Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019230.1 Corchorus olitorius cultivar O-4 contig19263, 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: 192316
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:458 original size:31 final size:31
Alignment explanation
Indices: 423--524 Score: 102
Period size: 31 Copynumber: 3.4 Consensus size: 31
413 CCCATTTCAC
423 AGAGGGACTAAATTGATCTGTTTTCAATAGT
1 AGAGGGACTAAATTGATCTGTTTTCAATAGT
* * * *
454 AGAGGGACTAAATTGA-CAGATTT-GATAAT
1 AGAGGGACTAAATTGATCTGTTTTCAATAGT
* * *
483 -GAAGGAACTAAATTGATCTTTTTTCTATAGT
1 AG-AGGGACTAAATTGATCTGTTTTCAATAGT
*
514 ACAGGGACTAA
1 AGAGGGACTAA
525 TCAGGTACTT
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
28 1 0.02
29 17 0.31
30 9 0.16
31 28 0.51
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (31 bp):
AGAGGGACTAAATTGATCTGTTTTCAATAGT
Found at i:1278 original size:22 final size:22
Alignment explanation
Indices: 1253--1297 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1243 CGAGGTTTTC
1253 AGTTGCTTTCATTACTTTCTTA
1 AGTTGCTTTCATTACTTTCTTA
1275 AGTTGCTTTCATTACTTTCTTA
1 AGTTGCTTTCATTACTTTCTTA
1297 A
1 A
1298 CACAATGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.09, T:0.53
Consensus pattern (22 bp):
AGTTGCTTTCATTACTTTCTTA
Found at i:3839 original size:25 final size:27
Alignment explanation
Indices: 3791--3845 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
3781 GTCAAATCAA
3791 ACTCAAATATTCTATGGCCAAAAAA-AT
1 ACTCAAATATTC-ATGGCCAAAAAACAT
*
3818 ACTCAAATATTC-TGGCCCAAAAACAT
1 ACTCAAATATTCATGGCCAAAAAACAT
3844 AC
1 AC
3846 ACTCAGTCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 10 0.38
26 4 0.15
27 12 0.46
ACGTcount: A:0.45, C:0.24, G:0.07, T:0.24
Consensus pattern (27 bp):
ACTCAAATATTCATGGCCAAAAAACAT
Found at i:6205 original size:13 final size:13
Alignment explanation
Indices: 6187--6212 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6177 ATAGGTTTTA
6187 TTTTTTTATTATT
1 TTTTTTTATTATT
6200 TTTTTTTATTATT
1 TTTTTTTATTATT
6213 GTCCAAACAG
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTATTATT
Found at i:12688 original size:53 final size:55
Alignment explanation
Indices: 12589--12695 Score: 150
Period size: 53 Copynumber: 2.0 Consensus size: 55
12579 TTTTTCTGAT
*
12589 TGTACTTTTTTTAAAAAATATATTTCTAAATTGTCATTATTAAAATATAATTTTG
1 TGTACTTTTTTTAAAAAATATATTTCTAAATTATCATTATTAAAATATAATTTTG
*
12644 TGTACTTTTTTT-CAAAA-ATATTTCTAAATTCAT-ATTAATT-AAATATAATTTT
1 TGTACTTTTTTTAAAAAATATATTTCTAAATT-ATCATT-ATTAAAATATAATTTT
12696 TTTTCATTAG
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
53 28 0.58
54 8 0.17
55 12 0.25
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (55 bp):
TGTACTTTTTTTAAAAAATATATTTCTAAATTATCATTATTAAAATATAATTTTG
Found at i:14631 original size:328 final size:327
Alignment explanation
Indices: 13295--15256 Score: 1637
Period size: 328 Copynumber: 6.0 Consensus size: 327
13285 AATCACATTG
* * * * * *
13295 GATTTAATCAGAAATTAATTTGGAAAAAATAGGAAAACCGATATTAGAAACGTGAAAAGCCTTTC
1 GATTTAATTAGAAATTAA-TTCGAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAGCCCTTC
* * * * * * *
13360 AATCTTTTTAGCGTTGA--ACTATATTTGTTATGAGGATCGTGACAAAAAATTGA-GGAATATTC
65 AATCTTTTTGGCGTTGATTA-TATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGGAA-AATC
* * * * * * *
13422 TTTTAGGTAAATTTTTTCAAAATTTTA-CCGAAATCATG--TAGCATCACGGCTCTT-AGCTAAA
128 TTTCAGTTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTATACCATCACGGTTTTTGA-CTAAA
* * *** *
13483 AACACG-TCCCGGGACCCAGACTCAGTTTTGCATGATTTTTGGTATCAAAACTTC-TTGAAATAT
192 AACACGTTCCGGGGTCCC-GACTCAGTTTTGCATGATTTTTGGCGCCAAGAC-TCATTGAAATAT
* * * * *
13546 CTATATTCATCCAACCAAATCTCATCCATATTGAATTTAAGAATTTGTTTTTACGAGTATCTGAA
255 -TATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAA
*
13611 TCTTGTCTC
319 TCTTGTTTC
* * * *
13620 GATTTAATTAAAAATTAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCA
1 GATTTAATTAGAAATTAATTCGAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCA
* * * * *
13685 ATCTTTTTGGCGTTGAATTATATATATTTTATGAGTAATATGGCTAAAAATTGAAGGAAAAACTT
66 ATCTTTTTGGCGTTG-ATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGGAAAATCTT
* * * *
13750 TC-GTTTAAATTTTTGCAAAAATTTAGCCGAAATCATGTATCAACCATTACGGTTTTTGGCTAAA
130 TCAG-TTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTAT--ACCATCACGGTTTTTGACTAAA
** * * ** * * * *
13814 AATGCGTTACAGGGTGTCGCCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTAATGAAATATCA
192 AACACGTTCCGGGGTCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATAT-T
* * ** * * *
13879 ATATTAATCTGATGAAATCTTAATCACATTGGATTTAA-AGATTTGTTTTTACGAGCATCTCAAT
256 ATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGA-ATTTGTTTTTACGAGCATCTGAAT
**
13943 CCGGTTTC
320 CTTGTTTC
** * * * *
13951 GATTTAATTAGAAATTAAATCTAAAAAAAACAAAGAAAAACGATATTAAAAGAGTGAGAAGCCCT
1 GATTTAATTAGAAATT-AAT-TCGAAAAAA-TAAGAAAAACGATATTAGAAGCGTGAAAAGCCCT
* * * ** *
14016 TAAAACTTTTTGGCATTGAGTTATATATTTTTTTATGAGTATTGCAGCAAAAAATTG-GGGAGAA
63 TCAATCTTTTTGGCGTTGA-TTATATA-TTTTTTATGAGTATTGTGGCTAAAAATTGAGGGA-AA
* * ** * * * *
14080 ATTTTTCAGGTCATTTTTTTGGAAAATTTTAGCCGAAATCGTGCACTAACCACCATGG----TGA
125 ATCTTTCA-GTTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-T-ACCATCACGGTTTTTGA
* * * * * *
14141 CTAAAAACGCGTTCTGTGG-CCTCGGA-T-ATGTTTTGCAAGATTTTTGGTGCCAAGTCTCATTG
187 CTAAAAACACGTTCCGGGGTCC-C-GACTCA-GTTTTGCATGATTTTTGGCGCCAAGACTCATTG
* * * * * * *
14203 AAGTATCTACATTCATATAACCAAATCTCACCCACATTGAATTTAAGAATTTGCTTTTAAGAGCA
249 AAATAT-TATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGAATTTGTTTTTACGAGCA
* * * *
14268 ACTGATTCTTATTTT
313 TCTGAATCTTGTTTC
* * ** *
14283 GATTTAATTAGAAATTAATTCGGAAAAATAAGAAAAACAATATTAGAAGCGT-AACAAAACTTTC
1 GATTTAATTAGAAATTAATTCGAAAAAATAAGAAAAACGATATTAGAAGCGTGAA-AAGCCCTTC
* * *
14347 AATCTTTTTGGCATTGTATTATATA-TTTTTATGAGCATTGTGGCTAAAAATTGAGGGAAAAACT
65 AATCTTTTTGGCGTTG-ATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGGAAAATCT
* * * * *
14411 TCCAATTAAATTTTTGCAAAAATTTACCCGAAATCGTGTACTAAACATCACGGTTTTTGACTAAA
129 TTCAGTTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-T-ACCATCACGGTTTTTGACTAAA
* * * *
14476 AACGCGTTCCGGGGTCCCGACTCAATTTTGCATGATTTTTGGCCCCAAGACTCATGGAAATA-TA
192 AACACGTTCCGGGGTCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATTA
* * **
14540 TATTCATCTAA-CAAAGTCAT-AACAATATTGGATTTAAGAATTTGTTTTTACGAGCATCCCAAT
257 TATTCATCTAACCAAA-TC-TCAACCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAAT
**
14603 CGGGTTTC
320 CTTGTTTC
* * * * * *
14611 GATTTAATTAGAAATTAATTCTGAAAAAAATAGGAAAAATGATGTTAGAAGTGTGAGATGCCCTT
1 GATTTAATTAGAAATTAATTC-G-AAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAGCCCTT
* *
14676 CAATCTTTTTTGCCTTGATTTATATATTTTTTATGAGTATTGTGGGC-AAAAATTGA-GGAGAAA
64 CAATCTTTTTGGCGTTGA-TTATATATTTTTTATGAGTATTGT-GGCTAAAAATTGAGGGA-AAA
* * * *
14739 TTTTTCGGGTT-AATTTTTGTAAAATTTTAGCCGAAATCGTGTAT---ATCACGGGTTTTGACTA
126 TCTTTC-AGTTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTATACCATCACGGTTTTTGACTA
* * * * *
14800 AAAACACATTCCGGGG-CCCTAGCTCTGTTTTGCATGATTTTTAGCGCCAAGTCTCATTGAAATA
190 AAAACACGTTCCGGGGTCCCGA-CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATA
* * * * *
14864 TTTATATCCATCTAACCAAATCTC-ACGCACGTTGGATTTGAGAATTTGTTTTTACAAGTATCTG
254 -TTATATTCATCTAACCAAATCTCAAC-CACATTGGATTTAAGAATTTGTTTTTACGAGCATCTG
*
14928 AATCATGTTTC
317 AATCTTGTTTC
* * * *
14939 AATTTAATTAAAAATTAATTCAGAAAAAATAA-AAAAACCGATATTAGAAACGTGAAAAGCCTTT
1 GATTTAATTAGAAATTAATTC-GAAAAAATAAGAAAAA-CGATATTAGAAGCGTGAAAAGCCCTT
* * * * * *
15003 CATTATTTTTGGCGTTTAATTATATATTTTTTATGAGTATCGTGACTAAAAATTGA-GGAATATT
64 CAATCTTTTTGGCG-TTGATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGGAA-AAT
* * *
15067 CTTTTGAG-TAAATTTTTGCAAAATTTTTA-CCGAAATCGTG--TAGCATCGCGGTTTTT-AGCT
127 C-TTTCAGTTAAATTTTTGCAAAA-TTTTAGCCGAAATCGTGTATACCATCACGGTTTTTGA-CT
* *** * * *
15127 AAAAACACG-TCCTGGGATTTAGACTCAGTTTTGCATGATTTTTGGCGGCAAGACTCCTTCAAAT
189 AAAAACACGTTCC-GGGGTCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAAT
* * * * * *
15191 ATTTATATTCATCTAACCAAATCTCATCCATACTGTATTTACGGATTTGTTTTTACGAGCATCTG
253 A-TTATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTG
15256 A
317 A
15257 TTCAAACTTT
Statistics
Matches: 1300, Mismatches: 270, Indels: 131
0.76 0.16 0.08
Matches are distributed among these distances:
324 55 0.04
325 23 0.02
326 162 0.12
327 156 0.12
328 270 0.21
329 59 0.05
330 116 0.09
331 194 0.15
332 133 0.10
333 11 0.01
334 53 0.04
335 30 0.02
336 36 0.03
337 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (327 bp):
GATTTAATTAGAAATTAATTCGAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCA
ATCTTTTTGGCGTTGATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGGAAAATCTTT
CAGTTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTATACCATCACGGTTTTTGACTAAAAACA
CGTTCCGGGGTCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATTATATT
CATCTAACCAAATCTCAACCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTT
TC
Found at i:16732 original size:331 final size:331
Alignment explanation
Indices: 15265--18197 Score: 2325
Period size: 331 Copynumber: 8.9 Consensus size: 331
15255 GATTCAAACT
* * * * * * * *
15265 TTTTTGTCGTTGTATTGTGTATTTTTTATGAGTATTTGTGGCTAAAAATTGTTGGAGAAA-CTTT
1 TTTTTGGCGTTGAATTATATATTTTTTATGAGTA-TTATGGCCAAAAATTG--AGAGAAATTTTT
* * * *
15329 CGGCTAAATTTTTGCAAAAATTTAGCCGAAATCGTGTAC-AA-CATCACGGTTTTTAGCTAAAAA
63 CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA
* * * *
15392 CGCGTTCCGGGGTCCCGGCTCAATTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCCAT
128 CGCGTTCCGAGGTCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTAT
* * *
15457 ATTCATCTAA-CAAAGTCGT-AGGCACATTGGATTTAAGGATTTAGTTTTTAC-ATGCATCTCAA
193 ATTCATCTAACCAAA-TC-TCAGCCACATTGGATTTAAAGATTT-GTTTTTACGA-GCATCTGAA
* * * *** * * *
15519 TCCGGTTTCAATTTAATTAGAAATAAATTTTTAAAAAAATAAGAAAAACGACATTAGAAGTGTGA
254 TCCTGTTTCGATTTAATTAGAAATTAA-TTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTGA
*
15584 GAAGCCCTTCAATC
318 AAAGCCCTTCAATC
* * * * *
15598 ATTTTGGCATTGAGTTATAT-TATTTTTATGAGT-TTGTGTCCAAAAATTGAGGAGAAATTTTT-
1 TTTTTGGCGTTGAATTATATAT-TTTTTATGAGTATTATGGCCAAAAATTGA-GAGAAATTTTTC
* * * *
15660 GGGTCAATTTTTTGCAGAATTTTAGCCGAAATCGTG---T-A-CGTCACGATTTTTGACTAAAAA
64 GGGTCAA-TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA
* * *
15720 CGCGTT-C-TGG----G---CA---TTGCATGATTTTTAGCGCTAA-ATCTCATTGAAATATCTA
128 CGCGTTCCGAGGTCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGA-CTCATTGAAATATCTA
* * * * * * * * *
15772 TATCCATATAACCAAATCTGAACCATATTGGA-TTAAAGGATTAGTTTTTACAAGTAAT-TAAAT
192 TATTCATCTAACCAAATCTCAGCCACATTGGATTTAAA-GATTTGTTTTTACGAG-CATCTGAAT
** * * * * *
15835 AATTTTTCGATTAAATTAGAAATTAATTCGG-AAAAATAGGAAAACCAATATTAATAATGC--GA
255 CCTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGATATT-AGAA-GCGTGA
* *
15897 AAAGCCTTTCAATT
318 AAAGCCCTTCAATC
* * ** *
15911 TTTTTGGCATTGAATTATATTTTCTTTTATGAGTATCGTGACCAAAAATTGAG-GAATATTCTTT
1 TTTTTGGCGTTGAATTATATATT-TTTTATGAGTATTATGGCCAAAAATTGAGAGAA-ATT-TTT
* * * * * * * * *
15975 TGTGTGAATTTTTGCAAAACTTTA-CCAAAAT--TCTA-T-AGCATCATGGTTCTTATAGCTAAA
63 CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTT-TT-TGGCTAAA
* * * * * * * * ** * *
16035 AACACG-TCCAATGACCCAGGCTCAGTTTTGCATTATATATGGCAACAAGATTCCTTGAAATATC
126 AACGCGTTCCGAGGTCCC-GACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATC
* * * *
16099 TATATTTATCTAACCAAATCTC-GTCCATATTGGATTTAAGGATTTGTTTTTACAAGCAGT-TGA
190 TATATTCATCTAACCAAATCTCAG-CCACATTGGATTTAAAGATTTGTTTTTACGAGCA-TCTGA
* * * * *** *
16162 CTCTTGTTTCGATTTAATTATAAATTAATTCAGAAATTTTTTTTATGAAAAACGATATTAGAAGC
253 ATCCTGTTTCGATTTAATTAGAAATTAATTCGGAAA----AAATAGGAAAAACGATATTAGAAGC
* * *
16227 ATGAAAAACTCTTCAATC
314 GTGAAAAGCCCTTCAATC
* * * * * * * * **
16245 TTTTTGGCGGTGAATTATATGTATTTTATAATTATTGTGGCTAAAAATTGAGGGAAAAACTTTCG
1 TTTTTGGCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGAG-AAATTTTTCG
* * * * * *
16310 GTTAAATTTTTGCAAAAATTTAGACGAAATCGTGTAATAA-CATTACGGTTTTTGGCTAAAAACG
65 GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACG
** * * * * *
16374 CGTT-TAAGGGCCCTGGCTCAGTTTTGCATGGTTTTTGGCGCCAAGAGTCATTGATATATCTATA
130 CGTTCCGAGGTCCC-GACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATA
* * * * * * * *
16438 TTCATCTAACGAAATCTCAGTCACATTGGATTCAAAGATTTCTTTTTATGAGCTTCTCAATCCGG
194 TTCATCTAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCCTG
* * *
16503 TTTCGATTTAATTAAAAATTAATTCGGAAAAAATTGGAAAAACAATATTAGAAGCGTGAAAAGCC
259 TTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCC
16568 CTTCAATC
324 CTTCAATC
* * * * * *
16576 TTCTTGGTGTTGAGTTATAAATTTTTTACGAGTATTATGGCCAAAAATTGATGAGAAATTTTTCA
1 TTTTTGGCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGA-GAGAAATTTTTCG
* * * *
16641 AGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAG-TTTTGGCTAAATATG
65 GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACG
* * * * *
16705 CGTTCCGAGGTCCCGACTCAATTTTGCATGACTTTTAGCGCCAAGAGTAATTGAAATATCTATAT
130 CGTTCCGAGGTCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATAT
* * ** * * * * *
16770 TCATCTAACGAAATATCAATCACATTGGATTTAAAGATTTGTTTTTAAGTGCATCTTACTCCGGT
195 TCATCTAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCCTGT
* * * * * * *
16835 TTCGATTCAA--AAAAATTAAATAGG---AAA-A--AAAAACGATATTAAAAGCGTGAGAAGCTC
260 TTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCC
* *
16892 TTTAAAC
325 TTCAATC
* * * * *
16899 TTTTTGGCGTTGAGTTATATATTTTTTATGAGAATTGGA-GG-CAAAGATTGGGCAGAATTTTTT
1 TTTTTGGCGTTGAATTATATATTTTTTATGAGTATT--ATGGCCAAAAATTGAG-AGAAATTTTT
*
16962 CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAA
63 CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA
* * * ** * * * * *
17027 CACGGTTCGGAGCTCTAG-CTCTGTTTTGCATGATTTTTAGTGCCACGTCTCATTGAAATATCTA
128 CGC-GTTCCGAGGTCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTA
* * * * * *
17091 TATCCATCTAACCAAATCTCACCCACATTGGATTTAAAGATTTGTTCTTACGATCATTTGAATCA
192 TATTCATCTAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCC
* * * *
17156 TGTTTCGATTTGATTATAAATTAATTC--AAATAAATAGGAAAATCGATATTAGAAACGTGAAAA
257 TGTTTCGATTTAATTAGAAATTAATTCGGAAA-AAATAGGAAAAACGATATTAGAAGCGTGAAAA
* *
17219 GGCTTTCAA--
321 GCCCTTCAATC
* * *
17228 ---TTGGCGTTGAATTATATTTTTTTTATGACTA-TAGTGACCAAAAATTGAG-GAATATTCTTT
1 TTTTTGGCGTTGAATTATATATTTTTTATGAGTATTA-TGGCCAAAAATTGAGAGAA-ATT-TTT
*** * * * * * *
17288 TTTGTTAATTTTTGCAAAATTTTA-CCGAAAT--TGT-GT-AGCATCACAGTTCTTAGCTAAAAA
63 CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA
* * * * * *
17348 CACG-TCCCAGGACCCAGACTCAGTTTTGTATGATTTTTGGTGCCAAGACTCCTT-AAGATATCT
128 CGCGTTCCGAGGTCCC-GACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAA-ATATCT
* * * *
17411 ATATTCATCTAACCAAATCTCACCCATATTGGATTTGAGGATTTGTTTTTAACGAGCATCTGAAT
191 ATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTT-ACGAGCATCTGAAT
* * * * *
17476 CTTGTTTCGATTTAATAAAAAATTAAATCTGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAA
255 CCTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAA
*
17541 AACCCTTCAATC
320 AGCCCTTCAATC
* * * * **
17553 TTTTTGGCGTTGAATTATATATATTTTATGAGTATTATGGCTAAAGATTGAGGGAAAAACTTTCG
1 TTTTTGGCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGAG-AAATTTTTCG
** * * * *
17618 ATTAAATTTTTGCAAAAATTTAGCCGAAATCGTGTACTAACCATTACGGTTTTGGGCTAAAAACG
65 GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACG
** * * * *
17683 CGTT-ATAGGGCCCCGTCTTAGTTTTGCATGA-TTTTGGCGCCAAGACTCAATGAAATATCTATA
130 CGTTCCGA-GGTCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATA
* * * * * * *
17746 TTTATGTAACGAAATCTCAGTCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTCAACCCGG
194 TTCATCTAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCCTG
* * * * *
17811 TTTCGTTTTAATTAGAAATTAAATT--GAAAAAAAAAGAAAAACGATATTAGAAGAGTGAGAAGC
259 TTTCGATTTAATTAGAAATT-AATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGC
*
17874 CCTTCAAAC
323 CCTTCAATC
* * * *
17883 TTTTTGGCATTGAGTTATATATTTTTTATGAGTATTGTGG-CAAAACATTGGGGAGAAATTTTTC
1 TTTTTGGCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAA-ATT-GAGAGAAATTTTTC
* * * *
17947 GGGTCATTTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCATGGTTTTTGACTAAAA
64 GGGTCA--ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAA
** * * * * * * *
18012 ACGCGTTTTGTGGCCCCAGA-TCTGTTTTACATGATTTTTGGAGGCAAGTCTCATTGAAATATCT
127 ACGCGTTCCGAGGTCCC-GACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCT
* * * *
18076 ATATTCATCTAACCAAGTCTCACCCACATTGGATTT-AAGATTTTGCTTTTACGAGCATATGAAT
191 ATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAAGA-TTTGTTTTTACGAGCATCTGAAT
* * * * * *
18140 CATATTTTGATTTAATTAGACATTAATTCGG-AAAAATAGGAAAAGCTATATTAGAAGC
255 CCTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGC
18198 AGGACTTTGC
Statistics
Matches: 2060, Mismatches: 427, Indels: 226
0.76 0.16 0.08
Matches are distributed among these distances:
312 1 0.00
313 52 0.03
314 28 0.01
315 78 0.04
316 69 0.03
317 16 0.01
318 1 0.00
319 7 0.00
320 4 0.00
321 103 0.05
322 39 0.02
323 167 0.08
324 120 0.06
325 22 0.01
326 75 0.04
327 1 0.00
328 90 0.04
329 125 0.06
330 110 0.05
331 346 0.17
332 168 0.08
333 226 0.11
334 59 0.03
335 136 0.07
336 7 0.00
337 9 0.00
338 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (331 bp):
TTTTTGGCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGAGAAATTTTTCGG
GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGC
GTTCCGAGGTCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATT
CATCTAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCCTGTT
TCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCT
TCAATC
Found at i:17601 original size:654 final size:651
Alignment explanation
Indices: 15335--18140 Score: 2236
Period size: 654 Copynumber: 4.3 Consensus size: 651
15325 CTTTCGGCTA
* * * * * *
15335 AATTTTTGCAAAAATTTAGCCGAAATCGTGTACAACATCACGGTTTTTAGCTAAAAACGCGTTCC
1 AATTTTTGCAAAATTTTAGCCGAAATTGTGTA-AGCATCACAGTTCTTAGCTAAAAACACGTTCC
* * * *
15400 GGGGTCCCGGCTCAATTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCCATATTCATCT
65 GAGGACCCGACTCAATTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCT
** *
15465 AA-CAAAGTCGT-AGGCACATTGGATTTAAGGATTTAGTTTTTAC-ATGCATCTCAATCCGGTTT
130 AACCAAA-TC-TCAACCACATTGGATTTAAGGATTT-GTTTTTACGA-GCATCTGAATCCGGTTT
* * * * * * * * *
15527 CAATTTAATTAGAAA-TAAATTTTTAAAAAAATAAGAAAAACGACATTAGAAGTGTGAGAAGCCC
191 CGATTTAATAAAAAATTAAA--TCTGAAAAAAT-AGAAAAACGATATTAGAAGCGTGAAAAACCC
* * * * * * *
15591 TTCAATCATTTTGGCATTGAGTTATAT-TATTTTTATGAGT-TTGTGTCCAAAAATTGA-GGAGA
253 TTCAATCTTTTTGGCGTTGAATTATATATA-TTTTATGAGTATTATGGCTAAAAATTGAGGGAAA
* * * * * * *
15653 AATTTTTGGGTCAATTTTTTGCAGAATTTTAGCCGAAATCGTG---T-ACGTCACGATTTTTGAC
317 AACTTTCGGGT-AAATTTTTGCAAAAATTTAGCCGAAATCGTGTACTAACATCACGGTTTTTGAC
* *
15714 TAAAAACGC-GTTCTGGG-C-A-------TTGCATGATTTTTAGCGCTAA-ATCTCATTGAAATA
381 TAAAAACGCGGTT-AGGGCCTAGTCTGTTTTGCATGATTTTTAGCGCCAAGA-CTCATTGAAATA
* * * * * * *
15768 TCTATATCCATATAACCAAATCTGAACCATATTGGA-TTAAAGGATTAGTTTTTACAAGT-AATT
444 TCTATATCCATCTAACCAAATCTCAGCCACATTGGATTTAAA-GATTTGTTTTTACGA-TCATTT
* * * * * * * *
15831 AAATAATTTTTCGATTAAATTAGAAATTAATTCGGAAAAATAGGAAAACCAATATTA-ATAATGC
507 AAATCATGTTTCGATTTAATTAAAAATTAATTCGAAAAAATAGGAAAAACAATATTAGA-AACGT
* *
15895 GAAAAGCCTTTCAATTTTTTTGGCATTGAATTATATTTTCTTTTATGAGTATCGTGACCAAAAAT
571 GAAAAGCCTTTCAA----TTTGGCGTTGAATTATATTTT-TTTTATGAGTATAGTGACCAAAAAT
* *
15960 TGAGGAATATTCTTTTGTGTG
631 TGAGGAATATTCTTTTATGTC
* * * * **
15981 AATTTTTGCAAAACTTTA-CCAAAATTCTAT-AGCATCATGGTTCTTATAGCTAAAAACACG-TC
1 AATTTTTGCAAAATTTTAGCCGAAATTGTGTAAGCATCACAGTTC-T-TAGCTAAAAACACGTTC
* * * * * * * ** * * *
16043 CAATGACCCAGGCTCAGTTTTGCATTATATATGGCAACAAGATTCCTTGAAATATCTATATTTAT
64 CGAGGACCC-GACTCAATTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCAT
** * * * **
16108 CTAACCAAATCTCGTCCATATTGGATTTAAGGATTTGTTTTTACAAGCAGT-TGACTCTTGTTTC
128 CTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCA-TCTGAATCCGGTTTC
* * * * *** * *
16172 GATTTAATTATAAATTAATTCAGAAATTTTTTTTATGAAAAACGATATTAGAAGCATGAAAAACT
192 GATTTAATAAAAAATTAAATCTGAAA----AAATA-GAAAAACGATATTAGAAGCGTGAAAAACC
* * * * *
16237 CTTCAATCTTTTTGGCGGTGAATTATATGTATTTTATAATTATTGTGGCTAAAAATTGAGGGAAA
252 CTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTATGGCTAAAAATTGAGGGAAA
* * * * *
16302 AACTTTCGGTTAAATTTTTGCAAAAATTTAGACGAAATCGTGTAATAACATTACGGTTTTTGGCT
317 AACTTTCGGGTAAATTTTTGCAAAAATTTAGCCGAAATCGTGTACTAACATCACGGTTTTTGACT
* * * * * * *
16367 AAAAACGCGTTTAAGGGCCCTGGCTCAGTTTTGCATGGTTTTTGGCGCCAAGAGTCATTGATATA
382 AAAAACGCGGTT-AGGG-CCTAG-TCTGTTTTGCATGATTTTTAGCGCCAAGACTCATTGAAATA
* * * * * * * *
16432 TCTATATTCATCTAACGAAATCTCAGTCACATTGGATTCAAAGATTTCTTTTTATGAGC-TTCTC
444 TCTATATCCATCTAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGATCATT-TA
** * *
16496 AATCCGGTTTCGATTTAATTAAAAATTAATTCGGAAAAAATTGGAAAAACAATATTAGAAGCGTG
508 AATCATGTTTCGATTTAATTAAAAATTAATTC-GAAAAAATAGGAAAAACAATATTAGAAACGTG
* * * ** * *
16561 AAAAGCCCTTCAATCTTCTTGGTGTTGAGTTATAAATTTTTTACGAGTATTA-TGGCCAAAAATT
572 AAAAGCCTTTCAA---T-TTGGCGTTGAATTATATTTTTTTTATGAGTA-TAGTGACCAAAAATT
* *
16625 GATGAGAA-ATT-TTTCAAGTC
632 GA-G-GAATATTCTTTTATGTC
* * * * **
16645 AATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTT-TTGGCTAAATATGCGTT
1 AATTTTTGCAAAATTTTAGCCGAAAT--TGT-GTAAGCATCACAGTTCTTAGCTAAAAACACGTT
* * * * *
16709 CCGAGGTCCCGACTCAATTTTGCATGACTTTTAGCGCCAAGAGTAATTGAAATATCTATATTCAT
63 CCGAGGACCCGACTCAATTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCAT
* * * * * * * *
16774 CTAACGAAATATCAATCACATTGGATTTAAAGATTTGTTTTTAAGTGCATCTTACTCCGGTTTCG
128 CTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCCGGTTTCG
* ** * * * * *
16839 A-TTCA-AAAAAATTAAA--T-AGGAAA-A-AAAAACGATATTAAAAGCGTGAGAAGCTCTTTAA
193 ATTTAATAAAAAATTAAATCTGAAAAAATAGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAA
* * * * * * ***
16897 ACTTTTTGGCGTTGAGTTATATATTTTTTATGAGAATTGGA-GGC-AAAGATTG-GGCAGAATTT
258 TCTTTTTGGCGTTGAATTATATATATTTTATGAGTATT--ATGGCTAAAAATTGAGGGA-AAAAC
* *
16959 TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAA
320 TTTCGGGTAAATTTTTGCAAAAATTTAGCCGAAATCGTGTACTAA-CATCACGGTTTTTGACTAA
* * * * *
17024 AAACACGGTTCGGAGCTCTAGCTCTGTTTTGCATGATTTTTAGTGCCACGTCTCATTGAAATATC
384 AAACGCGGTTAGG-GC-CTAG-TCTGTTTTGCATGATTTTTAGCGCCAAGACTCATTGAAATATC
* * *
17089 TATATCCATCTAACCAAATCTCACCCACATTGGATTTAAAGATTTGTTCTTACGATCATTTGAAT
446 TATATCCATCTAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGATCATTTAAAT
* * * *
17154 CATGTTTCGATTTGATTATAAATTAATTC-AAATAAATAGGAAAATCGATATTAGAAACGTGAAA
511 CATGTTTCGATTTAATTAAAAATTAATTCGAAA-AAATAGGAAAAACAATATTAGAAACGTGAAA
* *
17218 AGGCTTTCAA-TTGGCGTTGAATTATATTTTTTTTATGACTATAGTGACCAAAAATTGAGGAATA
575 AGCCTTTCAATTTGGCGTTGAATTATATTTTTTTTATGAGTATAGTGACCAAAAATTGAGGAATA
* *
17282 TTCTTTTTTGTT
640 TTCTTTTATGTC
*
17294 AATTTTTGCAAAATTTTA-CCGAAATTGTGT-AGCATCACAGTTCTTAGCTAAAAACACG-TCCC
1 AATTTTTGCAAAATTTTAGCCGAAATTGTGTAAGCATCACAGTTCTTAGCTAAAAACACGTTCCG
* * * *
17356 AGGACCCAGACTCAGTTTTGTATGATTTTTGGTGCCAAGACTCCTT-AAGATATCTATATTCATC
66 AGGACCC-GACTCAATTTTGCATGATTTTTGGCGCCAAGACTCATTGAA-ATATCTATATTCATC
* * * **
17420 TAACCAAATCTCACCCATATTGGATTTGAGGATTTGTTTTTAACGAGCATCTGAATCTTGTTTCG
129 TAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTT-ACGAGCATCTGAATCCGGTTTCG
17485 ATTTAATAAAAAATTAAATCTGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCA
193 ATTTAATAAAAAATTAAATCTGAAAAAATA-GAAAAACGATATTAGAAGCGTGAAAAACCCTTCA
*
17550 ATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTATGGCTAAAGATTGAGGGAAAAACTT
257 ATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTATGGCTAAAAATTGAGGGAAAAACTT
** * * *
17615 TCGATTAAATTTTTGCAAAAATTTAGCCGAAATCGTGTACTAACCATTACGGTTTTGGGCTAAAA
322 TCGGGTAAATTTTTGCAAAAATTTAGCCGAAATCGTGTACTAA-CATCACGGTTTTTGACTAAAA
* ** * *
17680 ACGCGTTATAGGGCCCCGTCTTAGTTTTGCATGA-TTTTGGCGCCAAGACTCAATGAAATATCTA
386 ACGCGGT-TAGGGCCTAGTC-T-GTTTTGCATGATTTTTAGCGCCAAGACTCATTGAAATATCTA
** * * * * * * * *
17744 TATTTATGTAACGAAATCTCAGTCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTCAACCC
448 TATCCATCTAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGATCATTTAAATCA
* * * * * * *
17809 GGTTTCGTTTTAATTAGAAATTAAATT-GAAAAAAAAAGAAAAACGATATTAGAAGA-GTGAGAA
513 TGTTTCGATTTAATTAAAAATT-AATTCGAAAAAATAGGAAAAACAATATTAGAA-ACGTGAAAA
* * * * * * *
17872 GCCCTTCAAACTTTTTGGCATTGAGTTATATATTTTTTATGAGTATTGTG-GCAAAACATTGGGG
576 GCCTTTC-AA---TTTGGCGTTGAATTATATTTTTTTTATGAGTATAGTGACCAAAA-ATTGAGG
* ***
17936 AGAAATT-TTTCGGGTC
636 A-ATATTCTTTTATGTC
* * * * ** * *
17952 ATTTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCATGGTT-TTTGACTAAAAACGC
1 A--ATTTTTGCAAAATTTTAGCCGAAAT--TGT-GTAAGCATCACAGTTCTTAG-CTAAAAACAC
** * * ** * * * *
18016 GTTTTGTGGCCCCAGA-TCTGTTTTACATGATTTTTGGAGGCAAGTCTCATTGAAATATCTATAT
60 GTTCCGAGGACCC-GACTCAATTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATAT
* * * *
18080 TCATCTAACCAAGTCTCACCCACATTGGATTTAA-GATTTTGCTTTTACGAGCATATGAATC
124 TCATCTAACCAAATCTCAACCACATTGGATTTAAGGA-TTTGTTTTTACGAGCATCTGAATC
18141 ATATTTTGAT
Statistics
Matches: 1705, Mismatches: 356, Indels: 180
0.76 0.16 0.08
Matches are distributed among these distances:
643 14 0.01
644 63 0.04
645 187 0.11
646 43 0.03
647 62 0.04
648 68 0.04
649 73 0.04
650 1 0.00
651 5 0.00
652 26 0.02
653 144 0.08
654 307 0.18
655 152 0.09
656 3 0.00
657 5 0.00
658 44 0.03
659 4 0.00
660 16 0.01
661 7 0.00
663 4 0.00
664 171 0.10
665 167 0.10
666 118 0.07
667 11 0.01
668 1 0.00
669 9 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (651 bp):
AATTTTTGCAAAATTTTAGCCGAAATTGTGTAAGCATCACAGTTCTTAGCTAAAAACACGTTCCG
AGGACCCGACTCAATTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCTA
ACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCCGGTTTCGATT
TAATAAAAAATTAAATCTGAAAAAATAGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATCT
TTTTGGCGTTGAATTATATATATTTTATGAGTATTATGGCTAAAAATTGAGGGAAAAACTTTCGG
GTAAATTTTTGCAAAAATTTAGCCGAAATCGTGTACTAACATCACGGTTTTTGACTAAAAACGCG
GTTAGGGCCTAGTCTGTTTTGCATGATTTTTAGCGCCAAGACTCATTGAAATATCTATATCCATC
TAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGATCATTTAAATCATGTTTCGA
TTTAATTAAAAATTAATTCGAAAAAATAGGAAAAACAATATTAGAAACGTGAAAAGCCTTTCAAT
TTGGCGTTGAATTATATTTTTTTTATGAGTATAGTGACCAAAAATTGAGGAATATTCTTTTATGT
C
Found at i:17654 original size:977 final size:981
Alignment explanation
Indices: 16390--18195 Score: 2463
Period size: 977 Copynumber: 1.8 Consensus size: 981
16380 AGGGCCCTGG
* * * * *
16390 CTCAGTTTTGCATGGTTTTTGGCGCCAAGAGTCATTGATATATCTATATTCATCTAACGAAATCT
1 CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTAAGATATCTATATTCATCTAACCAAATCT
** * * *
16455 CAGTCACATTGGATTCAAAGATTTCTTTTTATGAGCTTCTCAATCCGGTTTCGATTTAATTAAAA
66 CACCCACATTGGATTCAAAGATTTCTTTTTACGAGCATCTCAATCCGGTTTCGATTTAATAAAAA
* * * *
16520 ATTAATTCGGAAAAAATTGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTCTTGGTG
131 ATTAAATCGGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAATCTTCTTGGCG
* * * ** *
16585 TTGAGTTATAAATTTTTTACGAGTATTATGGCCAAAAATTGATGAGAAATTTTTCAAGTCAATTT
196 TTGAATTATAAATATTTTACGAGTATTATGGCCAAAAATTGAGGAGAAAACTTTCAAGTAAATTT
* * * *
16650 TTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTT-GGCTAAATATGCGTTCCGA-
261 TTGCAAAAATTTAGCCGAAATCGTGTACTAACCATCACAGTTTTGGGCTAAAAACGCGTT-AGAG
* *
16713 GGTCCCGACTCAATTTTGCATGACTTTTAGCGCCAAGAGT-AATTGAAATATCTATATTCATCTA
325 GGCCCCGACTCAATTTTGCATGA-TTTTAGCGCCAAGACTCAA-TGAAATATCTATATTCATCTA
* *
16777 ACGAAATATCAATCACATTGGATTTAAAGATTTGTTTTTAAGTGCATCT-TACTCCGGTTTCGAT
388 ACGAAATATCAATCACATTGGATTTAAAGATTTGTTTTTAAGAGCATCTCAAC-CCGGTTTCGAT
** * * *
16841 TCAA-AAAAATTAAA-T-AGGAAAA-AAAAACGATATTAAAAGCGTGAGAAGCTCTTTAAACTTT
452 TCAATAAAAATTAAATTAAAAAAAAGAAAAACGATATTAAAAGAGTGAGAAGCCCTTCAAACTTT
* * *
16902 TTGGCGTTGAGTTATATATTTTTTATGAGAATTGGAGGC-AAAGATTGGGCAGAATTTTTTCGGG
517 TTGGCATTGAGTTATATATTTTTTATGAGAATT-GAGGCAAAACATTGGGCAGAAATTTTTCGGG
*
16966 TCA-ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACAC
581 TCATATTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACAC
* * * * * *
17030 GGTTCG-GAGCTCTAGCTCTGTTTTGCATGATTTTTAGTGCCACGTCTCATTGAAATATCTATAT
646 GGTTCGTG-GCCCCAGATCTGTTTTACATGATTTTTAGAGCCAAGTCTCATTGAAATATCTATAT
* *
17094 CCATCTAACCAAATCTCACCCACATTGGATTTAAAGA-TTTG-TTCTTACGATCATTTGAATCAT
710 CCATCTAACCAAATCTCACCCACATTGGATTT-AAGATTTTGCTT-TTACGAGCATATGAATCAT
* * * *
17157 GTTTCGATTTGATTATAAATTAATTC-AAATAAATAGGAAAATCGATATTAGAAACGTGAAAAGG
773 ATTTCGATTTAATTAGAAATTAATTCGAAA-AAATAGGAAAAGCGATATTAGAAACGTGAAAAGG
17221 CTTTCAATTGGCGTTGAATTATATTTTTTTTATGACTATAGTGACCAAAAATTGAGGAATATTCT
837 CTTTCAATTGGCGTTGAATTATATTTTTTTTATGACTATAGTGACCAAAAATTGAGGAATATTCT
17286 TTTTTGTTAATTTTTGCAAAATTTTACCGAAATTGTGTAGCATCACAGTTCTTAGCTAAAAACAC
902 TTTTTGTTAATTTTTGCAAAATTTTACCGAAATTGTGTAGCATCACAGTTCTTAGCTAAAAACAC
17351 GTCCCAGGACCCAGA
967 GTCCCAGGACCCAGA
* * *
17366 CTCAGTTTTGTATGATTTTTGGTGCCAAGACTCCTTAAGATATCTATATTCATCTAACCAAATCT
1 CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTAAGATATCTATATTCATCTAACCAAATCT
* ** * * * **
17431 CACCCATATTGGATTTGAGGATTTGTTTTTAACGAGCATCTGAATCTTGTTTCGATTTAATAAAA
66 CACCCACATTGGATTCAAAGATTTCTTTTT-ACGAGCATCTCAATCCGGTTTCGATTTAATAAAA
* * *
17496 AATTAAATCTGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGC
130 AATTAAATCGGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAATCTTCTTGGC
* * * * * *
17561 GTTGAATTATATATATTTTATGAGTATTATGGCTAAAGATTGAGG-GAAAAACTTTCGATTAAAT
195 GTTGAATTATAAATATTTTACGAGTATTATGGCCAAAAATTGAGGAG-AAAACTTTCAAGTAAAT
* * *
17625 TTTTGCAAAAATTTAGCCGAAATCGTGTACTAACCATTACGGTTTTGGGCTAAAAACGCGTTATA
259 TTTTGCAAAAATTTAGCCGAAATCGTGTACTAACCATCACAGTTTTGGGCTAAAAACGCGTTAGA
* * * * * *
17690 GGGCCCCGTCTTAGTTTTGCATGATTTTGGCGCCAAGACTCAATGAAATATCTATATTTATGTAA
324 GGGCCCCGACTCAATTTTGCATGATTTTAGCGCCAAGACTCAATGAAATATCTATATTCATCTAA
* * * * *
17755 CGAAATCTCAGTCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTCAACCCGGTTTCGTTTT
389 CGAAATATCAATCACATTGGATTTAAAGATTTGTTTTTAAGAGCATCTCAACCCGGTTTCGATTC
* *
17820 AATTAGAAATTAAATTGAAAAAAAAAGAAAAACGATATTAGAAGAGTGAGAAGCCCTTCAAACTT
454 AA-TAAAAATTAAATT--AAAAAAAAGAAAAACGATATTAAAAGAGTGAGAAGCCCTTCAAACTT
* * *
17885 TTTGGCATTGAGTTATATATTTTTTATGAGTATTGTGGCAAAACATTGGGGAGAAATTTTTCGGG
516 TTTGGCATTGAGTTATATATTTTTTATGAGAATTGAGGCAAAACATTGGGCAGAAATTTTTCGGG
* * *
17950 TCATTTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCATGGTTTTTGACTAAAAACG
581 TCA-TATTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACA
* * * *
18015 CGTTTTGTGGCCCCAGATCTGTTTTACATGATTTTTGGAGGCAAGTCTCATTGAAATATCTATAT
645 CGGTTCGTGGCCCCAGATCTGTTTTACATGATTTTTAGAGCCAAGTCTCATTGAAATATCTATAT
* *
18080 TCATCTAACCAAGTCTCACCCACATTGGATTTAAGATTTTGCTTTTACGAGCATATGAATCATAT
710 CCATCTAACCAAATCTCACCCACATTGGATTTAAGATTTTGCTTTTACGAGCATATGAATCATAT
* * * *
18145 TTTGATTTAATTAGACATTAATTCGGAAAAATAGGAAAAGCTATATTAGAA
775 TTCGATTTAATTAGAAATTAATTCGAAAAAATAGGAAAAGCGATATTAGAA
18196 GCAGGACTTT
Statistics
Matches: 709, Mismatches: 101, Indels: 30
0.84 0.12 0.04
Matches are distributed among these distances:
976 81 0.11
977 271 0.38
978 36 0.05
979 9 0.01
980 1 0.00
983 9 0.01
984 91 0.13
985 4 0.01
986 202 0.28
987 5 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (981 bp):
CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTAAGATATCTATATTCATCTAACCAAATCT
CACCCACATTGGATTCAAAGATTTCTTTTTACGAGCATCTCAATCCGGTTTCGATTTAATAAAAA
ATTAAATCGGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAATCTTCTTGGCG
TTGAATTATAAATATTTTACGAGTATTATGGCCAAAAATTGAGGAGAAAACTTTCAAGTAAATTT
TTGCAAAAATTTAGCCGAAATCGTGTACTAACCATCACAGTTTTGGGCTAAAAACGCGTTAGAGG
GCCCCGACTCAATTTTGCATGATTTTAGCGCCAAGACTCAATGAAATATCTATATTCATCTAACG
AAATATCAATCACATTGGATTTAAAGATTTGTTTTTAAGAGCATCTCAACCCGGTTTCGATTCAA
TAAAAATTAAATTAAAAAAAAGAAAAACGATATTAAAAGAGTGAGAAGCCCTTCAAACTTTTTGG
CATTGAGTTATATATTTTTTATGAGAATTGAGGCAAAACATTGGGCAGAAATTTTTCGGGTCATA
TTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACACGGTTC
GTGGCCCCAGATCTGTTTTACATGATTTTTAGAGCCAAGTCTCATTGAAATATCTATATCCATCT
AACCAAATCTCACCCACATTGGATTTAAGATTTTGCTTTTACGAGCATATGAATCATATTTCGAT
TTAATTAGAAATTAATTCGAAAAAATAGGAAAAGCGATATTAGAAACGTGAAAAGGCTTTCAATT
GGCGTTGAATTATATTTTTTTTATGACTATAGTGACCAAAAATTGAGGAATATTCTTTTTTGTTA
ATTTTTGCAAAATTTTACCGAAATTGTGTAGCATCACAGTTCTTAGCTAAAAACACGTCCCAGGA
CCCAGA
Found at i:18553 original size:107 final size:105
Alignment explanation
Indices: 18330--18592 Score: 386
Period size: 107 Copynumber: 2.5 Consensus size: 105
18320 AATTTTTCTA
* **
18330 ACCCTTAAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTT
1 ACCCTT-AAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTT
* *
18393 ATCTCTAAAACCCTATAGCGATATTATTAATTATGGAATTT
65 ATCTCTAAAACCCTATAACGATATTATTAATTATGAAATTT
* * *
18434 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGTTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
* * *
18499 TTTCTAAAACCCTATAACAATATATTATTAATTTTGAAATTT
66 TCTCTAAAACCCTATAAC--GATATTATTAATTATGAAATTT
18541 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
18593 AGGCTAAACT
Statistics
Matches: 143, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
103 21 0.15
104 20 0.14
105 32 0.22
107 70 0.49
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.41
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TCTCTAAAACCCTATAACGATATTATTAATTATGAAATTT
Found at i:19620 original size:334 final size:326
Alignment explanation
Indices: 18751--20004 Score: 1183
Period size: 328 Copynumber: 3.8 Consensus size: 326
18741 TAACAAAACT
* *
18751 TTCAGTCTTTTTGGCGTTGTA-TTATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGGAAA
1 TTCAATCTTTTTGGCGTTG-AGTTATATATTTTTTATGAGTATTGTGGCCAAAAATTG-GGGAAA
* *
18815 AACTTTCGGTTAAATTTTTGCAAAAATTTA-CCTGAAATCGTGTACTAATCATCACGGTTTTTGG
64 AACTTTCGGTCAAATTTTTGCAAAAATTTAGCC-GAAATCGTGTACTAACCATCACGGTTTTTGG
* * * * * * * *
18879 CTAAAAATGCGTTCCGGGGTCCCGGCTAAATTTTGCAAGATTTTTGGTGCCAAGACTCCTTAAAA
128 CTAAAAACGCGTTCC-GTG-CCCAGCTCAATTTTGCATGATTTTTGGCGCCAAGACTCATTGAAA
* ** * * * *
18944 TATCTATATTCATCTAACTA-TATCTCTCCCATATTGGATTTGAGGATTTGTTTTTACGAGCATC
191 TATCTATATTCATCTAAC-AGAATCTCAGCCACATTGGATTTAAAGAATTGTTTTTACGAGCATC
* * * * *
19008 TGAATCTTGTTTCGATTTAATTA-ACATTATTAA--G-AAGAAAATAGTAAAAACGATATTAGAA
255 TCAAAC-AGTTTCGATTTAATTAGA-ATT-TAAATCGAAAAAAAAT-G-AAAAACGATATTAGAA
* *
19069 GCGTGAAAAACTC
315 GCGTGAGAAGC-C
* ** * **
19082 TTCAATCTTTTTGGCGTTGAATTATATAAATTTTATGAGTATTGTGGCTAAAAATTTATGGAAAA
1 TTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTATTGTGGCCAAAAA-TTGGGGAAAA
* * * * * **
19147 ACTTTCAGTTAAA-TTTTGCAAAAATTTAGACGAAATC-TATACT-ATCATTTCGGTTTTTGGCT
65 ACTTTCGGTCAAATTTTTGCAAAAATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCT
* * * * *
19209 AAAAACGCGTTTCAGGGCCCTGTCTCAGTTTTGCATGATTGTTT-GCGCCAACACTCATTGAAAT
130 AAAAACGCG-TTCCGTGCCCAG-CTCAATTTTGCATGATT-TTTGGCGCCAAGACTCATTGAAAT
* ** * * *
19273 ATCTATATTCATCTAACAGAATCTTAGTAACATTGGATTCAAAGAATTGTTTTGAAGAGCATCTC
192 ATCTATATTCATCTAACAGAATCTCAGCCACATTGGATTTAAAGAATTGTTTTTACGAGCATCTC
* *
19338 ACAACAGTTTCGATTTAATTAGAATTTAAATCGAAAAAAAATGAAAAACGATATTAGCAGAGTGA
257 A-AACAGTTTCGATTTAATTAGAATTTAAATCGAAAAAAAATGAAAAACGATATTAGAAGCGTGA
19403 GAAGCC
321 GAAGCC
* *
19409 GTTCAAACTTTTTGGCATTGAGTTATATATATTTTTATGAGTATTGTGGCCAAAAATTGGGGAGA
1 -TTCAATCTTTTTGGCGTTGAGTTATATAT-TTTTTATGAGTATTGTGGCCAAAAATTGGGGA-A
** ** * * * *
19474 AATTTTTCTGGTCATTTTTTGTGCAAAATTTTAGTCGAAATCGTGCACTAACCATCATGGTTTTT
63 AAACTTTC-GGTCAAATTTT-TGCAAAAATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT
* * * *
19539 GACTAAAAACGCGTTCCGTGACCCCAGATCAGTTTTGCATGATTTTTGGCGCCAAGAATCATTGA
126 GGCTAAAAACGCGTTCCGTG--CCCAGCTCAATTTTGCATGATTTTTGGCGCCAAGACTCATTGA
* *
19604 AATATCTATATTCATCTAAC-GAAATCTCAGCCACATTGGATAT-AAGAATTTGTATTTACGAGC
189 AATATCTATATTCATCTAACAG-AATCTCAGCCACATTGGATTTAAAGAA-TTGTTTTTACGAGC
* * * * ** * * *
19667 ATCTCAATCCGGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAACGGAAAAACAATAATATAA
252 ATCTCAA-ACAGTTTCGATTTAATTAGAATTTAAATC-GAAAAAAAATGAAAAACGATATTAGAA
*
19732 GCGAGAGAAGCCC
315 GCGTGAGAAG-CC
* * * * *
19745 TTCAATCTTTTCGACGTTGAGTTATATATTTTTTACGAGTATTTTGGCCAAAAATTGAGGAGAAA
1 TTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTATTGTGGCCAAAAATTGGGGA-AAA
** * * * * * *
19810 TTTTTCGAG-CCAATTTTTGTAAAATTTTAGCCGAAATTGTGTACTAACCACCACGGTTTTTTGC
65 ACTTTCG-GTCAAATTTTTGCAAAAATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGC
* ** * *
19874 TAAAAATGCG-TCGCAAAGTGCTTA-CTCAATTTTGCATGATTTTTGGCGACAAGACTTATTGAA
129 TAAAAACGCGTTC-C---GTGCCCAGCTCAATTTTGCATGATTTTTGGCGCCAAGACTCATTGAA
* * *
19937 ATATCTATATTAATC-AACAAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATC
190 ATATCTATATTCATCTAACAGAATCTCAGCCACATTGGATTTAAAGAATTGTTTTTACGAGCATC
20001 TCAA
255 TCAA
20005 TATGGTTTGC
Statistics
Matches: 766, Mismatches: 122, Indels: 70
0.80 0.13 0.07
Matches are distributed among these distances:
327 9 0.01
328 179 0.23
329 46 0.06
330 32 0.04
331 116 0.15
332 122 0.16
333 27 0.04
334 172 0.22
335 61 0.08
336 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (326 bp):
TTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTATTGTGGCCAAAAATTGGGGAAAAA
CTTTCGGTCAAATTTTTGCAAAAATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTA
AAAACGCGTTCCGTGCCCAGCTCAATTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCT
ATATTCATCTAACAGAATCTCAGCCACATTGGATTTAAAGAATTGTTTTTACGAGCATCTCAAAC
AGTTTCGATTTAATTAGAATTTAAATCGAAAAAAAATGAAAAACGATATTAGAAGCGTGAGAAGC
C
Found at i:20466 original size:473 final size:473
Alignment explanation
Indices: 19571--20476 Score: 1334
Period size: 473 Copynumber: 1.9 Consensus size: 473
19561 CCCAGATCAG
* * * *
19571 TTTTGCATGATTTTTGGCGCCAAGAATCATTGAAATATCTATATTCATCTAACGAAATCTCAGCC
1 TTTTGCATGATTTCTGGCGCCAAGAATCATTGAAATAACTATATTAATCTAACGAAATCTCAGAC
*
19636 ACATTGGATATAAGAATTTGTATTTACGAGCATCTCAATCCGGTTTCGATTTAATTAGAAATTAA
66 ACATTGGATATAAGAATTTGTATTTACGAGCATCTCAATCCGATTTCGATTTAATTAGAAATTAA
* * *
19701 TTCGGAAAAAAACGGAAAAACAATAATATAAGCGAGAGAAGCCCTTCAATCTTTTCGACGTTGAG
131 TTCGGAAAAAAAAGGAAAAACAATAATAGAAGCGAGAGAAGCCCTTCAATCTTTTCGACATTGAG
*
19766 TTATATATTTTTTACGAGTATTTTGGCCAAAAATTGAGGAGAAATTTTTCGAGCCAATTTTTGTA
196 TTATATATTTTTTACGAGTATTTTGGCCAAAAATTGAGGAGAAATTTTTCGAGCCAATTTTGGTA
** * * *
19831 AAATTTTAGCCGAAATTGTGTACTAACCACCACGGTTTTTTGCTAAAAATGCGTCGCAAAGTGCT
261 AAATTTTAGCCGAAATCATGTACTAACCACCACAGTTTTTTGCTAAAAATGCGTCGCAAAGTCCC
* * *
19896 TACTCAATTTTGCATGATTTTTGGCGACAAGACTTATTGAAATATCTATATTAATCAACAAAATC
326 GACTCAATTTTGCATGATTTTTGGCGACAAGACTCATTGAAATATATATATTAATCAACAAAATC
* *
19961 TCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTCAATATGGTTTGCTAAAAATGCGT
391 TCAGCCACACTGGATTCAAAGATTTGTTTTTACGAGCATCTCAATATGGTTTGCTAAAAATGCGT
20026 TACGGGGTCCTGACTCAA
456 TACGGGGTCCTGACTCAA
* *
20044 TTTTGCATGAATTTCT-GCGCCAAGACTTATTGAAATAACTATATTAATCTAACGAAATCTCAGA
1 TTTTGCATG-ATTTCTGGCGCCAAGAATCATTGAAATAACTATATTAATCTAACGAAATCTCAGA
* * **
20108 CACATTGGATTTAAGGATTTGT-TTTACGAGCATCTCAATCTTATTTCGATTTAATTAGAAATTA
65 CACATTGGATATAAGAATTTGTATTTACGAGCATCTCAATCCGATTTCGATTTAATTAGAAATTA
* * * * * *
20172 ATTCGGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAGAAGCCCTTTAATCTTTTTGGCATTG
130 ATTCGGAAAAAAA-AGGAAAAACAATAATAGAAGCGAGAGAAGCCCTTCAATCTTTTCGACATTG
* * * *
20237 AGTTATATATTTTTTACGAGTATTTTGGCTAAAAATTGAGGAGAAATTTTTTGGGTCAATTTTGG
194 AGTTATATATTTTTTACGAGTATTTTGGCCAAAAATTGAGGAGAAATTTTTCGAGCCAATTTTGG
* * ***
20302 TAAAATTTTAGCCGAAATCATGTACTAACCATCACAGTTTTTTGCTAAAAATGTGTTC-CGGGGT
259 TAAAATTTTAGCCGAAATCATGTACTAACCACCACAGTTTTTTGCTAAAAATGCG-TCGCAAAGT
* * * * *
20366 CCCGGCTCAATTTTGCATGATTTTTGGTGTCAAGACTCATTGAAATATATATATTCATCTAACGA
323 CCCGACTCAATTTTGCATGATTTTTGGCGACAAGACTCATTGAAATATATATATTAATC-AACAA
*
20431 AATCTCAGTCACACTGGATTCAAAGATTT-TTTTTACGAGCATCTCA
387 AATCTCAGCCACACTGGATTCAAAGATTTGTTTTTACGAGCATCTCA
20477 CTCCGGTTTC
Statistics
Matches: 383, Mismatches: 46, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
472 52 0.14
473 294 0.77
474 37 0.10
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (473 bp):
TTTTGCATGATTTCTGGCGCCAAGAATCATTGAAATAACTATATTAATCTAACGAAATCTCAGAC
ACATTGGATATAAGAATTTGTATTTACGAGCATCTCAATCCGATTTCGATTTAATTAGAAATTAA
TTCGGAAAAAAAAGGAAAAACAATAATAGAAGCGAGAGAAGCCCTTCAATCTTTTCGACATTGAG
TTATATATTTTTTACGAGTATTTTGGCCAAAAATTGAGGAGAAATTTTTCGAGCCAATTTTGGTA
AAATTTTAGCCGAAATCATGTACTAACCACCACAGTTTTTTGCTAAAAATGCGTCGCAAAGTCCC
GACTCAATTTTGCATGATTTTTGGCGACAAGACTCATTGAAATATATATATTAATCAACAAAATC
TCAGCCACACTGGATTCAAAGATTTGTTTTTACGAGCATCTCAATATGGTTTGCTAAAAATGCGT
TACGGGGTCCTGACTCAA
Found at i:20623 original size:332 final size:331
Alignment explanation
Indices: 20010--20642 Score: 858
Period size: 332 Copynumber: 1.9 Consensus size: 331
20000 CTCAATATGG
* *
20010 TTTGCTAAAAATGCGTTACGGGGTCCTGACTCAATTTTGCATGAATTTCTGCGCCAAGACTTATT
1 TTTGCTAAAAATGCGTTACGGGGTCCCGACTCAATTTTGCATGAATTTCTGCGCCAAGACTCATT
* * *
20075 GAAATAACTATATTAATCTAACGAAATCTCAGACACATTGGATTTAAGGATTTGTTTTACGAGCA
66 GAAATAACTATATTAATCTAACGAAATCTCAGACACACTGGATTCAAAGATTTGTTTTACGAGCA
** * * * *
20140 TCTCAATCTTATTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAGAA
131 TCTCAATCCGATTTCGATTTAATTAGAAATTAAATCAGAAAAAAAAAAGAAAAACGATATTAGAA
* * * * * * * * *
20205 GCGTGAGAAGCCCTTTAATCTTTTTGGCATTGAGTTATATATTTTTTACGAGTATTTTGGCTAAA
196 GCGTGAGAAGCCCTTCAAACTTTTTGGCACTGAGTAAAATAATTTTTACGAGTATTGTAGCCAAA
* * *
20270 AATTGAGGAGAAATTTTTTGGGTCAATTTTGGTAAAATTTTAGCCGAAATCATGTACTAACCATC
261 AAATGAGGAGAAATCTTTTGGGTCAATTTT-GCAAAATTTTAGCCGAAATCATGTACTAACCATC
20335 ACAGTTT
325 ACAGTTT
* * * * * *
20342 TTTGCTAAAAATGTGTTCCGGGGTCCCGGCTCAATTTTGCATG-ATTTTTGGTGTCAAGACTCAT
1 TTTGCTAAAAATGCGTTACGGGGTCCCGACTCAATTTTGCATGAATTTCT-GCGCCAAGACTCAT
* * *
20406 TGAAATATA-TATATTCATCTAACGAAATCTCAGTCACACTGGATTCAAAGATTTTTTTTACGAG
65 TGAAATA-ACTATATTAATCTAACGAAATCTCAGACACACTGGATTCAAAGATTTGTTTTACGAG
* * *
20470 CATCTCACTCCGGTTTCGATTTAATTAGAATTTAAAT-AGAATAAAAAAAAGAAAAACGATATTA
129 CATCTCAATCCGATTTCGATTTAATTAGAAATTAAATCAGAA-AAAAAAAAGAAAAACGATATTA
* *
20534 GAAGCGTGAGAAGCCCTTCAAACTTTTTGGCACTGTGTAAAATAATTTTTATGAGTATTGTAGCC
193 GAAGCGTGAGAAGCCCTTCAAACTTTTTGGCACTGAGTAAAATAATTTTTACGAGTATTGTAGCC
* *
20599 AAAAAATGGGGAGATATCTTTTGGGTCAATTTTGCAAAATTTTA
258 AAAAAATGAGGAGAAATCTTTTGGGTCAATTTTGCAAAATTTTA
20643 CAGGACCCTG
Statistics
Matches: 259, Mismatches: 39, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
331 18 0.07
332 240 0.93
333 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (331 bp):
TTTGCTAAAAATGCGTTACGGGGTCCCGACTCAATTTTGCATGAATTTCTGCGCCAAGACTCATT
GAAATAACTATATTAATCTAACGAAATCTCAGACACACTGGATTCAAAGATTTGTTTTACGAGCA
TCTCAATCCGATTTCGATTTAATTAGAAATTAAATCAGAAAAAAAAAAGAAAAACGATATTAGAA
GCGTGAGAAGCCCTTCAAACTTTTTGGCACTGAGTAAAATAATTTTTACGAGTATTGTAGCCAAA
AAATGAGGAGAAATCTTTTGGGTCAATTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCA
CAGTTT
Found at i:21334 original size:332 final size:331
Alignment explanation
Indices: 20659--21923 Score: 1573
Period size: 332 Copynumber: 3.8 Consensus size: 331
20649 CCTGGGTTAG
* * * *** *
20659 TTTTGCATGATTTTT-GTGCCAAGAATCAATGAAATATCTATATTAATCTGGTGAAATCTCAGTC
1 TTTTGCATGATTTTTGGCGCCAAGAATCATTGAAATATCTATATTCATCTAACGAAATCTCAGCC
* * * * * * *
20723 ACGTTGTATTTAAAGATTTGTTTTTACTAGCATCTCAA-CTCGGTTTTGTTTTAATTTGAAATTA
66 ACATTGGATTTAAAGATTTGTATTTACGAGCATCTCAATC-CGGTTTCGATTTAATTAGAAATTA
* * ** * * *
20787 AATC-TAAAAAAA-A-TAAAAATGATATTAGAAGAGTGAGAAGCCCTTCAAACATTTTGGCATTG
130 AATCGGAAAAAAATAGGAAAAACAATATTATAAGCGTGAGAAGCCCTTCAAACTTTTTGGCATTG
* * *
20849 AGTTATATA-TTTTTATGAGTATTGTGGCAAAAAAATTG-GTGAGAAATTTTTCGGGTCATTTTT
195 AGTTATATATTTTTTACGAGTATTTTGGC-CAAAAATTGAG-GAGAAATTTTTCGGGTCA-----
* *
20912 TTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAATGCGTTAC
253 ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAATGCGTT-C
20977 GGGGTCCCGGCTCAA
317 GGGGTCCCGGCTCAA
*
20992 TTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCTAACGAAATCTCAGCC
1 TTTTGCATGATTTTTGGCGCCAAGAATCATTGAAATATCTATATTCATCTAACGAAATCTCAGCC
* * * *
21057 ATATTGGATTTTAGGATTTGTATTTACCAGCATCTCAATCCGGTTTCGATTTAATTAGAAATTAA
66 ACATTGGATTTAAAGATTTGTATTTACGAGCATCTCAATCCGGTTTCGATTTAATTAGAAATTAA
* * * * * * * *
21122 TTCGGAAAAAAATCGGAAAAATAATATTATAAGCGAGAGAAGCCCTTCAATCTTTTCGACGTTGA
131 ATCGGAAAAAAATAGGAAAAACAATATTATAAGCGTGAGAAGCCCTTCAAACTTTTTGGCATTGA
*
21187 GTTATATATATTTTACGAGTATTTTGGCCAAAAATTGAGGAGAAATTTTTCGGGTCAATTTTTGC
196 GTTATATATTTTTTACGAGTATTTTGGCCAAAAATTGAGGAGAAATTTTTCGGGTCAATTTTTGC
* * *
21252 AAAATTTTAGCCGAAATTGTGTACTAACAATCACGATTTTTGGCAAAAATGCGTTCTGGGGTCCC
261 AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAATGCGTTC-GGGGTCCC
*
21317 AGCTCAA
325 GGCTCAA
* *
21324 TTTTGCATGATTTTTTGCGCCAAGACTCATTGAAATATCTATATTCATCTAACGAAATCTCAGCC
1 TTTTGCATGATTTTTGGCGCCAAGAATCATTGAAATATCTATATTCATCTAACGAAATCTCAGCC
*
21389 ACATTGGATTTAAGGATTTGTATTTACGAGCATCTCAAT-CGAGTTTCGATTTAATTAGAAATTA
66 ACATTGGATTTAAAGATTTGTATTTACGAGCATCTCAATCCG-GTTTCGATTTAATTAGAAATTA
* * **
21453 AATC-GAAAAAAATAGGAAAAACAATATCAAAAGCGTGAGAAGCCCTTCAATTTTTTTTGGCATT
130 AATCGGAAAAAAATAGGAAAAACAATATTATAAGCGTGAGAAGCCCTTCAA-ACTTTTTGGCATT
* *
21517 GAGTTATATATTTTTTGCGAGTATTTTGGCCAAAAATTGAGGAGAAATTTTTTGGGTCAATTTTT
194 GAGTTATATATTTTTTACGAGTATTTTGGCCAAAAATTGAGGAGAAATTTTTCGGGTCAATTTTT
* * * * *
21582 GTAAACTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAATGCGTTCCAGGGA
259 GCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGC-AAAAATGCGTT-CGGGGT
21647 CCCGGCTCAA
322 CCCGGCTCAA
* * * **
21657 TTTTGCATGAATTTTGGTGCCAAGAATCATTGAAATATATATATTCATCTAACGAAATCTCATTC
1 TTTTGCATGATTTTTGGCGCCAAGAATCATTGAAATATCTATATTCATCTAACGAAATCTCAGCC
* * * * * *
21722 ACACTGGATTCAAAGATTTTTTTTTACGAGCATCTCACTCCGGTTTCGATTTAATTAGAATTTAA
66 ACATTGGATTTAAAGATTTGTATTTACGAGCATCTCAATCCGGTTTCGATTTAATTAGAAATTAA
* * * * * ** *
21787 ATAGGAAAAAAA-AAGAAAAACGATAATATAAGTGTGAGAAGCCCTTCAAACTTTTTGGCGCTGT
131 ATCGGAAAAAAATAGGAAAAACAATATTATAAGCGTGAGAAGCCCTTCAAACTTTTTGGCATTGA
* * * * *
21851 GTAAAATATTTTTTATGAGTATTTTGGCCAAAAA-AGGGGAGAAATCTTTT-GGGTCAATTTTTG
196 GTTATATATTTTTTACGAGTATTTTGGCCAAAAATTGAGGAGAAAT-TTTTCGGGTCAATTTTTG
21914 CAAAATTTTA
260 CAAAATTTTA
21924 CAGGGCCCCG
Statistics
Matches: 816, Mismatches: 101, Indels: 32
0.86 0.11 0.03
Matches are distributed among these distances:
331 74 0.09
332 352 0.43
333 184 0.23
334 107 0.13
335 8 0.01
337 74 0.09
338 17 0.02
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (331 bp):
TTTTGCATGATTTTTGGCGCCAAGAATCATTGAAATATCTATATTCATCTAACGAAATCTCAGCC
ACATTGGATTTAAAGATTTGTATTTACGAGCATCTCAATCCGGTTTCGATTTAATTAGAAATTAA
ATCGGAAAAAAATAGGAAAAACAATATTATAAGCGTGAGAAGCCCTTCAAACTTTTTGGCATTGA
GTTATATATTTTTTACGAGTATTTTGGCCAAAAATTGAGGAGAAATTTTTCGGGTCAATTTTTGC
AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAATGCGTTCGGGGTCCCG
GCTCAA
Found at i:22363 original size:195 final size:197
Alignment explanation
Indices: 21993--22369 Score: 467
Period size: 195 Copynumber: 1.9 Consensus size: 197
21983 TAATCTGACG
* * * * * *
21993 AAATCTCAGTCACGTTGGATTTAAATATTTGTTTTTACGAGCATCTCAACTCGCTTTTGTTTTAA
1 AAATCTCAGCCACATTGGATTTAAAAATTTGCTTTTACGAGCATCTCAACTCGATTTTGATTTAA
* * * **
22058 TTAGAAATTAAATCTAAAAAAACAAGAAAAACGATATTAGAAGAGTGAGAAGCCCTTTAAACATT
66 TTAGAAATTAAATCTAAAAAAACAAGAAAAACAATATTAGAAGAGTAACAAGAACTTTAAACATT
* *
22123 TTGGCGTTGAGTTATGTATTTTTTATGAGTATTGTGGCAAAAAATTG-GGGAGAAATTTTTCTAA
131 TTGGCATTGAGTTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGGAGAAATTTTTCTAA
22187 CC
196 CC
* * *
22189 AAATCTCAGCCACATTGGATTTAAAAATTTGCTTTTACGAGCATCT-GAGTCATATTTTGATTTA
1 AAATCTCAGCCACATTGGATTTAAAAATTTGCTTTTACGAGCATCTCAACTC-GATTTTGATTTA
* ** * * * * *
22253 ATTAGAAATTAATTC-GGAAAAATAGGAAAAACAATATTAGAAGCGTAACAA-AACTTTCAATCT
65 ATTAGAAATTAAATCTAAAAAAACAAGAAAAACAATATTAGAAGAGTAACAAGAACTTT-AAACA
*
22316 TTTTGGCATTGTA-TTATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGGA
129 TTTTGGCATTG-AGTTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGGA
22370 AAAACTTCCA
Statistics
Matches: 152, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
194 4 0.03
195 78 0.51
196 70 0.46
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (197 bp):
AAATCTCAGCCACATTGGATTTAAAAATTTGCTTTTACGAGCATCTCAACTCGATTTTGATTTAA
TTAGAAATTAAATCTAAAAAAACAAGAAAAACAATATTAGAAGAGTAACAAGAACTTTAAACATT
TTGGCATTGAGTTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGGAGAAATTTTTCTAA
CC
Found at i:22754 original size:335 final size:332
Alignment explanation
Indices: 22207--22838 Score: 759
Period size: 335 Copynumber: 1.9 Consensus size: 332
22197 GCCACATTGG
* * * *
22207 ATTTAAAAATTTGCTTTTACGAGCATCTGAGTCATATTTTGATTTAATTAGAAATTAATTCGGAA
1 ATTTAAAAATTTGCTTTTACGAGCATCTCAATCAGATTTCGATTTAATTAGAAATTAATTCGGAA
*
22272 AAATAGGAAAAACAATATTAGAAGCGTAACAAAACTTTCAATCTTTTTGGCATTGTATTATATAT
66 AAATAGGAAAAACAATATTAGAAGCGTAACAAAACCTTCAATCTTTTTGGCATTGTATTATATAT
* * *
22337 TTTTTATGAGTATTGTGGCTAAAAATTGAGGGAAAAACTTCCAATTAAATTTTTTCAAAAATTTA
131 TTTTTATGAGTATTGTGGCGAAAAATTGAGGGAAAAACTTCCAATTAAATGTTTGCAAAAATTTA
* ** *
22402 CCCGAAATCGCGTACTAACCATCACGGTTTTTGGTTAAAAACGCGTTCCGGGGTCCC-GGCTCAA
196 CCCGAAATCGCGTACTAACCATCACGGGTTTTGACTAAAAACGCGTTCCGGGG-CCCTAGCTCAA
* *
22466 TTTTGTATGATTTTTTGCCCCAAGACTCATTGAATATATTCATCTAACGAAGTCTTAGCAATATT
260 TTTTGCATGATTTTTAGCCCCAAGACTCATTGAA-ATATTCATCTAACGAAGTCTTAGCAATATT
22531 AAAATTAAA
324 AAAATTAAA
* * *
22540 ATTTAAGAATTT-CTTTTTACGAGCATCTCAATCGGGTTTCGATTTAATTAGAAATTAATTCGGA
1 ATTTAAAAATTTGC-TTTTACGAGCATCTCAATCAGATTTCGATTTAATTAGAAATTAATTCGG-
** * * * *** * *
22604 AAAAAGTAGGAAAAATGATGTTAGAAGCGTGAGATGCCCTTCAATCTTTTTTGCCTTG-ATTTAT
64 AAAAA-TAGGAAAAACAATATTAGAAGCGTAACAAAACCTTCAATCTTTTTGGCATTGTA-TTAT
* ** *** ***
22668 ATATTTTTTATGAGTATTGTGGGGGGAAATTGAGGAGAAATTTTTCGGGTT-AATGTTTGCAAAA
127 ATATTTTTTATGAGTATTGTGGCGAAAAATTGAGG-GAAAAACTTCCAATTAAATGTTTGCAAAA
* * * * *
22732 TTTTAGCCGAAATTGTGTACTAATCATCACGGGTTTTGACTAAAAACGCGTTCCGGGGCCCTAGC
191 ATTTACCCGAAATCGCGTACTAACCATCACGGGTTTTGACTAAAAACGCGTTCCGGGGCCCTAGC
** ** *
22797 TCTGTTTTGCATGATTTTTAGCGTCAAGTCTCATTGAAATAT
256 TCAATTTTGCATGATTTTTAGCCCCAAGACTCATTGAAATAT
22839 CTATATCCAT
Statistics
Matches: 247, Mismatches: 46, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
332 1 0.00
333 54 0.22
334 13 0.05
335 170 0.69
336 9 0.04
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (332 bp):
ATTTAAAAATTTGCTTTTACGAGCATCTCAATCAGATTTCGATTTAATTAGAAATTAATTCGGAA
AAATAGGAAAAACAATATTAGAAGCGTAACAAAACCTTCAATCTTTTTGGCATTGTATTATATAT
TTTTTATGAGTATTGTGGCGAAAAATTGAGGGAAAAACTTCCAATTAAATGTTTGCAAAAATTTA
CCCGAAATCGCGTACTAACCATCACGGGTTTTGACTAAAAACGCGTTCCGGGGCCCTAGCTCAAT
TTTGCATGATTTTTAGCCCCAAGACTCATTGAAATATTCATCTAACGAAGTCTTAGCAATATTAA
AATTAAA
Found at i:24209 original size:332 final size:320
Alignment explanation
Indices: 23586--24635 Score: 969
Period size: 332 Copynumber: 3.2 Consensus size: 320
23576 CCCTGTTAAA
**
23586 AAAAAACGATATTAGAAGCGTGAGAAACCCTTCAAAATTTTTGGCGTTGAGTTATATATTTTTTA
1 AAAAAACGATATTAGAAGCGTGAGAAACCCTTCAATCTTTTTGGCGTTGAGTTATATATTTTTTA
* * * * * * * *
23651 TTAGTATTGTAGCCAAAAATTGGGGGAGATATTTTTTGGGTCATTTTTTACAAAATTTAAGCCGA
66 TGAGTATTGT-GGCAAAAAAT-GGGGAGA-AATTTTTCGGTCAATTTTTGCAAAATTTTAGCCGA
* * * * * * *
23716 TATCGTGTCACGAGTTTTAGCTAAAAATGCGTTACGGGGTCCTAACTCAATTTTGCATATTTTTT
128 AATCGTGTCACCAGTTTTAGCTAAAAAGGCATTACGGGGTCCCAACTCAATTTTCCATATTTTTG
*
23781 GCGCCAAGACTTATTGAAATATCTATATTAATCTAACGAAATCTCAGCCACATTGGATTTAAGGA
193 GCGCCAAGAC-TATTGAAATATCTAAATTAATCTAACGAAATCTCAGCCACATTGGATTTAAGGA
* * * *
23846 TTTGTTTTTACGAGCATCTCAATCTGGTTTCGATTTATTTAGAAATTAATTCGGAAAAAACATAG
257 TTTATTTTTACGAGCATCTCAATCCGGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAAATAG
* *
23911 AAAAAATGATATTAGAAGCGTGAGAAACCCTTCAATCTTTTTGGTGTTGAGTTATATATTTTTTA
1 AAAAAACGATATTAGAAGCGTGAGAAACCCTTCAATCTTTTTGGCGTTGAGTTATATATTTTTTA
* *
23976 TGAATATTGTGGCAAAAAATGGAGGAGAAATTTTTCAGGTCAATTTTTGCTAAATTTTAGCCGAA
66 TGAGTATTGTGGCAAAAAATGG-GGAGAAATTTTTC-GGTCAATTTTTGCAAAATTTTAGCCGAA
* * *
24041 ATCGTGTACTAACCATCACAGTTCTT-GACTAAAAAGGCATTATGGTGTCCCGACTCAATTTTCC
129 ATCGTG---T---CA-C-CAGTT-TTAG-CTAAAAAGGCATTACGGGGTCCCAACTCAATTTTCC
* * *
24105 ATGATTTTTGGCGCCAAGAC-ATTGAAATATTTAAATTCATCTAATGAAATCTCAGCCACATTGG
184 AT-ATTTTTGGCGCCAAGACTATTGAAATATCTAAATTAATCTAACGAAATCTCAGCCACATTGG
* * * *
24169 ATTTACGGATTTATTTTTACGAGCATCTCATTCCGGTTTCGATTTAATTGGAAGTTAATTCGAAA
248 ATTTAAGGATTTATTTTTACGAGCATCTCAATCCGGTTTCGATTTAATTAGAAATTAATTCGAAA
24234 AAAAATAG
313 AAAAATAG
* * * *
24242 GAAAAACAATATTAGAAGTC-TGAGAAGCCGTTCAATCTTTTTGGCGTTGAGTTATATATTTTTT
1 AAAAAACGATATTAGAAG-CGTGAGAAACCCTTCAATCTTTTTGGCGTTGAGTTATATATTTTTT
* * *
24306 ATGAGTATTGTGGCCAAAAAT--GGAGAAATTTTTCGAGTCAACTTTTGCAAAATTTTTCATGTT
65 ATGAGTATTGTGGCAAAAAATGGGGAGAAATTTTTCG-GTCAATTTTTGCAAAA-TTTT-A-G-C
* ** ** * * * * * ** *
24369 C-TAA-C-CATCA-TGGTTTTCGACT-AAAACGCATTTC-AGGT-CCAGGCTCTGTTTTGCATGA
125 CGAAATCGTGTCACCAGTTTTAG-CTAAAAAGGCATTACGGGGTCCCA-ACTCAATTTTCCAT-A
* * * * ** * **
24427 TTTTTAGAGCCAAGTCTCATTGAAATATCTATATCCATCTAACCAAATCTCA-CACACATAAGAT
187 TTTTTGGCGCCAAGACT-ATTGAAATATCTAAATTAATCTAACGAAATCTCAGC-CACATTGGAT
* * * * * * *
24491 TTAAGAATTTGTTTTTTCAAGCATCTGAATCAC-GTTTTGATTTAATTAAAAATTAATTCAGATA
250 TTAAGGATTTATTTTTACGAGCATCTCAATC-CGGTTTCGATTTAATTAGAAATTAATTC-GA-A
24555 AAAAAATAG
312 AAAAAATAG
* * * * * * * **
24564 GAAAACCGATATTAAAAGCGTGA-AAGCCTTTCAATATTTTTGACGTTGAAATATATATTTTTTT
1 AAAAAACGATATTAGAAGCGTGAGAAACCCTTCAATCTTTTTGGCGTTGAGTTATATA-TTTTTT
24628 ATGAGTAT
65 ATGAGTAT
24636 CGTGATAAAA
Statistics
Matches: 605, Mismatches: 91, Indels: 61
0.80 0.12 0.08
Matches are distributed among these distances:
317 2 0.00
318 27 0.04
319 12 0.02
320 90 0.15
321 33 0.05
322 42 0.07
323 10 0.02
324 42 0.07
325 69 0.11
326 1 0.00
327 2 0.00
328 27 0.04
329 4 0.01
330 4 0.01
331 90 0.15
332 101 0.17
333 33 0.05
334 16 0.03
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (320 bp):
AAAAAACGATATTAGAAGCGTGAGAAACCCTTCAATCTTTTTGGCGTTGAGTTATATATTTTTTA
TGAGTATTGTGGCAAAAAATGGGGAGAAATTTTTCGGTCAATTTTTGCAAAATTTTAGCCGAAAT
CGTGTCACCAGTTTTAGCTAAAAAGGCATTACGGGGTCCCAACTCAATTTTCCATATTTTTGGCG
CCAAGACTATTGAAATATCTAAATTAATCTAACGAAATCTCAGCCACATTGGATTTAAGGATTTA
TTTTTACGAGCATCTCAATCCGGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAATAG
Found at i:24549 original size:320 final size:327
Alignment explanation
Indices: 23587--24635 Score: 1011
Period size: 320 Copynumber: 3.2 Consensus size: 327
23577 CCTGTTAAAA
* **
23587 AAAAACGATATTAGAAGCGTGAGAAACCCTTCAAAATTTTTGGCGTTGAGTTATATATTTTTTAT
1 AAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAGTTATATATTTTTTAT
* * * * ** ** * *
23652 TAGTATTGTAGCCAAAAATTGGGGGAGATATTTTTTGGGTCATTTTTTACAAAATTTAAGCCGAT
66 GAGTATTGT-GGCAAAAAAT--GGGAGAAATTTTTCAGGTCAACTTTTGCAAAATTTTA-CC-A-
* * * ** *
23717 ATCGTG---T---CA-C-GAGTT-TT-AGCTAAAAATGCGTTACGGGGTCCTA-ACTCAATTTTG
125 ATCGTGTACTAACCATCACAGTTCTTGA-CTAAAAACGCATTATAGTGTCC-AGACTCAATTTTG
* * *
23771 CAT-ATTTTTTGCGCCAAGACTTATTGAAATATCTATATTAATCTAACGAAATCTCAGCCACATT
188 CATGATTTTTAGCGCCAAG-CTCATTGAAATATCTATATTCATCTAACGAAATCTCAGCCACATT
* * *
23835 GGATTTAAGGATTTGTTTTTACGAGCATCTCAATCTGGTTTCGATTTATTTAGAAATTAATTCGG
252 GGATTTAAGGATTTGTTTTTACGAGCATCTCAATC-CGTTTCGATTTAATTAGAAATTAATTCAG
* *
23900 AAAAAACATAGA
316 AAAAAAAATAGG
* * *
23912 AAAAATGATATTAGAAGCGTGAGAAACCCTTCAATCTTTTTGGTGTTGAGTTATATATTTTTTAT
1 AAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAGTTATATATTTTTTAT
* * *
23977 GAATATTGTGGCAAAAAATGGAGGAGAAATTTTTCAGGTCAATTTTTGCTAAATTTTAGCCGAAA
66 GAGTATTGTGGCAAAAAAT-G-GGAGAAATTTTTCAGGTCAACTTTTGCAAAATTTTA-CC--AA
* * * *
24042 TCGTGTACTAACCATCACAGTTCTTGACTAAAAAGGCATTATGGTGTCCCGACTCAATTTTCCAT
126 TCGTGTACTAACCATCACAGTTCTTGACTAAAAACGCATTATAGTGTCCAGACTCAATTTTGCAT
* * * * *
24107 GATTTTTGGCGCCAAG-ACATTGAAATATTTAAATTCATCTAATGAAATCTCAGCCACATTGGAT
191 GATTTTTAGCGCCAAGCTCATTGAAATATCTATATTCATCTAACGAAATCTCAGCCACATTGGAT
* * * * *
24171 TTACGGATTTATTTTTACGAGCATCTCATTCCGGTTTCGATTTAATTGGAAGTTAATTC-GAAAA
256 TTAAGGATTTGTTTTTACGAGCATCTCAATCC-GTTTCGATTTAATTAGAAATTAATTCAGAAAA
24235 AAAATAGG
320 AAAATAGG
* *
24243 AAAAACAATATTAGAAGTC-TGAGAAGCCGTTCAATCTTTTTGGCGTTGAGTTATATATTTTTTA
1 AAAAACGATATTAGAAG-CGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAGTTATATATTTTTTA
* *
24307 TGAGTATTGTGGCCAAAAAT-GGAGAAATTTTTC-GAGTCAACTTTTGCAAAATTTT-TC-AT-G
65 TGAGTATTGTGGCAAAAAATGGGAGAAATTTTTCAG-GTCAACTTTTGCAAAATTTTACCAATCG
** * **
24367 T-T-CTAACCATCATGGTT-TTCGACT-AAAACGCATT-TCAG-GTCCAGGCTCTGTTTTGCATG
129 TGTACTAACCATCACAGTTCTT-GACTAAAAACGCATTAT-AGTGTCCAGACTCAATTTTGCATG
* * * **
24426 ATTTTTAGAGCCAAGTCTCATTGAAATATCTATATCCATCTAACCAAATCTCA-CACACATAAGA
192 ATTTTTAGCGCCAAG-CTCATTGAAATATCTATATTCATCTAACGAAATCTCAGC-CACATTGGA
* * * * * *
24490 TTTAAGAATTTGTTTTTTCAAGCATCTGAATCACGTTTTGATTTAATTAAAAATTAATTCAGATA
255 TTTAAGGATTTGTTTTTACGAGCATCTCAATC-CGTTTCGATTTAATTAGAAATTAATTCAGA-A
24555 AAAAAATAGG
318 AAAAAATAGG
* * * * * **
24565 AAAACCGATATTAAAAGCGTGA-AAGCCTTTCAATATTTTTGACGTTGAAATATATATTTTTTTA
1 AAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAGTTATATA-TTTTTTA
24629 TGAGTAT
65 TGAGTAT
24636 CGTGATAAAA
Statistics
Matches: 610, Mismatches: 87, Indels: 57
0.81 0.12 0.08
Matches are distributed among these distances:
318 30 0.05
319 13 0.02
320 101 0.17
321 34 0.06
322 44 0.07
323 4 0.01
324 46 0.08
325 69 0.11
326 1 0.00
327 2 0.00
328 31 0.05
330 2 0.00
331 87 0.14
332 98 0.16
333 33 0.05
334 15 0.02
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (327 bp):
AAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAGTTATATATTTTTTAT
GAGTATTGTGGCAAAAAATGGGAGAAATTTTTCAGGTCAACTTTTGCAAAATTTTACCAATCGTG
TACTAACCATCACAGTTCTTGACTAAAAACGCATTATAGTGTCCAGACTCAATTTTGCATGATTT
TTAGCGCCAAGCTCATTGAAATATCTATATTCATCTAACGAAATCTCAGCCACATTGGATTTAAG
GATTTGTTTTTACGAGCATCTCAATCCGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAAATA
GG
Found at i:28208 original size:17 final size:17
Alignment explanation
Indices: 28183--28229 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
28173 CCATTGAAAA
*
28183 TTTTT-AATGCTTTAAT
1 TTTTTCAATGCGTTAAT
28199 TTTTTCAATGCGTTAAT
1 TTTTTCAATGCGTTAAT
28216 TTTTTCAATGCGTT
1 TTTTTCAATGCGTT
28230 TGATAATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 5 0.17
17 24 0.83
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.57
Consensus pattern (17 bp):
TTTTTCAATGCGTTAAT
Found at i:64648 original size:49 final size:49
Alignment explanation
Indices: 64587--64688 Score: 159
Period size: 49 Copynumber: 2.1 Consensus size: 49
64577 CACAGAACAA
* * *
64587 GATGATTACCAAAAACAAATGCCAATACTAATAATCAACAGAGAAATTT
1 GATGATTACCAAAAACAAATACCAACACTAATAATCAACAGAGAAAATT
* *
64636 GATGATTTCCAAAAACAATTACCAACACTAATAATCAACAGAGAAAATT
1 GATGATTACCAAAAACAAATACCAACACTAATAATCAACAGAGAAAATT
64685 GATG
1 GATG
64689 CTATAGTCTG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.23
Consensus pattern (49 bp):
GATGATTACCAAAAACAAATACCAACACTAATAATCAACAGAGAAAATT
Found at i:66827 original size:11 final size:11
Alignment explanation
Indices: 66813--66852 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
66803 TCAAATATTT
66813 GAAAAAAAAAA
1 GAAAAAAAAAA
66824 GAAAAAAAAAA
1 GAAAAAAAAAA
* *
66835 GAAGAAAAAAC
1 GAAAAAAAAAA
66846 GAAAAAA
1 GAAAAAA
66853 GCAAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:67052 original size:33 final size:33
Alignment explanation
Indices: 67005--67142 Score: 186
Period size: 33 Copynumber: 4.2 Consensus size: 33
66995 CGTTTCGGGT
* *
67005 ACCGCCGGAGATGCAGCGCAGAGTGTCTCCGAA
1 ACCGCCGGAGATGCAGCGGAAAGTGTCTCCGAA
* * *
67038 ACCGCCGGACATGCAACGGACAGTGTCTCCGAA
1 ACCGCCGGAGATGCAGCGGAAAGTGTCTCCGAA
* * * *
67071 GCCGCCGGAGAGGCAGGGGAAAGTATCTCCGAA
1 ACCGCCGGAGATGCAGCGGAAAGTGTCTCCGAA
*
67104 ACCGCCGGAGATGCATCGGAAAGTGTCTCCGAA
1 ACCGCCGGAGATGCAGCGGAAAGTGTCTCCGAA
67137 ACCGCC
1 ACCGCC
67143 TCCTCATGGA
Statistics
Matches: 89, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.26, C:0.30, G:0.32, T:0.12
Consensus pattern (33 bp):
ACCGCCGGAGATGCAGCGGAAAGTGTCTCCGAA
Found at i:68101 original size:17 final size:17
Alignment explanation
Indices: 68079--68111 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
68069 GGTGGTAGCT
*
68079 CATAGATTAGCGTTTCA
1 CATAGATTAACGTTTCA
68096 CATAGATTAACGTTTC
1 CATAGATTAACGTTTC
68112 GATAAGCTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (17 bp):
CATAGATTAACGTTTCA
Found at i:81764 original size:3 final size:3
Alignment explanation
Indices: 81756--81815 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
81746 AGAAGCTGGG
* * * * * *
81756 GCT GCT GCT GGT GTT GCT GCT GCT GTT GTT GTT GTT GCT GCT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
*
81804 GCT GCG GCT GCT
1 GCT GCT GCT GCT
81816 CCTCTTGCTG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.00, C:0.23, G:0.37, T:0.40
Consensus pattern (3 bp):
GCT
Found at i:115712 original size:68 final size:68
Alignment explanation
Indices: 115633--115769 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
115623 ATGAAGAGAA
115633 ATTGGTTGGTGGGCTGATGCATCCCTAAGCCTAACGAGAATTGCCGAAGTCAGCCACGAAGAGAC
1 ATTGGTTGGTGGGCTGATGCATCCCTAAGCCTAACGAGAATTGCCGAAGTCAGCCACGAAGAGAC
115698 AGG
66 AGG
115701 ATTGGTTGGTGGGCTGATGCATCCCTAAGCCTAACGAGAATTGCCGAAGTCAGCCACGAAGAGAC
1 ATTGGTTGGTGGGCTGATGCATCCCTAAGCCTAACGAGAATTGCCGAAGTCAGCCACGAAGAGAC
115766 AGG
66 AGG
115769 A
1 A
115770 CACCAACCGT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.28, C:0.22, G:0.31, T:0.19
Consensus pattern (68 bp):
ATTGGTTGGTGGGCTGATGCATCCCTAAGCCTAACGAGAATTGCCGAAGTCAGCCACGAAGAGAC
AGG
Found at i:116380 original size:59 final size:59
Alignment explanation
Indices: 116288--116405 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
116278 TGGCCGCAGC
116288 AAACAAGAATCCAACAAACCATGCTATGCAGTAAGTAAAACCAGAAGGAGATCTTTATT
1 AAACAAGAATCCAACAAACCATGCTATGCAGTAAGTAAAACCAGAAGGAGATCTTTATT
*
116347 AAACAAGAATCCAACAAACCATGCTATGCAGTAAGTAAAACCAGGAGGAGATCTTTATT
1 AAACAAGAATCCAACAAACCATGCTATGCAGTAAGTAAAACCAGAAGGAGATCTTTATT
116406 TTCTTCTTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.20
Consensus pattern (59 bp):
AAACAAGAATCCAACAAACCATGCTATGCAGTAAGTAAAACCAGAAGGAGATCTTTATT
Found at i:119613 original size:32 final size:32
Alignment explanation
Indices: 119572--119636 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
119562 ACATAAAATT
119572 ACAGAAATAGCGAAATTATGAAGAACAAAAGG
1 ACAGAAATAGCGAAATTATGAAGAACAAAAGG
119604 ACAGAAATAGCGAAATTATGAAGAACAAAAGG
1 ACAGAAATAGCGAAATTATGAAGAACAAAAGG
119636 A
1 A
119637 GGACACAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.57, C:0.09, G:0.22, T:0.12
Consensus pattern (32 bp):
ACAGAAATAGCGAAATTATGAAGAACAAAAGG
Found at i:125077 original size:237 final size:239
Alignment explanation
Indices: 124619--125224 Score: 804
Period size: 237 Copynumber: 2.5 Consensus size: 239
124609 ACACGAGCAG
** * * * **
124619 GAAGAAAAAATGTTACAAAGTTTT-ACATCAAATAATGCATTTATAAATCAAAGACGCGGAACAG
1 GAAGAAAAAA-GAAACAAA-TTTTGACATCAAAGAATTCATTTCTAAATCAAAGACATGGAACAG
* * * * * * *
124683 ACAATAACCTCATCGTTCTCACGAAGTAGTTGTTCACCTGGCAGGACAGATACGCTGTTGTCATT
64 ACAATAACCTCATTGTTCTCACGAAGCAGCTGTTCACCTGGCAGGACAGATGCACTGCTCTCATT
* *
124748 ACCTAAAGTGCTGACTAAACCAACTGCGTGTGGCTGCACAGTAAGCTCAACTTCCTTAGGTGATA
129 ACCTAAAGTGCTGACTAAACCAACTGCGTGTGGCTACACAGTAAGCTCAACTGCCTTAGGTGATA
124813 CTGTCCGGTCCAGTGAGTCCTACAAAGCACAGGAAATATATTA-TT
194 CTGTCCGGTCCAGTGAGTCCTACAAAGCACAGGAAATATATTATTT
* **
124858 GAAGAAAAAA-AAACAAATTTTGACATCAGAGAATTCATTTCTAAATCAAAGACATGGAATGGAC
1 GAAGAAAAAAGAAACAAATTTTGACATCAAAGAATTCATTTCTAAATCAAAGACATGGAACAGAC
* * * *
124922 AATAACCTCATTTTTCTCACGAAGCAGCTGTTCACCTAGCTGGACAGATGCACTGCTCTTATTAC
66 AATAACCTCATTGTTCTCACGAAGCAGCTGTTCACCTGGCAGGACAGATGCACTGCTCTCATTAC
* * * * ** * * *
124987 CTGAAGTGCTGCCTACATCAACTGCGTGTGGCTACTGAGTAGGTTCAACTGCCTTAGGTGATATT
131 CTAAAGTGCTGACTAAACCAACTGCGTGTGGCTACACAGTAAGCTCAACTGCCTTAGGTGATACT
* *
125052 GTCCGGTCTAGTGAGTCCTACAAAGCACATGAAATATATTATTT
196 GTCCGGTCCAGTGAGTCCTACAAAGCACAGGAAATATATTATTT
* * * * *
125096 GAAGAAAAAAGAAAGCAAATTTTGACATCATAGAATTCATCTCTCAATTAAAGACATTGAACAGA
1 GAAGAAAAAAGAAA-CAAATTTTGACATCAAAGAATTCATTTCTAAATCAAAGACATGGAACAGA
*
125161 CAATAACCTCATTGTTCTCACGAAGCAGCTGTTCACCTGGCCGGACAGATGCACTGCTCTCATT
65 CAATAACCTCATTGTTCTCACGAAGCAGCTGTTCACCTGGCAGGACAGATGCACTGCTCTCATT
125225 TCTTGATATG
Statistics
Matches: 318, Mismatches: 45, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
236 4 0.01
237 186 0.58
238 12 0.04
239 13 0.04
240 103 0.32
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (239 bp):
GAAGAAAAAAGAAACAAATTTTGACATCAAAGAATTCATTTCTAAATCAAAGACATGGAACAGAC
AATAACCTCATTGTTCTCACGAAGCAGCTGTTCACCTGGCAGGACAGATGCACTGCTCTCATTAC
CTAAAGTGCTGACTAAACCAACTGCGTGTGGCTACACAGTAAGCTCAACTGCCTTAGGTGATACT
GTCCGGTCCAGTGAGTCCTACAAAGCACAGGAAATATATTATTT
Found at i:125886 original size:97 final size:97
Alignment explanation
Indices: 125720--125914 Score: 354
Period size: 97 Copynumber: 2.0 Consensus size: 97
125710 AGAAATCCAT
*
125720 CATAACAAAGGTAAAATAAAATAAAATTCCTTCCAGCCAAAGTTTTCTCCAAGAAACTACTGGAC
1 CATAACAAAGGTAAAATAAAATAAAATTCCTTCCAGCCAAAGCTTTCTCCAAGAAACTACTGGAC
*
125785 ATGAGTGTCAAAGGCGTTAGCCTTACCATGCC
66 ATGAGTGTCAAAAGCGTTAGCCTTACCATGCC
* *
125817 CATAACAAAGGTAAAATAAATTAAATTTCCTTCCAGCCAAAGCTTTCTCCAAGAAACTACTGGAC
1 CATAACAAAGGTAAAATAAAATAAAATTCCTTCCAGCCAAAGCTTTCTCCAAGAAACTACTGGAC
125882 ATGAGTGTCAAAAGCGTTAGCCTTACCATGCC
66 ATGAGTGTCAAAAGCGTTAGCCTTACCATGCC
125914 C
1 C
125915 CCAGGTTCTT
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 94 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (97 bp):
CATAACAAAGGTAAAATAAAATAAAATTCCTTCCAGCCAAAGCTTTCTCCAAGAAACTACTGGAC
ATGAGTGTCAAAAGCGTTAGCCTTACCATGCC
Found at i:126958 original size:238 final size:240
Alignment explanation
Indices: 126536--127134 Score: 844
Period size: 238 Copynumber: 2.5 Consensus size: 240
126526 GGGTCCAGTG
* * * *
126536 AAGAAAGCAAATTTTAACATTAGAGAATGCATTTATAAATCAAAGACATGGAACGGACAATAACC
1 AAGAAAGCAAATTTTGACATTAGAGAATTCATTTCTAAATCAAAGACATGGAACAGACAATAACC
* * * * *
126601 TCATCGTTGTCACGAAGCAGATGTTCACCTGGCAGGACAGATACACTGTTGTCATTACCTAAAGT
66 TCATTGTTCTCACGAAGCAGATGTTCACCTGGCAGGACAGATGCACTGCTCTCATTACCTAAAGT
* * *
126666 GCTGACTGAACCAACTGCGTGTGGCTGCTCAGTAAGCTCAACTTCCTTAGGTGATACTGTCCGAT
131 GCTGACTGAACCAACTGCGTGCGACTGCTCAGTAAGCTCAACTGCCTTAGGTGATACTGTCCGAT
* *
126731 CCAGTGAGTCCTACAAAGCACATGAAATATATCA-TTGAAGAAAA
196 CCAGTAAGTCCTACAAAGCACAGGAAATATATCATTTGAAGAAAA
126775 AAG-AAGCAAATTTTGACATTAGAGAATTCATTTCTAAATCAAAGACATGGAACAGACAATAACC
1 AAGAAAGCAAATTTTGACATTAGAGAATTCATTTCTAAATCAAAGACATGGAACAGACAATAACC
* * * * * * *
126839 TCATTTTTCTCACAAAACAGCTGTTCACCTAGCTGGACAGATGCACTGCTCTCATTACCTGAAGT
66 TCATTGTTCTCACGAAGCAGATGTTCACCTGGCAGGACAGATGCACTGCTCTCATTACCTAAAGT
* * * * * *
126904 GCTGCCT-ACATCAACTGCGTGCGACTGCTGAGTAGGTTCAACTGCCTTAGGTGATACTGTCCGG
131 GCTGACTGA-ACCAACTGCGTGCGACTGCTCAGTAAGCTCAACTGCCTTAGGTGATACTGTCCGA
*
126968 TCCAGTAAGTCCTACAAAGCACAGGAAATATATTATTTGAAGAAAA
195 TCCAGTAAGTCCTACAAAGCACAGGAAATATATCATTTGAAGAAAA
* ** * * *
127014 AAGAAAGCAAATTATGACAGCAGAAAATTCATCTCTAAATCAAAGACATTGAACAGACAATAACC
1 AAGAAAGCAAATTTTGACATTAGAGAATTCATTTCTAAATCAAAGACATGGAACAGACAATAACC
* *
127079 TCATTGTTCTCACGAAGCAGTTGTTCACCTGGCCGGACAGATGCACTGCTCTCATT
66 TCATTGTTCTCACGAAGCAGATGTTCACCTGGCAGGACAGATGCACTGCTCTCATT
127135 TCTTGATGTG
Statistics
Matches: 317, Mismatches: 40, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
237 1 0.00
238 195 0.62
239 16 0.05
240 105 0.33
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (240 bp):
AAGAAAGCAAATTTTGACATTAGAGAATTCATTTCTAAATCAAAGACATGGAACAGACAATAACC
TCATTGTTCTCACGAAGCAGATGTTCACCTGGCAGGACAGATGCACTGCTCTCATTACCTAAAGT
GCTGACTGAACCAACTGCGTGCGACTGCTCAGTAAGCTCAACTGCCTTAGGTGATACTGTCCGAT
CCAGTAAGTCCTACAAAGCACAGGAAATATATCATTTGAAGAAAA
Found at i:128136 original size:18 final size:18
Alignment explanation
Indices: 128113--128167 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
128103 AATTTAACAG
*
128113 TAATTAACCCTAATAAAC
1 TAATTAACACTAATAAAC
128131 TAATTAACACTAATAAAC
1 TAATTAACACTAATAAAC
*
128149 TAATTAACACTAATTAAC
1 TAATTAACACTAATAAAC
128167 T
1 T
128168 GTAATTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (18 bp):
TAATTAACACTAATAAAC
Found at i:128144 original size:28 final size:29
Alignment explanation
Indices: 128106--128176 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
128096 TTTAGTTAAT
*
128106 TTAACAGTAATTAACCCTAA-TAA-ACTAA
1 TTAACAGTAATTAA-ACTAATTAACACTAA
*
128134 TTAACACTAA-TAAACTAATTAACACTAA
1 TTAACAGTAATTAAACTAATTAACACTAA
*
128162 TTAACTGTAATTAAA
1 TTAACAGTAATTAAA
128177 TTTAACAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 4 0.11
27 6 0.17
28 22 0.61
29 4 0.11
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (29 bp):
TTAACAGTAATTAAACTAATTAACACTAA
Found at i:128175 original size:10 final size:10
Alignment explanation
Indices: 128106--128166 Score: 76
Period size: 10 Copynumber: 6.5 Consensus size: 10
128096 TTTAGTTAAT
*
128106 TTAACAGTAA
1 TTAACACTAA
*
128116 TTAACCCTAA
1 TTAACACTAA
128126 -TAA-ACTAA
1 TTAACACTAA
128134 TTAACACTAA
1 TTAACACTAA
128144 -TAA-ACTAA
1 TTAACACTAA
128152 TTAACACTAA
1 TTAACACTAA
128162 TTAAC
1 TTAAC
128167 TGTAATTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
8 9 0.20
9 12 0.27
10 23 0.52
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.30
Consensus pattern (10 bp):
TTAACACTAA
Found at i:128202 original size:3 final size:3
Alignment explanation
Indices: 128194--128251 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
128184 ATTTCAAAAT
128194 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
128242 ATA ATA ATA A
1 ATA ATA ATA A
128252 ATAAATAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:128506 original size:47 final size:47
Alignment explanation
Indices: 128447--128544 Score: 178
Period size: 47 Copynumber: 2.1 Consensus size: 47
128437 TTTTAGTTTG
*
128447 AAGGTTTCAGAGGATTTGAAGTTAGAAAGTTTGAAGAAAATGAAGTA
1 AAGGTTTCAGAGGATTTGAAGTTAGAAAGTTTAAAGAAAATGAAGTA
*
128494 AAGGTTTTAGAGGATTTGAAGTTAGAAAGTTTAAAGAAAATGAAGTA
1 AAGGTTTCAGAGGATTTGAAGTTAGAAAGTTTAAAGAAAATGAAGTA
128541 AAGG
1 AAGG
128545 ATAAAAGTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.44, C:0.01, G:0.28, T:0.28
Consensus pattern (47 bp):
AAGGTTTCAGAGGATTTGAAGTTAGAAAGTTTAAAGAAAATGAAGTA
Found at i:128537 original size:24 final size:24
Alignment explanation
Indices: 128463--128539 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
128453 TCAGAGGATT
*
128463 TGAAGTTAGAAAGTTTGAAGAAAA
1 TGAAGTTAGAAAGTTTAAAGAAAA
* * * **
128487 TGAAG-TA-AAGGTTTTAGAGGATT
1 TGAAGTTAGAAAG-TTTAAAGAAAA
128510 TGAAGTTAGAAAGTTTAAAGAAAA
1 TGAAGTTAGAAAGTTTAAAGAAAA
128534 TGAAGT
1 TGAAGT
128540 AAAGGATAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
22 3 0.08
23 13 0.33
24 20 0.51
25 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (24 bp):
TGAAGTTAGAAAGTTTAAAGAAAA
Found at i:142403 original size:2 final size:2
Alignment explanation
Indices: 142398--142422 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
142388 TCCAAAATAA
142398 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
142423 TTCCTTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:151482 original size:2 final size:2
Alignment explanation
Indices: 151475--151503 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
151465 GCGGCTTCAT
151475 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
151504 GAGTATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:162007 original size:6 final size:6
Alignment explanation
Indices: 161996--162022 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
161986 TGAAGCTTCA
161996 TCATCT TCATCT TCATCT TCATCT TCA
1 TCATCT TCATCT TCATCT TCATCT TCA
162023 ATCAAACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.48
Consensus pattern (6 bp):
TCATCT
Found at i:175280 original size:12 final size:11
Alignment explanation
Indices: 175263--175308 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 11
175253 GTTAAACAAC
175263 TTATTATTATAA
1 TTATTA-TATAA
175275 TTATTA-A-AA
1 TTATTATATAA
175284 TTATTAT-TAA
1 TTATTATATAA
175294 TTATATATATAA
1 TTAT-TATATAA
175306 TTA
1 TTA
175309 CGTTTTACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 8 0.27
10 7 0.23
11 3 0.10
12 12 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTATTATATAA
Found at i:175457 original size:30 final size:29
Alignment explanation
Indices: 175379--175462 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 29
175369 TAATTTAGAT
175379 TTATTATTAT--TATAATAATTATTAAAC
1 TTATTATTATAATATAATAATTATTAAAC
** *
175406 TTATTATTAGTGGTATTATAATTATTAAAC
1 TTATTATTA-TAATATAATAATTATTAAAC
175436 TTATTATTATAATAATAATAATTATTA
1 TTATTATTATAAT-ATAATAATTATTA
175463 GTGGTATGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 9 0.18
28 1 0.02
29 2 0.04
30 37 0.76
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (29 bp):
TTATTATTATAATATAATAATTATTAAAC
Found at i:175460 original size:21 final size:21
Alignment explanation
Indices: 175419--175462 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
175409 TTATTAGTGG
* *
175419 TATTATAATTATTAAACTTAT
1 TATTATAATTAATAAAATTAT
175440 TATTATAA-TAATAATAATTAT
1 TATTATAATTAATAA-AATTAT
175461 TA
1 TA
175463 GTGGTATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTATAATTAATAAAATTAT
Found at i:175664 original size:26 final size:25
Alignment explanation
Indices: 175635--175689 Score: 94
Period size: 24 Copynumber: 2.2 Consensus size: 25
175625 AAAGTTCAAT
175635 TCAATTTAATTTTTCTTTGAAATATA
1 TCAA-TTAATTTTTCTTTGAAATATA
175661 TCAA-TAATTTTTCTTTGAAATATA
1 TCAATTAATTTTTCTTTGAAATATA
175685 TCAAT
1 TCAAT
175690 AGATCATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 24 0.86
26 4 0.14
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (25 bp):
TCAATTAATTTTTCTTTGAAATATA
Found at i:175669 original size:24 final size:24
Alignment explanation
Indices: 175641--175690 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
175631 CAATTCAATT
175641 TAATTTTTCTTTGAAATATATCAA
1 TAATTTTTCTTTGAAATATATCAA
175665 TAATTTTTCTTTGAAATATATCAA
1 TAATTTTTCTTTGAAATATATCAA
175689 TA
1 TA
175691 GATCATTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (24 bp):
TAATTTTTCTTTGAAATATATCAA
Found at i:177368 original size:271 final size:273
Alignment explanation
Indices: 176885--177429 Score: 1022
Period size: 271 Copynumber: 2.0 Consensus size: 273
176875 GGAACTAGCA
*
176885 CTGATATCTACAACAAAATTTTACCCTCTTAAAGTTAATAATTTTGGTTAAGATGCCGAGTTAAT
1 CTGATATCTACAACAAAATTTTACCCTCTTAAAGTTAATAATTTTGGTTAAAATGCCGAGTTAAT
176950 CAAAGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCGT
66 CAAAGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCGT
177015 GGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCAG
131 GGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCAG
* *
177080 ACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACC-AAACG-AAAAAGGA
196 ACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAAGA
177143 GTTGCAAGAAAAG
261 GTTGCAAGAAAAG
***
177156 CTGATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAAATGCCGAGTTAAT
1 CTGATATCTACAACAAAATTTTACCCTCTTAAAGTTAATAATTTTGGTTAAAATGCCGAGTTAAT
177221 CAAAGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCGT
66 CAAAGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCGT
177286 GGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCAG
131 GGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCAG
177351 ACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAAGA
196 ACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAAGA
177416 GTTGCAAGAAAAG
261 GTTGCAAGAAAAG
177429 C
1 C
177430 CAAGTTAGTC
Statistics
Matches: 266, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
271 241 0.91
272 4 0.02
273 21 0.08
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (273 bp):
CTGATATCTACAACAAAATTTTACCCTCTTAAAGTTAATAATTTTGGTTAAAATGCCGAGTTAAT
CAAAGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCGT
GGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCAG
ACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAAGA
GTTGCAAGAAAAG
Found at i:181527 original size:23 final size:20
Alignment explanation
Indices: 181490--181530 Score: 55
Period size: 23 Copynumber: 1.9 Consensus size: 20
181480 ACATGTAAAG
181490 TTTTTTCAACCCTTTTTCAC
1 TTTTTTCAACCCTTTTTCAC
181510 TTTTATTCACACCACTTTTTC
1 TTTT-TTCA-ACC-CTTTTTC
181531 TTAATTACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 3 0.17
23 7 0.39
ACGTcount: A:0.17, C:0.29, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTTCAACCCTTTTTCAC
Found at i:186411 original size:11 final size:11
Alignment explanation
Indices: 186395--186429 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
186385 TTTTTCTATT
186395 TTTTGTTTTTG
1 TTTTGTTTTTG
*
186406 TTTTGTTTTCG
1 TTTTGTTTTTG
186417 TTTTGTTTTTG
1 TTTTGTTTTTG
186428 TT
1 TT
186430 GCGCTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:191271 original size:20 final size:21
Alignment explanation
Indices: 191246--191289 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
191236 CTCCCTCTGG
191246 AAAGGGTGAGAAA-GAAAAA-A
1 AAAGGGTGA-AAATGAAAAAGA
191266 AAAGGGTGAAAATGAAAAAGA
1 AAAGGGTGAAAATGAAAAAGA
191287 AAA
1 AAA
191290 AAGAAAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 15 0.68
21 4 0.18
ACGTcount: A:0.66, C:0.00, G:0.27, T:0.07
Consensus pattern (21 bp):
AAAGGGTGAAAATGAAAAAGA
Found at i:191710 original size:23 final size:23
Alignment explanation
Indices: 191675--191718 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
191665 GAGACAAGGG
*
191675 AAAAAAGGGAAGG-AAGAAAAGA
1 AAAAAAGGCAAGGTAAGAAAAGA
191697 AAAAGAAGGCAAGGTAAGAAAA
1 AAAA-AAGGCAAGGTAAGAAAA
191719 ATCTTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.66, C:0.02, G:0.30, T:0.02
Consensus pattern (23 bp):
AAAAAAGGCAAGGTAAGAAAAGA
Done.