Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001667.1 Hibiscus syriacus cultivar Beakdansim tig00003339_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: 109801
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:3687 original size:24 final size:24
Alignment explanation
Indices: 3654--3714 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
3644 ACCTAGGTAG
3654 TGTACCGATACCCCAATTAAGGGA
1 TGTACCGATACCCCAATTAAGGGA
* *
3678 TGTACTGATACCCCAGTTAAGGGA
1 TGTACCGATACCCCAATTAAGGGA
3702 TGTACCGATACCC
1 TGTACCGATACCC
3715 TATAGCGGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (24 bp):
TGTACCGATACCCCAATTAAGGGA
Found at i:6815 original size:17 final size:17
Alignment explanation
Indices: 6795--6841 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
6785 ATAGTATAAC
6795 AAAAGATACAATACAAT
1 AAAAGATACAATACAAT
*
6812 AAAAGATATAGA-ACAAT
1 AAAAGATACA-ATACAAT
6829 AAAAGATACAATA
1 AAAAGATACAATA
6842 AGAGAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 24 0.92
18 1 0.04
ACGTcount: A:0.66, C:0.09, G:0.09, T:0.17
Consensus pattern (17 bp):
AAAAGATACAATACAAT
Found at i:6821 original size:34 final size:34
Alignment explanation
Indices: 6777--6841 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
6767 AAAATAAAAG
* * *
6777 TAAAATATATAGTATAACAAAAGATACAATACAA
1 TAAAAGATATAGAACAACAAAAGATACAATACAA
*
6811 TAAAAGATATAGAACAATAAAAGATACAATA
1 TAAAAGATATAGAACAACAAAAGATACAATA
6842 AGAGAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.22
Consensus pattern (34 bp):
TAAAAGATATAGAACAACAAAAGATACAATACAA
Found at i:6914 original size:35 final size:35
Alignment explanation
Indices: 6875--6965 Score: 84
Period size: 34 Copynumber: 2.6 Consensus size: 35
6865 ATGATATGGT
*
6875 AAAGGAATCAGTACAGAAAAAGGAACAATAT-GTTG
1 AAAGGAATCAGTACAGAAAAAGGAACAACATAG-TG
*
6910 AAAGGAA-C-GATACAGGAAAAA-GAATAACATAGTG
1 AAAGGAATCAG-TACA-GAAAAAGGAACAACATAGTG
*
6944 AAA-GAATTAGTACAAGAAAAAG
1 AAAGGAATCAGTAC-AGAAAAAG
6966 AGCAAATATA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
33 4 0.09
34 26 0.57
35 16 0.35
ACGTcount: A:0.56, C:0.08, G:0.22, T:0.14
Consensus pattern (35 bp):
AAAGGAATCAGTACAGAAAAAGGAACAACATAGTG
Found at i:12277 original size:17 final size:17
Alignment explanation
Indices: 12250--12282 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12240 GGTTGGTTTT
12250 GAAGCCTTAAGTGAAAGA
1 GAAGCCTTAAG-GAAAGA
12268 GAAG-CTTAAGGAAAG
1 GAAGCCTTAAGGAAAG
12283 CTTAAGAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.45, C:0.09, G:0.30, T:0.15
Consensus pattern (17 bp):
GAAGCCTTAAGGAAAGA
Found at i:12627 original size:54 final size:54
Alignment explanation
Indices: 12545--13221 Score: 946
Period size: 54 Copynumber: 12.6 Consensus size: 54
12535 TAGATAAGTG
* *
12545 ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGGGTGCAACTCATGGAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACTCACGGAATTC
12599 ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACTCACGGAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACTCACGGAATTC
* *
12653 ATAATGAGTTTGTGAATAACCGTATCGGCACTAAGGGTGCAACTCACGGAA--C
1 ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACTCACGGAATTC
* * * * * * * * *
12705 -TCATGAGTTTGTGAATTACCGTATCAGTAGTATGTGTTCAACCCATGAAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACTCACGGAATTC
* * *
12758 ATAATGAGTTTGTGAATTACCATATCGACACTAAGTGTACAACTCACGGAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACTCACGGAATTC
* * *
12812 ACAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACTCACGAAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACTCACGGAATTC
* *
12866 ATAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACTCACGAAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACTCACGGAATTC
* ** * * *
12920 ATAATGGGTTTGTGAATTACCACATCGACACTAAATGTGCAACTCACAGAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACTCACGGAATTC
* * * *
12974 ATAATGAGATTGTGAATGACCGTATCAGCACTAAGTGTGCAACCCACGGAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACTCACGGAATTC
* *
13028 ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACCCACGAAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACTCACGGAATTC
* *
13082 ATAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACTCATGGAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACTCACGGAATTC
* * * * * *
13136 ATAATGAGTTTGTGAATTATCGTATCGACACTATGTGAGCAACCCATGGAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACTCACGGAATTC
* *
13190 ATAAGGAGTTTGTGAATTACCATATCGGCACT
1 ATAATGAGTTTGTGAATTACCGTATCGGCACT
13222 TAGGTGCGAT
Statistics
Matches: 557, Mismatches: 63, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
51 39 0.07
52 1 0.00
53 1 0.00
54 516 0.93
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (54 bp):
ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACTCACGGAATTC
Found at i:18543 original size:54 final size:54
Alignment explanation
Indices: 18480--19266 Score: 972
Period size: 54 Copynumber: 14.6 Consensus size: 54
18470 TAGATAAGTG
* * *
18480 ATAATGAGTTTGTGAATTACCGTATCAACACTAAGTTTACAACTCATGAAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACTCATGAAATTC
* * *
18534 ATAATGAGTTTGTGAATTACTGTATCGGCACTAAGTGTGCAACTCAAGAAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACTCATGAAATTC
* * *
18588 ATAATGAGTTTGTG-ATTACCATATCGGCACTAAGTGTGCAACTCATGGAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACTCATGAAATTC
* * * * * * *
18641 ATAATGAGTTTGTAAAGTACCGTATCAACACTATGTGTGCAACCCACGGAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACTCATGAAATTC
* *
18695 ATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACTCA-CAGAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACTCATGA-AATTC
* * * * *
18749 ATAATGAGTTTGTTAATTACCTTATCGACACTAAGTGTGTAACTCACGGAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACTCATGAAATTC
* * * * *
18803 ATATTGAGTTTGTGACTTACCATATCGGCACTAAGTGTGCAACTCATGGAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACTCATGAAATTC
* *
18857 ATAATGAGTTTGTGAATTACAGTATCGACACTAAGTGTGCAACTCATGAAATTA
1 ATAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACTCATGAAATTC
*
18911 ATAATGAGTTTGTGAATTA-CGATATCGACACTAAGTGTGCAACTCA-CAGAATTC
1 ATAATGAGTTTGTGAATTACCG-TATCGACACTAAGTGTGCAACTCATGA-AATTC
* * * **
18965 ATAATGTGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACCCAACAAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACTCATGAAATTC
* * *
19019 ATAATGAGTTTGTGAATTACAGTGTCGACACTATGTGTGCAA-TCCATGAAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACT-CATGAAATTC
* ** * * *
19073 ATAATGAGTTTCTGAATTACAATATCAATACTAAGTGTGCAACTCACGAAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACTCATGAAATTC
* * * * *
19127 ATAATGAGTTTGTGAATTATCGTATCGGCACTATGTGTGCAACCCATGGAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACTCATGAAATTC
* * * * *
19181 ATAATGTGTTTGTGAATTACCATATCGACACTATGTGTGTAACCCATGAAATTC
1 ATAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACTCATGAAATTC
* * * *
19235 ATAATGTGTTTGTGAATTTCCATATTGACACT
1 ATAATGAGTTTGTGAATTACCGTATCGACACT
19267 TAGGTGCGAT
Statistics
Matches: 638, Mismatches: 86, Indels: 18
0.86 0.12 0.02
Matches are distributed among these distances:
53 50 0.08
54 583 0.91
55 5 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (54 bp):
ATAATGAGTTTGTGAATTACCGTATCGACACTAAGTGTGCAACTCATGAAATTC
Found at i:22657 original size:12 final size:12
Alignment explanation
Indices: 22624--22660 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 12
22614 GACGACTCCC
22624 AACATTTCAAAA
1 AACATTTCAAAA
22636 AATCATTTCAAAA
1 AA-CATTTCAAAA
*
22649 AACACTTCAAAA
1 AACATTTCAAAA
22661 CCTCATCGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.57, C:0.19, G:0.00, T:0.24
Consensus pattern (12 bp):
AACATTTCAAAA
Found at i:26240 original size:23 final size:23
Alignment explanation
Indices: 26214--26276 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
26204 CATATTATAT
**
26214 GGCACTTCGGTGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTACAC
* * *
26237 GGCACTACGGTGCAATTCTACAT
1 GGCACTTCGGTGCATTTCTACAC
26260 GGCACTTCGGTGCATTT
1 GGCACTTCGGTGCATTT
26277 ATACGAGCTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACAC
Found at i:28414 original size:19 final size:19
Alignment explanation
Indices: 28373--28415 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
28363 AATATTAATC
*
28373 ATTATTATTAATGAGTATT
1 ATTATTATTAATAAGTATT
*
28392 ATTATTATT-ATAATTATT
1 ATTATTATTAATAAGTATT
28410 AATTAT
1 -ATTAT
28416 ACTAACATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
ATTATTATTAATAAGTATT
Found at i:30038 original size:2 final size:2
Alignment explanation
Indices: 29999--30027 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29989 GGTGCTACAT
29999 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30028 TGTGGTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39069 original size:18 final size:17
Alignment explanation
Indices: 39046--39082 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
39036 TATCAAAATG
39046 AAATAAGACAACAATACA
1 AAATAAGACAACAA-ACA
*
39064 AAATAAGACTACAAACA
1 AAATAAGACAACAAACA
39081 AA
1 AA
39083 CTAAACCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.68, C:0.16, G:0.05, T:0.11
Consensus pattern (17 bp):
AAATAAGACAACAAACA
Found at i:39453 original size:39 final size:39
Alignment explanation
Indices: 39394--39477 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
39384 ACATCATTAC
*
39394 CAATTGATTTTATTTATTATTAAGTTCAATATAATACCT
1 CAATAGATTTTATTTATTATTAAGTTCAATATAATACCT
* *
39433 CAATAGATTTTATTTATTATTAAGTTTAATATAGTACCT
1 CAATAGATTTTATTTATTATTAAGTTCAATATAATACCT
39472 CAATAG
1 CAATAG
39478 TTTCTTCTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (39 bp):
CAATAGATTTTATTTATTATTAAGTTCAATATAATACCT
Found at i:40750 original size:22 final size:23
Alignment explanation
Indices: 40703--40750 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
40693 TCACGTTTTC
*
40703 AAAAGCTATTATTTTCCTATTTG
1 AAAAGCTATTATTTTCCTATTCG
40726 AAAA-CTATTATTTTTCC-ATTCG
1 AAAAGCTATTA-TTTTCCTATTCG
40748 AAA
1 AAA
40751 GAAGAAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (23 bp):
AAAAGCTATTATTTTCCTATTCG
Found at i:41987 original size:3 final size:3
Alignment explanation
Indices: 41979--42022 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
41969 CTAAAGTTTA
* *
41979 ATT ATT ATT ATT ACT A-T ATT ATT ATT ATT ATT AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42023 CCATTTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:45647 original size:21 final size:21
Alignment explanation
Indices: 45613--45663 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
45603 CATCAGCAAC
*
45613 TGTGAACTATCACGCTAGTGA
1 TGTGAACTAACACGCTAGTGA
* *
45634 TGTGAGCTAACACGTTAGT-A
1 TGTGAACTAACACGCTAGTGA
45654 TCGTGAACTA
1 T-GTGAACTA
45664 CCATATCAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (21 bp):
TGTGAACTAACACGCTAGTGA
Found at i:55504 original size:56 final size:56
Alignment explanation
Indices: 55424--55535 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
55414 CCCCAATGAC
*
55424 TCCAAATGGCTAGAATTATTGCAGAAGATATAAATTGAAGGTTAAAGCTTCCCAAG
1 TCCAAATGGCTAGAATTAATGCAGAAGATATAAATTGAAGGTTAAAGCTTCCCAAG
55480 TCCAAATGGCTAGAATTAATGCAGAAGATATAAATTGAAGGTTAAAGCTTCCCAAG
1 TCCAAATGGCTAGAATTAATGCAGAAGATATAAATTGAAGGTTAAAGCTTCCCAAG
55536 GTTAACAAGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (56 bp):
TCCAAATGGCTAGAATTAATGCAGAAGATATAAATTGAAGGTTAAAGCTTCCCAAG
Found at i:57800 original size:16 final size:17
Alignment explanation
Indices: 57769--57805 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
57759 GCTTTCAAAA
57769 TTGAAAAATAAGAATT-
1 TTGAAAAATAAGAATTG
57785 TTGAAAAA-AAGAAATTG
1 TTGAAAAATAAG-AATTG
57802 TTGA
1 TTGA
57806 CTTGAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.16
16 12 0.63
17 4 0.21
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (17 bp):
TTGAAAAATAAGAATTG
Found at i:64452 original size:3 final size:3
Alignment explanation
Indices: 64446--64486 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
64436 TTTTATTATT
*
64446 TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TGA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TA
64487 GGACAAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:64471 original size:16 final size:16
Alignment explanation
Indices: 64446--64483 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
64436 TTTTATTATT
64446 TAAT-AATAATAATAA
1 TAATAAATAATAATAA
64461 TAATAAATAATAATAA
1 TAATAAATAATAATAA
*
64477 TGATAAA
1 TAATAAA
64484 ATAGGACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
TAATAAATAATAATAA
Found at i:64664 original size:16 final size:16
Alignment explanation
Indices: 64643--64683 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
64633 GAACTTCTTC
64643 TTCTTCTTCA-GATGAA
1 TTCTTC-TCATGATGAA
*
64659 TTCTTCTCATTATGAA
1 TTCTTCTCATGATGAA
64675 TTCTT-TCAT
1 TTCTTCTCAT
64684 TAGAATGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.51
Consensus pattern (16 bp):
TTCTTCTCATGATGAA
Found at i:64685 original size:15 final size:16
Alignment explanation
Indices: 64654--64689 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
64644 TCTTCTTCAG
64654 ATGAATTCTTCTCATT
1 ATGAATTCTTCTCATT
64670 ATGAATTCTT-TCATT
1 ATGAATTCTTCTCATT
64685 A-GAAT
1 ATGAAT
64690 GACAATCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 6 0.30
16 10 0.50
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (16 bp):
ATGAATTCTTCTCATT
Found at i:65045 original size:15 final size:16
Alignment explanation
Indices: 65014--65049 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
65004 TCTTCTTCGG
65014 ATGAATTCTTCTCATT
1 ATGAATTCTTCTCATT
65030 ATGAATTCTT-TCATT
1 ATGAATTCTTCTCATT
65045 A-GAAT
1 ATGAAT
65050 GACAATCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 6 0.30
16 10 0.50
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (16 bp):
ATGAATTCTTCTCATT
Found at i:65140 original size:20 final size:17
Alignment explanation
Indices: 65099--65139 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
65089 TTGAACAAGC
65099 TCTTCTTATTATGAACT
1 TCTTCTTATTATGAACT
65116 TCTTCTTATTATGAACT
1 TCTTCTTATTATGAACT
65133 TCTTCTT
1 TCTTCTT
65140 CCTATTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.56
Consensus pattern (17 bp):
TCTTCTTATTATGAACT
Found at i:65145 original size:20 final size:19
Alignment explanation
Indices: 65099--65145 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 19
65089 TTGAACAAGC
65099 TCTTCTTATTATGAACTTCT
1 TCTTC-TATTATGAACTTCT
65119 TC-T-TATTATGAACTTCT
1 TCTTCTATTATGAACTTCT
65136 TCTTCCTATT
1 TCTT-CTATT
65146 TGGATGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 16 0.67
18 1 0.04
19 1 0.04
20 6 0.25
ACGTcount: A:0.19, C:0.21, G:0.04, T:0.55
Consensus pattern (19 bp):
TCTTCTATTATGAACTTCT
Found at i:65425 original size:123 final size:123
Alignment explanation
Indices: 65206--65573 Score: 528
Period size: 123 Copynumber: 3.0 Consensus size: 123
65196 CTATCTCATT
**
65206 TTCTTCTGGAAATATTGATGCTATTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATA
1 TTCTTCTGGAAATATTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATA
**
65271 AGTT-TTTCAGATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTTATTACGAAC
66 AGTTCTTT-AGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATTACGAAC
* * ** * *
65329 TTCTTCTAGAAATATTGATGTTGCTCTATCTTATTTTGAGATAGAGTCGAGCAAAAGGTTGAATA
1 TTCTTCTGGAAATATTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATA
65394 AGTTCTTTAGATTATGAACTTCTTCTTCCTCTTCAGACGAG---TTCTTATTACGAAC
66 AGTTCTTTAGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATTACGAAC
* * * **
65449 TTCTTCTGGAAATACTGATGCTGCTTTATCTCCTTCTGCGATAGAGTCAAGCAAAAATATTGAAT
1 TTCTTCTGGAAATATTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGC-AAAAGGTTGAAT
* * *
65514 AAGTTCTTTAGACTATGAACTTATTCTTCCTCTTCAGAGGAGTTCTTCTTATTACGAAC
65 AAGTTCTTTAGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATTACGAAC
65573 T
1 T
65574 CTATTTGGAA
Statistics
Matches: 216, Mismatches: 24, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
120 57 0.26
121 49 0.23
123 92 0.43
124 18 0.08
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (123 bp):
TTCTTCTGGAAATATTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATA
AGTTCTTTAGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATTACGAAC
Found at i:65706 original size:73 final size:73
Alignment explanation
Indices: 65585--65742 Score: 235
Period size: 73 Copynumber: 2.2 Consensus size: 73
65575 TATTTGGAAA
** *
65585 TGTTTTAAGAAAAACAATCGCAATTGAGATAAATTGCTATTTCGAGTGAAAATTTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCGCAAGCGAGATAAATTGCTATTTCAAGTGAAAATTTCTCAAGCGAG
65650 AAAAAGTT
66 AAAAAGTT
* * * * * *
65658 TGTTTTAATAAAAACAATCTCCAGCGAGATAAATTTCTATTTCAAGTGAAACTTTCTCTAGCGAG
1 TGTTTTAAGAAAAACAATCGCAAGCGAGATAAATTGCTATTTCAAGTGAAAATTTCTCAAGCGAG
65723 AAAAAGTT
66 AAAAAGTT
65731 TGTTTTAAGAAA
1 TGTTTTAAGAAA
65743 TCAATCTCAA
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (73 bp):
TGTTTTAAGAAAAACAATCGCAAGCGAGATAAATTGCTATTTCAAGTGAAAATTTCTCAAGCGAG
AAAAAGTT
Found at i:67060 original size:45 final size:46
Alignment explanation
Indices: 66995--67101 Score: 157
Period size: 45 Copynumber: 2.3 Consensus size: 46
66985 TGGGAGCGTC
66995 AGTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATAGC-CAG
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAA-A-CTCAG
* *
67040 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACTCTG
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACTCAG
67086 AGTGCATCGATGCATA
1 AGTGCATCGATGCATA
67102 GTATGTGCAT
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
45 30 0.54
46 23 0.41
47 3 0.05
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (46 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACTCAG
Found at i:67601 original size:2 final size:2
Alignment explanation
Indices: 67594--67638 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
67584 AATTGATTAA
67594 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
67636 AT A
1 AT A
67639 GCTTAAGCTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:69864 original size:23 final size:22
Alignment explanation
Indices: 69836--69918 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 22
69826 GCATGGCTGT
*
69836 ATGCATTGATGCACTTTCAAGG
1 ATGCATCGATGCACTTTCAAGG
* * *
69858 CATGCATCGGTGCACCTTCATGG
1 -ATGCATCGATGCACTTTCAAGG
* *
69881 -TGTATCGATGCACATTCAAAGGG
1 ATGCATCGATGCACTTTC-AA-GG
69904 ATGCATCGATGCACT
1 ATGCATCGATGCACT
69919 ATTAAGTGTA
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
21 14 0.30
22 1 0.02
23 20 0.43
24 12 0.26
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (22 bp):
ATGCATCGATGCACTTTCAAGG
Found at i:73787 original size:22 final size:21
Alignment explanation
Indices: 73745--73784 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
73735 GAGCTTATTT
*
73745 TCATTTTTAAATTTTGAAACA
1 TCATTTTTAAATTTTAAAACA
*
73766 TCATTTTTATATTTTAAAA
1 TCATTTTTAAATTTTAAAA
73785 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTAAATTTTAAAACA
Found at i:78191 original size:5 final size:5
Alignment explanation
Indices: 78181--78241 Score: 58
Period size: 5 Copynumber: 12.6 Consensus size: 5
78171 CTTGATTCAA
* *
78181 TTTCT TTTC- -TTCT TTT-T TTTCT TTTCT TTT-T TCATCT TTTAT TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T-TTCT TTTCT TTTCT
78228 TTTCTT TTTCT TTT
1 TTTC-T TTTCT TTT
78242 TTTCTAATAG
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
3 3 0.07
4 6 0.13
5 30 0.65
6 7 0.15
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:78218 original size:24 final size:25
Alignment explanation
Indices: 78185--78236 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
78175 ATTCAATTTC
*
78185 TTTTCTTCTTTT-TTTTCTTTTCTT
1 TTTTCATCTTTTATTTTCTTTTCTT
78209 TTTTCATCTTTTATTTTCTTTTCTT
1 TTTTCATCTTTTATTTTCTTTTCTT
78234 TTT
1 TTT
78237 CTTTTTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTTCATCTTTTATTTTCTTTTCTT
Found at i:78237 original size:24 final size:23
Alignment explanation
Indices: 78181--78244 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
78171 CTTGATTCAA
*
78181 TTTC-TTTTCTTCTTTTTTTTCT
1 TTTCTTTTTCATCTTTTTTTTCT
78203 TTTCTTTTTTCATCTTTTATTTTCT
1 TTTC-TTTTTCATCTTTT-TTTTCT
78228 TTTCTTTTTC-T-TTTTTT
1 TTTCTTTTTCATCTTTTTT
78245 CTAATAGATG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
21 2 0.05
22 8 0.21
23 1 0.03
24 17 0.45
25 10 0.26
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTCTTTTTCATCTTTTTTTTCT
Found at i:82403 original size:2 final size:2
Alignment explanation
Indices: 82396--82435 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
82386 TGAATTCTTC
82396 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
82436 TAACGTGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84142 original size:19 final size:17
Alignment explanation
Indices: 84118--84167 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
84108 CTGGGTCAAA
*
84118 TGTAATCGGGCCTCTTGGT
1 TGTAATCGGGCCTCCT--T
*
84137 TGTAATTGGGCCTCCTT
1 TGTAATCGGGCCTCCTT
84154 TGTAATCTGGGCCT
1 TGTAATC-GGGCCT
84168 ATAAAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 7 0.26
18 6 0.22
19 14 0.52
ACGTcount: A:0.12, C:0.22, G:0.28, T:0.38
Consensus pattern (17 bp):
TGTAATCGGGCCTCCTT
Found at i:84415 original size:20 final size:20
Alignment explanation
Indices: 84390--84428 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
84380 TACTGTTCAT
*
84390 AGTTTCAAAACTTTTTTAAG
1 AGTTTCAAAACTGTTTTAAG
*
84410 AGTTTCGAAACTGTTTTAA
1 AGTTTCAAAACTGTTTTAA
84429 CAGCAAGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (20 bp):
AGTTTCAAAACTGTTTTAAG
Found at i:88206 original size:21 final size:21
Alignment explanation
Indices: 88180--88220 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
88170 CATCAACAAC
*
88180 TGTGAACTATCACGCTAGTGA
1 TGTGAACTAACACGCTAGTGA
*
88201 TGTGAACTAACACGTTAGTG
1 TGTGAACTAACACGCTAGTG
88221 TCCACATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (21 bp):
TGTGAACTAACACGCTAGTGA
Found at i:92600 original size:20 final size:20
Alignment explanation
Indices: 92539--92617 Score: 97
Period size: 21 Copynumber: 3.9 Consensus size: 20
92529 TTTTTTTGCT
* *
92539 CAAAGGATCGATCCC-CTAT
1 CAAAGGATCGATCCCTTTAC
*
92558 CAAAAGATCGATCCCTTTGAC
1 CAAAGGATCGATCCCTTT-AC
92579 CAAAGGATCGATCCCTTTAC
1 CAAAGGATCGATCCCTTTAC
*
92599 CAAAATGATCGATCCCTTT
1 C-AAAGGATCGATCCCTTT
92618 GTTCCAACAA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 14 0.27
20 4 0.08
21 34 0.65
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (20 bp):
CAAAGGATCGATCCCTTTAC
Found at i:92632 original size:42 final size:39
Alignment explanation
Indices: 92539--92618 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 39
92529 TTTTTTTGCT
*
92539 CAAAGGATCGATCCCCTATCAAAAGATCGATCCCTTTGAC
1 CAAA-GATCGATCCCCTACCAAAAGATCGATCCCTTTGAC
*
92579 CAAAGGATCGATCCCTTTACCAAAATGATCGATCCCTTTG
1 CAAA-GATCGATCCC-CTACCAAAA-GATCGATCCCTTTG
92619 TTCCAACAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 15 0.42
41 7 0.19
42 14 0.39
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (39 bp):
CAAAGATCGATCCCCTACCAAAAGATCGATCCCTTTGAC
Found at i:98931 original size:18 final size:18
Alignment explanation
Indices: 98908--98942 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
98898 AGGGCCCAAT
98908 ATGAATTAAAAGGAAAAA
1 ATGAATTAAAAGGAAAAA
98926 ATGAATTAAAAGGAAAA
1 ATGAATTAAAAGGAAAA
98943 GTTAGGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (18 bp):
ATGAATTAAAAGGAAAAA
Found at i:99609 original size:21 final size:21
Alignment explanation
Indices: 99555--99612 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
99545 TTTTCCTATG
*
99555 AGTACTTTGTGTACTAGGAGT
1 AGTACTTAGTGTACTAGGAGT
* * *
99576 AGTATTTCA-TGTACTTGTAGT
1 AGTACTT-AGTGTACTAGGAGT
99597 AGTACTTAGTGTACTA
1 AGTACTTAGTGTACTA
99613 TGGTACTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.41
Consensus pattern (21 bp):
AGTACTTAGTGTACTAGGAGT
Found at i:105221 original size:23 final size:22
Alignment explanation
Indices: 105194--105237 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
105184 CATAAGGTAA
105194 GAGAAAATTTCATTTT-GATTTTT
1 GAGAAAA-TTC-TTTTGGATTTTT
105217 GAGAAAATTCTTTTGGATTTT
1 GAGAAAATTCTTTTGGATTTT
105238 GGATTATGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 9 0.45
23 7 0.35
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.50
Consensus pattern (22 bp):
GAGAAAATTCTTTTGGATTTTT
Done.