Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000085.1 Hibiscus syriacus cultivar Beakdansim tig00000156_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: 89855
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:10625 original size:14 final size:14
Alignment explanation
Indices: 10606--10645 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
10596 GTGATGACAT
10606 TCGGGTTGAAAATG
1 TCGGGTTGAAAATG
10620 TCGGGTTGAAAATG
1 TCGGGTTGAAAATG
10634 TCGGGTTGAAAA
1 TCGGGTTGAAAA
10646 ACGTAAGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.30, C:0.07, G:0.35, T:0.28
Consensus pattern (14 bp):
TCGGGTTGAAAATG
Found at i:13144 original size:16 final size:14
Alignment explanation
Indices: 13116--13151 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
13106 AAACAAATGA
13116 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
13130 AAAAATAAAATAAAAT
1 AAAAAT-AAA-AAAAT
13146 AAAAAT
1 AAAAAT
13152 GGGGTTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 3 0.15
16 11 0.55
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:22172 original size:10 final size:10
Alignment explanation
Indices: 22154--22194 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
22144 CAAATTTTTG
22154 CAAATATAAAA
1 CAAA-ATAAAA
*
22165 TAAAATAAAA
1 CAAAATAAAA
*
22175 CAAAACAAAA
1 CAAAATAAAA
22185 CAAAATAAAA
1 CAAAATAAAA
22195 GTGCAAAAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 23 0.88
11 3 0.12
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (10 bp):
CAAAATAAAA
Found at i:22519 original size:30 final size:28
Alignment explanation
Indices: 22485--22620 Score: 83
Period size: 30 Copynumber: 5.0 Consensus size: 28
22475 CCAAATTAAA
22485 AAAAACTTAAGGGACTAAAATAGCAAAAAC
1 AAAAA-TTAA-GGACTAAAATAGCAAAAAC
22515 AAAAATTAA--AC-AAAA-A-C-AAAA-
1 AAAAATTAAGGACTAAAATAGCAAAAAC
** *
22536 ATTAA--AAGGACTAAAATAGAAAAAAC
1 AAAAATTAAGGACTAAAATAGCAAAAAC
* * *
22562 TAAAACTTAAGAGATTAAAATAGCATAAAC
1 -AAAAATTAAG-GACTAAAATAGCAAAAAC
* *
22592 AGAAATTTAAAGGACTAAAATAGTAAAAA
1 A-AAAATT-AAGGACTAAAATAGCAAAAA
22621 TAGATAGTTA
Statistics
Matches: 80, Mismatches: 13, Indels: 26
0.67 0.11 0.22
Matches are distributed among these distances:
19 2 0.03
21 5 0.06
22 8 0.10
23 2 0.03
24 1 0.01
25 8 0.10
26 2 0.03
27 2 0.03
29 8 0.10
30 39 0.49
31 3 0.04
ACGTcount: A:0.64, C:0.09, G:0.10, T:0.17
Consensus pattern (28 bp):
AAAAATTAAGGACTAAAATAGCAAAAAC
Found at i:22530 original size:17 final size:17
Alignment explanation
Indices: 22508--22541 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
22498 ACTAAAATAG
22508 CAAAAACAAAAATTAAA
1 CAAAAACAAAAATTAAA
22525 CAAAAACAAAAATTAAA
1 CAAAAACAAAAATTAAA
22542 AGGACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (17 bp):
CAAAAACAAAAATTAAA
Found at i:22563 original size:15 final size:16
Alignment explanation
Indices: 22498--22566 Score: 54
Period size: 15 Copynumber: 4.4 Consensus size: 16
22488 AACTTAAGGG
*
22498 ACTAAAA-TAGCAAAA
1 ACTAAAATTAGAAAAA
* *
22513 ACAAAAATTAAACAAAA
1 ACTAAAATTAGA-AAAA
* **
22530 ACAAAAATTA-AAAGG
1 ACTAAAATTAGAAAAA
22545 ACTAAAA-TAGAAAAA
1 ACTAAAATTAGAAAAA
22560 ACTAAAA
1 ACTAAAA
22567 CTTAAGAGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
14 2 0.05
15 24 0.56
16 3 0.07
17 14 0.33
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (16 bp):
ACTAAAATTAGAAAAA
Found at i:22632 original size:30 final size:30
Alignment explanation
Indices: 22540--22656 Score: 96
Period size: 30 Copynumber: 3.9 Consensus size: 30
22530 ACAAAAATTA
22540 AAAGGACTAAAATAGAAAAAACTA-AAACTT
1 AAAGGACTAAAATAGAAAAAA-TAGAAACTT
* * * * *
22570 -AAGAGATTAAAATAGCATAAACAGAAATTT
1 AAAG-GACTAAAATAGAAAAAATAGAAACTT
* * *
22600 AAAGGACTAAAATAGTAAAAATAGATAGTT
1 AAAGGACTAAAATAGAAAAAATAGAAACTT
* *
22630 AAAGGACTAGAACA-ACAAAAATAGAAA
1 AAAGGACTAAAATAGA-AAAAATAGAAA
22657 GTTAGCCTAA
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
29 4 0.06
30 61 0.90
31 3 0.04
ACGTcount: A:0.61, C:0.08, G:0.14, T:0.18
Consensus pattern (30 bp):
AAAGGACTAAAATAGAAAAAATAGAAACTT
Found at i:23510 original size:10 final size:11
Alignment explanation
Indices: 23485--23510 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
23475 CTCTCAGGTT
23485 TTTTTTCTTTC
1 TTTTTTCTTTC
23496 TTTTTTCTTTC
1 TTTTTTCTTTC
23507 TTTT
1 TTTT
23511 GAAATCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:24581 original size:59 final size:59
Alignment explanation
Indices: 24517--24665 Score: 226
Period size: 59 Copynumber: 2.5 Consensus size: 59
24507 AATTCTCTAC
** * * * *
24517 AGGAAATGTTGGTCCCTCAAGTAAGGCGTAGCTGATTTGAAGTGTTGTGAATCGAGCAA
1 AGGAAATGTTAATCCCTCAAGTGAGGTGTAGCTGATTCGAAGTATTGTGAATCGAGCAA
*
24576 AGGAAATGTTAATCCCTCAAGTGAGGTGTTGCTGATTCGAAGTATTGTGAATCGAGCAA
1 AGGAAATGTTAATCCCTCAAGTGAGGTGTAGCTGATTCGAAGTATTGTGAATCGAGCAA
*
24635 ATGAAATGTTAATCCCTCAAGTGAGGTGTAG
1 AGGAAATGTTAATCCCTCAAGTGAGGTGTAG
24666 TTTGTTTTAA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 81 1.00
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.28
Consensus pattern (59 bp):
AGGAAATGTTAATCCCTCAAGTGAGGTGTAGCTGATTCGAAGTATTGTGAATCGAGCAA
Found at i:24762 original size:36 final size:37
Alignment explanation
Indices: 24666--25186 Score: 237
Period size: 38 Copynumber: 14.1 Consensus size: 37
24656 TGAGGTGTAG
**
24666 TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATC
1 TTTGTTTTAAGAAAAACAATCTCAAGCAAGATAAATC
** ** * **
24703 TTCTGTTTCGAGTGAAACTATCTCGGGCAAGATAAATC
1 TT-TGTTTTAAGAAAAACAATCTCAAGCAAGATAAATC
** *
24741 -TTGTTTTAAGAAAAACAATCTCAAGTGAGCTAAATC
1 TTTGTTTTAAGAAAAACAATCTCAAGCAAGATAAATC
*** ** * * **
24777 TTCTGTTCCGAGTGAAACTATCTCAAGCGAGATGCATC
1 TT-TGTTTTAAGAAAAACAATCTCAAGCAAGATAAATC
** ** *
24815 -TTGTTTTAAGAAAAACAATCTTGAGTGATATAAATC
1 TTTGTTTTAAGAAAAACAATCTCAAGCAAGATAAATC
* ** * * *
24851 TTCTGTTTCAAGTGAAACTATCTCAAGCGAGATGAATC
1 TT-TGTTTTAAGAAAAACAATCTCAAGCAAGATAAATC
** *
24889 -TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATAT
1 TTTGTTTTAAGAAAAACAATCTCAAGCAAGATAAAT-C
* * ** * * *
24926 TTTTTTTTGAGTGAAACTATCTCAAGCAGGATGAATC
1 TTTGTTTTAAGAAAAACAATCTCAAGCAAGATAAATC
* ** **
24963 -TTGTTTTAGGAAAAACAATCTCAAGTGATCTAAATC
1 TTTGTTTTAAGAAAAACAATCTCAAGCAAGATAAATC
** ** * * *
24999 TTATGTTTCGAGTGAAACTATCTCAAGCGAGATAAAAGC
1 TT-TGTTTTAAGAAAAACAATCTCAAGCAAGAT-AAATC
** ** * * *
25038 TTATGTTTCGAGTGAAACTATCTCAAGCGAGATGAATC
1 TT-TGTTTTAAGAAAAACAATCTCAAGCAAGATAAATC
* **
25076 -TTGTTTTAAGAAAAACAATCTAAAGTGAGATAAATC
1 TTTGTTTTAAGAAAAACAATCTCAAGCAAGATAAATC
** ** * * * * * *
25112 TTCTGTTTCGAGTGAAACTATCTAAATCGAGATGAGTC
1 TT-TGTTTTAAGAAAAACAATCTCAAGCAAGATAAATC
**
25150 -TTGTTTTAAG-AAAACAATCTCAAGTGAGATAAATC
1 TTTGTTTTAAGAAAAACAATCTCAAGCAAGATAAATC
25185 TT
1 TT
25187 CGTATTAAAT
Statistics
Matches: 354, Mismatches: 117, Indels: 27
0.71 0.23 0.05
Matches are distributed among these distances:
35 18 0.05
36 135 0.38
37 11 0.03
38 153 0.43
39 37 0.10
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.32
Consensus pattern (37 bp):
TTTGTTTTAAGAAAAACAATCTCAAGCAAGATAAATC
Found at i:24789 original size:74 final size:74
Alignment explanation
Indices: 24667--25031 Score: 532
Period size: 74 Copynumber: 4.9 Consensus size: 74
24657 GAGGTGTAGT
**
24667 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCGGGCA
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCA
*
24732 AGATAAATC
66 AGATGAATC
* * *
24741 TTGTTTTAAGAAAAACAATCTCAAGTGAGCTAAATCTTCTGTTCCGAGTGAAACTATCTCAAGCG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCA
*
24806 AGATGCATC
66 AGATGAATC
** * * *
24815 TTGTTTTAAGAAAAACAATCTTGAGTGATATAAATCTTCTGTTTCAAGTGAAACTATCTCAAGCG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCA
24880 AGATGAATC
66 AGATGAATC
* * * *
24889 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATATTTTTTTTTGAGTGAAACTATCTCAAGCA
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCA
*
24954 GGATGAATC
66 AGATGAATC
* ** * *
24963 TTGTTTTAGGAAAAACAATCTCAAGTGATCTAAATCTTATGTTTCGAGTGAAACTATCTCAAGCG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCA
25028 AGAT
66 AGAT
25032 AAAAGCTTAT
Statistics
Matches: 258, Mismatches: 33, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 258 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (74 bp):
TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCA
AGATGAATC
Found at i:25128 original size:74 final size:73
Alignment explanation
Indices: 25013--25187 Score: 260
Period size: 74 Copynumber: 2.4 Consensus size: 73
25003 GTTTCGAGTG
* * * * *
25013 AAACTATCTCAAGCGAGATAAAAGCTTATGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTT
1 AAACAATCTCAAGTGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTAAAGCGAGATGAATCTT
25078 GTTTTAAGAA
65 GTTTTAAG-A
* * *
25088 AAACAATCTAAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTAAATCGAGATGAGTCTTG
1 AAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTAAAGCGAGATGAATCTTG
25153 TTTTAAGA
66 TTTTAAGA
25161 AAACAATCTCAAGTGAGATAAATCTTC
1 AAACAATCTCAAGTGAGATAAATCTTC
25188 GTATTAAATG
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
73 27 0.30
74 48 0.53
75 16 0.18
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.30
Consensus pattern (73 bp):
AAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTAAAGCGAGATGAATCTTG
TTTTAAGA
Found at i:27532 original size:14 final size:14
Alignment explanation
Indices: 27515--27578 Score: 103
Period size: 14 Copynumber: 4.6 Consensus size: 14
27505 ATGGGACTGT
* *
27515 AAAATACAATAAGC
1 AAAATGCAAGAAGC
27529 AAAATGCAAGAAGC
1 AAAATGCAAGAAGC
27543 AAAATGCAAGAAGC
1 AAAATGCAAGAAGC
27557 AAAATGCAAGAAGC
1 AAAATGCAAGAAGC
27571 -AAATGCAA
1 AAAATGCAA
27579 CAAGGAATTG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
13 8 0.17
14 40 0.83
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATGCAAGAAGC
Found at i:31183 original size:22 final size:23
Alignment explanation
Indices: 31136--31184 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
31126 TCATAACCAT
*
31136 TTTTTACAAAACAATTAAATATTA
1 TTTTTACAAAACAATT-AATACTA
31160 TTTTTA-AAAACAATT-ATGACTA
1 TTTTTACAAAACAATTAAT-ACTA
31182 TTT
1 TTT
31185 ATTTTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 2 0.09
22 6 0.26
23 9 0.39
24 6 0.26
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTTTACAAAACAATTAATACTA
Found at i:31619 original size:10 final size:10
Alignment explanation
Indices: 31601--31641 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
31591 CAAATTTTTG
31601 CAAATATAAAA
1 CAAA-ATAAAA
*
31612 TAAAATAAAA
1 CAAAATAAAA
*
31622 CAAAACAAAA
1 CAAAATAAAA
31632 CAAAATAAAA
1 CAAAATAAAA
31642 GTTCACCGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 23 0.88
11 3 0.12
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (10 bp):
CAAAATAAAA
Found at i:38143 original size:4 final size:4
Alignment explanation
Indices: 38134--38160 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
38124 TCTATAATAC
38134 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
38161 GAGACTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:41698 original size:31 final size:31
Alignment explanation
Indices: 41645--41717 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
41635 GATAAGTCGA
*
41645 GACATATGGACAGGATTACCTATGTCCTTCGG
1 GACATATGGACA-GATTACCTATGTCCTTAGG
*
41677 GACATATGGACA-ATTTACCTATGTTCTTAGG
1 GACATATGGACAGA-TTACCTATGTCCTTAGG
*
41708 AACATATGGA
1 GACATATGGA
41718 TAGGTCCTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.03
31 24 0.65
32 12 0.32
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (31 bp):
GACATATGGACAGATTACCTATGTCCTTAGG
Found at i:46459 original size:14 final size:15
Alignment explanation
Indices: 46435--46464 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
46425 GTATGAATGG
46435 TATGATTATATGATA
1 TATGATTATATGATA
46450 TATG-TTATATGATA
1 TATGATTATATGATA
46464 T
1 T
46465 GAGATGGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (15 bp):
TATGATTATATGATA
Found at i:46695 original size:32 final size:31
Alignment explanation
Indices: 46611--46731 Score: 129
Period size: 31 Copynumber: 3.9 Consensus size: 31
46601 GAGTCGAGGG
* *
46611 TTACCTATG-CCTTCCGAGACATAAGGACAAA
1 TTACCTATGTCCTT-CGAGACATATGGACAGA
*
46642 TTACCTATGTCTTTCGAGACATATGGACAGGA
1 TTACCTATGTCCTTCGAGACATATGGACA-GA
* * *
46674 TTGCCTATGTCCTTCGGGACATATGGACAGT
1 TTACCTATGTCCTTCGAGACATATGGACAGA
* *
46705 TTACCTATGTTCTTAG-GAACATATGGA
1 TTACCTATGTCCTTCGAG-ACATATGGA
46732 TAGGTTCTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.01
31 46 0.60
32 30 0.39
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (31 bp):
TTACCTATGTCCTTCGAGACATATGGACAGA
Found at i:50567 original size:2 final size:2
Alignment explanation
Indices: 50560--50599 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
50550 TCCTATTTAA
50560 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
50600 TTTAGCGTAA
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:50854 original size:26 final size:26
Alignment explanation
Indices: 50809--50870 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 26
50799 ATATATATAT
50809 ATATATTATTCTTATATTAACTTAAAA
1 ATAT-TTATTCTTATATTAACTTAAAA
*
50836 ATATTTATTCTTATTTTAACTTAAAA
1 ATATTTATTCTTATATTAACTTAAAA
*
50862 ATATATATT
1 ATATTTATT
50871 TTACTCTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
26 29 0.88
27 4 0.12
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (26 bp):
ATATTTATTCTTATATTAACTTAAAA
Found at i:50880 original size:26 final size:26
Alignment explanation
Indices: 50809--50881 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
50799 ATATATATAT
*
50809 ATATATTATTCTTATATTAACTTAAAA
1 ATATA-TATTCTTATCTTAACTTAAAA
* *
50836 ATATTTATTCTTATTTTAACTTAAAA
1 ATATATATTCTTATCTTAACTTAAAA
50862 ATATATATT-TTACTCTTAAC
1 ATATATATTCTTA-TCTTAAC
50882 GTAATTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
25 3 0.07
26 34 0.83
27 4 0.10
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.51
Consensus pattern (26 bp):
ATATATATTCTTATCTTAACTTAAAA
Found at i:51064 original size:25 final size:23
Alignment explanation
Indices: 51011--51065 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
51001 ACATATATTT
* *
51011 TAATTTATCTTAACATAAAAGTG
1 TAATTTATTTTAACAAAAAAGTG
51034 T-A-TTATTTTAACTAAAAAATGTG
1 TAATTTATTTTAAC-AAAAAA-GTG
51057 TAATTTATT
1 TAATTTATT
51066 CTAATCTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 9 0.35
22 6 0.23
23 5 0.19
24 1 0.04
25 5 0.19
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (23 bp):
TAATTTATTTTAACAAAAAAGTG
Found at i:57971 original size:29 final size:28
Alignment explanation
Indices: 57911--57965 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
57901 ATTTAAGACG
* *
57911 AATTTTTTAAAATTTTAGAAAAAAAAGA
1 AATTTTATAAAATTTAAGAAAAAAAAGA
*
57939 AATTTTATAAAATTTGAAGAATAAAAA
1 AATTTTATAAAATTT-AAGAAAAAAAA
57966 TCAATTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (28 bp):
AATTTTATAAAATTTAAGAAAAAAAAGA
Found at i:58010 original size:16 final size:16
Alignment explanation
Indices: 57975--58007 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
57965 ATCAATTATT
57975 AATA-AAAATATTTAA
1 AATATAAAATATTTAA
57990 AATATAAAATAATTTAA
1 AATATAAAAT-ATTTAA
58007 A
1 A
58008 TATTTTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 5 0.31
17 7 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATATAAAATATTTAA
Found at i:59565 original size:16 final size:16
Alignment explanation
Indices: 59537--59570 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
59527 GAAAATTTAA
59537 ATTTTTTTGATTAATT
1 ATTTTTTTGATTAATT
59553 ATTTATTTT-ATTAATT
1 ATTT-TTTTGATTAATT
59569 AT
1 AT
59571 ATTTATCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
ATTTTTTTGATTAATT
Found at i:59573 original size:18 final size:18
Alignment explanation
Indices: 59552--59599 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
59542 TTTGATTAAT
*
59552 TATTTATTTTATTAATTA
1 TATTTATTTTATAAATTA
* *
59570 TATTTATCTTA-AAATTT
1 TATTTATTTTATAAATTA
59587 TATTTATATTTAT
1 TATTTAT-TTTAT
59600 CTTATATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTATTTTATAAATTA
Found at i:59625 original size:2 final size:2
Alignment explanation
Indices: 59615--59647 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
59605 ATAAAAATTT
59615 TA TA T- 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 TA TA TA
59648 CACATAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59633 original size:28 final size:28
Alignment explanation
Indices: 59580--59635 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
59570 TATTTATCTT
* *
59580 AAAATTTTATTTATATTTATCTTATATA
1 AAAATTTTATTTATATATATCATATATA
59608 AAAATTTTATATTATATATAT-ATATATA
1 AAAATTTTAT-TTATATATATCATATATA
59636 TATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (28 bp):
AAAATTTTATTTATATATATCATATATA
Found at i:59964 original size:23 final size:23
Alignment explanation
Indices: 59938--59985 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
59928 TTTAAATAAG
59938 AAAAATATCAATGAC-TTAATTAT
1 AAAAATATCAAT-ACTTTAATTAT
* *
59961 AAAAATATTAATACTTTTATTAT
1 AAAAATATCAATACTTTAATTAT
59984 AA
1 AA
59986 TTTAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (23 bp):
AAAAATATCAATACTTTAATTAT
Found at i:63943 original size:24 final size:24
Alignment explanation
Indices: 63895--63943 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
63885 TTTATATTAG
**
63895 AAATAAATTTATAAAAAAATTAAA
1 AAATAAATTTATAAAAAAACAAAA
* *
63919 AAATAAATTTTTAAAAATACAAAA
1 AAATAAATTTATAAAAAAACAAAA
63943 A
1 A
63944 TACAAAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATAAATTTATAAAAAAACAAAA
Found at i:66350 original size:40 final size:39
Alignment explanation
Indices: 66295--66371 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
66285 TGACTTAAAA
* * * *
66295 TGAAGGATCAATTGAATAAATAAAGAAATCATGAAAAGT
1 TGAAGGATAAATTGAAGAAATAAAAAAATCATCAAAAGT
*
66334 TGAAGGACTAAATTGAAGAATTAAAAAAATCATCAAAA
1 TGAAGGA-TAAATTGAAGAAATAAAAAAATCATCAAAA
66372 AGAGGAATTG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
39 7 0.22
40 25 0.78
ACGTcount: A:0.56, C:0.06, G:0.16, T:0.22
Consensus pattern (39 bp):
TGAAGGATAAATTGAAGAAATAAAAAAATCATCAAAAGT
Found at i:66989 original size:22 final size:23
Alignment explanation
Indices: 66942--66989 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
66932 TATCACATAC
*
66942 TTTCATCTACATTTATGATATGT
1 TTTCATCTACATTTATGATATAT
* *
66965 TTTCCTCTACCTTT-TGATATAT
1 TTTCATCTACATTTATGATATAT
66987 TTT
1 TTT
66990 AGGTCTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.21, C:0.17, G:0.06, T:0.56
Consensus pattern (23 bp):
TTTCATCTACATTTATGATATAT
Found at i:67639 original size:2 final size:2
Alignment explanation
Indices: 67632--67656 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
67622 AGAAAAGGAA
67632 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
67657 ATTTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76819 original size:10 final size:10
Alignment explanation
Indices: 76806--76834 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
76796 CATCATCTTC
76806 GCTTTCCTCA
1 GCTTTCCTCA
76816 GCTTTCCTCA
1 GCTTTCCTCA
76826 GCTTTCCTC
1 GCTTTCCTC
76835 CATCTCCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.07, C:0.41, G:0.10, T:0.41
Consensus pattern (10 bp):
GCTTTCCTCA
Found at i:81258 original size:12 final size:12
Alignment explanation
Indices: 81241--81265 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
81231 GTCAAATAAT
81241 TTAGGCACCAAA
1 TTAGGCACCAAA
81253 TTAGGCACCAAA
1 TTAGGCACCAAA
81265 T
1 T
81266 GGTGCTTTGT
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:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Done.