Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003515.1 Hibiscus syriacus cultivar Beakdansim tig00007433_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: 116718
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:227 original size:31 final size:32
Alignment explanation
Indices: 166--298 Score: 179
Period size: 31 Copynumber: 4.3 Consensus size: 32
156 TGAATTTAAG
*
166 ACAATTAGTGCA--GTCTTAACAGA-TAGGTA
1 ACAATTAGTGCAGTGTCTTGACAGATTAGGTA
195 ACAATTA-TGCAGTGTCTTGACAGATTAGGTA
1 ACAATTAGTGCAGTGTCTTGACAGATTAGGTA
226 AC-ATTAGTGCAGTGTCTTGACAGATTAGGTA
1 ACAATTAGTGCAGTGTCTTGACAGATTAGGTA
** * *
257 AC-ATTAGTGCAGTGTCTTGGTAGATTGGGCA
1 ACAATTAGTGCAGTGTCTTGACAGATTAGGTA
288 ACAATTAGTGC
1 ACAATTAGTGC
299 CCTTTCGCTA
Statistics
Matches: 94, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
28 4 0.04
29 7 0.07
30 14 0.15
31 61 0.65
32 8 0.09
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (32 bp):
ACAATTAGTGCAGTGTCTTGACAGATTAGGTA
Found at i:24498 original size:2 final size:2
Alignment explanation
Indices: 24493--24542 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
24483 ACACACACAC
24493 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
24535 AT AT AT AT
1 AT AT AT AT
24543 CAAGTAGTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24702 original size:60 final size:60
Alignment explanation
Indices: 24629--24761 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 60
24619 TAATTAGGGT
** * * *
24629 AAAG-TACACAAATGGTCCCTTGACTATTGA-ATATTTCTTTGTTGATTCC-CTCGACTATTA
1 AAAGTTACA-AAATGGTCCCTCAACTATAGAGA-ATTACTTTGTTGA-GCCTCTCGACTATTA
* *
24689 AAAGTTACAAAATGGTCTCTCAACTATAGAGAGTTACTTTGTTGAGCCTCTCGACTATTA
1 AAAGTTACAAAATGGTCCCTCAACTATAGAGAATTACTTTGTTGAGCCTCTCGACTATTA
*
24749 CAAGTTACAAAAT
1 AAAGTTACAAAAT
24762 TATCACCGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
59 2 0.03
60 55 0.89
61 5 0.08
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCTCAACTATAGAGAATTACTTTGTTGAGCCTCTCGACTATTA
Found at i:25496 original size:21 final size:21
Alignment explanation
Indices: 25466--25673 Score: 110
Period size: 21 Copynumber: 10.0 Consensus size: 21
25456 GATTTACATA
*
25466 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
25487 TTCGCGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
25508 TTTGCGTTGCGA-A-TCTGGAAA
1 TTCGCGTTGCGATAGTC--CAAG
* ** *
25529 CT-GATTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * * *
25549 TTCGCGTTACGATTTATTACAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
25572 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
25591 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
25614 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
25633 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
25656 TT--CGTTGTGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
25674 AATCTCAACG
Statistics
Matches: 140, Mismatches: 32, Indels: 32
0.69 0.16 0.16
Matches are distributed among these distances:
19 24 0.17
20 12 0.09
21 78 0.56
22 2 0.01
23 24 0.17
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:25585 original size:42 final size:42
Alignment explanation
Indices: 25534--25670 Score: 238
Period size: 42 Copynumber: 3.3 Consensus size: 42
25524 GGAAACTGAT
* *
25534 TTGCGATAGTCGAAGTTCGCGTTACGATTTATTACAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
25576 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
25618 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
25660 TTGTGATAGTC
1 TTGCGATAGTC
25671 CAAAATCTCA
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:26413 original size:5 final size:5
Alignment explanation
Indices: 26405--26445 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
26395 CCATCTCGTC
26405 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG
26446 TACGTGTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.27
Consensus pattern (5 bp):
TCGGG
Found at i:26434 original size:6 final size:6
Alignment explanation
Indices: 26408--26446 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
26398 TCTCGTCTCG
26408 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
26447 ACGTGTCTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.45
6 18 0.55
ACGTcount: A:0.00, C:0.18, G:0.54, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:26594 original size:42 final size:42
Alignment explanation
Indices: 26535--26696 Score: 265
Period size: 42 Copynumber: 3.9 Consensus size: 42
26525 TGCGATTTTG
* *
26535 GACTATCGCAACGAACTTGGAATAAATAGCAACGCGAGCTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
26577 GACTATCGCAACGAACTTGAAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
26619 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
26661 GACTATCGCAACGAACTTGGACT--ATCGCAACGCGAA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAA
26697 TTTGGAATAA
Statistics
Matches: 114, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 13 0.11
42 101 0.89
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:26711 original size:42 final size:41
Alignment explanation
Indices: 26526--26752 Score: 203
Period size: 42 Copynumber: 5.5 Consensus size: 41
26516 ACCAGCCGTT
* * *
26526 GCGATTTTGGACTATCGCAACGAACTTGGAATAAATAGCAAC
1 GCGAATTTGGAATATCGCAACGAACTTGGAAT-AATCGCAAC
** * * *
26568 GCGAGCTTCGACTATCGCAACGAACTTGAAATAAATCGCAAC
1 GCGAATTTGGAATATCGCAACGAACTTGGAAT-AATCGCAAC
* * *
26610 GCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAAC
1 GCGAATTTGGAATATCGCAACGAACTTGGAAT-AATCGCAAC
* *
26652 GCGAACTTT-GACTATCGCAACGAACTTGGACT-ATCGCAAC
1 GCGAA-TTTGGAATATCGCAACGAACTTGGAATAATCGCAAC
* *
26692 GCGAATTTGGAATAAATCGCAACGCGAACTTGGACT-ATCGTAA-
1 GCGAATTTGGAAT--ATCGCAA--CGAACTTGGAATAATCGCAAC
*
26735 -CGAATTTGGAAAATCGCA
1 GCGAATTTGGAATATCGCA
26753 TTGCGATAGT
Statistics
Matches: 167, Mismatches: 12, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
39 3 0.02
40 22 0.13
42 122 0.73
43 2 0.01
44 18 0.11
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (41 bp):
GCGAATTTGGAATATCGCAACGAACTTGGAATAATCGCAAC
Found at i:26711 original size:84 final size:83
Alignment explanation
Indices: 26538--26725 Score: 252
Period size: 84 Copynumber: 2.2 Consensus size: 83
26528 GATTTTGGAC
*
26538 TATCGCAACGAACTTGGAATAAATAGCAACGCGAGCTTCGACTATCGCAACGAACTTGAAATAAA
1 TATCGCAACGAACTTGGAATAAATAGCAACGCGAACTTCGACTATCGCAACGAACTTGAAAT-AA
*
26603 TCGCAACGCGAACTTCGAC
65 TCGCAACGCGAACTTCGAA
* * * *
26622 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTTGACTATCGCAACGAACTTGGACT-AT
1 TATCGCAACGAACTTGGAATAAATAGCAACGCGAACTTCGACTATCGCAACGAACTTGAAATAAT
* *
26686 CGCAACGCGAATTTGGAA
66 CGCAACGCGAACTTCGAA
26704 TAAATCGCAACGCGAACTTGGA
1 T--ATCGCAA--CGAACTTGGA
26726 CTATCGTAAC
Statistics
Matches: 92, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
82 18 0.20
84 64 0.70
86 10 0.11
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (83 bp):
TATCGCAACGAACTTGGAATAAATAGCAACGCGAACTTCGACTATCGCAACGAACTTGAAATAAT
CGCAACGCGAACTTCGAA
Found at i:26736 original size:21 final size:21
Alignment explanation
Indices: 26532--26736 Score: 174
Period size: 21 Copynumber: 9.8 Consensus size: 21
26522 CGTTGCGATT
26532 TTGGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
* * *
26551 TTGGAATAAATAGCAACGCGAGC
1 TTGGACT--ATCGCAACGCGAAC
*
26574 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
* *
26593 TTGAAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
26616 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
26635 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
26658 TTTGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
26677 TTGGACTATCGCAACGCGAAT
1 TTGGACTATCGCAACGCGAAC
*
26698 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
26721 TTGGACTATCGTAACG
1 TTGGACTATCGCAACG
26737 AATTTGGAAA
Statistics
Matches: 147, Mismatches: 23, Indels: 30
0.74 0.12 0.15
Matches are distributed among these distances:
19 42 0.29
21 58 0.39
23 47 0.32
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:26744 original size:63 final size:61
Alignment explanation
Indices: 26602--26744 Score: 205
Period size: 63 Copynumber: 2.3 Consensus size: 61
26592 CTTGAAATAA
* *
26602 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTTGACT
1 ATCGCAA--CGAACTTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
*
26665 ATCGCAACGAACTTGGACTATCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAACTTGGACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTGGACT
* *
26728 ATCGTAACGAATTTGGA
1 ATCGCAACGAACTTGGA
26745 AAATCGCATT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
61 18 0.25
63 55 0.75
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.22
Consensus pattern (61 bp):
ATCGCAACGAACTTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
Found at i:27053 original size:19 final size:21
Alignment explanation
Indices: 27016--27077 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 21
27006 TAAATATTTT
27016 AATCA-AAACTGAATAAATTA
1 AATCATAAACTGAATAAATTA
*
27036 AATCATAAACT-AAT-AATTC
1 AATCATAAACTGAATAAATTA
* * *
27055 GATCATAAA-TGATTAAAGTA
1 AATCATAAACTGAATAAATTA
27075 AAT
1 AAT
27078 TAGATATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
18 1 0.03
19 14 0.42
20 13 0.39
21 5 0.15
ACGTcount: A:0.55, C:0.10, G:0.06, T:0.29
Consensus pattern (21 bp):
AATCATAAACTGAATAAATTA
Found at i:30514 original size:43 final size:42
Alignment explanation
Indices: 30461--30812 Score: 418
Period size: 43 Copynumber: 8.2 Consensus size: 42
30451 TGAGAACCAA
*
30461 AAACGCCGCAATAGGTTAAGATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAATAGG-TCAGATCTATAGCGGCGTTTTTGGAAC
*
30504 AAACGCCGCAATAGGTCAAGATCTATAGTGGCG-TTTTGGAAC
1 AAACGCCGCAATAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
* * * * *
30546 AAACGCCGCAAAAGATTGATATCTATAGCGACGTTTTTGGAAC
1 AAACGCCGCAATAG-GTCAGATCTATAGCGGCGTTTTTGGAAC
* * *
30589 AAACGGCGCAATAGGTCAGATATATAGCAGCGTTTCTTGGAAC
1 AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTT-TTGGAAC
* * * *
30632 AAACGCTGTAAAAGGTCAGATCTGTAGCGGCGTTTTTGGAAC
1 AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTTTTGGAAC
* * * * *
30674 AAACGCCGCAAAAGGGTGATATCTATAGAGGCATTTTTTGGAAC
1 AAACGCCGCAATA-GGTCAGATCTATAGCGGC-GTTTTTGGAAC
30718 AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTTTTTGGAAC
1 AAACGCCGCAATAGGTCAGATCTATAGCGGCG-TTTTTGGAAC
* * * *
30761 AAACGCTGCAAAAGATCAGATATATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
30804 AAACGCCGC
1 AAACGCCGC
30813 TAATTTCTTT
Statistics
Matches: 261, Mismatches: 40, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
42 76 0.29
43 163 0.62
44 22 0.08
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (42 bp):
AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTTTTGGAAC
Found at i:30604 original size:85 final size:84
Alignment explanation
Indices: 30461--30812 Score: 418
Period size: 85 Copynumber: 4.1 Consensus size: 84
30451 TGAGAACCAA
* * *
30461 AAACGCCGCAATAGGTTAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAATAGGTCAAGAT
1 AAACGCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC-AGAT
* *
30526 CTATAGTGGCG-TTTTGGAAC
64 ATATAGCGGCGTTTTTGGAAC
* * * * * *
30546 AAACGCCGCAAAAGATTGATATCTATAGCGACGTTTTTGGAACAAACGGCGCAATAGGTCAGATA
1 AAACGCCGCAAAAG-GTCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAGATA
*
30611 TATAGCAGCGTTTCTTGGAAC
65 TATAGCGGCGTTT-TTGGAAC
* * * * * *
30632 AAACGCTGTAAAAGGTCAGATCTGTAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGGTGATATC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAA-GGTCAGATA
* *
30697 TATAGAGGCATTTTTTGGAAC
65 TATAGCGGC-GTTTTTGGAAC
* * *
30718 AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTTTTTGGAACAAACGCTGCAAAAGATCAGATA
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCG-TTTTTGGAACAAACGCCGCAAAAGGTCAGATA
30783 TATAGCGGCGTTTTTGGATAC
65 TATAGCGGCGTTTTTGGA-AC
30804 AAACGCCGC
1 AAACGCCGC
30813 TAATTTCTTT
Statistics
Matches: 225, Mismatches: 35, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
84 12 0.05
85 97 0.43
86 91 0.40
87 25 0.11
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (84 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAGATAT
ATAGCGGCGTTTTTGGAAC
Found at i:34898 original size:41 final size:41
Alignment explanation
Indices: 34837--35072 Score: 246
Period size: 41 Copynumber: 5.7 Consensus size: 41
34827 TTGTAAACTT
34837 GCGGCGTTTGT-TAAACAAACGCCACTAAAACATGAGTCTATA
1 GCGGCGTTTGTAT-AA-AAACGCCACTAAAACATGAGTCTATA
*
34879 GCGGCGTTTGTATAAAAACGCCACTAAAGTACA--AGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAA--ACATGAGTCTATA
* ***
34920 GTGGCGTTTGTATAAAAAC-CCACTAAGGTATGAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAACATGAGTCTATA
* * * * *
34960 GCGGCGTTTGTAAACACAAAAGCCACTAAATCACGATTCTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAACATGAGTCTATA
** *
35003 GCGGCGTTTGTATAAAAACGCCACTAAATGTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAA-ACATGAGTCTATA
* *
35045 GCGGCGTTTTTATGAAAACGCCACTAAA
1 GCGGCGTTTGTATAAAAACGCCACTAAA
35073 GTACAGTCTT
Statistics
Matches: 162, Mismatches: 23, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
38 1 0.01
40 26 0.16
41 51 0.31
42 51 0.31
43 33 0.20
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAACATGAGTCTATA
Found at i:35092 original size:40 final size:40
Alignment explanation
Indices: 34837--35194 Score: 310
Period size: 40 Copynumber: 8.7 Consensus size: 40
34827 TTGTAAACTT
** * *
34837 GCGGCGTTTGTTA-AACAAACGCCACTAAAACATGAGTCTATA
1 GCGGCGTTT-TTATAA-AAACGCCACTAAAGTA-CAGTCTTTA
*
34879 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTTTA
1 GCGGCGTTTTTATAAAAACGCCACTAAAGTAC-AGTCTTTA
* * * * *
34920 GTGGCGTTTGTATAAAAAC-CCACTAAGGTATGAGTCTATA
1 GCGGCGTTTTTATAAAAACGCCACTAAAGTA-CAGTCTTTA
* * * * *
34960 GCGGCGTTTGTAAACACAAAAGCCACTAAA-TCACGATTCTATA
1 GCGGCGTTTTTATA-A-AAACGCCACTAAAGT-AC-AGTCTTTA
* *
35003 GCGGCGTTTGTATAAAAACGCCACTAAATGTATGAGTCTTTA
1 GCGGCGTTTTTATAAAAACGCCACTAAA-GTA-CAGTCTTTA
*
35045 GCGGCGTTTTTATGAAAACGCCACTAAAGTACAGTCTTTA
1 GCGGCGTTTTTATAAAAACGCCACTAAAGTACAGTCTTTA
* * * *
35085 ACAGCGTTTTTACAGAAACGCCACTAAAGTACAGTCTTTA
1 GCGGCGTTTTTATAAAAACGCCACTAAAGTACAGTCTTTA
* * * *
35125 ACAGCGTTTTTATAGAAACGCCGCTAAAGTAC-GCATCTTTA
1 GCGGCGTTTTTATAAAAACGCCACTAAAGTACAG--TCTTTA
* *
35166 GCGGCGTTTGTTCTAAAAACGCCGCTAAA
1 GCGGCGTTT-TTATAAAAACGCCACTAAA
35195 AATGCTGCTA
Statistics
Matches: 268, Mismatches: 34, Indels: 28
0.81 0.10 0.08
Matches are distributed among these distances:
39 1 0.00
40 102 0.38
41 70 0.26
42 66 0.25
43 29 0.11
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (40 bp):
GCGGCGTTTTTATAAAAACGCCACTAAAGTACAGTCTTTA
Found at i:40466 original size:28 final size:28
Alignment explanation
Indices: 40433--40498 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
40423 AAATATAATT
40433 AAACTTTCATAGTAACAAATATCAAGTA
1 AAACTTTCATAGTAACAAATATCAAGTA
40461 AAACTTTCATAGTAACAAATATCAAGTA
1 AAACTTTCATAGTAACAAATATCAAGTA
40489 AAACTTTCAT
1 AAACTTTCAT
40499 CAATGAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.30
Consensus pattern (28 bp):
AAACTTTCATAGTAACAAATATCAAGTA
Found at i:40474 original size:14 final size:14
Alignment explanation
Indices: 40433--40498 Score: 64
Period size: 14 Copynumber: 4.7 Consensus size: 14
40423 AAATATAATT
40433 AAACTTTCATAGTA
1 AAACTTTCATAGTA
* *
40447 ACAAATATCA-AGTA
1 A-AACTTTCATAGTA
40461 AAACTTTCATAGTA
1 AAACTTTCATAGTA
* *
40475 ACAAATATCA-AGTA
1 A-AACTTTCATAGTA
40489 AAACTTTCAT
1 AAACTTTCAT
40499 CAATGAAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
13 12 0.30
14 16 0.40
15 12 0.30
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.30
Consensus pattern (14 bp):
AAACTTTCATAGTA
Found at i:41104 original size:15 final size:17
Alignment explanation
Indices: 41068--41105 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
41058 AGGTTAAAGA
*
41068 GGAGCCTGGAGCTGGCT
1 GGAGCCTAGAGCTGGCT
41085 GGAGCCTAGAGC-GG-T
1 GGAGCCTAGAGCTGGCT
41100 GGAGCC
1 GGAGCC
41106 AACTGCCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 2 0.10
17 11 0.55
ACGTcount: A:0.16, C:0.24, G:0.47, T:0.13
Consensus pattern (17 bp):
GGAGCCTAGAGCTGGCT
Found at i:48333 original size:2 final size:2
Alignment explanation
Indices: 48326--48355 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
48316 ACTAAAGATA
48326 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
48356 GATGTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51841 original size:42 final size:42
Alignment explanation
Indices: 51795--51877 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
51785 GTCGCCTCAC
*
51795 TCATTCAAGGATTATTCTTTCTGTTCTTCAATTAATAAGTGG
1 TCATTCAAGGATTATTCTTTCTGTTCTTCAATTAAAAAGTGG
* *
51837 TCATTCATGGATTATTCTTTTTGTTCTTCAATTAAAAAGTG
1 TCATTCAAGGATTATTCTTTCTGTTCTTCAATTAAAAAGTG
51878 ACGAAATTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (42 bp):
TCATTCAAGGATTATTCTTTCTGTTCTTCAATTAAAAAGTGG
Found at i:54068 original size:32 final size:33
Alignment explanation
Indices: 53968--54070 Score: 156
Period size: 33 Copynumber: 3.2 Consensus size: 33
53958 ACAAAGTTTA
* *
53968 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
**
54000 TAATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
54033 CGATAAATTCAAATACTTAAAAACTT-CAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
54065 CGATAA
1 CGATAA
54071 TTGAAACAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.22
33 50 0.78
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.32
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:54089 original size:21 final size:21
Alignment explanation
Indices: 54065--54106 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
54055 ACTTCAAGTT
54065 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
54086 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
54107 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:74864 original size:18 final size:18
Alignment explanation
Indices: 74841--74886 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
74831 GAAAATCATG
74841 GAAGACTACATCTATCCA
1 GAAGACTACATCTATCCA
74859 GAAGACTACATCTATCCA
1 GAAGACTACATCTATCCA
74877 GAAGACTACA
1 GAAGACTACA
74887 ACCTTAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.20
Consensus pattern (18 bp):
GAAGACTACATCTATCCA
Found at i:76032 original size:33 final size:33
Alignment explanation
Indices: 75989--76112 Score: 212
Period size: 33 Copynumber: 3.8 Consensus size: 33
75979 ACTTACAGTA
75989 CCTAGCCAGCATGCTCTTTTAACATCAATTGTG
1 CCTAGCCAGCATGCTCTTTTAACATCAATTGTG
*
76022 ACTAGCCAGCATGCTCTTTTAACATCAATTGTG
1 CCTAGCCAGCATGCTCTTTTAACATCAATTGTG
* * *
76055 CCTAGCCAGCATGCTCTTTTAACATAAAATGTT
1 CCTAGCCAGCATGCTCTTTTAACATCAATTGTG
76088 CCTAGCCAGCATGCTCTTTTAACAT
1 CCTAGCCAGCATGCTCTTTTAACAT
76113 GACCTGTATC
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 86 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.33
Consensus pattern (33 bp):
CCTAGCCAGCATGCTCTTTTAACATCAATTGTG
Found at i:81716 original size:26 final size:27
Alignment explanation
Indices: 81683--81734 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
81673 TTTTTACCTA
*
81683 TTAAAATTTTATAA-ATTATCTTCTAC
1 TTAAAATTATATAAGATTATCTTCTAC
81709 TTAAAATTATATAAGATTATCTTCTA
1 TTAAAATTATATAAGATTATCTTCTA
81735 GGAACAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (27 bp):
TTAAAATTATATAAGATTATCTTCTAC
Found at i:82420 original size:10 final size:10
Alignment explanation
Indices: 82405--82462 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
82395 CATTTAATAA
82405 ATAAACGAAC
1 ATAAACGAAC
82415 ATAAACGAAC
1 ATAAACGAAC
* *
82425 ATGAAC-ATAA
1 ATAAACGA-AC
82435 ATGAACACGAAC
1 AT-AA-ACGAAC
*
82447 ATAAACGAAT
1 ATAAACGAAC
82457 ATAAAC
1 ATAAAC
82463 ATTGGAGACC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
9 1 0.03
10 29 0.74
11 3 0.08
12 5 0.13
13 1 0.03
ACGTcount: A:0.59, C:0.17, G:0.10, T:0.14
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:82432 original size:16 final size:16
Alignment explanation
Indices: 82409--82455 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
82399 TAATAAATAA
82409 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
82425 ATGAACATAAATGAAC
1 ACGAACATAAACGAAC
82441 ACGAACATAAACGAA
1 ACGAACATAAACGAA
82456 TATAAACATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.57, C:0.19, G:0.13, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:82446 original size:32 final size:30
Alignment explanation
Indices: 82401--82464 Score: 92
Period size: 32 Copynumber: 2.1 Consensus size: 30
82391 CGTTCATTTA
*
82401 ATAAATAAACGAACATAAACGAACATGAAC
1 ATAAATAAACGAACATAAACGAACATAAAC
*
82431 ATAAATGAACACGAACATAAACGAATATAAAC
1 ATAAAT-AA-ACGAACATAAACGAACATAAAC
82463 AT
1 AT
82465 TGGAGACCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 6 0.20
31 2 0.07
32 22 0.73
ACGTcount: A:0.59, C:0.16, G:0.09, T:0.16
Consensus pattern (30 bp):
ATAAATAAACGAACATAAACGAACATAAAC
Found at i:82828 original size:10 final size:10
Alignment explanation
Indices: 82813--82842 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
82803 TTAAGCATAA
82813 ATAAACGAAC
1 ATAAACGAAC
82823 ATAAACGAAC
1 ATAAACGAAC
*
82833 ATAACCGAAC
1 ATAAACGAAC
82843 GAACATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.57, C:0.23, G:0.10, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:84787 original size:60 final size:59
Alignment explanation
Indices: 84679--84793 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 59
84669 AAAAGACGAG
** *
84679 TTTTGTAACTTTTAATAGTAGGAGAACTCAACAAAGCAACGTCTTATAGTCGAAAGATTA
1 TTTTGTAACTTTTAATAGTAGGAGAACTCAACAAAGCAACACCCTATAGTC-AAAGATTA
*
84739 TTTTGTAACTTTTAATAGTCAGGAG-ACTCAACAAAGCAGCACCCTATAGTCAAAG
1 TTTTGTAACTTTTAATAGT-AGGAGAACTCAACAAAGCAACACCCTATAGTCAAAG
84794 GACCATTTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 4 0.08
60 41 0.82
61 5 0.10
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (59 bp):
TTTTGTAACTTTTAATAGTAGGAGAACTCAACAAAGCAACACCCTATAGTCAAAGATTA
Found at i:84810 original size:60 final size:60
Alignment explanation
Indices: 84670--84810 Score: 162
Period size: 60 Copynumber: 2.3 Consensus size: 60
84660 TTTTACGGAA
* ** *
84670 AAAGACGAGTTTTGTAACTTTTAATAGTAGGAGAACTCAACAAAGCAACGTCTTATAGTCG
1 AAAGACCA-TTTTGTAACTTTTAATAGTAGGAGAACTCAACAAAGCAACACCCTATAGTCG
** *
84731 AAAGATTATTTTGTAACTTTTAATAGTCAGGAG-ACTCAACAAAGCAGCACCCTATAGTC-
1 AAAGACCATTTTGTAACTTTTAATAGT-AGGAGAACTCAACAAAGCAACACCCTATAGTCG
84790 AAAGGACCATTTGTGT-ACTTT
1 AAA-GACCATTT-TGTAACTTT
84811 ACCCCAAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
59 3 0.04
60 52 0.75
61 14 0.20
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (60 bp):
AAAGACCATTTTGTAACTTTTAATAGTAGGAGAACTCAACAAAGCAACACCCTATAGTCG
Found at i:89374 original size:2 final size:2
Alignment explanation
Indices: 89367--89400 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
89357 TGATTTATTG
89367 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
89401 GTGAGAACTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:95807 original size:41 final size:41
Alignment explanation
Indices: 95749--95826 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
95739 TTGACGTTAC
*
95749 AATTCGATCGATGATAATATCAAGTTTGATAAAATTTCAAT
1 AATTCGATCGATAATAATATCAAGTTTGATAAAATTTCAAT
*
95790 AATTCGACTC-ATAATAATATCGAGTTTGATAAAATTT
1 AATTCGA-TCGATAATAATATCAAGTTTGATAAAATTT
95827 TGATAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
41 32 0.94
42 2 0.06
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (41 bp):
AATTCGATCGATAATAATATCAAGTTTGATAAAATTTCAAT
Found at i:102507 original size:21 final size:22
Alignment explanation
Indices: 102481--102521 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
102471 ATTCATACCT
102481 TATAAA-ACATAATTAAATCGA
1 TATAAAGACATAATTAAATCGA
* *
102502 TATAAAGATATATTTAAATC
1 TATAAAGACATAATTAAATC
102522 TACATACGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (22 bp):
TATAAAGACATAATTAAATCGA
Found at i:105411 original size:27 final size:27
Alignment explanation
Indices: 105379--105433 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
105369 ACAAAAAGAA
* *
105379 GAAATATAATTACATGACAATAGTTTT
1 GAAATATAATTACACGACAATAGATTT
105406 GAAATATAATTACACGACAATAGATTT
1 GAAATATAATTACACGACAATAGATTT
105433 G
1 G
105434 TCCCTGACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (27 bp):
GAAATATAATTACACGACAATAGATTT
Found at i:108813 original size:2 final size:2
Alignment explanation
Indices: 108806--108833 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
108796 AGATAGTGTT
108806 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
108834 AAATTTTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:109881 original size:17 final size:17
Alignment explanation
Indices: 109859--109891 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
109849 AATTTTTGAA
109859 GAAATATAT-TAAAATTT
1 GAAATA-ATGTAAAATTT
109876 GAAATAATGTAAAATT
1 GAAATAATGTAAAATT
109892 ATAAAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (17 bp):
GAAATAATGTAAAATTT
Found at i:116555 original size:21 final size:21
Alignment explanation
Indices: 116502--116555 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
116492 TTAATGAGAA
116502 ATAATAAAAAAT---TACAAT
1 ATAATAAAAAATAAATACAAT
* * * *
116520 TTAACAATAAGTAAATACAAT
1 ATAATAAAAAATAAATACAAT
116541 ATAATAAAAAATAAA
1 ATAATAAAAAATAAA
116556 ACTACTATCG
Statistics
Matches: 25, Mismatches: 8, Indels: 3
0.69 0.22 0.08
Matches are distributed among these distances:
18 8 0.32
21 17 0.68
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.26
Consensus pattern (21 bp):
ATAATAAAAAATAAATACAAT
Done.