Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013301.1 Corchorus olitorius cultivar O-4 contig13334, 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: 28017
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:175 original size:27 final size:27
Alignment explanation
Indices: 145--243 Score: 126
Period size: 27 Copynumber: 3.6 Consensus size: 27
135 GAAAAGGACC
* * *
145 AAAATACCCCTAAATGTACAAATGACT
1 AAAATGCCCCTAGATGTGCAAATGACT
*
172 AAAATGCCCCCAGATGTGCAAATGACT
1 AAAATGCCCCTAGATGTGCAAATGACT
* *
199 AAAATGCCCCCTTGATGTGCAAATGACC
1 AAAATG-CCCCTAGATGTGCAAATGACT
*
227 AAAATGCCCCTGGATGT
1 AAAATGCCCCTAGATGT
244 CCCCAATGCC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 39 0.62
28 24 0.38
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.21
Consensus pattern (27 bp):
AAAATGCCCCTAGATGTGCAAATGACT
Found at i:671 original size:28 final size:28
Alignment explanation
Indices: 631--706 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
621 GGGTCACTCT
* *
631 CAGGGGCATTTTGGTCATTTTACATATC
1 CAGGGGCATTTTGGTCATTTGACACATC
* *
659 CAGGGGCATTTTGGTAATTTGGCACATC
1 CAGGGGCATTTTGGTCATTTGACACATC
*
687 TAGGGAGCATTTTGGGTCAT
1 CAGGG-GCATTTT-GGTCAT
707 CTCAAGTACT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
28 28 0.70
29 7 0.17
30 5 0.12
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.36
Consensus pattern (28 bp):
CAGGGGCATTTTGGTCATTTGACACATC
Found at i:5141 original size:36 final size:36
Alignment explanation
Indices: 5030--5142 Score: 137
Period size: 35 Copynumber: 3.2 Consensus size: 36
5020 CCTAATCTAT
*
5030 TTGAAGATTCGCTGCACCGAGCCCACTGAGTCCATA
1 TTGAAGATTTGCTGCACCGAGCCCACTGAGTCCATA
* * *
5066 TTGAAGA--TGCTACACCGAG-TCATCCTGA-TCTAT-
1 TTGAAGATTTGCTGCACCGAGCCCA--CTGAGTCCATA
5099 TTGAAGATTTGCTGCACCGAGCCCACTGAGTCCATA
1 TTGAAGATTTGCTGCACCGAGCCCACTGAGTCCATA
5135 TTGAAGAT
1 TTGAAGAT
5143 GCTACACCGA
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
33 9 0.14
34 18 0.29
35 19 0.30
36 17 0.27
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (36 bp):
TTGAAGATTTGCTGCACCGAGCCCACTGAGTCCATA
Found at i:5181 original size:35 final size:35
Alignment explanation
Indices: 5066--5492 Score: 564
Period size: 35 Copynumber: 12.2 Consensus size: 35
5056 TGAGTCCATA
*
5066 TTGAAGATGCTACACCGAGTCATCCTG-A-TCTA-T
1 TTGAAGATGCTACACCGAGTCAT-CTGAATTCAACT
* * * *
5099 TTGAAGATTTGCTGCACCGAGCCCA-CTG-AGTCCA-T
1 TTGAAGA--TGCTACACCGAG-TCATCTGAATTCAACT
* *
5134 ATTGAAGATGCTACACCGAGTCATCTGAATCCATCT
1 -TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
* *
5170 TTGAAGATGCTACACCGAGTCAT-TCGAGTTCATCT
1 TTGAAGATGCTACACCGAGTCATCT-GAATTCAACT
* * *
5205 TTGAAGATGCTGCACCGAGTCATCTGGATTCACCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
*
5240 TTGAAGATGCTACACCGAGTCATCTGAGTTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
* *
5275 TTGAAGATGCTACACCGAGTCATCTGGATTCAAAT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
*
5310 TTGAAGATGCTACACCGAGTCATCTGAGTTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
*
5345 TTGAAGATGCTACACCGAGTCATCTGATTTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
*
5380 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
*
5415 TTGAAGATGCTACACCGAGTCATCTGAGTTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
5450 TTGAAGATGCTACACCGAGTCATCTGAA-TCTAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTC-AACT
5485 TTGAAGAT
1 TTGAAGAT
5493 AAACCTAAAT
Statistics
Matches: 352, Mismatches: 31, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
33 9 0.03
34 21 0.06
35 311 0.88
36 11 0.03
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
Found at i:5574 original size:54 final size:54
Alignment explanation
Indices: 5485--5645 Score: 198
Period size: 54 Copynumber: 3.0 Consensus size: 54
5475 GAATCTAACT
* * * * *
5485 TTGAAGATAAACCTAAATCACTGAAAACTTCCTTGACTGGCCGCACTGGATCAC
1 TTGAAGATAAACTTAAACCACTGAAAATTTCCTTGATTGACCGCACTGGATCAC
* * * *
5539 TTGAAGATAAACTTAAACCACTGTAAATTTTCTTGATTGATCGCACTAGATCAC
1 TTGAAGATAAACTTAAACCACTGAAAATTTCCTTGATTGACCGCACTGGATCAC
* * **
5593 TTGAGGA-AAACTTAAACCACTGCAAATTTGATTGATTGACCGCACTGGATCAC
1 TTGAAGATAAACTTAAACCACTGAAAATTTCCTTGATTGACCGCACTGGATCAC
5646 CTTTAGGAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
53 41 0.45
54 51 0.55
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (54 bp):
TTGAAGATAAACTTAAACCACTGAAAATTTCCTTGATTGACCGCACTGGATCAC
Found at i:5621 original size:53 final size:53
Alignment explanation
Indices: 5525--5655 Score: 181
Period size: 53 Copynumber: 2.4 Consensus size: 53
5515 CCTTGACTGG
* * **
5525 CCGCACTGGATCACTTGAAGATAAACTTAAACCACTGTAAATTTTCTTGATTGA
1 CCGCACTGGATCACTTGAGGA-AAACTTAAACCACTGCAAATTTGATTGATTGA
* *
5579 TCGCACTAGATCACTTGAGGAAAACTTAAACCACTGCAAATTTGATTGATTGA
1 CCGCACTGGATCACTTGAGGAAAACTTAAACCACTGCAAATTTGATTGATTGA
*
5632 CCGCACTGGATCACCTTTAGGAAA
1 CCGCACTGGATCA-CTTGAGGAAA
5656 CTTCCTTGAT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
53 40 0.60
54 27 0.40
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (53 bp):
CCGCACTGGATCACTTGAGGAAAACTTAAACCACTGCAAATTTGATTGATTGA
Found at i:5748 original size:50 final size:50
Alignment explanation
Indices: 5694--5833 Score: 183
Period size: 50 Copynumber: 2.8 Consensus size: 50
5684 TTTTAGGAAC
* * *
5694 CTTAAACCACTGTAAACTTGACTGATCGCACTAGATCACTTGAAGAAAAA
1 CTTAAACCACTGTAAACTTGATTGATCGCACTGGATCACTTAAAGAAAAA
* * * * *
5744 CTTAAGCCATTGTAAATTTGATTGATCGCATTGGATCACTTAAAGATAAA
1 CTTAAACCACTGTAAACTTGATTGATCGCACTGGATCACTTAAAGAAAAA
*
5794 -TTCGAACCACTGTAAACTTGATTGATCGCACTGGATCACT
1 CTT-AAACCACTGTAAACTTGATTGATCGCACTGGATCACT
5834 CGAAACCACC
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 2 0.03
50 74 0.97
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (50 bp):
CTTAAACCACTGTAAACTTGATTGATCGCACTGGATCACTTAAAGAAAAA
Found at i:6061 original size:25 final size:25
Alignment explanation
Indices: 6028--6088 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
6018 TCAATTGAAG
* *
6028 TAAACTGAAGAATGATCGCCCTAGA
1 TAAATTGAAGAAAGATCGCCCTAGA
* * *
6053 TCAGTTGAAGAAAGATCGCCCTGGA
1 TAAATTGAAGAAAGATCGCCCTAGA
6078 TAAATTGAAGA
1 TAAATTGAAGA
6089 GAGACCACCC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.21
Consensus pattern (25 bp):
TAAATTGAAGAAAGATCGCCCTAGA
Found at i:6191 original size:35 final size:35
Alignment explanation
Indices: 6144--6512 Score: 309
Period size: 35 Copynumber: 10.5 Consensus size: 35
6134 CTCGATCATT
* * *
6144 CTGACATAAACTGAAGAAAAACCGCCTTGGGTCAA
1 CTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
*
6179 CTGAAATAAACTGCAA-AAAGACCGCCATGGGTCAA
1 CTGAAATAAACTG-AAGAAAGACCGCCCTGGGTCAA
* * *
6214 CTAAAATAAACTGAAGAAAGACCACTCTGGGTCAA
1 CTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
* * * * * * * *
6249 CTAAAATTAACTTAAGAATGATCACCCTGGATCGA
1 CTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
* * *
6284 CATGAGAAT-AACTGAAGAAAGACCACTCTAGGTCAA
1 C-TGA-AATAAACTGAAGAAAGACCGCCCTGGGTCAA
* * * * * * *
6320 CTAAAATAAAATGAAGAATGATCACCCTAGATCAA
1 CTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
*
6355 CTTGAGAAT-AACTGAAGAAAGACCACCCTGGGTCAA
1 C-TGA-AATAAACTGAAGAAAGACCGCCCTGGGTCAA
*
6391 CTAAAATAAACTGAAGAAAGACCGCCCT-GGTCAA
1 CTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
* * * * **
6425 CTTAAATAAACTGAGGAATGATCGCCCTGGACCAA
1 CTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
* * *
6460 CTTGAAA-ATAACTGAAGAAAGACC-ACTTTGGTCAA
1 C-TGAAATA-AACTGAAGAAAGACCGCCCTGGGTCAA
6495 CTGAAATAAACTGAAGAA
1 CTGAAATAAACTGAAGAA
6513 TAATCACCCT
Statistics
Matches: 271, Mismatches: 51, Indels: 25
0.78 0.15 0.07
Matches are distributed among these distances:
34 53 0.20
35 146 0.54
36 66 0.24
37 6 0.02
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (35 bp):
CTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
Found at i:6232 original size:70 final size:69
Alignment explanation
Indices: 6149--6512 Score: 292
Period size: 71 Copynumber: 5.2 Consensus size: 69
6139 TCATTCTGAC
* * * *
6149 ATAAACTGAAGAAAAACCGCCTTGGGTCAACTGAAATAAACTGCAA-AAAGACCGCCATGGGTCA
1 ATAAACTGAAGAAAGACC-CCTTGGGTCAACTAAAATAAACTG-AAGAAAGACCACCCTGGGTCA
6213 ACTAAA
64 ACTAAA
* * * * * * *
6219 ATAAACTGAAGAAAGACCACTCTGGGTCAACTAAAATTAACTTAAGAATGATCACCCTGGATCGA
1 ATAAACTGAAGAAAGACCCCT-TGGGTCAACTAAAATAAACTGAAGAAAGACCACCCTGGGTCAA
*
6284 CATGAGA
65 C-T-AAA
* * * * * * *
6291 AT-AACTGAAGAAAGACCACTCTAGGTCAACTAAAATAAAATGAAGAATGATCACCCTAGATCAA
1 ATAAACTGAAGAAAGACCCCT-TGGGTCAACTAAAATAAACTGAAGAAAGACCACCCTGGGTCAA
*
6355 CTTGAGA
65 C-T-AAA
* *
6362 AT-AACTGAAGAAAGACCACCCTGGGTCAACTAAAATAAACTGAAGAAAGACCGCCCT-GGTCAA
1 ATAAACTGAAGAAAGACC-CCTTGGGTCAACTAAAATAAACTGAAGAAAGACCACCCTGGGTCAA
*
6425 CTTAA
65 CTAAA
* * ** * *
6430 ATAAACTGAGGAATGATCGCCC-TGGACCAACTTGAAAAT-AACTGAAGAAAGACCA-CTTTGGT
1 ATAAACTGAAGAAAGA-C-CCCTTGGGTCAAC-T-AAAATAAACTGAAGAAAGACCACCCTGGGT
*
6492 CAACTGAA
62 CAACTAAA
6500 ATAAACTGAAGAA
1 ATAAACTGAAGAA
6513 TAATCACCCT
Statistics
Matches: 246, Mismatches: 37, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
68 3 0.01
69 25 0.10
70 96 0.39
71 117 0.48
72 5 0.02
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (69 bp):
ATAAACTGAAGAAAGACCCCTTGGGTCAACTAAAATAAACTGAAGAAAGACCACCCTGGGTCAAC
TAAA
Found at i:6302 original size:71 final size:71
Alignment explanation
Indices: 6222--6408 Score: 302
Period size: 71 Copynumber: 2.6 Consensus size: 71
6212 AACTAAAATA
* * * *
6222 AACTGAAGAAAGACCACTCTGGGTCAACTAAAATTAACTTAAGAATGATCACCCTGGATCGACAT
1 AACTGAAGAAAGACCACTCTGGGTCAACTAAAATAAACTGAAGAATGATCACCCTAGATCAACAT
6287 GAGAAT
66 GAGAAT
* * *
6293 AACTGAAGAAAGACCACTCTAGGTCAACTAAAATAAAATGAAGAATGATCACCCTAGATCAACTT
1 AACTGAAGAAAGACCACTCTGGGTCAACTAAAATAAACTGAAGAATGATCACCCTAGATCAACAT
6358 GAGAAT
66 GAGAAT
*
6364 AACTGAAGAAAGACCACCCTGGGTCAACTAAAATAAACTGAAGAA
1 AACTGAAGAAAGACCACTCTGGGTCAACTAAAATAAACTGAAGAA
6409 AGACCGCCCT
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 106 1.00
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (71 bp):
AACTGAAGAAAGACCACTCTGGGTCAACTAAAATAAACTGAAGAATGATCACCCTAGATCAACAT
GAGAAT
Found at i:6307 original size:106 final size:104
Alignment explanation
Indices: 6152--6512 Score: 345
Period size: 105 Copynumber: 3.4 Consensus size: 104
6142 TTCTGACATA
* * * * *
6152 AACTGAAGAAAAACCGCCTTGGGTCAACTGAAATAAACTGCAA-AAAGACCGCCATGGGTCAACT
1 AACTGAAGAAAGACCACCCTGGATCAACTAAAATAAACTG-AAGAAAGACCGCC-T-GGTCAACT
* * *
6216 AAAATAAACTGAAGAAAGACCACTCTGGGTCAAC-T-AAAATT
63 AAAATAAACTGAAGAAAGACCACCCTAGATCAACTTGAAAA-T
* * * * * *
6257 AACTTAAGAATGATCACCCTGGATCGACATGAGAAT-AACTGAAGAAAGACCACTCTAGGTCAAC
1 AACTGAAGAAAGACCACCCTGGATCAAC-T-AAAATAAACTGAAGAAAGACCGC-CT-GGTCAAC
* * * *
6321 TAAAATAAAATGAAGAATGATCACCCTAGATCAACTTGAGAAT
62 TAAAATAAACTGAAGAAAGACCACCCTAGATCAACTTGAAAAT
* *
6364 AACTGAAGAAAGACCACCCTGGGTCAACTAAAATAAACTGAAGAAAGACCGCCCTGGTCAACTTA
1 AACTGAAGAAAGACCACCCTGGATCAACTAAAATAAACTGAAGAAAGACCG-CCTGGTCAACTAA
* * * * * *
6429 AATAAACTGAGGAATGATCGCCCTGGACCAACTTGAAAAT
65 AATAAACTGAAGAAAGACCACCCTAGATCAACTTGAAAAT
** *
6469 AACTGAAGAAAGACCACTTTGG-TCAACTGAAATAAACTGAAGAA
1 AACTGAAGAAAGACCACCCTGGATCAACTAAAATAAACTGAAGAA
6513 TAATCACCCT
Statistics
Matches: 212, Mismatches: 36, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
104 21 0.10
105 89 0.42
106 69 0.33
107 30 0.14
108 3 0.01
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (104 bp):
AACTGAAGAAAGACCACCCTGGATCAACTAAAATAAACTGAAGAAAGACCGCCTGGTCAACTAAA
ATAAACTGAAGAAAGACCACCCTAGATCAACTTGAAAAT
Found at i:8380 original size:26 final size:26
Alignment explanation
Indices: 8328--8381 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
8318 CTTAAAAGAC
* *
8328 TCAAAACCTTTTTGGAAACCTATTTT
1 TCAAAACCTTTTTGGAAAACTAATTT
*
8354 TCAAAACCTTTTCTTGAAAAC-AATTT
1 TCAAAACCTTTT-TGGAAAACTAATTT
8380 TC
1 TC
8382 TTGAAAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (26 bp):
TCAAAACCTTTTTGGAAAACTAATTT
Found at i:9627 original size:44 final size:44
Alignment explanation
Indices: 9553--9695 Score: 181
Period size: 43 Copynumber: 3.3 Consensus size: 44
9543 CGACCTATGC
* *
9553 ATGAACATATATACAAA-G-GA-ATGGATAATGCATGATGGATGT
1 ATGAACATATAT-CAAATGAGACATGGACAATGCATGAAGGATGT
* *
9595 ATGAACTTATAT-ATATGGAGACATGGACAATGCATGAAGGATGT
1 ATGAACATATATCAAAT-GAGACATGGACAATGCATGAAGGATGT
*
9639 ATG-ACATATATCAAATGAGATATGGACAATGCATGAAGGATGT
1 ATGAACATATATCAAATGAGACATGGACAATGCATGAAGGATGT
9682 ATG-ACATATATCAA
1 ATGAACATATATCAA
9696 TGGATATGAT
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
40 2 0.02
42 12 0.13
43 49 0.55
44 26 0.29
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (44 bp):
ATGAACATATATCAAATGAGACATGGACAATGCATGAAGGATGT
Found at i:11656 original size:15 final size:15
Alignment explanation
Indices: 11622--11669 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
11612 AATTTTCTAA
*
11622 TTTTTCAATTTTTTCAT
1 TTTTTC-ATTTCTTC-T
*
11639 TTTTTCCTTTCTTCT
1 TTTTTCATTTCTTCT
*
11654 TTTTTCATTTTTTCT
1 TTTTTCATTTCTTCT
11669 T
1 T
11670 CAACTTTGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 15 0.56
16 6 0.22
17 6 0.22
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTCATTTCTTCT
Found at i:11666 original size:8 final size:8
Alignment explanation
Indices: 11622--11667 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
11612 AATTTTCTAA
11622 TTTTTCAAT
1 TTTTTC-AT
11631 TTTTTCAT
1 TTTTTCAT
*
11639 TTTTTCCT
1 TTTTTCAT
*
11647 TTCTTC-T
1 TTTTTCAT
11654 TTTTTCAT
1 TTTTTCAT
11662 TTTTTC
1 TTTTTC
11668 TTCAACTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.18
8 21 0.64
9 6 0.18
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTCAT
Found at i:15027 original size:27 final size:27
Alignment explanation
Indices: 14997--15089 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
14987 GAAAAGGACC
* * *
14997 AAAATACCCCTAAATGTACAAATAACT
1 AAAATGCCCCTAAATGTGCAAATGACT
* *
15024 AAAATGCCCCCAGATGTGCAAATGACT
1 AAAATGCCCCTAAATGTGCAAATGACT
*
15051 AAAATGCCCCCTAAATGTGCAAATGACC
1 AAAATG-CCCCTAAATGTGCAAATGACT
15079 AAAATGCCCCT
1 AAAATGCCCCT
15090 GGATGTCCCC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 33 0.58
28 24 0.42
ACGTcount: A:0.42, C:0.27, G:0.12, T:0.19
Consensus pattern (27 bp):
AAAATGCCCCTAAATGTGCAAATGACT
Found at i:15070 original size:28 final size:28
Alignment explanation
Indices: 15003--15088 Score: 129
Period size: 28 Copynumber: 3.1 Consensus size: 28
14993 GACCAAAATA
* *
15003 CCCCTAAATGTACAAATAACTAAAATGC
1 CCCCTAAATGTGCAAATGACTAAAATGC
*
15031 CCCC-AGATGTGCAAATGACTAAAATGC
1 CCCCTAAATGTGCAAATGACTAAAATGC
*
15058 CCCCTAAATGTGCAAATGACCAAAATGC
1 CCCCTAAATGTGCAAATGACTAAAATGC
15086 CCC
1 CCC
15089 TGGATGTCCC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
27 24 0.46
28 28 0.54
ACGTcount: A:0.40, C:0.29, G:0.13, T:0.19
Consensus pattern (28 bp):
CCCCTAAATGTGCAAATGACTAAAATGC
Found at i:16236 original size:52 final size:52
Alignment explanation
Indices: 16085--16238 Score: 227
Period size: 52 Copynumber: 3.0 Consensus size: 52
16075 TCCTTCAAAG
* * *
16085 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTTAAAGTATTCGATTTAGATC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCGATTTAGGTC
*
16137 TTTTCAAAGTGGGAAAGTTCGCATCAAGTTTTCAAAGTGTTCGATTTAGGTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCGATTTAGGTC
* * * * *
16189 TTTTCAAACTGGGAAACTTCCCATCAGGTTTTCAAAGCGTTCAATTTAGG
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCGATTTAGG
16239 GAAAGATCCC
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 92 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (52 bp):
TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCGATTTAGGTC
Found at i:17556 original size:47 final size:47
Alignment explanation
Indices: 17453--17587 Score: 218
Period size: 47 Copynumber: 2.9 Consensus size: 47
17443 TTTTCTTGTG
* *
17453 TGATAACTTCTGGTGTCAATTAAATTTACT-AAAGAAAATTTTGATT
1 TGATAACTTCTGGTGTCAATTAAATTTACTAAAACAAAATTTTAATT
* *
17499 TGACAACTTCTGGTGTCAATTAAATTTACTAAAATAAAATTTTAATT
1 TGATAACTTCTGGTGTCAATTAAATTTACTAAAACAAAATTTTAATT
*
17546 TGATAACTTCTGGTGTCAATTAAATTTACTAGAACAAAATTT
1 TGATAACTTCTGGTGTCAATTAAATTTACTAAAACAAAATTT
17588 GGCTAATTGC
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 29 0.35
47 53 0.65
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (47 bp):
TGATAACTTCTGGTGTCAATTAAATTTACTAAAACAAAATTTTAATT
Found at i:17692 original size:60 final size:60
Alignment explanation
Indices: 17599--17763 Score: 276
Period size: 60 Copynumber: 2.8 Consensus size: 60
17589 GCTAATTGCT
*
17599 CAAATAAGGGCCTAAAGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
** * *
17659 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATATTGACCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
*
17719 CAAATAAGGGCCTAACGTTTGCTAAAATGCTCAAATAAGGGCCTG
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTG
17764 GTGTCGAAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 95 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
Found at i:17757 original size:31 final size:31
Alignment explanation
Indices: 17595--17762 Score: 127
Period size: 31 Copynumber: 5.5 Consensus size: 31
17585 TTTGGCTAAT
* *
17595 TGCTCAAATAAGGGCCTAAAGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCTAAAA
* **
17626 TGCTCAAATAAGGGCCTGATC-TTT--TAATT
1 TGCTCAAATAAGGGCCT-AACGTTTGCTAAAA
*
17655 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCTAAAA
* ** * * **
17686 TGCTCAAATATTGACCCGATC-TTT--TAATT
1 TGCTCAAATA-AGGGCCTAACGTTTGCTAAAA
17715 TGGC-CAAATAAGGGCCTAACGTTTGCTAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCTAAAA
17746 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
17763 GGTGTCGAAA
Statistics
Matches: 101, Mismatches: 24, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
28 7 0.07
29 31 0.31
30 8 0.08
31 49 0.49
32 6 0.06
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCTAAAA
Found at i:17841 original size:31 final size:29
Alignment explanation
Indices: 17803--17968 Score: 115
Period size: 31 Copynumber: 5.5 Consensus size: 29
17793 CTGACGACAT
* *
17803 GCCCTTATTTGAGCATTTTCGATAACGTTGG
1 GCCCTTATTTGAGCATTTT-GA-AAAGTTAG
** **
17834 GCCCTTATTTG-GCCAAATT-AAAAGATCGG
1 GCCCTTATTTGAG-CATTTTGAAAAG-TTAG
17863 GCCCTTATTTGAGCATTTTCGATAAAGTTAG
1 GCCCTTATTTGAGCATTTT-GA-AAAGTTAG
** *
17894 GCCCTTATTTG-GCCAAATT-AAAAGATTTG
1 GCCCTTATTTGAG-CATTTTGAAAAG-TTAG
* *
17923 GTCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTT-G-AAAAGTTAG
17954 GCCCTTATTTGAGCA
1 GCCCTTATTTGAGCA
17969 ATTAGCCACA
Statistics
Matches: 106, Mismatches: 17, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
28 7 0.07
29 37 0.35
30 4 0.04
31 50 0.47
32 8 0.08
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (29 bp):
GCCCTTATTTGAGCATTTTGAAAAGTTAG
Found at i:17871 original size:29 final size:29
Alignment explanation
Indices: 17830--17933 Score: 104
Period size: 29 Copynumber: 3.5 Consensus size: 29
17820 TTCGATAACG
17830 TTGGGCCCTTATTTGGCCAAATTAAAAGA
1 TTGGGCCCTTATTTGGCCAAATTAAAAGA
* **
17859 TCGGGCCCTTATTTGAG-CATTTTCGATAAAG-
1 TTGGGCCCTTATTTG-GCCAAATT--A-AAAGA
*
17890 TTAGGCCCTTATTTGGCCAAATTAAAAGA
1 TTGGGCCCTTATTTGGCCAAATTAAAAGA
* *
17919 TTTGGTCCTTATTTG
1 TTGGGCCCTTATTTG
17934 AGCATTTTGG
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.07
29 32 0.53
30 2 0.03
31 18 0.30
32 4 0.07
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (29 bp):
TTGGGCCCTTATTTGGCCAAATTAAAAGA
Found at i:17879 original size:60 final size:60
Alignment explanation
Indices: 17803--17964 Score: 254
Period size: 60 Copynumber: 2.7 Consensus size: 60
17793 CTGACGACAT
*
17803 GCCCTTATTTGAGCATTTTCGATAACGTTGGGCCCTTATTTGGCCAAATTAAAAGATCGG
1 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGG
* **
17863 GCCCTTATTTGAGCATTTTCGATAAAGTTAGGCCCTTATTTGGCCAAATTAAAAGATTTG
1 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGG
* *
17923 GTCCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTG
1 GCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
17965 AGCAATTAGC
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 93 0.99
61 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGG
Found at i:26753 original size:27 final size:29
Alignment explanation
Indices: 26696--26757 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 29
26686 TTTCTTAATT
* *
26696 GGCATTTTGGTCATTTTGGCACGTCCGGG
1 GGCATTTTGGTCATTTTGGCACATCCAGG
*
26725 GGCATTTTGGTCA-TTT-GCACATTCAGG
1 GGCATTTTGGTCATTTTGGCACATCCAGG
26752 GGCATT
1 GGCATT
26758 GGAGTCAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 14 0.47
28 3 0.10
29 13 0.43
ACGTcount: A:0.15, C:0.19, G:0.31, T:0.35
Consensus pattern (29 bp):
GGCATTTTGGTCATTTTGGCACATCCAGG
Done.