Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014981.1 Corchorus olitorius cultivar O-4 contig15014, 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: 110365
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--100 Score: 191
Period size: 2 Copynumber: 50.0 Consensus size: 2
*
1 TC TC TC TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
85 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
101 GGTAGTATTA
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 96 1.00
ACGTcount: A:0.00, C:0.49, G:0.01, T:0.50
Consensus pattern (2 bp):
TC
Found at i:10294 original size:16 final size:17
Alignment explanation
Indices: 10269--10302 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
10259 ACACAAACAT
*
10269 ATTTTCATTTGAA-AGC
1 ATTTTAATTTGAAGAGC
10285 ATTTTAATTTGAAGAGC
1 ATTTTAATTTGAAGAGC
10302 A
1 A
10303 AGATGAGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (17 bp):
ATTTTAATTTGAAGAGC
Found at i:11362 original size:2 final size:2
Alignment explanation
Indices: 11357--11390 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
11347 TTTCTAATCA
11357 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11391 CTAAATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:14594 original size:144 final size:140
Alignment explanation
Indices: 14338--14620 Score: 503
Period size: 144 Copynumber: 2.0 Consensus size: 140
14328 TAACAATTAT
14338 GATGAACGGGGACTTGGTTTGGGAATATGGATATAATTGCCTAACCTAGTTGTGAATCATAATGG
1 GATGAACGGGGACTTGGTTTGGGAATATGGATATAATTGCCTAACCTAGTTGTGAATCATAATGG
*
14403 AAAAGGAAAATCCAAGGCTATAATTAAATTTGATGATACCAACTTCTTGAAATTTTCTACTTATT
66 AAAAGGAAAATCCAAGGCTATAATTAAATTTGATGATACCAACTTCTTGAAATTTTCTACTTATG
14468 TACGCAACAG
131 TACGCAACAG
14478 GATGAACGGGGACTTGGTTTGGGAATATGGATATATATAATTGCCTAACCTAGTTGTGAATCATA
1 GATGAACGGGGACTTGGTTTGGGAATATGG----ATATAATTGCCTAACCTAGTTGTGAATCATA
*
14543 ATGGAAAAGGAAAATCCAAGGCTATAATTAGATTTGATGATACCAACTTCTTGAAATTTTCTACT
62 ATGGAAAAGGAAAATCCAAGGCTATAATTAAATTTGATGATACCAACTTCTTGAAATTTTCTACT
*
14608 TATGTACGTAACA
127 TATGTACGCAACA
14621 ACCTCCGTTG
Statistics
Matches: 136, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
140 30 0.22
144 106 0.78
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (140 bp):
GATGAACGGGGACTTGGTTTGGGAATATGGATATAATTGCCTAACCTAGTTGTGAATCATAATGG
AAAAGGAAAATCCAAGGCTATAATTAAATTTGATGATACCAACTTCTTGAAATTTTCTACTTATG
TACGCAACAG
Found at i:15518 original size:15 final size:16
Alignment explanation
Indices: 15493--15522 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15483 AATAATTATT
15493 TTTAGATTATAATATA
1 TTTAGATTATAATATA
15509 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
15523 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:16972 original size:314 final size:315
Alignment explanation
Indices: 15906--19497 Score: 881
Period size: 340 Copynumber: 10.9 Consensus size: 315
15896 ATTTAAAAAC
* * * *
15906 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATAAGAA
1 TTGTTTTTACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAA
* * ** * * *
15971 ATACGATATTAAAAGTGCAAAAAGCTCTCCAATCTTTTTGCCGTTGAATTATATATTTTT-ATGA
66 AAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTCATGA
* ** * * * * * *
16035 GTATT-TCAGCCAAAAATTGAGGAGAAATCTTTCGTGTCA-ATTTTCGCAAAATTTTAGCCGAAA
131 GTATTAT-GGATAAAAATTGAGGAAAAATATTTCGGGT-AGATTTTTGCAAAATATTAGCCAAAA
* *** * * * *
16098 TCGTGTAATAGAAACCATCATGGTTTTTTTTTTTTGCTAAAAACGTGTTGCAGGGACCC-GCCTC
194 TCGTG---T--AAA--ATCAT-G-CTCGGTTTTTGGCTAAAAACGCGTT-CCGGGACCCAG-GTC
* ** ** * * *
16162 AATTTTTTCATGATTTTTGGCTTCGAGACTACTTGAAATATCTATAT-TCATCTAATCAAATCTC
248 -AGTTTTGAATGATTTTTGGCACCGAGACTCCTTGAAATATCTATATAT-ATCTAACCAAATCCC
16226 AGCCACATTGGATTTAAGAA
311 AG-C-C-------------A
* * * * *
16246 TTTGTTTTTTCAAGCATCTAAATCTTGTTTTC-ATTTAGTTAGAAATTAATTCA-AAAAAATATG
1 -TTGTTTTTACAAGCATCTGAATCATG-TTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGG
*** * * * * *
16309 AAAAATTCTATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGACGTTAAATTATATATTTTT-AT
64 AAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTCAT
* * * * * * *
16373 GAGTATT-T-TATCCAAAAATTGAGCAAAATTTTTTTGCGTCA-TTTTTTGCAAAAT-TCTAGCC
129 GAGTATTATGGAT--AAAAATTGAGGAAAAATATTTCGGGT-AGATTTTTGCAAAATAT-TAGCC
* ** * ** * *
16434 AAAATCATGT-ACGTCA---T-GGTTTTTGGCT-AAAACGCGTTTCGGGGTCCTGTCTCAGTTTT
190 AAAATCGTGTAAAATCATGCTCGGTTTTTGGCTAAAAACGCGTTCCGGGACCCAG-GTCAGTTTT
* * * * * * **
16493 GCATTATTTTTGGCGCCTACATTCCTTGAAATATCTATAT-TCATCTAATAAAATCTTAGTCACA
254 GAATGATTTTTGGCACCGAGACTCCTTGAAATATCTATATAT-ATCTAACCAAATC-----C-CA
*
16557 TTGCATTTAAGGA
312 --GC-------CA
* * * *
16570 TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAATAAATATGA
1 -TTGTTTTTACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGA
* * *
16635 AAGACGATATTAAAAGCGTGAAAAGTCGTTCAATCTTTTT-GCGTTGAATTATATATTTTTCATG
65 AAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTCATG
* * *
16699 AGTATTATGGATAAAAATTGAGGAAATATCTTTCGGGTCA-ATTTTTGCAAAAT-TGTAGCCGAA
130 AGTATTATGGATAAAAATTGAGGAAAAATATTTCGGGT-AGATTTTTGCAAAATAT-TAGCCAAA
* * **
16762 ATCGTGTAATAATCAT-CTCGGTTTTTGGCTAAATATGCGTTCCGGGGTCC-GGTTCAGTTTTGA
193 ATCGTGTAA-AATCATGCTCGGTTTTTGGCTAAAAACGCGTTCCGGGACCCAGG-TCAGTTTTGA
* *
16825 ATGTTTTTTGGCACCGAGACTCTTTGAAATATCTATATATATCTAACCAAATCCCAGCCA
256 ATGATTTTTGGCACCGAGACTCCTTGAAATATCTATATATATCTAACCAAATCCCAGCCA
* * *
16885 TTGTTTTTACAAGCATCTGAATCATGTTTCGTTTTAATTAGAAATTTATTCGGAAAAAATAGGAA
1 TTGTTTTTACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAA
** *
16950 AAACGATATTCGAA-CAGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATG
66 AAACGATATTAAAAGC-GTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTCATG
* * * *
17014 GGTATTGTGGCTAAAAATTGAGGAAAAATATTTTGGGTAGATTTTTGCAAAATATTAGCCAAAAT
130 AGTATTATGGATAAAAATTGAGGAAAAATATTTCGGGTAGATTTTTGCAAAATATTAGCCAAAAT
* * *** *
17079 CGTGTAACATCATGGTTTTTTTTTTGGCTAAAAACGCGTTCCGGGACCCAGGTCAGTTTTGCATG
195 CGTGTAAAATCAT-GCTCGGTTTTTGGCTAAAAACGCGTTCCGGGACCCAGGTCAGTTTTGAATG
* * * * *
17144 ATTTTTGGCACCTAGACTCCTTGAAATATCTATAT-TCATCAAATCATATCTCAGCCACA
259 ATTTTTGGCACCGAGACTCCTTGAAATATCTATATAT-ATCTAACCAAATCCCAG-C-CA
**** * * * ** *
17203 TTGGATTTTTTTTTTGGCAATCAGCCA-CATTGGATTTAAGGATTTGTTTTTACAAACATCTAAA
1 TT-G---TTTTTACAAGC-ATCTG-AATCA-T-G-TTT--CGA-TT-TAATTA-GAA-AT-T-AA
** * **
17267 TCTTGTTTC-GATTTAATTA-GAAATTAATTCGGA-A--AAAGTAG-GAAAAACGATATTAGAAG
49 ------TTCAGA-AAAAATAGGAAA--AA--C-GATATTAAA--AGCG--TG-----A--A-AA-
* * * * * * **
17326 CGTAATAAACCCATCAATATTTTTGACGTTGAACTATATATTTTT-ATGAGTATTTTAGCCAAAA
89 -G-------CCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTCATGAGTATTATGGATAAAA
* * * * * * * * *
17390 ATTGAGGAAATATCTTTCCGATCA-ATTTTTGCAAAATTTTAGACGAAATCATATAATAATCAT-
146 ATTGAGGAAAAATATTTCGGGT-AGATTTTTGCAAAATATTAGCCAAAATCGTGTAA-AATCATG
* * * * * * * * * **
17453 CACCGTTTTTGGCTAAAAACGCATTTCAGGG-CCCAATGTTAGTTTTGCATGTTTTTTGGCGCTA
209 CTCGGTTTTTGGCTAAAAACGC-GTTCCGGGACCC-AGGTCAGTTTTGAATGATTTTTGGCACCG
* * * * *
17517 AGACTCCTTGAGATACCCATAT-TCATCTAATCAAATCTCAGCCACCTTACATTTAAGGAA
272 AGACTCCTTGAAATATCTATATAT-ATCTAACCAAA--TC--CCAGC---C---------A
* * ** * * *
17577 TTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAACTAATTCATAAAAAATATGAA
1 TTGTTTTTACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATA-GGA
* * * * * * *
17642 AAAACGATATGAAAAGCGTGAAAAGTCCTCCAAACTTTTTGGCATTAAATTATATATATTTCATG
65 AAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTCATG
* * * * ** * * *
17707 AGTATTTTAG-TCAAAAATTGAGGAAAAATTTTTCTGGTCATTTTTTTTGCAGAATTTTAGCCGA
130 AGTATTATGGAT-AAAAATTGAGGAAAAATATTTCGGGT-A-GATTTTTGCAAAATATTAGCCAA
* * ** * * * * *
17771 AATCGTGTACGTTAGTCGAAAT-CAAGATTTTTGGCTAAAAATGTGTTCCAGGGCCCCAGTTCAG
192 AATCGTGTA---AAATC---ATGCTCGGTTTTTGGCTAAAAACGCGTTCC-GGGACCCAGGTCAG
** * ***
17835 CGTT-ACATGATTTTTGGCACCGAGACTCCTTGAAATATTTATAT-TCATCTAACCAAATTTTAG
250 TTTTGA-ATGATTTTTGGCACCGAGACTCCTTGAAATATCTATATAT-ATCTAACCAAATCCCAG
*
17898 CTAGA
313 C--CA
* **
17903 TTGGATTTAGGGAGTTGTAAAATAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTTG
1 TT-G--TT------TT-T---ACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCA
* * * * *
17968 GAAAATAATAGGAAAAACGATATTAGAACCATGAAAAGCCCTTCAATTTTTTTGGTGTTGAATTA
53 GAAAA-AATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTA
* * *
18033 TATAATTTTT-ATGAGTATTGTGGCTAAAAATTGA-GAAATTAA-CTTT-GGAGTCA-ATTTTTG
117 TAT-ATTTTTCATGAGTATTATGGATAAAAATTGAGGAAA--AATATTTCGG-GT-AGATTTTTG
* * * * * * * *
18093 CAAACT-TCTAGTCGAAATCGTGTAATAACCAT-CACAGTTTTTGGCTAAAAACACGTTCTGGGG
177 CAAAATAT-TAGCCAAAATCGTGTAA-AATCATGCTCGGTTTTTGGCTAAAAACGCGTTC-CGGG
*** * * * * * ** * * * * * * * * * *
18156 GTTCGGGTAAATTTTGCATTATTTTTTCCGCCAAGAATCTTTGAGATATCCACATACATCAAATC
239 ACCCAGGTCAGTTTTGAATGATTTTTGGCACCGAGACTCCTTGAAATATCTATATATATCTAACC
**
18221 AAATCTTAGCTACATTGGATTTAAAA
304 AAATC----C--CA---G-----CCA
* * * * * ** *
18247 TTTTGTTTTTACGAGTATGTGAATCTTGTTTCGATTTAATTAAAAATTGCTTCAG--AAAATATG
1 --TTGTTTTTACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGG
* * * * *
18310 AAAAACGATATTAAAAGCATGAAAAGTCCTCCAATATTTTTGGCGTTAAATTATATATATTTT-A
64 AAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTCA
* * * * ** * * * * *
18374 TGAGTATTTTAGACAAAAATTGATGGAAAAATTTTTCAAGTCA-TTTTTTGTAAAATTTTTGCCG
128 TGAGTATTATGGATAAAAATTGA-GGAAAAATATTTCGGGT-AGATTTTTGCAAAATATTAGCCA
* * * * * * ** *
18438 AAATCGTGT---ACCAT-CACGGTTTTTGACTAAAAACGCATTTCGGGGTCCCATCTTAGTTTTG
191 AAATCGTGTAAAATCATGCTCGGTTTTTGGCTAAAAACGC-GTTCCGGGACCCAGGTCAGTTTTG
* * ** * * *
18499 CACGATTTTTGGTGCCGAGACTCCTTGAAATATTTATAT-TCATCTAATCAAATCTCATCCGCAT
255 AATGATTTTTGGCACCGAGACTCCTTGAAATATCTATATAT-ATCTAACCAAATC-C--CAGC--
18563 TAAATCTAAGGA
314 -----C-----A
* * * * *
18575 TTTCTTTTTTCGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCA-AAAAAATATGA
1 -TTGTTTTTACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGA
* * * * *
18639 AAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGCTTTTAATTATATATATTTT-AT
65 AAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTCAT
* * * * *
18703 GAGTATTGTGGTTAAAAATTGAGGAAAAATATTTCGCGTCA-ATTTTTGCAAAATTTTAGCCGAA
129 GAGTATTATGGATAAAAATTGAGGAAAAATATTTCGGGT-AGATTTTTGCAAAATATTAGCCAAA
** * * * * * * *
18767 ATCGTGTACCATCACGAT---TTTTTGGTTAAAAACGCGTTCCGGCACCCCGAGTCTGTTTTGCA
193 ATCGTGTAAAATCATGCTCGGTTTTTGGCTAAAAACGCGTTCCGGGACCCAG-GTCAGTTTTGAA
* * * * **
18829 TGATTTTCGATGGTA---AAACTCCTTGAAATATCTATATTTATTTAA--GGAT--------
257 TGATTTT---TGGCACCGAGACTCCTTGAAATATCTATATATATCTAACCAAATCCCAGCCA
* * * * * * *
18878 TTTTTTTTCCAAGCATTTGAATTATGTTTCGATTAAATTAGAAATTAATTTTA-ATAAAATAGAA
1 TTGTTTTTACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAA-TTCAGAAAAAATAG--
* * * * * * *
18942 AAAAAAAAACAAAATTAGAAGCGTGAGAAGCCCTTCAATCTTTATGGCATTGAATTATATATTTT
63 ---GAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTT
* * * * *
19007 T-ATGAGTATTGTGGCTAAAATTTGA-GTAAAATAATTT-GGGTCA-ATTTTTGCAAAATTTTAG
125 TCATGAGTATTATGGATAAAAATTGAGGAAAAAT-ATTTCGGGT-AGATTTTTGCAAAATATTAG
* * ** * * * *
19068 TCGAAATCGTGTATCATCATGAT---TCTTTGGCTAAAAATGCGTTCCGAGG-CCCTGGGTCAGT
188 CCAAAATCGTGTAAAATCATGCTCGGTTTTTGGCTAAAAACGCGTTCCG-GGACCC-AGGTCAGT
* ** * * * **
19129 TTTGCATGATTTTTGGCGTCAAGACTCCTTAAAATATATCTATAT-TCATCAAACCAAATTTCAG
251 TTTGAATGATTTTTGGCACCGAGACTCCTT-GAA-ATATCTATATAT-ATCTAACCAAATCCCAG
19193 CCACA
313 -C-CA
* * * * * *
19198 TTGTATTTA-AGGATTTGTTTTTACGAGTTTCGAAATCTTATTTCGATTTAATCATAAATTAATT
1 TTGTTTTTACA--A---G------C-A-TCT-G-AATCATGTTTCGATTTAATTAGAAATTAATT
** * * * * **
19262 TTGAAATAAAATAGGAAAAACGATATTAGAAGCGTGAAAAAGGCTTTCAATTTTTTTTACGTTGA
51 CAG-AA-AAAATAGGAAAAACGATATTAAAAGCGTG-AAAAGCCCTTCAATCTTTTTGGCGTTGA
* * * * * *
19327 ATTATATATTTTTTATGAGTATTATTGCTAGAAATCGAGGAAAAATCTTTCGGGTCA-ATTTTTG
113 ATTATATATTTTTCATGAGTATTATGGATAAAAATTGAGGAAAAATATTTCGGGT-AGATTTTTG
* * * * * * * * *
19391 CAAAAT-TCAGTCGAAATCGTGTACTAACCAT-CACAGTTTTTGGCTAAAAACACGTTTCGAGG-
177 CAAAATATTAGCCAAAATCGTGTA-AAATCATGCTCGGTTTTTGGCTAAAAACGCGTTCCG-GGA
* ** *
19453 CCC-GGCTCAGTTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAA
240 CCCAGG-TCAG-TTTTGAATGATTTTTGGCACCGAGACTCCTTGAA
19498 TATGTAACTT
Statistics
Matches: 2474, Mismatches: 518, Indels: 524
0.70 0.15 0.15
Matches are distributed among these distances:
302 41 0.02
303 13 0.01
306 98 0.04
307 35 0.01
308 62 0.03
310 2 0.00
313 1 0.00
314 96 0.04
315 86 0.03
316 84 0.03
317 3 0.00
318 4 0.00
319 2 0.00
320 6 0.00
321 2 0.00
322 9 0.00
323 10 0.00
324 126 0.05
325 115 0.05
326 18 0.01
327 179 0.07
328 148 0.06
329 8 0.00
330 153 0.06
331 76 0.03
332 141 0.06
333 115 0.05
334 57 0.02
335 39 0.02
336 66 0.03
337 31 0.01
338 7 0.00
339 124 0.05
340 203 0.08
341 51 0.02
342 6 0.00
343 5 0.00
344 4 0.00
345 1 0.00
346 2 0.00
349 3 0.00
350 4 0.00
351 2 0.00
352 14 0.01
353 1 0.00
354 4 0.00
358 2 0.00
359 21 0.01
360 119 0.05
361 40 0.02
362 6 0.00
363 3 0.00
364 4 0.00
365 2 0.00
366 3 0.00
367 1 0.00
368 2 0.00
369 3 0.00
370 7 0.00
373 1 0.00
374 3 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (315 bp):
TTGTTTTTACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAA
AAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTCATGA
GTATTATGGATAAAAATTGAGGAAAAATATTTCGGGTAGATTTTTGCAAAATATTAGCCAAAATC
GTGTAAAATCATGCTCGGTTTTTGGCTAAAAACGCGTTCCGGGACCCAGGTCAGTTTTGAATGAT
TTTTGGCACCGAGACTCCTTGAAATATCTATATATATCTAACCAAATCCCAGCCA
Found at i:17557 original size:360 final size:360
Alignment explanation
Indices: 16885--17561 Score: 846
Period size: 360 Copynumber: 1.9 Consensus size: 360
16875 ATCCCAGCCA
* * * *
16885 TTGTTTTTACAAGCATCTGAATCATGTTTCGTTTTAATTAGAAATTTATTCGGAAAAAATAGGAA
1 TTGTTTTTACAAACATCTAAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAA
* * * * * * *
16950 AAACGATATTCGAACAGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGG
66 AAACGATATTAGAACAGTGAAAAACCCATCAATATTTTTGACGTTGAACTATATATTTTTTATGA
* * ** * *
17015 GTATTGTGGCTAAAAATTGAGGAAAAATATTTTGGGTAGATTTTTGCAAAATATTAGCCAAAATC
131 GTATTGTAGCCAAAAATTGAGGAAAAATATTTCCGATAGATTTTTGCAAAATATTAGACAAAATC
* * * ***** *
17080 GTGTAACATCATGGTTTTTTTTTTGGCTAAAAACGCGTTCCGGGACCCAGGTCAGTTTTGCATGA
196 ATATAAAATCAT-GCACCGTTTTTGGCTAAAAACGCGTTCAGGGACCCAGGTCAGTTTTGCATGA
* * *
17145 TTTTTGGCACCTAGACTCCTTGAAATATCTATATTCATCAAATCATATCTCAGCCACATTGGATT
260 TTTTTGGCACCTAGACTCCTTGAAATACCCATATTCATCAAATCAAATCTCAGCCACATTGGATT
17210 TTTTTTTTGGCAATCAGCCACATTGGATTTAAGGAT
325 TTTTTTTTGGCAATCAGCCACATTGGATTTAAGGAT
* *
17246 TTGTTTTTACAAACATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAGTAGGAA
1 TTGTTTTTACAAACATCTAAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAA
17311 AAACGATATTAGAAGC-GT-AATAAACCCATCAATATTTTTGACGTTGAACTATATA-TTTTTAT
66 AAACGATATTAGAA-CAGTGAA-AAACCCATCAATATTTTTGACGTTGAACTATATATTTTTTAT
* * * * *
17373 GAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCCGATCA-ATTTTTGCAAAATTTTAGACGAA
129 GAGTATTGTAGCCAAAAATTGAGGAAAAATATTTCCGAT-AGATTTTTGCAAAATATTAGACAAA
* * *
17437 ATCATATAATAATCAT-CACCGTTTTTGGCTAAAAACGCATTTCAGGG-CCCAATGTTAGTTTTG
193 ATCATATAA-AATCATGCACCGTTTTTGGCTAAAAACGC-GTTCAGGGACCC-AGGTCAGTTTTG
* * * *
17500 CATGTTTTTTGGC-GCTAAGACTCCTTGAGATACCCATATTCATCTAATCAAATCTCAGCCAC
255 CATGATTTTTGGCACCT-AGACTCCTTGAAATACCCATATTCATCAAATCAAATCTCAGCCAC
17562 CTTACATTTA
Statistics
Matches: 266, Mismatches: 43, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
359 22 0.08
360 134 0.50
361 109 0.41
362 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (360 bp):
TTGTTTTTACAAACATCTAAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAA
AAACGATATTAGAACAGTGAAAAACCCATCAATATTTTTGACGTTGAACTATATATTTTTTATGA
GTATTGTAGCCAAAAATTGAGGAAAAATATTTCCGATAGATTTTTGCAAAATATTAGACAAAATC
ATATAAAATCATGCACCGTTTTTGGCTAAAAACGCGTTCAGGGACCCAGGTCAGTTTTGCATGAT
TTTTGGCACCTAGACTCCTTGAAATACCCATATTCATCAAATCAAATCTCAGCCACATTGGATTT
TTTTTTTGGCAATCAGCCACATTGGATTTAAGGAT
Found at i:18613 original size:327 final size:326
Alignment explanation
Indices: 17223--19497 Score: 1457
Period size: 327 Copynumber: 6.9 Consensus size: 326
17213 TTTTTGGCAA
* * * * *
17223 TCAGCCACATTGGATTTAAGGATTTGTTTTTACAAACATCTAAATCTTGTTTCGATTTAATTAGA
1 TCAGCCACATTAGATTTAAGGATTTGTTTTTTCGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* * * **
17288 AATTAATTCGGAAAAAGTAGGAAAAACGATATTAGAAGCGT-AATAAACCCAT-CAATATTTTTG
66 AATTAATTCAG-AAAA-TATGAAAAACGATATTAAAAGCGTGAA-AAGTCC-TCCAATATTTTTG
* * * * *
17351 ACGTTGAACTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCCGA-TCA
127 GCGTTAAATTATATATATTTTATGAGTATTTTAGTCAAAAATTGAGGAAAAATCTTT-CGAGTCA
* * * * *
17414 ATTTTTGCAAAATTTTAGACGAAATCATATAATAATCATCACCGTTTTTGGCTAAAAACGCATTT
191 ATTTTTGCAAAATTTTAGCCGAAATC--GT-GT-ACCATCACGGTTTTTGGCTAAAAACGCATTT
* * * *
17479 CAGGG-CCCAATGTTAGTTTTGCATGTTTTTTGGCGCTAAGACTCCTTGAGATACCCATATTCAT
252 CAGGGTCCC-ATGTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCCATATTCAT
17543 CTAATCAAATC
316 CTAATCAAATC
* * * * * *
17554 TCAGCCACCTTACATTTAAGGAATTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTAATTAGA
1 TCAGCCACATTAGATTTAAGGATTTGTTTTTTCGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* * *
17619 AACTAATTCATAAAAAATATGAAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAA-ACTTTTTG
66 AATTAATTC--AGAAAATATG-AAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATA-TTTTTG
* * *
17683 GCATTAAATTATATATATTTCATGAGTATTTTAGTCAAAAATTGAGGAAAAATTTTTCTG-GTCA
127 GCGTTAAATTATATATATTTTATGAGTATTTTAGTCAAAAATTGAGGAAAAATCTTTC-GAGTCA
* * * *
17747 TTTTTTTTGCAGAATTTTAGCCGAAATCGTGTACGTTAGTCGAAATCAAGATTTTTGGCTAAAAA
191 --ATTTTTGCAAAATTTTAGCCGAAATCGTGTAC------C---ATCACGGTTTTTGGCTAAAAA
* ** * * ** * * * **
17812 TGTGTTCCAGGGCCCCA-GTTCAGCGTTACATGATTTTTGGCACCGAGACTCCTTGAAATATTTA
245 CGCATTTCAGGGTCCCATGTT-AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCCA
* *
17876 TATTCATCTAACCAAATT
309 TATTCATCTAATCAAATC
* * * * * * **** * *
17894 TTAGCTAGATTGGATTTAGGGAGTTGTAAAAT-AAGCATCTGAATCATGTTTCGATTTAATTAGA
1 TCAGCCACATTAGATTTAAGGATTTGTTTTTTCGAGCATCTGAATCTTGTTTCGATTTAATTAGA
** * * * * * *
17958 AATTAATTTGGAAAATAATAGGAAAAACGATATTAGAACCATGAAAAGCCCTTCAATTTTTTTGG
66 AATTAATTCAGAAAAT-AT--GAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGG
* * * * *
18023 TGTTGAATTATATA-ATTTTTATGAGTATTGT-GGCTAAAAATTGA-GAAATTAA-CTTTGGAGT
128 CGTTAAATTATATATA-TTTTATGAGTATTTTAGTC-AAAAATTGAGGAAA--AATCTTTCGAGT
* * * * * *
18084 CAATTTTTGCAAACTTCTAGTCGAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAACACGT
189 CAATTTTTGCAAAATTTTAGCCGAAATCGTG---T-ACCATCACGGTTTTTGGCTAAAAACGCAT
** * ** * * * ** * * * * *
18149 TCTGGGGGT-TCGGGTAAATTTTGCATTATTTTTTCCGCCAAGAATCTTTGAGATATCCACATAC
250 T-TCAGGGTCCCATGTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCCATATTC
*
18213 ATCAAATCAAATC
314 ATCTAATCAAATC
* * * * * * * *
18226 TTAGCTACATTGGATTTAA-AATTTTGTTTTTACGAGTATGTGAATCTTGTTTCGATTTAATTAA
1 TCAGCCACATTAGATTTAAGGA-TTTGTTTTTTCGAGCATCTGAATCTTGTTTCGATTTAATTAG
** *
18290 AAATTGCTTCAGAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATATTTTTGGCG
65 AAATTAATTCAGAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGCG
* * * *
18355 TTAAATTATATATATTTTATGAGTATTTTAGACAAAAATTGATGGAAAAATTTTTCAAGTCATTT
130 TTAAATTATATATATTTTATGAGTATTTTAGTCAAAAATTGA-GGAAAAATCTTTCGAGTCAATT
* * * *
18420 TTTGTAAAATTTTTGCCGAAATCGTGTACCATCACGGTTTTTGACTAAAAACGCATTTCGGGGTC
194 TTTGCAAAATTTTAGCCGAAATCGTGTACCATCACGGTTTTTGGCTAAAAACGCATTTCAGGGTC
* * * * **
18485 CCATCTTAGTTTTGCACGATTTTTGGTGCCGAGACTCCTTGAAATATTTATATTCATCTAATCAA
259 CCATGTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCCATATTCATCTAATCAA
18550 ATC
324 ATC
* * * * *
18553 TCATCCGCATTAAATCTAAGGATTTCTTTTTTCGAGCATCTGAATCTTGTTTCGATTTAATTAGA
1 TCAGCCACATTAGATTTAAGGATTTGTTTTTTCGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* *
18618 AATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGCT
66 AATTAATTC-AGAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGCG
* * * * * *
18683 TTTAATTATATATATTTTATGAGTATTGTGGTTAAAAATTGAGGAAAAATATTTCGCGTCAATTT
130 TTAAATTATATATATTTTATGAGTATTTTAGTCAAAAATTGAGGAAAAATCTTTCGAGTCAATTT
* * * * **
18748 TTGCAAAATTTTAGCCGAAATCGTGTACCATCACGATTTTTTGGTTAAAAACGC-GTTCCGGCAC
195 TTGCAAAATTTTAGCCGAAATCGTGTACCATCACG-GTTTTTGGCTAAAAACGCATTTCAGG-GT
* ** ** *
18812 CCCGA-GTCT-GTTTTGCATGATTTTCGATGGTAAAACTCCTTG----A---A-A-T-ATCT-AT
258 CCC-ATGT-TAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCCATATTCATCTAAT
18864 ---A--
321 CAAATC
* * * * ** *
18865 T--------TT--ATTTAAGGATTTTTTTTTCCAAGCATTTGAATTATGTTTCGATTAAATTAGA
1 TCAGCCACATTAGATTTAAGGATTTGTTTTTTCGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* * * * * * * * *
18920 AATTAATTTTAATAAAATA-GAAAAAAAAAAACAAAATTAGAAGCGTGAGAAGCCCTTCAATCTT
66 AATTAA--TTCAGAAAATATG------AAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATT
* * * * * * * *
18984 TATGGCATTGAATTATATAT-TTTTATGAGTATTGT-GGCTAAAATTTGA-GTAAAATAATTT-G
123 TTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGTC-AAAAATTGAGGAAAAAT-CTTTCG
* * * * * * *
19045 GGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTATCATCATGATTCTTTGGCTAAAAATGC-G
186 AGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCATCACGGTT-TTTGGCTAAAAACGCAT
* * * * *
19109 TTCCGAGG-CCC-TGGGTCAGTTTTGCATGATTTTTGGCGTCAAGACTCCTTAAAATATATCTAT
250 TTCAG-GGTCCCAT--GTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT-GAA-ATATCCAT
* * *
19172 ATTCATCAAACCAAATT
310 ATTCATCTAATCAAATC
* ** * *
19189 TCAGCCACATT-GTATTTAAGGATTTGTTTTTACGAGTTTC-GAAATCTTATTTCGATTTAATCA
1 TCAGCCACATTAG-ATTTAAGGATTTGTTTTTTCGAGCATCTG-AATCTTGTTTCGATTTAATTA
* * * * * * * * *
19252 TAAATTAATTTTGAAATAAAATAGGAAAAACGATATTAGAAGCGTGAAAAAGGCTTTCAATTTTT
64 GAAATTAA--TT--CAGAAAATATGAAAAACGATATTAAAAGCGTG-AAAAGTCCTCCAATATTT
** * * * * *
19317 TTTACGTTGAATTATATATTTTTTATGAGTATTATT-G-CTAGAAATCGAGGAAAAATCTTTCGG
124 TTGGCGTTAAATTATATATATTTTATGAGTATT-TTAGTC-AAAAATTGAGGAAAAATCTTTCGA
* * * *
19380 GTCAATTTTTGCAAAA-TTCAGTCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACAC
187 GTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---T-ACCATCACGGTTTTTGGCTAAAAACGC
* * * *
19444 GTTTC-GAGG-CCC-GGCTCAGTTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAA
248 ATTTCAG-GGTCCCATG-TTAG-TTTTGCATGATTTTTGGCGCCAAGACTCCTTGAA
19498 TATGTAACTT
Statistics
Matches: 1524, Mismatches: 309, Indels: 218
0.74 0.15 0.11
Matches are distributed among these distances:
302 51 0.03
303 7 0.00
304 4 0.00
305 5 0.00
306 95 0.06
307 28 0.02
308 48 0.03
312 2 0.00
314 1 0.00
315 1 0.00
316 1 0.00
317 3 0.00
318 7 0.00
319 2 0.00
320 1 0.00
321 1 0.00
322 1 0.00
324 2 0.00
326 6 0.00
327 188 0.12
328 136 0.09
329 2 0.00
330 76 0.05
331 126 0.08
332 171 0.11
333 127 0.08
334 75 0.05
335 30 0.02
336 59 0.04
337 42 0.03
338 10 0.01
339 113 0.07
340 98 0.06
341 5 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (326 bp):
TCAGCCACATTAGATTTAAGGATTTGTTTTTTCGAGCATCTGAATCTTGTTTCGATTTAATTAGA
AATTAATTCAGAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGCGT
TAAATTATATATATTTTATGAGTATTTTAGTCAAAAATTGAGGAAAAATCTTTCGAGTCAATTTT
TGCAAAATTTTAGCCGAAATCGTGTACCATCACGGTTTTTGGCTAAAAACGCATTTCAGGGTCCC
ATGTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCCATATTCATCTAATCAAAT
C
Found at i:24933 original size:22 final size:22
Alignment explanation
Indices: 24908--24996 Score: 101
Period size: 23 Copynumber: 4.0 Consensus size: 22
24898 AGTAATCACA
* *
24908 CTATGAAATTGTGAT-AACCTC
1 CTATAAAATTTTGATAAACCTC
* *
24929 GCTATGAAATTTTGATAAACATTC
1 -CTATAAAATTTTGATAAAC-CTC
24953 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAACCT-C
24976 CTATAAAATTTTGAT-AACCTC
1 CTATAAAATTTTGATAAACCTC
24997 ATGAAATCTT
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
21 1 0.02
22 20 0.33
23 37 0.62
24 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
CTATAAAATTTTGATAAACCTC
Found at i:25057 original size:20 final size:20
Alignment explanation
Indices: 25019--25057 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25009 TAACAACAAA
*
25019 TTTTGATAACCTCCCTATGT
1 TTTTGATAACCTCACTATGT
* *
25039 TTTTTATAACCTCATTATG
1 TTTTGATAACCTCACTATG
25058 AAATTTTGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.21, G:0.08, T:0.49
Consensus pattern (20 bp):
TTTTGATAACCTCACTATGT
Found at i:25127 original size:22 final size:21
Alignment explanation
Indices: 24908--25261 Score: 125
Period size: 22 Copynumber: 16.9 Consensus size: 21
24898 AGTAATCACA
* *
24908 CTATGAAATTGTGATAACCTCG
1 CTATGAAATTTTGATAACC-CT
**
24930 CTATGAAATTTTGATAAACATT
1 CTATGAAATTTTGAT-AACCCT
* *
24952 CCTATAAAATTTTGATAAACCTCC
1 -CTATGAAATTTTGAT-AACC-CT
*
24976 CTATAAAATTTTGATAA-CCT
1 CTATGAAATTTTGATAACCCT
*
24996 C-ATGAAATCTTGATAA----
1 CTATGAAATTTTGATAACCCT
** *
25012 C-AACAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAACC-CT
* *
25033 CTATG--TTTTTTATAA-CCT
1 CTATGAAATTTTGATAACCCT
*
25051 CATTATGAAATTTTGTTAATCTCC-
1 C--TATGAAATTTTGATAA-C-CCT
* *
25075 CTATGAAATTTTGATCTA-CAT
1 CTATGAAATTTTGAT-AACCCT
*
25096 ACTATAAAATTTTGATAACCCT
1 -CTATGAAATTTTGATAACCCT
* ***
25118 CTTATGAAATTTTGAAAACTAAA
1 C-TATGAAATTTTGATAAC-CCT
*
25141 CTATGAAATTTTGATAACCTT
1 CTATGAAATTTTGATAACCCT
* *
25162 CATATGAAATTTTAAT-ATCCT
1 C-TATGAAATTTTGATAACCCT
* *
25183 C-CTGAAATTTTGATTACTCCAT
1 CTATGAAATTTTGATAAC-CC-T
* * * * *
25205 -AATAAAAGTTTAATAACCTT
1 CTATGAAATTTTGATAACCCT
*
25225 CT-T--AA-TTTGATAACCAT
1 CTATGAAATTTTGATAACCCT
25242 ACTATGAAATTTTGATAACC
1 -CTATGAAATTTTGATAACC
25262 TCCCCAGAAA
Statistics
Matches: 247, Mismatches: 52, Indels: 66
0.68 0.14 0.18
Matches are distributed among these distances:
16 13 0.05
17 10 0.04
18 6 0.02
19 26 0.11
20 18 0.07
21 14 0.06
22 119 0.48
23 38 0.15
24 1 0.00
25 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCCT
Found at i:25331 original size:21 final size:22
Alignment explanation
Indices: 25302--25514 Score: 100
Period size: 22 Copynumber: 9.8 Consensus size: 22
25292 GATCACATTT
*
25302 TGAAAATTTGATAACCTCTATA
1 TGAAATTTTGATAACCTCTATA
25324 TGAAATTTTGAT-ACCTCTATA
1 TGAAATTTTGATAACCTCTATA
* * * *
25345 --AAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTATA
* *
25365 TGAAATTTTGATAATCAC-ATTA
1 TGAAATTTTGATAACCTCTA-TA
* * ** *
25387 TGTAATTTTGATAACTTCGCTT
1 TGAAATTTTGATAACCTCTATA
* **
25409 TGAAATTTTGAT-ATCAATACTA
1 TGAAATTTTGATAACCTCTA-TA
* *
25431 TGAAATTTTGATAATCT-TCCTA
1 TGAAATTTTGATAACCTCT-ATA
* *
25453 T-AAATTTTGATAATCTGATCTCTA
1 TGAAATTTTGATAA-C--CTCTATA
* * * *
25477 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTATA
*
25499 TGAGA-TTTGATAACCT
1 TGAAATTTTGATAACCT
25515 TCTACCAAAT
Statistics
Matches: 143, Mismatches: 35, Indels: 27
0.70 0.17 0.13
Matches are distributed among these distances:
19 9 0.06
20 7 0.05
21 30 0.21
22 77 0.54
23 3 0.02
24 5 0.03
25 12 0.08
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTATA
Found at i:25413 original size:44 final size:44
Alignment explanation
Indices: 25362--25467 Score: 139
Period size: 44 Copynumber: 2.4 Consensus size: 44
25352 GTTGACCCCT
*
25362 CTATGAAATTTTGATAATCACAT-TATGTAATTTTGATAA-CTTC
1 CTATGAAATTTTGATAATCA-ATATATGAAATTTTGATAATCTTC
*
25405 GCTTTGAAATTTTGAT-ATCAATACTATGAAATTTTGATAATCTTC
1 -CTATGAAATTTTGATAATCAATA-TATGAAATTTTGATAATCTTC
25450 CTAT-AAATTTTGATAATC
1 CTATGAAATTTTGATAATC
25468 TGATCTCTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
42 2 0.04
43 14 0.25
44 35 0.64
45 4 0.07
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.44
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCAATATATGAAATTTTGATAATCTTC
Found at i:25580 original size:22 final size:21
Alignment explanation
Indices: 25551--25712 Score: 87
Period size: 22 Copynumber: 7.4 Consensus size: 21
25541 AAATTGAGAC
25551 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* * **
25572 TTTTGATAATCACACTAAAAAA
1 TTTTGATAACCTCA-TATGAAA
*
25594 TTTTGATAACCACACTATGAAA
1 TTTTGATAACCTCA-TATGAAA
* **
25616 TTTTAATAACCTCCCCATGAAA
1 TTTTGATAACCT-CATATGAAA
* *
25638 TATT-AGTAACCTCCTTATGAAA
1 TTTTGA-TAACCT-CATATGAAA
* * *
25660 GTTTGTTAACCACACTATGAAA
1 TTTTGATAACCTCA-TATGAAA
* *
25682 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-ATATGAAA
25704 TTTTGATAA
1 TTTTGATAA
25713 TCTCTTTGAT
Statistics
Matches: 108, Mismatches: 24, Indels: 17
0.72 0.16 0.11
Matches are distributed among these distances:
21 10 0.09
22 95 0.88
23 3 0.03
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.36
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:25636 original size:66 final size:66
Alignment explanation
Indices: 25551--25930 Score: 254
Period size: 66 Copynumber: 5.6 Consensus size: 66
25541 AAATTGAGAC
* * * *
25551 TTTT-ATAACCTTCATATGAAATTTTGATAATCACACTAAAAAATTTTGATAACCACACTATGAA
1 TTTTAATAACCTCCCTATGAAATTTTGATAACCACACTATAAAATTTTGATAACCACACTATGAA
25615 A
66 A
* * * * * *
25616 TTTTAATAACCTCCCCATGAAATATT-AGTAACCTC-CTTATGAAAGTTTGTTAACCACACTATG
1 TTTTAATAACCTCCCTATGAAATTTTGA-TAACCACAC-TATAAAATTTTGATAACCACACTATG
25679 AAA
64 AAA
* * * *
25682 TTCTT-ATAACCTCGCTATGACATTTTGATAATCTCTTTGATAACCTTTCTATAAAATTGTGATA
1 TT-TTAATAACCTCCCTATGAAATTTTGATAA-C-C-------A-C--ACTATAAAATTTTGATA
25746 ACCACACTATGAAA
53 ACCACACTATGAAA
* * * * * * *
25760 TTTCAATAACCTTCCTAAGAAATTTTAATAACCTGATC-CTATGAAATTTTGATAACCTTC-CCA
1 TTTTAATAACCTCCCTATGAAATTTTGATAACC--A-CACTATAAAATTTTGATAACC-ACACTA
25823 TGAAA
62 TGAAA
* * * * * *
25828 TTTTGATAACTTCCATATGAAATTTTGGTAACCACACTATAGAATTTTGATAACCTC-CTCATGA
1 TTTTAATAACCTCCCTATGAAATTTTGATAACCACACTATAAAATTTTGATAACCACACT-ATGA
25892 AA
65 AA
* *
25894 TTATAATAACCATCTC-ATGAAATTTTGATAACCACAC
1 TTTTAATAACC-TCCCTATGAAATTTTGATAACCACAC
25931 AGAGACAAGA
Statistics
Matches: 244, Mismatches: 48, Indels: 45
0.72 0.14 0.13
Matches are distributed among these distances:
65 10 0.04
66 121 0.50
67 6 0.02
68 50 0.20
69 1 0.00
71 3 0.01
76 2 0.01
77 2 0.01
78 48 0.20
79 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (66 bp):
TTTTAATAACCTCCCTATGAAATTTTGATAACCACACTATAAAATTTTGATAACCACACTATGAA
A
Found at i:25701 original size:44 final size:42
Alignment explanation
Indices: 25551--25930 Score: 196
Period size: 44 Copynumber: 8.8 Consensus size: 42
25541 AAATTGAGAC
* * **
25551 TTTTATAACCTTCATATGAAATTTTGATAATCACACTAAAAAA
1 TTTTATAACC-TCCTATGAAATTTTGATAACCACACTATGAAA
* * * * *
25594 TTTTGATAACCACACTATGAAATTTTAATAACCTCCCCATGAAA
1 TTTT-ATAACCTC-CTATGAAATTTTGATAACCACACTATGAAA
* * *
25638 TATTAGTAACCTCCTTATGAAAGTTTGTTAACCACACTATGAAA
1 TTTTA-TAACCTCC-TATGAAATTTTGATAACCACACTATGAAA
* * *
25682 TTCTTATAACCTCGCTATGACATTTTGAT----A-A-TCT---C
1 TT-TTATAACCTC-CTATGAAATTTTGATAACCACACTATGAAA
* * * *
25717 TTTGATAACCTTTCTATAAAATTGTGATAACCACACTATGAAA
1 TTTTATAACC-TCCTATGAAATTTTGATAACCACACTATGAAA
* * *
25760 TTTCAATAACCTTCCTAAGAAATTTTAATAACCTGATC-CTATGAAA
1 TTT-TATAACC-TCCTATGAAATTTTGATAACC--A-CACTATGAAA
*
25806 TTTTGATAACCTTCCCATGAAATTTTGATAACTTC-CA-TATGAAA
1 TTTT-ATAACC-TCCTATGAAATTTTGATAAC--CACACTATGAAA
* * *
25850 TTTTGGTAACCACACTAT-AGAATTTTGATAACCTC-CTCATGAAA
1 TTTT-ATAACCTC-CTATGA-AATTTTGATAACCACACT-ATGAAA
*
25894 TTATAATAACCAT-CTCATGAAATTTTGATAACCACAC
1 TT-TTATAACC-TCCT-ATGAAATTTTGATAACCACAC
25931 AGAGACAAGA
Statistics
Matches: 256, Mismatches: 47, Indels: 66
0.69 0.13 0.18
Matches are distributed among these distances:
34 19 0.07
35 3 0.01
38 3 0.01
39 2 0.01
40 3 0.01
42 1 0.00
43 16 0.06
44 164 0.64
45 7 0.03
46 36 0.14
47 1 0.00
48 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (42 bp):
TTTTATAACCTCCTATGAAATTTTGATAACCACACTATGAAA
Found at i:25816 original size:46 final size:43
Alignment explanation
Indices: 25752--25860 Score: 128
Period size: 46 Copynumber: 2.4 Consensus size: 43
25742 GATAACCACA
** *
25752 CTATGAAATTTCAATAACCTTCCTAAGAAATTTTAATAACCTGATC
1 CTATGAAATTTTGATAACCTTCCCAAGAAATTTTAATAA-CT--TC
* *
25798 CTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACTTC
1 CTATGAAATTTTGATAACCTTCCCAAGAAATTTTAATAACTTC
*
25841 CATATGAAATTTTGGTAACC
1 C-TATGAAATTTTGATAACC
25861 ACACTATAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
43 3 0.05
44 17 0.30
45 2 0.04
46 34 0.61
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCTTCCCAAGAAATTTTAATAACTTC
Found at i:25828 original size:22 final size:22
Alignment explanation
Indices: 25717--25926 Score: 180
Period size: 22 Copynumber: 9.5 Consensus size: 22
25707 TGATAATCTC
* *
25717 TTTGATAACCTTTCTATAAAAT
1 TTTGATAACCTTCCTATGAAAT
* *
25739 TGTGATAACC-ACACTATGAAAT
1 TTTGATAACCTTC-CTATGAAAT
** *
25761 TTCAATAACCTTCCTAAGAAAT
1 TTTGATAACCTTCCTATGAAAT
*
25783 TTTAATAACCTGATCCTATGAAAT
1 TTTGATAACCT--TCCTATGAAAT
*
25807 TTTGATAACCTTCCCATGAAAT
1 TTTGATAACCTTCCTATGAAAT
25829 TTTGATAA-CTTCCATATGAAAT
1 TTTGATAACCTTCC-TATGAAAT
* *
25851 TTTGGTAACC-ACACTAT-AGAAT
1 TTTGATAACCTTC-CTATGA-AAT
25873 TTTGATAACC-TCCTCATGAAAT
1 TTTGATAACCTTCCT-ATGAAAT
* * *
25895 TATAATAACCAT-CTCATGAAAT
1 TTTGATAACCTTCCT-ATGAAAT
25917 TTTGATAACC
1 TTTGATAACC
25927 ACACAGAGAC
Statistics
Matches: 155, Mismatches: 22, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
21 8 0.05
22 122 0.79
23 5 0.03
24 20 0.13
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.36
Consensus pattern (22 bp):
TTTGATAACCTTCCTATGAAAT
Found at i:27797 original size:16 final size:16
Alignment explanation
Indices: 27772--27802 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27762 GTCATTTATT
27772 TTTTTAAAAAAAATTC
1 TTTTTAAAAAAAATTC
*
27788 TTTTTCAAAAAAATT
1 TTTTTAAAAAAAATT
27803 TACCCTAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTTTAAAAAAAATTC
Found at i:30976 original size:35 final size:35
Alignment explanation
Indices: 30930--30999 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
30920 CCTACAAGGA
30930 GTCTCAAATTTTAACCACTTAGGAGTCTCAAGTTT
1 GTCTCAAATTTTAACCACTTAGGAGTCTCAAGTTT
30965 GTCTCAAATTTTAACCACTTAGGAGTCTCAAGTTT
1 GTCTCAAATTTTAACCACTTAGGAGTCTCAAGTTT
31000 TAACCACTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (35 bp):
GTCTCAAATTTTAACCACTTAGGAGTCTCAAGTTT
Found at i:31405 original size:31 final size:31
Alignment explanation
Indices: 31370--31464 Score: 109
Period size: 31 Copynumber: 3.1 Consensus size: 31
31360 ACAGTGTCCG
* * *
31370 ACGTGGCATACCATATGTATCAAAAAGTGAC
1 ACGTGGCACACCACATGTACCAAAAAGTGAC
* * *
31401 ACGTGGCACGCCACATGTGCCAAAGAGTGAC
1 ACGTGGCACACCACATGTACCAAAAAGTGAC
* * *
31432 ACGTGTCGCACCACGTGTACCAAAAAGTGAC
1 ACGTGGCACACCACATGTACCAAAAAGTGAC
31463 AC
1 AC
31465 CACATGTCAT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (31 bp):
ACGTGGCACACCACATGTACCAAAAAGTGAC
Found at i:32842 original size:24 final size:24
Alignment explanation
Indices: 32815--32863 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
32805 GATTTCCATG
32815 TCCGAGATTTGAGAGGGATTATGA
1 TCCGAGATTTGAGAGGGATTATGA
32839 TCCGAGATTTGAGAGGGATTATGA
1 TCCGAGATTTGAGAGGGATTATGA
32863 T
1 T
32864 GAATGGGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.08, G:0.33, T:0.31
Consensus pattern (24 bp):
TCCGAGATTTGAGAGGGATTATGA
Found at i:34078 original size:18 final size:18
Alignment explanation
Indices: 34055--34094 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
34045 AATCTTTTCC
34055 TAATTTCCTTGCATCCAG
1 TAATTTCCTTGCATCCAG
34073 TAATTTCCTTGCATCCAG
1 TAATTTCCTTGCATCCAG
34091 TAAT
1 TAAT
34095 GGTTTGAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (18 bp):
TAATTTCCTTGCATCCAG
Found at i:34586 original size:29 final size:29
Alignment explanation
Indices: 34526--34604 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
34516 GCTTAAATAC
* *
34526 CAAAAAAATCCCTTAGCTTTTTCATTTGGA
1 CAAATAAATCCCTTAGCTTTTTCA-TGGGA
*
34556 CAAATAAATCCCTTATCTTTTTTC-TGGGA
1 CAAATAAATCCCTTAGC-TTTTTCATGGGA
* *
34585 CAAATAAATCCTTTTGCTTT
1 CAAATAAATCCCTTAGCTTT
34605 CAAAAATGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
28 3 0.07
29 18 0.43
30 15 0.36
31 6 0.14
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (29 bp):
CAAATAAATCCCTTAGCTTTTTCATGGGA
Found at i:39729 original size:71 final size:72
Alignment explanation
Indices: 39638--39771 Score: 200
Period size: 71 Copynumber: 1.9 Consensus size: 72
39628 TAATCAAAAA
* * *
39638 TCTCATCGCAATTATATATCTTTATATACTCAAACAATTCGATGAGAAATCA-AAAACACAAATC
1 TCTCATCGCAATCATATATCTCTATATACTCAAACAATTCAATGAGAAATCACAAAACACAAATC
39702 TTTGAAG
66 TTTGAAG
* *
39709 TCTCAT-GACAATCATATATCTCTGTATACTCAAACAATTCAATGAGAAATCACAAAATACAAA
1 TCTCATCG-CAATCATATATCTCTATATACTCAAACAATTCAATGAGAAATCACAAAACACAAA
39772 CTACCTTATG
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
70 1 0.02
71 46 0.82
72 9 0.16
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.29
Consensus pattern (72 bp):
TCTCATCGCAATCATATATCTCTATATACTCAAACAATTCAATGAGAAATCACAAAACACAAATC
TTTGAAG
Found at i:55553 original size:38 final size:38
Alignment explanation
Indices: 55506--55664 Score: 219
Period size: 38 Copynumber: 3.9 Consensus size: 38
55496 TTGATTCGTT
55506 AAAGTCTTCTCAACAAATGCGCTCTGAATTTGTAGTTA
1 AAAGTCTTCTCAACAAATGCGCTCTGAATTTGTAGTTA
55544 AAAGTCTTCTCAACAAATGCGCTCTGAATTTGTAGTTA
1 AAAGTCTTCTCAACAAATGCGCTCTGAATTTGTAGTTA
55582 AAAGTCTTCTCAACAAATACGCTACAAATGCGCTCTGAATTTGTAGTTA
1 AAAGTCTTCT---C----A----ACAAATGCGCTCTGAATTTGTAGTTA
55631 AAAGTCTTCTCAACAAATGCGCTCTGAATTTGTA
1 AAAGTCTTCTCAACAAATGCGCTCTGAATTTGTA
55665 CTCTGAATTT
Statistics
Matches: 110, Mismatches: 0, Indels: 22
0.83 0.00 0.17
Matches are distributed among these distances:
38 70 0.64
41 1 0.01
42 1 0.01
45 1 0.01
46 1 0.01
49 36 0.33
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (38 bp):
AAAGTCTTCTCAACAAATGCGCTCTGAATTTGTAGTTA
Found at i:55628 original size:49 final size:49
Alignment explanation
Indices: 55556--55653 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
55546 AGTCTTCTCA
55556 ACAAATGCGCTCTGAATTTGTAGTTAAAAGTCTTCTCAACAAATACGCT
1 ACAAATGCGCTCTGAATTTGTAGTTAAAAGTCTTCTCAACAAATACGCT
*
55605 ACAAATGCGCTCTGAATTTGTAGTTAAAAGTCTTCTCAACAAATGCGCT
1 ACAAATGCGCTCTGAATTTGTAGTTAAAAGTCTTCTCAACAAATACGCT
55654 CTGAATTTGT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (49 bp):
ACAAATGCGCTCTGAATTTGTAGTTAAAAGTCTTCTCAACAAATACGCT
Found at i:55670 original size:13 final size:13
Alignment explanation
Indices: 55652--55677 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55642 AACAAATGCG
55652 CTCTGAATTTGTA
1 CTCTGAATTTGTA
55665 CTCTGAATTTGTA
1 CTCTGAATTTGTA
55678 ATCTCGCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
CTCTGAATTTGTA
Found at i:57792 original size:2 final size:2
Alignment explanation
Indices: 57785--57811 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57775 TGATATGGAT
57785 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
57812 TGCGTTTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61093 original size:103 final size:103
Alignment explanation
Indices: 60914--61121 Score: 353
Period size: 103 Copynumber: 2.0 Consensus size: 103
60904 TTTTTATTTG
* *
60914 TTTGTTTAATTTGTTGTTAGTGTATGTATAGTAATTTCTTAGTTTAAGTTGAATTCTCATAAGAT
1 TTTGTTTAATTTGTAGTTAGTGTATGTATAGTAATATCTTAGTTTAAGTTGAATTCTCATAAGAT
60979 GTTTGACATATAAGGAAATAATCTGATTGTAATGAGAT
66 GTTTGACATATAAGGAAATAATCTGATTGTAATGAGAT
* *
61017 TTTGTTTAATTTGTAGTTGGTGTATGTATAGTAATATCTTAGTTTAGGTTGAATTCTCATAAGAT
1 TTTGTTTAATTTGTAGTTAGTGTATGTATAGTAATATCTTAGTTTAAGTTGAATTCTCATAAGAT
* * *
61082 GTTTGGCATATAAGTAAATATTCTGATTGTAATGAGAT
66 GTTTGACATATAAGGAAATAATCTGATTGTAATGAGAT
61120 TT
1 TT
61122 CATTGTACCA
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.46
Consensus pattern (103 bp):
TTTGTTTAATTTGTAGTTAGTGTATGTATAGTAATATCTTAGTTTAAGTTGAATTCTCATAAGAT
GTTTGACATATAAGGAAATAATCTGATTGTAATGAGAT
Found at i:61814 original size:31 final size:31
Alignment explanation
Indices: 61766--61825 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
61756 CCATGATGTG
61766 GCAACTCACACAGGTGCTCCCCGGAGCACGT
1 GCAACTCACACAGGTGCTCCCCGGAGCACGT
* *
61797 GCAACTCGCAC-GAGTGCTCCCCTGAGCAC
1 GCAACTCACACAG-GTGCTCCCCGGAGCAC
61826 ATGACCAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.22, C:0.40, G:0.25, T:0.13
Consensus pattern (31 bp):
GCAACTCACACAGGTGCTCCCCGGAGCACGT
Found at i:63498 original size:20 final size:20
Alignment explanation
Indices: 63461--63498 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
63451 TGATTGATAC
*
63461 TATTGATTAGTAGTAGAATT
1 TATTGATGAGTAGTAGAATT
63481 TATTGATGA-TAGTCAGAA
1 TATTGATGAGTAGT-AGAA
63499 ATTCAAGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.39
Consensus pattern (20 bp):
TATTGATGAGTAGTAGAATT
Found at i:70627 original size:13 final size:12
Alignment explanation
Indices: 70609--70642 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
70599 TAATTTTCCC
70609 TTTTTTTTTCTAT
1 TTTTTTTTTC-AT
70622 TTTTTTTTTCAT
1 TTTTTTTTTCAT
70634 TTTTTTTTT
1 TTTTTTTTT
70643 GTTTAAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTCAT
Found at i:76862 original size:21 final size:21
Alignment explanation
Indices: 76826--76884 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
76816 TCTAACCCTA
* *
76826 AAATAATGCCCGTAGCAAATGT
1 AAATAA-GCTCGTAGCAAACGT
*
76848 AAATAAGCTCGTAGCAACCGT
1 AAATAAGCTCGTAGCAAACGT
*
76869 ACATAAGCTCGTAGCA
1 AAATAAGCTCGTAGCA
76885 TATAGGAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
21 27 0.82
22 6 0.18
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (21 bp):
AAATAAGCTCGTAGCAAACGT
Found at i:83282 original size:40 final size:40
Alignment explanation
Indices: 83226--83318 Score: 127
Period size: 40 Copynumber: 2.3 Consensus size: 40
83216 CATATTTATA
* *
83226 ATTA-GGGGCTAAACCTGGATTTAATTT-TTTACCTTAATT
1 ATTAGGGGGTTAAACCTGAATTTAATTTATTT-CCTTAATT
*
83265 ATTAGGGGGTTAAACCTGAATTTAATTTATTTTCTTAATT
1 ATTAGGGGGTTAAACCTGAATTTAATTTATTTCCTTAATT
83305 ATTAGGAGGGTTAA
1 ATTAGG-GGGTTAA
83319 GTTGGAGGGA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
39 4 0.08
40 34 0.71
41 10 0.21
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (40 bp):
ATTAGGGGGTTAAACCTGAATTTAATTTATTTCCTTAATT
Found at i:94988 original size:2 final size:2
Alignment explanation
Indices: 94981--95039 Score: 65
Period size: 2 Copynumber: 31.5 Consensus size: 2
94971 ACTTGATACA
*
94981 AT AT AT AT A- AT A- AT AT A- AT AT AT AT AT AT AT AT AT AC ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
95021 AT AT AT A- AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
95040 CTAAATATTA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
1 5 0.10
2 43 0.88
3 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:95002 original size:17 final size:17
Alignment explanation
Indices: 94980--95039 Score: 77
Period size: 17 Copynumber: 3.4 Consensus size: 17
94970 AACTTGATAC
94980 AATATATATAATAATAT
1 AATATATATAATAATAT
94997 AATATATATATATATATAT
1 AATATATATA-ATA-ATAT
95016 ACACTATATATAAT-ATAT
1 A-A-TATATATAATAATAT
95034 AATATA
1 AATATA
95040 CTAAATATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.10
17 11 0.28
18 8 0.21
19 5 0.13
20 3 0.08
21 8 0.21
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATATATAATAATAT
Found at i:95040 original size:23 final size:21
Alignment explanation
Indices: 94981--95039 Score: 72
Period size: 19 Copynumber: 2.9 Consensus size: 21
94971 ACTTGATACA
94981 ATATAT-ATA-ATAATATAAT
1 ATATATAATATATAATATAAT
95000 ATATAT-ATATAT-ATATACACT
1 ATATATAATATATAATATA-A-T
95021 ATATATAATATATAATATA
1 ATATATAATATATAATATA
95040 CTAAATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 14 0.40
20 3 0.09
21 7 0.20
22 6 0.17
23 5 0.14
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATATAATATATAATATAAT
Found at i:95047 original size:23 final size:22
Alignment explanation
Indices: 94980--95047 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 22
94970 AACTTGATAC
*
94980 AATATATATA-ATAATATAATA
1 AATATATATATATAATATACTA
* *
95001 TATATATATATAT-ATACACTA
1 AATATATATATATAATATACTA
*
95022 TATATA-ATATATAATATACTA
1 AATATATATATATAATATACTA
95043 AATAT
1 AATAT
95048 TATTTGAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 6 0.15
21 32 0.80
22 2 0.05
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (22 bp):
AATATATATATATAATATACTA
Found at i:100870 original size:50 final size:49
Alignment explanation
Indices: 100790--100892 Score: 179
Period size: 50 Copynumber: 2.1 Consensus size: 49
100780 TTTTGTTTAA
100790 TTTCCTCCAATAATTCAATTTTCACAACTTATTCTATAGTACTCTATAC
1 TTTCCTCCAATAATTCAATTTTCACAACTTATTCTATAGTACTCTATAC
* *
100839 TTTCCTCCAAATAATTCAATTTTCTCGACTTATTCTATAGTACTCTATAC
1 TTTCCTCC-AATAATTCAATTTTCACAACTTATTCTATAGTACTCTATAC
100889 TTTC
1 TTTC
100893 TTTACCTGCT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 8 0.16
50 43 0.84
ACGTcount: A:0.28, C:0.24, G:0.03, T:0.45
Consensus pattern (49 bp):
TTTCCTCCAATAATTCAATTTTCACAACTTATTCTATAGTACTCTATAC
Found at i:101104 original size:3 final size:3
Alignment explanation
Indices: 101096--101155 Score: 104
Period size: 3 Copynumber: 20.0 Consensus size: 3
101086 TTCTTTTAAA
101096 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
101144 GT-T TAT TAT TAT
1 -TAT TAT TAT TAT
101156 GTAAATTTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 1 0.02
3 53 0.96
4 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:101246 original size:28 final size:27
Alignment explanation
Indices: 101190--101246 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
101180 TATTTAGATA
* * **
101190 TAAATGAAGAATTTGTTTAGTATTTGT
1 TAAATAAAGAAATTGTTTAGTACATGT
101217 TAAATAAAGAAATTGTTTATGTACATGT
1 TAAATAAAGAAATTGTTTA-GTACATGT
101245 TA
1 TA
101247 GTAATTTCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.44
Consensus pattern (27 bp):
TAAATAAAGAAATTGTTTAGTACATGT
Found at i:105698 original size:21 final size:21
Alignment explanation
Indices: 105672--105712 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
105662 CAAAAGTTTC
105672 CTAGCTACTAAGAAATACATT
1 CTAGCTACTAAGAAATACATT
105693 CTAGCTACTAAGAAATACAT
1 CTAGCTACTAAGAAATACAT
105713 ACCCTCCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (21 bp):
CTAGCTACTAAGAAATACATT
Done.