Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016432.1 Corchorus olitorius cultivar O-4 contig16465, 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: 78127
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:14750 original size:41 final size:41
Alignment explanation
Indices: 14697--14776 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
14687 TGGGAAGGGG
14697 TTTGTTGACTCATAGATTAGCATTTCAGTAATGTAGCTACA
1 TTTGTTGACTCATAGATTAGCATTTCAGTAATGTAGCTACA
*
14738 TTTGTTGGCTCATAGATTAGCATTTCAGTAATGTAGCTA
1 TTTGTTGACTCATAGATTAGCATTTCAGTAATGTAGCTA
14777 ATCATGCAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (41 bp):
TTTGTTGACTCATAGATTAGCATTTCAGTAATGTAGCTACA
Found at i:19022 original size:30 final size:30
Alignment explanation
Indices: 18982--19038 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
18972 TGAACCTACG
*
18982 AACTAGAAACTATATCTACCTACAAACCAA
1 AACTAAAAACTATATCTACCTACAAACCAA
19012 AACTAAAAACTATATCTACCTACAAAC
1 AACTAAAAACTATATCTACCTACAAAC
19039 TAAATAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.51, C:0.26, G:0.02, T:0.21
Consensus pattern (30 bp):
AACTAAAAACTATATCTACCTACAAACCAA
Found at i:19039 original size:24 final size:24
Alignment explanation
Indices: 18975--19042 Score: 64
Period size: 30 Copynumber: 2.6 Consensus size: 24
18965 GTGTTCTTGA
* *
18975 ACCTACGAACTAGAAACTATATCT
1 ACCTACAAACTAAAAACTATATCT
18999 ACCTACAAACCAAAACTAAAAACTATATCT
1 ACCT----A-C-AAACTAAAAACTATATCT
19029 ACCTACAAACTAAA
1 ACCTACAAACTAAA
19043 TAAACAACCA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
24 12 0.33
25 1 0.03
26 1 0.03
28 1 0.03
29 1 0.03
30 20 0.56
ACGTcount: A:0.50, C:0.26, G:0.03, T:0.21
Consensus pattern (24 bp):
ACCTACAAACTAAAAACTATATCT
Found at i:19040 original size:17 final size:17
Alignment explanation
Indices: 18988--19040 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
18978 TACGAACTAG
18988 AAACTATATCTACCTAC
1 AAACTATATCTACCTAC
* * *
19005 AAACCA-A---AACTAA
1 AAACTATATCTACCTAC
19018 AAACTATATCTACCTAC
1 AAACTATATCTACCTAC
19035 AAACTA
1 AAACTA
19041 AATAAACAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 8
0.65 0.15 0.20
Matches are distributed among these distances:
13 9 0.35
14 1 0.04
16 1 0.04
17 15 0.58
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (17 bp):
AAACTATATCTACCTAC
Found at i:31106 original size:19 final size:20
Alignment explanation
Indices: 31078--31115 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31068 TTTATTCTCT
31078 AATGGATAG-TTTTATTTTA
1 AATGGATAGTTTTTATTTTA
*
31097 AATGGGTAGTTTTTATTTT
1 AATGGATAGTTTTTATTTT
31116 GTTTTGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.55
Consensus pattern (20 bp):
AATGGATAGTTTTTATTTTA
Found at i:31199 original size:2 final size:2
Alignment explanation
Indices: 31192--31224 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
31182 TTATAATTAG
*
31192 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31225 GACAAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:36302 original size:19 final size:20
Alignment explanation
Indices: 36278--36336 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
36268 CTATTTAACA
36278 ACTGTACAGATGAGATTAT-
1 ACTGTACAGATGAGATTATG
* *
36297 ACTGTACATATTAGATTAGGTG
1 ACTGTACAGATGAGATTA--TG
*
36319 A-TCTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
36337 TAGAGCTGCG
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 17 0.53
21 14 0.44
22 1 0.03
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (20 bp):
ACTGTACAGATGAGATTATG
Found at i:36381 original size:139 final size:139
Alignment explanation
Indices: 36131--36398 Score: 500
Period size: 139 Copynumber: 1.9 Consensus size: 139
36121 CATTGATACA
36131 ATTTAACAACTGTACAGATGAGATTATACTATACATATTAGATTAGGCGATCTACAGATGAGATT
1 ATTTAACAACTGTACAGATGAGATTATACTATACATATTAGATTAGGCGATCTACAGATGAGATT
*
36196 ATTAGAGTTGCGATTGAAACGGAGTTTACACTTAAACTCCGTTTGAACCCAAAACGATGGTCAAG
66 ATTAGAGCTGCGATTGAAACGGAGTTTACACTTAAACTCCGTTTGAACCCAAAACGATGGTCAAG
36261 ATTAACACT
131 ATTAACACT
* *
36270 ATTTAACAACTGTACAGATGAGATTATACTGTACATATTAGATTAGGTGATCTACAGATGAGATT
1 ATTTAACAACTGTACAGATGAGATTATACTATACATATTAGATTAGGCGATCTACAGATGAGATT
*
36335 ATTAGAGCTGCGATTGAAACGGAGTTTACACTTAAACTCCGTTTGAACCCAAAATGATGGTCAA
66 ATTAGAGCTGCGATTGAAACGGAGTTTACACTTAAACTCCGTTTGAACCCAAAACGATGGTCAA
36399 ACGATGATGA
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 125 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (139 bp):
ATTTAACAACTGTACAGATGAGATTATACTATACATATTAGATTAGGCGATCTACAGATGAGATT
ATTAGAGCTGCGATTGAAACGGAGTTTACACTTAAACTCCGTTTGAACCCAAAACGATGGTCAAG
ATTAACACT
Found at i:37432 original size:18 final size:18
Alignment explanation
Indices: 37392--37432 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
37382 AATTTATTTA
*
37392 TGTCAT-TTTAAAAAAAC
1 TGTCATATTAAAAAAAAC
*
37409 T-ACATATTAAAAAAAAC
1 TGTCATATTAAAAAAAAC
37426 TGTCATA
1 TGTCATA
37433 AACCACTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.16
17 12 0.63
18 4 0.21
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (18 bp):
TGTCATATTAAAAAAAAC
Found at i:37570 original size:2 final size:2
Alignment explanation
Indices: 37563--37606 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
37553 TTTAATACAA
37563 AT AT AT AT AT AT AT A- AGT AT AT AT AT A- AT AT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
37602 AT AT A
1 AT AT A
37607 ATTTCTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
1 4 0.11
2 32 0.86
3 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:37585 original size:12 final size:11
Alignment explanation
Indices: 37563--37606 Score: 63
Period size: 12 Copynumber: 3.9 Consensus size: 11
37553 TTTAATACAA
37563 ATAT-ATATAT
1 ATATAATATAT
37573 ATATAAGTATAT
1 ATATAA-TATAT
37585 ATATAATATAT
1 ATATAATATAT
37596 AATATAATATA
1 -ATATAATATA
37607 ATTTCTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.13
11 6 0.19
12 21 0.68
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
ATATAATATAT
Found at i:37638 original size:129 final size:128
Alignment explanation
Indices: 37441--37686 Score: 406
Period size: 129 Copynumber: 1.9 Consensus size: 128
37431 TAAACCACTC
37441 ATATATATATATATATATAAAAGTAAAGTATAATATAATTTCTTAATACAAATGTCAACCTCATG
1 ATATATATATATATATATAAAAGTAAAGTATAATATAATTTCTTAATACAAATGTCAACCTCATG
* * *
37506 TCAGGTACATGTCTCAGAAAGTTTACAGATTTTAAATTATTGCAGATTTTAATACAAATATAT
66 TCAGGTACATATCTCAAAAAGTTTACAGATATTAAATTATTGCAGATTTTAATACAAATATAT
* *
37569 ATATATATAAGTATATATATAATA-TATAA-TATAATATAATTTCTTAATACAAATGTCAAGCTC
1 ATATATAT-A-TATATATATAAAAGTA-AAGTATAATATAATTTCTTAATACAAATGTCAACCTC
37632 ATGTCAGGTACATATCTCAAAAAGTTTACAGATATTAAATTATTGCAGATTTTAA
63 ATGTCAGGTACATATCTCAAAAAGTTTACAGATATTAAATTATTGCAGATTTTAA
37687 AGTTGTATAT
Statistics
Matches: 110, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
128 8 0.07
129 88 0.80
130 14 0.13
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (128 bp):
ATATATATATATATATATAAAAGTAAAGTATAATATAATTTCTTAATACAAATGTCAACCTCATG
TCAGGTACATATCTCAAAAAGTTTACAGATATTAAATTATTGCAGATTTTAATACAAATATAT
Found at i:49188 original size:99 final size:99
Alignment explanation
Indices: 49015--49214 Score: 373
Period size: 99 Copynumber: 2.0 Consensus size: 99
49005 TTGATCTGAA
*
49015 ATTTGATCCCTCATAACATGTTTTTACACGGTTGGTCCAATAGACTGGTCCTACCACTACTTGAA
1 ATTTGATCCCTCATAACATGTTTTTACACGGTTGGTCCAATAGACTGGTCCCACCACTACTTGAA
*
49080 TGAAGTTTTACTACATAATATAGGATGACTGGCC
66 TGAAATTTTACTACATAATATAGGATGACTGGCC
*
49114 ATTTGATCCCTCATAACGTGTTTTTACACGGTTGGTCCAATAGACTGGTCCCACCACTACTTGAA
1 ATTTGATCCCTCATAACATGTTTTTACACGGTTGGTCCAATAGACTGGTCCCACCACTACTTGAA
49179 TGAAATTTTACTACATAATATAGGATGACTGGCC
66 TGAAATTTTACTACATAATATAGGATGACTGGCC
49213 AT
1 AT
49215 GACACGTCAT
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (99 bp):
ATTTGATCCCTCATAACATGTTTTTACACGGTTGGTCCAATAGACTGGTCCCACCACTACTTGAA
TGAAATTTTACTACATAATATAGGATGACTGGCC
Found at i:66993 original size:12 final size:12
Alignment explanation
Indices: 66976--67002 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
66966 CTAATATATC
66976 AAACCTAGTCAT
1 AAACCTAGTCAT
66988 AAACCTAGTCAT
1 AAACCTAGTCAT
67000 AAA
1 AAA
67003 AAGACTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.22
Consensus pattern (12 bp):
AAACCTAGTCAT
Found at i:67282 original size:6 final size:6
Alignment explanation
Indices: 67271--67298 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
67261 TATTACGTAG
67271 AATAGA AATAGA AATAGA AATAGA AATA
1 AATAGA AATAGA AATAGA AATAGA AATA
67299 TAATTGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (6 bp):
AATAGA
Found at i:71214 original size:79 final size:79
Alignment explanation
Indices: 71083--71242 Score: 302
Period size: 79 Copynumber: 2.0 Consensus size: 79
71073 AAATATAGCT
* *
71083 ATGACTGCAGTCACTTAAGCTAATCAATGACAAGTAATAAGAAGGGCAAATAATTTTTCTTGGCC
1 ATGACTGCAGTCACTTAAGCTAATCAATGACAAGTAATAAGAAAGACAAATAATTTTTCTTGGCC
71148 ATGGTGCAGCTGTG
66 ATGGTGCAGCTGTG
71162 ATGACTGCAGTCACTTAAGCTAATCAATGACAAGTAATAAGAAAGACAAATAATTTTTCTTGGCC
1 ATGACTGCAGTCACTTAAGCTAATCAATGACAAGTAATAAGAAAGACAAATAATTTTTCTTGGCC
71227 ATGGTGCAGCTGTG
66 ATGGTGCAGCTGTG
71241 AT
1 AT
71243 TCTTTGTTTA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (79 bp):
ATGACTGCAGTCACTTAAGCTAATCAATGACAAGTAATAAGAAAGACAAATAATTTTTCTTGGCC
ATGGTGCAGCTGTG
Found at i:75738 original size:331 final size:329
Alignment explanation
Indices: 74806--75740 Score: 1100
Period size: 331 Copynumber: 2.8 Consensus size: 329
74796 TTAGTATACA
* * * * * ** * *
74806 ATTTCGGCTAAAATTTTGCAAAAACTAACCAGAAAAACAATTCATCAA-TTTTTGGC-CATTACA
1 ATTTCGGCTAAAATTTTGCAAAAACTGACCAAAAAAATATTTCCTCAATTTTTTACCACAATACT
*
74869 CAT-AAAAAATATATAATTTAACACCAAAAAGATTGAAGAGTTTTTCACGCTTCGAATATCGTTT
66 CATAAAAAAATATATAATTTAACGCCAAAAAGATTGAAGAGTTTTTCACGCTTCGAATATCGTTT
* *
74933 TTCATATTTTTTCCGAATTAATATCTAATTAAATCGAAACATGATTCAGATGATCGTAAAAACAA
131 TTCATATTTTTTCAGAATTAATATCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAA
* * *
74998 ATCATTAAATCCAATGTGTCTGAGATTTGGTTAGATGAATATAGATATCTCAAA-GAGTCTTGGC
196 ATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATAT-TTAAAGGAGTCTTGGC
* * * *
75062 GCCAAAAATCATGCAAAACTGAGTCGGGTCCCGGAACGCGTTTTTAGCCAGAAAACGTGATGGTT
260 GCCAAAAATCATGCAAAACTGAGCCGAGCCCCGAAACGCGTTTTTAGCCAGAAAACGTGATGG--
75127 ATTACACG
323 -TTACACG
* * * * *
75135 ATTTTGCCTAAAATTTTACAAAAACTGACCAAAAAAATATTT-CTACAATTTTTGACCACAATAG
1 ATTTCGGCTAAAATTTTGCAAAAACTGACCAAAAAAATATTTCCT-CAATTTTTTACCACAATAC
* ** * * *
75199 T--TAGAAAAAATTTATAATTTAACGCCAGTAAGATTGAAAAATTTTTCACGCTTCGAAAATCGT
65 TCATA-AAAAAATATATAATTTAACGCCAAAAAGATTGAAGAGTTTTTCACGCTTCGAATATCGT
* *
75262 TTTTCCTATTTTTTCAGAATTAATATATAAAATATAATTAAATCGAAACATGATTCAGATGCTCG
129 TTTTCATATTTTTTCAGAA-T--TA-AT---ATCTAATTAAATCGAAACATGATTCAGATGCTCG
* * ** * * *
75327 TAAAAACAAATCTTTAATTATAATGTGGCAGAGATTTGGTTAGATGAATATAAATATTTCAAGGA
187 TAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTAAAGGA
* * * *
75392 TTCTTGGCGCCAAAAATCATTCAAAATTGAGCCAGAGCCCCGAAACGTGTTTTTAGCCA-AAAAC
252 GTCTTGGCGCCAAAAATCATGCAAAACTGAGCC-GAGCCCCGAAACGCGTTTTTAGCCAGAAAA-
75456 CGTGAT-G-TACACG
315 CGTGATGGTTACACG
* *
75469 ATTTCGGCTAAAATTTTGCAAAAACTGACCAAAAAAATATTTCCTCAATTTTTTTTATCACAACA
1 ATTTCGGCTAAAATTTTGCAAAAACTGACCAAAAAAATATTTCCTCAA--TTTTTTACCACAATA
*
75534 CTCATAAAAAAATATATAAATTAACGCCAAAAAGATTGAAGAGTTTTTCACGCTTCGAATATCGT
64 CTCATAAAAAAATATATAATTTAACGCCAAAAAGATTGAAGAGTTTTTCACGCTTCGAATATCG-
* * * * * *
75599 TTTTTCTTATTTTTTCTGAATTAACT-TCTAATCAAATCGAAACAAGATTCAGATGCTTGTTAAA
128 TTTTTCATATTTTTTCAGAATTAA-TATCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAA
* * * *
75663 ACAAATCCTTCAATCCAACGTGGCTGAGATTTGGTTATATGAATATTGATATTTAAAGGAGTCTT
192 ACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTT
* *
75728 GCCACCAAAAATC
257 GGCGCCAAAAATC
75741 GTAAAATTGA
Statistics
Matches: 507, Mismatches: 77, Indels: 42
0.81 0.12 0.07
Matches are distributed among these distances:
328 1 0.00
329 39 0.08
330 5 0.01
331 170 0.34
332 1 0.00
334 51 0.10
335 7 0.01
336 13 0.03
337 55 0.11
338 138 0.27
339 27 0.05
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.32
Consensus pattern (329 bp):
ATTTCGGCTAAAATTTTGCAAAAACTGACCAAAAAAATATTTCCTCAATTTTTTACCACAATACT
CATAAAAAAATATATAATTTAACGCCAAAAAGATTGAAGAGTTTTTCACGCTTCGAATATCGTTT
TTCATATTTTTTCAGAATTAATATCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAA
ATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTGGCG
CCAAAAATCATGCAAAACTGAGCCGAGCCCCGAAACGCGTTTTTAGCCAGAAAACGTGATGGTTA
CACG
Found at i:75891 original size:193 final size:193
Alignment explanation
Indices: 75551--75920 Score: 476
Period size: 193 Copynumber: 1.9 Consensus size: 193
75541 AAAAATATAT
* *
75551 AAATTAACGCCAAAAAGATTGAAGAGTTTTTCACGCTTCGAATATCGTTTTTTCTTATTTTTTCT
1 AAATTAACGCCAAAAAGATTAAAGAGTTTTTCACGCTTCGAATATCGTTTTTTCTTATTTTTTCC
* * * * * *
75616 GAATTAACTTCTAATCAAATCGAAACAAGATTCAGATGCTTGTTAAAACAAATCCTTCAATCCAA
66 AAATTAACTTCAAATCAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* * * **
75681 CGTGGCTGAGATTTGGTTATATGAATATTGATATTTAAAGGAGTCTTGCCACCAAAAATCGTA
131 CGTGGCTGAGATTTGGTTAGACGAATATAGATACATAAAGGAGTCTTGCCACCAAAAATCGTA
* * * * * *
75744 AAATTGACGCTAAAAAGATTAAAGTGTTTTTCATGCTTCTAATATTG-TTTTTCTTATTTTTTCC
1 AAATTAACGCCAAAAAGATTAAAGAGTTTTTCACGCTTCGAATATCGTTTTTTCTTATTTTTTCC
* *
75808 AAATTAA-TATCAAATTAAATCGAAATTC-TGATTAAGATGCTCGTAAAAACAAATCCTTAAATC
66 AAATTAACT-TCAAATCAAATCGAAA--CAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATC
* * *
75871 CAATGTGGCTTAGATTTGGTTAGACGAATATAGATACATCAAGGAGTCTT
128 CAACGTGGCTGAGATTTGGTTAGACGAATATAGATACATAAAGGAGTCTT
75921 AATGCCAAAA
Statistics
Matches: 150, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
191 1 0.01
192 36 0.24
193 112 0.75
194 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (193 bp):
AAATTAACGCCAAAAAGATTAAAGAGTTTTTCACGCTTCGAATATCGTTTTTTCTTATTTTTTCC
AAATTAACTTCAAATCAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAA
CGTGGCTGAGATTTGGTTAGACGAATATAGATACATAAAGGAGTCTTGCCACCAAAAATCGTA
Found at i:77203 original size:330 final size:331
Alignment explanation
Indices: 75750--77860 Score: 2375
Period size: 331 Copynumber: 6.4 Consensus size: 331
75740 CGTAAAATTG
* * * * * * **
75750 ACGCTAAAAAGATTAAAGTGTTTTTCA-TGCTTCTAATATTGTTTTTCTTATTTTTTCCAAATTA
1 ACGCCAAAAAAATTGAAGAGTTTTTCACT-CTTCGAATATCGTTTTTCTTATTTTTTCTGAATTA
* * * * * *
75814 ATATCAAATTAAATCGAAATTC-TGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
65 ATTTCTAATTAAATCGAAA--CATAATTCAGATGCTCGTAAAAACAAATCCTTAATTCCAATTTG
* * ** ****
75878 GCTTAGATTTGGTTAGACGAATATAGATACATCAAGGAGTCTTAATGCCAAAAATCATGCAAAAT
128 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAAT
** * * * *
75943 TGAACCGGGGCACCGGAATGCGTTTTCAGCCAGAAACCGTGATGGTTAGTACACGATTTCGGCTA
193 TGTGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
* * * * * * * * *
76008 AAATTTTACAAAAACTGA-CTAGAAAATATTTCCTTAATTTTTGGCCACAATATTCCTAAAAAGT
258 AAATTTTGCAAAAACTGATCAAAAAAAT-TTTCCTCAATTTTCGGCCACAACACTCATAAAAAAT
76072 ATATAATTTA
322 ATATAATTTA
* ** * * * * *
76082 ATGCCAGTAAGATTGGAGAATTTTTCACGT-TTCGAATATCGTTTTTCCTATTTTTTCAGAATTA
1 ACGCCAAAAAAATTGAAGAGTTTTTCAC-TCTTCGAATATCGTTTTTCTTATTTTTTCTGAATTA
* * * * *
76146 ATATCCAATTAAATCGAAACATGATTCAGATGTTCGTAAAAACAAATGCTTAATTCCAATTTGGC
65 ATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAACAAATCCTTAATTCCAATTTGGC
*
76211 TGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAATTG
130 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAATTG
* ** * * *
76276 TGCCGGGGCCTCGGAACGCGTTTTTTTCCAAAAACCGTGATGGTTGGTACACGATTTTGGTTAAA
195 TGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* * ** *
76341 AATTTGCAAAAACAT-ATGAAAAATTTTTTCCTCATTTTTCGGCCACAACACTCATAAGAAAATA
260 ATTTTGCAAAAAC-TGATCAAAAAAATTTTCCTCAATTTTCGGCCACAACACTCATAA-AAAATA
76405 TATAATTTA
323 TATAATTTA
*
76414 ACGCC-AAAAAATTGAAGAGTTTTTCACTCTTCGAATATCGTTTTTCTTATTTTTTCTAAATTAA
1 ACGCCAAAAAAATTGAAGAGTTTTTCACTCTTCGAATATCGTTTTTCTTATTTTTTCTGAATTAA
* *
76478 TTTCTAATTAAATCGAAACA-AGATTCAGATGCTCGCAAAAACAAATCCTTAGTTCCAATTTGGC
66 TTTCTAATTAAATCGAAACATA-ATTCAGATGCTCGTAAAAACAAATCCTTAATTCCAATTTGGC
* * * * *
76542 TGAGATTTGGTTAGATGGATGTAGATATTTTAAGGAGTCTTAGCACAAAAAATCATGCAAAATTG
130 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAATTG
* *
76607 TGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACC---CT-G--A-TA-ACGATTTCGGTTAAA
195 TGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* ** * * * *
76664 ATTCTGCAAAAACAAATCAAAAAATTTTTCCTCAATTTTCAGCCACAACATTCATAAAAAAACAT
260 ATTTTGCAAAAACTGATCAAAAAAATTTTCCTCAATTTTCGGCCACAACACTCAT-AAAAAATAT
*
76729 AAAATTTA
324 ATAATTTA
* * * *
76737 ACGCCAAAAAAATTTGAAGAGTTTTTCACGCTTCGAAAATCCTTTTTCTTATTTTTTCTAAATTA
1 ACGCCAAAAAAA-TTGAAGAGTTTTTCACTCTTCGAATATCGTTTTTCTTATTTTTTCTGAATTA
* *
76802 ATTTCTAATTAAATCGAAACA-AGATTCAGATGCTCGCAAAAACAAATCCTTAATTACAATTTGG
65 ATTTCTAATTAAATCGAAACATA-ATTCAGATGCTCGTAAAAACAAATCCTTAATTCCAATTTGG
* * * * *
76866 CTGAGATTTGGTTAAAT-AGATATAGATATTTCAAGGAGCCTTGCCATCAAAAATCAAGCAAAAT
129 CTGAGATTTGGTTAGATGA-ATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAAT
* * * *
76930 TGTGCTGTGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGGTGGTTAGTACACGATTTCGGTTA
193 TGTGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
* * * * *
76995 AAATTATGTAAAAACAT-ATCAAAAAAATTTTCCTCAAATTTCGTCCACAACACTCATAAAATA-
258 AAATTTTGCAAAAAC-TGATCAAAAAAATTTTCCTCAATTTTCGGCCACAACACTCATAAAAAAT
77058 ATATAATTTA
322 ATATAATTTA
* * * * *
77068 ATGCCAAAAAAAATGAAGTGTTTTTCACTCTTCAAATATCATTTTTCTTATGTTTTT-TGAATTA
1 ACGCCAAAAAAATTGAAGAGTTTTTCACTCTTCGAATATCGTTTTTCTTAT-TTTTTCTGAATTA
* * * *
77132 ATTTCTAATTAAATCGAAACATAATTCAGATGCTCATACAAACAAATCCTTCATTCCAACTTGGC
65 ATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAACAAATCCTTAATTCCAATTTGGC
* ** * *
77197 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTATTGGTGCCAAAAATCATGCAAAACTA
130 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAATTG
* * * * *
77262 AGCCGGGGTCCCGAAACGCGTTTTTAGCCAGAAACC---AT-G--ATTACACGATTTCGGCTAAA
195 TGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* * * * * * *
77321 ATTTTACAAAAACTGACCAGAAAATATTTT-CTCAAGTTTT-GGACACAATACTCCTAAAAAGTA
260 ATTTTGCAAAAACTGATCA-AAAAAATTTTCCTCAA-TTTTCGGCCACAACACTCATAAAAAATA
77384 TATAATTTA
323 TATAATTTA
* ** * ** * *
77393 ATGCTC-GTAAGATTG-AGAAAATTTTCACGT-TTCGAATATCGTTTTTCCTATTTTTTCAGAAT
1 ACGC-CAAAAAAATTGAAG-AGTTTTTCAC-TCTTCGAATATCGTTTTTCTTATTTTTTCTGAAT
* * * *
77455 TAATATCCAATTAAATCGAAACATGATTCAGATGCTCGTAAAAAGAAATCCTTAATTCCAATTTG
63 TAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAACAAATCCTTAATTCCAATTTG
* * * *
77520 GCTGAGATTTGGTTAGATGAATATAGATATTTTAAGCAGTCTTGGCACCAAAAATCATGTATAAT
128 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAAT
** * * *
77585 TGTAACGGGGCCTCGGAACGTGTTTTT-GCCAAAAACCGTGATGGTTAATACACGATTTCGGCTA
193 TGTGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
* *
77649 AAATTTTGCAAAGACTGACCAAAAAATATTTT-CTCAATTTTCGGCCACAACACTCATAAAAAAT
258 AAATTTTGCAAAAACTGATCAAAAAA-ATTTTCCTCAATTTTCGGCCACAACACTCATAAAAAAT
77713 ATATAATTTA
322 ATATAATTTA
* * *
77723 ACGCCAAAAAATTTGAAGAGTTGTTCACGCTTCGAATATCGTTTTTCTTATTTTTTCTGAATTAA
1 ACGCCAAAAAAATTGAAGAGTTTTTCACTCTTCGAATATCGTTTTTCTTATTTTTTCTGAATTAA
* * * *
77788 TTTTTAATTAAATCGAAACA-AGATTCAGATGCTCGTTAAAACAAATCCTTCAA-CCCAATGTGG
66 TTTCTAATTAAATCGAAACATA-ATTCAGATGCTCGTAAAAACAAATCCTT-AATTCCAATTTGG
77851 CTGAGATTTG
129 CTGAGATTTG
77861 TTTAAAAATT
Statistics
Matches: 1505, Mismatches: 228, Indels: 94
0.82 0.12 0.05
Matches are distributed among these distances:
323 79 0.05
324 77 0.05
325 393 0.26
326 3 0.00
327 4 0.00
328 3 0.00
329 10 0.01
330 364 0.24
331 414 0.28
332 96 0.06
333 61 0.04
334 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (331 bp):
ACGCCAAAAAAATTGAAGAGTTTTTCACTCTTCGAATATCGTTTTTCTTATTTTTTCTGAATTAA
TTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAACAAATCCTTAATTCCAATTTGGCT
GAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAATTGT
GCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
TTTTGCAAAAACTGATCAAAAAAATTTTCCTCAATTTTCGGCCACAACACTCATAAAAAATATAT
AATTTA
Found at i:77485 original size:655 final size:651
Alignment explanation
Indices: 75750--77860 Score: 2676
Period size: 655 Copynumber: 3.2 Consensus size: 651
75740 CGTAAAATTG
* * * * * * *
75750 ACGCTAAAAAGATTAAAGTGTTTTTCA-TGCTTCTAATATTGTTTTTCTTATTTTTTCCAAATTA
1 ACGCCAAAAAAATTGAAGAGTTTTTCACT-CTTCGAATATCGTTTTTCTTATTTTTTCTAAATTA
* * * * *
75814 ATATCAAATTAAATCGAAATTC-TGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
65 ATTTCTAATTAAATCGAAA--CAAGATTCAGATGCTCGTAAAAACAAATCCTTCAATCCAATGTG
* * ** *
75878 GCTTAGATTTGGTTAGACGAATATAGATACATCAAGGAGTCTTAATGCCAAAAATCATGCAAAAT
128 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTAGTGCCAAAAATCATGCAAAAT
* *
75943 TGAA-CCGGGGCACCGGAATGCGTTTTCAGCCAGAAACCGTGATGGTTAGTACACGATTTCGGCT
193 T-AAGCCGGGGC-CCGGAACGCGTTTTTAGCCAGAAACC---AT-G--A-TACACGATTTCGGCT
* * *
76007 AAAATTTTACAAAAACTGACTAGAAAATATTTCCTTAATTTTTGGCCACAATATTCCTAAAAAGT
249 AAAATTTTACAAAAACTGACCAGAAAATATTTTCTCAA-TTTTGGCCACAATATTCCTAAAAAGT
76072 ATATAATTTAATGCCAGTAAGATTG-GAGAATTTTTCACGTTTCGAATATCGTTTTTCCTATTTT
313 ATATAATTTAATGCCAGTAAGATTGAGAGAATTTTTCACGTTTCGAATATCGTTTTTCCTATTTT
* *
76136 TTCAGAATTAATATCCAATTAAATCGAAACATGATTCAGATGTTCGTAAAAACAAATGCTTAATT
378 TTCAGAATTAATATCCAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAATT
*
76201 CCAATTTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCA
443 CCAATTTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCA
* *
76266 TGCAAAATTGTGCCGGGGCCTCGGAACGCGTTTTTTTCCAAAAACCGTGATGGTTGGTACACGAT
508 TGCAAAATTGTG-CGGGGCCTCGGAACGCG-TTTTTGCCAAAAACCGTGATGGTTAGTACACGAT
* * ** *
76331 TTTGGTTAAAAATTTGCAAAAACATATGAAAAATTTTTTCCTCATTTTTCGGCCACAACACTCAT
571 TTCGGTT-AAAATTTGCAAAAACATATCAAAAAAATTTTCCTCAATTTTCGGCCACAACACTCAT
76396 AAGAAAATATATAATTTA
635 AA-AAAATATATAATTTA
76414 ACGCC-AAAAAATTGAAGAGTTTTTCACTCTTCGAATATCGTTTTTCTTATTTTTTCTAAATTAA
1 ACGCCAAAAAAATTGAAGAGTTTTTCACTCTTCGAATATCGTTTTTCTTATTTTTTCTAAATTAA
* * *
76478 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGCAAAAACAAATCCTT-AGTTCCAATTTGGC
66 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTCA-ATCCAATGTGGC
* * * ** * *
76542 TGAGATTTGGTTAGATGGATGTAGATATTTTAAGGAGTCTTAGCACAAAAAATCATGCAAAATTG
130 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTAGTGCCAAAAATCATGCAAAATTA
* * * * * *
76607 TGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCCTGATA-ACGATTTCGGTTAAAATTCTGC
195 AGCCGGGG-CCCGGAACGCGTTTTTAGCCAGAAACCATGATACACGATTTCGGCTAAAATTTTAC
** * * * * * ** *
76671 AAAAACAAATCAAAAAAT-TTTTCCTCAATTTTCAGCCACAACATTCATAAAAAAACATAAAATT
259 AAAAACTGACCAGAAAATATTTT-CTCAATTTT-GGCCACAATATTCCT-AAAAAGTATATAATT
* ** * * * * * *
76735 TAACGCCAAAAAAATTTGA-AGAGTTTTTCACGCTTCGAAAATCCTTTTTCTTATTTTTTCTA-A
321 TAATGCCAGTAAGA-TTGAGAGAATTTTTCACGTTTCGAATATCGTTTTTCCTATTTTTTC-AGA
* * * * *
76798 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGCAAAAACAAATCCTTAATTACAATT
384 ATTAATATCCAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAATTCCAATT
* * * * *
76863 TGGCTGAGATTTGGTTAAAT-AGATATAGATATTTCAAGGAGCCTTGCCATCAAAAATCAAGCAA
449 TGGCTGAGATTTGGTTAGATGA-ATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAA
* * *
76927 AATTGTGCTGTGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGGTGGTTAGTACACGATTTCGG
513 AATTGTGC-GGGGCCTCGGAACGCGTTTTT-GCCAAAAACCGTGATGGTTAGTACACGATTTCGG
* * * *
76992 TTAAAATTATGTAAAAACATATCAAAAAAATTTTCCTCAAATTTCGTCCACAACACTCATAAAAT
576 TTAAAATT-TGCAAAAACATATCAAAAAAATTTTCCTCAATTTTCGGCCACAACACTCATAAAAA
77057 A-ATATAATTTA
640 ATATATAATTTA
* * * * * *
77068 ATGCCAAAAAAAATGAAGTGTTTTTCACTCTTCAAATATCATTTTTCTTATGTTTTT-TGAATTA
1 ACGCCAAAAAAATTGAAGAGTTTTTCACTCTTCGAATATCGTTTTTCTTAT-TTTTTCTAAATTA
* * *
77132 ATTTCTAATTAAATCGAAACATA-ATTCAGATGCTCATACAAACAAATCCTTCATTCCAACT-TG
65 ATTTCTAATTAAATCGAAACA-AGATTCAGATGCTCGTAAAAACAAATCCTTCAATCCAA-TGTG
* * *
77195 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTATTGGTGCCAAAAATCATGCAAAAC
128 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTAGTGCCAAAAATCATGCAAAAT
*
77260 TAAGCCGGGGTCCCGAAACGCGTTTTTAGCCAGAAACCATGATTACACGATTTCGGCTAAAATTT
193 TAAGCCGGGG-CCCGGAACGCGTTTTTAGCCAGAAACCATGA-TACACGATTTCGGCTAAAATTT
* *
77325 TACAAAAACTGACCAGAAAATATTTTCTCAAGTTTTGGACACAATACTCCTAAAAAGTATATAAT
256 TACAAAAACTGACCAGAAAATATTTTCTCAA-TTTTGGCCACAATATTCCTAAAAAGTATATAAT
*
77390 TTAATGCTC-GTAAGATTGAGA-AAATTTTCACGTTTCGAATATCGTTTTTCCTATTTTTTCAGA
320 TTAATGC-CAGTAAGATTGAGAGAATTTTTCACGTTTCGAATATCGTTTTTCCTATTTTTTCAGA
*
77453 ATTAATATCCAATTAAATCGAAACATGATTCAGATGCTCGTAAAAAGAAATCCTTAATTCCAATT
384 ATTAATATCCAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAATTCCAATT
* * * *
77518 TGGCTGAGATTTGGTTAGATGAATATAGATATTTTAAGCAGTCTTGGCACCAAAAATCATGTATA
449 TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAA
* * * *
77583 ATTGTAACGGGGCCTCGGAACGTGTTTTTGCCAAAAACCGTGATGGTTAATACACGATTTCGGCT
514 ATTGT-GCGGGGCCTCGGAACGCGTTTTTGCCAAAAACCGTGATGGTTAGTACACGATTTCGGTT
* *
77648 AAAATTTTGCAAAGAC-TGACCAAAAAATATTTT-CTCAATTTTCGGCCACAACACTCATAAAAA
578 AAAA-TTTGCAAAAACAT-ATCAAAAAA-ATTTTCCTCAATTTTCGGCCACAACACTCATAAAAA
77711 ATATATAATTTA
640 ATATATAATTTA
* * * *
77723 ACGCCAAAAAATTTGAAGAGTTGTTCACGCTTCGAATATCGTTTTTCTTATTTTTTCTGAATTAA
1 ACGCCAAAAAAATTGAAGAGTTTTTCACTCTTCGAATATCGTTTTTCTTATTTTTTCTAAATTAA
* * *
77788 TTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAACAAATCCTTCAACCCAATGTGGCT
66 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTCAATCCAATGTGGCT
77853 GAGATTTG
131 GAGATTTG
77861 TTTAAAAATT
Statistics
Matches: 1237, Mismatches: 174, Indels: 81
0.83 0.12 0.05
Matches are distributed among these distances:
653 8 0.01
654 150 0.12
655 538 0.43
656 287 0.23
657 50 0.04
658 9 0.01
659 1 0.00
661 2 0.00
662 119 0.10
663 68 0.05
664 5 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (651 bp):
ACGCCAAAAAAATTGAAGAGTTTTTCACTCTTCGAATATCGTTTTTCTTATTTTTTCTAAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTCAATCCAATGTGGCT
GAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTAGTGCCAAAAATCATGCAAAATTAA
GCCGGGGCCCGGAACGCGTTTTTAGCCAGAAACCATGATACACGATTTCGGCTAAAATTTTACAA
AAACTGACCAGAAAATATTTTCTCAATTTTGGCCACAATATTCCTAAAAAGTATATAATTTAATG
CCAGTAAGATTGAGAGAATTTTTCACGTTTCGAATATCGTTTTTCCTATTTTTTCAGAATTAATA
TCCAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAATTCCAATTTGGCTGA
GATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAATTGTGC
GGGGCCTCGGAACGCGTTTTTGCCAAAAACCGTGATGGTTAGTACACGATTTCGGTTAAAATTTG
CAAAAACATATCAAAAAAATTTTCCTCAATTTTCGGCCACAACACTCATAAAAAATATATAATTT
A
Done.