Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021116.1 Corchorus olitorius cultivar O-4 contig21149, 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: 14564
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:407 original size:28 final size:29
Alignment explanation
Indices: 366--426 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
356 ACTTGTAGTG
* * *
366 TTTGGACGTTTTG-CCCTTAAACTTCAAT
1 TTTGGACATGTTGCCCCATAAACTTCAAT
394 TTTGGACATGTTGCCCCATAAACTTCAAT
1 TTTGGACATGTTGCCCCATAAACTTCAAT
423 TTTG
1 TTTG
427 TGACGTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (29 bp):
TTTGGACATGTTGCCCCATAAACTTCAAT
Found at i:3549 original size:15 final size:16
Alignment explanation
Indices: 3524--3553 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3514 AATAATTATT
3524 TTTAGATTATAATATA
1 TTTAGATTATAATATA
3540 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
3554 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:3708 original size:15 final size:15
Alignment explanation
Indices: 3688--3718 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3678 GGAATACTTT
3688 TTTATATAATTTAAA
1 TTTATATAATTTAAA
3703 TTTATATAATTTAAA
1 TTTATATAATTTAAA
3718 T
1 T
3719 AAATTATGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATATAATTTAAA
Found at i:5215 original size:331 final size:328
Alignment explanation
Indices: 4509--7007 Score: 1396
Period size: 320 Copynumber: 7.5 Consensus size: 328
4499 ATACTTTACA
* * *
4509 TCATCTAACCAAATCTCAGCAACATTGGATTTAAAATTTTGTTTTTACGAGTATCTGAATCTTAT
1 TCATCTAATCAAATCTCAGCAACATTGGATTTAAAA-TTTGTTTTTACGAGCATCTGAATCTTGT
* *
4574 TTCAATTTAATTAGAAATTAATTTAGAAAAAATAAGAAATACGATATTAAAAGCGTAAAAGCC-C
65 TTCAATTTAATTAGAAATTAATTT-GAAAAAATATGAAAAACGATATTAAAAGCGTAAAAGCCTC
** * *
4638 TCCAATCTTTTTGGCGTTGAATT-TATATTTTTATGAGTATTTT-AGTCAAAAATTAAGGAGAAA
129 T-CAATCTTTTTGGCGTTGAATTATATA-TTTTATGAGTATTTTAAAAC-AAAATTGAGGAAAAA
* * * *
4701 TCTTCCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGAACTAACAAACCATCATGGTTTTT
191 TCTTTCGAGTCAATTTTTGCAAAATTTTAGCCAAAATCGTG---TAACAAACCATCACGGTTTTT
* * * * *
4766 GGCTAAAAATGCGTTC-CGAGGACCCGGCTC-GATTTTGCATGATTTTTGGCTCCGAGACTACTT
253 GGCTAAAAAAGCGTTCTAGA-GCCCCGGCTCAG-TTTTGCATGATTTTTGGCCCCGAGACTCCTT
4829 GAAATATCTATAT
316 GAAATATCTATAT
*
4842 TCATCTAATCAAATCTTAGCCAA-ATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTG
1 TCATCTAATCAAATCTCAG-CAACATTGGATTTAAA-ATTTGTTTTTACGAGCATCTGAATCTTG
* * * *
4906 TTTCGATTTAATTAGAAATTAATTTGGAAAAAAATACGAAAAACGATATTGAAA-CATCAAAA-C
64 TTTCAATTTAATTAGAAATTAATTT-G-AAAAAATATGAAAAACGATATTAAAAGCGT-AAAAGC
* *
4969 CTCTTAAATTTTTTTGGCGTTGAATTATATATTCTTATGAGTATTTTAAAACAAAATTGA-GAAA
126 CTC-TCAATCTTTTTGGCGTTGAATTATATATT-TTATGAGTATTTTAAAACAAAATTGAGGAAA
* **
5033 ATATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAAC-AACCGTCACACTTTTT
189 A-ATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAACAAACCATCACGGTTTTT
* * * *
5097 GGCTAAAAAAGCATTCTAGAGCCCCGGTTCAGTTTTGCATGATTTTTTGCCCCAAGACTCCTTGA
253 GGCTAAAAAAGCGTTCTAGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCCCCGAGACTCCTTGA
* *
5162 GATATCCATAT
318 AATATCTATAT
* *
5173 TCATCCAATCAAATCTCAGCAACATTGGATTTAAGAATTTGTTTTTACAAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCAACATTGGATTTAA-AATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * *
5238 TTC--GTTAATTAGAATTTAA-TTCAGAAAATATGAAAAAATGATATTAAAAGCGTGAAAAGTCC
65 TTCAATTTAATTAGAAATTAATTTGAAAAAATATG-AAAAACGATATTAAAAGCGT-AAAAG-CC
* * * *
5300 TC-CAATCTTTTCGGCGTTAAATTATATA-TTTATGAGGATTTTATATA-AAAATTGAGGAAAAA
127 TCTCAATCTTTTTGGCGTTGAATTATATATTTTATGAGTATTTTA-AAACAAAATTGAGGAAAAA
* * * * * * *
5362 TTTTTCGGGTCATTTTTTGTAAAATTTTAGCCATAATCGTG-GACTAAA-CATTACGGTTTTTGG
191 TCTTTCGAGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAAC-AAACCATCACGGTTTTTGG
* * * * * * * *
5425 CTAAAAACGTGTT-TAAGGGCCCTGACTCAGTTTTGCATGATTTTTGGCGCTGACACTCCTTGAA
255 CTAAAAAAGCGTTCT-AGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCCCCGAGACTCCTTGAA
*
5489 ATATTTATAT
319 ATATCTATAT
* * * * * * **
5499 TCATAATATAATAAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTAAGAGCATAAGAATCT
1 TC---ATCTAATCAAATCTCAGCAACATTGGATTTAA-AATTTGTTTTTACGAGCATCTGAATCT
* * *
5564 TGTTTCAATTTAATTAGAAATTAATTCTGAAAAGATATGAAAAACGATATAAAAAGTGTGAAAAG
62 TGTTTCAATTTAATTAGAAATTAATT-TGAAAAAATATGAAAAACGATATTAAAAGCGT-AAAAG
* * *
5629 CC-CTTCAATCTTTTTGGCATTGAATTATATATATATATATATATATGTATATATATATATATAT
125 CCTC-TCAATCTTTTTGGCGTTGAA-T-TATATAT-T-T-TAT-GA-GTAT-T-T-TA-A-A-AC
** * * *
5693 ATTATGAGTATT-ATGGCGAAAAA---TT-GAGGAAATATCTTT-CAGGTCAATTTTTGCAAAAT
176 A--A--A--ATTGA--G-GAAAAATCTTTCGAGTCAAT-T-TTTGCA---AAATTTTAGCCAAA-
* * ** * * * *
5752 TTTAGTCGAGACTCGTCTAA-TAATCATCATAGTTTTTGGCTAAAAACGAGTTC-AGGGGCCCGG
226 ---A-TC--G--T-G--TAACAAACCATCACGGTTTTTGGCTAAAAAAGCGTTCTAGAGCCCCGG
* * * * *
5815 -TACAATTTTGAATGATTTTTTGCACCGACACTCCTTGAAATATCTATAT
280 CT-CAGTTTTGCATGATTTTTGGCCCCGAGACTCCTTGAAATATCTATAT
* * * *
5864 TCATATAACCAAATCTCAGC--C------------A-TTGTTTTTACAAGCATCTGAATCATGTT
1 TCATCTAATCAAATCTCAGCAACATTGGATTTAAAATTTGTTTTTACGAGCATCTGAATCTTGTT
** * *
5914 TCGTTTTAATTAGAAATTAATTCGTAAAAAATAGGAAAAACGATATTAGTTAGAAGCGTGAAAAG
66 TCAATTTAATTAGAAATTAATTTG-AAAAAATATGAAAAACGATATTA---A-AAGCGT-AAAAG
* **** * *
5979 CC-CTTAAATCTTTTTGGCGTTGAATTATATAATTTTCTATGAGTATTATGGCTA-AAAATTTAA
125 CCTC-TCAATCTTTTTGGCGTTGAATTATAT-A-TTT-TATGAGTATT-TTAAAACAAAATTGAG
* * * * * ****
6042 GAAAAATATTTCGGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTAAC--ATCA-CTTTTTT
185 GAAAAATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAACAAACCATC-ACGGT
* * * * * * * ** * * * *
6104 TTTTTGCTTAAAACGTGTTTTGGGGCCTTGGGTCAGTTTTGCATAATTTTTGGCGCCAAGACTCC
249 TTTTGGCTAAAAAAGCGTTCTAGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCCCCGAGACTCC
*
6169 TTGAAATATATATAT
314 TTGAAATATCTATAT
* * *
6184 TCATCTAATCAAATCTCAGCCACATGGGATTTAAGGATTTG--TTT------A----AATCTTGT
1 TCATCTAATCAAATCTCAGCAACATTGGATTTAA-AATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
6237 TTCAATTTAATTAGAAATTAATTCAT-AAAAAGTAGGAAAAACGATATTAGAAGCGTAAAAACC-
65 TTCAATTTAATTAGAAATTAATT--TGAAAAAATATGAAAAACGATATTAAAAGCGTAAAAGCCT
* * **
6300 CTTCAATATTTTTGGCGTTGAATTATATATCTTTTATGATTATTTTAGCTA-AAAATTGAGGAAA
128 C-TCAATCTTTTTGGCGTTGAATTATATA--TTTTATGAGTATTTTA-AAACAAAATTGAGGAAA
* * * * * * *
6364 TATCCTTCTG-GTCATTTTTTTTGCAAAATTTTAGCCGAAATCGTAT-ACTAACCAACACGGTTT
189 AATCTTTC-GAGTCA--ATTTTTGCAAAATTTTAGCCAAAATCGTGTAACAAACCATCACGGTTT
* * * * * * * * *
6427 TT-GATAAAAACGCGTT-TCGGGGCTCCGGCTTAATTTTGCATGATTTTTGACGCCGAGACTCCT
251 TTGGCTAAAAAAGCGTTCT-AGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCCCCGAGACTCCT
6490 TGAAATATCTATAT
315 TGAAATATCTATAT
** * * * ** * *
6504 TCATCTAATCAAATCTCAGTGACATTGAATTCAAGGATTAATTTTTACGAGCATATTAATCTCTT
1 TCATCTAATCAAATCTCAGCAACATTGGATTTAA-AATTTGTTTTTACGAGCATCTGAA--TCTT
* * * *
6569 GTTTCGATTTAATTAAAAATTAA-TTCAGAAAAATATGAAAAACGATATTAAAAGCATGAAAAGT
63 GTTTCAATTTAATTAGAAATTAATTTGA-AAAAATATGAAAAACGATATTAAAAGCGT-AAAAG-
* **
6633 CCTC-CAATCTTTTTGGCATTGAATTATATATATATATAT-A-TATATTATGAGTACTTTGGTTA
125 CCTCTCAATCTTTTTGGCGTTGAATTATATAT-T-T-TATGAGTAT-TT-T-AAAAC--------
* * * * *
6695 AAAATTGAGAAAAAATATTTCGGGTCAACTTTTACAAAATTTTAGCC-AAATC--GT---AAACC
176 AAAATTGAGGAAAAATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAACAAACC
* * * * * * * *
6754 ATCATGGTGTTTTAGCTAAAAATGCGTT-TCG-GACCCCATG-TCAGTTTTGTATGATTTTTTGT
241 ATCACGGT-TTTTGGCTAAAAAAGCGTTCTAGAG-CCCC-GGCTCAGTTTTGCATGATTTTTGGC
**** * *
6816 GGAAAAACTCCTTCAAATATCTATAT
303 CCCGAGACTCCTTGAAATATCTATAT
* * * * * * * * *
6842 TCATCTAACCAAATATTAACCACATTGGATTTAAGGATTTGTTTTTATGAGCATTTGAATCATGT
1 TCATCTAATCAAATCTCAGCAACATTGGATTTAA-AATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * *
6907 TTCGATTTAATTAAAAATTAATTTGAAAAAAAAATAGGAAGAACGATATTAGAAGC-------CC
65 TTCAATTTAATTAGAAATTAATTTG---AAAAAATATGAAAAACGATATTAAAAGCGTAAAAGCC
6965 T-TCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATT
127 TCTCAATCTTTTTGGCGTTGAATTATATA--TTTTATGAGTATT
7008 GTGGCTAAAA
Statistics
Matches: 1719, Mismatches: 279, Indels: 339
0.74 0.12 0.15
Matches are distributed among these distances:
317 1 0.00
318 34 0.02
319 61 0.04
320 193 0.11
321 9 0.01
322 6 0.00
323 1 0.00
324 50 0.03
325 4 0.00
326 136 0.08
327 26 0.02
328 33 0.02
329 73 0.04
330 39 0.02
331 152 0.09
332 68 0.04
333 123 0.07
334 129 0.08
335 79 0.05
336 40 0.02
337 14 0.01
338 95 0.06
339 40 0.02
340 5 0.00
341 7 0.00
342 18 0.01
343 5 0.00
344 21 0.01
345 5 0.00
346 68 0.04
347 2 0.00
348 10 0.01
349 4 0.00
350 39 0.02
351 5 0.00
352 6 0.00
353 1 0.00
354 16 0.01
358 1 0.00
359 2 0.00
360 1 0.00
361 1 0.00
362 16 0.01
363 1 0.00
364 2 0.00
365 52 0.03
366 24 0.01
367 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Consensus pattern (328 bp):
TCATCTAATCAAATCTCAGCAACATTGGATTTAAAATTTGTTTTTACGAGCATCTGAATCTTGTT
TCAATTTAATTAGAAATTAATTTGAAAAAATATGAAAAACGATATTAAAAGCGTAAAAGCCTCTC
AATCTTTTTGGCGTTGAATTATATATTTTATGAGTATTTTAAAACAAAATTGAGGAAAAATCTTT
CGAGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAACAAACCATCACGGTTTTTGGCTAAAA
AAGCGTTCTAGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCCCCGAGACTCCTTGAAATATCTA
TAT
Found at i:5485 original size:326 final size:324
Alignment explanation
Indices: 4509--5660 Score: 1153
Period size: 331 Copynumber: 3.5 Consensus size: 324
4499 ATACTTTACA
* * * *
4509 TCATCTAACCAAATCTCAGCAACATTGGATTTAAAATTTTGTTTTTACGAGTATCTGAATCTTAT
1 TCATCTAATCAAATCTCAGCAACATTGGATTTAAAA-TTTGTTTTTACAAGCATCTGAATCTTGT
* *
4574 TTCAATTTAATTAGAAATTAATTTAG-AAAAAATAAGAAATACGATATTAAAAGCGT-AAAAGCC
65 TTC-AGTTAATTAGAAATTAATTCAGAAAAAAATAA-AAA-ACGATATTAAAAGCGTGAAAAGCC
* * * * *
4637 CTCCAATCTTTTTGGCGTTGAATTTATATTTTTATGAGTATTTTAGT-CAAAAATTAAGGAGAAA
127 CTCCAATCTTTTTGGCGTT-AAATTATATATTTATGAGTATTTTA-TAAAAAAATTGAGGAAAAA
* * *
4701 TCTTCCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGAACTAACAAACCATCATGGTTTTT
190 TCTTTCGAGTCAATTTTTGCAAAATTTTAGCC-AAATCGTGAACT---AAA-CATCACGGTTTTT
* * * * *
4766 GGCTAAAAATGCGTTCCGAGGACCCGGCTC-GATTTTGCATGATTTTTGGCTCCGAGACTACTTG
250 GGCTAAAAAAGCGTT-CTAGGGCCCGGCTCAG-TTTTGCATGATTTTTGGCCCCGAGACTCCTTG
4830 AAATATCTATAT
313 AAATATCTATAT
* *
4842 TCATCTAATCAAATCTTAGCCAA-ATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTG
1 TCATCTAATCAAATCTCAG-CAACATTGGATTTAAA-ATTTGTTTTTACAAGCATCTGAATCTTG
* ** * * *
4906 TTTCGATTTAATTAGAAATTAATTTGGAAAAAAATACGAAAAACGATATTGAAA-CATCAAAA-C
64 TTTC-AGTTAATTAGAAATTAATTCAGAAAAAAATA--AAAAACGATATTAAAAGCGTGAAAAGC
** * *
4969 CTCTTAAATTTTTTTGGCGTTGAATTATATATTCTTATGAGTATTTTA-AAACAAAATTGA-GAA
126 C-CTCCAATCTTTTTGGCGTTAAATTATATA-T-TTATGAGTATTTTATAAA-AAAATTGAGGAA
* * **
5032 AATATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAAC-AACCGTCACACTTTT
187 AA-ATCTTTCGAGTCAATTTTTGCAAAATTTTAGCC-AAATCGTG-AACTAAACATCACGGTTTT
* * * * *
5096 TGGCTAAAAAAGCATTCTAGAGCCCCGGTTCAGTTTTGCATGATTTTTTGCCCCAAGACTCCTTG
249 TGGCTAAAAAAGCGTTCTAG-GGCCCGGCTCAGTTTTGCATGATTTTTGGCCCCGAGACTCCTTG
* *
5161 AGATATCCATAT
313 AAATATCTATAT
*
5173 TCATCCAATCAAATCTCAGCAACATTGGATTTAAGAATTTGTTTTTACAAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCAACATTGGATTTAA-AATTTGTTTTTACAAGCATCTGAATCTTGT
* * * *
5238 TTC-GTTAATTAGAATTTAATTCAG-AAAATATGAAAAAATGATATTAAAAGCGTGAAAAGTCCT
65 TTCAGTTAATTAGAAATTAATTCAGAAAAAAAT-AAAAAACGATATTAAAAGCGTGAAAAGCCCT
* * * *
5301 CCAATCTTTTCGGCGTTAAATTATATATTTATGAGGATTTTATATAAAAATTGAGGAAAAATTTT
129 CCAATCTTTTTGGCGTTAAATTATATATTTATGAGTATTTTATAAAAAAATTGAGGAAAAATCTT
* * * * *
5366 TCGGGTCATTTTTTGTAAAATTTTAGCCATAATCGTGGACTAAACATTACGGTTTTTGGCTAAAA
194 TCGAGTCAATTTTTGCAAAATTTTAGCCA-AATCGTGAACTAAACATCACGGTTTTTGGCTAAAA
* * * * * * *
5431 ACGTGTT-TAAGGGCCCTGACTCAGTTTTGCATGATTTTTGGCGCTGACACTCCTTGAAATATTT
258 AAGCGTTCT-AGGGCCC-GGCTCAGTTTTGCATGATTTTTGGCCCCGAGACTCCTTGAAATATCT
5495 ATAT
321 ATAT
* * * * * **
5499 TCATAATATAATAAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTA-AGAGCATAAGAATC
1 TC---ATCTAATCAAATCTCAGCAACATTGGATTTAA-AATTTGTTTTTACA-AGCATCTGAATC
* * * * * *
5563 TTGTTTCAATTTAATTAGAAATTAATTCTGAAAAGATATGAAAAACGATATAAAAAGTGTGAAAA
61 TTGTTTC-AGTTAATTAGAAATTAATTCAGAAAA-AAATAAAAAACGATATTAAAAGCGTGAAAA
* * *
5628 GCCCTTCAATCTTTTTGGCATTGAATTATATAT
124 GCCCTCCAATCTTTTTGGCGTTAAATTATATAT
5661 ATATATATAT
Statistics
Matches: 685, Mismatches: 100, Indels: 69
0.80 0.12 0.08
Matches are distributed among these distances:
325 8 0.01
326 125 0.18
327 22 0.03
328 37 0.05
329 75 0.11
330 6 0.01
331 145 0.21
332 57 0.08
333 94 0.14
334 49 0.07
335 63 0.09
336 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (324 bp):
TCATCTAATCAAATCTCAGCAACATTGGATTTAAAATTTGTTTTTACAAGCATCTGAATCTTGTT
TCAGTTAATTAGAAATTAATTCAGAAAAAAATAAAAAACGATATTAAAAGCGTGAAAAGCCCTCC
AATCTTTTTGGCGTTAAATTATATATTTATGAGTATTTTATAAAAAAATTGAGGAAAAATCTTTC
GAGTCAATTTTTGCAAAATTTTAGCCAAATCGTGAACTAAACATCACGGTTTTTGGCTAAAAAAG
CGTTCTAGGGCCCGGCTCAGTTTTGCATGATTTTTGGCCCCGAGACTCCTTGAAATATCTATAT
Found at i:5661 original size:2 final size:2
Alignment explanation
Indices: 5654--5694 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
5644 GGCATTGAAT
*
5654 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5695 TATGAGTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7269 original size:260 final size:251
Alignment explanation
Indices: 6822--7282 Score: 638
Period size: 260 Copynumber: 1.8 Consensus size: 251
6812 TTGTGGAAAA
* * * **
6822 ACTCCTTCAAATATCTATATTCATCTAACCAAATATTAACCACATTGGATTTAAGGATTTGTTTT
1 ACTCCTTAAAATATCTATATTCATATAACCAAATATCAACCACATTGGATTTAAGGATTTGTTAA
* ** * * * *
6887 TATGAGCATTTGAATCATGTTTCGATTTAATTAAAAATTAATTTGAAAAAAAAATAGGAAGAACG
66 AACAAGCATCTAAATCATGTTTCGATTTAATTAAAAATTAATTTCAAAAAAAAATAGGAAAAACG
* *
6952 ATATTAGAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCTAAA
131 ATATTAGAAGCCCTTCAATCTTTTTCGCGTTGAATTATATAATTTTTATGAGTATTGTGGCTAAA
7017 AATTGACAAAAATATTTCGGGTCAATGGTCAGTTTTGCATAATTTTTGGCGTCAAG
196 AATTGACAAAAATATTTCGGGTCAATGGTCAGTTTTGCATAATTTTTGGCGTCAAG
*
7073 ACTCCTTAAAATATTTCTATATTCATATAACCAAATCTCAACCACATTGGATTTAAGGATTTG-T
1 ACTCCTTAAAATA--TCTATATTCATATAACCAAATATCAACCACATTGGATTTAAGGATTTGTT
* * *
7137 AAAACAAGCATCTAAATCATGTTTCGATTTCATTAAAAATTAA-TTCAGAAAATAATAGGAAAAA
64 AAAACAAGCATCTAAATCATGTTTCGATTTAATTAAAAATTAATTTCAAAAAAAAATAGGAAAAA
*
7201 CGATATTAGAAACATGAAAAGCCCTTCAATCTTTTTCGCGTTGAATTATATAATTTTTATGGGTA
129 CGATATT------A-G--AAGCCCTTCAATCTTTTTCGCGTTGAATTATATAATTTTTATGAGTA
7266 TTGTGGCTAAAAATTGA
185 TTGTGGCTAAAAATTGA
7283 GGAAATAATT
Statistics
Matches: 180, Mismatches: 19, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
251 36 0.20
252 36 0.20
253 45 0.25
257 1 0.01
258 1 0.01
260 61 0.34
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (251 bp):
ACTCCTTAAAATATCTATATTCATATAACCAAATATCAACCACATTGGATTTAAGGATTTGTTAA
AACAAGCATCTAAATCATGTTTCGATTTAATTAAAAATTAATTTCAAAAAAAAATAGGAAAAACG
ATATTAGAAGCCCTTCAATCTTTTTCGCGTTGAATTATATAATTTTTATGAGTATTGTGGCTAAA
AATTGACAAAAATATTTCGGGTCAATGGTCAGTTTTGCATAATTTTTGGCGTCAAG
Found at i:7724 original size:335 final size:331
Alignment explanation
Indices: 7043--8922 Score: 1434
Period size: 335 Copynumber: 5.7 Consensus size: 331
7033 TCGGGTCAAT
* * * * *
7043 GGTCAGTTTTGCATAATTTTTGGCGTCAAGACTCCTTAAAATATTTCTATATTCATATAACCAAA
1 GGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCTTTGAAATA--TCTATATTCATCTAACCAAA
* * *** * * * *
7108 TCTCAACCACATTGGATTTAAGGATTTG-TAAAACAAGCATCTAAATCATGTTTCGATTTCATTA
64 TCTC-AGCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
* * *
7172 AAAATTAATTCAGAAAATAATAGGAAAAACGATATTAGAAA-CATGAAAAGCCCTTCAATCTTTT
128 GAAATTAATTCAGAAAA-AATAGGAAAAACGATATTA-AAAGCGTGAAAAG-TCTTCAATCTTTT
* * * *
7236 TCGCGTTGAATTATATA-ATTTTTATGGGTATTGT-GGCTAAAAATTGAGGAAATAA-TTTTC-G
190 TGGCGTTAAATTATATATA-TTTTATGAGTATTTTAGGCTAAAAATTGAGGAAA-AATTTTTCGG
* * * * ** *
7297 ACTCAATTTTTGCAAAATTCTAGTCGAAATCGTGTAATAA-TCATCACGGTTTTTAACTAAAAAT
253 A-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACT-ATCACGATTTTTGGCTAAAAAC
** *
7361 GCGTTCTGGGGCCCCA
316 GCGTTCCAGGGTCCCA
* * * *
7377 GCTAAGTTTTGCATGATTTTTGGCGCCAAGACTCTTTTTGATAT-TC-ATATTCATCTAATCAAA
1 GGTCAGTTTTGCATGATTTTTGGCGCCAAGACTC--TTTGAAATATCTATATTCATCTAACCAAA
* * * *
7440 TCTCATGTACATTAGATTTAAGAATTTGTTTTTACGAACATTTGAATCTTGTTTCGATTTAATTA
64 TCTCA-GCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
* ** * *
7505 AAAATTAATTCAGAAAAAATATAAAAAACAATATTAAAAGCGTGAAAAGTCTTCCAATCTTTTTC
128 GAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTCTT-CAATCTTTTTG
* **
7570 GCGTTAAATTATATATATTTTATTAGTATTTTAGGGAAAAAAATTGATGGAAAAATTTTTCGGAT
192 GCGTTAAATTATATATATTTTATGAGTATTTTA-GGCTAAAAATTGA-GGAAAAATTTTTCGGAT
* * * *
7635 CATTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACTATCACGGTTTTTGGCTAAAAACGTGT
255 CAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACTATCACGATTTTTGGCTAAAAACGCGT
7700 TCCAGGGTCCCA
320 TCCAGGGTCCCA
* * * *
7712 GGTTAGTTTTGCATGATTTTTGGTGGCAAAACTCTTTGAAATATCTATATTCATCTAACCAAATC
1 GGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCTTTGAAATATCTATATTCATCTAACCAAATC
* * * * *
7777 TTAGTCACATTGGATTT-AGAGATTTGTTTTTACGAGCATTTTAATCATGTTTTGATTTAATTAG
66 TCAG-CACATTGGATTTAAGA-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
* * * *
7841 AAATTAATT-TGAAAAAATAGGAAAAACGATATTAGAAGC--------CCTTCAAAC---TTGGC
129 AAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTCTTCAATCTTTTTGGC
** * * * *
7894 ACTAAATTATATAT-TTTTGTGAGTATTGTA-ACTAAAAATTGA-GAAAAATATTTCGG------
194 GTTAAATTATATATATTTTATGAGTATTTTAGGCTAAAAATTGAGGAAAAATTTTTCGGATCAAT
* * * * * ***** * * *
7950 --GT-C-AAATTTTAGCCGGAATCGTATACCATC-ATGTTTTTTTTTTTGTTAAAAACGTGTT-C
259 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACTAT-CACGATTTTTGGCTAAAAACGCGTTCC
* * *
8009 TGGGGCCCT
323 AGGGTCCCA
** *
8018 GCGTCAGTTTTGCATGATTTTTAACGCCAAGACTCTTTAAAATATATCTATATTCATCTAACCAA
1 G-GTCAGTTTTGCATGATTTTTGGCGCCAAGACTCTTT-GAA-ATATCTATATTCATCTAACCAA
* * * * * ** * * * *
8083 ATTTCAACCACATTGTATTTAAGGATTTATTTTTACGAGTTTTTAAATCTTGTTTCGATTTAGTC
63 ATCTC-AGCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
** * *
8148 AGAAATTAATTTGGAAATAAAATAGGAAAAACGATATTAGAAGCGTGAAAAAGGCTTTCAAT-TT
127 AGAAATTAATTCAG-AA-AAAATAGGAAAAACGATATTAAAAGCGTG-AAAAGTC-TTCAATCTT
* * * * * * *
8212 TCTTGGTGTTGAGTTATATA-ATTTTTATGAATATTTT-CGCTAAAAA-TCAGGGAAAAA-CTTT
188 T-TTGGCGTTAAATTATATATA-TTTTATGAGTATTTTAGGCTAAAAATTGA-GGAAAAATTTTT
* * *
8273 CGGGTCAATTTTTGTAAAATTTTAG-CGAAATCGTGTACTAACTATCACGATTTTCGGCTAAAAA
250 CGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACTATCACGATTTTTGGCTAAAAA
* * * *
8337 CGCATTTCGGGGT--CT
315 CGCGTTCCAGGGTCCCA
* *** *
8352 GGCTCAGTTTTGCATGATTTTAGG-TTTAAGGACTCCTTGAAATATCTATATTCATCTAACCAAA
1 GG-TCAGTTTTGCATGATTTTTGGCGCCAA-GACTCTTTGAAATATCTATATTCATCTAACCAAA
* * * * * *
8416 TCTCAGCCACATTAGG-TTTAAGGATTTGCTTTTATGAGTATCTGAATTTTGTTTTGATTTAATT
64 TCTCAG-CACATT-GGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
* * * * *
8480 AGAAATTATTTCGGAAAAAATAGGAAAAACAATATTAGAAGCGTTAAAAGTCCTTCAATCTTTTT
127 AGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGT-CTTCAATCTTTTT
*** * * * * * * *
8545 TATGTCGAAA-TATACACTTTTTTATGAGTATTTTA-GCCAAAAAATGAGGAAATATTTTTCGGG
191 GGCGT-TAAATTATATA-TATTTTATGAGTATTTTAGGCTAAAAATTGAGGAAAAATTTTTCGGA
* * *
8608 TGAATTTTTGCAAAATTTTAGCCGAAATCGTG---T-ACTATCACGATTTTTGACTAGAAACGCG
254 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACTATCACGATTTTTGGCTAAAAACGCG
*
8669 TTCCAGGGTCAC-
319 TTCCAGGGTCCCA
* * * * * * * *
8681 GGCTCTGTTTTGTATGATTTTTTGCGCCAAAACTCCTTGAAATATCTTTATTCATCTAATCGAAT
1 GG-TCAGTTTTGCATGATTTTTGGCGCCAAGACTCTTTGAAATATCTATATTCATCTAACCAAAT
* *
8746 CTCAGCCACATTGGATTTAA-AGATTT-TCTTTTATGTGCATCTGAATCTTGTTTCGATTTAATT
65 CTCAG-CACATTGGATTTAAGA-ATTTGT-TTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
* * * * * *
8809 AGAAATTAATTCTA-AAAAAATATGAAAAAGGATATTAAAAGTGTAAAAAGTCATCTAATATTTT
127 AGAAATTAATTC-AGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTCTTC-AATCTTTT
* * * *
8873 TGGCTTTGAATTATATATA--TTATGAGTATTTTTGTC-AAAAATTGA-GAAAA
190 TGGCGTTAAATTATATATATTTTATGAGTATTTTAGGCTAAAAATTGAGGAAAA
8923 TATCTTTCAG
Statistics
Matches: 1238, Mismatches: 228, Indels: 169
0.76 0.14 0.10
Matches are distributed among these distances:
306 10 0.01
307 70 0.06
308 3 0.00
309 81 0.07
310 4 0.00
311 2 0.00
312 26 0.02
317 13 0.01
319 9 0.01
321 14 0.01
322 21 0.02
325 23 0.02
326 49 0.04
327 7 0.01
328 39 0.03
329 181 0.15
330 62 0.05
331 38 0.03
332 190 0.15
333 60 0.05
334 103 0.08
335 210 0.17
336 23 0.02
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (331 bp):
GGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCTTTGAAATATCTATATTCATCTAACCAAATC
TCAGCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
ATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTCTTCAATCTTTTTGGCGT
TAAATTATATATATTTTATGAGTATTTTAGGCTAAAAATTGAGGAAAAATTTTTCGGATCAATTT
TTGCAAAATTTTAGCCGAAATCGTGTACTAACTATCACGATTTTTGGCTAAAAACGCGTTCCAGG
GTCCCA
Found at i:12238 original size:32 final size:32
Alignment explanation
Indices: 12196--12258 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
12186 AATTTTAATG
*
12196 TTGGATATTTTA-CCTTTTGAACTCTTAATTTT
1 TTGGACATTTTATCC-TTTGAACTCTTAATTTT
12228 TTGGACATTTTATCCTTTGAACTCTTAATTT
1 TTGGACATTTTATCCTTTGAACTCTTAATTT
12259 GAGCCTCTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 27 0.93
33 2 0.07
ACGTcount: A:0.22, C:0.14, G:0.10, T:0.54
Consensus pattern (32 bp):
TTGGACATTTTATCCTTTGAACTCTTAATTTT
Found at i:12374 original size:31 final size:31
Alignment explanation
Indices: 12339--12406 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
12329 GTCGAACAGA
* **
12339 GTTTTGGATGTTTTGCCTCATGAACTTGTAC
1 GTTTTGGATATTTCACCTCATGAACTTGTAC
*
12370 GTTTTGGATATTTCACCTCTTGAACTTGTAC
1 GTTTTGGATATTTCACCTCATGAACTTGTAC
12401 GTTTTG
1 GTTTTG
12407 CCCCCTAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (31 bp):
GTTTTGGATATTTCACCTCATGAACTTGTAC
Found at i:13381 original size:2 final size:2
Alignment explanation
Indices: 13374--13409 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
13364 TAATATTTAG
13374 TA TA TA TA GTA 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 TA TA TA TA T
13410 TGGGTACGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13675 original size:25 final size:25
Alignment explanation
Indices: 13647--13695 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
13637 TTACAAATTA
13647 TCCAAATGTAAGAAATATTAATATG
1 TCCAAATGTAAGAAATATTAATATG
13672 TCCAAATGTAAGAAATATTAATAT
1 TCCAAATGTAAGAAATATTAATAT
13696 ATAAGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (25 bp):
TCCAAATGTAAGAAATATTAATATG
Done.