Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014523.1 Corchorus olitorius cultivar O-4 contig14556, 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: 63754
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:335 original size:18 final size:18
Alignment explanation
Indices: 312--346 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
302 AAATCATAGA
312 ATATAATAATATAATAAC
1 ATATAATAATATAATAAC
* *
330 ATATAATGATTTAATAA
1 ATATAATAATATAATAA
347 TTACAACTTT
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:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (18 bp):
ATATAATAATATAATAAC
Found at i:1548 original size:96 final size:94
Alignment explanation
Indices: 1302--1548 Score: 257
Period size: 96 Copynumber: 2.6 Consensus size: 94
1292 TAACCTTAGC
* ** * * *
1302 TATAATATTTTTTTATGGCACGCTAAATTATTATTATTTTGGATACTCTATACTTAATTGTAGAA
1 TATAATATTTTTTTTTGATACACTAAATTATAATTATTTTGGATACTCTATACTTAATTATAGAA
** *
1367 ATTGGGAAATGTCATTGTCCTGCCTTAAT
66 ATTGGGAAATGTCATCATCCTGCCATAAT
* * * * * *
1396 AATAATATTTTTCCTTT-ATAACACTCAATTATAATTA-TTTGGAATACTCCACACTTACTTATA
1 TATAATATTTTT-TTTTGAT-ACACTAAATTATAATTATTTTGG-ATACTCTATACTTAATTATA
* *
1459 -AAATTCTGGGACATGTCATCATCCTTCCATAAT
63 GAAA-T-TGGGAAATGTCATCATCCTGCCATAAT
*
1492 TATAATATTTTTTGTTTGATACACTAAATCATAATTATTTTGGATACTCTATACTTA
1 TATAATATTTTTT-TTTGATACACTAAATTATAATTATTTTGGATACTCTATACTTA
1549 TTTGAAAAAA
Statistics
Matches: 122, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
94 19 0.16
95 33 0.27
96 63 0.52
97 7 0.06
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (94 bp):
TATAATATTTTTTTTTGATACACTAAATTATAATTATTTTGGATACTCTATACTTAATTATAGAA
ATTGGGAAATGTCATCATCCTGCCATAAT
Found at i:3732 original size:318 final size:316
Alignment explanation
Indices: 2644--5586 Score: 2121
Period size: 318 Copynumber: 8.9 Consensus size: 316
2634 TTGTTTCATA
* * * * * *
2644 TTTTTTGAATTAATTTCTAATTAAATCAAAATAAGATTTAAATACTCGTAAAAACAAATCCTTAA
1 TTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAT
* * * * * * ** *
2709 ATCCAATATGCCTTAGATTTGATTAGAT-AATATAGATATTTCAAGAAGTCTCGGTGCAAAAAAT
66 ATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAAT
** * * * * * * * *
2773 CATGC-ATTCTTAGTTCCATGGCCCCGGAACGCATTTTTAGTAAAAAATCATGATGGTTATAGTA
131 CATGCAAAACTGAG-T-C-GGGACCCGAAACGCGTTTTTAG-CAAAAACCGTGATGG-T-TAGTA
* * * *
2837 CACAATTTCGGCTAAAAACTGACCCGAAACGTTTATACTCAATTTTTTGCCACAATACTCAG-AA
190 CACGATTTCGGCTAAAAACTGACCCGAAAAGTTT-TCCTCAATTTTTTG-CAAAATACTCAGAAA
* *
2901 AAATATATAATTCAATGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGTTTTTCCATT
253 AAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCC---
2966 TT
315 TT
* *
2968 TTTTTTCAGAATTAATTTCTAATTAAATCGGAACAAGATTCAGATGCTCGTAAAAACAAATTCTT
1 TTTTTT--GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * * * * * *
3033 ATATTCAATGTGGCTGACATTTGTTTCGATGAATATAGATATTTTAATGAGTCTTTGCGCTAAAA
64 ATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAA
* * * * * *
3098 ATTATGCAAAATTGAGTCGGGGCTCC-AGAACGCGTTTTTAGCCAAAAGCAGTGA---TAACGTA
129 ATCATGCAAAACTGAGTCGGGAC-CCGA-AACGCGTTTTTAG-CAAAAACCGTGATGGTTA-GTA
* * *
3159 CACGATTTCGGCTAAAATTTTGCAAAAACTGATCCGAAAAGTTTTTCCCCAATTTTTTGCCACAA
190 CACGATTTCGGC--------T--AAAAACTGACCCGAAAAG-TTTTCCTCAATTTTTTG-CAAAA
* * * * *
3224 TACTCTGAAAAAATATATAATTTAACGTCAAAAAAATTGAAGGG-TTTTCACGCTTCTAATATCG
243 TACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCG
3288 TTTTTCCTT
308 TTTTTCCTT
* * * * *
3297 TTTTTTCCAAATTTATTTCTAATTAAATCGAAATAAAGATTGAGATGCTCGTAAAAACTAATCCT
1 TTTTTT--GAATTAATTTCTAATTAAATCGAAA-CAAGATTCAGATGCTCGTAAAAACAAATCCT
* * * * * *
3362 TAAATCCATTGTGGCTGAGATTTTGTTAGATGAATATAGATATTTTAAGGAGTCTTTTTGCCAAA
63 TATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAA
* * * *
3427 AATCATGCAAAACTAAG-CGGGGCCCGAAACGCGTTTTTAGCTAACAACCGTGATGGTAAGTACA
128 AATCATGCAAAACTGAGTCGGGACCCGAAACGCGTTTTTAGC-AAAAACCGTGATGGTTAGTACA
* * *
3491 CGATTTAGGCTAAAAACTGACCCGAAAAGTTTT-CTCAATTTTCTGCAAAATAGTCAGAAAAAAT
192 CGATTTCGGCTAAAAACTGACCCGAAAAGTTTTCCTCAATTTTTTGCAAAATACTCAGAAAAAAT
* * *
3555 ATATAATTCAACACCAAAAAGATTGACGGCCTTTTTCACGCTTCTCATATCGTTTTTCCATT
257 ATATAATTCAACGCCAAAAAGATTGACGGGC-TTTTCACGCTTCTAATATCGTTTTTCC-TT
*
3617 TTATTTTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAAAT-CTT
1 TT-TTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC-AAATCCTT
* * * *
3681 ATATACAATGTGGTTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGGCAAAA
64 ATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAA
* * * * * * * *
3746 ATCATGCCAAATTGAGCCGAGACTCTGGAATGCGTTTTTAGGCAAAAACCGTGATGATTAGTACA
129 ATCATGCAAAACTGAGTCGGGAC-CCGAAACGCGTTTTTA-GCAAAAACCGTGATGGTTAGTACA
* *** ** ** ** *
3811 CGATTTCGTTGGCAAAAAAAAAATAC-ACGA-TTTTCGACT-AAAATTTTGCAAAAATTGAC-CC
192 CGATTTC---GGCTAAAAACTGACCCGAAAAGTTTTC--CTCAATTTTTTGC-AAAA-T-ACTCA
*** * * ** * * ** *
3872 GAAAGGTTTTTTCTCAATGTTTTGCCACAATAATCAGAAAGAATAAATAATTCAATGCCAAAAAA
249 GAAA--AAATATAT-AA----TT----C---AA-C-G--CCAA-AAA-GATTGACGGGC------
** *
3937 TATTGAAAGGTTTTTCACAGTTCTAATATCGTTTTTCCATT
288 T-TT------TCA--CGC--TTCTAATATCGTTTTTCC-TT
* * * *
3978 TTTTTTGAATTTATTTCTAATTAAATCAAAACAAAGATTTAGATGCTCTTAAAAACAAATCCTTA
1 TTTTTTGAATTAATTTCTAATTAAATCGAAAC-AAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * * * * * *
4043 AATCTATTGTGGCTGAGATTTGGTTAGATGAATGTAGATATTTCAAGCAGTTTTTCTGCCAAAAA
65 TATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAA
* * * * *
4108 TCTTGGAAAACTGAGTCGAGGCCCCGAAACACGTTTTTAGCCGAAAACCGTGATGGTTAGTACAC
130 TCATGCAAAACTGAGTCG-GGACCCGAAACGCGTTTTTAG-CAAAAACCGTGATGGTTAGTACAC
* * ** * * * * * *
4173 GATTTCGACTAAAAACTAACCTTAAAATTTTTTTCTCAATTTTTTACGAAATATTCAAAAAAAAA
193 GATTTCGGCTAAAAACTGACCCGAAAA-GTTTTCCTCAATTTTTTGCAAAATACTC-AGAAAAAA
* * * *
4238 TATATAATTCAATGCCAGAAAGATTGACGGGCTTTTCACGCTACTAATATCATTTTTCCTT
256 TATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCTT
* *
4299 TTTTTTCCGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCTTT
1 TTTTTT--GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * *
4364 ATATCCAATGTGGCTGATATTTGGTACGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAA
64 ATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCC-AAA
* ** * *
4429 AATCATGCAAAATTGAACCGGCACTCC-AGAACGCGTTTTTAGCCACAAACCGTGATGGTTAGTA
128 AATCATGCAAAACTGAGTCGGGAC-CCGA-AACGCGTTTTTAG-CAAAAACCGTGATGGTTAGTA
* * *
4493 CACGGTTTCGGCTAAATTTTGCAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATA
190 CACGATTTCGGCT--A------AAAACTGACCCGAAAAG-TTTTCCTCAATTTTTTG-CAAAATA
* * *** *
4558 GTCAGAAAAAATATATAATTCAACGCCAAACAA-ATTGAAGTATTTTTCACGATTCTAATATCGT
245 CTCAGAAAAAATATATAATTCAACGCCAAA-AAGATTGACGGGCTTTTCACGCTTCTAATATCGT
4622 TTTTCCATT
309 TTTTCC-TT
* * * **
4631 TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAAGAATAATATGCTCGTAAAAACAAATTTTT
1 TTTTT-TGAATTAATTTCTAATTAAATCGAAAC-AAGATTCAGATGCTCGTAAAAACAAATCCTT
* *
4696 ATATCCAATGTGGCTGGGATTTGGTTCGATGAGGATGGATATAGATATTTCAAGGAGT-TTTATG
64 ATATCCAATGTGGCTGAGATTTGGTTCGAT---GA---ATATAGATATTTCAAGGAGTCTTTGTG
* * * * * *
4760 CAAAAAAAATCATGCAAAACTGTGTCGGGACCCCGAAGCGCCTTTTTTTGCAGAAAAAAAAAACT
123 C--CAAAAATCATGCAAAACTGAGTCGGGA-CCCGAAACG-C-GTTTTT--AG----CAAAAACC
* * * * *
4825 TTGATGGTTAGTGCAGGATTTCGGTTAAAATTTTGCAAAAACTGACCC-AAAATTTTTTTTCCTC
177 GTGATGGTTAGTACACGATTTCGG--------CT--AAAAACTGACCCGAAAA---GTTTTCCTC
* *
4889 AATTCTTTGCAACAATACTCAGAAAAAATATGTAATTCAACGCCAAAAA-ATTGACAGGG-TTTT
229 AATTTTTTGCAA-AATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAC-GGGCTTTT
* *
4952 CAAGCTTCTAATATCG----TCTTT
292 CACGCTTCTAATATCGTTTTTCCTT
* * * * * *
4973 TTTTTTGAATTTATTTCTTATTAAATCGAAACAAGATTCAGATACTCGTTAAAAGAAATCCTTAA
1 TTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAT
* * * * * * **
5038 ATCCATTGTTGTTTAGATTTGGTTAGATTAATATAGATATTTCAAGGAGTCTTTCAGCCAAAAAT
66 ATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAAT
* * ** *
5103 CATGCAAAACTGAGTTGGGGCCCCGAAACATGTTTTTAGCCGAAAACCGTGAT-G---GTACACG
131 CATGCAAAACTGAG-TCGGGACCCGAAACGCGTTTTTAG-CAAAAACCGTGATGGTTAGTACACG
* * * ** * * * * * *
5164 ATTTCGACCAAAAACTAACCTTAAAATTTTTTTCTCAAATTTTTACGAAATATTCAGAAAAAATA
194 ATTTCGGCTAAAAACTGACCCGAAAA-GTTTTCCTCAATTTTTTGCAAAATACTCAGAAAAAATA
* *
5229 TATAATTCAACGCCAAAAAGATTAACGGGCTCTTCACGCTTCTAATATCGTTTTTCCTTT
258 TATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCC-TT
* *
5289 TTTTTTCCGAATTAATTTCTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCTT
1 TTTTTT--GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * *
5354 ATATCCAATGTGGCTGATATTTGGTACGATGAATATAGATATTTGAAGGAGTCTTTGTGCCAAAA
64 ATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCC-AAA
* * * * *
5419 AATCATGCAAAATTGAGCCGGCACTCCAAAACGTGTTTTTAGCCAAAAACCGTGATGGTTAGTAC
128 AATCATGCAAAACTGAGTCGGGAC-CCGAAACGCGTTTTTAG-CAAAAACCGTGATGGTTAGTAC
* ** *
5484 ACGGTTTCGGCTAAAATTTTGCAAAACTTGACCCGAAAAGTTTTTCCTCAATTTTTACCACAATA
191 ACGATTTCGGCT---A------AAAAC-TGACCCGAAAAG-TTTTCCTCAATTTTTTGCAAAATA
5549 CTCAGAAAAAATATATAATTCAACGCCAAACAA-ATTGA
245 CTCAGAAAAAATATATAATTCAACGCCAAA-AAGATTGA
5587 AGTGTTTTTT
Statistics
Matches: 2062, Mismatches: 390, Indels: 325
0.74 0.14 0.12
Matches are distributed among these distances:
310 37 0.02
311 40 0.02
312 10 0.00
313 4 0.00
315 2 0.00
316 8 0.00
317 40 0.02
318 205 0.10
319 107 0.05
320 60 0.03
321 19 0.01
322 126 0.06
323 118 0.06
324 14 0.01
325 11 0.01
326 106 0.05
327 38 0.02
328 29 0.01
329 40 0.02
330 110 0.05
331 114 0.06
332 146 0.07
333 121 0.06
334 26 0.01
335 7 0.00
336 1 0.00
337 6 0.00
338 46 0.02
339 11 0.01
340 55 0.03
341 26 0.01
342 9 0.00
343 5 0.00
344 3 0.00
345 34 0.02
346 4 0.00
347 37 0.02
348 50 0.02
350 1 0.00
351 2 0.00
352 2 0.00
353 2 0.00
356 2 0.00
357 5 0.00
358 11 0.01
359 12 0.01
360 40 0.02
361 158 0.08
362 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (316 bp):
TTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAT
ATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAAT
CATGCAAAACTGAGTCGGGACCCGAAACGCGTTTTTAGCAAAAACCGTGATGGTTAGTACACGAT
TTCGGCTAAAAACTGACCCGAAAAGTTTTCCTCAATTTTTTGCAAAATACTCAGAAAAAATATAT
AATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCTT
Found at i:7443 original size:31 final size:31
Alignment explanation
Indices: 7399--7539 Score: 151
Period size: 31 Copynumber: 4.5 Consensus size: 31
7389 ACGGTGTCCG
* *
7399 ACGTGTCATGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* * *
7430 ATGTGGCACGCCACGTGTACCAGAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* *
7461 A--TGGATCATACCATGTGTACCAAAAAGTGAC
1 ACGTGG--CATGCCACGTGTACCAAAAAGTGAC
* * **
7492 ACATGGCATGCCATGTGTTTCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
7523 ACGTGGCATGCCACGTG
1 ACGTGGCATGCCACGTG
7540 CACAAAAGGA
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
29 3 0.03
31 86 0.93
33 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (31 bp):
ACGTGGCATGCCACGTGTACCAAAAAGTGAC
Found at i:10515 original size:33 final size:33
Alignment explanation
Indices: 10470--10548 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
10460 TGAAGATCGT
*
10470 ATAGGATTTAGTTCCAGGGCCAGGGTTTTCGAG
1 ATAGGATCTAGTTCCAGGGCCAGGGTTTTCGAG
*
10503 ATAGGATCTAGTTCCAGTGCCAGGGTTTTCGAG
1 ATAGGATCTAGTTCCAGGGCCAGGGTTTTCGAG
10536 ATAGGATCTAGTT
1 ATAGGATCTAGTT
10549 TCGCCGGTGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (33 bp):
ATAGGATCTAGTTCCAGGGCCAGGGTTTTCGAG
Found at i:10582 original size:21 final size:22
Alignment explanation
Indices: 10556--10614 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
10546 GTTTCGCCGG
10556 TGGAGGGCAGCTCGTGCT-CGA
1 TGGAGGGCAGCTCGTGCTGCGA
* *
10577 TGGAGGGCATCTCGTG-TGCGG
1 TGGAGGGCAGCTCGTGCTGCGA
*
10598 TGCAGGGCAGCTCGTGC
1 TGGAGGGCAGCTCGTGC
10615 CTGGTTGAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.12, C:0.24, G:0.44, T:0.20
Consensus pattern (22 bp):
TGGAGGGCAGCTCGTGCTGCGA
Found at i:10647 original size:21 final size:21
Alignment explanation
Indices: 10621--10736 Score: 160
Period size: 21 Copynumber: 5.5 Consensus size: 21
10611 GTGCCTGGTT
10621 GAGGTGAGCCCTTGCCCGCTG
1 GAGGTGAGCCCTTGCCCGCTG
* * * *
10642 GGGGTGAGCCCGTGCCCGTTT
1 GAGGTGAGCCCTTGCCCGCTG
10663 GAGGTGAGCCCTTGCCCGCTG
1 GAGGTGAGCCCTTGCCCGCTG
* * * *
10684 GGGGTGAGCCCGTGCCCGTTT
1 GAGGTGAGCCCTTGCCCGCTG
10705 GAGGTGAGCCCTTGCCCGCTG
1 GAGGTGAGCCCTTGCCCGCTG
10726 GAGGTGAGCCC
1 GAGGTGAGCCC
10737 GAAGCCGGGG
Statistics
Matches: 79, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 79 1.00
ACGTcount: A:0.09, C:0.31, G:0.41, T:0.20
Consensus pattern (21 bp):
GAGGTGAGCCCTTGCCCGCTG
Found at i:10669 original size:42 final size:42
Alignment explanation
Indices: 10610--10737 Score: 229
Period size: 42 Copynumber: 3.0 Consensus size: 42
10600 CAGGGCAGCT
* *
10610 CGTGCCTGGTTGAGGTGAGCCCTTGCCCGCTGGGGGTGAGCC
1 CGTGCCCGTTTGAGGTGAGCCCTTGCCCGCTGGGGGTGAGCC
10652 CGTGCCCGTTTGAGGTGAGCCCTTGCCCGCTGGGGGTGAGCC
1 CGTGCCCGTTTGAGGTGAGCCCTTGCCCGCTGGGGGTGAGCC
*
10694 CGTGCCCGTTTGAGGTGAGCCCTTGCCCGCTGGAGGTGAGCC
1 CGTGCCCGTTTGAGGTGAGCCCTTGCCCGCTGGGGGTGAGCC
10736 CG
1 CG
10738 AAGCCGGGGT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 83 1.00
ACGTcount: A:0.08, C:0.30, G:0.41, T:0.21
Consensus pattern (42 bp):
CGTGCCCGTTTGAGGTGAGCCCTTGCCCGCTGGGGGTGAGCC
Found at i:14259 original size:45 final size:45
Alignment explanation
Indices: 14195--14280 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
14185 ATCCAGTATC
* * * *
14195 CAGGGTTTTGCTCTGATTAATCCGGATTTGACCCGCGTCGCACAT
1 CAGGGCTTTGCCCTGATTAATCCGGATCTGACCCACGTCGCACAT
14240 CAGGGCTTTGCCCTGATTAATCCGGATCTGACCCACGTCGC
1 CAGGGCTTTGCCCTGATTAATCCGGATCTGACCCACGTCGC
14281 GCACCTGGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.17, C:0.30, G:0.24, T:0.28
Consensus pattern (45 bp):
CAGGGCTTTGCCCTGATTAATCCGGATCTGACCCACGTCGCACAT
Found at i:14360 original size:68 final size:69
Alignment explanation
Indices: 14249--14382 Score: 216
Period size: 68 Copynumber: 2.0 Consensus size: 69
14239 TCAGGGCTTT
* *
14249 GCCCTGATTAATCCGGATCTGACCCACGTCGCGCACCTGGTTATGGTGGGTGAGTCTACCAACGG
1 GCCCTGACTAATCCGGATCTGACCCACGTCGCGCACCTAGTTATGGTGGGTGAGTCTACCAACGG
14314 GAAA
66 GAAA
** *
14318 GCCCTGACTAATCCGG-TCTGACCTGCGTCGCGCACCTAGTTATGGTGGGTGAGTCTATCAACGG
1 GCCCTGACTAATCCGGATCTGACCCACGTCGCGCACCTAGTTATGGTGGGTGAGTCTACCAACGG
14382 G
66 G
14383 GACAGCTACG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
68 45 0.75
69 15 0.25
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.23
Consensus pattern (69 bp):
GCCCTGACTAATCCGGATCTGACCCACGTCGCGCACCTAGTTATGGTGGGTGAGTCTACCAACGG
GAAA
Found at i:17382 original size:332 final size:325
Alignment explanation
Indices: 16721--17904 Score: 1218
Period size: 332 Copynumber: 3.6 Consensus size: 325
16711 CTTTGTTACA
* * * * * * * *
16721 AAAAATCGTGATGGTTAATAAACGATTTCGGTTAAACTTTTGCAAAATTTTACCCGAAAGAATTT
1 AAAAACCGTGATGGTTAGTAAACGATTTCGGCTAAAATTTTGTAAAAATTGACACG-AA-AATTT
* ** * * * *
16786 TCCTAAATTTTTTTGCCATGATA-CTCATAAAAAATATATAATTAAACACCAAAAAGATTGAAAG
64 TCCTCAA-TTTTCGGCCA-CATATCT-A-AAAAAATATATAAATCAACGCCAAAAAGATTGAAAG
* *
16850 GCTTTTCACGCTTCTAATATCGGTTTTCCTAATTTTTCCGAATTAATTTCTAATTAAATCGAAAC
125 GCTTTTCACGCTTCTAATATCGTTTTTCCTACTTTTTCCGAATTAATTTCTAATTAAATCGAAAC
* *
16915 ATGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGATTAGATGGAT
190 ATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGGAT
* * *
16980 ATAGACATTTCAATGA-TACTTGGCGTCAAAAATCATGCAAAA-TAGAGCCGGGACCCCGAATCG
255 ATAGATATTTCAATGAGT-CTTGG-ATCAAAAATCATGCAAAACT-GAGCCGGG-CCCGGAA-CG
17043 CATTTTTAGTC
315 CATTTTTAGTC
* *
17054 AAAAACTGTGATGGTTAGTAAACGATTTCGGCTAAAATTTTGTAAAAAATGACACGAAACATTTC
1 AAAAACCGTGATGGTTAGTAAACGATTTCGGCTAAAATTTTGTAAAAATTGACACGAAA-ATTT-
* * * *
17119 TCCTCAATTTCCGGCCACCATATTCTTAAAAAAAAATATAAATCAACGTCAAAAAAATT-AAAGG
64 TCCTCAATTTTCGGCCA-CATA-TC-TAAAAAAATATATAAATCAACGCCAAAAAGATTGAAA-G
* * * *
17183 GCTTATCACACTTCTAATATTCTTTTTTTCTA-TTTTTCCGAATTAATTT-TCAATTAAATCGAA
125 GCTTTTCACGCTTCTAATA-TCGTTTTTCCTACTTTTTCCGAATTAATTTCT-AATTAAATCGAA
** * * **
17246 ACCGGATTGAGATGCTCGTAAAAA-AAATCCTTAAATCCAATGTGGCTGAGATTTCATTAGATAA
188 ACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGG
* * *
17310 ATATAGATATTTGAATGAGTCTTGGATACAAAAATCATGCAAAACTGAGTCGAGGCCACGGTACG
253 ATATAGATATTTCAATGAGTCTTGGAT-CAAAAATCATGCAAAACTGAGCCG-GGCC-CGGAACG
* *
17375 TATTTTTAGGC
315 CATTTTTAGTC
* * *
17386 AAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGAATTT
1 AAAAACCGTGATGGTTAGTAAACGATTTCGGCTAAAATTTTGTAAAAATTGACACG-AA-AATTT
* ** * * *
17451 TCCTCAATTTTTGGCCATGGTA-CTCATAAAAAATTTATAATTCAACACCAAAAAGATTGAAAGG
64 TCCTCAATTTTCGGCCA-CATATCT-A-AAAAAATATATAAATCAACGCCAAAAAGATTGAAAGG
* * * * * *
17515 CTTTTCACGCTTCTAATAACATTTTTCCTATTTTTTCCGAATTAATTCCTAATTGAACCGAAACA
126 CTTTTCACGCTTCTAATATCGTTTTTCCTACTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * * * * * * *
17580 TGATTCATATGCTCGTAAAAATAAATCATTAAATCTAATCTGGGTAAGATTTGGTTAGATGGATA
191 TGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGGATA
* ** * * * * *
17645 TAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGCCGGAACTTCGAAACGCGT
256 TAGATATTTCAATGAGTCTTGG-ATCAAAAATCATGCAAAACTGAGCCGG-GC-CCGGAACGCAT
17710 TTTTAGTC
318 TTTTAGTC
* * * *
17718 AAAAACCGTGATGGTTAGTATACGATTTCAGCTAAAATTTTGCAAAAATTGACTCGATAAATTTG
1 AAAAACCGTGATGGTTAGTAAACGATTTCGGCTAAAATTTTGTAAAAATTGACACGA-AAATTT-
* * *
17783 TCCTCAATTTTGGGCCACACTA-CTAATAAGAAATATATAACTCAACGCCAAAAAGACTG-AAGG
64 TCCTCAATTTTCGGCCACA-TATCTAA-AA-AAATATATAAATCAACGCCAAAAAGATTGAAAGG
* *
17846 GTTTCTCACGCTTCTAATATCGTTTTTCCTACCTTTTCCTGAATTAATTTCTAATTAAA
126 CTTT-TCACGCTTCTAATATCGTTTTTCCTACTTTTTCC-GAATTAATTTCTAATTAAA
17905 AAAATGATAT
Statistics
Matches: 708, Mismatches: 112, Indels: 62
0.80 0.13 0.07
Matches are distributed among these distances:
329 1 0.00
330 12 0.02
331 108 0.15
332 400 0.56
333 174 0.25
334 12 0.02
335 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (325 bp):
AAAAACCGTGATGGTTAGTAAACGATTTCGGCTAAAATTTTGTAAAAATTGACACGAAAATTTTC
CTCAATTTTCGGCCACATATCTAAAAAAATATATAAATCAACGCCAAAAAGATTGAAAGGCTTTT
CACGCTTCTAATATCGTTTTTCCTACTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATT
CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGGATATAGAT
ATTTCAATGAGTCTTGGATCAAAAATCATGCAAAACTGAGCCGGGCCCGGAACGCATTTTTAGTC
Found at i:21227 original size:33 final size:34
Alignment explanation
Indices: 21185--21349 Score: 138
Period size: 33 Copynumber: 4.5 Consensus size: 34
21175 CGGACCCTTA
**
21185 GTGAATGGGGCATAAT-TTGTGATAGCTAATTTG
1 GTGAATGGGGCATAATAAAGTGATAGCTAATTTG
*
21218 GTGAATGGGGCATAATAAAAAGTGATAGCTATTTGGTGATAATTTA
1 GTGAATGGGGCATAAT--AAAGTGATAGC----------TAATTTG
**
21264 GTGAATGGGGCATAAT-TTGTGATAGCTAATTTG
1 GTGAATGGGGCATAATAAAGTGATAGCTAATTTG
21297 GTGAATGGGGCATAATAAAAAGTGATAGCT-ATTTG
1 GTGAATGGGGCATAAT--AAAGTGATAGCTAATTTG
21332 GTGAATGGGGCATAATAA
1 GTGAATGGGGCATAATAA
21350 TGGGGCACAC
Statistics
Matches: 108, Mismatches: 8, Indels: 32
0.73 0.05 0.22
Matches are distributed among these distances:
33 40 0.37
35 21 0.19
36 17 0.16
43 8 0.07
46 22 0.20
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.32
Consensus pattern (34 bp):
GTGAATGGGGCATAATAAAGTGATAGCTAATTTG
Found at i:21280 original size:19 final size:18
Alignment explanation
Indices: 21256--21312 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
21246 CTATTTGGTG
21256 ATAATTTAGTGAATGGGGC
1 ATAATTT-GTGAATGGGGC
*
21275 ATAATTTGTG-AT--AGC
1 ATAATTTGTGAATGGGGC
21290 -TAATTTGGTGAATGGGGC
1 ATAATTT-GTGAATGGGGC
21308 ATAAT
1 ATAAT
21313 AAAAAGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 6 0.19
15 5 0.16
16 2 0.06
17 2 0.06
18 5 0.16
19 11 0.35
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (18 bp):
ATAATTTGTGAATGGGGC
Found at i:21313 original size:79 final size:79
Alignment explanation
Indices: 21182--21335 Score: 308
Period size: 79 Copynumber: 1.9 Consensus size: 79
21172 AAACGGACCC
21182 TTAGTGAATGGGGCATAATTTGTGATAGCTAATTTGGTGAATGGGGCATAATAAAAAGTGATAGC
1 TTAGTGAATGGGGCATAATTTGTGATAGCTAATTTGGTGAATGGGGCATAATAAAAAGTGATAGC
21247 TATTTGGTGATAAT
66 TATTTGGTGATAAT
21261 TTAGTGAATGGGGCATAATTTGTGATAGCTAATTTGGTGAATGGGGCATAATAAAAAGTGATAGC
1 TTAGTGAATGGGGCATAATTTGTGATAGCTAATTTGGTGAATGGGGCATAATAAAAAGTGATAGC
21326 TATTTGGTGA
66 TATTTGGTGA
21336 ATGGGGCATA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (79 bp):
TTAGTGAATGGGGCATAATTTGTGATAGCTAATTTGGTGAATGGGGCATAATAAAAAGTGATAGC
TATTTGGTGATAAT
Found at i:21336 original size:35 final size:36
Alignment explanation
Indices: 21257--21349 Score: 131
Period size: 35 Copynumber: 2.7 Consensus size: 36
21247 TATTTGGTGA
* **
21257 TAATTTAGTGAATGGGGCATAAT---TTGTGATAGC
1 TAATTTGGTGAATGGGGCATAATAAAAAGTGATAGC
21290 TAATTTGGTGAATGGGGCATAATAAAAAGTGATAGC
1 TAATTTGGTGAATGGGGCATAATAAAAAGTGATAGC
21326 T-ATTTGGTGAATGGGGCATAATAA
1 TAATTTGGTGAATGGGGCATAATAA
21350 TGGGGCACAC
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
33 22 0.41
35 23 0.43
36 9 0.17
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.32
Consensus pattern (36 bp):
TAATTTGGTGAATGGGGCATAATAAAAAGTGATAGC
Found at i:21694 original size:92 final size:94
Alignment explanation
Indices: 21532--21719 Score: 308
Period size: 92 Copynumber: 2.0 Consensus size: 94
21522 GCGGTTTGTT
*
21532 CCAGTTTAAGCAGATCTCGAGCCCTGTTGGGAGACTCACCCACCATAACCAGGTGCGCGACGCGG
1 CCAGCTTAAGCAGATCTCGAGCCCTGTTGGGAGACTCACCCACCATAACCAGGTGCGCGACGCGG
21597 GTCGGATC-T-GGATTAGTCAGGGCAAAA
66 GTCGGATCGTCGGATTAGTCAGGGCAAAA
* *
21624 CCAGCTTAAGCAGGTCTCGAGCCCTGTTGGGAGACTCACCCACCATAACCAGGTGCGCGACGTGG
1 CCAGCTTAAGCAGATCTCGAGCCCTGTTGGGAGACTCACCCACCATAACCAGGTGCGCGACGCGG
21689 GTCGGATCGGATCCGGATTAGTCAGGGCAAA
66 GTCGGATC-G-T-CGGATTAGTCAGGGCAAA
21720 GTCTTGGATA
Statistics
Matches: 88, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
92 70 0.80
95 1 0.01
97 17 0.19
ACGTcount: A:0.24, C:0.28, G:0.30, T:0.18
Consensus pattern (94 bp):
CCAGCTTAAGCAGATCTCGAGCCCTGTTGGGAGACTCACCCACCATAACCAGGTGCGCGACGCGG
GTCGGATCGTCGGATTAGTCAGGGCAAAA
Found at i:21739 original size:22 final size:22
Alignment explanation
Indices: 21714--21758 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
21704 GATTAGTCAG
*
21714 GGCAAAGTCTTGGATACCGGAT
1 GGCAAAGCCTTGGATACCGGAT
21736 GGCAAAGCCTTGGATACCGGAT
1 GGCAAAGCCTTGGATACCGGAT
21758 G
1 G
21759 TGATAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.20
Consensus pattern (22 bp):
GGCAAAGCCTTGGATACCGGAT
Found at i:23322 original size:42 final size:42
Alignment explanation
Indices: 23276--23355 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
23266 TGTTGTTTCC
23276 TTTTATTAGGACCAATTAGCATATTCTTTTTGTATTTATGTT
1 TTTTATTAGGACCAATTAGCATATTCTTTTTGTATTTATGTT
* *
23318 TTTTATTAGGACCAATTAGCATGTTTTTTTTGTATTTA
1 TTTTATTAGGACCAATTAGCATATTCTTTTTGTATTTA
23356 CGTTAAATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (42 bp):
TTTTATTAGGACCAATTAGCATATTCTTTTTGTATTTATGTT
Found at i:25040 original size:21 final size:20
Alignment explanation
Indices: 25014--25055 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
25004 TGATCTCACA
*
25014 TAATAGAGCTTAGTTAGAGCT
1 TAATAGAGCTTAATT-GAGCT
25035 TAATAGAGCTTAATTGAGCT
1 TAATAGAGCTTAATTGAGCT
25055 T
1 T
25056 CAGGTAGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (20 bp):
TAATAGAGCTTAATTGAGCT
Found at i:25043 original size:10 final size:10
Alignment explanation
Indices: 25014--25055 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
25004 TGATCTCACA
25014 TAATAGAGCT
1 TAATAGAGCT
*
25024 TAGTTAGAGCT
1 TA-ATAGAGCT
25035 TAATAGAGCT
1 TAATAGAGCT
*
25045 TAATTGAGCT
1 TAATAGAGCT
25055 T
1 T
25056 CAGGTAGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (10 bp):
TAATAGAGCT
Found at i:40859 original size:60 final size:60
Alignment explanation
Indices: 40793--40955 Score: 197
Period size: 60 Copynumber: 2.7 Consensus size: 60
40783 ACTAATTGTT
* ** *
40793 CAAATAAGGGTCTAACGTTTGTCAAAATGTTCAAATAAGGGTTTGGTTTTTTAATTTGGC
1 CAAATAAGGGTCTAACGTTTGTCAAAATGCTCAAATAAGGGTCCGGTCTTTTAATTTGGC
* * *
40853 CAAATAAGGGTTTAACG-TTATCGAAAATGCTCAAATAAGGGCCCGGTCTTTTAATTTGGC
1 CAAATAAGGGTCTAACGTTTGTC-AAAATGCTCAAATAAGGGTCCGGTCTTTTAATTTGGC
* *
40913 TAAATAAGGGCCTAACGTTATAG--AAAATGCTCAAATAAGGGTC
1 CAAATAAGGGTCTAACGTT-T-GTCAAAATGCTCAAATAAGGGTC
40956 TGGCGTTGAA
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
59 4 0.05
60 81 0.93
61 1 0.01
62 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (60 bp):
CAAATAAGGGTCTAACGTTTGTCAAAATGCTCAAATAAGGGTCCGGTCTTTTAATTTGGC
Found at i:41010 original size:31 final size:31
Alignment explanation
Indices: 40975--41058 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 31
40965 AAATTCTCAC
* *
40975 ACGTTAGATCCTTATTTGAGCATTTTCGATA
1 ACGTTAGACCCTTATTTGAGCATTTTCGAAA
* * ** *
41006 ACGTTAGACCCTTGTTTAAATATTTTGGAAA
1 ACGTTAGACCCTTATTTGAGCATTTTCGAAA
* *
41037 ACGTTAGGCTCTTATTTGAGCA
1 ACGTTAGACCCTTATTTGAGCA
41059 ATTAGCCATT
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.39
Consensus pattern (31 bp):
ACGTTAGACCCTTATTTGAGCATTTTCGAAA
Found at i:42004 original size:179 final size:178
Alignment explanation
Indices: 41670--42006 Score: 532
Period size: 179 Copynumber: 1.9 Consensus size: 178
41660 GCTAAAGAAT
* *
41670 CCCATCAACTTTTAATGTGGAGAGACCTTATCGTCCCGTTTTGCTCTTTTCTCATGTGGTTGATT
1 CCCATCAACCTTTAATGTGGAGAGACCTTATCGTCCCGTTTTGCTCTTTTCTCACGTGGTTGATT
* ** * *
41735 ACTGAAATATCCCCTAAGTTTAATATGTTTTCTTCAGATCCATTGTCTTTGTGTGTAATTTGGCC
66 ACTGAAATATCCCATAAGCCTAACATGTTTTCTTCAGATCCATTGTCTTTGTGTGTAATTTGACC
41800 ATTGAATTCTAATAAGTGATGTTCCCACGGGAATTTACTAAAAGATCC
131 ATTGAATTCTAATAAGTGATGTTCCCACGGGAATTTACTAAAAGATCC
* * *
41848 CCCATCAACCTTTAATGTTGAGAGACCTTATCG-CCCTGTTTTGGTTTTTTCTCACGTGGTTGAT
1 CCCATCAACCTTTAATGTGGAGAGACCTTATCGTCCC-GTTTTGCTCTTTTCTCACGTGGTTGAT
*
41912 TAGTGAAATATCCTCATAAGCCTAACATGTTTTCTTCAGATCCATTGTCTTTGTGTGTAATTTGA
65 TACTGAAATATCC-CATAAGCCTAACATGTTTTCTTCAGATCCATTGTCTTTGTGTGTAATTTGA
* *
41977 CCATTGAGTTCTAATAAGTGTTGTTCCCAC
129 CCATTGAATTCTAATAAGTGATGTTCCCAC
42007 TATAATTTTT
Statistics
Matches: 144, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
177 3 0.02
178 67 0.47
179 74 0.51
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (178 bp):
CCCATCAACCTTTAATGTGGAGAGACCTTATCGTCCCGTTTTGCTCTTTTCTCACGTGGTTGATT
ACTGAAATATCCCATAAGCCTAACATGTTTTCTTCAGATCCATTGTCTTTGTGTGTAATTTGACC
ATTGAATTCTAATAAGTGATGTTCCCACGGGAATTTACTAAAAGATCC
Found at i:42287 original size:45 final size:45
Alignment explanation
Indices: 42238--42332 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
42228 AACAATCGTT
42238 AATATTAGTTTTATTTTGATAAATTACCTAGAGATGAAGGAGTAG
1 AATATTAGTTTTATTTTGATAAATTACCTAGAGATGAAGGAGTAG
* *
42283 AATATTAGTTTTATTTTGATGAATTACCTAGAGATGAGGGAGTAG
1 AATATTAGTTTTATTTTGATAAATTACCTAGAGATGAAGGAGTAG
*
42328 GATAT
1 AATAT
42333 AGGTAATGCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (45 bp):
AATATTAGTTTTATTTTGATAAATTACCTAGAGATGAAGGAGTAG
Found at i:43327 original size:23 final size:24
Alignment explanation
Indices: 43270--43327 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
43260 TATAGCACAC
43270 TTTTGGATATCTTAAGATTAAATTT
1 TTTTGG-TATCTTAAGATTAAATTT
* *
43295 TTTGGTGTATCTTAAG-TTCAATTT
1 TTTTG-GTATCTTAAGATTAAATTT
43319 TTTTGGTAT
1 TTTTGGTAT
43328 AACACACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.14
24 11 0.38
25 13 0.45
26 1 0.03
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.55
Consensus pattern (24 bp):
TTTTGGTATCTTAAGATTAAATTT
Found at i:60039 original size:2 final size:2
Alignment explanation
Indices: 60030--60068 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
60020 AAAAAGTGTC
60030 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60069 GTGCTTCCGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:61796 original size:11 final size:11
Alignment explanation
Indices: 61777--61811 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
61767 TTTTTCTGTT
61777 TTTTGTTTTTG
1 TTTTGTTTTTG
* *
61788 TTTTATTTTCG
1 TTTTGTTTTTG
61799 TTTTGTTTTTG
1 TTTTGTTTTTG
61810 TT
1 TT
61812 GCGCTGTCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.03, C:0.03, G:0.14, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:62380 original size:14 final size:14
Alignment explanation
Indices: 62361--62387 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
62351 TCCTTGCAAT
62361 ATCTTATATATATG
1 ATCTTATATATATG
62375 ATCTTATATATAT
1 ATCTTATATATAT
62388 TTGATACATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (14 bp):
ATCTTATATATATG
Done.