Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016340.1 Corchorus olitorius cultivar O-4 contig16373, 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: 96942
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:176 original size:30 final size:30
Alignment explanation
Indices: 116--175 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
106 GTTTATCGTT
* *
116 ATTTAAAATATATATTCTTCTTAGCAAAAA
1 ATTTAAAATATATATTCTTCTAACCAAAAA
146 ATTTAAAATATAATATT-TT-TAACCAAAAA
1 ATTTAAAATAT-ATATTCTTCTAACCAAAAA
175 A
1 A
176 AATTCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 9 0.33
30 13 0.48
31 5 0.19
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (30 bp):
ATTTAAAATATATATTCTTCTAACCAAAAA
Found at i:669 original size:21 final size:21
Alignment explanation
Indices: 645--686 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
635 TTTCCTTATT
645 TGAACTCCAAATTAATCCAAC
1 TGAACTCCAAATTAATCCAAC
666 TGAACTCCAAATTAATCCAAC
1 TGAACTCCAAATTAATCCAAC
687 GTAAATATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.29, G:0.05, T:0.24
Consensus pattern (21 bp):
TGAACTCCAAATTAATCCAAC
Found at i:6614 original size:15 final size:15
Alignment explanation
Indices: 6594--6625 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6584 GAAATTATAC
*
6594 AATGTACCGTAAGTG
1 AATGTACCATAAGTG
6609 AATGTACCATAAGTG
1 AATGTACCATAAGTG
6624 AA
1 AA
6626 GTTTAGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (15 bp):
AATGTACCATAAGTG
Found at i:12150 original size:7 final size:7
Alignment explanation
Indices: 12126--12160 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
12116 AAAGGAGGGA
12126 GCCATAG
1 GCCATAG
* *
12133 CCCAAAG
1 GCCATAG
12140 GCCATAG
1 GCCATAG
12147 GCCATAG
1 GCCATAG
12154 GCCATAG
1 GCCATAG
12161 TCCCCAACCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.31, C:0.31, G:0.26, T:0.11
Consensus pattern (7 bp):
GCCATAG
Found at i:21914 original size:17 final size:17
Alignment explanation
Indices: 21878--21910 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21868 ATTATATCTT
21878 TATCATATTTTATTTTA
1 TATCATATTTTATTTTA
*
21895 TATCGTATTTT-TTTTA
1 TATCATATTTTATTTTA
21911 ATATTCTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (17 bp):
TATCATATTTTATTTTA
Found at i:30899 original size:284 final size:280
Alignment explanation
Indices: 30368--30899 Score: 692
Period size: 284 Copynumber: 1.9 Consensus size: 280
30358 CCAGGGCCCG
* * * *
30368 GGAACGCGTTTTTAGTAAAAAAACCATGATGGTACATGATTTCATCTAAAATCTTGCAAAATTTG
1 GGAACGCGTTTTTAGGAAAAAAACCATGATGGTACACGATTTCAGCTAAAATCTTGCAAAATATG
* * * *
30433 ACTCGAAATATTTTTCTCACTTTTTAGCCACAATACTCATAAAAAATATATAATGCAACACCAAA
66 ACCCAAAATATTTTTATCACTTTTTAGCCACAATACTCATAAAAAATATATAATGAAACACCAAA
*
30498 AAAATTGAAGGACTTCTCACGCTTTTAATATCGTTTTCCGATTTTTTTCAAATTAATTTCTAATT
131 AAAATTGAAGGACTTCTCACGCTTTTAATATCGTTTTCCGATATTTTTCAAATTAATTTCTAATT
* * *
30563 AAATCGAAATATGATTCAAATGCTCGTAAAAACACATCTTTAAATCCAATGTGTCTAAAATCATG
196 AAATCGAAATAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGTCTAAAATCATG
30628 CAAAACTAACTCGAGGCTTC
261 CAAAACTAACTCGAGGCTTC
* ** * *
30648 GGAACGCG-TTTTAGGCAAAAAACTGTGATGGTACACGATTTCGGCTAAAATTTTGCAGAAA-AT
1 GGAACGCGTTTTTAGGAAAAAAACCATGATGGTACACGATTTCAGCTAAAATCTTGCA-AAATAT
* * * *
30711 GACCCAAAATATTTTTATCAATTTTTTAGCCACAATCAATACTCATAGAATATATATAATTAAAC
65 GACCCAAAATATTTTTATC-ACTTTTTAG-C-C-A-CAATACTCATAAAAAATATATAATGAAAC
* ** * * * * *
30776 GCCAAAAAGTTTGAAGGACTTTTCACGTTTTTAATATCGTTTTTC-ATATTTTTCTGATTTAATT
125 ACCAAAAAAATTGAAGGACTTCTCACGCTTTTAATATCGTTTTCCGATATTTTTC-AAATTAATT
* * *
30840 TCTAATTAAATTGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTG
189 TCTAATTAAATCGAAATAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
30900 GCTGAGATTT
Statistics
Matches: 213, Mismatches: 32, Indels: 10
0.84 0.13 0.04
Matches are distributed among these distances:
279 58 0.27
280 19 0.09
281 1 0.00
282 1 0.00
283 9 0.04
284 125 0.59
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (280 bp):
GGAACGCGTTTTTAGGAAAAAAACCATGATGGTACACGATTTCAGCTAAAATCTTGCAAAATATG
ACCCAAAATATTTTTATCACTTTTTAGCCACAATACTCATAAAAAATATATAATGAAACACCAAA
AAAATTGAAGGACTTCTCACGCTTTTAATATCGTTTTCCGATATTTTTCAAATTAATTTCTAATT
AAATCGAAATAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGTCTAAAATCATG
CAAAACTAACTCGAGGCTTC
Found at i:31763 original size:2 final size:2
Alignment explanation
Indices: 31756--31780 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31746 AATACTCATA
31756 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
31781 ATTCAACTCC
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:32256 original size:289 final size:286
Alignment explanation
Indices: 31772--32293 Score: 716
Period size: 289 Copynumber: 1.8 Consensus size: 286
31762 ATATATATAT
* * *
31772 ATATATATAATTCAACTCCAAAAATATTGGAGGACTTTTCAGGCTTTTAATATCGTTTTTCATAT
1 ATATATATAATTCAACTCCAAAAAGATTGGAGGACTTTTCACGCTTTTAACATCGTTTTTCATAT
* * *
31837 CTTTCTAGATTGAATTCTAATTAAATTGAAATAAGATTCAGATGCTCGCAAAACAAATCCTTAAA
66 CTTTCTAGATTGAATTCTAATTAAATCGAAACAAGATTCAGATGCTCGAAAAACAAATCCTTAAA
* *
31902 TGCAATGTGGCTAAGATTCGATTAGATGAATATAGATATTTCAAGGAGTTTCGATGCCAAAAATC
131 TGCAATGTGGCTAAGATTCGATTAGATGAATACAGATATCTCAAGGAGTTTC-ATGCCAAAAATC
* *
31967 ATGAAAAATTGAGTCAG-GGCCCTGAAACGCGTTTTTAGAAAAAAAACTGACCAGAAAAGTTTTC
195 ATGAAAAACTGA-CCAGAGGCCCTGAAACGCGTTTTTAGAAAAAAAACTGACCAGAAAAGTTTTC
32031 CTCAATTTTTGGCTAAAATACTCATGAA
259 CTCAATTTTTGGCTAAAATACTCATGAA
* * *
32059 ATATATATAATTTAA-TGCCAAGAAGATTGGAGGACTTTTTCACGCTTTTCACATCGTTTTTCAT
1 ATATATATAATTCAACT-CCAAAAAGATTGGAGGAC-TTTTCACGCTTTTAACATCGTTTTTCAT
* *
32123 A-CTTTTCT-GAATT-AATTTTTAATTAAATCGAAACAATATTCAGATGCTCGTAAAAACAAATC
64 ATC-TTTCTAG-ATTGAA-TTCTAATTAAATCGAAACAAGATTCAGATGCTCG-AAAAACAAATC
* * * *
32185 CTTAAATGCAATGTGGCTGAGATTTGATTAGATTAATACGGATATCTCAAGGAGTCTT-A-GCAC
125 CTTAAATGCAATGTGGCTAAGATTCGATTAGATGAATACAGATATCTCAAGGAGT-TTCATGC-C
*
32248 AAAAAATCATGCAAAACTGACCAGAGGCCCTGAAACGCGTTTTTAG
188 -AAAAATCATGAAAAACTGACCAGAGGCCCTGAAACGCGTTTTTAG
32294 CCAAAAACAG
Statistics
Matches: 205, Mismatches: 20, Indels: 18
0.84 0.08 0.07
Matches are distributed among these distances:
286 1 0.00
287 36 0.18
288 69 0.34
289 97 0.47
290 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (286 bp):
ATATATATAATTCAACTCCAAAAAGATTGGAGGACTTTTCACGCTTTTAACATCGTTTTTCATAT
CTTTCTAGATTGAATTCTAATTAAATCGAAACAAGATTCAGATGCTCGAAAAACAAATCCTTAAA
TGCAATGTGGCTAAGATTCGATTAGATGAATACAGATATCTCAAGGAGTTTCATGCCAAAAATCA
TGAAAAACTGACCAGAGGCCCTGAAACGCGTTTTTAGAAAAAAAACTGACCAGAAAAGTTTTCCT
CAATTTTTGGCTAAAATACTCATGAA
Found at i:33809 original size:332 final size:330
Alignment explanation
Indices: 32029--34186 Score: 1653
Period size: 330 Copynumber: 6.6 Consensus size: 330
32019 AGAAAAGTTT
* * * * * * * * *
32029 TCCTCAATTTTTGGCTAAAATACTCATGAAATATATATAATTTAATGCCAAGAAGATTGGAGGAC
1 TCCTTAATTTTTGGATAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGAC
* * * * *
32094 TTTTTCACGCTTTTCACATCGTTTTTC-ATACTTTTCTGAATTAATTTTTAATTAAATCGAAACA
66 -TTTTCACGCTTTTAATATCGTTTTTCTATATTTTTCTAAATTAATTTCTAATTAAATCGAAACA
* * *
32158 ATATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATTAATA
130 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
** * * * *
32223 CGGATATCTCAAGGAGTCTTAGCAC--AAAAAATCATGCAAAACTGA-CCAGAGGCCCTGAAACG
195 TAGATATTTCAAGGAGTCTT-G-ACGTCAAAAATCATGCAAAACTAAGCC-G-GGCCCCG-AACG
* * * *
32285 CGTTTTTAGCCAAAAA-CAGTGATGCTTATTACATGATTTCGGCTAAAATTTTGTAAAAATTGA-
255 CGTTTTTAGCCAAAAACCTGTGATGATTA-TACACGATTTCGGCTAAAATTTTGTCAAAATTGAC
*
32348 GCGAAAAGATAT-
319 CCG-AAAGATATA
* * * * * * *
32360 TTCTCCAATTTTTGGCTAGGAA-ACTCATAAAAAAT-TTTCAATTCAATG-TAAAAAATATTGAA
1 TCCT-TAATTTTTGGATA-AAATACTCATAAAAAATATAT-AATTCAACGCCAAAAAA-ATTGAA
* * * * * * * * * *
32422 GG-GTTTTTAAGCTGTTAATATCATTTTTCCTA-CTTTTTCCAATTTAATTTC-CATCT-AATTG
62 GGACTTTTCACGCTTTTAATATCGTTTTT-CTATATTTTTCTAAATTAATTTCTAAT-TAAATCG
* * * *
32483 AAACAAGATTTAGATGCTGGTAAAAACAAATCCTTAAATCCAATGCGGCTGAGATTTGATTTGAT
125 AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGAT
* * * * * *
32548 GAATATAGATTTTTCAAGGAATCTTGGCG-CCAAAATCATGCAAAACTGA-CTCGGGGCCTCGGA
190 GAATATAGATATTTCAAGGAGTCTTGACGTCAAAAATCATGCAAAACTAAGC-C-GGGCC-CCGA
* **
32611 ACGC-TTTTTCA-CAAAAAAAAAAAATTGTGATG-TTA-A-ACGATTTCGGCTAATAA-TTTG-C
252 ACGCGTTTTT-AGC-----CAAAAACCTGTGATGATTATACACGATTTCGGCTAA-AATTTTGTC
* * *
32669 AAAAATTGACCCGAAATATTTT
310 -AAAATTGACCCGAAAGATATA
* * ** * * * * * **
32691 TCGTT--TTTTTAGCCACAATACTCAT-AAAAATATATACTTCAATGCCAAAAAGATTAAAGGGG
1 TCCTTAATTTTTGGATAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGAC
* * * *
32753 TTTTCACG-TTTCTAATATCGTATTTGTGAT-TTTTTTTCGAATTAATTTCTAATTAAAAT-GAA
66 TTTTCACGCTTT-TAATATCGTTTTTCT-ATATTTTTCT-AAATTAATTTCTAATT-AAATCGAA
* *
32815 ACATGATTCAGATGCTTGT-------AA-----AAAT--AA--TGGCT-AGGATTTGATTAGATG
127 ACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGA-GATTTGATTAGATG
* * *
32863 AACATAGATATTTCAAGGAGTC-TGATGTCAAAAATCATTCAAAACTGAA-CCGGGCCCCGAGAC
191 AATATAGATATTTCAAGGAGTCTTGACGTCAAAAATCATGCAAAACT-AAGCCGGGCCCCGA-AC
* *
32926 GCGTTTTTAGCCAAAAATC-GTGATGATTATTACACGATTTCGGCTAAAATTTTG-CAAAAAACT
254 GCGTTTTTAGCCAAAAACCTGTGATGATTA-TACACGATTTCGGCTAAAATTTTGTC--AAAATT
32989 GACCCGAAAGATA-A
316 GACCCGAAAGATATA
* **** ** *
33003 TTCCTTAATTTTTAGCCGTAATACTCATAAAAAATATATAATTCAAC-ATAAAAAAATTGAAGGG
1 -TCCTTAATTTTTGGATAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGA
* * * * *
33067 CTTTTCACGGC-TTTCATATCGTTTTT-AATATTTTTCTCAATTAATTTCTAATTAAATAGAAAT
65 CTTTTCAC-GCTTTTAATATCGTTTTTCTATATTTTTCTAAATTAATTTCTAATTAAATCGAAAC
* * * * **
33130 AA-ATTTCAGATACTTGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTTTTAGATGAA
129 AAGA-TTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAA
* * * * ** * **
33194 TATATATATTTCAAGGAGTGTCGGCACCAAAAAT-ATGCAAAACTGAGCCGGCGTACCGAAACGC
193 TATAGATATTTCAAGGAGTCTTGACGTCAAAAATCATGCAAAACTAAGCCGG-GCCCCG-AACGC
* * * * ** * * *
33258 GTTTTTAGCCAAAAATCT-T-AGTGGTTAGTTCATGATTTTTGCTAAAATTTTGTAAAAAAATAA
256 GTTTTTAGCCAAAAACCTGTGA-TGATTA-TACACGATTTCGGCTAAAATTTTGT-CAAAATTGA
* *
33321 CCCGAAAAATTTA
318 CCCGAAAGATATA
* ** ** * *
33334 TCCTTAATTTTTGGATAAAATACTAATAAAATCTATATTTTTTAACGCCAAAAAAATTGGAGGAC
1 TCCTTAATTTTTGGATAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGAC
* * * *
33399 CTTTCACGCTTTTCATATCATTTTTC-ATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAA
66 TTTTCACGCTTTTAATATCGTTTTTCTATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAA
* *
33463 GATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTAGCTGAGATTTGATTAGATGAATAT
131 GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT
* *
33528 GGATATCTT-AAGGAGTCTTGACG-CAAAAAATCATGCAAAACAAAGCCGGGGCCCCAGAACGC-
196 AGATAT-TTCAAGGAGTCTTGACGTC-AAAAATCATGCAAAACTAAGCC-GGGCCCC-GAACGCG
* * *
33590 TTTTTAGTCAAAAA-CTGTGATAATTATCACACGATTTCGGCTAAAATTTTGTCAAAATTGATCC
257 TTTTTAGCCAAAAACCTGTGATGATTAT-ACACGATTTCGGCTAAAATTTTGTCAAAATTGACCC
*
33654 GGAAGATATA
321 GAAAGATATA
* * **
33664 TCCTCAACTTTTGTTTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGAC
1 TCCTTAATTTTTGGATAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGAC
* *
33729 TTTTGACG-TTTCTAATATCGTTTTTCCTATTTTTTTCTAAATTAATTTCTAATTAAATCGAAAC
66 TTTTCACGCTTT-TAATATCGTTTTT-CTATATTTTTCTAAATTAATTTCTAATTAAATCGAAAC
33793 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
129 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * * * * **
33858 ATAGATATTTTAAGTAGTCTCGGA-GTCAAAAATCATGCAAAATTGAGCCGGGTCCAGGAACGCG
194 ATAGATATTTCAAGGAGTCT-TGACGTCAAAAATCATGCAAAACTAAGCCGGG-CCCCGAACGCG
* * * * * *
33922 TTTTTAGGCAAAAAACC-GTGATGGTTTGTTAATAAATGATTTCAGCTAAAATTTTGCCAAAATT
257 TTTTTA-GCCAAAAACCTGTGAT-G---ATT-ATACACGATTTCGGCTAAAATTTTGTCAAAATT
* * * * *
33986 TACGCGAAATATTTC
316 GACCCGAAAGATATA
* * * * * * * *
34001 TCTTTGATTTTTGGCTAAAATAGTCAT-AAAAATATATAATTCAACACCAAAAAGATTGGAGGGC
1 TCCTTAATTTTTGGATAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGAC
* * * *
34065 TTTTTACGCTTTTAATACCGTATCTCT-TATTTTTTCTAAATTAATTTCTAATTAAATCGAAACA
66 TTTTCACGCTTTTAATATCGTTTTTCTATA-TTTTTCTAAATTAATTTCTAATTAAATCGAAACA
* ** ** * *
34129 AGATTCAGATGCTCGTAAAAATAAATTTTTAAATTTAATGTTGCTGAGATTTGGTTAG
130 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAG
34187 GCGATGTAAA
Statistics
Matches: 1466, Mismatches: 253, Indels: 212
0.76 0.13 0.11
Matches are distributed among these distances:
308 6 0.00
309 8 0.01
311 3 0.00
312 27 0.02
313 69 0.05
314 65 0.04
315 51 0.03
316 21 0.01
318 4 0.00
320 2 0.00
323 2 0.00
325 4 0.00
327 28 0.02
328 53 0.04
329 93 0.06
330 361 0.25
331 230 0.16
332 205 0.14
333 27 0.02
334 8 0.01
335 87 0.06
336 50 0.03
337 60 0.04
338 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (330 bp):
TCCTTAATTTTTGGATAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGAC
TTTTCACGCTTTTAATATCGTTTTTCTATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAA
GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT
AGATATTTCAAGGAGTCTTGACGTCAAAAATCATGCAAAACTAAGCCGGGCCCCGAACGCGTTTT
TAGCCAAAAACCTGTGATGATTATACACGATTTCGGCTAAAATTTTGTCAAAATTGACCCGAAAG
ATATA
Found at i:34756 original size:5 final size:5
Alignment explanation
Indices: 34746--34771 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
34736 TATATAATAG
34746 TAAGA TAAGA TAAGA TAAGA TAAGA T
1 TAAGA TAAGA TAAGA TAAGA TAAGA T
34772 GTGCTAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (5 bp):
TAAGA
Found at i:65009 original size:24 final size:24
Alignment explanation
Indices: 64971--65042 Score: 126
Period size: 24 Copynumber: 3.0 Consensus size: 24
64961 GTTTCCTTCT
* *
64971 CAGTAGTTGCTTATGAAACAATCC
1 CAGTAGGTGCCTATGAAACAATCC
64995 CAGTAGGTGCCTATGAAACAATCC
1 CAGTAGGTGCCTATGAAACAATCC
65019 CAGTAGGTGCCTATGAAACAATCC
1 CAGTAGGTGCCTATGAAACAATCC
65043 AGGGATAGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (24 bp):
CAGTAGGTGCCTATGAAACAATCC
Found at i:73782 original size:15 final size:15
Alignment explanation
Indices: 73758--73787 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
73748 CTTAGAAACT
*
73758 TTGTAGAAAAAAAAA
1 TTGTAAAAAAAAAAA
73773 TTGTAAAAAAAAAAA
1 TTGTAAAAAAAAAAA
73788 ACTAAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (15 bp):
TTGTAAAAAAAAAAA
Found at i:73783 original size:14 final size:15
Alignment explanation
Indices: 73758--73786 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
73748 CTTAGAAACT
73758 TTGTAGAAAAAAAAA
1 TTGTAGAAAAAAAAA
73773 TTGTA-AAAAAAAAA
1 TTGTAGAAAAAAAAA
73787 AACTAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (15 bp):
TTGTAGAAAAAAAAA
Found at i:74073 original size:22 final size:22
Alignment explanation
Indices: 74048--74097 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
74038 ATAAAAAAAA
74048 TTTCATAATGAGATTATCAAAC
1 TTTCATAATGAGATTATCAAAC
** * *
74070 TTTCATGGTTAGATTATCAAAT
1 TTTCATAATGAGATTATCAAAC
74092 TTTCAT
1 TTTCAT
74098 GAGGAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (22 bp):
TTTCATAATGAGATTATCAAAC
Found at i:74709 original size:164 final size:164
Alignment explanation
Indices: 74420--74744 Score: 429
Period size: 164 Copynumber: 2.0 Consensus size: 164
74410 GAGTCAAGAT
* * * * * *
74420 TCCTTGAGATATCCATATTCATCTAATCAAATCTTAGCCACATTGCATTTAAGGATTTGTTTATA
1 TCCTTGAAATATCCATATCCATCTAACCAAACCTTAGCCACAATGAATTTAAGGATTTGTTTATA
** *
74485 CGAGTATCTGAATTTTATTTGATTTAATTAGAAATTAATTAAAAAAAATATATGAAAAACGATAT
66 CGAACATCTGAATCTTATTTGATTTAATTAGAAATTAATTAAAAAAAATATA-GAAAAACGATAT
* * *
74550 GAAAAGTG-GGAAAGTCCTCCAATCTTTTTGAGAC
130 GAAAAGCGTGAAAAATCCTCCAATCTTTTTGAGAC
* * *
74584 TCCTTGAAATATCTATATCCATCTAACCAAACCTTAGCGACAATGAATTTAAGGATTTGTTTTTA
1 TCCTTGAAATATCCATATCCATCTAACCAAACCTTAGCCACAATGAATTTAAGGATTTGTTTATA
* * * *
74649 CGAACATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAGAATAT-GAAAAAACGATA
66 CGAACATCTGAATCTTATTT-GATTTAATTAGAAATTAATTAAAAAAAATATAG-AAAAACGATA
*
74713 TTAAAAGCGTGAAAAATCCTCCAATCTTTTTG
129 TGAAAAGCGTGAAAAATCCTCCAATCTTTTTG
74745 GAGTTGAATG
Statistics
Matches: 138, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
163 1 0.01
164 89 0.64
165 48 0.35
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (164 bp):
TCCTTGAAATATCCATATCCATCTAACCAAACCTTAGCCACAATGAATTTAAGGATTTGTTTATA
CGAACATCTGAATCTTATTTGATTTAATTAGAAATTAATTAAAAAAAATATAGAAAAACGATATG
AAAAGCGTGAAAAATCCTCCAATCTTTTTGAGAC
Found at i:75277 original size:331 final size:329
Alignment explanation
Indices: 74580--76505 Score: 1797
Period size: 331 Copynumber: 5.8 Consensus size: 329
74570 AATCTTTTTG
* * * * * * *
74580 AGACTCCTTGAAATATCTATATCCATCTAACCAAACCTTAGCGACAATGAATTTAAGGATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
* * * *
74645 TTTACGAACATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAGAATATGAAAAAAC
66 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATA-GGAAAAAC
* * * *
74709 GATATTAAAAGCGTGAAAAATCCTCCAATCTTTTTGGA-GTTGAATGATATATATTTTATGAGTT
130 GATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTT-GACGTTGAATTATATATATTTTATGAGTA
** * * * *
74773 TTTTAGAAAAAAAATTGAGGAAAAATACTTCT-GGTCAATTTTTGCAAAATATTAGCTGAAATCG
194 TTTT-G-GCAAAAATTGAGG-AAAA-ACTTTTGGGTCAATTTTTGTAAAATTTTAGCCGAAATCG
* * * * * *
74837 TGTACGTTAGTCGAAATCACGATTTTTGGCTAAAAACGCGTTCCAGGGCCCCGGTTCAGTGTTGC
255 TGTAC--TA-AC--CATCACGGTTTTAGGCTAAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGC
74902 ATGATTTTTGGCAG--A
314 ATGATTTTTGGC-GCCA
* * *
74917 GAGACTCCTTGAAATATCTATATTCATCTAACCAAATTTCAGCCACATTGGATTTAAGGATATG-
1 -AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGT
*** * * *
74981 TAAAACAAGCATCTGAATCATGTTTCGATTTAATTGGAAATTAATTCGGAAAATAATAGGAAAAA
65 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAA-AATAGGAAAAA
* * * * *
75046 CGATATTAGAAGCATGAAAAGCCCTTCAATATTTTTGACGTTAAATTATATA-ATTTTTATGAGT
129 CGATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGACGTTGAATTATATATA-TTTTATGAGT
* ** * *
75110 ATTATGGTTAAAATTGAGGATATAACTTTTAGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTG
193 ATTTTGGCAAAAATTGAGGA-AAAACTTTTGGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTG
* * * * *
75175 TAATAATCATCACGGTTTTAGGCTAAAAACGCATTCCGGGACCCCGGCTAAGTTTTGCTTGATTT
257 TACTAACCATCACGGTTTTAGGCTAAAAACGCGTTCCGGG-CCCCGGCTCAGTTTTGCATGATTT
75240 TTGGCGCCA
321 TTGGCGCCA
* * * * * *
75249 AGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCATCTACATTGGATCTAAGAATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
* * * *
75314 TTTTCGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTC-TAGAAAAATATGAAAAAC
66 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGA-AAAAATAGGAAAAAC
* * * * * * *
75378 GATATTAAAAGCGTGAAAAATCCTCCAATCTTTTTGGCGTTAAATTGTATATATTTTGTGAGAAT
130 GATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTAT
* * * * *
75443 TTTAGCCAAAAATTGAGGAAAAAATTTTCGGTTCATTTTTTTTATTGAAAAATTTTAGCCGAAAT
195 TTT-GGCAAAAATTGAGGAAAAACTTTT-GGGTCA----ATTT-TTGTAAAATTTTAGCCGAAAT
* * * * * * * * * *
75508 CGTATACTAACTATCATGGGTTTT-CGCTAAAAATGCATTTCGGGGCTCCGACTTAGTTTTGCAT
253 CGTGTACTAACCATCA-CGGTTTTAGGCTAAAAACGC-GTTCCGGGCCCCGGCTCAGTTTTGCAT
*
75572 GATTTTTGGCGCCG
316 GATTTTTGGCGCCA
* * *
75586 AGACTCCTTAAAATATCTATATTCATCTAATCAAATCTCAGTCACATTGAATTTAAGGATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
* * ** * * *
75651 TTTGCGAGCATCTGAATCTTATTTTAATTTAATTAGAAATTAATTCAG-AAAAATATG-AAAACA
66 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACG
* * * *
75714 ATATTAAAAGCATGAGAAGTCCTTCAATTTTTTTGACGTTGAATTACATATATTTTATGAGTATT
131 ATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATT
**
75779 GCGGCTAAAAATTGAGGAAAAA-TATTTCGGGTCAATTTTTGTAAAATTTTAGCCGAAATC--GT
196 TTGGC-AAAAATTGAGGAAAAACT-TTT-GGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGT
* * * ** * * * *
75841 ACGTGTACCATCACGATTTTTAAGCTGGAAACGCGTTTCGGGGCCCTGGATCACTTTTGCATG--
258 AC-T-AACCATCACG-GTTTTAGGCTAAAAACGCG-TTCCGGGCCCCGGCTCAGTTTTGCATGAT
75904 ---T---GCCA
319 TTTTGGCGCCA
* *
75909 AGACTCCTTAAGATATATCTATATTCATCTAATCAAATCTCAGCCACA-TGGTATCTAAGGATTT
1 AGACTCCTT--GAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGG-ATTTAAGGATTT
* * ** * *
75973 GTTTTTACGAGTATCTAAATCTTGTTTTAATTTAATCAGAAATTAATTTGGAAATATAATAGGAA
63 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAA-A-AATAGGAA
* * * * * * * *
76038 AAATGATATCAGAAGCGTGAAAAAGGCTTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATG
126 AAACGATATTAAAAGCGTG-AAAAGTCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATG
* * ** * *
76103 AGTAGTTTT-GCTAGAAATTGAGGAAAAATCTTTCGGGT-TGTTTTTTTCAAAAATTTAGCCGAA
190 AGTA-TTTTGGC-AAAAATTGAGGAAAAA-CTTTTGGGTCAATTTTTGT-AAAATTTTAGCCGAA
* * *
76166 ATCGTGTACTAACCATCACAGTTTTTA-GCTAAAAACGCGTTCCAGGG-CCCGACTTAGTTTTGC
251 ATCGTGTACTAACCATCAC-GGTTTTAGGCTAAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGC
* *
76229 ATGATTTTTGGTGTCA
314 ATGATTTTTGGCGCCA
*
76245 AGACTCCTTAAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGA-TTAAGGATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
* * *
76309 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATTAATTCGG-AAAAATATGAAAAA-A
66 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACG
* ** * * * * *
76372 ATATTAGAAGTTTTAAAAGCCCTTCAATCTTTTTGACGTCGGATTATATATTTTTTTATGAGTAT
131 ATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGACGTTGAATTATATA-TATTTTATGAGTAT
* * * * * * * *
76437 TTTAGCCAAAATTGAGCAAATATTTTTCGGGTCAATTTTTGCAAAAGTTTAACCGAAATCGTGTA
195 TTTGGCAAAAATTGAGGAAAAACTTTT-GGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTA
76502 CTAA
259 CTAA
76506 GCGAACAGGA
Statistics
Matches: 1306, Mismatches: 224, Indels: 126
0.79 0.14 0.08
Matches are distributed among these distances:
323 12 0.01
324 2 0.00
325 89 0.07
326 3 0.00
327 4 0.00
328 100 0.08
329 66 0.05
330 141 0.11
331 218 0.17
332 67 0.05
333 54 0.04
334 41 0.03
335 93 0.07
336 69 0.05
337 214 0.16
338 129 0.10
339 4 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (329 bp):
AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACG
ATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATT
TTGGCAAAAATTGAGGAAAAACTTTTGGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTACT
AACCATCACGGTTTTAGGCTAAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGC
GCCA
Found at i:75592 original size:337 final size:329
Alignment explanation
Indices: 74580--76505 Score: 1865
Period size: 337 Copynumber: 5.8 Consensus size: 329
74570 AATCTTTTTG
* * * * * * *
74580 AGACTCCTTGAAATATCTATATCCATCTAACCAAACCTTAGCGACAATGAATTTAAGGATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
* *
74645 TTTACGAACATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAGAATATGAAAAAACG
66 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATG-AAAAACG
* * *
74710 ATATTAAAAGCGTGAAAAATCCTCCAATCTTTTTGGA-GTTGAATGATATATATTTTATGAGTTT
130 ATATTAAAAGCGTGAAAAATCCTTCAATCTTTTT-GACGTTGAATTATATATATTTTATGAGTAT
** * * * *
74774 TTTAGAAAAAAAATTGAGGAAAAATACTTCTGGTCAATTTTTGCAAAATATTAGCTGAAATCGTG
194 TTTAG-CTAAAAATTGAGGAAAAATATTTC-GGTCAATTTTTGAAAAATTTTAGCCGAAATCGTG
* * * * * * *
74839 TACGTTAGTCGAAATCACGATTTTTGGCTAAAAACGCGTTCCAGGGCCCCG-GTTCAGTGTTGCA
257 TAC--TA-AC--CATCACGGTTTTTAGCTAAAAACGCGTTCC-GGGGCCCGACTT-AGTTTTGCA
74903 TGATTTTTGGCAG--A
315 TGATTTTTGGC-GCCA
* * *
74917 GAGACTCCTTGAAATATCTATATTCATCTAACCAAATTTCAGCCACATTGGATTTAAGGATATG-
1 -AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGT
*** * * * * *
74981 TAAAACAAGCATCTGAATCATGTTTCGATTTAATTGGAAATTAATTCGGAAAATAATAGGAAAAA
65 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAA-AATATGAAAAA
* * ** * *
75046 CGATATTAGAAGCATGAAAAGCCCTTCAATATTTTTGACGTTAAATTATATA-ATTTTTATGAGT
128 CGATATTAAAAGCGTGAAAAATCCTTCAATCTTTTTGACGTTGAATTATATATA-TTTTATGAGT
* * * * * *
75110 ATTAT-GGTTAAAATTGAGGATATAACT-TTTAGGTCAATTTTTGTAAAATTTTAGCCGAAATCG
192 ATTTTAGCTAAAAATTGAGGA-A-AAATATTTCGGTCAATTTTTGAAAAATTTTAGCCGAAATCG
* * * * * * *
75173 TGTAATAATCATCACGG-TTTTAGGCTAAAAACGCATTCCGGGACCCCGGCTAAGTTTTGCTTGA
255 TGTACTAACCATCACGGTTTTTA-GCTAAAAACGCGTTCCGGG-GCCCGACTTAGTTTTGCATGA
75237 TTTTTGGCGCCA
318 TTTTTGGCGCCA
* * * * * *
75249 AGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCATCTACATTGGATCTAAGAATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
* *
75314 TTTTCGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCTAGAAAAATATGAAAAACG
66 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-AGAAAAATATGAAAAACG
* * * * * *
75379 ATATTAAAAGCGTGAAAAATCCTCCAATCTTTTTGGCGTTAAATTGTATATATTTTGTGAGAATT
130 ATATTAAAAGCGTGAAAAATCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATT
* *
75444 TTAGCCAAAAATTGAGGAAAAA-ATTTTCGGTTCATTTTTTTTATTGAAAAATTTTAGCCGAAAT
195 TTAGCTAAAAATTGAGGAAAAATA-TTTCGG-TCA----ATTT-TTGAAAAATTTTAGCCGAAAT
* * * * * * * *
75508 CGTATACTAACTATCATGGGTTTTCGCTAAAAATGCATTTCGGGGCTCCGACTTAGTTTTGCATG
253 CGTGTACTAACCATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGC-CCGACTTAGTTTTGCATG
*
75573 ATTTTTGGCGCCG
317 ATTTTTGGCGCCA
* * *
75586 AGACTCCTTAAAATATCTATATTCATCTAATCAAATCTCAGTCACATTGAATTTAAGGATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
* * ** *
75651 TTTGCGAGCATCTGAATCTTATTTTAATTTAATTAGAAATTAATTCAGAAAAATATG-AAAACAA
66 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGA
* * * * * *
75715 TATTAAAAGCATGAGAAGTCCTTCAATTTTTTTGACGTTGAATTACATATATTTTATGAGTATTG
131 TATTAAAAGCGTGAAAAATCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTT
** *
75780 CGGCTAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGTAAAATTTTAGCCGAAATC--GTAC
196 TAGCTAAAAATTGAGGAAAAATATTTC-GGTCAATTTTTGAAAAATTTTAGCCGAAATCGTGTAC
* * ** * * *
75843 GTGTACCATCACGATTTTTAAGCTGGAAACGCGTTTCGGGGCCCTGGA-TCACTTTTGCATG---
260 -T-AACCATCACGGTTTTT-AGCTAAAAACGCGTTCCGGGGCCC--GACTTAGTTTTGCATGATT
75904 --T---GCCA
320 TTTGGCGCCA
* *
75909 AGACTCCTTAAGATATATCTATATTCATCTAATCAAATCTCAGCCACA-TGGTATCTAAGGATTT
1 AGACTCCTT--GAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGG-ATTTAAGGATTT
* * ** * ** *
75973 GTTTTTACGAGTATCTAAATCTTGTTTTAATTTAATCAGAAATTAATTTGGAAATATAATAGGAA
63 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AA-A-AATATGAA
* * * * * * * *
76038 AAATGATATCAGAAGCGTGAAAAAGGCTTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATG
125 AAACGATATTAAAAGCGTGAAAAA-TCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATG
* * *** *
76103 AGTAGTTTT-GCTAGAAATTGAGGAAAAATCTTTCGGGTTGTTTTTTTCAAAAA-TTTAGCCGAA
189 AGTA-TTTTAGCTAAAAATTGAGGAAAAATATTTC-GG-TCAATTTTTGAAAAATTTTAGCCGAA
* *
76166 ATCGTGTACTAACCATCACAGTTTTTAGCTAAAAACGCGTTCCAGGGCCCGACTTAGTTTTGCAT
251 ATCGTGTACTAACCATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGCCCGACTTAGTTTTGCAT
* *
76231 GATTTTTGGTGTCA
316 GATTTTTGGCGCCA
*
76245 AGACTCCTTAAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGA-TTAAGGATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
* * *
76309 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATTAATTCGGAAAAATATGAAAAA-AA
66 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGA
* ** * ** * * *
76373 TATTAGAAGTTTTAAAAGCCCTTCAATCTTTTTGACGTCGGATTATATATTTTTTTATGAGTATT
131 TATTAAAAGCGTGAAAAATCCTTCAATCTTTTTGACGTTGAATTATATA-TATTTTATGAGTATT
* * * * * * *
76438 TTAGC-CAAAATTGAGCAAATATTTTTCGGGTCAATTTTTGCAAAAGTTTAACCGAAATCGTGTA
195 TTAGCTAAAAATTGAGGAAAAATATTTC-GGTCAATTTTTGAAAAATTTTAGCCGAAATCGTGTA
76502 CTAA
259 CTAA
76506 GCGAACAGGA
Statistics
Matches: 1311, Mismatches: 220, Indels: 124
0.79 0.13 0.07
Matches are distributed among these distances:
323 12 0.01
324 2 0.00
325 89 0.07
326 3 0.00
327 13 0.01
328 89 0.07
329 68 0.05
330 145 0.11
331 215 0.16
332 68 0.05
333 55 0.04
334 38 0.03
335 87 0.07
336 74 0.06
337 225 0.17
338 123 0.09
339 5 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (329 bp):
AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGA
TATTAAAAGCGTGAAAAATCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTT
TAGCTAAAAATTGAGGAAAAATATTTCGGTCAATTTTTGAAAAATTTTAGCCGAAATCGTGTACT
AACCATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGCCCGACTTAGTTTTGCATGATTTTTGGC
GCCA
Found at i:89850 original size:21 final size:22
Alignment explanation
Indices: 89805--89851 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 22
89795 CCACGTATAT
89805 TGTCAAAGCATACTTCAGTACATC
1 TGTCAAAGCATACTTCA--ACATC
89829 TGTCAAAGCATACTTC-ACATC
1 TGTCAAAGCATACTTCAACATC
89850 TG
1 TG
89852 CCAATCTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.30
24 16 0.70
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.30
Consensus pattern (22 bp):
TGTCAAAGCATACTTCAACATC
Found at i:92493 original size:30 final size:31
Alignment explanation
Indices: 92457--92515 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
92447 ATTAATAAGC
*
92457 CATTAAAATTTGAGGGTATAAGA-GAAAAGT
1 CATTAAAATTTGAGGATATAAGAGGAAAAGT
92487 CATTAAAATTTGAGGATATAAGAGGAAAA
1 CATTAAAATTTGAGGATATAAGAGGAAAA
92516 TCAAGATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.49, C:0.03, G:0.22, T:0.25
Consensus pattern (31 bp):
CATTAAAATTTGAGGATATAAGAGGAAAAGT
Found at i:94250 original size:15 final size:16
Alignment explanation
Indices: 94227--94274 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
94217 CATCTTCTTA
*
94227 TTATAATTATTA-AAC
1 TTATTATTATTATAAC
94242 TTATTATTATTATAAC
1 TTATTATTATTATAAC
94258 AATTATTATTAGTTATA
1 --TTATTATTA-TTATA
94275 TGATCACTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
18 9 0.32
19 5 0.18
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (16 bp):
TTATTATTATTATAAC
Found at i:94263 original size:18 final size:17
Alignment explanation
Indices: 94224--94274 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
94214 AAACATCTTC
* *
94224 TTATTATAATTATTAAAC
1 TTATTATTATTA-TAAAA
94242 TTATTATTATTATAACAA
1 TTATTATTATTATAA-AA
94260 TTATTATTAGTTATA
1 TTATTATTA-TTATA
94275 TGATCACTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.10
18 21 0.72
19 5 0.17
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
TTATTATTATTATAAAA
Found at i:95678 original size:22 final size:22
Alignment explanation
Indices: 95653--95694 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
95643 AAAATAATAA
* *
95653 TATAGTTTTTAAAATAATCACT
1 TATACTTTTTAAAACAATCACT
*
95675 TATACTTTTTAGAACAATCA
1 TATACTTTTTAAAACAATCA
95695 TTGAAGCTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (22 bp):
TATACTTTTTAAAACAATCACT
Found at i:96168 original size:22 final size:22
Alignment explanation
Indices: 96137--96218 Score: 155
Period size: 22 Copynumber: 3.7 Consensus size: 22
96127 AAAATGGCAT
*
96137 GGCACGGCACGACCCACGTGCC
1 GGCACAGCACGACCCACGTGCC
96159 GGCACAGCACGACCCACGTGCC
1 GGCACAGCACGACCCACGTGCC
96181 GGCACAGCACGACCCACGTGCC
1 GGCACAGCACGACCCACGTGCC
96203 GGCACAGCACGACCCA
1 GGCACAGCACGACCCA
96219 TTTTTAATGT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 59 1.00
ACGTcount: A:0.23, C:0.45, G:0.28, T:0.04
Consensus pattern (22 bp):
GGCACAGCACGACCCACGTGCC
Done.