Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022468.1 Corchorus olitorius cultivar O-4 contig22501, 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: 32671
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:727 original size:37 final size:37
Alignment explanation
Indices: 674--744 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
664 TACTAGTTAT
** * *
674 TCATAAAGTTGTGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTACGTCTATATGAAAAGACATGTATTGA
711 TCATAAAGTTACGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTACGTCTATATGAAAAGACATGTAT
745 GTTGATCAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (37 bp):
TCATAAAGTTACGTCTATATGAAAAGACATGTATTGA
Found at i:5141 original size:340 final size:320
Alignment explanation
Indices: 3698--6171 Score: 1779
Period size: 318 Copynumber: 7.5 Consensus size: 320
3688 ATACTTTACA
* * * *
3698 TCATCTAACCAAATCTCAGCAACATTGGATTTAAGAATTTGTTTTTACGAGCATTTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * *
3763 TTCGATTTAATTAAAAATTAATTTAGAAAAAAATAAGAAATACCATATTAAAAGCGTAAAAA-CC
66 TTCGATTTAATTAGAAATTAATTT--AAAAAAATAGGAAAAACGATATTAAAAGCGTAAAAAGTC
* * * * * *
3827 CTCTAATCTTTTTGGCGTTGAATTATATA-CTTTTATGAGTATTTTAGCCAAAAATTGATGAGAA
129 CTC-AAT-TTTTTGGCGTTAAATTATATATTTTTTATGAGTATTATGGCTAAAAATTGA-GAAAA
* * * * ** *
3891 ATCTTTCGTGTCAAATTTTGTAAAATTTTAGTCAAAAATCGTGTACTAACAAACAATCACAGTTT
191 ATATTTCGAGTCAATTTTTGCAAAATTTTAG-CCGAAATCGTG---T--------ATCACGGTTT
* ** * * *
3956 TTGGCTAAAAACGCGTTCCGGGGACCCGCCTCAATTTTGCATGA-TTTTTG-GCTCCGAGGCTAC
244 TTGGCTAAAAACGCATTCCGGGG-CCCGAGTCAGTTTTGCATGATTTTTTGTGCT--AAGGCTCC
4019 TTGAAATATCTATAT
306 TTGAAATATCTATAT
* *
4034 TCATCTAATCAAATCTCAGCCACATTGGATTCAAGGATTTGTTTTT-CGAGCATCCGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* *
4098 TTCGATTTAATTAGAAAATAATTTGGAAAAAATTAGGAAAAACGATATTAGAAA-CGTCAAAAA-
66 TTCGATTTAATTAGAAATTAATTT--AAAAAAATAGGAAAAACGATATTA-AAAGCGT-AAAAAG
* * * * *
4161 CCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGAAA
127 TCC-TCAA-TTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTATGGCTAAAAATTGAGAAA
* * *
4226 ATATCTTTCGAGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTG
190 A-ATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---T----ATCACGGTTTTTG
* ** * ** * * * * *
4291 GATAAAAAAACGTTTTGAGGCCCCG-GCTCAGTTTTACATGATTTTTGGCGCCAAGGCTCCTTGA
247 GCTAAAAACGCATTCCG-GGGCCCGAG-TCAGTTTTGCATGATTTTTTGTGCTAAGGCTCCTTGA
* *
4355 GATATCCATAT
310 AATATCTATAT
* * * *
4366 TCATCTAATCAAATCTCAGCCATATTGGATTTAAGAATTGGTTTTTACGAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * * *
4431 TTCGATTTAATAAAAAATTAATTCAGAAAACAT--GAAAAATGATGTTAAAAGCGTGAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTTA-AAAAAATAGGAAAAACGATATTAAAAGCGTAAAAAGTCC
* *
4494 TCCAATCTTTTTGGCGTTAAATTATATATATTTTATGAGTAATTTAT--CTAAAAATTTAGGAAA
130 T-CAAT-TTTTTGGCGTTAAATTATATATTTTTTATGAGT-A-TTATGGCTAAAAATTGA-GAAA
* * *
4557 AATTTTTCGAGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTATCACGGTTTTTGGCTAAAAA
190 AATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATCACGGTTTTTGGCTAAAAA
* * * * * * ***
4622 CGCGTT-TGGGGCCTGACTCAGTTTT-CTATGATTTTTTTTTACGCCGGCACTCCTTGAAATATC
255 CGCATTCCGGGGCCCGAGTCAGTTTTGC-ATGA-TTTTTTGTGCTAAGG--CTCCTTGAAATATC
4685 TATAT
316 TATAT
* * * *
4690 TCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
4755 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAACCGATATTAAAAGCGTAAAAAGTCCT
66 TTCGATTTAATTAGAAATTAATTTAAAAAAATAGGAAAAACGATATTAAAAGCGTAAAAAGTCCT
* * *
4820 ACGATTTTTTCGGCGTTTAATTTTCTATATATATATATATATTCTATGAGTACTATGGTTAAAAA
131 -CAATTTTTT-GGCG-TTAA------AT-TATATAT-T-T-TT-TATGAGTATTATGGCTAAAAA
* * *
4885 ATGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTACCATCACGGTT
182 TTGA-GAAAAATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT---ATCACGG-T
* * *
4950 TTTTGGCTAAAAACGTATTCCGGGGCTCCGAGTCAGTTTTGCATGATTTTTTGTGGTAAAGCTCC
242 TTTTGGCTAAAAACGCATTCCGGGGC-CCGAGTCAGTTTTGCATGATTTTTTGTGCTAAGGCTCC
5015 TTGAAATATCTATAT
306 TTGAAATATCTATAT
* * * * * * * * *
5030 ACATCTAACCAAATCTTAACCACATAGAATTTGAGGATTTGTTTTTACGAGCATTTGAATCATGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
5095 TTCGATTTAATTAGAAATTAATTTAAAAAAATAGGAAAAACGATATTAGAAGCGTGAGAAGCCCT
66 TTCGATTTAATTAGAAATTAATTTAAAAAAATAGGAAAAACGATATTAAAAGCGTAAAAAGTCC-
* * *
5160 TCAATACTTTT-GCG----GTTATATATTTTTTATGAGTATTATGGCTAAAAATTGATAAAAATA
130 TCAAT-TTTTTGGCGTTAAATTATATATTTTTTATGAGTATTATGGCTAAAAATTGAGAAAAATA
* * ** * * *
5220 TTTAGGGTCAATTTTTGCAAAATTTTAGTAGAAATCGCGT-T-ATGTTTTTTGGCTAAAAACGCA
194 TTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATCACGGTTTTTGGCTAAAAACGCA
** * * * * * *
5283 TTCCGGAACCCTAGGTTAGTTTTGCATGA-TTTTTG-ACGTCAGGACTCCTTAAAATATATCTTT
259 TTCCGGGGCCCGA-GTCAGTTTTGCATGATTTTTTGTGC-TAAGG-CTCCTT-GAA-ATATCTAT
5346 AT
319 AT
* * * ** *
5348 TCATCTAACCAAATCTCAGTCACATTGTATTTAAGGATTTGTTTTTACGAGTTTCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* *
5413 TTCGATTTTATTAGAAATTAATTTGGAAATAAAATAGGAAAAACGATATTAGAAGCGTGAAAAAG
66 TTCGATTTAATTAGAAATTAATTT--AAA-AAAATAGGAAAAACGATATTAAAAGCGT-AAAAAG
* * *** * * * * * * *
5478 GCTTTCAATTTTTTTTATGTTGAATTATCTATTTTTTATGAGTATTTTTGTTAGAAATCGAGGAA
127 TC-CTCAA-TTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTATGGCTAAAAATTGA-GAA
** * * * * **
5543 AAATCGTTCGAGACAATTTTTGTAAAA-TTTAGCCGAAATCGTGTACGTTAATTATGGTTTTCAG
189 AAATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATC--GT--G-T-ATCACGGTTTTTGG
* * ** * * * * *
5607 CAAAAAAACGCGTTATGGGACCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAA
248 C-TAAAAACGCATTCCGGGGCCCGAGTCAGTTTTGCATGATTTTTTGTGCTAAGGCTCCTTGAAA
*
5672 TATCTATAC
312 TATCTATAT
* * * * *
5681 TCAT-TAAACCAAATCTCAGCCATATTAGATTTAAGGATTTGTTTTTACAAGCATTTGAATCTTG
1 TCATCT-AATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* ** * * ** *
5745 TTTCGATTTAATCAG----------AAACGAA-A--AAAAACAATATTAGAAGCGTTGAAAGCCC
65 TTTCGATTTAATTAGAAATTAATTTAAAAAAATAGGAAAAACGATATTAAAAGCGTAAAAAGTCC
** ** * * * *
5797 TTCAATCTTTTTGATGTCGAATTATATATTTTTTATGAGTATTTTAG-TCAAAAATTGGGGAAAT
130 -TCAAT-TTTTTGGCGTTAAATTATATATTTTTTATGAGTATTATGGCT-AAAAATT-GAGAAAA
* ** *
5861 ATCTTTCG-GATCAATTTTTATAAATTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGG
191 ATATTTCGAG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTG------T-ATCACGGTTTTTGG
** * * * * * * ** ** *
5925 CTAAAATTGCCTTACAGGGCTACGACTCTGTTTTGCATGATTTTTTACGCCGAGACTCCTTGAAA
248 CTAAAAACGCATTCCGGGGC-CCGAGTCAGTTTTGCATGATTTTTTGTGCTAAGGCTCCTTGAAA
*
5990 TATCTTTAT
312 TATCTATAT
* * * * * *
5999 TCATCTAATCAAATTTCAACCAAATTGGGTTTAAGGATTTGTTTTTATGTGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * *
6064 TTCGATTTAATTAGAAATTAGTTCAGAAAAAATATGAAAAACAATATTAAAAGCCTAAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTTA-AAAAAATAGGAAAAACGATATTAAAAGCGTAAAAAGTCC
* * *
6129 TCCAATCTTTTTGGCATTGAATTATATATATTTTATGAGTATT
130 T-CAAT-TTTTTGGCGTTAAATTATATATTTTTTATGAGTATT
6172 TTTGCCAAAA
Statistics
Matches: 1742, Mismatches: 289, Indels: 218
0.77 0.13 0.10
Matches are distributed among these distances:
313 1 0.00
315 17 0.01
316 117 0.07
317 49 0.03
318 209 0.12
319 2 0.00
320 6 0.00
321 48 0.03
322 66 0.04
323 52 0.03
324 106 0.06
325 35 0.02
326 5 0.00
327 50 0.03
328 25 0.01
329 14 0.01
330 99 0.06
331 9 0.01
332 177 0.10
333 124 0.07
334 5 0.00
335 94 0.05
336 119 0.07
337 118 0.07
339 3 0.00
340 140 0.08
341 23 0.01
342 13 0.01
343 15 0.01
344 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (320 bp):
TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATTAGAAATTAATTTAAAAAAATAGGAAAAACGATATTAAAAGCGTAAAAAGTCCT
CAATTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTATGGCTAAAAATTGAGAAAAATATT
TCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATCACGGTTTTTGGCTAAAAACGCATT
CCGGGGCCCGAGTCAGTTTTGCATGATTTTTTGTGCTAAGGCTCCTTGAAATATCTATAT
Found at i:6815 original size:13 final size:13
Alignment explanation
Indices: 6797--6828 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6787 CTAAAAACAT
*
6797 AAAAAAAACGCAG
1 AAAAAAAACCCAG
6810 AAAAAAAACCCAG
1 AAAAAAAACCCAG
6823 AAAAAA
1 AAAAAA
6829 TAGCGGGTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.75, C:0.16, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAAACCCAG
Found at i:7292 original size:22 final size:21
Alignment explanation
Indices: 7247--7294 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
7237 CGCCCCTCCA
*
7247 TGATTTTAGATGTTGTTGGGT
1 TGATTTTAGATGTTGTTGGAT
* *
7268 TGATTTTTGATGTTGTTTTGAT
1 TGATTTTAGATGTTG-TTGGAT
7290 TGATT
1 TGATT
7295 AAGGTTGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (21 bp):
TGATTTTAGATGTTGTTGGAT
Found at i:7451 original size:20 final size:20
Alignment explanation
Indices: 7394--7441 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
7384 TCTTTTGGCG
7394 GGGCGGTAGCTAGTAAAACA
1 GGGCGGTAGCTAGTAAAACA
7414 GGGCGGTAGCTAGTAAAACA
1 GGGCGGTAGCTAGTAAAACA
7434 GGGCGGTA
1 GGGCGGTA
7442 CTTTGTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.40, T:0.15
Consensus pattern (20 bp):
GGGCGGTAGCTAGTAAAACA
Found at i:11940 original size:27 final size:25
Alignment explanation
Indices: 11885--11940 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
11875 TATATTCTTC
*
11885 ATATATTCTTTCCCTATATAATGAG
1 ATATATTCTTTCCCCATATAATGAG
11910 ATATATTCTTTCCCCATATAATGAG
1 ATATATTCTTTCCCCATATAATGAG
*
11935 CTATAT
1 ATATAT
11941 CTATATTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (25 bp):
ATATATTCTTTCCCCATATAATGAG
Found at i:12830 original size:13 final size:12
Alignment explanation
Indices: 12807--12836 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
12797 TATATTTGGA
12807 ATTTAAAATAAT
1 ATTTAAAATAAT
12819 ATTTATAAATAAT
1 ATTTA-AAATAAT
12832 ATTTA
1 ATTTA
12837 GAACATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTTAAAATAAT
Found at i:16056 original size:88 final size:87
Alignment explanation
Indices: 15897--16152 Score: 446
Period size: 88 Copynumber: 3.0 Consensus size: 87
15887 TCTCTTTTAT
*
15897 TTGTGTATTTGGTAGGTAGTTTGAGTTGATCTCTCATTTAG---GTTTGGGCATATAGAGATTTA
1 TTGTGTATTTGGTAGGTAGTTTGAGTTGATTTCTCATTTAGTATGTTTGGGCATATAGAGATTTA
15959 TTCAGATTGTAATGAGATCTCG
66 TTCAGATTGTAATGAGATCTCG
*
15981 TTGTGTATTTGGTAGGTAGTTTGAGTTGATTTCTCATTTAGGTATGTTTGAGCATATAGAGATTT
1 TTGTGTATTTGGTAGGTAGTTTGAGTTGATTTCTCATTTA-GTATGTTTGGGCATATAGAGATTT
16046 ATTCAGATTGTAATGAGATCTCG
65 ATTCAGATTGTAATGAGATCTCG
16069 TTGTGTATTTGGTAGGTAGTTTGAGTTGATTTCTCATTTATGTATGTTTGGGCATATAGAGATTT
1 TTGTGTATTTGGTAGGTAGTTTGAGTTGATTTCTCATTTA-GTATGTTTGGGCATATAGAGATTT
*
16134 ATTCAGATGGTAATGAGAT
65 ATTCAGATTGTAATGAGAT
16153 TTCACATGTA
Statistics
Matches: 163, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
84 39 0.24
85 1 0.01
88 123 0.75
ACGTcount: A:0.23, C:0.07, G:0.26, T:0.44
Consensus pattern (87 bp):
TTGTGTATTTGGTAGGTAGTTTGAGTTGATTTCTCATTTAGTATGTTTGGGCATATAGAGATTTA
TTCAGATTGTAATGAGATCTCG
Found at i:16256 original size:106 final size:107
Alignment explanation
Indices: 16071--16279 Score: 357
Period size: 106 Copynumber: 2.0 Consensus size: 107
16061 AGATCTCGTT
* * * *
16071 GTGTATTTGGTAGGTAGTTTGAGTTGATTTCTCATTTATGTATGTTTGGGCATATAGAGATTTAT
1 GTGTATTTGGTAGGTAGCTTGAGTTGATCTCTCATTTAGGTATGTTTGGGCATATAAAGATTTAT
16136 TCAGATGGTAATGAGATTTCACATGTAATCACT-AAAATGAG
66 TCAGATGGTAATGAGATTTCACATGTAATCACTCAAAATGAG
*
16177 GTGTATTTGTTAGGTAGCTTGAGTTGATCTCTCATTTAGGTATGTTTGGGCATATAAAGATTTAT
1 GTGTATTTGGTAGGTAGCTTGAGTTGATCTCTCATTTAGGTATGTTTGGGCATATAAAGATTTAT
*
16242 TCAGATTGTAATGAGATTTCACATGTAATCACTCAAAA
66 TCAGATGGTAATGAGATTTCACATGTAATCACTCAAAA
16280 AAATTGCCTT
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
106 92 0.96
107 4 0.04
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (107 bp):
GTGTATTTGGTAGGTAGCTTGAGTTGATCTCTCATTTAGGTATGTTTGGGCATATAAAGATTTAT
TCAGATGGTAATGAGATTTCACATGTAATCACTCAAAATGAG
Found at i:16406 original size:144 final size:147
Alignment explanation
Indices: 16143--16418 Score: 414
Period size: 144 Copynumber: 1.9 Consensus size: 147
16133 TATTCAGATG
*
16143 GTAATGAGATTTCACATGTAATCACTAAAATGAGGTGTATTTGTTAGGTAGCTTGAGTTGATCTC
1 GTAATGAGATTTCACATGTAATCACTAAAATGAGGTGTATTTGGTAGGTAGCTTGAGTTGATCTC
*
16208 TCATTTAGGTATGTTTGGGCATATAAAGATTTATTCAGATTGTAATGAGATTTCACATGTAATCA
66 TCATTTAGGTATGTTTGGACATATAAAGATTTATTCAGATTGTAATGAGATTTCACATGTAATCA
16273 CTCAAAAAAATTGCCTT
131 CTCAAAAAAATTGCCTT
* *** ** * *
16290 GTAATGAGATTTCACATGTAATCTCTTTTAT-TTGTGTATTTGGTAGGTAGTTTGAGTTGATTTC
1 GTAATGAGATTTCACATGTAATCACTAAAATGAGGTGTATTTGGTAGGTAGCTTGAGTTGATCTC
* * *
16354 TCATTTA-G-ATGTTTGGACATATAGAGATTTATTTAGATTGTAATGATATTTCACATGTAATCA
66 TCATTTAGGTATGTTTGGACATATAAAGATTTATTCAGATTGTAATGAGATTTCACATGTAATCA
16417 CT
131 CT
16419 TAAATGAGAT
Statistics
Matches: 116, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
144 53 0.46
145 1 0.01
146 35 0.30
147 27 0.23
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (147 bp):
GTAATGAGATTTCACATGTAATCACTAAAATGAGGTGTATTTGGTAGGTAGCTTGAGTTGATCTC
TCATTTAGGTATGTTTGGACATATAAAGATTTATTCAGATTGTAATGAGATTTCACATGTAATCA
CTCAAAAAAATTGCCTT
Found at i:16960 original size:14 final size:14
Alignment explanation
Indices: 16941--16974 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
16931 TACATTAAAT
16941 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
16955 ATTTTATTTTTACT
1 ATTTTATTTTTACC
16969 ATTTTA
1 ATTTTA
16975 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:20230 original size:310 final size:310
Alignment explanation
Indices: 19758--20638 Score: 796
Period size: 323 Copynumber: 2.8 Consensus size: 310
19748 ATTATCACAT
* * * * *
19758 GATTTCGGCCAAAATTTTGTAAAAATTGACCCAAAAGATATTTCCTCAATTTTTAGCCATAATAC
1 GATTTCGGCCAAAATTTTGCAAAAAATGACCCAAAAAATATTTCCTCAATTTTTAGACAAAATAC
* * *
19823 TCATAAAAAATATATAAGTCAATGCGAAAAAGATTGAAGGACTTTTCATGCTTCTAATATCGTTT
66 TCATAAAAAATAAATAAGTCAATACGAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTT
* * *
19888 TTCATATTTTTCAGAATAAATTTCTAATTAAATTGAAACAAGATTCAGATGC-TCTTAAAAATAA
131 TTCATATTTTTCAGAATAAATTTCCAATTAAATCGAAACAAGATTCAGATGCAT-TTAAAAACAA
* * * * *
19952 A-TCTTTAAATGCAATGTGGCT-AAGATTTTATTAGATGAATATAGATATTTCAAGGAGTGTCAG
195 ATTC-TTAAATCCAATGTGGCTGAA-ATTTGATTAGATGAATATAGATATCTCAAGGAATCTCAG
*
20015 CG-CAAAAAATCATGCAAAACTGAGCTGGAGCATTTTTAGCCAAAAACCGGAC
258 CGCCAAAAAATCATACAAAACTGAGCTGGAGCATTTTTAGCCAAAAACCGGAC
* * * * * *
20067 GATTTTGGCTAAAATTTTGCAAAAAATGACTCAAAAAATTTTTCCTCAATTTTTGGATAAAATAC
1 GATTTCGGCCAAAATTTTGCAAAAAATGACCCAAAAAATATTTCCTCAATTTTTAGACAAAATAC
* * * * *
20132 TCATAAAATATAAATAATTTAATAC-AAAAAGGGATTGGAGGACTTTTCACGCTTTTAATATCGT
66 TCATAAAAAATAAATAAGTCAATACGAAAAA--GATTGAAGGACTTTTCACGCTTCTAATATCGT
* * * * *
20196 TTTTCGTATTTTTCTGAGTTAATTTCCCATTAAATCGAAACAAGATTCAGATGCATTTAAAAACA
129 TTTTCATATTTTTCAGAATAAATTTCCAATTAAATCGAAACAAGATTCAGATGCATTTAAAAACA
* * ** *
20261 AATTCTTAAATCCAATGTGGTTGAAATTTGATTAGATGAATATGGATATCTCAAGGAATCTTGGT
194 AATTCTTAAATCCAATGTGGCTGAAATTTGATTAGATGAATATAGATATCTCAAGGAATCTCAGC
* * * ** *
20326 GCCAAAAAATCATACAAAACTGAGTTGGGGCCCCAAAACACTTTTTTAGCTAAAAATTGTGATT
259 GCCAAAAAATCATACAAAACTGAGCT--GG------AGCA--TTTTTAGCCAAAAACCG-GA-C
** ** * * * *
20390 G-TTAT--TACACGATTTCGGCAAAAATTTGACCCAAAAGATATTTCCTTAATTTTT-GACTAAA
1 GATT-TCGGCCAAAATTT-TGCAAAAA-ATGACCCAAAAAATATTTCCTCAATTTTTAGAC-AAA
* * ** * ** * *
20451 ATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTGGACGTTTCTAATAT
62 ATACTCATAAAAAATAAATAAGTCAATACGAAAAAGATTGAAGGACTTTT-CACGCTTCTAATAT
* * * * *
20516 C-ATTTTCCTATTTTTTCCA-AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC-TCGTA
126 CGTTTTTCATA-TTTTT-CAGAATAAATTTCCAATTAAATCGAAACAAGATTCAGATGCAT-TTA
* * ** * * *
20578 AAAATAAATCCTTAAATCCAATGTGATTGAGATTTGATTAAATGAATATAGATATTTCAAG
188 AAAACAAATTCTTAAATCCAATGTGGCTGAAATTTGATTAGATGAATATAGATATCTCAAG
20639 TAGTCTTGGA
Statistics
Matches: 464, Mismatches: 81, Indels: 40
0.79 0.14 0.07
Matches are distributed among these distances:
308 5 0.01
309 74 0.16
310 134 0.29
311 27 0.06
313 2 0.00
319 3 0.01
321 19 0.04
322 33 0.07
323 161 0.35
324 6 0.01
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (310 bp):
GATTTCGGCCAAAATTTTGCAAAAAATGACCCAAAAAATATTTCCTCAATTTTTAGACAAAATAC
TCATAAAAAATAAATAAGTCAATACGAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTT
TTCATATTTTTCAGAATAAATTTCCAATTAAATCGAAACAAGATTCAGATGCATTTAAAAACAAA
TTCTTAAATCCAATGTGGCTGAAATTTGATTAGATGAATATAGATATCTCAAGGAATCTCAGCGC
CAAAAAATCATACAAAACTGAGCTGGAGCATTTTTAGCCAAAAACCGGAC
Found at i:26645 original size:17 final size:17
Alignment explanation
Indices: 26609--26652 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
26599 GGTCATTTGG
*
26609 GTTCGGGTCAATTCTAAA
1 GTTCGGGTC-TTTCTAAA
* *
26627 GTTTGGGTCTTTCTCAA
1 GTTCGGGTCTTTCTAAA
26644 GTTCGGGTC
1 GTTCGGGTC
26653 ATGTGGTTCG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.39
Consensus pattern (17 bp):
GTTCGGGTCTTTCTAAA
Found at i:28461 original size:70 final size:70
Alignment explanation
Indices: 28386--28527 Score: 275
Period size: 70 Copynumber: 2.0 Consensus size: 70
28376 ACCCAGTGAA
*
28386 ATCTCATTACAATTCAAATAAATCTCTATGCCCAAACATCTAAATGAGAATTCAACCCAAAGTAG
1 ATCTCATTACAATTCAAATAAATCTCTATGCCCAAACATCTAAATGAGAATTCAACCCAAACTAG
28451 AAACT
66 AAACT
28456 ATCTCATTACAATTCAAATAAATCTCTATGCCCAAACATCTAAATGAGAATTCAACCCAAACTAG
1 ATCTCATTACAATTCAAATAAATCTCTATGCCCAAACATCTAAATGAGAATTCAACCCAAACTAG
28521 AAACT
66 AAACT
28526 AT
1 AT
28528 AGCATAAATA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.44, C:0.23, G:0.06, T:0.26
Consensus pattern (70 bp):
ATCTCATTACAATTCAAATAAATCTCTATGCCCAAACATCTAAATGAGAATTCAACCCAAACTAG
AAACT
Done.