Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000645.1 Hibiscus syriacus cultivar Beakdansim tig00001250_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: 82290
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:531 original size:20 final size:20
Alignment explanation
Indices: 506--545 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
496 GCGCTATGTA
506 AATCGCGTAGCGAAAGTCAG
1 AATCGCGTAGCGAAAGTCAG
*
526 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTAGCGAAAGTCAG
546 TATCTCGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.20, G:0.30, T:0.17
Consensus pattern (20 bp):
AATCGCGTAGCGAAAGTCAG
Found at i:554 original size:20 final size:20
Alignment explanation
Indices: 515--660 Score: 186
Period size: 20 Copynumber: 7.2 Consensus size: 20
505 AAATCGCGTA
* * *
515 GCGAAAGTCAGAATCGCGTT
1 GCGATAGTCAGTATCGCATT
* * *
535 GCGAAAGTCAGTATCTCGTT
1 GCGATAGTCAGTATCGCATT
* *
555 GCGATTTTGT-ATTATCGCATT
1 GCGA--TAGTCAGTATCGCATT
*
576 GCGATAGTAAGTATCGCATT
1 GCGATAGTCAGTATCGCATT
596 GCGATAGTCAGTATCGCATT
1 GCGATAGTCAGTATCGCATT
616 GCGATAGTCAGTATCGCATT
1 GCGATAGTCAGTATCGCATT
636 GCGATAGTCAGTATCGCATT
1 GCGATAGTCAGTATCGCATT
656 GCGAT
1 GCGAT
661 TTTCCCAATT
Statistics
Matches: 113, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
19 3 0.03
20 96 0.85
21 12 0.11
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (20 bp):
GCGATAGTCAGTATCGCATT
Found at i:771 original size:21 final size:21
Alignment explanation
Indices: 731--771 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
721 ATTGTATACC
**
731 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
752 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
772 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:4741 original size:24 final size:24
Alignment explanation
Indices: 4707--4762 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
4697 TAGAAGTTCG
* *
4707 ATTGAAACCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTCGAGCTCA
*
4731 ATTGAAGCCTAAAATTCGGGCTCA
1 ATTGAAGCCTAAAATTCGAGCTCA
4755 ATTGAAGC
1 ATTGAAGC
4763 GAAAGAATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTCGAGCTCA
Found at i:9665 original size:32 final size:31
Alignment explanation
Indices: 9623--9750 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
9613 AGAGTCGAGG
9623 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
9654 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
9686 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
9717 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
9748 GTT
1 GTT
9751 GTCAAGGTTC
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
31 54 0.66
32 28 0.34
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:12333 original size:91 final size:91
Alignment explanation
Indices: 12177--12356 Score: 292
Period size: 91 Copynumber: 2.0 Consensus size: 91
12167 TACCAAATTG
*
12177 TCTGCAAGTTTACCAGAACATATCACTTGAAACCTTGTTTCTCATCTCTTTTTGACCCTAGTTCT
1 TCTGCAAGTTTACCAGAACATATCACTTGAAACCTTGTTTCTCATCTCTTTTTGACCCTAATTCT
* *
12242 GTCTTTAAGGTATGGTGTGCTGCTTA
66 GTCATTAAGGTATGCTGTGCTGCTTA
*
12268 TCTGCAAGTTTACCAGAACATATCACTTGAAGCCTTGTTTCTCATCT-TCTTTT-ACCCCTAATT
1 TCTGCAAGTTTACCAGAACATATCACTTGAAACCTTGTTTCTCATCTCT-TTTTGA-CCCTAATT
12331 CTGTCATTAAGGTATGCTGTGCTGCT
64 CTGTCATTAAGGTATGCTGTGCTGCT
12357 CTTGCAGGTA
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
90 2 0.02
91 81 0.98
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (91 bp):
TCTGCAAGTTTACCAGAACATATCACTTGAAACCTTGTTTCTCATCTCTTTTTGACCCTAATTCT
GTCATTAAGGTATGCTGTGCTGCTTA
Found at i:20708 original size:30 final size:30
Alignment explanation
Indices: 20672--20741 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
20662 ATTCAGGCAA
20672 AAGAAATACATTAAGCTCATGTGTTGGCTC
1 AAGAAATACATTAAGCTCATGTGTTGGCTC
20702 AAGAAATACATTAAGCTCATGTGTTGGCTC
1 AAGAAATACATTAAGCTCATGTGTTGGCTC
20732 AAGAAATACA
1 AAGAAATACA
20742 ATCATGTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.27
Consensus pattern (30 bp):
AAGAAATACATTAAGCTCATGTGTTGGCTC
Found at i:28867 original size:16 final size:16
Alignment explanation
Indices: 28846--28876 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28836 ATAAATAAAT
28846 GAACATAAACGAACAC
1 GAACATAAACGAACAC
28862 GAACATAAACGAACA
1 GAACATAAACGAACA
28877 ATTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:29003 original size:10 final size:10
Alignment explanation
Indices: 28968--29031 Score: 65
Period size: 10 Copynumber: 6.1 Consensus size: 10
28958 AACGAACATA
*
28968 ATAAATGAAC
1 ATAAACGAAC
* *
28978 ATAAAAGAAA
1 ATAAACGAAC
28988 ATAAACGAAC
1 ATAAACGAAC
28998 ATAAACGAACAC
1 ATAAACG-A-AC
*
29010 AATAAACGAAT
1 -ATAAACGAAC
29021 ATAAACGAAC
1 ATAAACGAAC
29031 A
1 A
29032 ACACAAACAC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
10 33 0.73
11 2 0.04
12 3 0.07
13 7 0.16
ACGTcount: A:0.64, C:0.14, G:0.09, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:29013 original size:23 final size:22
Alignment explanation
Indices: 28958--29032 Score: 91
Period size: 23 Copynumber: 3.4 Consensus size: 22
28948 AACACAAACG
*
28958 AACGAACATAATAAATGAACATA
1 AACGAACA-AATAAACGAACATA
*
28981 AAAG-A-AAATAAACGAACATA
1 AACGAACAAATAAACGAACATA
*
29001 AACGAACACAATAAACGAATATA
1 AACGAACA-AATAAACGAACATA
29024 AACGAACAA
1 AACGAACAA
29033 CACAAACACA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
20 16 0.36
21 2 0.04
22 3 0.07
23 24 0.53
ACGTcount: A:0.64, C:0.15, G:0.09, T:0.12
Consensus pattern (22 bp):
AACGAACAAATAAACGAACATA
Found at i:29015 original size:33 final size:32
Alignment explanation
Indices: 28978--29047 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
28968 ATAAATGAAC
*
28978 ATAAAAGAAAATAAACGAACATAAACGAACACA
1 ATAAAAGAAAATAAACGAACA-AAACAAACACA
* * *
29011 ATAAACGAATATAAACGAACAACACAAACACA
1 ATAAAAGAAAATAAACGAACAAAACAAACACA
29043 A-AAAA
1 ATAAAA
29048 CAAACTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 3 0.09
32 10 0.31
33 19 0.59
ACGTcount: A:0.67, C:0.17, G:0.07, T:0.09
Consensus pattern (32 bp):
ATAAAAGAAAATAAACGAACAAAACAAACACA
Found at i:29039 original size:23 final size:23
Alignment explanation
Indices: 28990--29039 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
28980 AAAAGAAAAT
*
28990 AAACGAACATAAACGAACACAAT
1 AAACGAACATAAACGAACACAAC
*
29013 AAACGAATATAAACGAACA-ACAC
1 AAACGAACATAAACGAACACA-AC
29036 AAAC
1 AAAC
29040 ACAAAAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.62, C:0.22, G:0.08, T:0.08
Consensus pattern (23 bp):
AAACGAACATAAACGAACACAAC
Found at i:29314 original size:14 final size:14
Alignment explanation
Indices: 29295--29321 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29285 CCTCTGTTCA
29295 AACATAAATGAACG
1 AACATAAATGAACG
29309 AACATAAATGAAC
1 AACATAAATGAAC
29322 ATAAATGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:29324 original size:24 final size:24
Alignment explanation
Indices: 29295--29358 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
29285 CCTCTGTTCA
*
29295 AACATAAATGAACGAACATAAATG
1 AACATAAATGAACGAACATAAACG
* *
29319 AACATAAATGAATGAATATAAACG
1 AACATAAATGAACGAACATAAACG
*
29343 AATATATAATCGAACG
1 AACATA-AAT-GAACG
29359 TTCACGAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
24 26 0.79
25 3 0.09
26 4 0.12
ACGTcount: A:0.56, C:0.11, G:0.12, T:0.20
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:39932 original size:29 final size:29
Alignment explanation
Indices: 39891--39968 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
39881 CTCAACAAAG
* *
39891 TAACTCCTT-ATAGTCGAAG-GATCATTTTG
1 TAACT-CTTAATAGTC-AAGTGACCATTTTA
* *
39920 TAACTTTTAATAGTCAGGTGACCATTTTA
1 TAACTCTTAATAGTCAAGTGACCATTTTA
39949 TAACTCTTAATAGTCAAGTG
1 TAACTCTTAATAGTCAAGTG
39969 GCTCAACAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 4 0.10
29 37 0.90
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (29 bp):
TAACTCTTAATAGTCAAGTGACCATTTTA
Found at i:40377 original size:61 final size:61
Alignment explanation
Indices: 40282--40401 Score: 163
Period size: 61 Copynumber: 2.0 Consensus size: 61
40272 AATTTAATTT
* * * *
40282 ATTTAATCGTTAATTAGATGATAGCATGTGTCAATCATCTGATTGGATATAA-AACAAATAA
1 ATTTAATCGCTAATTAAATGATAACATGTGTCAATCACCTGATTGGATA-AAGAACAAATAA
*
40343 ATTTAATCGCTAATTAAATAGA-AACATTTGTCAATCACCTGATTGGATAAAGAACAAAT
1 ATTTAATCGCTAATTAAAT-GATAACATGTGTCAATCACCTGATTGGATAAAGAACAAAT
40402 TGTAAGAGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
60 2 0.04
61 48 0.92
62 2 0.04
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (61 bp):
ATTTAATCGCTAATTAAATGATAACATGTGTCAATCACCTGATTGGATAAAGAACAAATAA
Found at i:48403 original size:22 final size:22
Alignment explanation
Indices: 48378--48438 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
48368 GTTCGTCTCC
*
48378 TCGCCGTCACTTCCCTCTCTGG
1 TCGCCGTCACTGCCCTCTCTGG
*
48400 TCGCCGTCACTGCCCTCTCTTG
1 TCGCCGTCACTGCCCTCTCTGG
* *
48422 TCGTCGTCACTGGCCTC
1 TCGCCGTCACTGCCCTC
48439 GTTGAGATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.05, C:0.44, G:0.20, T:0.31
Consensus pattern (22 bp):
TCGCCGTCACTGCCCTCTCTGG
Found at i:48518 original size:21 final size:21
Alignment explanation
Indices: 48493--48532 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
48483 AAAGTTTTAT
48493 TTAAAAAA-ACTTTTTTTAAGA
1 TTAAAAAATA-TTTTTTTAAGA
48514 TTAAAAAATATTTTTTTAA
1 TTAAAAAATATTTTTTTAA
48533 AGTACCACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (21 bp):
TTAAAAAATATTTTTTTAAGA
Found at i:49605 original size:34 final size:34
Alignment explanation
Indices: 49567--49634 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
49557 ATTTTCGTAA
* * *
49567 AATTATCGAAGTTTAAATCCCATTTGCTAAAAAG
1 AATTATCAAAATTTAAATCCCACTTGCTAAAAAG
* *
49601 AATTATCAAAATTTAAATCTCACTTGCTGAAAAG
1 AATTATCAAAATTTAAATCCCACTTGCTAAAAAG
49635 GAAAAACAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (34 bp):
AATTATCAAAATTTAAATCCCACTTGCTAAAAAG
Found at i:50310 original size:2 final size:2
Alignment explanation
Indices: 50303--50409 Score: 75
Period size: 2 Copynumber: 57.0 Consensus size: 2
50293 TAAAAATAAT
50303 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * *
50342 -A TA AA TT TA -A TT TA AA TA -A AA AA TA TA TA TT TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
50381 TA -A TT TA AA 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
50410 CCCGGCCCGA
Statistics
Matches: 81, Mismatches: 17, Indels: 14
0.72 0.15 0.12
Matches are distributed among these distances:
1 7 0.09
2 74 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:50442 original size:12 final size:12
Alignment explanation
Indices: 50427--50461 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
50417 CGATTCTCGG
50427 CCCAATACCCGA
1 CCCAATACCCGA
*
50439 CCCAATACCCGG
1 CCCAATACCCGA
50451 CCCAATACCCG
1 CCCAATACCCG
50462 TTTAAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:60563 original size:12 final size:12
Alignment explanation
Indices: 60546--60570 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60536 GCGCCAACTG
60546 TTAATAAGCATA
1 TTAATAAGCATA
60558 TTAATAAGCATA
1 TTAATAAGCATA
60570 T
1 T
60571 GAAGAGAGGA
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:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (12 bp):
TTAATAAGCATA
Found at i:60809 original size:15 final size:15
Alignment explanation
Indices: 60785--60822 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
60775 GTCATCATCT
*
60785 TATTAGATAAAAAAA
1 TATTAAATAAAAAAA
*
60800 TATTAAATAAAAATA
1 TATTAAATAAAAAAA
60815 TA-TAAATA
1 TATTAAATA
60823 TTAAGAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (15 bp):
TATTAAATAAAAAAA
Found at i:61200 original size:42 final size:41
Alignment explanation
Indices: 61103--61207 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 41
61093 TGCCTTTATC
* *
61103 GAAATCAATTAAGGGTTAGTGAATAATCAAAATTAATTTGT
1 GAAATCAATTTAGGGTTTGTGAATAATCAAAATTAATTTGT
*
61144 GAAATCGATCTTAGGGTTTGTG-A-AATCAAAATT-ATTTGAGCTT
1 GAAATCAAT-TTAGGGTTTGTGAATAATCAAAATTAATTT--G--T
61187 GAAATCAATTTAGGGTTTGTG
1 GAAATCAATTTAGGGTTTGTG
61208 TTTATATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
39 4 0.07
40 10 0.18
41 10 0.18
42 22 0.40
43 9 0.16
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (41 bp):
GAAATCAATTTAGGGTTTGTGAATAATCAAAATTAATTTGT
Found at i:63945 original size:81 final size:75
Alignment explanation
Indices: 63746--63965 Score: 219
Period size: 75 Copynumber: 2.9 Consensus size: 75
63736 CCACAGTAAG
** * * * ** * *
63746 GTGGATGATACCTTTTCAACAGAGCTCTACCAGCCAACACCATCAAAAGA-CCTAAGCATAAGGA
1 GTGGATGATAAATTCTCAACAGAGCTTTACCAGCCAGCACCATCAAGGGAGTC-AAGCACAAGGA
63810 CCATGCACCAC
65 CCATGCACCAC
* *
63821 GTGGATGATGAATTCTTAACAGAGCTTTACCAGCCAGCACCATCAAGGGAGTCAAGCACAAGGAC
1 GTGGATGATAAATTCTCAACAGAGCTTTACCAGCCAGCACCATCAAGGGAGTCAAGCACAAGGAC
63886 CATGCACCAC
66 CATGCACCAC
* * * *
63896 GATAAGGTGAATGATAAATTCTCAATAGAG-TTATACTAGCCAGCGCCATCAAGGGAGTCAAGTA
1 G-T---G-G-ATGATAAATTCTCAACAGAGCTT-TACCAGCCAGCACCATCAAGGGAGTCAAGCA
63960 CAAGGA
59 CAAGGA
63966 TCAGACGCCA
Statistics
Matches: 120, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
75 63 0.52
76 2 0.02
79 1 0.01
80 3 0.03
81 51 0.43
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.19
Consensus pattern (75 bp):
GTGGATGATAAATTCTCAACAGAGCTTTACCAGCCAGCACCATCAAGGGAGTCAAGCACAAGGAC
CATGCACCAC
Found at i:63983 original size:81 final size:81
Alignment explanation
Indices: 63761--64008 Score: 246
Period size: 81 Copynumber: 3.1 Consensus size: 81
63751 TGATACCTTT
* * ** * *
63761 TCAACAGAGCTCTACCAGCCAACACCATCAAAAGA-CCTAAGCATAAGGACCATGCACCACG-T-
1 TCAACAGAGCTTTACCAGCCAGCACCATCAAGGGAGTC-AAGCACAAGGACCATGCACCACGATA
63823 --G-G-ATGATGAATTC
65 AGGTGAATGATGAATTC
*
63836 TTAACAGAGCTTTACCAGCCAGCACCATCAAGGGAGTCAAGCACAAGGACCATGCACCACGATAA
1 TCAACAGAGCTTTACCAGCCAGCACCATCAAGGGAGTCAAGCACAAGGACCATGCACCACGATAA
*
63901 GGTGAATGATAAATTC
66 GGTGAATGATGAATTC
* * * * * *
63917 TCAATAGAG-TTATACTAGCCAGCGCCATCAAGGGAGTCAAGTACAAGGATCA-GACGCCAC-AG
1 TCAACAGAGCTT-TACCAGCCAGCACCATCAAGGGAGTCAAGCACAAGGACCATG-CACCACGA-
* *
63979 TAAGGTGGATAATGAATTC
63 TAAGGTGAATGATGAATTC
63998 TCAACAGAGCT
1 TCAACAGAGCT
64009 CCATCAGTCA
Statistics
Matches: 143, Mismatches: 19, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
75 52 0.36
76 2 0.01
79 1 0.01
80 5 0.03
81 82 0.57
82 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.18
Consensus pattern (81 bp):
TCAACAGAGCTTTACCAGCCAGCACCATCAAGGGAGTCAAGCACAAGGACCATGCACCACGATAA
GGTGAATGATGAATTC
Found at i:64944 original size:42 final size:42
Alignment explanation
Indices: 64896--64983 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
64886 CCCATTGCAT
* * *
64896 AAACCATCCTTAAACTTCAATATCTACTACAAAAGTTACCAA
1 AAACCATCCTCAAAATTCAATAGCTACTACAAAAGTTACCAA
* * *
64938 AAACCATCCTCAAAATTCAATAGCTATTGCATAAGTTACCAA
1 AAACCATCCTCAAAATTCAATAGCTACTACAAAAGTTACCAA
64980 AAAC
1 AAAC
64984 TATATTCAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (42 bp):
AAACCATCCTCAAAATTCAATAGCTACTACAAAAGTTACCAA
Found at i:66349 original size:2 final size:2
Alignment explanation
Indices: 66344--66375 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
66334 TTTTTTTTCC
66344 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
66376 CTTAGCTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73814 original size:16 final size:16
Alignment explanation
Indices: 73784--73815 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
73774 TTAATATGGT
73784 ATAAAATGTTAAAAAA
1 ATAAAATGTTAAAAAA
73800 ATAAACATGTTAAAAA
1 ATAAA-ATGTTAAAAA
73816 GGTATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (16 bp):
ATAAAATGTTAAAAAA
Found at i:80189 original size:65 final size:64
Alignment explanation
Indices: 80119--80243 Score: 223
Period size: 65 Copynumber: 1.9 Consensus size: 64
80109 CGTTTTTAAT
*
80119 TTTATTATTTTAAGTGTTTATTTTTGTTAAAAAAATATTATCAATCACTCAAAATATAATACATC
1 TTTATTATTTTAAGTGTTTATTTTTGTTAAAAAAAT-TCATCAATCACTCAAAATATAATACATC
*
80184 TTTATTATTTTAAGTGTTTATTTTTGTTAAAACAATTCATCAATCACTCAAAATATAATA
1 TTTATTATTTTAAGTGTTTATTTTTGTTAAAAAAATTCATCAATCACTCAAAATATAATA
80244 TATCAGGCAT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 23 0.40
65 35 0.60
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (64 bp):
TTTATTATTTTAAGTGTTTATTTTTGTTAAAAAAATTCATCAATCACTCAAAATATAATACATC
Found at i:81280 original size:20 final size:20
Alignment explanation
Indices: 81257--81294 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
81247 TTTTATTGAA
81257 TTTTATT-CACTTTTAATTAT
1 TTTTATTGCA-TTTTAATTAT
81277 TTTTATTGCATTTTAATT
1 TTTTATTGCATTTTAATT
81295 GGTTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTATTGCATTTTAATTAT
Found at i:81300 original size:20 final size:20
Alignment explanation
Indices: 81257--81300 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
81247 TTTTATTGAA
*
81257 TTTTATTCACTTTTAATTAT
1 TTTTATTCACTTTTAATTAG
*
81277 TTTTATTGCA-TTTTAATTGG
1 TTTTATT-CACTTTTAATTAG
81297 TTTT
1 TTTT
81301 TAAAAAAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTTATTCACTTTTAATTAG
Found at i:81445 original size:25 final size:24
Alignment explanation
Indices: 81417--81463 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
81407 AAGTCAATTT
81417 TTTTCAAAATATATAAAATTTATAA
1 TTTTCAAAATATA-AAAATTTATAA
** *
81442 TTTTTTAAATATAAATATTTAT
1 TTTTCAAAATATAAAAATTTAT
81464 CATCATCATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTTCAAAATATAAAAATTTATAA
Done.