Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000561.1 Hibiscus syriacus cultivar Beakdansim tig00001095_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: 332011
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:268740 original size:25 final size:25
Alignment explanation
Indices: 268706--268760 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
268696 TTTCATGCTC
268706 ATTCTACAAATCGGTTCTTGAAATT
1 ATTCTACAAATCGGTTCTTGAAATT
268731 ATTCTACAAATCGGTTCTTGAAATT
1 ATTCTACAAATCGGTTCTTGAAATT
268756 ATTCT
1 ATTCT
268761 GATAACATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (25 bp):
ATTCTACAAATCGGTTCTTGAAATT
Found at i:270420 original size:3 final size:3
Alignment explanation
Indices: 270412--270440 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
270402 CAGCAAAAAT
270412 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
270441 TTTTAAGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:272030 original size:11 final size:11
Alignment explanation
Indices: 272014--272043 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
272004 AAAATCATAG
272014 GTTGATTTTAA
1 GTTGATTTTAA
272025 GTTGATTTTAA
1 GTTGATTTTAA
272036 GTTGATTT
1 GTTGATTT
272044 GATAGTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (11 bp):
GTTGATTTTAA
Found at i:273629 original size:21 final size:20
Alignment explanation
Indices: 273602--273700 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
273592 AATCAGTTTC
*
273602 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAATGCGATT-TT
* * *
273623 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAATGCGAT-TTT
* *
273644 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAATGCGATTTT
* * *
273664 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAATGCGATTTT
*
273685 GAAAATCGCAATGCGA
1 CAAAATCGCAATGCGA
273701 ACACATAAAT
Statistics
Matches: 60, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
20 15 0.25
21 45 0.75
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
CAAAATCGCAATGCGATTTT
Found at i:273691 original size:20 final size:19
Alignment explanation
Indices: 273665--273719 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
273655 TGCGATTTTC
*
273665 CAAAATCGCAACGCGAATA
1 CAAAATCGCAACGCGAACA
* *
273684 TGAAAATCGCAATGCGAACA
1 -CAAAATCGCAACGCGAACA
273704 CATAAATCGCAACGCG
1 CA-AAATCGCAACGCG
273720 TATCCGTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.13
Consensus pattern (19 bp):
CAAAATCGCAACGCGAACA
Found at i:273729 original size:20 final size:20
Alignment explanation
Indices: 273706--273936 Score: 261
Period size: 20 Copynumber: 11.6 Consensus size: 20
273696 TGCGAACACA
273706 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
273726 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
*
273746 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
273766 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
273786 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
273806 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
273826 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
273846 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
273866 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
273886 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
273906 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
273926 TAAATCACAAC
1 TAAATCGCAAC
273937 ACTGAAATTT
Statistics
Matches: 180, Mismatches: 25, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
19 1 0.01
20 179 0.99
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:273731 original size:40 final size:39
Alignment explanation
Indices: 273667--273936 Score: 252
Period size: 40 Copynumber: 6.8 Consensus size: 39
273657 CGATTTTCCA
** * * * *
273667 AAATCGCAACGCGAATATGAAAATCGCAATGCGAACACAT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGAGAAC-CGT
* * *
273707 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGAG-AACCGT
* * * * *
273747 ATATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGAG-AACCGT
* * *
273787 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGAGAA-CCGT
* * *
273827 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGAGAA-CCGT
* * *
273867 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGAGAA-CCGT
* * *
273907 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGCGAATCCGTAAATCGCAAC
273937 ACTGAAATTT
Statistics
Matches: 208, Mismatches: 20, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
39 1 0.00
40 205 0.99
41 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (39 bp):
AAATCGCAACGCGAATCCGTAAATCGCAACGAGAACCGT
Found at i:274655 original size:24 final size:24
Alignment explanation
Indices: 274616--274662 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
274606 AAATTTGGTC
274616 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
274640 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
274663 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:277191 original size:33 final size:34
Alignment explanation
Indices: 277154--277350 Score: 190
Period size: 33 Copynumber: 5.8 Consensus size: 34
277144 GCAACGAGAG
*
277154 AATCGCAATGCGAAATGAAAATC-CAAATATGAA
1 AATCGCAATGCGAAATGAAAATCGCAAAGATGAA
* *
277187 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAAAGATGAA
*
277221 AATCGCAATGCGAAATGAAAATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAAAATCGC-A---AAGATGAA
* * * *
277259 AATCGCAACGAGAGAATCG-CAAT-GCGAA-ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCGCAAAGATGAA
* *
277292 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAAAGATGAA
*
277325 AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
277351 TTGCGATTCT
Statistics
Matches: 135, Mismatches: 17, Indels: 24
0.77 0.10 0.14
Matches are distributed among these distances:
31 1 0.01
32 6 0.04
33 71 0.53
34 29 0.21
35 4 0.03
37 2 0.01
38 15 0.11
39 6 0.04
40 1 0.01
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAAAGATGAA
Found at i:277245 original size:19 final size:19
Alignment explanation
Indices: 277154--277356 Score: 194
Period size: 19 Copynumber: 11.7 Consensus size: 19
277144 GCAACGAGAG
277154 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
277173 AATC-CAA----ATATGAA
1 AATCGCAATGCGAAATGAA
277187 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
277207 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
277221 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
277240 AATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
*
277259 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
277273 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
277292 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
277311 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
277325 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
277344 AATCGCATTGCGA
1 AATCGCAATGCGA
277357 TTCTCCCGTT
Statistics
Matches: 151, Mismatches: 12, Indels: 42
0.74 0.06 0.20
Matches are distributed among these distances:
14 40 0.26
15 6 0.04
16 6 0.04
17 4 0.03
18 7 0.05
19 74 0.49
20 14 0.09
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:277267 original size:52 final size:52
Alignment explanation
Indices: 277182--277356 Score: 314
Period size: 52 Copynumber: 3.3 Consensus size: 52
277172 AAATCCAAAT
277182 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
277235 ATGAAAATCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
277287 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
277339 ATTAAAATCGCATTGCGA
1 ATGAAAATCGCAATGCGA
277357 TTCTCCCGTT
Statistics
Matches: 118, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 102 0.86
53 16 0.14
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:277405 original size:19 final size:19
Alignment explanation
Indices: 277365--277462 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
277355 GATTCTCCCG
277365 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
277385 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
277404 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
277418 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
277437 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
277456 TTGCGAT
1 TTGCGAT
277463 AGTCAATTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 34 0.49
20 15 0.22
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:277459 original size:52 final size:53
Alignment explanation
Indices: 277346--277462 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
277336 GAAATTAAAA
*
277346 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCAATTTTCATT
*
277399 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCAATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCAATTTTCATT
277451 TCGCATTGCGAT
1 TCGCATTGCGAT
277463 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCAATTTTCATT
Found at i:277588 original size:14 final size:14
Alignment explanation
Indices: 277569--277605 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
277559 CATCAATTAC
277569 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
277583 ACAAATCATCTTTT
1 ACAAATCAACTTTT
277597 ACAAATCAA
1 ACAAATCAA
277606 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:279555 original size:20 final size:20
Alignment explanation
Indices: 279530--279595 Score: 91
Period size: 19 Copynumber: 3.4 Consensus size: 20
279520 TAGTTTACTT
* *
279530 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
279550 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
*
279569 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACTCAAAA
279588 TCGCAACG
1 TCGCAACG
279596 ACAGAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.45, C:0.27, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:279605 original size:14 final size:14
Alignment explanation
Indices: 279586--279640 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
279576 GCGAAATGAA
*
279586 AATCGCAACGACAG
1 AATCGCAACGAAAG
279600 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
279617 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
279633 AATCGCAA
1 AATCGCAA
279641 TGCGATTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 16 0.46
16 5 0.14
17 6 0.17
19 8 0.23
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:279613 original size:33 final size:33
Alignment explanation
Indices: 279567--279645 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
279557 GCGAAACCAA
* *
279567 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
279600 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
279633 AATCGCAATGCGA
1 AATCGCAATGCGA
279646 TTTTGGTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAG
Found at i:279624 original size:19 final size:17
Alignment explanation
Indices: 279546--279634 Score: 78
Period size: 19 Copynumber: 5.1 Consensus size: 17
279536 CACGAAACTT
*
279546 AAAATCGCAACGCGAAACC
1 AAAATCGCAA-GCGAAA-G
279565 AAAATCGCAACGCGAAATG
1 AAAATCGCAA-GCGAAA-G
*
279584 AAAATCGCAA-CGACAG
1 AAAATCGCAAGCGAAAG
279600 --AATCGCAATGCGAAATG
1 AAAATCGCAA-GCGAAA-G
279617 AAAATCGCAA-CGAAAG
1 AAAATCGCAAGCGAAAG
279633 AA
1 AA
279635 TCGCAATGCG
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
14 8 0.13
16 8 0.13
17 10 0.16
19 35 0.57
ACGTcount: A:0.49, C:0.22, G:0.19, T:0.09
Consensus pattern (17 bp):
AAAATCGCAAGCGAAAG
Found at i:279663 original size:19 final size:19
Alignment explanation
Indices: 279641--279769 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
279631 AGAATCGCAA
279641 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
279660 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
279674 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
279693 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
279707 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
279726 TGCGATTTTGGTTCCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
279745 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
279765 TGCGA
1 TGCGA
279770 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 47 0.53
20 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:279683 original size:33 final size:33
Alignment explanation
Indices: 279641--279732 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
279631 AGAATCGCAA
279641 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
279674 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
279707 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
279733 TTGGTTCCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:279933 original size:93 final size:93
Alignment explanation
Indices: 279817--280099 Score: 550
Period size: 93 Copynumber: 3.1 Consensus size: 93
279807 ATGGATTGCA
279817 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
279881 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
279909 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
279974 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
280002 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
280067 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
280095 TTACT
1 TTACT
280100 AAGCAATCTA
Statistics
Matches: 189, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
92 4 0.02
93 185 0.98
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:281879 original size:14 final size:14
Alignment explanation
Indices: 281862--281918 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
281852 TTTGGTTTTG
281862 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
281876 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
281895 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
281909 CGTTGCGATT
1 CGTTGCGATT
281919 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:281898 original size:33 final size:33
Alignment explanation
Indices: 281846--281926 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
281836 AAAATCGCAA
** *
281846 TGCGATTTTGGTTTTGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
281879 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
281912 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
281927 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.22, T:0.48
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:281929 original size:21 final size:21
Alignment explanation
Indices: 281903--281978 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
281893 CGCGTTGCGA
281903 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
281924 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
281944 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
281965 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
281979 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:281959 original size:41 final size:41
Alignment explanation
Indices: 281902--281979 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
281892 TCGCGTTGCG
*
281902 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
281943 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
281980 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:282100 original size:33 final size:33
Alignment explanation
Indices: 282058--282128 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
282048 AATACTAACT
*
282058 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
282091 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
282124 TGAAA
1 TGAAA
282129 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:282536 original size:20 final size:20
Alignment explanation
Indices: 282511--282664 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
282501 CTTTAAATAT
282511 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
282531 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
282553 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
282572 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
282592 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
282612 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
282632 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
282652 CGCGTTGCGATTT
1 CGCGTTGCGATTT
282665 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:282638 original size:40 final size:40
Alignment explanation
Indices: 282510--282664 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
282500 GCTTTAAATA
*
282510 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
282551 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
282591 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
282631 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
282665 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:282681 original size:21 final size:21
Alignment explanation
Indices: 282651--282733 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
282641 ATTTTCATAT
*
282651 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
282672 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
* *
282693 TCGCATTGCAATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
282714 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
282734 CTGATTTGCG
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
20 1 0.02
21 42 0.93
22 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:287216 original size:22 final size:22
Alignment explanation
Indices: 287184--287232 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
287174 CACGTGTCAC
*
287184 TTAACTGTCAAATTTTACGGTA
1 TTAACTATCAAATTTTACGGTA
287206 TTAACTATCAAATTTTACGGTA
1 TTAACTATCAAATTTTACGGTA
287228 TTAAC
1 TTAAC
287233 AATCCATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TTAACTATCAAATTTTACGGTA
Found at i:295053 original size:16 final size:16
Alignment explanation
Indices: 295028--295060 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
295018 TAATAAATAA
*
295028 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
295044 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
295060 A
1 A
295061 AAATGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:295141 original size:10 final size:10
Alignment explanation
Indices: 295126--295199 Score: 59
Period size: 10 Copynumber: 7.6 Consensus size: 10
295116 CATTTAATAA
295126 ATAAACGAAC
1 ATAAACGAAC
295136 ATAAACGAAC
1 ATAAACGAAC
*
295146 ----ACAAAC
1 ATAAACGAAC
295152 ATAAACGAAC
1 ATAAACGAAC
* *
295162 ATGAAC-ATAA
1 ATAAACGA-AC
295172 ATGAACACGAAC
1 AT-AA-ACGAAC
295184 ATAAACGAAC
1 ATAAACGAAC
295194 ATAAAC
1 ATAAAC
295200 ATTGGAGACC
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
6 5 0.10
9 1 0.02
10 35 0.70
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.20, G:0.09, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:295154 original size:16 final size:16
Alignment explanation
Indices: 295133--295201 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
295123 TAAATAAACG
295133 AACATAAACGAACACA
1 AACATAAACGAACACA
**
295149 AACATAAACGAACATG
1 AACATAAACGAACACA
* *
295165 AACATAAATGAACACG
1 AACATAAACGAACACA
*
295181 AACATAAACGAACATA
1 AACATAAACGAACACA
295197 AACAT
1 AACAT
295202 TGGAGACCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.59, C:0.20, G:0.09, T:0.12
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:295168 original size:32 final size:32
Alignment explanation
Indices: 295132--295201 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
295122 ATAAATAAAC
295132 GAACATAAACGAACACAAACATAAACGAACAT
1 GAACATAAACGAACACAAACATAAACGAACAT
* *
295164 GAACATAAATGAACACGAACATAAACGAACAT
1 GAACATAAACGAACACAAACATAAACGAACAT
*
295196 AAACAT
1 GAACAT
295202 TGGAGACCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.59, C:0.20, G:0.10, T:0.11
Consensus pattern (32 bp):
GAACATAAACGAACACAAACATAAACGAACAT
Found at i:295921 original size:14 final size:14
Alignment explanation
Indices: 295875--295930 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
295865 AATGAACATA
*
295875 AACGAACATAACCG
1 AACGAACATAACTG
*
295889 AACAAACAT-A---
1 AACGAACATAACTG
295899 AACGAACATAACTG
1 AACGAACATAACTG
295913 AACGAACATAACTG
1 AACGAACATAACTG
295927 AACG
1 AACG
295931 TTCACGAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 8 0.22
11 1 0.03
13 1 0.03
14 26 0.72
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAACTG
Found at i:295929 original size:24 final size:24
Alignment explanation
Indices: 295855--295923 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
295845 GATTGGCTTA
* *
295855 AACATAAATGAATGAACATAAACG
1 AACATAACTGAACGAACATAAACG
* *
295879 AACATAACCGAACAAACATAAACG
1 AACATAACTGAACGAACATAAACG
295903 AACATAACTGAACGAACATAA
1 AACATAACTGAACGAACATAA
295924 CTGAACGTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.58, C:0.19, G:0.10, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGAACATAAACG
Found at i:298893 original size:20 final size:20
Alignment explanation
Indices: 298868--298905 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
298858 CGCATGTTAA
298868 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
298888 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
298906 TCAAAGGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:311409 original size:2 final size:2
Alignment explanation
Indices: 311402--311449 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
311392 ATCTTATCTC
311402 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
311444 AT AT AT
1 AT AT AT
311450 TTTGAAGATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:313620 original size:15 final size:15
Alignment explanation
Indices: 313600--313632 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
313590 TGAGACATTA
*
313600 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
313615 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
313630 CCC
1 CCC
313633 ACCTAGCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.70, G:0.15, T:0.06
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:315499 original size:2 final size:2
Alignment explanation
Indices: 315492--315540 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
315482 TACTTTCTTT
315492 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
315534 TA TA TA T
1 TA TA TA T
315541 GTGATGAGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:316829 original size:21 final size:22
Alignment explanation
Indices: 316790--316830 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
316780 TTTTATTTTA
*
316790 TTTATTTAAATTGAGAATTAGG
1 TTTATTTAAATTGACAATTAGG
*
316812 TTTATTT-ACTTGACAATTA
1 TTTATTTAAATTGACAATTA
316831 CGACGCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (22 bp):
TTTATTTAAATTGACAATTAGG
Found at i:322960 original size:2 final size:2
Alignment explanation
Indices: 322953--323051 Score: 198
Period size: 2 Copynumber: 49.5 Consensus size: 2
322943 TTTACTTTCT
322953 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
322995 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
323037 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
323052 TTGTGATGAG
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 97 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:331190 original size:28 final size:29
Alignment explanation
Indices: 331158--331215 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
331148 CAATGCTAAG
331158 CATGATCTAAT-CATGCTTAGCTAAATCT
1 CATGATCTAATCCATGCTTAGCTAAATCT
331186 CATGATCTAATCCATGCTTAGCTAAATCT
1 CATGATCTAATCCATGCTTAGCTAAATCT
331215 C
1 C
331216 TTTAGCCGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (29 bp):
CATGATCTAATCCATGCTTAGCTAAATCT
Done.