Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008052.1 Hibiscus syriacus cultivar Beakdansim tig00110547_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: 532719
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:513342 original size:14 final size:14
Alignment explanation
Indices: 513317--513349 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
513307 CTCGGATAGT
513317 CTCGGTCGGATGCC
1 CTCGGTCGGATGCC
*
513331 CTCGGTCGGATGGC
1 CTCGGTCGGATGCC
513345 CTCGG
1 CTCGG
513350 ATGCCCAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.33, G:0.39, T:0.21
Consensus pattern (14 bp):
CTCGGTCGGATGCC
Found at i:516896 original size:28 final size:28
Alignment explanation
Indices: 516858--516913 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
516848 GATCGTTATC
* * *
516858 GTGTTACCGTGACAGTTCACGGTGTTAA
1 GTGTTAACGTGACAGCTCACAGTGTTAA
*
516886 GTGTTAACGTGACGGCTCACAGTGTTAA
1 GTGTTAACGTGACAGCTCACAGTGTTAA
516914 CGTAGAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (28 bp):
GTGTTAACGTGACAGCTCACAGTGTTAA
Found at i:521788 original size:23 final size:23
Alignment explanation
Indices: 521762--521809 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
521752 ATAAATATAA
*
521762 AAATTGGATGAAACAAAA-AAATG
1 AAATTGAAT-AAACAAAATAAATG
*
521785 AAATTGAATAAATAAAATAAATG
1 AAATTGAATAAACAAAATAAATG
521808 AA
1 AA
521810 GATAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.21
Consensus pattern (23 bp):
AAATTGAATAAACAAAATAAATG
Found at i:521939 original size:21 final size:21
Alignment explanation
Indices: 521888--521998 Score: 79
Period size: 23 Copynumber: 5.1 Consensus size: 21
521878 GCAAAGAAAC
521888 TAAAA-ATATA-ATAAAATAA
1 TAAAATATATATATAAAATAA
*
521907 -ATAAATAGTATACATAAAATAA
1 TA-AAATA-TATATATAAAATAA
521929 TAAAATATATATTTATAAAA-ATA
1 TAAAATATATA--TATAAAATA-A
* *
521952 TAAAATATATGTATAATATAA
1 TAAAATATATATATAAAATAA
*
521973 T-AAATACTAAATAGTAATAATAA
1 TAAAATA-TATATA-TAA-AATAA
521996 TAA
1 TAA
521999 TAAATAAATG
Statistics
Matches: 73, Mismatches: 6, Indels: 21
0.73 0.06 0.21
Matches are distributed among these distances:
18 1 0.01
19 3 0.04
20 6 0.08
21 20 0.27
22 19 0.26
23 23 0.32
24 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (21 bp):
TAAAATATATATATAAAATAA
Found at i:522006 original size:23 final size:22
Alignment explanation
Indices: 521894--522007 Score: 74
Period size: 21 Copynumber: 4.9 Consensus size: 22
521884 AAACTAAAAA
521894 TATAATAA-AATAAATAAATAG
1 TATAATAATAATAAATAAATAG
* *
521915 TATACATAAAATAATAAAATATATATT
1 TATA-AT--AATAAT-AAATAAATA-G
* *
521942 TATAAAAAT-ATAAA-ATATATG
1 TATAATAATAATAAATAAATA-G
521963 TATAAT-ATAATAAATACTAAATAG
1 TATAATAATAAT-AA-A-TAAATAG
521987 TAATAATAATAATAAATAAAT
1 T-ATAATAATAATAAATAAAT
522008 GAAAAATAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 24
0.71 0.06 0.23
Matches are distributed among these distances:
20 2 0.03
21 17 0.23
22 7 0.09
23 8 0.11
24 8 0.11
25 14 0.19
26 14 0.19
27 4 0.05
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (22 bp):
TATAATAATAATAAATAAATAG
Found at i:522161 original size:22 final size:22
Alignment explanation
Indices: 522133--522183 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
522123 ATAAGTAAAC
522133 ATATATAA-AAAAAATATAATAT
1 ATATATAATAAAAAA-ATAATAT
522155 ATATATAATAAAAAAATAATAT
1 ATATATAATAAAAAAATAATAT
522177 A-ATATAA
1 ATATATAA
522184 CGCAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.21
22 16 0.57
23 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
ATATATAATAAAAAAATAATAT
Found at i:522190 original size:22 final size:22
Alignment explanation
Indices: 522133--522193 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
522123 ATAAGTAAAC
522133 ATATATAA-AAAAAATATAATAT
1 ATATATAAGAAAAAA-ATAATAT
*
522155 ATATATAATAAAAAAATAATAT
1 ATATATAAGAAAAAAATAATAT
*
522177 A-ATATAACGCAAAAAAT
1 ATATATAA-GAAAAAAAT
522194 GAAAAAAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 6 0.17
22 23 0.66
23 6 0.17
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (22 bp):
ATATATAAGAAAAAAATAATAT
Found at i:523626 original size:21 final size:20
Alignment explanation
Indices: 523540--523697 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
523530 AAATGACCAA
**
523540 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
523559 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
523579 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
523599 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
523620 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
523641 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
523661 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
523682 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
523698 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:523713 original size:40 final size:40
Alignment explanation
Indices: 523664--523837 Score: 172
Period size: 40 Copynumber: 4.3 Consensus size: 40
523654 CGATTTTCCA
* ** *
523664 AAATCGCAACGCGAATATGAAAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAAC-CAT
* * *
523704 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCAT
** * * *
523744 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCAT
* * *
523784 ATATCGCAACGCGTATCCGTAAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAA-CCAT
523824 AAAATCGCAACGCG
1 -AAATCGCAACGCG
523838 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
39 2 0.02
40 95 0.86
41 14 0.13
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCAT
Found at i:523726 original size:20 final size:20
Alignment explanation
Indices: 523664--523814 Score: 187
Period size: 20 Copynumber: 7.5 Consensus size: 20
523654 CGATTTTCCA
* ** *
523664 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
523684 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
523704 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
523724 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
523744 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
523764 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
523784 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
523804 AAATCGCAACG
1 AAATCGCAACG
523815 ATAATACATA
Statistics
Matches: 112, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
19 1 0.01
20 109 0.97
21 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:523748 original size:60 final size:60
Alignment explanation
Indices: 523664--523837 Score: 213
Period size: 60 Copynumber: 2.9 Consensus size: 60
523654 CGATTTTCCA
* ** * *
523664 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
523724 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
523784 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCG
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCG
523838 ATATTTAAAG
Statistics
Matches: 93, Mismatches: 20, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
60 81 0.87
61 12 0.13
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:524008 original size:22 final size:22
Alignment explanation
Indices: 523983--524037 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
523973 CTCTCTACGG
523983 CGAAGAAATCCGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
524005 CGAAGATTTCCGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
524027 CGGCGAAATCC
1 CGAAGAAATCC
524038 CTCACAACCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.20
Consensus pattern (22 bp):
CGAAGAAATCCGTCCCCATCTC
Found at i:524257 original size:33 final size:33
Alignment explanation
Indices: 524218--524288 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
524208 TTCACTTAGA
* *
524218 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
524251 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
524284 TTTCA
1 TTTCA
524289 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:524409 original size:20 final size:21
Alignment explanation
Indices: 524378--524441 Score: 80
Period size: 20 Copynumber: 3.1 Consensus size: 21
524368 GAACGATATA
524378 AATGAAAA-TCGCAACGAGAG
1 AATGAAAAGTCGCAACGAGAG
**
524398 AATG-ACTGTCGCAACGAGAG
1 AATGAAAAGTCGCAACGAGAG
524418 AAATGAAAAG-CGCAACGAGAG
1 -AATGAAAAGTCGCAACGAGAG
524439 AAT
1 AAT
524442 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
19 1 0.03
20 19 0.51
21 15 0.41
22 2 0.05
ACGTcount: A:0.47, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AATGAAAAGTCGCAACGAGAG
Found at i:524426 original size:41 final size:35
Alignment explanation
Indices: 524377--524486 Score: 111
Period size: 33 Copynumber: 3.1 Consensus size: 35
524367 CGAACGATAT
524377 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGAG
1 AAATGAAAATCGCAACGAGAGAAT-A---TCGCAAC--GAG
* *
524418 AAATGAAAAGCGCAACGAGAG-A-ATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATATCGCAACGAG
*
524451 AAATGAAAATCGCAACGAGAG-A-ATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATATCGCAACGAG
524484 AAA
1 AAA
524487 CCAAATCGCA
Statistics
Matches: 66, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
33 37 0.56
35 7 0.11
38 1 0.02
40 1 0.02
41 20 0.30
ACGTcount: A:0.46, C:0.19, G:0.25, T:0.09
Consensus pattern (35 bp):
AAATGAAAATCGCAACGAGAGAATATCGCAACGAG
Found at i:524431 original size:21 final size:21
Alignment explanation
Indices: 524377--524440 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
524367 CGAACGATAT
*
524377 AAATGAAAATCGCAACGAGAG
1 AAATGAAAAGCGCAACGAGAG
**
524398 -AATG-ACTGTCGCAACGAGAG
1 AAATGAAAAG-CGCAACGAGAG
524418 AAATGAAAAGCGCAACGAGAG
1 AAATGAAAAGCGCAACGAGAG
524439 AA
1 AA
524441 TCGCAACGCG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 1 0.03
20 15 0.43
21 17 0.49
22 2 0.06
ACGTcount: A:0.48, C:0.16, G:0.27, T:0.09
Consensus pattern (21 bp):
AAATGAAAAGCGCAACGAGAG
Found at i:524447 original size:14 final size:14
Alignment explanation
Indices: 524428--524481 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
524418 AAATGAAAAG
524428 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
524442 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
524461 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
524475 CGCAACG
1 CGCAACG
524482 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:524457 original size:33 final size:33
Alignment explanation
Indices: 524417--524486 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
524407 CGCAACGAGA
524417 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
524450 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
524483 GAAA
1 GAAA
524487 CCAAATCGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:524519 original size:19 final size:19
Alignment explanation
Indices: 524492--524574 Score: 88
Period size: 19 Copynumber: 4.7 Consensus size: 19
524482 CGAAACCAAA
*
524492 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
524511 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
524525 TCTCGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
* *
524543 TCGCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
524562 TCGCGTTGCGATT
1 TCGCGTTGCGATT
524575 CTCTCGTTGC
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
14 10 0.19
15 3 0.06
17 3 0.06
18 10 0.19
19 28 0.52
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:524533 original size:14 final size:15
Alignment explanation
Indices: 524514--524588 Score: 64
Period size: 14 Copynumber: 4.7 Consensus size: 15
524504 TTTCATTTCG
524514 CGTTGCGATTC-TCT
1 CGTTGCGATTCATCT
*
524528 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTCA--TCT
524546 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TCATCT
524563 CGCGTTGCGATTC-TCT
1 --CGTTGCGATTCATCT
524579 CGTTGCGATT
1 CGTTGCGATT
524589 TTCATTTCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
14 18 0.35
15 3 0.06
16 3 0.06
17 4 0.08
18 13 0.25
19 11 0.21
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.41
Consensus pattern (15 bp):
CGTTGCGATTCATCT
Found at i:524573 original size:51 final size:52
Alignment explanation
Indices: 524492--524596 Score: 176
Period size: 51 Copynumber: 2.0 Consensus size: 52
524482 CGAAACCAAA
* *
524492 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGA-TTTCATT
1 TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
*
524543 TCGCGTTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
524595 TC
1 TC
524597 AACCAAAAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
51 41 0.82
52 9 0.18
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:526557 original size:93 final size:93
Alignment explanation
Indices: 526265--526639 Score: 649
Period size: 93 Copynumber: 4.1 Consensus size: 93
526255 TAGATTGCTT
*
526265 AGTAAATTTATTC-GTTGCTGCC-ATTCTGCTAAAC--TGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
526326 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
526354 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACAC--TGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
526417 TTTGTC-TTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
526444 AGTAAATTTGTTCGGTTGCTGCCACATTCTGCTAAACTGTGTA-TCTATAACACTGTGAAATAGT
1 AGTAAATTTGTTCGGTTGCTGCCA-ATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
526508 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
526537 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
526602 TTTGTCTTTGTTTTGTTTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTG--TCTTTTGGTTGAA
526632 AGTAAATT
1 AGTAAATT
526640 ATCCATTCAA
Statistics
Matches: 272, Mismatches: 3, Indels: 16
0.93 0.01 0.05
Matches are distributed among these distances:
89 12 0.04
90 63 0.23
91 46 0.17
92 34 0.12
93 96 0.35
95 21 0.08
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:526724 original size:19 final size:19
Alignment explanation
Indices: 526700--526809 Score: 93
Period size: 19 Copynumber: 6.5 Consensus size: 19
526690 ACGAAAACTT
526700 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
**
526719 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACC
526738 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
526752 AGAAT-GCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
526770 -AAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
526783 AAGATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
526802 -AAATCGCA
1 AAAATCGCA
526810 TTGCGATTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 25
0.69 0.07 0.24
Matches are distributed among these distances:
13 5 0.07
14 13 0.18
15 3 0.04
16 4 0.06
17 6 0.08
18 13 0.18
19 28 0.39
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.07
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:526777 original size:31 final size:32
Alignment explanation
Indices: 526722--526809 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
526712 CGAAACCAAA
**
526722 ATCGCAACGCGAAATGAAAATCGCAACGAC-AG
1 ATCGCAACGCGAAA-CCAAATCGCAACGACAAG
526754 AAT-GCAACGCGAAACCAAATCGCAACGACAAG
1 -ATCGCAACGCGAAACCAAATCGCAACGACAAG
526786 ATCGCAACGCGAAACCAAATCGCA
1 ATCGCAACGCGAAACCAAATCGCA
526810 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
31 15 0.29
32 34 0.67
33 2 0.04
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.08
Consensus pattern (32 bp):
ATCGCAACGCGAAACCAAATCGCAACGACAAG
Found at i:526846 original size:14 final size:14
Alignment explanation
Indices: 526827--526882 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
526817 TTTCATTTCG
526827 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
526841 CGTTGCGATTTTCATT
1 CGTTGCGA--TTCTTT
*
526857 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
526873 CGTTGCGATT
1 CGTTGCGATT
526883 TTATTTAGCG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.46
16 13 0.37
18 6 0.17
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:526865 original size:32 final size:33
Alignment explanation
Indices: 526810--526900 Score: 132
Period size: 32 Copynumber: 2.8 Consensus size: 33
526800 CCAAATCGCA
* *
526810 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
526843 TTGCGATTTTCA-TTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
* *
526875 TTGCGATTTT-ATTTAGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
526901 TTGGTTTCGC
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
31 1 0.02
32 40 0.75
33 12 0.23
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
Found at i:526896 original size:18 final size:18
Alignment explanation
Indices: 526873--526922 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
526863 GCGATTCTGT
526873 CGTTGCGATTTTATTTAG
1 CGTTGCGATTTTATTTAG
* *
526891 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTT-ATTTAG
526910 CGTTGCGATTTTA
1 CGTTGCGATTTTA
526923 AGTTTCGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.48
Consensus pattern (18 bp):
CGTTGCGATTTTATTTAG
Found at i:528871 original size:13 final size:14
Alignment explanation
Indices: 528839--528873 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
528829 ATTGTTTAAT
528839 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
528853 TGATTTGTAAAAG-
1 TGATTTGTAAAAGA
528866 TGATTTGT
1 TGATTTGT
528874 GTAATTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:529002 original size:19 final size:19
Alignment explanation
Indices: 528978--529075 Score: 129
Period size: 19 Copynumber: 5.5 Consensus size: 19
528968 AAAATTGACT
528978 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
528997 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
529016 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
529030 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
529048 ATCGCAATGCGGAAATG-AA
1 ATCGCAATGC-GAAATGAAA
529067 ATCGCAATG
1 ATCGCAATG
529076 GGAGAATCGC
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 12 0.17
19 44 0.62
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:529104 original size:51 final size:52
Alignment explanation
Indices: 528978--529092 Score: 189
Period size: 51 Copynumber: 2.2 Consensus size: 52
528968 AAAATTGACT
528978 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATG-AAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
529030 ATCGCAATGCGAAATGAAATCGCAATGCGGAAATG-AAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
529081 ATCGCAATGCGA
1 ATCGCAATGCGA
529093 TTTTAATTCG
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
51 38 0.63
52 22 0.37
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:529141 original size:19 final size:19
Alignment explanation
Indices: 529117--529225 Score: 116
Period size: 19 Copynumber: 6.3 Consensus size: 19
529107 GCGATTCTCG
529117 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
529136 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
529155 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
529169 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
529188 TTGCGA--TTC---TCG--
1 TTGCGATTTTCATTTCGCA
529200 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
529220 TTGCGA
1 TTGCGA
529226 AATGTAATGG
Statistics
Matches: 75, Mismatches: 2, Indels: 25
0.74 0.02 0.25
Matches are distributed among these distances:
12 6 0.08
14 12 0.16
16 7 0.09
17 11 0.15
18 2 0.03
19 31 0.41
20 6 0.08
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:529180 original size:52 final size:49
Alignment explanation
Indices: 529082--529195 Score: 183
Period size: 52 Copynumber: 2.3 Consensus size: 49
529072 AATGGGAGAA
*
529082 TCGCAATGCGATTTTAATTCGCATTGCGATTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTCGCATTGCGATTCTCGTTGCGATTTTCATT
*
529131 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTT-AATTCGCATTGCGA-T-TCTCGTTGCGATTTTCATT
529183 TCGCATTGCGATT
1 TCGCATTGCGATT
529196 CTCGTTGCGA
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
49 14 0.23
50 13 0.22
51 1 0.02
52 32 0.53
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (49 bp):
TCGCATTGCGATTTTAATTCGCATTGCGATTCTCGTTGCGATTTTCATT
Found at i:529202 original size:31 final size:33
Alignment explanation
Indices: 529136--529225 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
529126 TCATTTCGCA
529136 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
529169 TTGCGATTTTCATTTCGCATTGCGA-T-TCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
529200 TTGCGATTTTCATTTCCGCATTGCGA
1 TTGCGATTTTCATTT-CGCATTGCGA
529226 AATGTAATGG
Statistics
Matches: 56, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
31 20 0.36
32 11 0.20
33 25 0.45
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:529307 original size:19 final size:19
Alignment explanation
Indices: 529283--529377 Score: 137
Period size: 19 Copynumber: 5.2 Consensus size: 19
529273 AAAATTGACT
529283 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
529302 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
529321 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
529335 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
529354 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
529374 ATCG
1 ATCG
529378 TAACGAGAGA
Statistics
Matches: 68, Mismatches: 2, Indels: 11
0.84 0.02 0.14
Matches are distributed among these distances:
14 10 0.15
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.57
20 13 0.19
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:529412 original size:53 final size:53
Alignment explanation
Indices: 529283--529399 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
529273 AAAATTGACT
529283 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
529335 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
529388 ATCGCAATGCGA
1 ATCGCAATGCGA
529400 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:531707 original size:12 final size:12
Alignment explanation
Indices: 531690--531714 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
531680 TCTTCGGGGA
531690 CTTTTTCTTCTT
1 CTTTTTCTTCTT
531702 CTTTTTCTTCTT
1 CTTTTTCTTCTT
531714 C
1 C
531715 AGGATATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:532636 original size:20 final size:20
Alignment explanation
Indices: 532608--532717 Score: 161
Period size: 20 Copynumber: 5.6 Consensus size: 20
532598 AAATTTCAGT
*
532608 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACAGATTCTC
* *
532628 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCTC
532648 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTCTC
* *
532668 GTTGCGATTTACGGA-TATC
1 GTTGCGATTTACAGATTCTC
532687 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTCTC
532707 G-TGCGATTTAC
1 GTTGCGATTTAC
532718 GG
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
19 27 0.34
20 53 0.66
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCTC
Found at i:532698 original size:39 final size:40
Alignment explanation
Indices: 532608--532719 Score: 201
Period size: 40 Copynumber: 2.9 Consensus size: 40
532598 AAATTTCAGT
*
532608 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
532648 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGA-TATC
1 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
532687 GTTGCGATTTACAGATTCTCG-TGCGATTTACGG
1 GTTGCGATTTACAGATTCTCGTTGCGATTTACGG
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
38 12 0.17
39 25 0.35
40 34 0.48
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (40 bp):
GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
Done.