Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017683.1 Corchorus olitorius cultivar O-4 contig17716, 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: 58017
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:757 original size:335 final size:326
Alignment explanation
Indices: 1--1019 Score: 1037
Period size: 329 Copynumber: 3.1 Consensus size: 326
* * * * *
1 TCGT-AAAATAAATCCTTAAATGCAATGAGGCTAAGATTTTATTAGATGAATATAGATATTTCAA
1 TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTC-A
* * * *
65 AGAGTGTC-GACGCAAAAAATCATGCAAAACTGAGCTGGGGCCCCGAAACGCGTTTTTAACCAAA
65 AGAGTCTCGGA-GCAAAAAATCATGCAAAACTGAGCCGGGACCCCGAAA--TGTTTTT-ACCAAA
* * * * *
129 AACCATGATGGTAAGTACTCGAGTTT-GGCTAAAATTTT-TCAAAAAAATAACCCAAAAA-ATTT
126 AACCGTGATGGTTAGTACACGA-TTTCGGCTAAAATTTTGT--AAAAATTGACCCAAAAATATTT
* * * * *
191 TACCCAATTTTTGGATAAAATTCGCATAAAATATATATAATTTAACGCCAAAAAGATTGGAGGAC
188 T-CTCAATTTTTGGCTAAAATACTCATAAAA-ATATATAATTTAACGCCAAAAAAATT-GAGGAC
* * *
256 TTTTCATGTTTTTAATATCA-TTTT-C-ATATTTTCCGAATTAATTTATAATTAAATCGAAACAA
250 TTTTCACGTTTTTAATATCATTTTTCCTATATTTTCCAAATTAATTTCTAATTAAATCGAAACAA
318 GATTT-AGATGC
315 GATTTCAGATGC
* * * *
329 TTGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATGGATATCTCAA
1 TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAA
* * * *
394 CGAGTTTTGGCA-TAAAAAATCATGCAAAACTGAGCCGGGACCCCAAAATGATTTTTTAGCCAAA
66 -GAGTCTCGG-AGCAAAAAATCATGCAAAACTGAGCCGGGACCCCGAAATG--TTTTTA-CCAAA
* * *
458 AACTGTGATGATTATTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCAAAATATATTTTC
126 AACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCAAAA-ATATTTTC
* * * **
523 TCAATTTTTGGCTAAAAAACTCATAAAAGATATATAATTCAACACCAAAAAAATTGAAGGGGTTT
190 TCAATTTTTGGCTAAAATACTCATAAAA-ATATATAATTTAACGCCAAAAAAATTG-AGGACTTT
* * *
588 TGACGTTTCTAATATCATTTTTCCTATATTTTCCAAATTAATTTCTAATTAAATTGAAACAAGAT
253 TCACGTTTTTAATATCATTTTTCCTATATTTTCCAAATTAATTTCTAATTAAATCGAAACAAGAT
653 TGATCAGATGC
318 T--TCAGATGC
*
664 TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATTTTTCAA
1 TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAA
* * * * * * *
729 GTAGCCTCGGAGCCAAAAATCATGCAAAATTGAGTCGGGTCCCTGGAACTCGTTTTTACCAAAAA
66 G-AGTCTCGGAGCAAAAAATCATGCAAAACTGAGCCGGGACCC-CGAAAT-GTTTTTACCAAAAA
* * *
794 CCGCGATGGTTTGTTAGTACACGATTTCGGCTAAAATTTTG---CAATTGA--CATAAAAGATTT
128 CCGTGAT-G---GTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCA-AAAATATTT
* *
854 CTCCTCAATTTTTGGCTAAAATACTCGTAAAAATATATAATTTAACGCCAAAAAGATTTGAGGAC
188 -T-CTCAATTTTTGGCTAAAATACTCATAAAAATATATAATTTAACGCCAAAAA-AATTGAGGAC
* * ** * * **
919 TTTTTAC-TTTTTAATATCGTAGTTCTTATTTTTTTTAAAATTAATTTCTAATTAAATCGAAACA
250 TTTTCACGTTTTTAATATCATTTTTCCTA-TATTTTCCAAATTAATTTCTAATTAAATCGAAACA
983 AGA-TTCAGATGC
314 AGATTTCAGATGC
* **
995 TCGTAAAAATAAATTTTTAAATCCA
1 TCGTAAAAACAAATCCTTAAATCCA
1020 TTGTTACTGA
Statistics
Matches: 577, Mismatches: 83, Indels: 59
0.80 0.12 0.08
Matches are distributed among these distances:
327 1 0.00
328 24 0.04
329 193 0.33
330 11 0.02
331 32 0.06
332 38 0.07
333 24 0.04
334 82 0.14
335 141 0.24
336 3 0.01
337 1 0.00
338 27 0.05
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (326 bp):
TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAA
GAGTCTCGGAGCAAAAAATCATGCAAAACTGAGCCGGGACCCCGAAATGTTTTTACCAAAAACCG
TGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCAAAAATATTTTCTCAATT
TTTGGCTAAAATACTCATAAAAATATATAATTTAACGCCAAAAAAATTGAGGACTTTTCACGTTT
TTAATATCATTTTTCCTATATTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTTCAGATG
C
Found at i:1400 original size:15 final size:16
Alignment explanation
Indices: 1380--1409 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1370 ACTATTGATA
1380 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
1395 ATATTATAATCTAAA
1 ATATTATAATCTAAA
1410 AATAATTATT
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:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:3198 original size:26 final size:26
Alignment explanation
Indices: 3169--3220 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
3159 ATATATCTCA
3169 ATTTAGTAATATGAATCAAATAATTT
1 ATTTAGTAATATGAATCAAATAATTT
* *
3195 ATTTGGTACTATGAATCAAATAATTT
1 ATTTAGTAATATGAATCAAATAATTT
3221 CTTCTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (26 bp):
ATTTAGTAATATGAATCAAATAATTT
Found at i:5590 original size:335 final size:327
Alignment explanation
Indices: 4958--6301 Score: 1336
Period size: 335 Copynumber: 4.1 Consensus size: 327
4948 GTACTTTACA
* *** * *
4958 TCATCTAACCAAATCTCATGAATATTGGATTTAAGAATTTGCTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAACCATATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
* * ** * *
5023 TTCGATTTAATTAGAAATTAATTTAGAAAAAATAAGAAATACGATATTAAAAGAATAAAAAGCCC
66 TTCGATTTAATTAGAAATTAATTT-GAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
** * *
5088 TCCAATCTTTTTGGTATTGAATTATATA-TTTTTATGAGTATTTTAGCGAAAAATTGAGAAGAAA
130 TCCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGA-AAA
* * * *
5152 TCTTTTGTGTCAAATTTTGCAAAATTTTAGCCGAAATCGTGTACTAACAAACTATCACGGTTTTT
194 TC-TTTGGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTACTAAC---C-ATCACAGTTTTT
* * * * *
5217 GACTAAAAACGCGTTTTGGGGACCGGACTCAATTTTGCATGATTTTTGGCTCCGAGACTACTTAA
254 GACTAAAAAAGCG-TTTCGGGACCCGACTCAATTTTGCATGATTTTTGGCGCC-AGACTACTTGA
5282 AATATCTATAT
317 AATATCTATAT
* * * *
5293 TCATTTAATCAAATCTCAACCATATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAACCATATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
5358 TTCGATTTAATTAGAAATTAATTTGGAAAAATAGGAAAAACGATATTAGAAA-CCTACAATAAAA
66 TTCGATTTAATTAGAAATTAATTTGAAAAAATATGAAAAACGATATTA-AAAGCGT----GAAAA
* * *
5422 GTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATTACTATTTTAGCCAAAAATTGAGGA
126 GTCCTCCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGA
* *
5487 AATATCTTTCAGGTCAATTTTTACAAAATTTTAGTCGAAATCGTGTACTAACCATCACAGTTTTT
191 AA-ATCTTT-GGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACAGTTTTT
* * * * * *
5552 -AGCTAAAAAAGCGTTTAGGGACCCCGACTCAGTTTTGCATGATTTTTGACGTCATGTCTCCTTG
254 GA-CTAAAAAAGCGTTTCGGGA-CCCGACTCAATTTTGCATGATTTTTGGCGCCA-GACTACTTG
* *
5616 AGATATCCATAT
316 AAATATCTATAT
* * * * * *
5628 TCATCTAATCAAATATCAGCCACATTGCATTAAAGAATTTGATTTTA-TAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAACCATATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
5692 TTCGATTTAATTTGAAATT-AGTTCAGAAAAACATGAAAAACGATATTAAAAGCGTGAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTTGA-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
* * * * * * * *
5756 TCCAATATATTTGGTGTTAAATTATATATATTTTATGATTATTTTATCCAAAAATTAGGGGAAAA
130 TCCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATT-GAGGAAAA
* * * * ** *
5821 TGTTTGGGTTATTTTTTGTAAAATTTTAGTAAAAATCGTGTACTAACCATCACGGTTTTTGACTA
194 TCTTTGGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACAGTTTTTGACTA
* * * *
5886 AAAAAGCGTTTCGGGGCCCCGGCTTAATTTTGCATGGTTTTTGGCGCC-GAC-AC------TATC
259 AAAAAGCGTTTC-GGGACCCGACTCAATTTTGCATGATTTTTGGCGCCAGACTACTTGAAATATC
5943 TATAT
323 TATAT
* * * * * * *
5948 TCATCTAATAAAATCTTAGCC-TCATTGCATTTCAGGATTTGTTTTTATGAGCATCTAAATCTTG
1 TCATCTAATCAAATCTCAACCAT-ATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTG
* *
6012 TTTCGATTTAATTAGAAATTAATTCAGAAAAAAAAAATGAAAAAGCGATATTAAAAGCGTGAAAA
65 TTTCGATTTAATTAGAAATTAATT-TG--AAAAAATATGAAAAA-CGATATTAAAAGCGTGAAAA
* * * * * * *
6077 GTCCTTCAATTTTTTTGGCGTTGAATTATAAATTCTTTATGAGTATTATGGCTAAAAATTGAGGA
126 GTCCTCCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGA
* * * *
6142 AACATCTTTCGGGTCAATTTTTGCAAAATTTTAG-CCAATATCGGGTAATAATCATCACAGTTTT
191 AA-ATCTTT-GGGTCAATTTTTGCAAAATTTTAGTCGAA-ATCGTGTACTAACCATCACAGTTTT
* * * * * * *
6206 TGGCTAAAAACGCGTTCCGAGG-CCCTA-TGAAATTTTGAATGATTTTTGGCGCCGAGACTCCTT
253 TGACTAAAAAAGCGTTTCG-GGACCCGACT-CAATTTTGCATGATTTTTGGCGCC-AGACTACTT
6269 GAAATATCTATAT
315 GAAATATCTATAT
* *
6282 TCATCTAACCAAATCCCAAC
1 TCATCTAATCAAATCTCAAC
6302 AATTGTTTTT
Statistics
Matches: 832, Mismatches: 140, Indels: 75
0.79 0.13 0.07
Matches are distributed among these distances:
320 46 0.06
321 33 0.04
322 2 0.00
324 20 0.02
325 100 0.12
326 60 0.07
327 5 0.01
328 1 0.00
329 86 0.10
330 64 0.08
331 6 0.01
333 6 0.01
334 111 0.13
335 186 0.22
336 1 0.00
338 37 0.04
339 68 0.08
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Consensus pattern (327 bp):
TCATCTAATCAAATCTCAACCATATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATTAGAAATTAATTTGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
CCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAATC
TTTGGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACAGTTTTTGACTAAA
AAAGCGTTTCGGGACCCGACTCAATTTTGCATGATTTTTGGCGCCAGACTACTTGAAATATCTAT
AT
Found at i:7684 original size:331 final size:329
Alignment explanation
Indices: 7040--8478 Score: 1078
Period size: 331 Copynumber: 4.3 Consensus size: 329
7030 ACAAAGGGAG
* * * * * * *
7040 TAATTCGGAAAATAATAGGAAAAACGATATTAGAAGCATGAAAAGCCCTTCATTCT-TTTTGGCA
1 TAATTCAGAAAA-AATATGAAAAACGATATTAAAAGCGTGAAAAGGCCTTCAATCTCTTTTGGCG
* * * * * *
7104 TTGAATTATATA-ATTTTTAAGAGTA-TTATGGCTAAAAATTAAGGAATTAA-CTTTCGAGTCAA
65 TTGAATTATATATA-TTTTATGAGTAGTT-TAGCCAAAAATTGAGGAA-AAATCTTTCGGGTC-A
* ** * * * *
7166 TTTTTGCAAAATTCTAGCCGATCGAAATTTTGTAATAATCATAATGGATTTTGGCTAAAAACGCG
126 TTTTTGCAAAATTTTAG-C---CGAAATCATGTACT--CCATCACGG-TTTTGGCTAAAAACGCG
* ** * * * * ** * *
7231 TTCCGGGGCCCCGGGTAAGCTTTGCATGATTTATGGCGCCAAAACTATTTGAGATATCCATATTC
184 TTCCAGGGCCCCGACTTAGTTTTGCATGATTTATGGCGCCGAGACTCCTTGAAATATCTATATTC
* * * * * *
7296 ATTTAATCAAATCTCAGCTAAATTGGATTTAATAATTTGTTTTTACGAGCATCTGAATTTTGTTT
249 ATCTAATCAAATCTCAGCCACATTGAATTTAATGATTTGTTTTTACGAGCATCTGAATCTTGTTT
*
7361 CGATTTAATTAGAAAT
314 CAATTTAATTAGAAAT
* * * * * *
7377 TAATTCAG-AAAAATATGAAAAATGATGTTTAAAGCTTGAAAAGTCCTCCAATCT-TTTTGGCGT
1 TAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGGCCTTCAATCTCTTTTGGCGT
*
7440 TGAATTATATATATTTTATGAGTAGTTTAGCCAAAAATTGACGGAAAAATTTTTCGGGTCATTTT
66 TGAATTATATATATTTTATGAGTAGTTTAGCCAAAAATTGA-GGAAAAATCTTTCGGGTCA-TTT
* *
7505 TTGCAAAATTTTAGCCGAAATCATGTACTAACCATCACAGGTTTTGGTTAAAAACGCGTTTC-GG
129 TTGCAAAATTTTAGCCGAAATCATGTACT--CCATCAC-GGTTTTGGCTAAAAACGCGTTCCAGG
* * *
7569 GCCCCGACTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATTTATATTTATCTAAT
191 GCCCCGACTTAGTTTTGCATGATTTATGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAAT
* *
7634 CAAATCTTAGCCACATTGAATTTAATGATTTGTTTTTACGAGCATCTGAATCTTATTTCAATTTA
256 CAAATCTCAGCCACATTGAATTTAATGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTA
7699 ATTAGAAAT
321 ATTAGAAAT
* * *
7708 TAATTCAG--AAAATATGAAAAACGATATTAAAAGCGTGAAAAAGGCTTTCAA-CTGTTTTGGCA
1 TAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTG-AAAAGGCCTTCAATCTCTTTTGGCG
* * * ** * * *
7770 TTGAATTATATGTTTTTTATGAGTATTTTCTCTAGAAA-TCAGGGAAAAATCTTTC--GT-A---
65 TTGAATTATATATATTTTATGAGTAGTTTAGCCAAAAATTGA-GGAAAAATCTTTCGGGTCATTT
* ** * *
7828 -T-C--AATTTTTG-C-AAA--AT-T--TCGGT-ACGGTTTTCAGCTAAAAATC-CGTTAC-GGG
129 TTGCAAAATTTTAGCCGAAATCATGTACTCCATCACGGTTTT-GGCTAAAAA-CGCGTTCCAGGG
* * * * *
7879 GCCCGGCTCAGTTTTGCATGATTTATGACG-C-A-A-TCCTTGAAATATCTATATTCATCTAAAA
192 CCCCGACTTAGTTTTGCATGATTTATGGCGCCGAGACTCCTTGAAATATCTATATTCATCT-AAT
* * *
7940 AAAATCTCAGCCACATT-AGATTT-ATGGATTTGTTTTTACAAGCATCTGAATCTTGTTACAATT
256 CAAATCTCAGCCACATTGA-ATTTAAT-GATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATT
8003 TAATTAGAAAT
319 TAATTAGAAAT
* * * * * * **
8014 TAATTCGGGAAAGAAATAGGATAAACAATATTAGAAGCGTTAAAAGGCCTTCAATCT-TTTTGAT
1 TAATTC-AGAAA-AAATATGAAAAACGATATTAAAAGCGTGAAAAGGCCTTCAATCTCTTTTGGC
* * *
8078 GTCGAATTATATATTTTTTATGAGTA-TTATAGCCAAAAATTGAGGAAATATCTTTCGGGTCAAT
64 GTTGAATTATATATATTTTATGAGTAGTT-TAGCCAAAAATTGAGGAAAAATCTTTCGGGTC-AT
* * * *
8142 TTTTGCAAAATTTTAGCTGAAATCATGTAC-GCATCACGGTTTTTGGCTAAAAATGTGTTCCAGG
127 TTTTGCAAAATTTTAGCCGAAATCATGTACTCCATCACGG-TTTTGGCTAAAAACGCGTTCCAGG
* * *
8206 GCCAC-AGCTCT-G-TTTGCTTGATTTTTGGCGCCGAGACTCATTGAAATATCTTTTTTTTAAGT
191 GCCCCGA-CT-TAGTTTTGCATGATTTATGGCGCCGAGACTC----------C------------
* * * * * * *
8268 GGTTGAAATATCTTTATTCATCTAATCAAATCTCAGGCACATTGGATTTAAGGATTTATTTTAAT
232 --TTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAATGATTTGTTTTTAC
* * * *
8333 GTGTATTTGAATCTTGTATT-GATTTAATTAGAAAT
295 GAGCATCTGAATCTTGT-TTCAATTTAATTAGAAAT
* *
8368 TAATTCAGAAAAAATATGAAAAACTATATTAAAAGCGTGAAAAGTCCTTCAAT-TCTTTTGGCGT
1 TAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGGCCTTCAATCTCTTTTGGCGT
* *
8432 TGAATTATATATATTTTATGAGTAGTTTTGCCAAAAAATGAGGAAAA
66 TGAATTATATATATTTTATGAGTAGTTTAGCCAAAAATTGAGGAAAA
8479 TTTTTTACCA
Statistics
Matches: 876, Mismatches: 149, Indels: 139
0.75 0.13 0.12
Matches are distributed among these distances:
305 25 0.03
306 73 0.08
307 2 0.00
308 9 0.01
309 101 0.12
310 30 0.03
311 2 0.00
312 1 0.00
313 1 0.00
314 1 0.00
315 2 0.00
317 4 0.00
318 2 0.00
319 7 0.01
320 7 0.01
321 1 0.00
322 4 0.00
324 2 0.00
325 1 0.00
326 1 0.00
327 32 0.04
328 15 0.02
329 1 0.00
330 42 0.05
331 177 0.20
332 36 0.04
333 2 0.00
335 78 0.09
336 34 0.04
337 7 0.01
341 1 0.00
351 1 0.00
352 82 0.09
353 6 0.01
354 64 0.07
355 22 0.03
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (329 bp):
TAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGGCCTTCAATCTCTTTTGGCGT
TGAATTATATATATTTTATGAGTAGTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCATTTTT
GCAAAATTTTAGCCGAAATCATGTACTCCATCACGGTTTTGGCTAAAAACGCGTTCCAGGGCCCC
GACTTAGTTTTGCATGATTTATGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAAT
CTCAGCCACATTGAATTTAATGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAG
AAAT
Found at i:10123 original size:32 final size:32
Alignment explanation
Indices: 10087--10185 Score: 135
Period size: 32 Copynumber: 3.1 Consensus size: 32
10077 TTGAGTCAGG
* *
10087 TCGGGTTAAATTTGGGTTATGTTGATTCGAGT
1 TCGGGTTAAATTTGGGTCAGGTTGATTCGAGT
*
10119 TCGGGTTAAATTTGGGTCAGGTTGATTCAAGT
1 TCGGGTTAAATTTGGGTCAGGTTGATTCGAGT
* * * *
10151 TCGGGTCAATTTTGGGTCAGGTTAATTCGGGT
1 TCGGGTTAAATTTGGGTCAGGTTGATTCGAGT
10183 TCG
1 TCG
10186 AGTTCGGGCT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.18, C:0.10, G:0.32, T:0.39
Consensus pattern (32 bp):
TCGGGTTAAATTTGGGTCAGGTTGATTCGAGT
Found at i:10353 original size:19 final size:20
Alignment explanation
Indices: 10329--10366 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
10319 CATAAATGAA
*
10329 ATTTTCAAA-ATTATTATTT
1 ATTTTCAAATATTAGTATTT
10348 ATTTTCAAATATTAGTATT
1 ATTTTCAAATATTAGTATT
10367 GAATTCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTTTCAAATATTAGTATTT
Found at i:15777 original size:106 final size:106
Alignment explanation
Indices: 15647--15861 Score: 412
Period size: 106 Copynumber: 2.0 Consensus size: 106
15637 GTTGTCCCAT
*
15647 AATCTATACTAATTATAAAGCCAAGTTCTGAGTTTGTGTCACGAGTTGACTCAGACACAAACTCA
1 AATCTATACTAATTATAAAGCCAAGTTCTGAGTTTATGTCACGAGTTGACTCAGACACAAACTCA
15712 GTTTATAAAAATTCAAAACAAAATAAAAACTACCCATTTTA
66 GTTTATAAAAATTCAAAACAAAATAAAAACTACCCATTTTA
15753 AATCTATACTAATTATAAAGCCAAGTTCTGAGTTTATGTCACGAGTTGACTCAGACACAAACTCA
1 AATCTATACTAATTATAAAGCCAAGTTCTGAGTTTATGTCACGAGTTGACTCAGACACAAACTCA
*
15818 GTTTATAAAAATTCAAAACAAAATAAAAACTACTCATTTTA
66 GTTTATAAAAATTCAAAACAAAATAAAAACTACCCATTTTA
15859 AAT
1 AAT
15862 AAAACTAGAG
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 107 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (106 bp):
AATCTATACTAATTATAAAGCCAAGTTCTGAGTTTATGTCACGAGTTGACTCAGACACAAACTCA
GTTTATAAAAATTCAAAACAAAATAAAAACTACCCATTTTA
Found at i:20228 original size:284 final size:284
Alignment explanation
Indices: 19719--20257 Score: 947
Period size: 284 Copynumber: 1.9 Consensus size: 284
19709 GCCTCATTTG
* *
19719 GTGCCCCATTCACCAAATCATGTCACATATCCTTTTTATTATAATTTGTTTGTTTTCAAGTTTTA
1 GTGCCCCATTCACCAAATCATGCCACATATCCTTTTTATTATAACTTGTTTGTTTTCAAGTTTTA
* * *
19784 ACAAATAATAAAAATACCAATTAAATACCAAGTTTAGCTCCAAATTAATAACAAATAATTATATA
66 ACAAATAATAAAAATACCAATTAAACACCAAGTTTAGCCCCAAATTAACAACAAATAATTATATA
*
19849 TAAGAGTTAGTTCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATTTAA
131 GAAGAGTTAGTTCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATTTAA
19914 TTTAACTAGCCAAACAAGGAATAACATTAGAAACTGAAAAAAGACATATGTCATT-TTTGTGCCC
196 TTTAACTAGCCAAACAAGGAATAACATTAGAAACTGAAAAAAGACATATGTCATTATTTGTGCCC
19978 CACTCTGTGCCCCATTCACCATCC
261 CACTCTGTGCCCCATTCACCATCC
* *
20002 GTGCCCCATTCACCAAATCATGCCACGTATCCTTTTTATTATAGCTTGTTTGTTTTCAAGTTTTA
1 GTGCCCCATTCACCAAATCATGCCACATATCCTTTTTATTATAACTTGTTTGTTTTCAAGTTTTA
**
20067 ACAAATAATAAAAATGTCAATTAAACACCAAGTTTAGACCCCAAATTAACAACAAATAATTATAT
66 ACAAATAATAAAAATACCAATTAAACACCAAGTTTAG-CCCCAAATTAACAACAAATAATTATAT
20132 AGAAGAGTTAGTTCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATTTA
130 AGAAGAGTTAGTTCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATTTA
*
20197 ATTTAACTAGCCAAAC-AGGAAATAACATTAGAAACTGAAAAAAGACATGTGTCATTATTTG
195 ATTTAACTAGCCAAACAAGG-AATAACATTAGAAACTGAAAAAAGACATATGTCATTATTTG
20258 GTGGATGAGA
Statistics
Matches: 242, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
283 98 0.40
284 140 0.58
285 4 0.02
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (284 bp):
GTGCCCCATTCACCAAATCATGCCACATATCCTTTTTATTATAACTTGTTTGTTTTCAAGTTTTA
ACAAATAATAAAAATACCAATTAAACACCAAGTTTAGCCCCAAATTAACAACAAATAATTATATA
GAAGAGTTAGTTCTAAATTTTAATACATTCCCCATAGGGTTTTAGAATGAAAATATAAAATTTAA
TTTAACTAGCCAAACAAGGAATAACATTAGAAACTGAAAAAAGACATATGTCATTATTTGTGCCC
CACTCTGTGCCCCATTCACCATCC
Found at i:22734 original size:20 final size:20
Alignment explanation
Indices: 22709--22746 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
22699 TAATATTGGA
22709 CAAAACTCACATACAATGAG
1 CAAAACTCACATACAATGAG
22729 CAAAACTCACATACAATG
1 CAAAACTCACATACAATG
22747 TGTATCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.26, G:0.08, T:0.16
Consensus pattern (20 bp):
CAAAACTCACATACAATGAG
Found at i:25159 original size:13 final size:13
Alignment explanation
Indices: 25143--25167 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25133 AAGTCAACAC
25143 GCCACGTCATCCT
1 GCCACGTCATCCT
25156 GCCACGTCATCC
1 GCCACGTCATCC
25168 ATTGACTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (13 bp):
GCCACGTCATCCT
Found at i:25478 original size:18 final size:18
Alignment explanation
Indices: 25455--25515 Score: 97
Period size: 18 Copynumber: 3.4 Consensus size: 18
25445 CTATTTTCTG
25455 CCTGTTTGACCTCTTGGT
1 CCTGTTTGACCTCTTGGT
*
25473 CCTGTTTAACCTCTTGGT
1 CCTGTTTGACCTCTTGGT
25491 CCTGTTTGACC-CTTTGGT
1 CCTGTTTGACCTC-TTGGT
25509 CCTGTTT
1 CCTGTTT
25516 TCTGCTTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
17 1 0.03
18 39 0.98
ACGTcount: A:0.07, C:0.28, G:0.20, T:0.46
Consensus pattern (18 bp):
CCTGTTTGACCTCTTGGT
Found at i:25511 original size:65 final size:64
Alignment explanation
Indices: 25428--25562 Score: 182
Period size: 65 Copynumber: 2.1 Consensus size: 64
25418 GAAGTTTGCT
* *
25428 CTGTTTGACCTTTCGTCCTATTTTCTGCCTGTTTGACCTCTTGGTCCTGTTTAACCTCTT-GGTC
1 CTGTTTGACCTTTCGTCCTATTTTCTGCCTGTTCGACCTCTTGGTCATGTTTAACCT-TTCGGTC
* * * *
25492 CTGTTTGACCCTTTGGTCCTGTTTTCTGCTTGTTCGACCTCTTGGTCATGTTTGACCTTTCGGTC
1 CTGTTTGA-CCTTTCGTCCTATTTTCTGCCTGTTCGACCTCTTGGTCATGTTTAACCTTTCGGTC
*
25557 TTGTTT
1 CTGTTT
25563 TATGCATGTT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
64 10 0.16
65 52 0.84
ACGTcount: A:0.07, C:0.26, G:0.19, T:0.48
Consensus pattern (64 bp):
CTGTTTGACCTTTCGTCCTATTTTCTGCCTGTTCGACCTCTTGGTCATGTTTAACCTTTCGGTC
Found at i:25535 original size:47 final size:48
Alignment explanation
Indices: 25481--25611 Score: 185
Period size: 48 Copynumber: 2.8 Consensus size: 48
25471 GTCCTGTTTA
* *
25481 ACCTCTTGGTCCTGTTTGACCCTTT-GGTCCTGTTTTCTGCTTG-TTCG
1 ACCTCTTGGTCCTGTTTGA-CCTTTCGGTCCTGTTTTATGCATGTTTCG
* * *
25528 ACCTCTTGGTCATGTTTGACCTTTCGGTCTTGTTTTATGCATGTTTTG
1 ACCTCTTGGTCCTGTTTGACCTTTCGGTCCTGTTTTATGCATGTTTCG
*
25576 ACCCCTTGGTCCTGTTTGACCTTTCGGTCCTGTTTT
1 ACCTCTTGGTCCTGTTTGACCTTTCGGTCCTGTTTT
25612 TTTAGCCCTT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
46 5 0.07
47 33 0.45
48 36 0.49
ACGTcount: A:0.07, C:0.25, G:0.21, T:0.47
Consensus pattern (48 bp):
ACCTCTTGGTCCTGTTTGACCTTTCGGTCCTGTTTTATGCATGTTTCG
Found at i:25595 original size:18 final size:18
Alignment explanation
Indices: 25572--25610 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25562 TTATGCATGT
25572 TTTGACCCCTT-GGTCCTG
1 TTTGA-CCCTTCGGTCCTG
*
25590 TTTGACCTTTCGGTCCTG
1 TTTGACCCTTCGGTCCTG
25608 TTT
1 TTT
25611 TTTTAGCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.05, C:0.28, G:0.21, T:0.46
Consensus pattern (18 bp):
TTTGACCCTTCGGTCCTG
Found at i:29508 original size:335 final size:336
Alignment explanation
Indices: 28688--31367 Score: 967
Period size: 336 Copynumber: 8.2 Consensus size: 336
28678 GTACACGATT
* * * * * * *
28688 TAATTAAATCTAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTATATTCAATGTT-GTTGAG
1 TAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAAT-TTAGCTGAA
** * * * * *
28752 ATTTGATTAGGTGAATATAGATAAT-TCAAGGAGTCTCGGCGTC-AAAAATCATGAAAAAC-TAA
65 ATTTGATTAAATGAATATAAAT-ATCTCAACGAGTATCAGCG-CAAAAAATCATGCAAAACTTAA
* * * * * * *
28814 GTCGGGGCCTC-GAAACACGTTTTTAGCCAAAAAACCGTGATGGTTAGTACACGGTTTCGA-C--
128 -CCGGGGCC-CAGGAACGCGTTTTTAGCC-AAAAACCGTGATGATTATTACATGATTTCGATCGG
* * * * * * * *
28875 -TAAAATTTTGTAAAAAATGGCCCGAAAAATT-CTTCCGTCAATTTTTGGCTCAAATACTCATAA
190 ATAGAATTTTGTAGAAATTGACTCG-AAATTTATTTCCGTCAATTTTTAGCTCAAATACTCATAA
* * * * * *
28938 TATATGTATAATTCAACGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATATCATTTTTCATA
254 AATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCATTTATCATA
**
29003 TTTTTCTGAATTAATTTC
319 TTTTTCCAAATTAATTTC
* * * *
29021 TAATTGAATCGAAACAAGATTCAGATGCTCATAAAAACAAATTCTTAAATCTAATTTAGCTGAGA
1 TAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATTTAGCTGAAA
** * * * * **
29086 TTTGATTAAATGAATATGGATATCTCAACGAGTCTTAGCGCCAAAAATCATTCAAAACTTAGTCG
66 TTTGATTAAATGAATATAAATATCTCAACGAGTATCAGCGCAAAAAATCATGCAAAACTTAACCG
* *
29151 GGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGATTATTACATGATTTCGATCGGATAGAA
131 GGGCCCAGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTACATGATTTCGATCGGATAGAA
29216 TTTTGTAGAAATTGACTCGAAATTTATTTCC-TCAATTTTTAGC-CACAATACTCATAAAA-ATT
196 TTTTGTAGAAATTGACTCGAAATTTATTTCCGTCAATTTTTAGCTCA-AATACTCATAAAATA-T
* * * ** *
29278 ATATAATTCTACGCCAAAAAGATTGAAGGGCTTTTCATGCTTCTAATATTGTTTATCCTATTATT
259 ATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCATTTATCATA-T-TT
29343 TTCCAAATTAATTTC
322 TTCCAAATTAATTTC
** *** *
29358 TAATTAAATCGAAACATA-ATTCAGATGCTTGT-TTTACAAATCCTTAAATCCAATTTGGCTGAA
1 TAATTAAATCGAAACA-AGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATTTAGCTGAA
* * * * ** * * *
29421 ATTTGGTTAGATGAATGTAAATATTTCATGGAGTATCGGTGCAAAAAATCATGCAACA-TTGAAC
65 ATTTGATTAAATGAATATAAATATCTCAACGAGTATCAGCGCAAAAAATCATGCAAAACTT-AAC
* * * *
29485 CGGGGCCTAGGAACGCG-TTTTAGCCAAAAACCGTGATTTCGACTAACGTACACGATTTC-A---
129 CGGGGCCCAGGAACGCGTTTTTAGCCAAAAACCGTGA--T-GA-TTA-TTACATGATTTCGATCG
* * * * * * **
29545 GCTA-ATATTTTGCAAAAATTGAC-CAGAAATATTTTTTCC-TCAA--TTGAACTTCAAA-A-AG
189 GATAGA-ATTTTGTAGAAATTGACTC-GAAAT-TTATTTCCGTCAATTTTTAGC-TCAAATACTC
** ** * * * *
29603 ATTGGAGGAT-T-T--TTC-ACG-C------TTTTAA-TATCGTTT-----TTC--ATAT--TTT
250 A-TAAAATATATATAATTCAACGCCAAAAAGATTGAAGGA-CTTTTCACGCTTCTAATATCATTT
** * ** *
29646 -TC-TA-AATT-AATTTC------
313 ATCATATTTTTCCAAATTAATTTC
* * *
29660 TAATTAAATCGAAACAAGATTCATATGCT-AGTAAAAACAAATCCTTAAATGCAATGT-GTCTGA
1 TAATTAAATCGAAACAAGATTCAGATGCTCA-TAAAAACAAATCCTTAAATCCAATTTAG-CTGA
* * * * * * * * * *
29723 GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC-GACGCCAAAAATCATGCAGAACTGAG
64 AATTTGATTAAATGAATATAAATATCTCAACGAGTATCAG-CGCAAAAAATCATGCAAAACTTAA
* * * * * **
29787 CTGGGGCCCCA-AAACGCGTTTTTAG-CATAAAATCGTGATGATTAGTACACGATTTCG---GCT
128 CCGGGG-CCCAGGAACGCGTTTTTAGCCA-AAAACCGTGATGATTATTACATGATTTCGATCGGA
* * * * *
29847 TA-AATTTTGCA-AAACATGAC-CAGAAAAATT-TTTCC-TCAATTTTTATC-CACAATACTCGT
191 TAGAATTTTGTAGAAA-TTGACTC-G-AAATTTATTTCCGTCAATTTTTAGCTCA-AATACTCAT
* * * ** *
29906 AAAA-AGTATATAATTCAACGTCGAAAAGATTGAA-AAGCTTTTCACGCTTCTAATATTGTTTTT
252 AAAATA-TATATAATTCAACGCCAAAAAGATTGAAGGA-CTTTTCACGCTTCTAATATCATTTAT
* *
29969 CCTATTTTTTTCCCGAATTAATTTC
315 -C-ATATTTTT-CCAAATTAATTTC
** * * * ** * *
29994 TAATTAAAAAGAAACATGATTCTGATG-T--T---------T--GTAAAAACAA--TGGCTGAGA
1 TAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATTTAGCTGAAA
* * * * * * * * * *
30043 TTTGGTTAGATGAATATAGATATTTTAAGGAGTCTCGGCGCCAAAAATCATTCAAAA-TTGAA-C
66 TTTGATTAAATGAATATAAATATCTCAACGAGTATCAGCGCAAAAAATCATGCAAAACTT-AACC
* * * * * *
30106 TGGG-CAACGGAACCCGTTTTTAGCCAAAAACCGTGATGGA-TAGTACACGATTT--A--GGCTA
130 GGGGCCCA-GGAACGCGTTTTTAGCCAAAAACCGTGAT-GATTATTACATGATTTCGATCGGATA
* ** * ** *
30165 AAATTTTACAAAAATTGAC-CTGAAAGATATTTTTC-TCAATTTTTAGC-CATAATACTCATAAA
193 GAATTTTGTAGAAATTGACTC-GAAATTTA-TTTCCGTCAATTTTTAGCTCA-AATACTCATAAA
** * * * * *
30227 AGCT-TATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACTCTTTTAATATCGATAT-TCATA
255 ATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATC-ATTTATCATA
** *
30290 TTTTTCTTATTTAATTTC
319 TTTTTCCAAATTAATTTC
* * * * * * *
30308 TAATTAAATTGAAATAAGATTTAGAATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTG
1 TAATTAAATCG--A-AACA---AG-ATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATTTA
* * * * * * *
30373 GCT-AAGATTTTG-TTAGATGAATATAGATATTTCAAGGAGTGTCAGCGCCAAAAA-CAACGCAA
59 GCTGAA-A-TTTGATTAAATGAATATAAATATCTCAACGAGTATCAGCGCAAAAAATC-ATGCAA
* ** * * * ** **
30435 AACTGAGTCGGGGTCCC-GAAACGAGTTTTTAGCCAAAACACCGTGATGGTTAGCACACAATTT-
121 AACTTAACCGGGG-CCCAGGAACGCGTTTTTAGCCAAAA-ACCGTGATGATTATTACATGATTTC
* * * * * * * ** * * * *
30498 --T-GGCTAAAATTTTGCAAAAAATAACCCGAAAAAT-TTTCC-CCAATTTTTGGATAAAATACT
184 GATCGGATAGAATTTTGTAGAAATTGACTCGAAATTTATTTCCGTCAATTTTTAGCTCAAATACT
* * * * * * * *
30558 CATAATATATATATAATTTAACACCAAAAATATTGGAGGACTTTTCACGCTTTTAATATCGTTTT
249 CATAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCATTTA
***
30623 TCATATTTTTTTGAATTAATTTC
314 TCATATTTTTCCAAATTAATTTC
* * * ** * * *
30646 TAATTAAATCGAATCAAGATCCATATGCTTGTAAAAA-AAATTCTTAAATCCAATGTGGCTGAAA
1 TAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATTTAGCTGAAA
* ** * * * * *
30710 TTTGATTAGATGAATATGGATATCTCAAGGAGTCT-TG-GCATCAAAAATCATGCAAAACTGAGC
66 TTTGATTAAATGAATATAAATATCTCAACGAGTATCAGCGCA--AAAAATCATGCAAAACTTAAC
* * ** * *
30773 CGGAGCCCTA-GAACGCTTTTTTTAGCCAAAAAATGTGATG-TTATTACACGA-TT---TCGGCT
129 CGGGGCCC-AGGAACGC-GTTTTTAGCCAAAAACCGTGATGATTATTACATGATTTCGATCGGAT
* * * * * * * *
30832 AAAATTTTGTAAAAATTGACCCGAAA--GATGTTCCCTCAATTTCTGGCTAAAATACTCATAAAA
192 AGAATTTTGTAGAAATTGACTCGAAATTTAT-TTCCGTCAATTTTTAGCTCAAATACTCATAAAA
* ** * * * *
30895 AATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTTACG-TCTCTAATATCGTTTTTCCTAT
256 TATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCT-TCTAATATCATTTATCATA-
*
30959 TTTTTCCAAATTAATTTT
319 TTTTTCCAAATTAATTTC
* * * * *
30977 TAATTAAATCAAAAAAAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT-AA
1 TAATTAAATC-GAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATTTAGCTGAA
* * * * * * *
31041 GATTTGATTAGATGAATATAGATATTTCAA-GTAGTCTCGGAGCCAAAAATCATGCAAAA-TTGA
65 -ATTTGATTAAATGAATATAAATATCTCAACG-AGTATCAGCGCAAAAAATCATGCAAAACTT-A
** * * * **
31104 GTCGGGTCCGC-GGAACGCGTTTTTAGCCAAAAACCGTGATAGTTTGTTA-AT-A-CACGATTTC
127 ACCGGGGCC-CAGGAACGCGTTTTTAGCCAAAAACCGTGAT-GATTATTACATGATTTCGA--TC
* * * ** ** * * * * *
31165 GGCTAAAATTTT-TCAAAAATTGAAAC-AAA-AGATTTCTCCTTAATTTTTGGCTAAAATGCTCA
188 GGATAGAATTTTGT-AGAAATTGACTCGAAATTTATTTC-CGTCAATTTTTAGCTCAAATACTCA
* * * * * * * *
31227 TAAAA-ATATATAATTCAATGCCAAAAATATTGGAGGGCTTTTTACTCTTTTAATATCGTATT-T
251 TAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCAT-TTAT
* * *
31290 CTTATTTTTTCTAAATTAATTTT
315 CATA-TTTTTCCAAATTAATTTC
* * *
31313 TAATTAATTCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAAT
1 TAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAAT
31368 GTTGTTGAGA
Statistics
Matches: 1846, Mismatches: 332, Indels: 336
0.73 0.13 0.13
Matches are distributed among these distances:
298 14 0.01
299 32 0.02
300 16 0.01
301 4 0.00
302 31 0.02
303 84 0.05
304 22 0.01
305 3 0.00
306 1 0.00
308 2 0.00
309 2 0.00
312 11 0.01
313 2 0.00
314 22 0.01
315 9 0.00
316 13 0.01
317 100 0.05
318 101 0.05
319 6 0.00
320 8 0.00
321 10 0.01
322 3 0.00
323 9 0.00
324 1 0.00
325 1 0.00
326 2 0.00
328 7 0.00
329 49 0.03
330 159 0.09
331 59 0.03
332 79 0.04
333 209 0.11
334 36 0.02
335 161 0.09
336 220 0.12
337 193 0.10
338 104 0.06
339 49 0.03
340 12 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (336 bp):
TAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATTTAGCTGAAA
TTTGATTAAATGAATATAAATATCTCAACGAGTATCAGCGCAAAAAATCATGCAAAACTTAACCG
GGGCCCAGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTACATGATTTCGATCGGATAGAA
TTTTGTAGAAATTGACTCGAAATTTATTTCCGTCAATTTTTAGCTCAAATACTCATAAAATATAT
ATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCATTTATCATATTTTTCC
AAATTAATTTC
Found at i:31754 original size:15 final size:16
Alignment explanation
Indices: 31736--31765 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31726 ATAAATAATA
31736 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
31751 ATATTATAATCTAAA
1 ATATTATAATCTAAA
31766 AATAATTATT
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:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:32046 original size:24 final size:25
Alignment explanation
Indices: 31999--32053 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
31989 TTAGAATTTT
* *
31999 TAAGTTCGTGATTTTTTTTAAGTAA
1 TAAGTTCGTGATTTTATATAAGTAA
*
32024 TAAGTTCGTGATTTTATAT-AGTAG
1 TAAGTTCGTGATTTTATATAAGTAA
32048 TAAGTT
1 TAAGTT
32054 TAGGCTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (25 bp):
TAAGTTCGTGATTTTATATAAGTAA
Found at i:39113 original size:36 final size:36
Alignment explanation
Indices: 39066--39135 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
39056 ACATGGAGAT
39066 TTAGCCAATGTCTTGAGACATTGATGAAATAAATGA
1 TTAGCCAATGTCTTGAGACATTGATGAAATAAATGA
*
39102 TTAGCCAATGTCTTTAGACATTGATGAAATAAAT
1 TTAGCCAATGTCTTGAGACATTGATGAAATAAAT
39136 TGGAGAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (36 bp):
TTAGCCAATGTCTTGAGACATTGATGAAATAAATGA
Found at i:48323 original size:39 final size:39
Alignment explanation
Indices: 48269--48348 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
48259 CCATCCCTAT
48269 AGGGGGCCATTGGAAAGAGTAAGAAATTTCATAGTTTGA
1 AGGGGGCCATTGGAAAGAGTAAGAAATTTCATAGTTTGA
48308 AGGGGGCCATTGGAAAGAGTAAGAAATTTCATAGTTTGA
1 AGGGGGCCATTGGAAAGAGTAAGAAATTTCATAGTTTGA
48347 AG
1 AG
48349 CATATGAAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.36, C:0.07, G:0.31, T:0.25
Consensus pattern (39 bp):
AGGGGGCCATTGGAAAGAGTAAGAAATTTCATAGTTTGA
Found at i:49541 original size:12 final size:12
Alignment explanation
Indices: 49526--49555 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
49516 TGAACTGCCC
49526 GGTGAACCTTCG
1 GGTGAACCTTCG
*
49538 GGTGAACCTTCT
1 GGTGAACCTTCG
49550 GGTGAA
1 GGTGAA
49556 TAAGAAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.27
Consensus pattern (12 bp):
GGTGAACCTTCG
Found at i:54279 original size:12 final size:12
Alignment explanation
Indices: 54262--54290 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
54252 TCATAACAAT
54262 CTCTCTAGCAAA
1 CTCTCTAGCAAA
54274 CTCTCTAGCAAA
1 CTCTCTAGCAAA
54286 CTCTC
1 CTCTC
54291 AATTTAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.38, G:0.07, T:0.28
Consensus pattern (12 bp):
CTCTCTAGCAAA
Found at i:56448 original size:47 final size:49
Alignment explanation
Indices: 56394--56518 Score: 125
Period size: 48 Copynumber: 2.6 Consensus size: 49
56384 GAGCGTGTCA
* * *
56394 ATCAATTTTGA-C-CAGAAATTGATAAAAGGAACAA-TAAAAAGTAAAAG
1 ATCAATTTTGATCTCAGAAATTGAGAAAAAGAACAAGGAAAAA-TAAAAG
* **
56441 ATCAATTTT-ATCTTAGAAATTGAGAAAAAGTGCAAGGAAAAATAAAAG
1 ATCAATTTTGATCTCAGAAATTGAGAAAAAGAACAAGGAAAAATAAAAG
* * *
56489 ATCAATTTTGTTGT-AAAAATTGAGAAAAAG
1 ATCAATTTTGATCTCAGAAATTGAGAAAAAG
56519 TGCAAAAAAG
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
46 1 0.02
47 10 0.15
48 47 0.72
49 7 0.11
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (49 bp):
ATCAATTTTGATCTCAGAAATTGAGAAAAAGAACAAGGAAAAATAAAAG
Found at i:56509 original size:48 final size:46
Alignment explanation
Indices: 56429--56536 Score: 146
Period size: 48 Copynumber: 2.3 Consensus size: 46
56419 AAGGAACAAT
* *
56429 AAAAAGTAAAAGATCAATTTTATCTTAGAAATTGAGAAAAAGTGCA
1 AAAAAATAAAAGATCAATTTTATCTTAAAAATTGAGAAAAAGTGCA
*
56475 AGGAAAAATAAAAGATCAATTTTGT-TGTAAAAATTGAGAAAAAGTGCA
1 A--AAAAATAAAAGATCAATTTTATCT-TAAAAATTGAGAAAAAGTGCA
*
56523 AAAAAGTAAAAGAT
1 AAAAAATAAAAGAT
56537 TGCTTTTAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
46 13 0.24
47 1 0.02
48 41 0.75
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.24
Consensus pattern (46 bp):
AAAAAATAAAAGATCAATTTTATCTTAAAAATTGAGAAAAAGTGCA
Done.