Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005537.1 Hibiscus syriacus cultivar Beakdansim tig00012816_pilon, 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: 154793
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:3869 original size:23 final size:24
Alignment explanation
Indices: 3825--3871 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
3815 TTGTTGAATT
3825 CCAAAGCCCCCAATTTTGACTTCC
1 CCAAAGCCCCCAATTTTGACTTCC
*
3849 CCAAAGCCTCCAA-TTTGACTTCC
1 CCAAAGCCCCCAATTTTGACTTCC
3872 AACAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.26, C:0.40, G:0.09, T:0.26
Consensus pattern (24 bp):
CCAAAGCCCCCAATTTTGACTTCC
Found at i:6427 original size:22 final size:21
Alignment explanation
Indices: 6402--6449 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
6392 TTTGAAATCA
6402 TGTTGTCATGTCAGACTATTTT
1 TGTT-TCATGTCAGACTATTTT
* * *
6424 TGTTTCCTTTCATACTATTTT
1 TGTTTCATGTCAGACTATTTT
6445 TGTTT
1 TGTTT
6450 GCATTGTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.58
Consensus pattern (21 bp):
TGTTTCATGTCAGACTATTTT
Found at i:9600 original size:30 final size:30
Alignment explanation
Indices: 9555--9627 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
9545 TTCATTTAAG
*
9555 TACTTAAAATA-TTTTTTGGTTAAAATAAA
1 TACTTAAAATATTTTTTTGGTCAAAATAAA
* *
9584 TACTTAAATTTATTTTTTTGGTCAAAATAAG
1 TACTTAAA-ATATTTTTTTGGTCAAAATAAA
* *
9615 TACATAAAGTATT
1 TACTTAAAATATT
9628 CATTTTTTCC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 8 0.22
30 6 0.16
31 23 0.62
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.45
Consensus pattern (30 bp):
TACTTAAAATATTTTTTTGGTCAAAATAAA
Found at i:9789 original size:32 final size:33
Alignment explanation
Indices: 9734--9799 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
9724 CTATTTTGAC
* *
9734 AAAAAATATTTTAGATACCTATTTT-GATAAAA
1 AAAAAATACTTTAGATACCTATTTTACATAAAA
* **
9766 AAAAAATACTTTATATATTTATTTTACATAAAA
1 AAAAAATACTTTAGATACCTATTTTACATAAAA
9799 A
1 A
9800 CACTTCAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 21 0.75
33 7 0.25
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (33 bp):
AAAAAATACTTTAGATACCTATTTTACATAAAA
Found at i:12320 original size:13 final size:15
Alignment explanation
Indices: 12290--12321 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
12280 AGTGAGCAAA
12290 AGAAAAATATACGAG
1 AGAAAAATATACGAG
12305 AGAAAAA-ATA-GAG
1 AGAAAAATATACGAG
12318 AGAA
1 AGAA
12322 TTGAGAGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 3 0.18
15 7 0.41
ACGTcount: A:0.66, C:0.03, G:0.22, T:0.09
Consensus pattern (15 bp):
AGAAAAATATACGAG
Found at i:17850 original size:30 final size:30
Alignment explanation
Indices: 17816--17918 Score: 188
Period size: 30 Copynumber: 3.4 Consensus size: 30
17806 GGTTCTTCGG
* *
17816 GACCTATGGATAATTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
17846 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
17876 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
17906 GACCTCTGGATAG
1 GACCTCTGGATAG
17919 GTCATTCGGA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:23084 original size:22 final size:22
Alignment explanation
Indices: 23059--23113 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
23049 GACATAGAAA
23059 GAATATGAAATATGTAGCATAT
1 GAATATGAAATATGTAGCATAT
23081 GAATATGAAATATGTAGCATAT
1 GAATATGAAATATGTAGCATAT
23103 GAATATGAAAT
1 GAATATGAAAT
23114 CATATGAGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (22 bp):
GAATATGAAATATGTAGCATAT
Found at i:23546 original size:31 final size:30
Alignment explanation
Indices: 23508--23603 Score: 79
Period size: 31 Copynumber: 3.1 Consensus size: 30
23498 GTCAAAGAAC
23508 TACCTATGTCTTTCGAGACATATGGATAGT
1 TACCTATGTCTTTCGAGACATATGGATAGT
*** *
23538 ATACCTATGTTCTAAGGA-ATATATGGATAGTT
1 -TACCTATG-TCTTTCGAGACATATGGATAG-T
* * *
23570 TACCTAGGT-TCTTCGGGACCTATGGATAGT
1 TACCTATGTCT-TTCGAGACATATGGATAGT
23600 TACC
1 TACC
23604 GAGGATCTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
29 1 0.02
30 7 0.14
31 36 0.72
32 6 0.12
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (30 bp):
TACCTATGTCTTTCGAGACATATGGATAGT
Found at i:23621 original size:30 final size:30
Alignment explanation
Indices: 23559--23688 Score: 179
Period size: 30 Copynumber: 4.3 Consensus size: 30
23549 CTAAGGAATA
* * ***
23559 TATGGATAGTTTACCTAGGTTCTTCGGGACC
1 TATGGATAG-TTACCGAGGATCTTTATGACC
*
23590 TATGGATAGTTACCGAGGATCTTTATAACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
23620 TATGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
*
23650 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
*
23680 TCTGGATAG
1 TATGGATAG
23689 GTCATTCGGA
Statistics
Matches: 91, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
30 82 0.90
31 9 0.10
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (30 bp):
TATGGATAGTTACCGAGGATCTTTATGACC
Found at i:24599 original size:13 final size:15
Alignment explanation
Indices: 24569--24600 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
24559 AGTGAGCAAA
24569 AGAAAAATATACGAG
1 AGAAAAATATACGAG
24584 AGAAAAA-ATA-GAG
1 AGAAAAATATACGAG
24597 AGAA
1 AGAA
24601 TTGAGAGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 3 0.18
15 7 0.41
ACGTcount: A:0.66, C:0.03, G:0.22, T:0.09
Consensus pattern (15 bp):
AGAAAAATATACGAG
Found at i:27481 original size:24 final size:24
Alignment explanation
Indices: 27443--27490 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
27433 CCAAGTCATT
*
27443 ATTTGCACAACACTTTTAATTCTA
1 ATTTGCACAACACTTTCAATTCTA
* *
27467 ATTTGCAGAATACTTTCAATTCTA
1 ATTTGCACAACACTTTCAATTCTA
27491 TTTTTCATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (24 bp):
ATTTGCACAACACTTTCAATTCTA
Found at i:29380 original size:311 final size:303
Alignment explanation
Indices: 29003--29750 Score: 792
Period size: 311 Copynumber: 2.4 Consensus size: 303
28993 GCAGTGGAGC
* * ** *
29003 TCTTCCTTCTTCTTTTTCGTTTCTCTGTAACATTTGGAAGATCAGTGCAAGATTGGTTTATCATC
1 TCTTCTTTCTCCTTTTTCGTTTCTCCATAACATTTGGAAGATCAGTGCAAGACTGGTTT-TCATC
* * * *
29068 TTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATTCCTGTAACAAAATATTAATGAAATTG
65 TTCTCTATTTCTGGTTCAGATCCCATTGATTGATCAATACCTGTAACAAAATAATAATGAAATCG
* * * * * * * *
29133 GCTTCAACTTTGTCGTGTTTATGGGAA-TC-TTAGTAATAAATAATCACGCGTGTTGATGTGTAT
130 ACTTCAACTTTATCATGTTCATGGGAACTCTTTAGTAAGAAATAATCACGCATGATGATCTG-A-
** * * *
29196 ATTTTGAAGTCCAATGATGAAAC-TGATTGAGTAGATGACGAACCCGATTGTGTAGATGTTTCC-
193 A-TTTG-AG-----TGAT-AAACACAATTGAGTAGATGACGAACCCAATTGAGTAGACG-TTCCA
* * * * * * * *
29259 TTGGTCTTGGACAATCTTTGTGATTTCGAGGAAGATGA-CTC-GGAAGTGGAAGTTT
249 TTCGTCTTGGACAATCGTTGAGATTTCAAGGAACAGGAGC-CAGCAA-TGGAAGTGT
29314 TCTTCTTTCTCCTTTTTCGTTTCTCCATAACATTTGGAAGATCAGTGCAAGACTGGTTTCTCATC
1 TCTTCTTTCTCCTTTTTCGTTTCTCCATAACATTTGGAAGATCAGTGCAAGACTGGTTT-TCATC
* * * *
29379 TTCTCTACTTCTAGTTCAGATCCCATTGATTGATCAATACCTGCT-GCAAAATAGTAATGAAATC
65 TTCTCTATTTCTGGTTCAGATCCCATTGATTGATCAATACCTG-TAACAAAATAATAATGAAATC
* * * *
29443 GATTTCAACTTTATTATGTTCATGGGAATCTCTAATATTTTAGTAAGAAATAGTCATGCATGATG
129 GACTTCAACTTTATCATGTTCATGGGAA-CTC------TTTAGTAAGAAATAATCACGCATGATG
*
29508 ATCTGAATTTGAGTGATAAACACAATTGAGTAGATGGCGAACCCAATTGAGTAGACGTTCCATTC
187 ATCTGAATTTGAGTGATAAACACAATTGAGTAGATGACGAACCCAATTGAGTAGACGTTCCATTC
29573 GTCTTGGACAATCGTTGAGATTTCAAGGAACAGGAGCCAGCAATGGAAGTGT
252 GTCTTGGACAATCGTTGAGATTTCAAGGAACAGGAGCCAGCAATGGAAGTGT
* * * ** *
29625 TCTTCTTTCTCCTTTTTGGTTTCTCCCTAACATCTAAAAGATCAGTGCATGACTGGATTTTCATC
1 TCTTCTTTCTCCTTTTTCGTTTCTCCATAACATTTGGAAGATCAGTGCAAGACTGG-TTTTCATC
* *
29690 TTCTCTATTT-TCGGTTCATATCCCACTGATTGATCAATACCTGTAACAAAATAATAATGAA
65 TTCTCTATTTCT-GGTTCAGATCCCATTGATTGATCAATACCTGTAACAAAATAATAATGAA
29751 TTTTATTGTG
Statistics
Matches: 369, Mismatches: 51, Indels: 34
0.81 0.11 0.07
Matches are distributed among these distances:
310 10 0.03
311 316 0.86
312 8 0.02
313 2 0.01
316 2 0.01
317 4 0.01
318 1 0.00
319 1 0.00
320 25 0.07
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (303 bp):
TCTTCTTTCTCCTTTTTCGTTTCTCCATAACATTTGGAAGATCAGTGCAAGACTGGTTTTCATCT
TCTCTATTTCTGGTTCAGATCCCATTGATTGATCAATACCTGTAACAAAATAATAATGAAATCGA
CTTCAACTTTATCATGTTCATGGGAACTCTTTAGTAAGAAATAATCACGCATGATGATCTGAATT
TGAGTGATAAACACAATTGAGTAGATGACGAACCCAATTGAGTAGACGTTCCATTCGTCTTGGAC
AATCGTTGAGATTTCAAGGAACAGGAGCCAGCAATGGAAGTGT
Found at i:29630 original size:615 final size:619
Alignment explanation
Indices: 28249--29750 Score: 1522
Period size: 624 Copynumber: 2.4 Consensus size: 619
28239 AGAATCTTAA
** * * * * *
28249 TAAGAAATAATCATGCATGATGATCTTCATATTTTGAAGTCTAGTGACGAACCTAATTGTGTAGA
1 TAAGAAATAATCATGCATGATGATCTTCATATTTTGAACACTACTAACGAACCCAATTGAGAAGA
* * ** * * * * *
28314 TATTTTCTTCATCTTGGTTAATCGTTTATATTTCG--A-AGAAGAAGAAGCCTCAGCAGTGGAAG
66 TAGTTCCTTCATCTTGGACAATCGTTGAGATTTTGAAAGAGAAGAAGAAGACTCAGCAAT-G--G
* *
28376 AGCTCTTCCTTCTTCTTTTTCGTTTCTCTGTAACATTTGAAAGATCAATGCAAGACTGGTTTCTC
128 AGCTC--CTTTCTTCTTTTTCGTTTCTCTGTAACATTTGAAAGATCAGTGCAAGACTGGTTT-TC
* * * * *
28441 ATTTTCTCTGCTTCTGCTTCAG-CCTCCATTGATTGATCAATACCTGTAACAAAATATTAATAAA
190 ATCTTCTCTGTTTCTGGTTCAGATC-CCATTGATTGATCAATACCTGTAACAAAATATTAATGAA
* ** * *
28505 ATTTACTTGGAGTTTGTTGTGTTTATGAGAATCTTAAATATATTAGTAAGAAATAAGCTTGCACG
254 ATTGACTTCAACTTTGTCGTGTTTATGAGAATCTTAAATATATTAG-AAGAAATAAGC-TGCACG
* *** *
28570 GTGATCTTTATATTTTGAAGTTGGATGATGAAACTGATTAAGTACATAATGAACCCAATTGAGTA
317 GTGATCTGTATATTTTGAAGTCCAATGATGAAACTGATTAAGTACATAACGAACCCAATTGAGTA
* * * *
28635 GATGTTTCTTTAGTTTTGGATAATCGTTGAGATTTCGAGGAGGATGACTCGGAAGTGGAACTTCT
382 GATGTTTCCTTAGTCTTGGACAATCGTTGAGATTTCGAGGAAGATGACTCGGAAGTGGAACTTCT
* * *
28700 CTTCTTTCTCCTTTTTGGTTTCTCCATAACATTTGGGAGATCAGTGCAAGACTGGTTTTTCATCT
447 CTTCTTTCTCCTTTTTCGTTTCTCCATAACATTTGGAAGATCAGTGCAAGACTGGTTTCTCATCT
* * * *
28765 TCTCTGCTGCTGGTTCAGATCCAATAAATTGATCAATATCTGTAACAAAAAGTAATAATGAAATT
512 TCTCTACTGCTAGTTCAGATCCAATAAATTGATCAATACCTGTAACAAAAAGTAATAATGAAATC
* * * *
28830 GATTTCGACTTTCTTGTGTTGATAAGAATCTCAAATATATTAG
577 GATTTCAACTTTATTATGTTCATAAGAATCTCAAATATATTAG
**
28873 TAAGAAATAATCATGCATGATGATCTTCATATTTTGAAGTCTACTAACGAACCCAATTGAGAAGA
1 TAAGAAATAATCATGCATGATGATCTTCATATTTTGAACACTACTAACGAACCCAATTGAGAAGA
* * * * * * *
28938 TATTTTCTTCATCTTGGATAATCGTTTATATTTTGAAAGAGAAGAAGAAGACTCGGCAGTGGAGC
66 TAGTTCCTTCATCTTGGACAATCGTTGAGATTTTGAAAGAGAAGAAGAAGACTCAGCAATGGAGC
* * *
29003 TCTTCCTTCTTCTTTTTCGTTTCTCTGTAACATTTGGAAGATCAGTGCAAGATTGGTTTATCATC
131 TC--CTTTCTTCTTTTTCGTTTCTCTGTAACATTTGAAAGATCAGTGCAAGACTGGTTT-TCATC
*
29068 TTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATTCCTGTAACAAAATATTAATGAAATTG
193 TTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTGTAACAAAATATTAATGAAATTG
* * * * * ** * *
29133 GCTTCAACTTTGTCGTGTTTATGGGAATCTT-AGTA-A-TA-AA-TAATCA-C-GCGTGTTGATG
258 ACTTCAACTTTGTCGTGTTTATGAGAATCTTAAATATATTAGAAGAAATAAGCTGCACGGTGATC
* * * * *
29191 TGTATATTTTGAAGTCCAATGATGAAACTGATTGAGTAGATGACGAACCCGATTGTGTAGATGTT
323 TGTATATTTTGAAGTCCAATGATGAAACTGATTAAGTACATAACGAACCCAATTGAGTAGATGTT
* * * * *
29256 TCCTTGGTCTTGGACAATCTTTGTGATTTCGAGGAAGATGACTCGGAAGTGGAAGTTTTCTTCTT
388 TCCTTAGTCTTGGACAATCGTTGAGATTTCGAGGAAGATGACTCGGAAGTGGAACTTCTCTTCTT
29321 TCTCCTTTTTCGTTTCTCCATAACATTTGGAAGATCAGTGCAAGACTGGTTTCTCATCTTCTCTA
453 TCTCCTTTTTCGTTTCTCCATAACATTTGGAAGATCAGTGCAAGACTGGTTTCTCATCTTCTCTA
* * ** * *
29386 CTTCTAGTTCAGATCCCATTGATTGATCAATACCTGCT-GC-AAAA-TAGTAATGAAATCGATTT
518 CTGCTAGTTCAGATCCAATAAATTGATCAATACCTG-TAACAAAAAGTAATAATGAAATCGATTT
** * *
29448 CAACTTTATTATGTTCATGGGAATCTCTAATATTTTAG
582 CAACTTTATTATGTTCATAAGAATCTCAAATATATTAG
* * *
29486 TAAGAAATAGTCATGCATGATGATC-TGA-ATTTGAGTGATAAACACAATTGAGTAGATGGCGAA
1 TAAGAAATAATCATGCATGATGATCTTCATATTT---TG---AACAC---T-ACTA-A---CGAA
* * * * * *
29549 CCCAATTGAGTAGA-CGTTCCATTCGTCTTGGACAATCGTTGAGA-TTT-CAAG-GAA-CAGGAG
52 CCCAATTGAGAAGATAGTTCC-TTCATCTTGGACAATCGTTGAGATTTTGAAAGAGAAGAAGAAG
* * * ** * *
29609 -C-CAGCAATGGAAGTGTTCTTCTTTCTCCTTTTTGGTTTCTCCCTAACATCTAAAAGATCAGTG
116 ACTCAGCAATGG-A--G--CTCCTTTCTTCTTTTTCGTTTCTCTGTAACATTTGAAAGATCAGTG
* * * *
29672 CATGACTGGATTTTCATCTTCTCTATTT-TCGGTTCATATCCCACTGATTGATCAATACCTGTAA
176 CAAGACTGG-TTTTCATCTTCTCTGTTTCT-GGTTCAGATCCCATTGATTGATCAATACCTGTAA
*
29736 CAAAATAATAATGAA
239 CAAAATATTAATGAA
29751 TTTTATTGTG
Statistics
Matches: 744, Mismatches: 107, Indels: 56
0.82 0.12 0.06
Matches are distributed among these distances:
611 4 0.01
612 2 0.00
613 70 0.09
614 6 0.01
615 210 0.28
616 1 0.00
617 4 0.01
618 4 0.01
619 9 0.01
620 3 0.00
621 10 0.01
622 107 0.14
623 9 0.01
624 247 0.33
625 37 0.05
626 2 0.00
627 19 0.03
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (619 bp):
TAAGAAATAATCATGCATGATGATCTTCATATTTTGAACACTACTAACGAACCCAATTGAGAAGA
TAGTTCCTTCATCTTGGACAATCGTTGAGATTTTGAAAGAGAAGAAGAAGACTCAGCAATGGAGC
TCCTTTCTTCTTTTTCGTTTCTCTGTAACATTTGAAAGATCAGTGCAAGACTGGTTTTCATCTTC
TCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTGTAACAAAATATTAATGAAATTGACT
TCAACTTTGTCGTGTTTATGAGAATCTTAAATATATTAGAAGAAATAAGCTGCACGGTGATCTGT
ATATTTTGAAGTCCAATGATGAAACTGATTAAGTACATAACGAACCCAATTGAGTAGATGTTTCC
TTAGTCTTGGACAATCGTTGAGATTTCGAGGAAGATGACTCGGAAGTGGAACTTCTCTTCTTTCT
CCTTTTTCGTTTCTCCATAACATTTGGAAGATCAGTGCAAGACTGGTTTCTCATCTTCTCTACTG
CTAGTTCAGATCCAATAAATTGATCAATACCTGTAACAAAAAGTAATAATGAAATCGATTTCAAC
TTTATTATGTTCATAAGAATCTCAAATATATTAG
Found at i:38935 original size:31 final size:29
Alignment explanation
Indices: 38864--38940 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 29
38854 ATTCATTTTT
38864 ATTTTAATTATTATTTCGTTTAGTACCTAA
1 ATTTTAATT-TTATTTCGTTTAGTACCTAA
* *
38894 ATTATCAATTTTAATTT-GTTTTAGTATCTAA
1 ATT-TTAATTTT-ATTTCG-TTTAGTACCTAA
38925 ACTTTTAATTTT-TTTC
1 A-TTTTAATTTTATTTC
38941 AAAACCATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
29 3 0.08
30 6 0.15
31 28 0.72
32 2 0.05
ACGTcount: A:0.29, C:0.09, G:0.05, T:0.57
Consensus pattern (29 bp):
ATTTTAATTTTATTTCGTTTAGTACCTAA
Found at i:40584 original size:21 final size:22
Alignment explanation
Indices: 40558--40599 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
40548 GATGAAAAAA
40558 CCGGATCGG-TTTTTATCCGAT
1 CCGGATCGGTTTTTTATCCGAT
40579 CCGGATCGGTTTTTTATCCGA
1 CCGGATCGGTTTTTTATCCGA
40600 CTTTGTGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.38
Consensus pattern (22 bp):
CCGGATCGGTTTTTTATCCGAT
Found at i:50730 original size:228 final size:228
Alignment explanation
Indices: 50307--50990 Score: 733
Period size: 228 Copynumber: 3.0 Consensus size: 228
50297 AGCTTAGAAA
* * * * * * * * * *
50307 CCACCACGAAGACGCAAGACAAGGTGAAGAGTGGATTCCTTCTGGATATTGTAATCAG-CAAGAG
1 CCACCACGAAGACGCAAAACCAGATGAAGGGTCGACTCCTTCTGAATGTTATAATCGGCCAA-AG
** * * ** * * * * * * *
50371 TCCTTCCATCTTCCAATTGTTTCCCAGCGAAAATCAACCTCTGCTGATCTGGGGGAATCCCTTCT
65 TCCGGCCGTCTTCGAGCTGTTTTCCAGCGAAGATGAGCCTCTGCTGATCCGGTGGAATCCCTTCC
* * * * * * * * * * *
50436 TTGTCCTGAATCTTCGCCTTAACATTATCGATCGTATCAGAACTCTCCACCTCTAGGGTTATGGT
130 TTGTCTTGGATCTTGGCCTTGACGTTGTCGATCGTATCGGAACTCTCAACTTCCAAGGTTATGGT
* *
50501 TTTTCCAGTCAAAGTCTTGACGAAGATCTGCATC
195 TTTTCCGGTCAGAGTCTTGACGAAGATCTGCATC
* * * *
50535 CCACCACGAAGCCTCAAAACCAGATGAAGGGTCGATTCCTTCTGAATGTTATAATCGGCCAAGGT
1 CCACCACGAAGACGCAAAACCAGATGAAGGGTCGACTCCTTCTGAATGTTATAATCGGCCAAAGT
*
50600 CCGGCCGTCTTCGAGCTGTTTTCCAGCGAAGATGAGCCTCTGCTGGTCCGGTGGAATCCCTTCCT
66 CCGGCCGTCTTCGAGCTGTTTTCCAGCGAAGATGAGCCTCTGCTGATCCGGTGGAATCCCTTCCT
* * *
50665 TGTCTTGGATCTTGGCCTTGACGTTGTCGATCGTGTCGGAGCTCTCAACTTCCAAAGTTATGGTT
131 TGTCTTGGATCTTGGCCTTGACGTTGTCGATCGTATCGGAACTCTCAACTTCCAAGGTTATGGTT
* * *
50730 TTTCCGGTGAGAGTTTTGACGAAGATCTGCATG
196 TTTCCGGTCAGAGTCTTGACGAAGATCTGCATC
* * ** * * * * * *
50763 CCTCCACGAAGACGGAGGACGAGGTGGAGGGTTGACTCCTTCTGGATGTTGTAATCGGCCAAAGT
1 CCACCACGAAGACGCAAAACCAGATGAAGGGTCGACTCCTTCTGAATGTTATAATCGGCCAAAGT
* * * *
50828 CCGGCCGTCTTCGAGCTGTTTTCCGGCGAAGATGAGACGCTGCTGATCCGGTGGGATCCCTTCCT
66 CCGGCCGTCTTCGAGCTGTTTTCCAGCGAAGATGAGCCTCTGCTGATCCGGTGGAATCCCTTCCT
* * * *
50893 TGTCTTGGATCTTGGCCTTGACGTTGTCGATGGTATCGGAACTCTCGACTT-CAAGGGTGATTGT
131 TGTCTTGGATCTTGGCCTTGACGTTGTCGATCGTATCGGAACTCTCAACTTCCAA-GGTTATGGT
* *
50957 CTTTCCGGTCAGGGTCTTGACGAAGATCTGCATC
195 TTTTCCGGTCAGAGTCTTGACGAAGATCTGCATC
50991 TTGTTTGGCT
Statistics
Matches: 378, Mismatches: 76, Indels: 4
0.83 0.17 0.01
Matches are distributed among these distances:
227 3 0.01
228 372 0.98
229 3 0.01
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (228 bp):
CCACCACGAAGACGCAAAACCAGATGAAGGGTCGACTCCTTCTGAATGTTATAATCGGCCAAAGT
CCGGCCGTCTTCGAGCTGTTTTCCAGCGAAGATGAGCCTCTGCTGATCCGGTGGAATCCCTTCCT
TGTCTTGGATCTTGGCCTTGACGTTGTCGATCGTATCGGAACTCTCAACTTCCAAGGTTATGGTT
TTTCCGGTCAGAGTCTTGACGAAGATCTGCATC
Found at i:54247 original size:65 final size:65
Alignment explanation
Indices: 54087--54247 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
54077 TTGTTTAAGG
* * * **
54087 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
54150 A
65 A
*
54151 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
54215 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
54248 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:55763 original size:824 final size:823
Alignment explanation
Indices: 54177--55828 Score: 3295
Period size: 824 Copynumber: 2.0 Consensus size: 823
54167 GAGTGCATCG
54177 ATGCATCCCCATTAAATACAAACATCGAATAGGATTTATGCATCGATGCATGGTGTAGTGCATCG
1 ATGCATCCCCATTAAATACAAACATCGAATAGGATTTATGCATCGATGCATGGTGTAGTGCATCG
54242 ATGCATACCTTCATTAAAAGATGAAATTGGCTTTTCTTTGAGACTAAGGAGTGATAGTTTCGAAT
66 ATGCATACCTTCATTAAAAGATGAAATTGGCTTTTCTTTGAGACTAAGGAGTGATAGTTTCGAAT
54307 ATATCAATCAGTATACTGATAAGTATTAATGTATTATTATGTAGATATAGAATGAAAGCTTGTTC
131 ATATCAATCAGTATACTGATAAGTATTAATGTATTATTATGTAGATATAGAATGAAAGCTTGTTC
54372 CGGAACAATTAAGGATTAGGATTGATTCAAACAACGAGGCCCAGGTGAGTGCATCTTATCGTATA
196 CGGAACAATTAAGGATTAGGATTGATTCAAACAACGAGGCCCAGGTGAGTGCATCTTATCGTATA
54437 AGATTATATGGAAATTGGACTTGTGATAAGTCTATTCCTATAGTAATAGCTCATTAAGCCTTGAT
261 AGATTATATGGAAATTGGACTTGTGATAAGTCTATTCCTATAGTAATAGCTCATTAAGCCTTGAT
54502 TATAAGTATGTTAACGATATGAAGTGTATGTATGTTGGATTATATGAATTGATAGGTTTTGTTTT
326 TATAAGTATGTTAACGATATGAAGTGTATGTATGTTGGATTATATGAATTGATAGGTTTTGTTTT
54567 GCATGTGCTATGTGGTTTATGTAAAAATACGGTTAAGTGTTAATGAGATAATATAAAATAAGTTA
391 GCATGTGCTATGTGGTTTATGTAAAAATACGGTTAAGTGTTAATGAGATAATATAAAATAAGTTA
54632 TGAAATTATATGAATATAGAAGATAAGTCAAGAGATGTAGGGAAATGAAAATAGATGTTTATAAA
456 TGAAATTATATGAATATAGAAGATAAGTCAAGAGATGTAGGGAAATGAAAATAGATGTTTATAAA
54697 GAGTCATAGGAGAACAAATATAAGTAATATGATAATGAAATATAAGGCTATGTAAATACATGGTT
521 GAGTCATAGGAGAACAAATATAAGTAATATGATAATGAAATATAAGGCTATGTAAATACATGGTT
54762 ATGAGATAAAATATGTAGGAATAAGAAAAGATGATGAGAGTGAGTTCATGAGAAGTGATATGAAC
586 ATGAGATAAAATATGTAGGAATAAGAAAAGATGATGAGAGTGAGTTCATGAGAAGTGATATGAAC
54827 TAGGTAAACATGAGTTGGACAATTAAATAGTGGTATGATCCATTATGGGAATTAGTATAATAGAG
651 TAGGTAAACATGAGTTGGACAATTAAATAGTGGTATGATCCATTATGGGAATTAGTATAATAGAG
54892 TTTTTTTGATTTAAAAAGAGTTAAGGGAACTAAATAAGATTGAATTATAGAATGAAATGGGAATA
716 TTTTTTTGATTTAAAAAGAGTTAAGGGAACTAAATAAGATTGAATTATAGAATGAAATGGGAATA
54957 GTATATCAATTAGGAATCTTGAATATAAAGGGACGATACGAAT
781 GTATATCAATTAGGAATCTTGAATATAAAGGGACGATACGAAT
55000 ATGCATCCCCATTAAATACAAACATCGAATAGGATTTATGCATCGATGCATGGTGTAGTGCATCG
1 ATGCATCCCCATTAAATACAAACATCGAATAGGATTTATGCATCGATGCATGGTGTAGTGCATCG
55065 ATGCATACCTTCATTAAAAGATGAAATTGGCTTTTCTTTGAGACTAAGGAGTGATAGTTTCGAAT
66 ATGCATACCTTCATTAAAAGATGAAATTGGCTTTTCTTTGAGACTAAGGAGTGATAGTTTCGAAT
55130 ATATCAATCAGTATACTGATAAGTATTAATGTATTATTATGTAGATATAGAATGAAAGCTTGTTC
131 ATATCAATCAGTATACTGATAAGTATTAATGTATTATTATGTAGATATAGAATGAAAGCTTGTTC
55195 CGGAACAAATTAAGGATTAGGATTGATTCAAACAACGAGGCCCAGGTGAGTGCATCTTATCGTAT
196 CGGAAC-AATTAAGGATTAGGATTGATTCAAACAACGAGGCCCAGGTGAGTGCATCTTATCGTAT
55260 AAGATTATATGGAAATTGGACTTGTGATAAGTCTATTCCTATAGTAATAGCTCATTAAGCCTTGA
260 AAGATTATATGGAAATTGGACTTGTGATAAGTCTATTCCTATAGTAATAGCTCATTAAGCCTTGA
55325 TTATAAGTATGTTAACGATATGAAGTGTATGTATGTTGGATTATATGAATTGATAGGTTTTGTTT
325 TTATAAGTATGTTAACGATATGAAGTGTATGTATGTTGGATTATATGAATTGATAGGTTTTGTTT
55390 TGCATGTGCTATGTGGTTTATGTAAAAATACGGTTAAGTGTTAATGAGATAATATAAAATAAGTT
390 TGCATGTGCTATGTGGTTTATGTAAAAATACGGTTAAGTGTTAATGAGATAATATAAAATAAGTT
55455 ATGAAATTATATGAATATAGAAGATAAGTCAAGAGATGTAGGGAAATGAAAATAGATGTTTATAA
455 ATGAAATTATATGAATATAGAAGATAAGTCAAGAGATGTAGGGAAATGAAAATAGATGTTTATAA
55520 AGAGTCATAGGAGAACAAATATAAGTAATATGATAATGAAATATAAGGCTATGTAAATACATGGT
520 AGAGTCATAGGAGAACAAATATAAGTAATATGATAATGAAATATAAGGCTATGTAAATACATGGT
55585 TATGAGATAAAATATGTAGGAATAAGAAAAGATGATGAGAGTGAGTTCATGAGAAGTGATATGAA
585 TATGAGATAAAATATGTAGGAATAAGAAAAGATGATGAGAGTGAGTTCATGAGAAGTGATATGAA
55650 CTAGGTAAACATGAGTTGGACAATTAAATAGTGGTATGATCCATTATGGGAATTAGTATAATAGA
650 CTAGGTAAACATGAGTTGGACAATTAAATAGTGGTATGATCCATTATGGGAATTAGTATAATAGA
55715 GTTTTTTTGATTTAAAAAGAGTTAAGGGAACTAAATAAGATTGAATTATAGAATGAAATGGGAAT
715 GTTTTTTTGATTTAAAAAGAGTTAAGGGAACTAAATAAGATTGAATTATAGAATGAAATGGGAAT
55780 AGTATATCAATTAGGAATCTTGAATATAAAGGGACGATACGAAT
780 AGTATATCAATTAGGAATCTTGAATATAAAGGGACGATACGAAT
55824 ATGCA
1 ATGCA
55829 AGATAAGTTA
Statistics
Matches: 828, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
823 201 0.24
824 627 0.76
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (823 bp):
ATGCATCCCCATTAAATACAAACATCGAATAGGATTTATGCATCGATGCATGGTGTAGTGCATCG
ATGCATACCTTCATTAAAAGATGAAATTGGCTTTTCTTTGAGACTAAGGAGTGATAGTTTCGAAT
ATATCAATCAGTATACTGATAAGTATTAATGTATTATTATGTAGATATAGAATGAAAGCTTGTTC
CGGAACAATTAAGGATTAGGATTGATTCAAACAACGAGGCCCAGGTGAGTGCATCTTATCGTATA
AGATTATATGGAAATTGGACTTGTGATAAGTCTATTCCTATAGTAATAGCTCATTAAGCCTTGAT
TATAAGTATGTTAACGATATGAAGTGTATGTATGTTGGATTATATGAATTGATAGGTTTTGTTTT
GCATGTGCTATGTGGTTTATGTAAAAATACGGTTAAGTGTTAATGAGATAATATAAAATAAGTTA
TGAAATTATATGAATATAGAAGATAAGTCAAGAGATGTAGGGAAATGAAAATAGATGTTTATAAA
GAGTCATAGGAGAACAAATATAAGTAATATGATAATGAAATATAAGGCTATGTAAATACATGGTT
ATGAGATAAAATATGTAGGAATAAGAAAAGATGATGAGAGTGAGTTCATGAGAAGTGATATGAAC
TAGGTAAACATGAGTTGGACAATTAAATAGTGGTATGATCCATTATGGGAATTAGTATAATAGAG
TTTTTTTGATTTAAAAAGAGTTAAGGGAACTAAATAAGATTGAATTATAGAATGAAATGGGAATA
GTATATCAATTAGGAATCTTGAATATAAAGGGACGATACGAAT
Found at i:56434 original size:22 final size:21
Alignment explanation
Indices: 56368--56447 Score: 142
Period size: 21 Copynumber: 3.8 Consensus size: 21
56358 AGGGTTTCAT
56368 AGGTCCTTCGGGACAACTCAC
1 AGGTCCTTCGGGACAACTCAC
56389 AGGTCCTTCGGGACAACTCAC
1 AGGTCCTTCGGGACAACTCAC
*
56410 AGGTCCTTCGGGACATATTCAC
1 AGGTCCTTCGGGACA-ACTCAC
56432 AGGTCCTTCGGGACAA
1 AGGTCCTTCGGGACAA
56448 ATTTCATATG
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
21 37 0.65
22 20 0.35
ACGTcount: A:0.24, C:0.30, G:0.25, T:0.21
Consensus pattern (21 bp):
AGGTCCTTCGGGACAACTCAC
Found at i:57498 original size:24 final size:24
Alignment explanation
Indices: 57453--57499 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
57443 TTTTTATATA
*
57453 TAATAATATTACACATTTAATTAT
1 TAATAATATTACACATTAAATTAT
* * *
57477 TAATAATTTTATATATTAAATTA
1 TAATAATATTACACATTAAATTA
57500 AACTAATAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATAATATTACACATTAAATTAT
Found at i:62340 original size:20 final size:20
Alignment explanation
Indices: 62315--62364 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
62305 AGGGAAATAG
* *
62315 TATCGATACTTATCCTTTGA
1 TATCGATACTGACCCTTTGA
62335 TATCGATACTGACCCTTTGA
1 TATCGATACTGACCCTTTGA
62355 TATCGATACT
1 TATCGATACT
62365 AAGGGTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (20 bp):
TATCGATACTGACCCTTTGA
Found at i:62452 original size:20 final size:20
Alignment explanation
Indices: 62407--62468 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
62397 TCAAGACTGA
*
62407 TGGTCTTCATACTA-AAGAAC
1 TGGTCTTCATA-TAGAAGGAC
* *
62427 TAGTCTTCATATAGAAGGAT
1 TGGTCTTCATATAGAAGGAC
*
62447 TGGTCTTCATATCGAAGGAC
1 TGGTCTTCATATAGAAGGAC
62467 TG
1 TG
62469 ATCTCCATAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 2 0.06
20 33 0.94
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (20 bp):
TGGTCTTCATATAGAAGGAC
Found at i:62477 original size:20 final size:20
Alignment explanation
Indices: 62434--62483 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
62424 AACTAGTCTT
* * * *
62434 CATATAGAAGGATTGGTCTT
1 CATATCGAAGGACTGATCTC
62454 CATATCGAAGGACTGATCTC
1 CATATCGAAGGACTGATCTC
*
62474 CATACCGAAG
1 CATATCGAAG
62484 ATTGAGTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (20 bp):
CATATCGAAGGACTGATCTC
Found at i:63554 original size:31 final size:31
Alignment explanation
Indices: 63511--63604 Score: 107
Period size: 31 Copynumber: 2.9 Consensus size: 31
63501 GTGAGACTAG
63511 ATACTAGTCAAGGTGCATTCAAATAATGCACA
1 ATAC-AGTCAAGGTGCATTCAAATAATGCACA
* *
63543 ATACAGTCAAGGTGCATTCAGATAGTGCACA
1 ATACAGTCAAGGTGCATTCAAATAATGCACA
* * * *
63574 GTAAAATTAAGGTTTGCATTCAAATAATGCA
1 ATACAGTCAAGG--TGCATTCAAATAATGCA
63605 TATAAGTATC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
31 33 0.63
32 4 0.08
33 15 0.29
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (31 bp):
ATACAGTCAAGGTGCATTCAAATAATGCACA
Found at i:67847 original size:2 final size:2
Alignment explanation
Indices: 67840--67918 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
67830 CTTTTTCGTG
67840 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67882 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
67919 CTTTTGTTTG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:69057 original size:194 final size:191
Alignment explanation
Indices: 68675--69031 Score: 441
Period size: 194 Copynumber: 1.9 Consensus size: 191
68665 ATTATATATG
* * *
68675 GTGACGTTATGCATAATCATCATTCGTAATATTATTAGGTAATGATATATTATGTCACTAAAAAT
1 GTGACATTATGCATAAACATCATTCATAATATTATTAGGTAATGATATATTATGTCACTAAAAAT
* *
68740 GTGACTATCTTTTTCGTCACATATAAGTTGATTTTAATGCATTATTTGTGACAATATAAACTATC
66 GTGACTATCTTTTTCGTCACATATAAGTTGATTTTAATACATTATCTGTGACAATATAAACTATC
** ** * **
68805 AATAATGAAATCTTATTTAATTTTGTGATGTAACCAATTGCCATAGAATATAAATTATAAA
131 AATAACAAAATCTTACATAATTTAGTGACATAACCAATTGCCATAGAATATAAATTATAAA
* * *
68866 GTGACATTATGCATAAACGTCATTCATAATATTATTAGGTAACAT-TTATATTATGTTACTAAAA
1 GTGACATTATGCATAAACATCATTCATAATATTATTAGGT-A-ATGATATATTATGTCACTAAAA
* * * **
68930 ATTTGACAATAT-TTCTTTCGTCACATATATGTTGATTTTAATATATTATCTGTGATGATATAAA
64 ATGTGAC--TATCTT-TTTCGTCACATATAAGTTGATTTTAATACATTATCTGTGACAATATAAA
* *
68994 -TCATCAATAACAAAATTTTACATAATTTAGTTACATAA
126 CT-ATCAATAACAAAATCTTACATAATTTAGTGACATAA
69032 TTAGTTTTCA
Statistics
Matches: 138, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
191 36 0.26
192 24 0.17
193 5 0.04
194 73 0.53
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (191 bp):
GTGACATTATGCATAAACATCATTCATAATATTATTAGGTAATGATATATTATGTCACTAAAAAT
GTGACTATCTTTTTCGTCACATATAAGTTGATTTTAATACATTATCTGTGACAATATAAACTATC
AATAACAAAATCTTACATAATTTAGTGACATAACCAATTGCCATAGAATATAAATTATAAA
Found at i:78936 original size:2 final size:2
Alignment explanation
Indices: 78929--78979 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
78919 TGGCCCCAAT
78929 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
78971 TA TA TA TA T
1 TA TA TA TA T
78980 TAAATTCTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:80990 original size:104 final size:104
Alignment explanation
Indices: 80645--81715 Score: 1851
Period size: 105 Copynumber: 10.3 Consensus size: 104
80635 GGAAACTACG
80645 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
1 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
80710 TTATCTTTATTTTTCTTCTTCTCTAATTGTAGATTAACAT
66 TTATCTTTATTTTT-TTCTTCTCTAATTGTAGATTAACAT
* *
80750 GGATGAAGCTACGAAAACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTA
1 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
80815 TTATCTTTATTTTTTTTCTTCTCTAATTGTAGATTAACAT
66 TTATCTTTA-TTTTTTTCTTCTCTAATTGTAGATTAACAT
* * *
80855 GGATGAAGTTACGAAGACATCACTGGAATTTGATGGTTCTTTAGACAAAAACAGATAATTTTCTT
1 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
80920 TTATCTTTATTTTTTTCTTCTCTAATTGTAGATTAACAT
66 TTATCTTTATTTTTTTCTTCTCTAATTGTAGATTAACAT
* *
80959 GGATGAAGCTACAAAGACATCATCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
1 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
81024 TTATCTTTATTTTTTTCTTCTCTAATTGTAGATTAACAT
66 TTATCTTTATTTTTTTCTTCTCTAATTGTAGATTAACAT
* *
81063 TGATGAAGCTACGAAGACATCACCGGAATTTAATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
1 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
81128 TTATCTTTATTTTGTTTCTTCTCTAATTGTAGATTAACAT
66 TTATCTTTATTTT-TTTCTTCTCTAATTGTAGATTAACAT
* * *
81168 GGATGAAGCTACGAAAACATCACCGGAATTTGATGGTTCTTTAGA-TAAAGTAGATAATTTT-TT
1 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
81231 TTATCTTTATTTTTTTTCTTCTCTAATTGTAGATTAACAT
66 TTATCTTTA-TTTTTTTCTTCTCTAATTGTAGATTAACAT
* *
81271 GGATGAAGCTACGAAGACATCACTGGAATTTGATGGTTCTTTAGACAAAAGTAGATAATTTTCTT
1 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
*
81336 TTATCTTTATTTTTTTCTTCTCTAATTGTATATTAACAT
66 TTATCTTTATTTTTTTCTTCTCTAATTGTAGATTAACAT
*
81375 GGATGAAGCTACGAAGACATCACCAGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
1 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
81440 TTATCTTTATTTTTTT-TTCTCTAATTGTAGATTAACAT
66 TTATCTTTATTTTTTTCTTCTCTAATTGTAGATTAACAT
* *
81478 GGATGAAGCTACGAAGACATCACTGGAATTTGATGGTACTTTAGACAAAAGCAGATAATTTTCTT
1 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
*
81543 TTATCTTTATTTTTTTCCTTCTCTAATTGTAGATTAATAT
66 TTATCTTTATTTTTTT-CTTCTCTAATTGTAGATTAACAT
* *
81583 GGATGAAGCTACGAAGACATCACCAGAATTTGATGGTTCTTTAGACAAAAACAGATAATTTTCTT
1 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
*
81648 TTATCTTTATTTTTTTTCTTCTTTAATTGTAGATTAACAT
66 TTATCTTTA-TTTTTTTCTTCTCTAATTGTAGATTAACAT
* *
81688 GGATGAAACTACGAAAACATCACCGGAA
1 GGATGAAGCTACGAAGACATCACCGGAA
81716 CTTGGCTTAA
Statistics
Matches: 916, Mismatches: 42, Indels: 16
0.94 0.04 0.02
Matches are distributed among these distances:
103 179 0.20
104 343 0.37
105 382 0.42
106 12 0.01
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (104 bp):
GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
TTATCTTTATTTTTTTCTTCTCTAATTGTAGATTAACAT
Found at i:81131 original size:208 final size:209
Alignment explanation
Indices: 80645--81715 Score: 1841
Period size: 208 Copynumber: 5.1 Consensus size: 209
80635 GGAAACTACG
80645 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
1 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
80710 TTATCTTTATTTTTCTTCTTCTCTAATTGTAGATTAACATGGATGAAGCTACGAAA-ACATCACC
66 TTATCTTTATTTTT-TTCTTCTCTAATTGTAGATTAACATGGATGAAGCTAC-AAAGACATCACC
*
80774 GGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTATTATCTTTATTTTTTTTCTTCTCT
129 GGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTTTTATCTTTATTTTTTTTCTTCTCT
80839 AATTGTAGATTAACAT
194 AATTGTAGATTAACAT
* * *
80855 GGATGAAGTTACGAAGACATCACTGGAATTTGATGGTTCTTTAGACAAAAACAGATAATTTTCTT
1 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
*
80920 TTATCTTTATTTTTTTCTTCTCTAATTGTAGATTAACATGGATGAAGCTACAAAGACATCATCGG
66 TTATCTTTATTTTTTTCTTCTCTAATTGTAGATTAACATGGATGAAGCTACAAAGACATCACCGG
80985 AATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTTTTATCTTTA-TTTTTTTCTTCTCTAA
131 AATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTTTTATCTTTATTTTTTTTCTTCTCTAA
81049 TTGTAGATTAACAT
196 TTGTAGATTAACAT
* *
81063 TGATGAAGCTACGAAGACATCACCGGAATTTAATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
1 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
81128 TTATCTTTATTTTGTTTCTTCTCTAATTGTAGATTAACATGGATGAAGCTACGAAA-ACATCACC
66 TTATCTTTATTTT-TTTCTTCTCTAATTGTAGATTAACATGGATGAAGCTAC-AAAGACATCACC
* *
81192 GGAATTTGATGGTTCTTTAGA-TAAAGTAGATAATTTT-TTTTATCTTTATTTTTTTTCTTCTCT
129 GGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTTTTATCTTTATTTTTTTTCTTCTCT
81255 AATTGTAGATTAACAT
194 AATTGTAGATTAACAT
* *
81271 GGATGAAGCTACGAAGACATCACTGGAATTTGATGGTTCTTTAGACAAAAGTAGATAATTTTCTT
1 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
* * *
81336 TTATCTTTATTTTTTTCTTCTCTAATTGTATATTAACATGGATGAAGCTACGAAGACATCACCAG
66 TTATCTTTATTTTTTTCTTCTCTAATTGTAGATTAACATGGATGAAGCTACAAAGACATCACCGG
81401 AATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTTTTATCTTTA-TTTTTTT-TTCTCTAA
131 AATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTTTTATCTTTATTTTTTTTCTTCTCTAA
81464 TTGTAGATTAACAT
196 TTGTAGATTAACAT
* *
81478 GGATGAAGCTACGAAGACATCACTGGAATTTGATGGTACTTTAGACAAAAGCAGATAATTTTCTT
1 GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
* * *
81543 TTATCTTTATTTTTTTCCTTCTCTAATTGTAGATTAATATGGATGAAGCTACGAAGACATCACCA
66 TTATCTTTATTTTTTT-CTTCTCTAATTGTAGATTAACATGGATGAAGCTACAAAGACATCACCG
* *
81608 GAATTTGATGGTTCTTTAGACAAAAACAGATAATTTTCTTTTATCTTTATTTTTTTTCTTCTTTA
130 GAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTTTTATCTTTATTTTTTTTCTTCTCTA
81673 ATTGTAGATTAACAT
195 ATTGTAGATTAACAT
* *
81688 GGATGAAACTACGAAAACATCACCGGAA
1 GGATGAAGCTACGAAGACATCACCGGAA
81716 CTTGGCTTAA
Statistics
Matches: 820, Mismatches: 31, Indels: 20
0.94 0.04 0.02
Matches are distributed among these distances:
206 2 0.00
207 177 0.22
208 339 0.41
209 177 0.22
210 125 0.15
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (209 bp):
GGATGAAGCTACGAAGACATCACCGGAATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTT
TTATCTTTATTTTTTTCTTCTCTAATTGTAGATTAACATGGATGAAGCTACAAAGACATCACCGG
AATTTGATGGTTCTTTAGACAAAAGCAGATAATTTTCTTTTATCTTTATTTTTTTTCTTCTCTAA
TTGTAGATTAACAT
Found at i:82418 original size:31 final size:31
Alignment explanation
Indices: 82383--82459 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
82373 AATTACTTGG
* *
82383 GGGACCATATTGCAAACAGACTAAATGTTGA
1 GGGACCGTATTGCAAACAGACTAAATATTGA
** * *
82414 GGGACCGTATTATAAATAGACTAAATATTGG
1 GGGACCGTATTGCAAACAGACTAAATATTGA
*
82445 GGGACTGTATTGCAA
1 GGGACCGTATTGCAA
82460 GTTTTAAAAG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (31 bp):
GGGACCGTATTGCAAACAGACTAAATATTGA
Found at i:96098 original size:21 final size:21
Alignment explanation
Indices: 96065--96114 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
96055 CTAACAAAAA
* *
96065 TCGGAT-TCGGATCCGGATATT
1 TCGGATATCCGATCC-GAAATT
96086 T-GGATATCCGATCCGAAATT
1 TCGGATATCCGATCCGAAATT
96106 TCGGATATC
1 TCGGATATC
96115 TGAATGTTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (21 bp):
TCGGATATCCGATCCGAAATT
Found at i:104468 original size:25 final size:24
Alignment explanation
Indices: 104440--104489 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
104430 AAGACACGAA
*
104440 TTTCTCTGTTTTCATAGCACGTTTT
1 TTTCTCTGCTTTCATAGCAC-TTTT
*
104465 TTTCTCTGCTTTCATATCACTTTT
1 TTTCTCTGCTTTCATAGCACTTTT
104489 T
1 T
104490 CTCTGTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.12, C:0.22, G:0.08, T:0.58
Consensus pattern (24 bp):
TTTCTCTGCTTTCATAGCACTTTT
Found at i:104491 original size:22 final size:23
Alignment explanation
Indices: 104440--104499 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 23
104430 AAGACACGAA
*
104440 TTTCTCTGTTTTCATAGCACGTTTT
1 TTTCTCTGCTTTCATAGCAC--TTT
*
104465 TTTCTCTGCTTTCATATCAC-TT
1 TTTCTCTGCTTTCATAGCACTTT
104487 TTTCTCTGTCTTT
1 TTTCTCTG-CTTT
104500 TGACACGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 10 0.31
23 4 0.12
25 18 0.56
ACGTcount: A:0.10, C:0.23, G:0.08, T:0.58
Consensus pattern (23 bp):
TTTCTCTGCTTTCATAGCACTTT
Found at i:106696 original size:28 final size:28
Alignment explanation
Indices: 106636--106702 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
106626 GGTGGCAAGG
* *
106636 CCGACCATATATCATTCAGGCGATATAA
1 CCGACCATATATCAATCAGGCGACATAA
106664 CCGACCATATATCAATCAGGCGACA-AA
1 CCGACCATATATCAATCAGGCGACATAA
*
106691 GTCGACCATATA
1 -CCGACCATATA
106703 ATATAACTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 2 0.06
28 33 0.94
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.21
Consensus pattern (28 bp):
CCGACCATATATCAATCAGGCGACATAA
Found at i:108657 original size:41 final size:43
Alignment explanation
Indices: 108589--108749 Score: 145
Period size: 43 Copynumber: 3.9 Consensus size: 43
108579 CAAAATGGTA
*
108589 ACTTTAGCGGCGTTTTCAAAGACAAACGCCGCAACAGAGTTTT
1 ACTTTAGCGGCGTTTTCAAAGACAAACGCCGCAACAGAGTTCT
* * * * *
108632 ACTTTAGCGGCTTTTTTATA-A-AAACGCCGCAATAGA-TTCC
1 ACTTTAGCGGCGTTTTCAAAGACAAACGCCGCAACAGAGTTCT
* * * * * **
108672 ATCTTTAGTGGCATTTT--TA-ATAAACACCGCAACAGAGTAGT
1 A-CTTTAGCGGCGTTTTCAAAGACAAACGCCGCAACAGAGTTCT
*
108713 AGTTTAGCGGCGTTTTCAAAGACAAACGCCGCAACAG
1 ACTTTAGCGGCGTTTTCAAAGACAAACGCCGCAACAG
108750 GCAAAATTTA
Statistics
Matches: 93, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
39 3 0.03
40 28 0.30
41 29 0.31
42 2 0.02
43 31 0.33
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (43 bp):
ACTTTAGCGGCGTTTTCAAAGACAAACGCCGCAACAGAGTTCT
Found at i:111596 original size:24 final size:21
Alignment explanation
Indices: 111546--111590 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
111536 ATAGAGCGAT
111546 GAAGAAGGTTCCGATGAAGAG
1 GAAGAAGGTTCCGATGAAGAG
111567 GAAGAAGGTTCCGATGAAGAG
1 GAAGAAGGTTCCGATGAAGAG
111588 GAA
1 GAA
111591 CAAGAAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.09, G:0.38, T:0.13
Consensus pattern (21 bp):
GAAGAAGGTTCCGATGAAGAG
Found at i:115927 original size:53 final size:53
Alignment explanation
Indices: 115863--115963 Score: 184
Period size: 53 Copynumber: 1.9 Consensus size: 53
115853 TTCAATCAGT
115863 GGGTTCACTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCTTAC
1 GGGTTCACTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCTTAC
* *
115916 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTTGAACAATCTTCTG
1 GGGTTCACTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTG
115964 GTGTGATTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.31
Consensus pattern (53 bp):
GGGTTCACTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCTTAC
Found at i:116449 original size:41 final size:42
Alignment explanation
Indices: 116404--116484 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
116394 TGGATGACAC
* *
116404 GAAGGATTT-TTCATCTTGCCCGAACA-ACTTACTGATGGCCT
1 GAAGGATTTCATCATCATGCCCGAA-AGACTTACTGATGGCCT
*
116445 GAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGC
1 GAAGGATTTCATCATCATGCCCGAAAGACTTACTGATGGC
116485 ACTTACTGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 10 0.29
42 25 0.71
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (42 bp):
GAAGGATTTCATCATCATGCCCGAAAGACTTACTGATGGCCT
Found at i:116490 original size:13 final size:13
Alignment explanation
Indices: 116472--116496 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
116462 TGCTCGAAAG
116472 ACTTACTGATGGC
1 ACTTACTGATGGC
116485 ACTTACTGATGG
1 ACTTACTGATGG
116497 ATTTGCTTCA
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:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:116553 original size:93 final size:93
Alignment explanation
Indices: 116445--116669 Score: 414
Period size: 93 Copynumber: 2.4 Consensus size: 93
116435 CTGATGGCCT
*
116445 GAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCACTA
1 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCACTA
*
116510 CTCTTCCGTGAAGGTTTACAAATTACCC
66 CTCTTCCGTGAAGGCTTACAAATTACCC
*
116538 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGGTTTGCTTCACTA
1 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCACTA
*
116603 CTCTTCGGTGAAGGCTTACAAATTACCC
66 CTCTTCCGTGAAGGCTTACAAATTACCC
116631 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
116670 ACCGAAGGAC
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 128 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (93 bp):
GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCACTA
CTCTTCCGTGAAGGCTTACAAATTACCC
Found at i:116583 original size:13 final size:13
Alignment explanation
Indices: 116565--116589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
116555 TGCTCGAAAG
116565 ACTTACTGATGGC
1 ACTTACTGATGGC
116578 ACTTACTGATGG
1 ACTTACTGATGG
116590 GTTTGCTTCA
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:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:116846 original size:41 final size:41
Alignment explanation
Indices: 116791--116897 Score: 133
Period size: 42 Copynumber: 2.6 Consensus size: 41
116781 CCCGAAGGTT
* * * *
116791 TTACGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGC
1 TTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAC
* * *
116832 TTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAC
1 TTACAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGAC
*
116874 TTACTGATGGCCCGAAGGACTTAT
1 TTACAGATGGCCCGAAGGACTTAT
116898 AAATTGTGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 20 0.37
42 34 0.63
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.25
Consensus pattern (41 bp):
TTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAC
Found at i:116982 original size:214 final size:214
Alignment explanation
Indices: 116613--117014 Score: 705
Period size: 214 Copynumber: 1.9 Consensus size: 214
116603 CTCTTCGGTG
* *
116613 AAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
1 AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
* *
116678 ACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTCAAAAC
66 ACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTCAAAAC
* *
116743 ATCGTTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGGCCCGAAG
131 ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTACGGATGGCCCGAAG
116808 GACTTATCATCTTGCTCTA
196 GACTTATCATCTTGCTCTA
* *
116827 AAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
*
116892 ACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAAC
66 ACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTCAAAAC
* *
116957 ATCATTTTTTATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTATGGATGG
131 ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTACGGATGG
117015 TTTGCTTCAC
Statistics
Matches: 177, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
214 177 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (214 bp):
AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
ACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTCAAAAC
ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTACGGATGGCCCGAAG
GACTTATCATCTTGCTCTA
Found at i:126185 original size:44 final size:45
Alignment explanation
Indices: 126121--126210 Score: 164
Period size: 44 Copynumber: 2.0 Consensus size: 45
126111 ATGCATACAC
126121 AAGCAAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGT
1 AAGCAAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGT
*
126166 AAGCAAATTA-AAAAACAATTGAGAATGGAAACATAGAAATAAGT
1 AAGCAAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGT
126210 A
1 A
126211 CCCCTTTTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 34 0.77
45 10 0.23
ACGTcount: A:0.60, C:0.08, G:0.14, T:0.18
Consensus pattern (45 bp):
AAGCAAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGT
Found at i:127602 original size:28 final size:28
Alignment explanation
Indices: 127542--127608 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
127532 GGTGGCAAGG
* *
127542 CCGACCATATATCATTCAGGCGATATAA
1 CCGACCATATATCAATCAGGCGACATAA
127570 CCGACCATATATCAATCAGGCGACA-AA
1 CCGACCATATATCAATCAGGCGACATAA
*
127597 GTCGACCATATA
1 -CCGACCATATA
127609 ATATAACTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 2 0.06
28 33 0.94
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.21
Consensus pattern (28 bp):
CCGACCATATATCAATCAGGCGACATAA
Found at i:127821 original size:19 final size:20
Alignment explanation
Indices: 127767--127812 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
127757 CTCTAGCTCA
127767 CACTTTTGGCACTCTTTTAT
1 CACTTTTGGCACTCTTTTAT
127787 CACTTTTGGCACTCTTTTAT
1 CACTTTTGGCACTCTTTTAT
127807 CA-TTTT
1 CACTTTT
127813 TTCACTCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.15, C:0.24, G:0.09, T:0.52
Consensus pattern (20 bp):
CACTTTTGGCACTCTTTTAT
Found at i:130862 original size:43 final size:42
Alignment explanation
Indices: 130783--131108 Score: 356
Period size: 43 Copynumber: 7.6 Consensus size: 42
130773 TACAAATGCA
* * *
130783 CTAAATACACAGTTAATAGCGGCATTTAT-AAAGACAAACACG
1 CTAAATACACAGTCAATAGCGGCGTTT-TCAAAGACAAACCCG
* * *
130825 CTAAATACACAATCAAATAACGGCATTTTCAAAGACAAACGCCG
1 CTAAATACACAGTC-AATAGCGGCGTTTTCAAAGACAAAC-CCG
* ** * *
130869 CTAAATACACAATCAATAGCAACGTTAT-AAATACAAACGCCG
1 CTAAATACACAGTCAATAGCGGCGTTTTCAAAGACAAAC-CCG
*
130911 CTAAATACACAGTCAATAGC-GCATTTTCAAAGACAAACGCCG
1 CTAAATACACAGTCAATAGCGGCGTTTTCAAAGACAAAC-CCG
* *
130953 CTAAATACACAGTTAATAGCGGCGTTTAT-AAAGTA-AAATGCCG
1 CTAAATACACAGTCAATAGCGGCGTTT-TCAAAG-ACAAA-CCCG
** *
130996 CTAAATACACAGTCAATAGCGGCGTTTTCAAAGTTAAACGCGG
1 CTAAATACACAGTCAATAGCGGCGTTTTCAAAGACAAAC-CCG
* *
131039 CTAAATACACAGTCAATAGCGGCGTTTTCAAAGTCAAACGCGG
1 CTAAATACACAGTCAATAGCGGCGTTTTCAAAGACAAAC-CCG
131082 CTAAATACACAGTCAATAGCGGCGTTT
1 CTAAATACACAGTCAATAGCGGCGTTT
131109 GTCTTTACAA
Statistics
Matches: 250, Mismatches: 23, Indels: 21
0.85 0.08 0.07
Matches are distributed among these distances:
41 4 0.02
42 78 0.31
43 150 0.60
44 18 0.07
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.21
Consensus pattern (42 bp):
CTAAATACACAGTCAATAGCGGCGTTTTCAAAGACAAACCCG
Found at i:131082 original size:21 final size:21
Alignment explanation
Indices: 131006--131075 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
130996 CTAAATACAC
131006 AGTCAATAGCGGCGTTTTCAA
1 AGTCAATAGCGGCGTTTTCAA
* * * *
131027 AGTTAA-ACGCGGC-TAAATACAC
1 AGTCAATA-GCGGCGT--TTTCAA
131049 AGTCAATAGCGGCGTTTTCAA
1 AGTCAATAGCGGCGTTTTCAA
131070 AGTCAA
1 AGTCAA
131076 ACGCGGCTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
20 2 0.06
21 19 0.53
22 13 0.36
23 2 0.06
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (21 bp):
AGTCAATAGCGGCGTTTTCAA
Found at i:131096 original size:22 final size:22
Alignment explanation
Indices: 131031--131097 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
131021 TTTCAAAGTT
131031 AAACGCGGCTAAATACACAGTC
1 AAACGCGGCTAAATACACAGTC
* * *
131053 AATA-GCGGCGT--TTTCAAAGTC
1 AA-ACGCGGC-TAAATACACAGTC
131074 AAACGCGGCTAAATACACAGTC
1 AAACGCGGCTAAATACACAGTC
131096 AA
1 AA
131098 TAGCGGCGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
20 2 0.06
21 14 0.41
22 16 0.47
23 2 0.06
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (22 bp):
AAACGCGGCTAAATACACAGTC
Found at i:131122 original size:86 final size:86
Alignment explanation
Indices: 130783--131104 Score: 429
Period size: 86 Copynumber: 3.8 Consensus size: 86
130773 TACAAATGCA
* * * * * *
130783 CTAAATACACAGTTAATAGCGGCATTTATAAAGACAAAC-ACGCTAAATACACAATCAAATAACG
1 CTAAATACACAGTCAATAGCGGCGTTTATAAAGTCAAACGCCGCTAAATACACAGTC-AATAGCG
130847 GCATTTTCAAAGACAAACGCCG
65 GCATTTTCAAAGACAAACGCCG
* **
130869 CTAAATACACAATCAATAGCAACG-TTATAAA-TACAAACGCCGCTAAATACACAGTCAATAGC-
1 CTAAATACACAGTCAATAGCGGCGTTTATAAAGT-CAAACGCCGCTAAATACACAGTCAATAGCG
130931 GCATTTTCAAAGACAAACGCCG
65 GCATTTTCAAAGACAAACGCCG
* * *
130953 CTAAATACACAGTTAATAGCGGCGTTTATAAAGTAAAATGCCGCTAAATACACAGTCAATAGCGG
1 CTAAATACACAGTCAATAGCGGCGTTTATAAAGTCAAACGCCGCTAAATACACAGTCAATAGCGG
* ** *
131018 CGTTTTCAAAGTTAAACGCGG
66 CATTTTCAAAGACAAACGCCG
*
131039 CTAAATACACAGTCAATAGCGGCGTTT-TCAAAGTCAAACGCGGCTAAATACACAGTCAATAGCG
1 CTAAATACACAGTCAATAGCGGCGTTTAT-AAAGTCAAACGCCGCTAAATACACAGTCAATAGCG
131103 GC
65 GC
131105 GTTTGTCTTT
Statistics
Matches: 207, Mismatches: 23, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
84 42 0.20
85 52 0.25
86 113 0.55
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (86 bp):
CTAAATACACAGTCAATAGCGGCGTTTATAAAGTCAAACGCCGCTAAATACACAGTCAATAGCGG
CATTTTCAAAGACAAACGCCG
Found at i:131162 original size:129 final size:128
Alignment explanation
Indices: 130783--131108 Score: 378
Period size: 128 Copynumber: 2.5 Consensus size: 128
130773 TACAAATGCA
* * * *
130783 CTAAATACACAGTTAATAGCGGCATTTAT-AAAGACAAAC-ACGCTAAATACACAATCAAATAAC
1 CTAAATACACAGTCAATAGC-GCATTT-TCAAAGACAAACGCCGCTAAATACACAGTC-AATAGC
* ** ** *
130846 GGCATTT-TCAAAG-ACAAACGCCGCTAAATACACAATCAATAGCAACGTTATAAA--TACAAAC
63 GGCGTTTAT-AAAGTA-AAACGCCGCTAAATACACAGCCAATAGCGGCGTTTTAAAGTTA-AAAC
130907 GCCG
125 GCCG
*
130911 CTAAATACACAGTCAATAGCGCATTTTCAAAGACAAACGCCGCTAAATACACAGTTAATAGCGGC
1 CTAAATACACAGTCAATAGCGCATTTTCAAAGACAAACGCCGCTAAATACACAGTCAATAGCGGC
* * *
130976 GTTTATAAAGTAAAATGCCGCTAAATACACAGTCAATAGCGGCGTTTTCAAAGTT-AAACGCGG
66 GTTTATAAAGTAAAACGCCGCTAAATACACAGCCAATAGCGGCGTTTT-AAAGTTAAAACGCCG
* * *
131039 CTAAATACACAGTCAATAGCGGCGTTTTCAAAGTCAAACGCGGCTAAATACACAGTCAATAGCGG
1 CTAAATACACAGTCAATAGC-GCATTTTCAAAGACAAACGCCGCTAAATACACAGTCAATAGCGG
131104 CGTTT
65 CGTTT
131109 GTCTTTACAA
Statistics
Matches: 174, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
126 1 0.01
127 62 0.36
128 65 0.37
129 45 0.26
130 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.21
Consensus pattern (128 bp):
CTAAATACACAGTCAATAGCGCATTTTCAAAGACAAACGCCGCTAAATACACAGTCAATAGCGGC
GTTTATAAAGTAAAACGCCGCTAAATACACAGCCAATAGCGGCGTTTTAAAGTTAAAACGCCG
Found at i:132093 original size:21 final size:21
Alignment explanation
Indices: 132068--132132 Score: 121
Period size: 21 Copynumber: 3.1 Consensus size: 21
132058 CTTTTATTAG
132068 TCCCTTAACTTTGCATTTTAC
1 TCCCTTAACTTTGCATTTTAC
132089 TCCCTTAACTTTGCATTTTAC
1 TCCCTTAACTTTGCATTTTAC
*
132110 TTCCTTAACTTTGCATTTTAC
1 TCCCTTAACTTTGCATTTTAC
132131 TC
1 TC
132133 AATTTGGTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.18, C:0.28, G:0.05, T:0.49
Consensus pattern (21 bp):
TCCCTTAACTTTGCATTTTAC
Found at i:133807 original size:16 final size:16
Alignment explanation
Indices: 133782--133813 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
133772 TTCGCTAATT
*
133782 TTTGGGTCGGGTATGG
1 TTTGGATCGGGTATGG
133798 TTTGGATCGGGTATGG
1 TTTGGATCGGGTATGG
133814 GCCGGGTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.47, T:0.38
Consensus pattern (16 bp):
TTTGGATCGGGTATGG
Found at i:135921 original size:6 final size:6
Alignment explanation
Indices: 135854--135919 Score: 114
Period size: 6 Copynumber: 11.0 Consensus size: 6
135844 ATTCAGACAC
135854 TACTGG TACTGG TACTGG TACTGG TACTGG TACTGG TACTGG TACTGG
1 TACTGG TACTGG TACTGG TACTGG TACTGG TACTGG TACTGG TACTGG
* *
135902 TACTGG CACTGG CACTGG
1 TACTGG TACTGG TACTGG
135920 CAGCAGTATT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (6 bp):
TACTGG
Found at i:146110 original size:17 final size:16
Alignment explanation
Indices: 146074--146112 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
146064 TAGAGTTCCC
*
146074 AGCTTCAAACTGCCAA
1 AGCTTTAAACTGCCAA
146090 AGCTTTAAACTGCCAAA
1 AGCTTTAAACTGCC-AA
146107 AGCTTT
1 AGCTTT
146113 GATGTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (16 bp):
AGCTTTAAACTGCCAA
Found at i:150498 original size:30 final size:32
Alignment explanation
Indices: 150449--150524 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
150439 ATAATGATGG
*
150449 AGTGGCCATTTTG-TTAGAAATCTA-TA-ATT
1 AGTGACCATTTTGTTTAGAAATCTATTATATT
150478 AGTGACCATTTTGTTTAGAAATCTATTATATT
1 AGTGACCATTTTGTTTAGAAATCTATTATATT
150510 AGTGACCATTTTGTT
1 AGTGACCATTTTGTT
150525 ACAAACCGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
29 12 0.28
30 11 0.26
31 2 0.05
32 18 0.42
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (32 bp):
AGTGACCATTTTGTTTAGAAATCTATTATATT
Done.