTTTACTACTTAGTTT-AGTTACCTAGAATTAAACTAATTTCTTCTTCTT
47296 TTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTCTTCT
454 TTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTCTTCT
47342 TTTA
1 TTTA
47346 GTTTAAAATT
Statistics
Matches: 489, Mismatches: 10, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
498 6 0.01
499 478 0.98
500 5 0.01
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.48
Consensus pattern (499 bp):
TTTACTACTTAGTTTAATTACCTAGAATTAAAAGAATTTCTTCTTCTTTTACTACTTAGTTTAAT
TACCCAGAATTAAACTAATTTCTTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAA
TTTCTTCTTCTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTAGTTTAATTACCTAG
AATTAAACTAATTTCTTCTTTTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTC
TTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTACTTAGTT
TGATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTACTTAGTTTAATTACCCAGAATTAAA
CTAATCTTCTCTTCTTTTACTACTTAGTTTAGTTACCTAGAATTAAACTAATTTCTTCTTCTTTT
ACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTCTTCT
Found at i:51262 original size:27 final size:25
Alignment explanation
Indices: 51224--51298 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 25
51214 ACAGTAATTT
51224 TGACCAAAATGCCCCTGGGATGAAAAA
1 TGACCAAAATGCCCCTGGG-TG-AAAA
*
51251 TGACCAAAATGCCCCCGAGGTGAAAA
1 TGACCAAAATGCCCCTG-GGTGAAAA
51277 TGACCAAAATGCCCCT-GGTGAA
1 TGACCAAAATGCCCCTGGGTGAA
51299 TTTTTAAGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
24 6 0.13
26 19 0.42
27 18 0.40
28 2 0.04
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (25 bp):
TGACCAAAATGCCCCTGGGTGAAAA
Found at i:63170 original size:2 final size:2
Alignment explanation
Indices: 63163--63187 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63153 TAGGCAGCAC
63163 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 A
63188 CATGTGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65698 original size:27 final size:27
Alignment explanation
Indices: 65668--65740 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
65658 GGTCATCTAT
65668 GGGGCATTTTGGTCATTTGCGAAT-T-CA
1 GGGGCATTTTGGTCATTTGC--ATGTCCA
* *
65695 GGGGTATTTTAGTCATTTTGCATGTCCA
1 GGGGCATTTTGGTCA-TTTGCATGTCCA
*
65723 AGGGCATTTTGGTCATTT
1 GGGGCATTTTGGTCATTT
65741 CTACTTCATT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 2 0.05
27 17 0.45
28 19 0.50
ACGTcount: A:0.18, C:0.14, G:0.27, T:0.41
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTGCATGTCCA
Found at i:65866 original size:21 final size:20
Alignment explanation
Indices: 65838--65886 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
65828 TGTTATGTTC
**
65838 TTTTGCATATTCGTATCACA
1 TTTTGCATATTAATATCACA
*
65858 TTTTCGCATATTAATTTCACA
1 TTTT-GCATATTAATATCACA
65879 TTTTGCAT
1 TTTTGCAT
65887 TTACATAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.24, C:0.18, G:0.08, T:0.49
Consensus pattern (20 bp):
TTTTGCATATTAATATCACA
Done.