Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014522.1 Corchorus olitorius cultivar O-4 contig14555, 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: 74166
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--171 Score: 315
Period size: 3 Copynumber: 57.0 Consensus size: 3
* * *
1 TAA TAA TAA TAA TAA TAA TAA TAT TAT TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
49 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
97 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
145 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
172 CAACAACAAC
Statistics
Matches: 166, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
3 166 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1852 original size:24 final size:20
Alignment explanation
Indices: 1807--1852 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 20
1797 GACGTAATTA
1807 TTCTTTTTCTTCTTTTTAAT
1 TTCTTTTTCTTCTTTTTAAT
1827 TTCTTTGTTCTTACTATTTTATAT
1 TTCTTT-TTCTT-CT-TTTTA-AT
1851 TT
1 TT
1853 TAGTTATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.27
21 5 0.23
22 2 0.09
23 5 0.23
24 4 0.18
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.72
Consensus pattern (20 bp):
TTCTTTTTCTTCTTTTTAAT
Found at i:4237 original size:15 final size:14
Alignment explanation
Indices: 4219--4262 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
4209 AAGTTTCATG
4219 ATTATAAATAATAAT
1 ATTATAAATAA-AAT
*
4234 ATTATAATTAAATAT
1 ATTATAAATAAA-AT
4249 ATTATAATATAAAA
1 ATTATAA-ATAAAA
4263 ATAATTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.04
15 20 0.80
16 4 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTATAAATAAAAT
Found at i:4272 original size:35 final size:34
Alignment explanation
Indices: 4221--4286 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
4211 GTTTCATGAT
* *
4221 TATAAATAATAATATTATAATTAAATATATTATAA
1 TATAAATAATAATATTAGAAGTAAAT-TATTATAA
4256 TATAAA-AATAATTATTAGAAGTAAATTATTA
1 TATAAATAATAA-TATTAGAAGTAAATTATTA
4287 GTTACAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 10 0.36
35 18 0.64
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (34 bp):
TATAAATAATAATATTAGAAGTAAATTATTATAA
Found at i:6197 original size:332 final size:329
Alignment explanation
Indices: 4434--7084 Score: 1859
Period size: 332 Copynumber: 8.0 Consensus size: 329
4424 ACCAAGATGG
* * * * * * * * *
4434 TACACAATTTCGGTTAAAATTTTACAAAAATTGACCCGAAATAT-TTTTCTAAATTTTTAGCCAC
1 TACACGATTTCGGCTAAAATTTTGCAAAAAATGA-CCGAAAGATATTTCCTCAATTTTTAG-TAA
* * *
4498 CATACTCATAAAAAATATATAATTCAACGCCAAAAAGATT----GA----T-ACGGTTCTAATAT
64 AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATAT
* * * * *
4554 CGTTTTTCCTATTTGTTTTCAAATTAATTTCTAATTAAATTGAAACATGATTCAAATGCTCGTAA
129 CGTTTTTCATATTT-TTCT-GAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAA
* * * * * * **
4619 AAACAAATCTTTAAATCCAATGTGGCTAAGATATGGTTAGATGAATATAGATATTTCAA-TAAAC
192 AAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC
* * *
4683 GTT-GC-CACTAAAAATCATGCAAAACTGACCCGGGGCCCCAGAACGCGTTTTTAGCCAAAAAAA
257 -TTAGCGC-C-AAAAATCATGCAAAACTAACCCAGGGCCCCGGAACGCGTTTTTAGCC----AAA
* *
4746 AACCGTGATG----G
315 AACTGTGATGATTAT
* * * * * * * *
4757 TACACGATTTCGACTAAAATTTTCCAAAAATTGACCTGAAATATTTTTCCTCCATTTTTAGCCAC
1 TACACGATTTCGGCTAAAATTTTGCAAAAAATGACC-GAAAGATATTTCCTCAATTTTTAG-TAA
* * * ** * **
4822 AATACTCATAGAATATATATAATTAAAATCCAAAAAGATTGGAA-AACACTTCACGCTTTTAATA
64 AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATT-GAAGGACTTTTCACGCTTTTAATA
* * *
4886 TTGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCGGATGCTCGTAAA
128 TCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAAA
* * *
4951 AACAAATCCTTAAATTG-AATGTGGCTAATATTTGATTAGATAAATATAGATATTTCAAGGAGTC
193 AACAAATCCTTAAA-TGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC
* * * * * *
5015 TTGGCGCCAAAAATCATGCAAAACTAAGCC-GGAGTCCCGAAACGTGTTTTTAGCCAAAAACCGT
257 TTAGCGCCAAAAATCATGCAAAACTAACCCAGG-GCCCCGGAACGCGTTTTTAGCCAAAAACTGT
5079 GATGATTAT
321 GATGATTAT
* * * * ***
5088 TACACGATTTCGACTAAAATTTTGCAAAAATTGACTCGAAAGTTATTTCCTCAAGTTTTAGCCGC
1 TACACGATTTCGGCTAAAATTTTGCAAAAAATGAC-CGAAAGATATTTCCTCAATTTTTAG-TAA
** * ** * *
5153 AATACTCAGT--AAAATCATATAATTCAACATCAAAAAGATTGAAGGGCTTTTCATACTTCTAGT
64 AATACTCA-TAAAAAAT-ATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAAT
* * *
5216 ATCGTTTTTCCTATAATTTTC-AAGATTAATTTCTAATTAAATTGAAATTTTCAATATCATAATT
127 ATCGTTTTT-C-ATATTTTTCTGA-ATTAATTTCTAATTAAATTGAAA----C---A--A-GATT
* *** * * * * * * * *
5280 CAGATGCTTGT-TTTACAAATCCCTATATCCATTATGGATGAGATTTGGTTAGATTAATATAGAT
179 CAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGAT
** * *
5344 ATTTCAAGGAGTCTCGGCGCAAAAAATCATG-AAACACTGAA-CCAAGGCCCCGGAACGCGTTTT
244 ATTTCAAGGAGTCTTAGCGCCAAAAATCATGCAAA-ACT-AACCCAGGGCCCCGGAACGCGTTTT
** * *
5407 TAGGAAAAAAACTGTGATTTCGACTAACG
307 TA-GCCAAAAACTGTGA--T-GA-TTA-T
* ** * * * * *
5436 TACACGTTTTCACCTAATATTTGGC-AAAAATCAAAC-ATAA-ATAGTTTACCTCAATTTTT-TT
1 TACACGATTTCGGCTAAAATTTTGCAAAAAAT-GACCGA-AAGATA-TTT-CCTCAATTTTTAGT
* * *
5497 CGAAAATACCCATAAATATATATATATATATATATAATTCAACTCCAAAAATATT-ACAGGACTT
62 --AAAATA--C-T---CATA-A-A-A-A-ATATATAATTCAACGCCAAAAAGATTGA-AGGACTT
* * ** *
5561 TTCATGCTTTTAATACCGTTTTTCATATTTTTCTGAATTAAAATCTAATTAAATTGAAAAAAGAT
113 TTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATTGAAACAAGAT
* * *
5626 TCAGATGCTCGTAAAAACAAATCTTTAAATGTAATGTGGCTGAGATTTGATTAGATGAATATATA
178 TCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGA
* * * ** * * * **
5691 TATTTCAATGAGCCTCAATGCCAAAAATCATGCAAAACTGAGCC-GGGGCCCAAAACGCGTTTTT
243 TATTTCAAGGAGTCTTAGCGCCAAAAATCATGCAAAACTAACCCAGGGCCCCGGAACGCGTTTTT
* * * *
5755 AGCAAAAAAAAACCGTGATGGTTAG
308 AGC---CAAAAACTGTGATGATTAT
* * ** * *
5780 TGCACGATTTCGCCTAAAATTTTATAAAAAA-GACC-AAAAAAATTTTCCTCAATTTTTAGCTAA
1 TACACGATTTCGGCTAAAATTTTGCAAAAAATGACCGAAAGATA-TTTCCTCAATTTTTAG-TAA
* * * * * * *
5843 AATACTCATGAAATATATATAATTTAACGCCAAAAAGATTGGAGGACGTTTCACGATTTTCATAT
64 AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATAT
* * *
5908 CGTTTTTCATAATTTTTCTGAATTAATTTCTAATTTAATTGAAATAAGATTTAGATGCTCGTAAA
129 CGTTTTTCAT-ATTTTTCTGAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAAA
* * * *
5973 AACAAATCCTTAAATGCAATGTGTCTGAGATTTGATTAGATGAATATGGATATCTCAAGTAGTCT
193 AACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCT
** * *
6038 TAGCGCCAAAAATCATGCAAAACTAACCCAGGGCCATGGAACGCATTTTTAGCCAAAAACTATGA
258 TAGCGCCAAAAATCATGCAAAACTAACCCAGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGA
6103 TGATTAT
323 TGATTAT
* * *
6110 TACACGATTTCGGTTAAAATTTTGCAAAAAATGACCGGAAAGATATTTCCTCAATTTTTTGTTAA
1 TACACGATTTCGGCTAAAATTTTGCAAAAAATGACC-GAAAGATATTTCCTCAATTTTTAGTAAA
* * * * * *
6175 AT-CATCATAAAAAATAATATAATTCTATGCCAAAAATATTGAAGGATTTTTTACGCTTCTAATA
65 ATAC-TCATAAAAAAT-ATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATA
* * * * * * *
6239 TAGTTTTTCCTACTATTTCTGAATTAATTTATAATTAAATCGAAAGAAGATTTAGATGCTCGTAA
128 TCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAA
* * * * * **
6304 AAACAAATCCTTAAATCCAATGTGGATGAGATTTGATTAGTTTAAAATAGATGGTTCAAGGAGTC
192 AAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC
* * ** * * * *
6369 TT-GACGCCAAAAATCATGCAATACTGACCTGGGGCCCTGAAACGTGTTTTTAGCAAAAAAAAAA
257 TTAG-CGCCAAAAATCATGCAAAACTAACCCAGGGCCCCGGAACGCGTTTTTAGC----CAAAAA
6433 CTGTGATG----T
317 CTGTGATGATTAT
* * * ** * *
6442 TGCACGATTTCGGCTAATATTTTGCAAAAAATGACGTGAACTATTTTTCCTCAATTTTTAGTCAC
1 TACACGATTTCGGCTAAAATTTTGCAAAAAATGAC-CGAAAGATATTTCCTCAATTTTTAGT-AA
* * * * *
6507 AATACTCAT-AAAAATATATAATTCAAGGCCAAAAAGATTGAAGGGCTTTTCATGCTTCTAATAC
64 AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATAT
* * ** * *
6571 CGTTTTTCCTATTTTTCCGAATTAATTTCTAATTAAAAAGAAACATGATTCAAATGCT--T----
129 CGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAA
* * * * *
6630 A-TAA-----AAA--CAA--TGGCTGGGATTTGGTTAGATGAATATAGACATTTCCAGGAGTC-T
194 ACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTT
* * * * *
6684 CGACGGCAAAAATCATTCAAATCTGAA---ATGGGCCTCC-GAACGCGTTTTTAGCCAAAACCCG
259 AG-CGCCAAAAATCATGCAAAACT-AACCCA-GGGCC-CCGGAACGCGTTTTTAGCCAAAA-AC-
*
6745 TGTGATAATTAT
318 TGTGATGATTAT
6757 TACACGATTTCGGC-AAAATTTTGCAAAAAATTGACCCGAAAGATATTTCCTCAATTTTTA-TCC
1 TACACGATTTCGGCTAAAATTTTGCAAAAAA-TGA-CCGAAAGATATTTCCTCAATTTTTAGT--
** * * *
6820 TTAATATTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGCTTTTAAT
62 AAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAAT
* * * * * *
6885 ATCGTTTTTCATTTTTTTTCTAAATTAATTTCTAATTAAATCGAAACATGTTTCTGATGCTCGTT
127 ATCGTTTTTCA-TATTTTTCTGAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTCG-T
* * * *
6950 AAAAACAAGAAATAAAATCTTAAATGCAATGTGGCTAAGATTTTATTAGATGAATATAGTTATTT
190 AAAAAC---AAAT----CCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTT
* * * * * * * * *
7015 CAAGGAGTGTCAGTGCCAAAAATCATGTAAAACTGA-GCTGGTGCCCCGAAACGCGTTTTTAGCA
248 CAAGGAGTCTTAGCGCCAAAAATCATGCAAAACTAACCCAGG-GCCCCGGAACGCGTTTTTAGCC
7079 AAAAAC
312 AAAAAC
7085 CATATATATA
Statistics
Matches: 1840, Mismatches: 349, Indels: 260
0.75 0.14 0.11
Matches are distributed among these distances:
309 4 0.00
310 1 0.00
311 6 0.00
313 19 0.01
314 69 0.04
315 47 0.03
316 62 0.03
317 41 0.02
318 3 0.00
320 1 0.00
322 2 0.00
323 39 0.02
324 53 0.03
327 13 0.01
328 4 0.00
330 88 0.05
331 356 0.19
332 409 0.22
333 84 0.05
334 2 0.00
335 1 0.00
336 14 0.01
337 4 0.00
339 4 0.00
340 3 0.00
341 60 0.03
342 130 0.07
343 34 0.02
344 20 0.01
345 8 0.00
346 7 0.00
347 45 0.02
348 105 0.06
349 14 0.01
350 2 0.00
351 1 0.00
353 1 0.00
354 1 0.00
357 30 0.02
358 4 0.00
359 47 0.03
360 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (329 bp):
TACACGATTTCGGCTAAAATTTTGCAAAAAATGACCGAAAGATATTTCCTCAATTTTTAGTAAAA
TACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCG
TTTTTCATATTTTTCTGAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAAC
AAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAG
CGCCAAAAATCATGCAAAACTAACCCAGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGA
TTAT
Found at i:7282 original size:247 final size:252
Alignment explanation
Indices: 6836--7299 Score: 582
Period size: 247 Copynumber: 1.8 Consensus size: 252
6826 TTCATAAAAA
* * * *
6836 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATTTTT
1 ATATATAATTCAACGCCAAAAAGATTGAAGGACGTTTCACGCTTTTAATATCGTTTTTCATTCTT
* *
6901 TTTCTAAATTAATTTCTAATTAAATCGAAACATGTTTCTGATGCTCGTTAAAAACAAGAAATAAA
66 TTTCTAAATTAATTTCTAATTAAATCGAAACAAGTTTCAGATGC-CGTT---AACAAGAAATAAA
* * * * * * *
6966 ATCTTAAATGCAATGTGGCTAAGATTTTATTAGATGAATATAGTTATTTCAAGGAGTGTCAGTGC
127 ATCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATAAAGATATCTCAAGGAGTCTCAGCGC
*
7031 CAAAAATCATGTAAAACTGAGCTGGTGCCCCGAAACGCGTTTTTAGCAAAAAACCATATAT
192 CAAAAATCATGCAAAACTGAGCTGGTGCCCCGAAACGCGTTTTTAGCAAAAAACCATATAT
* * *
7092 ATATATAATTTAACTG-CAAAAAGATTGGAGGACGTTTCATGCTTTTAATATCGTTTTTCA-TCT
1 ATATATAATTCAAC-GCCAAAAAGATTGAAGGACGTTTCACGCTTTTAATATCGTTTTTCATTCT
** * *
7155 TTTTCTGTATTAATTTCTAATTAAATCGAAACAAGATTT-AGATG-C-TT-ATAA-AAATAAATT
65 TTTTCTAAATTAATTTCTAATTAAATCGAAACAAG-TTTCAGATGCCGTTAACAAGAAATAAAAT
* ** * **
7215 TTTAAATCCAATGTGGCTGTGATTTGATTAGATGAGTAAAGATATCTCAAGGAGTCTTGGCGCCA
129 CTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATAAAGATATCTCAAGGAGTCTCAGCGCCA
7280 AAAATCATGCAAAACTGAGC
194 AAAATCATGCAAAACTGAGC
7300 CGGGGGCACA
Statistics
Matches: 179, Mismatches: 27, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
247 79 0.44
248 3 0.02
252 2 0.01
253 1 0.01
255 38 0.21
256 55 0.31
257 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (252 bp):
ATATATAATTCAACGCCAAAAAGATTGAAGGACGTTTCACGCTTTTAATATCGTTTTTCATTCTT
TTTCTAAATTAATTTCTAATTAAATCGAAACAAGTTTCAGATGCCGTTAACAAGAAATAAAATCT
TAAATCCAATGTGGCTAAGATTTGATTAGATGAATAAAGATATCTCAAGGAGTCTCAGCGCCAAA
AATCATGCAAAACTGAGCTGGTGCCCCGAAACGCGTTTTTAGCAAAAAACCATATAT
Found at i:8293 original size:15 final size:15
Alignment explanation
Indices: 8265--8300 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
8255 GTTTCATGAC
* *
8265 TATAAATAATTATAT
1 TATAATTAAATATAT
8280 TATAATTAAATATAT
1 TATAATTAAATATAT
8295 TATAAT
1 TATAAT
8301 CTTAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAATTAAATATAT
Found at i:8585 original size:8 final size:8
Alignment explanation
Indices: 8559--8594 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
8549 TTTTATAATT
8559 TAGTAAGA
1 TAGTAAGA
8567 TAAGATAAGA
1 T-AG-TAAGA
8577 TAGTAAGA
1 TAGTAAGA
8585 TAGTAAGA
1 TAGTAAGA
8593 TA
1 TA
8595 TTAGTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 16 0.62
9 4 0.15
10 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (8 bp):
TAGTAAGA
Found at i:10337 original size:48 final size:49
Alignment explanation
Indices: 10266--10383 Score: 202
Period size: 49 Copynumber: 2.4 Consensus size: 49
10256 ACTGCCAGAT
*
10266 TTTGCAATTTTCAAGTCTAAACTTGGGTGGCTTT-CAAAATTTTGATTG
1 TTTGCCATTTTCAAGTCTAAACTTGGGTGGCTTTGCAAAATTTTGATTG
**
10314 TTTGCCATTTTCAAGTCTAAACTTGGGTGTTTTTGCAAAATTTTGATTG
1 TTTGCCATTTTCAAGTCTAAACTTGGGTGGCTTTGCAAAATTTTGATTG
10363 TTTGCCATTTTCAAGTCTAAA
1 TTTGCCATTTTCAAGTCTAAA
10384 AAACCATACT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
48 31 0.47
49 35 0.53
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.45
Consensus pattern (49 bp):
TTTGCCATTTTCAAGTCTAAACTTGGGTGGCTTTGCAAAATTTTGATTG
Found at i:18997 original size:12 final size:12
Alignment explanation
Indices: 18980--19018 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
18970 AAGATCTATT
18980 CATCATCTTCAC
1 CATCATCTTCAC
18992 CATCATCTTCAC
1 CATCATCTTCAC
19004 CATCA-CTTCAC
1 CATCATCTTCAC
19015 CATC
1 CATC
19019 CCAGCCTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.26, C:0.44, G:0.00, T:0.31
Consensus pattern (12 bp):
CATCATCTTCAC
Found at i:19066 original size:26 final size:24
Alignment explanation
Indices: 19029--19078 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
19019 CCAGCCTTGC
19029 ATTATTTCTTTTAATCCTTCACTT
1 ATTATTTCTTTTAATCCTTCACTT
*
19053 ATTAGTTTCATTTTCATCCTTCACTT
1 ATTA-TTTC-TTTTAATCCTTCACTT
19079 CATCATCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.17
25 4 0.17
26 15 0.65
ACGTcount: A:0.20, C:0.22, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTATTTCTTTTAATCCTTCACTT
Found at i:19094 original size:12 final size:12
Alignment explanation
Indices: 19079--19106 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
19069 TCCTTCACTT
19079 CATCATCTTCAC
1 CATCATCTTCAC
19091 CATCATCTTCAC
1 CATCATCTTCAC
19103 CATC
1 CATC
19107 CCAACCTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.43, G:0.00, T:0.32
Consensus pattern (12 bp):
CATCATCTTCAC
Found at i:22510 original size:9 final size:9
Alignment explanation
Indices: 22496--22522 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
22486 GTAGATCTTT
22496 GAAAGAAAA
1 GAAAGAAAA
22505 GAAAGAAAA
1 GAAAGAAAA
22514 GAAAGAAAA
1 GAAAGAAAA
22523 CGTATGAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
GAAAGAAAA
Found at i:22847 original size:16 final size:16
Alignment explanation
Indices: 22826--22867 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
22816 CAGCCCCTTT
22826 TTTCTTTTTCTTTTCA
1 TTTCTTTTTCTTTTCA
*
22842 TTTCTTCTTT-TTTTCT
1 TTTCTT-TTTCTTTTCA
*
22858 TTTTTTTTTC
1 TTTCTTTTTC
22868 AGCCTCGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.14
16 16 0.73
17 3 0.14
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTCTTTTTCTTTTCA
Found at i:30123 original size:19 final size:19
Alignment explanation
Indices: 30089--30138 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
30079 TCCCAACAGT
30089 TATA-AATATAATTATTTAA
1 TATATAATAT-ATTATTTAA
* * *
30108 TTTATATTATATTATTTTA
1 TATATAATATATTATTTAA
30127 TATATAATATAT
1 TATATAATATAT
30139 AATACGGGCC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATAATATATTATTTAA
Found at i:31163 original size:3 final size:3
Alignment explanation
Indices: 31152--31208 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
31142 AATAAATACC
*
31152 AAT AGAT AAT AAT AAT AAT AAT -AT AAT ATT AAT AAAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
31198 AAT AAT -AT AAT
1 AAT AAT AAT AAT
31209 TAGATCAAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 4 0.08
3 38 0.79
4 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:31193 original size:30 final size:30
Alignment explanation
Indices: 31139--31208 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
31129 TACATAAGTA
*
31139 AATAATA-AATACCAATAGATAATAATAAT
1 AATAATATAATACCAATAAATAATAATAAT
**
31168 AATAATATAATATTAATAAATAATAATAAT
1 AATAATATAATACCAATAAATAATAATAAT
31198 AATAATATAAT
1 AATAATATAAT
31209 TAGATCAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 7 0.19
30 30 0.81
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (30 bp):
AATAATATAATACCAATAAATAATAATAAT
Found at i:31441 original size:2 final size:2
Alignment explanation
Indices: 31434--31467 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31424 GGAACTGGGA
31434 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
31468 TTAAGAGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:36818 original size:46 final size:46
Alignment explanation
Indices: 36740--36831 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
36730 TACCAACACT
* *
36740 TTTGATTTTAAATTGCAAATTCATAAGCCTATAAAAGTTGGGTGGC
1 TTTGATTTTAAATTGCAAAGTCACAAGCCTATAAAAGTTGGGTGGC
*
36786 TTTGATTTTAAATTGCAAAGTCACAAGTCTATAAAAGTTGGGTGGC
1 TTTGATTTTAAATTGCAAAGTCACAAGCCTATAAAAGTTGGGTGGC
36832 AGGAAATTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.36
Consensus pattern (46 bp):
TTTGATTTTAAATTGCAAAGTCACAAGCCTATAAAAGTTGGGTGGC
Found at i:39229 original size:29 final size:28
Alignment explanation
Indices: 39186--39248 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 28
39176 GTATGTGGCA
* *
39186 ATTTTTAACATGTGGCATGCCACGTGTC
1 ATTTTTAACACGTGGCATGCCACATGTC
39214 ATTTTTAATCACGTGGCATGCCACATGTC
1 ATTTTTAA-CACGTGGCATGCCACATGTC
39243 ATTTTT
1 ATTTTT
39249 GGTACATGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 8 0.25
29 24 0.75
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (28 bp):
ATTTTTAACACGTGGCATGCCACATGTC
Found at i:44219 original size:37 final size:37
Alignment explanation
Indices: 44178--44248 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
44168 AATTACCCAT
44178 TCAAAAAATGGAAATGTGTCAACTCCACAACCCAGAG
1 TCAAAAAATGGAAATGTGTCAACTCCACAACCCAGAG
* *
44215 TCAAAAAATGGACATGTGTCAACTCCCCAACCCA
1 TCAAAAAATGGAAATGTGTCAACTCCACAACCCA
44249 CACCGCCTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.41, C:0.28, G:0.14, T:0.17
Consensus pattern (37 bp):
TCAAAAAATGGAAATGTGTCAACTCCACAACCCAGAG
Found at i:44299 original size:30 final size:30
Alignment explanation
Indices: 44263--44329 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
44253 GCCTGTGTAG
*
44263 CAAATAGTGTATCAAATAGTATTAGATAAT
1 CAAATAGTGTACCAAATAGTATTAGATAAT
44293 CAAATAGTGTACCAAATAGTATTAGATAAT
1 CAAATAGTGTACCAAATAGTATTAGATAAT
44323 CATAATA
1 CA-AATA
44330 CCTACGACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (30 bp):
CAAATAGTGTACCAAATAGTATTAGATAAT
Found at i:46066 original size:36 final size:36
Alignment explanation
Indices: 46016--46089 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
46006 ACTTGTTCGG
*
46016 CAGGGAGCCGACTTAGCACGTCGATTGTCACATCAT
1 CAGGGAGCCGACTTAGCACGTCGACTGTCACATCAT
* * *
46052 CAGGGAGGCC-ACTTATCATGTCGACTGTCACATGAT
1 CAGGGA-GCCGACTTAGCACGTCGACTGTCACATCAT
46088 CA
1 CA
46090 TCGAAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 30 0.91
37 3 0.09
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (36 bp):
CAGGGAGCCGACTTAGCACGTCGACTGTCACATCAT
Found at i:46640 original size:15 final size:15
Alignment explanation
Indices: 46620--46650 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
46610 AAACATTAAT
46620 TCTTGTGCCGATTTC
1 TCTTGTGCCGATTTC
46635 TCTTGTGCCGATTTC
1 TCTTGTGCCGATTTC
46650 T
1 T
46651 AGAAATGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.26, G:0.19, T:0.48
Consensus pattern (15 bp):
TCTTGTGCCGATTTC
Found at i:48924 original size:14 final size:16
Alignment explanation
Indices: 48905--48936 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48895 TCTAAGTTGA
48905 TTGTGAA-A-ATTTTT
1 TTGTGAAGATATTTTT
48919 TTGTGAAGATATTTTT
1 TTGTGAAGATATTTTT
48935 TT
1 TT
48937 TCATATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 1 0.06
16 8 0.50
ACGTcount: A:0.25, C:0.00, G:0.16, T:0.59
Consensus pattern (16 bp):
TTGTGAAGATATTTTT
Found at i:54536 original size:22 final size:22
Alignment explanation
Indices: 54508--54572 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
54498 TAGAGATGTG
54508 CATTACAATGCTTCATCAAATT
1 CATTACAATGCTTCATCAAATT
*
54530 CATTACAGA-GCTTC-CCAAATT
1 CATTACA-ATGCTTCATCAAATT
*
54551 CTTCCATACAATGCTTCATCAA
1 CAT---TACAATGCTTCATCAA
54573 GAAACAAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
21 8 0.24
22 12 0.35
23 2 0.06
24 9 0.26
25 3 0.09
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (22 bp):
CATTACAATGCTTCATCAAATT
Found at i:56288 original size:12 final size:13
Alignment explanation
Indices: 56258--56297 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
56248 TTTAAAATAC
*
56258 TTGTCACAATTAG
1 TTGTCACAATTAA
56271 TTGTCACAA-TAA
1 TTGTCACAATTAA
56283 TTGTCACAATTAA
1 TTGTCACAATTAA
56296 TT
1 TT
56298 TTATAATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (13 bp):
TTGTCACAATTAA
Found at i:59936 original size:20 final size:18
Alignment explanation
Indices: 59897--59932 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
59887 CTAGCCCTAA
*
59897 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAAATAG
59915 AACTAGAAGAGAAAAATA
1 AACTAGAAGA-AAAAATA
59933 AGAAGAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (18 bp):
AACTAGAAGAAAAAATAG
Found at i:60141 original size:13 final size:13
Alignment explanation
Indices: 60117--60148 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
60107 TTAAAATAGG
60117 ATCCTG-AAAAAA
1 ATCCTGAAAAAAA
60129 ATCCTGAAAAAAA
1 ATCCTGAAAAAAA
60142 ATCCTGA
1 ATCCTGA
60149 TTTCGTGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.53, C:0.19, G:0.09, T:0.19
Consensus pattern (13 bp):
ATCCTGAAAAAAA
Done.