Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002913.1 Hibiscus syriacus cultivar Beakdansim tig00006023_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: 65456
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4069 original size:125 final size:125
Alignment explanation
Indices: 3845--4218 Score: 527
Period size: 125 Copynumber: 3.0 Consensus size: 125
3835 AAGTTAGGAT
* * *
3845 ATATTGGGGCACGACTGAACCCACATCATGTTGAGATGATAAGATTCAGACCAATGAGGCATGAA
1 ATATTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAAGAGGCATGAA
* * *
3910 GAATGATCCTTACAATTTGAAGTGATGGGACATTTTGAAGGCCCGTACCGGTATAAGTTA
66 GAATGATCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGTTA
* * *
3970 ATATTGGGGCATGACTGAACCCACATCATATTGAGATGACAAAATTCAGACCAAAGAGGCGTGAA
1 ATATTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAAGAGGCATGAA
* * *
4035 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCACGTACCAGTATAAGGTA
66 GAATGATCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGTTA
* * * * *
4095 ATGTTGGGGCGTGACTAAACCCACATCATGTTGAGATGACAAGATACAGACC-AAGAAGGCCTTG
1 ATATTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAAG-AGG-CATG
* * * *
4159 -AGAATAATCCTTACAATTTGAGGTGTTGTGGAATTTTGAAGGCCCGTACCAGTATAAGTT
64 AAGAATGATCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGTT
4219 GACGTTGTGG
Statistics
Matches: 221, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
124 3 0.01
125 215 0.97
126 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (125 bp):
ATATTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAAGAGGCATGAA
GAATGATCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGTTA
Found at i:5540 original size:37 final size:37
Alignment explanation
Indices: 5488--5646 Score: 198
Period size: 37 Copynumber: 4.3 Consensus size: 37
5478 ATGAGATTGG
* *
5488 AGCAAAGTCAATCTTAAGCCTTCACTGAAGAGTAGTGA
1 AGCAAA-TCCATCTTAAGCCTTCACCGAAGAGTAGTGA
* *
5526 AGCAAATCCATCTTAATCCTTCACCAAAGAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGA
*
5563 AGCAAA-CCATCTTAAGTCTTCACCGAAGAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGA
* * * *
5599 AGCAAATCCATTTTAAGCCTTCTCAGAAGAGT-GTTGG
1 AGCAAATCCATCTTAAGCCTTCACCGAAGAGTAG-TGA
5636 AGCAAA-CCATC
1 AGCAAATCCATC
5647 AAATTATCAG
Statistics
Matches: 106, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
36 38 0.36
37 62 0.58
38 6 0.06
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (37 bp):
AGCAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGA
Found at i:5585 original size:73 final size:73
Alignment explanation
Indices: 5498--5646 Score: 212
Period size: 73 Copynumber: 2.0 Consensus size: 73
5488 AGCAAAGTCA
* *
5498 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCCATCTTAATCCTTCACCA-AAGAGTAG-T
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTC-CCAGAAGAGT-GTT
5561 GAAGCAAACC
64 GAAGCAAACC
* * * *
5571 ATCTTAAGTCTTCACCGAAGAGTAGTGAAGCAAATCCATTTTAAGCCTTCTCAGAAGAGTGTTGG
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCCCAGAAGAGTGTTGA
5636 AGCAAACC
66 AGCAAACC
5644 ATC
1 ATC
5647 AAATTATCAG
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
72 3 0.04
73 65 0.96
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (73 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCCCAGAAGAGTGTTGA
AGCAAACC
Found at i:6083 original size:54 final size:54
Alignment explanation
Indices: 6024--6287 Score: 332
Period size: 54 Copynumber: 4.9 Consensus size: 54
6014 ATGAAGCAAG
*
6024 AGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCATAAGA
1 AGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGA
* * * * **
6078 AGAAGATGTTTGAGTTCCATACTTCCTAGAGAAAGAGGGAACGAACTCGTTTGA
1 AGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGA
* * * * ** *
6132 AGAAGATGTTCGAGTTCTATACTCCCTAGATAAAGAGAGAGCAAACCCGTTTGT
1 AGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGA
* * *
6186 AGAAGATGTCCGAGTTCTATACTCCCT-GAAGAAAGAGGGAGTGAACCCGTAAGA
1 AGAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTAAGA
* * *
6240 AGAAGATGTTCGAGTTTCATACTTCTTAGAGAAAGAGGGAGCGAACCC
1 AGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCC
6288 ATTTGTTGAA
Statistics
Matches: 178, Mismatches: 30, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
53 1 0.01
54 176 0.99
55 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (54 bp):
AGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGA
Found at i:6219 original size:108 final size:108
Alignment explanation
Indices: 6024--6328 Score: 355
Period size: 108 Copynumber: 2.8 Consensus size: 108
6014 ATGAAGCAAG
* ** * *
6024 AGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCATAAGAAGAAGATGTTT
1 AGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGTAGAAGATGTTC
* * * **
6089 GAGTTCCATACTTCCT-AGAGAAAGAGGGAACGAACTCGTTTGA
66 GAGTTCTATACTCCCTGA-AGAAAGAGGGAACGAACCCGTAAGA
* * * * *
6132 AGAAGATGTTCGAGTTCTATACTCCCTAGATAAAGAGAGAGCAAACCCGTTTGTAGAAGATGTCC
1 AGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGTAGAAGATGTTC
**
6197 GAGTTCTATACTCCCTGAAGAAAGAGGGAGTGAACCCGTAAGA
66 GAGTTCTATACTCCCTGAAGAAAGAGGGAACGAACCCGTAAGA
* * * *
6240 AGAAGATGTTCGAGTT-TCATACTTCTTAGAGAAAGAGGGAGCGAACCCATTTGTTGAAAATTGT
1 AGAAGATGTTCGAGTTCT-ATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGTAGAAGA-TGT
*
6304 TCGAG-TCTTATACTCTCTGAAGAAA
64 TCGAGTTC-TATACTCCCTGAAGAAA
6329 TAAGGAGCAG
Statistics
Matches: 166, Mismatches: 27, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
107 1 0.01
108 141 0.85
109 24 0.14
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (108 bp):
AGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGTAGAAGATGTTC
GAGTTCTATACTCCCTGAAGAAAGAGGGAACGAACCCGTAAGA
Found at i:6328 original size:55 final size:54
Alignment explanation
Indices: 6170--6876 Score: 519
Period size: 55 Copynumber: 13.2 Consensus size: 54
6160 GATAAAGAGA
* * * *
6170 GAGCAAACCCGTTTGTAGAAGA-TGTCCGAGT-TCTATACTCCCTGAAGAAAGAGG
1 GAGC-AACCCGTTTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGG
* ** ** * *
6224 GAGTGAACCCGTAAGAAGAAGA-TGTTCGAGT-TTCATACT-TCTTAGAGAAAGAGG
1 GAG-CAACCCGTTTGTTGAAGATTGTTCGAGTCTT-ATACTCTCTGA-AGAAATAGG
* * *
6278 GAGCGAACCCATTTGTTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAAG
1 GAGC-AACCCGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
* ** ** *
6333 GAGCAGACACAATTGTTGAAGATTACTCGAGTCTTATACTCTCTGAAGGAATAGG
1 GAGCA-ACCCGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
* * * *
6388 GAGCAAACACGATTGTTGAAGATTGTTTGAGTCTTATACTCTCTGAAGAAATAGA
1 GAGC-AACCCGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
* * * *
6443 GAGCAGACACGATTGCTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGA
1 GAGCA-ACCCGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
* *
6498 GAGCAGACAC-TATTATTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
1 GAGCA-ACCCGT-TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
** * * *
6553 GAGCATATACGATTATTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
1 GAGCA-ACCCGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
* * * *
6608 GAGTAGA--C--------ACGATTGTTCGAGCCTTATACTCTCTGAAGAAAGAGG
1 GAGCA-ACCCGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
* ** ** *
6653 GAGCAGACACGTTTGTTGAAGGCTGTTTAAGTCCTATACTCTCTGAAGGAAATAGG
1 GAGCA-ACCCGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAA-GAAATAGG
* * * *
6709 GAGCGAACACGTTTGTTGAAGA----TCGAGTCCTATACTCTCTGAAGGAATAGA
1 GAGC-AACCCGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
* * * *
6760 GAGCAGACACGTTTGTT-AA-A--GATCGAGTCCTATACTCTCTGAAGGAATAGG
1 GAGCA-ACCCGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
* * * * * * *
6811 GAACGAACCCGTTT-TATGAAGATTGTTTGAGTTTTACACTCCCTGAAGCAAGAGG
1 GAGC-AACCCGTTTGT-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
6866 GAGCAAACCCG
1 GAGC-AACCCG
6877 CTGGTCGAAC
Statistics
Matches: 547, Mismatches: 73, Indels: 65
0.80 0.11 0.09
Matches are distributed among these distances:
45 39 0.07
47 1 0.00
49 1 0.00
50 4 0.01
51 60 0.11
52 22 0.04
53 6 0.01
54 56 0.10
55 324 0.59
56 33 0.06
57 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (54 bp):
GAGCAACCCGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
Found at i:6587 original size:165 final size:165
Alignment explanation
Indices: 6294--6871 Score: 574
Period size: 165 Copynumber: 3.6 Consensus size: 165
6284 ACCCATTTGT
* * *
6294 TGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATA-AGGAGCAGACAC-AATTGTTGAAGATT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGA-GAGCAGACACGTATTATTGAAGATT
** * * *
6357 ACTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAAACACGATTGTTGAAGATTGTTTGAGTCT
65 GTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGC-AACACGATTGTTGAAAATTGTTCGAGTCT
6422 TATACTCTCTGAAGAAATAGAGAGCAGACACGATTGC
129 TATACTCTCTGAAGAAATAGAGAGCAGACACGATTGC
6459 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAGCAGACAC-TATTATTGAAGATTG
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAGCAGACACGTATTATTGAAGATTG
* *
6523 TTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCATATACGATTATTGAAAATTGTTCGAGTCTT
66 TTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCA-ACACGATTGTTGAAAATTGTTCGAGTCTT
*
6588 ATACTCTCTGAAGAAATAG-G-G-AG-TA-GA---C
130 ATACTCTCTGAAGAAATAGAGAGCAGACACGATTGC
* * * * * **
6616 --ACGATTGTTCGAGCCTTATACTCTCTGAAGAAAGAGGGAGCAGACACGT-TTGTTGAAGGCTG
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAGCAGACACGTATTATTGAAGATTG
** * * * *
6678 TTTAAGTCCTATACTCTCTGAAGGAAATAGGGAGCGAACACGTTTGTTG--AA--GATCGAGTCC
66 TTCGAGTCTTATACTCTCTGAA-GAAATAGGGAGC-AACACGATTGTTGAAAATTGTTCGAGTCT
* *
6739 TATACTCTCTGAAGGAATAGAGAGCAGACACGTTTG-
129 TATACTCTCTGAAGAAATAGAGAGCAGACACGATTGC
* * * * * * * *
6775 TTAA-A--GATCGAGTCCTATACTCTCTGAAGGAATAGGGAAC-GAACCCGTTTTA-TGAAGATT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAGCAG-ACACGTATTATTGAAGATT
* * * * * *
6835 GTTTGAGTTTTACACTCCCTGAAGCAAGAGGGAGCAA
65 GTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAA
6872 ACCCGCTGGT
Statistics
Matches: 349, Mismatches: 47, Indels: 43
0.79 0.11 0.10
Matches are distributed among these distances:
152 27 0.08
153 1 0.00
154 3 0.01
155 74 0.21
156 25 0.07
157 14 0.04
158 58 0.17
159 2 0.01
160 3 0.01
161 2 0.01
162 2 0.01
163 1 0.00
164 2 0.01
165 134 0.38
166 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (165 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAGCAGACACGTATTATTGAAGATTG
TTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAACACGATTGTTGAAAATTGTTCGAGTCTTA
TACTCTCTGAAGAAATAGAGAGCAGACACGATTGC
Found at i:6604 original size:29 final size:29
Alignment explanation
Indices: 6519--6604 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 29
6509 ATTATTGAAG
6519 ATTGTTCGAGTCTTATACTCTCTGAAGAA
1 ATTGTTCGAGTCTTATACTCTCTGAAGAA
* * * *
6548 ATAG--GGAG-CATATACGAT-TATTG-A-AA
1 ATTGTTCGAGTCTTATAC--TCT-CTGAAGAA
6574 ATTGTTCGAGTCTTATACTCTCTGAAGAA
1 ATTGTTCGAGTCTTATACTCTCTGAAGAA
6603 AT
1 AT
6605 AGGGAGTAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 18
0.61 0.12 0.27
Matches are distributed among these distances:
26 11 0.28
27 8 0.20
28 8 0.20
29 13 0.32
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (29 bp):
ATTGTTCGAGTCTTATACTCTCTGAAGAA
Found at i:6611 original size:27 final size:27
Alignment explanation
Indices: 6526--6611 Score: 63
Period size: 27 Copynumber: 3.1 Consensus size: 27
6516 AAGATTGTTC
6526 GAGTCTTATACTCTCTGAAGAAATAGG
1 GAGTCTTATACTCTCTGAAGAAATAGG
* * * *
6553 GAG-CATATACGAT-TATTG-A-AAATTGTTC
1 GAGTCTTATAC--TCT-CTGAAGAAATAG--G
6581 GAGTCTTATACTCTCTGAAGAAATAGG
1 GAGTCTTATACTCTCTGAAGAAATAGG
6608 GAGT
1 GAGT
6612 AGACACGATT
Statistics
Matches: 42, Mismatches: 8, Indels: 18
0.62 0.12 0.26
Matches are distributed among these distances:
26 11 0.26
27 12 0.29
28 8 0.19
29 11 0.26
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (27 bp):
GAGTCTTATACTCTCTGAAGAAATAGG
Found at i:6663 original size:45 final size:45
Alignment explanation
Indices: 6574--6669 Score: 156
Period size: 45 Copynumber: 2.1 Consensus size: 45
6564 ATTATTGAAA
* * *
6574 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGTAGACACG
1 ATTGTTCGAGCCTTATACTCTCTGAAGAAAGAGGGAGCAGACACG
6619 ATTGTTCGAGCCTTATACTCTCTGAAGAAAGAGGGAGCAGACACG
1 ATTGTTCGAGCCTTATACTCTCTGAAGAAAGAGGGAGCAGACACG
*
6664 TTTGTT
1 ATTGTT
6670 GAAGGCTGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (45 bp):
ATTGTTCGAGCCTTATACTCTCTGAAGAAAGAGGGAGCAGACACG
Found at i:6691 original size:100 final size:98
Alignment explanation
Indices: 6518--6812 Score: 287
Period size: 100 Copynumber: 2.9 Consensus size: 98
6508 TATTATTGAA
* * * * *
6518 GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCATATACGATTATTGAAA-ATTGTTCG
1 GATTGTTCGAGCCTTATACTCTCTGAAGAAATAGGGAGCAGACACGTTTGTTGAAAGA-TGTT--
*
6582 AGTCTTATACTCTCTGAAGAAATAGGGAGTAG-ACAC
63 AGTCCTATACTCTCTGAAGAAATAGGGAG-AGAACAC
* * *
6618 GATTGTTCGAGCCTTATACTCTCTGAAGAAAGAGGGAGCAGACACGTTTGTTGAAGGCTGTTTAA
1 GATTGTTCGAGCCTTATACTCTCTGAAGAAATAGGGAGCAGACACGTTTGTTGAAAGATG-TT-A
*
6683 GTCCTATACTCTCTGAAGGAAATAGGGAGCGAACAC
64 GTCCTATACTCTCTGAA-GAAATAGGGAGAGAACAC
* * *
6719 GTTTGTTGAAGATCGAGTCC-TATACTCTCTGAAGGAATAGAGAGCAGACACGTTTGTT-AAAGA
1 GATTG-T-----TCGAG-CCTTATACTCTCTGAAGAAATAGGGAGCAGACACGTTTGTTGAAAGA
*
6782 TCG--AGTCCTATACTCTCTGAAGGAATAGGGA
59 T-GTTAGTCCTATACTCTCTGAAGAAATAGGGA
6813 ACGAACCCGT
Statistics
Matches: 165, Mismatches: 18, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
100 69 0.42
101 21 0.13
102 10 0.06
103 18 0.11
106 4 0.02
107 41 0.25
108 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (98 bp):
GATTGTTCGAGCCTTATACTCTCTGAAGAAATAGGGAGCAGACACGTTTGTTGAAAGATGTTAGT
CCTATACTCTCTGAAGAAATAGGGAGAGAACAC
Found at i:7026 original size:3 final size:3
Alignment explanation
Indices: 7000--7039 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
6990 ATATTATAAA
*
7000 TAT TAAT TAT ATAT TAT TAC TAT TAT TAT TAT TAT TAT TA
1 TAT T-AT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
7040 ATGTTACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 27 0.82
4 6 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:19514 original size:20 final size:20
Alignment explanation
Indices: 19472--19514 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
19462 TTATTTTCAT
* *
19472 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
19492 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
19512 TTT
1 TTT
19515 CTCATAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:21381 original size:19 final size:20
Alignment explanation
Indices: 21345--21382 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21335 TGGAGCGTGG
21345 GGGGAATCGGTACCCCTAAT
1 GGGGAATCGGTACCCCTAAT
21365 GGGGAATCGGT-CCCCTAA
1 GGGGAATCGGTACCCCTAA
21383 GTGTAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.24, C:0.26, G:0.32, T:0.18
Consensus pattern (20 bp):
GGGGAATCGGTACCCCTAAT
Found at i:21818 original size:2 final size:2
Alignment explanation
Indices: 21811--21836 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21801 GAATCAAATG
21811 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
21837 TTATGTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22736 original size:21 final size:21
Alignment explanation
Indices: 22710--22770 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
22700 AGAAACTATC
22710 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
* *
22731 TCAA--G-G--AAAA-CTGTC
1 TCAAGGGAGACAAAATTTGTT
22746 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
22767 TCAA
1 TCAA
22771 TGGAAACTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 7 0.23
16 4 0.13
17 1 0.03
18 2 0.07
19 1 0.03
20 4 0.13
21 11 0.37
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTGTT
Found at i:22742 original size:36 final size:36
Alignment explanation
Indices: 22701--22997 Score: 351
Period size: 36 Copynumber: 8.0 Consensus size: 36
22691 TGTTTCGTGA
*
22701 GAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGG
1 GAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGG
* * * *
22737 AAAACTGTCTCAAGGGAGACAAAATTTGTTTCAATG
1 GAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGG
* *
22773 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGG
1 GAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGG
*
22809 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGG
1 GAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGG
*
22845 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGG
1 GAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGG
* * *
22881 GAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCGAGG
1 GAAACTATCTCAAGAGAGACAAAA---TTTGTTTCAAGG
* * * *
22920 AAAACTATCTCAAAAGAGATAAAATCTTCTGTTTCGAGG
1 GAAACTATCTCAAGAGAGACAAAA--TT-TGTTTCAAGG
* *
22959 GAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCAAGG
1 GAAACTATCTCAAGAGAGACAAAA--TT-TGTTTCAAGG
22998 AAAAACAATC
Statistics
Matches: 236, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
36 157 0.67
38 2 0.01
39 77 0.33
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (36 bp):
GAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGG
Found at i:23026 original size:40 final size:40
Alignment explanation
Indices: 22896--23578 Score: 1039
Period size: 40 Copynumber: 17.0 Consensus size: 40
22886 TATCTCAAGC
* * * ** **
22896 GAGATAAAATCTTTTGTTTCGAGG-AAAACTATCTCAAAA
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * * ** *
22935 GAGATAAAATCTTCTGTTTCGAGG-GAAACTATCTCAAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
22974 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
23014 GAGATAAAATCTTCTGTTTAAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
23054 GAGATAAAATCTTCTGTTTCAA-GAAAAAAAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
23093 GAGATAAAATCTTCTGTTTAAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
23133 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * *
23173 GAGATAAAATATTTTGTTTCAAGGAAAAACAATATTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
23213 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
23253 GAGATGAAATCTTCTGTTTCAAGGAAAAACAATCTTGATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAAC-A-----ATCTTGAGT
*
23299 GAGATGAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
23339 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
23379 GAGATAAAATCTTCTGTTTCAAGGAAAAGCAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
23419 GAGATGAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
23459 GAGATAAAATCTTCTGTTTCAAGGAGAAATAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
23499 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
23539 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCATGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
23579 CAAATGAAAT
Statistics
Matches: 603, Mismatches: 33, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
39 95 0.16
40 467 0.77
41 1 0.00
45 1 0.00
46 39 0.06
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
Found at i:23485 original size:23 final size:23
Alignment explanation
Indices: 23459--23523 Score: 56
Period size: 23 Copynumber: 3.1 Consensus size: 23
23449 AATCTTGAGT
23459 GAGATAAAATCTTCTGTTTCAAG
1 GAGATAAAATCTTCTGTTTCAAG
23482 GAGA-AATAATC-T-TG-----AG
1 GAGATAA-AATCTTCTGTTTCAAG
23498 TGAGATAAAATCTTCTGTTTCAAG
1 -GAGATAAAATCTTCTGTTTCAAG
23522 GA
1 GA
23524 AAAACAATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 20
0.62 0.00 0.38
Matches are distributed among these distances:
16 2 0.06
17 8 0.25
18 3 0.09
19 2 0.06
21 2 0.06
22 3 0.09
23 10 0.31
24 2 0.06
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (23 bp):
GAGATAAAATCTTCTGTTTCAAG
Found at i:32541 original size:18 final size:18
Alignment explanation
Indices: 32498--32535 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
32488 GTGAAGTATG
*
32498 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
32516 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
32534 AA
1 AA
32536 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:35883 original size:117 final size:117
Alignment explanation
Indices: 35677--35902 Score: 443
Period size: 117 Copynumber: 1.9 Consensus size: 117
35667 CCTTCTTATG
35677 GATCGTTTGAACATATTTGGATCTCCCAACTTTGACTACATGATTAAGAATTTCTTGTCTCATTA
1 GATCGTTTGAACATATTTGGATCTCCCAACTTTGACTACATGATTAAGAATTTCTTGTCTCATTA
*
35742 TGACCAGCCTTTTTATTAGTCAATCACTTGTGAAGTAACACCTTTGGAGAAT
66 TGACCAGCCTTTTTATTAATCAATCACTTGTGAAGTAACACCTTTGGAGAAT
35794 GATCGTTTGAACATATTTGGATCTCCCAACTTTGACTACATGATTAAGAATTTCTTGTCTCATTA
1 GATCGTTTGAACATATTTGGATCTCCCAACTTTGACTACATGATTAAGAATTTCTTGTCTCATTA
35859 TGACCAGCCTTTTTATTAATCAATCACTTGTGAAGTAACACCTT
66 TGACCAGCCTTTTTATTAATCAATCACTTGTGAAGTAACACCTT
35903 CGGATGACAT
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 108 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (117 bp):
GATCGTTTGAACATATTTGGATCTCCCAACTTTGACTACATGATTAAGAATTTCTTGTCTCATTA
TGACCAGCCTTTTTATTAATCAATCACTTGTGAAGTAACACCTTTGGAGAAT
Found at i:37351 original size:30 final size:29
Alignment explanation
Indices: 37278--37351 Score: 69
Period size: 30 Copynumber: 2.5 Consensus size: 29
37268 CTTAGGAATT
*
37278 AAATAATAAAAATTAAAAATTAAAATACCA
1 AAATAATAAAAA-CAAAAATTAAAATACCA
* ** *
37308 AAAT-ATCACAAACAAAAACTTAATGTACTA
1 AAATAAT-AAAAACAAAAA-TTAAAATACCA
37338 AAATAATAAAAACA
1 AAATAATAAAAACA
37352 GATAGTTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
29 7 0.20
30 26 0.74
31 2 0.06
ACGTcount: A:0.66, C:0.11, G:0.01, T:0.22
Consensus pattern (29 bp):
AAATAATAAAAACAAAAATTAAAATACCA
Found at i:39113 original size:31 final size:28
Alignment explanation
Indices: 39055--39131 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 28
39045 CTTTTTCATT
*
39055 TAAGTACTTAAAGTATTTTTGGTCAAAA
1 TAAGTACTTAAAGTATTTTTGGACAAAA
39083 TAAGTACTTAAAGTTATCTTTTTGGACAAAA
1 TAAGTACTTAAAG-TA--TTTTTGGACAAAA
*
39114 T-AGATACCTAAAGTATTT
1 TAAG-TACTTAAAGTATTT
39132 AATTTTTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 16 0.37
29 2 0.05
30 4 0.09
31 21 0.49
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (28 bp):
TAAGTACTTAAAGTATTTTTGGACAAAA
Found at i:39277 original size:32 final size:32
Alignment explanation
Indices: 39207--39278 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
39197 AAAAATATTG
* *
39207 AATAA-TTTATGTACATGTTTTGACAAAAAAA
1 AATAATTTTAGGTACATATTTTGACAAAAAAA
**
39238 AAT-ATTTTAGGTACATATTTTGACCCAAAAA
1 AATAATTTTAGGTACATATTTTGACAAAAAAA
*
39269 GATAATTTTA
1 AATAATTTTA
39279 AATATTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 1 0.03
31 27 0.79
32 6 0.18
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (32 bp):
AATAATTTTAGGTACATATTTTGACAAAAAAA
Found at i:45524 original size:60 final size:60
Alignment explanation
Indices: 45397--45529 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 60
45387 ATAGTCGGGT
* * * *
45397 GACCATTTTATAACTTTTAATAGTTGAGAGACTCAACAAAGCAACTCCCTATAGTTGGAG
1 GACCATTTTGTAACTTTTAATAGTGGAGAGACTCAACAAAGCAACTCCATATAGTAGGAG
* * *
45457 GATCATTTTGTAATTTTTAATAGCTGGAG-GACTCAACAAAGCAA-TATCATATAGCTAGG-G
1 GACCATTTTGTAACTTTTAATAG-TGGAGAGACTCAACAAAGCAACT-CCATATAG-TAGGAG
45517 GACCATTTGTGTA
1 GACCATTT-TGTA
45530 CTTCACCCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
59 1 0.02
60 49 0.80
61 11 0.18
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTGGAGAGACTCAACAAAGCAACTCCATATAGTAGGAG
Found at i:47255 original size:29 final size:31
Alignment explanation
Indices: 47216--47303 Score: 101
Period size: 31 Copynumber: 2.9 Consensus size: 31
47206 TTTTAATTTG
47216 ACACCTAAACTTTAGATAAAATA-CTAAT-TT
1 ACACCTAAACTTTAGATAAAATATC-AATCTT
* * * *
47246 A-ACTTAAACTTTATATACAATATCATTCTT
1 ACACCTAAACTTTAGATAAAATATCAATCTT
*
47276 ACCCCTAAACTTTAGATAAAATATCAAT
1 ACACCTAAACTTTAGATAAAATATCAAT
47304 TTTGATCTCT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 20 0.43
30 5 0.11
31 21 0.46
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.35
Consensus pattern (31 bp):
ACACCTAAACTTTAGATAAAATATCAATCTT
Found at i:63540 original size:25 final size:25
Alignment explanation
Indices: 63493--63563 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 25
63483 TTTAAATTAT
**
63493 TTAAAATATATTTATATCA-TATTCA
1 TTAAAATATAAATATAT-ATTATTCA
**
63518 TTAAAATATAAATATATATTATTTT
1 TTAAAATATAAATATATATTATTCA
* *
63543 TTAAAAT-TCAATAAATATTAT
1 TTAAAATATAAATATATATTAT
63564 ATTTATAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
24 13 0.33
25 26 0.67
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (25 bp):
TTAAAATATAAATATATATTATTCA
Done.