Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014252.1 Corchorus olitorius cultivar O-4 contig14285, 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: 119227
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4633 original size:19 final size:19
Alignment explanation
Indices: 4602--4640 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4592 ACATCTCTTT
4602 ATTTAGAATATTTTATATA
1 ATTTAGAATATTTTATATA
4621 ATTTCAGAA-ATTTTATATA
1 ATTT-AGAATATTTTATATA
4640 A
1 A
4641 AAATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (19 bp):
ATTTAGAATATTTTATATA
Found at i:33587 original size:31 final size:32
Alignment explanation
Indices: 33549--33610 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
33539 GTACTAGTAG
*
33549 TTTTTTTTTGTGCT-AAATGTCAAAGAACACT
1 TTTTTTTTTGGGCTAAAATGTCAAAGAACACT
*
33580 TTTTTTTTTGGGTTAAAAATGTCAAAGAACA
1 TTTTTTTTTGGGCT-AAAATGTCAAAGAACA
33611 TTTACCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 12 0.44
33 15 0.56
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.44
Consensus pattern (32 bp):
TTTTTTTTTGGGCTAAAATGTCAAAGAACACT
Found at i:37315 original size:18 final size:18
Alignment explanation
Indices: 37289--37323 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37279 TCCCTTTTTC
*
37289 AAGGGAGGCTTACAGATT
1 AAGGCAGGCTTACAGATT
*
37307 AAGGCAGGCTTTCAGAT
1 AAGGCAGGCTTACAGAT
37324 CTGGTTCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.23
Consensus pattern (18 bp):
AAGGCAGGCTTACAGATT
Found at i:37931 original size:24 final size:24
Alignment explanation
Indices: 37891--37937 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
37881 TTTTTTGGAT
37891 ACGATCTGAATGAGAAAGAGTGGC
1 ACGATCTGAATGAGAAAGAGTGGC
*
37915 ACGATCTGGAA-GGGAAAGAGTGG
1 ACGATCT-GAATGAGAAAGAGTGG
37938 GACCGCATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.36, C:0.11, G:0.38, T:0.15
Consensus pattern (24 bp):
ACGATCTGAATGAGAAAGAGTGGC
Found at i:37989 original size:18 final size:18
Alignment explanation
Indices: 37966--38002 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
37956 CTTAAATCCT
37966 CTGATGGATTTGAGGATC
1 CTGATGGATTTGAGGATC
37984 CTGATGGATTTGAGGATC
1 CTGATGGATTTGAGGATC
38002 C
1 C
38003 CGAGTTGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (18 bp):
CTGATGGATTTGAGGATC
Found at i:48857 original size:1 final size:1
Alignment explanation
Indices: 48851--48882 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
48841 TCCTCAGTTC
48851 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
48883 CATGGCCAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:49494 original size:15 final size:15
Alignment explanation
Indices: 49470--49500 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49460 CAACTCTCTG
*
49470 TCTCTGTGATATATA
1 TCTCTCTGATATATA
49485 TCTCTCTGATATATA
1 TCTCTCTGATATATA
49500 T
1 T
49501 AGTAATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (15 bp):
TCTCTCTGATATATA
Found at i:67692 original size:25 final size:25
Alignment explanation
Indices: 67645--67692 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
67635 TGCAGCTACA
*
67645 CAATTTAGTATACTACTAGAATTTG
1 CAATTTAGTATACTACTACAATTTG
*
67670 CAATTTAGTAGTA-TACTCCAATT
1 CAATTTAGTA-TACTACTACAATT
67693 GAATCCATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (25 bp):
CAATTTAGTATACTACTACAATTTG
Found at i:73716 original size:127 final size:128
Alignment explanation
Indices: 73584--73842 Score: 339
Period size: 127 Copynumber: 2.0 Consensus size: 128
73574 CATCGTTTAA
* * *
73584 ACTTTTATAGTTTTATTCAATTAAAAACTCTAATTTTATTTATTTAAATCTAATAT-C-T-T-TA
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
73645 -TGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATATATTAGAATTTTTTAAAT
66 TTGATTTTTACCATTTTACTATTTTAATTAAAAAAC---T-TATATATATTAGAATTTTTTAAAT
73709 AT
127 AT
*
73711 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTAT--C
* * * * *
73776 TATTTTATTTTTACTATTTTATTATTTTATTTTAAAAACTTATATATATTAGAATTTTTTAAATA
64 TA-TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
73841 T
128 T
73842 A
1 A
73843 TTTCTTAAAT
Statistics
Matches: 115, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
127 52 0.45
128 1 0.01
129 1 0.01
130 1 0.01
131 27 0.23
132 1 0.01
133 2 0.02
135 30 0.26
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.53
Consensus pattern (128 bp):
ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:73864 original size:14 final size:13
Alignment explanation
Indices: 73828--73866 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
73818 TATATATTAG
73828 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
73841 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
73855 AATTTTTTAAAT
1 AATTTTTTAAAT
73867 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:76290 original size:47 final size:47
Alignment explanation
Indices: 76221--76326 Score: 194
Period size: 47 Copynumber: 2.3 Consensus size: 47
76211 AGGGCTTTAC
* *
76221 GACCTCACAGCCCACTCACCTACTTACCAAACTACTATATAATCCAG
1 GACCTCACAGTCCACGCACCTACTTACCAAACTACTATATAATCCAG
76268 GACCTCACAGTCCACGCACCTACTTACCAAACTACTATATAATCCAG
1 GACCTCACAGTCCACGCACCTACTTACCAAACTACTATATAATCCAG
76315 GACCTCACAGTC
1 GACCTCACAGTC
76327 TAGGCACGAG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.33, C:0.38, G:0.08, T:0.21
Consensus pattern (47 bp):
GACCTCACAGTCCACGCACCTACTTACCAAACTACTATATAATCCAG
Found at i:76354 original size:21 final size:21
Alignment explanation
Indices: 76315--76354 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
76305 TATAATCCAG
* *
76315 GACCTCACAGTCTAGGCACGA
1 GACCTCACAGTCCACGCACGA
76336 GACCTCACAGTCCACGCAC
1 GACCTCACAGTCCACGCAC
76355 CTACTTACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.40, G:0.20, T:0.12
Consensus pattern (21 bp):
GACCTCACAGTCCACGCACGA
Found at i:76377 original size:68 final size:68
Alignment explanation
Indices: 76268--76400 Score: 257
Period size: 68 Copynumber: 2.0 Consensus size: 68
76258 TATAATCCAG
*
76268 GACCTCACAGTCCACGCACCTACTTACCAAACTACTATATAATCCAGGACCTCACAGTCTAGGCA
1 GACCTCACAGTCCACGCACCTACTTACCAAACTACTATATAATCCAGGACCTCACAGTCCAGGCA
76333 CGA
66 CGA
76336 GACCTCACAGTCCACGCACCTACTTACCAAACTACTATATAATCCAGGACCTCACAGTCCAGGCA
1 GACCTCACAGTCCACGCACCTACTTACCAAACTACTATATAATCCAGGACCTCACAGTCCAGGCA
76401 TGGTGTGAGC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.32, C:0.36, G:0.13, T:0.19
Consensus pattern (68 bp):
GACCTCACAGTCCACGCACCTACTTACCAAACTACTATATAATCCAGGACCTCACAGTCCAGGCA
CGA
Found at i:86974 original size:38 final size:38
Alignment explanation
Indices: 86923--86997 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
86913 AAAAGTTCGT
*
86923 CATAACTTTTGAGACGAAGAAACGGAAATTAATAAAAG
1 CATAACTTTTGAGACGAAGAAACGGAAATCAATAAAAG
*
86961 CATAACTTTTGAGATGAAGAAACGGAAATCAATAAAA
1 CATAACTTTTGAGACGAAGAAACGGAAATCAATAAAA
86998 AGTACTACTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.51, C:0.11, G:0.17, T:0.21
Consensus pattern (38 bp):
CATAACTTTTGAGACGAAGAAACGGAAATCAATAAAAG
Found at i:87026 original size:15 final size:15
Alignment explanation
Indices: 87006--87034 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
86996 AAAGTACTAC
87006 TCCCTTCGTCTCAAT
1 TCCCTTCGTCTCAAT
87021 TCCCTTCGTCTCAA
1 TCCCTTCGTCTCAA
87035 CTACTTTCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.41, G:0.07, T:0.38
Consensus pattern (15 bp):
TCCCTTCGTCTCAAT
Found at i:90610 original size:22 final size:22
Alignment explanation
Indices: 90550--90611 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
90540 ACGTTACAAA
* * *
90550 TTATCATGACATGTTAATACCG
1 TTATCATGACACGTTGATACAG
90572 TTATCATGACACGTTGATACAG
1 TTATCATGACACGTTGATACAG
*
90594 TTATCATGACACATTGAT
1 TTATCATGACACGTTGAT
90612 CTATAAATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (22 bp):
TTATCATGACACGTTGATACAG
Found at i:105285 original size:101 final size:104
Alignment explanation
Indices: 105104--105383 Score: 297
Period size: 107 Copynumber: 2.7 Consensus size: 104
105094 TTAGTCCTAG
* * * * * *
105104 TAATTT-TTATTATAGAGTTTTATAAATAAAATATAAAATTAATTTAAAACTAAGTTTAGCCTCA
1 TAATTTATTGTTATAGGGTTTTAGAAATAAAATATAAAACTAATTT--CACTAAGTTTAGCCCCA
** **
105168 AATT-ATTTTTTCA-TT-TTT-AGGATAAATTTTAAAATTAA
64 AATTAAAATTTTCATTTATTTAAGG-TAAATTCCAAAATTAA
*
105206 TAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCAAA
1 TAATTTATTGTTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAA
*
105271 TTAAAATTTT-ATTTTTATTTCAAAGGTAAATTCCATAATTAA
66 TTAAAATTTTCA--TTTATTT--AAGGTAAATTCCAAAATTAA
* * * *
105313 TAACTCATTGTTATAGGGTTTTAGAAATAAGATATATAACTAA-TTCACTAAGTTTAG-CCCAAA
1 TAATTTATTGTTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAA
105376 TTAAAATT
66 TTAAAATT
105384 AAAATTATAT
Statistics
Matches: 152, Mismatches: 17, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
101 20 0.13
102 11 0.07
103 34 0.22
104 2 0.01
105 17 0.11
106 14 0.09
107 51 0.34
108 3 0.02
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (104 bp):
TAATTTATTGTTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAA
TTAAAATTTTCATTTATTTAAGGTAAATTCCAAAATTAA
Found at i:108475 original size:28 final size:28
Alignment explanation
Indices: 108443--108498 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
108433 TCAACTTAAA
*
108443 AAAGGTTATAACTTTCAAACCATAAGTC
1 AAAGGTCATAACTTTCAAACCATAAGTC
108471 AAAGGTCATAACTTTCAAACCATAAGTC
1 AAAGGTCATAACTTTCAAACCATAAGTC
108499 GGTTTGACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.27
Consensus pattern (28 bp):
AAAGGTCATAACTTTCAAACCATAAGTC
Found at i:117634 original size:331 final size:328
Alignment explanation
Indices: 116920--119203 Score: 2637
Period size: 331 Copynumber: 6.9 Consensus size: 328
116910 TTTGTGACAT
* * * * * *
116920 GACTCCTTGAAACATCTATATTTC-TCTATCCAAATCTCAGCCACAT-TGGATTGAAGGATCTGT
1 GACTCCTTGAAATATCTA-AATTCATCTAACCAAATCTCAGTCACATAT-GATTTAAGGATTTGT
* * * *
116983 TTTTTCAAGCATCTGAATCATATTTCAATTTAATTA-AACATTAATTCAGAAAAAAATAGGAAAA
64 TTTTACGAGCATCTGAATCATGTTTCAATTTAATTAGAA-ATTAATTC-G-GAAAAATAGGAAAA
** * * * * * * *
117047 ATAATATTAGAAGCGTGAATAGTCCTTCAATATTTTTGGTGTTAAATATATATTTA--TTTCAGT
126 ACGATATTAGAAGCGTGAAAAG-CCCTAAATCTTTTTGGTGTTGAAT-TATTTTTATTTTTTAGT
* * *
117110 ATTGTGGCCAAAAATAAAAGGAAAAAATATTTCGGGTCAA-TTTTGACAAAATTTTAGCCAAAAT
189 ATTGTGGCCAAAAAT-TAAGG-AAAAATCTTTCGGGTCAATTTTTG-CAAAATTTTAGCCGAAAT
** * *
117174 CGTGTACTAATTATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGACCCGGCTCAATTTTGCATG
251 CGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTC-ATTTTGCATG
117239 ATTTTTGGCGGCAA
315 ATTTTTGGCGGCAA
* * * *
117253 AACTCCTTGAAATATCTAAATTCATC-AAACAAATTCTCAGTCAGATATGATTTAAGGATTTTTT
1 GACTCCTTGAAATATCTAAATTCATCTAACCAAA-TCTCAGTCACATATGATTTAAGGATTTGTT
* * *
117317 TTTACGAGCATTTGAATTATGTTTCTATTTAATTAGAAATTAATTCGGAAACAATAGGAAAAACG
65 TTTACGAGCATCTGAATCATGTTTCAATTTAATTAGAAATTAATTCGGAAA-AATAGGAAAAACG
* * *
117382 ATATTAGAAGTGTAAAAAGCCTCTAAATCTTTTTGGCGTTGAATTATTTTTATGTTTTTAGTATT
129 ATATTAGAAGCGTGAAAAGCC-CTAAATCTTTTTGGTGTTGAATTATTTTTAT-TTTTTAGTATT
* *
117447 GTGGCCAAAAATTAAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATTGTTTA
192 GTGGCCAAAAATTAAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA
* * *
117512 CTAACCATCACGGTTTTTTGC-AAAAGCGCGTTCCGGGGCCCCGGCTCATATTTGCATGATTTTT
257 CTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAT-TTTGCATGATTTTT
117576 GGCGGCAA
321 GGCGGCAA
* * * * *
117584 GAATCCTTGAAATATCTATATTCATCTAACCAAATCTAAGTCACATATGATTTAATGATTCGTTT
1 GACTCCTTGAAATATCTAAATTCATCTAACCAAATCTCAGTCACATATGATTTAAGGATTTGTTT
* *
117649 TTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAGGAAAAACGAT
66 TTACGAGCATCTGAATCATGTTTCAATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAACGAT
* * * * * *
117714 ACTAGAAGCGTGAAAAGCGCGTAAATATTTTTGGAGTTGAATTA--TATATTTTTATGGGTATTG
131 ATTAGAAGCGTGAAAAGC-CCTAAATCTTTTTGGTGTTGAATTATTTTTATTTTT-T-AGTATTG
* * * *
117777 TGGCAAAAAAATT-AGGAAAAATTTTTCGGGTCAGA-TTTTGAAAAATTTCAG-CGAAA------
193 TGGC-CAAAAATTAAGGAAAAATCTTTCGGGTCA-ATTTTTGCAAAATTTTAGCCGAAATCGTGT
* * * * *
117833 A-T----GTCACGGGTTTTGGATAAAAACGCGTTCCTGGGCCTCGACTCATTTTTGCATGATTTT
256 ACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCA-TTTTGCATGATTTT
*
117893 TGGTGGCAA
320 TGGCGGCAA
** * * *
117902 GACTCCTTGAAATATCTAAATTCATCTAAATAAATATCAATCACATATGATTTAAGGATTAGTTT
1 GACTCCTTGAAATATCTAAATTCATCTAACCAAATCTCAGTCACATATGATTTAAGGATTTGTTT
* * * *
117967 TTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAGAAAATGGGGAAAACGA
66 TTACGAGCATCTGAATCATGTTTCAATTTAATTAGAAATTAATTCGGA-AAAATAGGAAAAACGA
* * * * * *
118032 TATTAGAAGCGTTAAAAGCCCTTAAATCTTTTTGTTGTTGAATTATATATATATATTAGTATTGT
130 TATTAGAAGCGTGAAAAGCCC-TAAATCTTTTTGGTGTTGAATTATTTTTATTTTTTAGTATTGT
*
118097 GGCCAAAAATTAAGGAAAAATCTTTCGGGTCAATTTTTGCCAAATTTTAGCCGAAATCGTGTACT
194 GGCCAAAAATTAAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT
* * * * * *
118162 -A-CATCACAGTTTTTGGCTAAAATCACGTTCCGGGCCCCCGACTCATTTTGGCATAATTTTTTG
259 AACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCATTTT-GCATGATTTTTGG
*
118225 TGGCAA
323 CGGCAA
*
118231 GACTCCTTGAAATAACTAAATTCATCTAACCAAATCTCAGTCACATATGATTTAAGGACTTTGTT
1 GACTCCTTGAAATATCTAAATTCATCTAACCAAATCTCAGTCACATATGATTTAAGGA-TTTGTT
* * *
118296 TTTACGAGCATCTGAATCATGTTTCAATTTAACTAGAAATCAATTCGGAAAAAATA-GAAAAAGT
65 TTTACGAGCATCTGAATCATGTTTCAATTTAATTAGAAATTAATTCGG-AAAAATAGGAAAAA-C
*
118360 GATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGTGTTGAATTATATATATATATATATATA
128 GATATTAGAAGCGTGAAAAGCCC-TAAATCTTTTTGGTGTTG--------A-AT-TAT-T-T-T-
* * *
118425 TATATATATTATAGTATTATGGCCAAAAATTAAGGAAAAATCTTTCAGGTCAATTTTTGCCAAAT
178 TAT-T-T-TT-TAGTATTGTGGCCAAAAATTAAGGAAAAATCTTTCGGGTCAATTTTTGCAAAAT
* * *
118490 TTTAGCCGAAATCGTGTACAAACCATCACAGTATTTTGGCTAAAAACGCGTTCCTGGGCCCCGAC
239 TTTAGCCGAAATCGTGTACTAACCATCACGGT-TTTTGGCTAAAAACGCGTTCCGGGGCCCCGAC
* *
118555 TCATTTTGGCATAATTTTTGGTGGCAA
303 TCATTTT-GCATGATTTTTGGCGGCAA
118582 GACTCCTTGAAATATCTAAATTCATCTAACCAAATCTCAGTCACATATGATTTAAGGATTTGTTT
1 GACTCCTTGAAATATCTAAATTCATCTAACCAAATCTCAGTCACATATGATTTAAGGATTTGTTT
*
118647 TTACGAGCATCTGAATCATGTTTCAATTTAACTAGAAATTAATTCGGAGAAAATAGGAAAAACGA
66 TTACGAGCATCTGAATCATGTTTCAATTTAATTAGAAATTAATTCGGA-AAAATAGGAAAAACGA
* *
118712 TATTAGAAGCGTGAAAAGCACTTAAATCTTTTTGGCT-TTGAATTATTTTTCTTTTTTAGTATTG
130 TATTAGAAGCGTGAAAAGC-CCTAAATCTTTTTGG-TGTTGAATTATTTTTATTTTTTAGTATTG
* * * * *
118776 TAGCAAAAAATTAAGGAAAAATCATTCGGGTCAACTTCTGCAAAATTTTAGCCGAAATCGTGTAC
193 TGGCCAAAAATTAAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC
* ** * *
118841 TAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGACCCCTTCTCATTTTTGCTTGATTTTTA
258 TAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCA-TTTTGCATGATTTTTG
*
118906 GCGGCAG
322 GCGGCAA
* * * * * * *
118913 GACTTCTTGAAATATCTGAATACGTCTAACCAAATCTGAGTCACACATGATTTAAGGATTTGTGT
1 GACTCCTTGAAATATCTAAATTCATCTAACCAAATCTCAGTCACATATGATTTAAGGATTTGTTT
* * * * * *
118978 TTACGAGTATTTGAATCATGTTACTATTTAATTAGAAATTAATTCAGGAAAAA-AAGAAAAATGA
66 TTACGAGCATCTGAATCATGTTTCAATTTAATTAGAAATTAATTC-GGAAAAATAGGAAAAACGA
* *
119042 TATTAGAAGCGTGAAAAGCCCTTAAATCTTTTTTGTGTTGAATTATATATATATTTTTTAGTATT
130 TATTAGAAGCGTGAAAAGCCC-TAAATCTTTTTGGTGTTGAATTAT-T-TTTATTTTTTAGTATT
* * *
119107 GTGGCCAAAAATTAACGAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTTTA
192 GTGGCCAAAAATTAAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA
* **
119172 CTAAACATCACTATTTTTGGCTAAAAACGCGT
257 CTAACCATCACGGTTTTTGGCTAAAAACGCGT
119204 AGCGGGACCC
Statistics
Matches: 1688, Mismatches: 193, Indels: 141
0.83 0.10 0.07
Matches are distributed among these distances:
317 11 0.01
318 156 0.09
319 93 0.06
320 6 0.00
321 8 0.00
322 1 0.00
326 1 0.00
327 5 0.00
328 14 0.01
329 154 0.09
330 202 0.12
331 304 0.18
332 299 0.18
333 89 0.05
334 25 0.01
335 1 0.00
336 2 0.00
337 1 0.00
338 2 0.00
339 3 0.00
340 6 0.00
341 2 0.00
342 2 0.00
344 3 0.00
346 1 0.00
347 1 0.00
348 71 0.04
349 2 0.00
350 104 0.06
351 119 0.07
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (328 bp):
GACTCCTTGAAATATCTAAATTCATCTAACCAAATCTCAGTCACATATGATTTAAGGATTTGTTT
TTACGAGCATCTGAATCATGTTTCAATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAACGAT
ATTAGAAGCGTGAAAAGCCCTAAATCTTTTTGGTGTTGAATTATTTTTATTTTTTAGTATTGTGG
CCAAAAATTAAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
CCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCATTTTGCATGATTTTTGGCGG
CAA
Found at i:118412 original size:2 final size:2
Alignment explanation
Indices: 118405--118437 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
118395 GGTGTTGAAT
118405 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
118438 GTATTATGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:118442 original size:8 final size:7
Alignment explanation
Indices: 118403--118444 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 7
118393 TTGGTGTTGA
118403 ATTATAT
1 ATTATAT
118410 A-TATAT
1 ATTATAT
118416 ATATATAT
1 AT-TATAT
118424 ATATATAT
1 AT-TATAT
118432 ATTATAGT
1 ATTATA-T
118440 ATTAT
1 ATTAT
118445 GGCCAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.19
7 5 0.16
8 21 0.66
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (7 bp):
ATTATAT
Done.