Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004919.1 Hibiscus syriacus cultivar Beakdansim tig00011074_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: 69199
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:1904 original size:30 final size:30
Alignment explanation
Indices: 1868--1934 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
1858 TATATTGATT
1868 CTTAAACTTTTCTATAACTCTTTAACTTTC
1 CTTAAACTTTTCTATAACTCTTTAACTTTC
1898 CTTAAACTTTTCTATAACTCTTTAACTTTC
1 CTTAAACTTTTCTATAACTCTTTAACTTTC
1928 CTTAAAC
1 CTTAAAC
1935 ATATGAATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (30 bp):
CTTAAACTTTTCTATAACTCTTTAACTTTC
Found at i:3461 original size:23 final size:23
Alignment explanation
Indices: 3424--3487 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
3414 TAGCTCATAT
*
3424 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAA
* * *
3447 AATTGCACCGTAGTGCCGCGTAA
1 AAATGCACCGAAGTGCCACGTAA
3470 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
3488 TATTAGATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAA
Found at i:25367 original size:23 final size:23
Alignment explanation
Indices: 25341--25409 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
25331 TAGGGTTCTT
* *
25341 TCCTTCGAGACAATTCTACGTGG
1 TCCTTCGGGACATTTCTACGTGG
**
25364 TCCTTCGGGACATTTCTACGCAG
1 TCCTTCGGGACATTTCTACGTGG
25387 TCCTTCGGGACATTTCTACGTGG
1 TCCTTCGGGACATTTCTACGTGG
25410 CACTTTGGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (23 bp):
TCCTTCGGGACATTTCTACGTGG
Found at i:25592 original size:32 final size:32
Alignment explanation
Indices: 25556--25620 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
25546 ATGAATGAAT
*
25556 AGTGTATAATATTACATGTTCTTGTTTGGTGA
1 AGTGTATAATATTACATGTTATTGTTTGGTGA
* * *
25588 AGTGTGTAATGTTACATGTTATTGTTTTGTGA
1 AGTGTATAATATTACATGTTATTGTTTGGTGA
25620 A
1 A
25621 ATATATGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.48
Consensus pattern (32 bp):
AGTGTATAATATTACATGTTATTGTTTGGTGA
Found at i:27379 original size:30 final size:30
Alignment explanation
Indices: 27356--27440 Score: 161
Period size: 30 Copynumber: 2.8 Consensus size: 30
27346 ATCTATCAAC
27356 ACAAGCTTGAAATGCAAGCCATCTAACAGA
1 ACAAGCTTGAAATGCAAGCCATCTAACAGA
*
27386 ACAAGCTTGAAATGCAAGCTATCTAACAGA
1 ACAAGCTTGAAATGCAAGCCATCTAACAGA
27416 ACAAGCTTGAAATGCAAGCCATCTA
1 ACAAGCTTGAAATGCAAGCCATCTA
27441 GCCACATCTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.19
Consensus pattern (30 bp):
ACAAGCTTGAAATGCAAGCCATCTAACAGA
Found at i:27693 original size:4 final size:4
Alignment explanation
Indices: 27684--27708 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
27674 ATTTAACACA
27684 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
27709 TAAAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:36290 original size:15 final size:15
Alignment explanation
Indices: 36270--36326 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 15
36260 TGGTTTTCTA
36270 GAAAATGAATTACTG
1 GAAAATGAATTACTG
* *
36285 GAAAATAAATTATTG
1 GAAAATGAATTACTG
**
36300 GAATTTGAATT-CTG
1 GAAAATGAATTACTG
36314 GAAAATGAATTAC
1 GAAAATGAATTAC
36327 ATTTTTTGAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
14 11 0.33
15 22 0.67
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.32
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:36722 original size:23 final size:23
Alignment explanation
Indices: 36673--36723 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
36663 GTGTTATATT
**
36673 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
36696 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
36719 ATATT
1 ATATT
36724 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:36800 original size:27 final size:28
Alignment explanation
Indices: 36736--36800 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
36726 TAGATTATTA
* *
36736 TATTA-ATATTAAATATATAAATAATAT
1 TATTATATATTAAATATACAAATAAAAT
36763 TATTCAT-TATTAAATATACAAA-AAAAT
1 TATT-ATATATTAAATATACAAATAAAAT
36790 TATTATATATT
1 TATTATATATT
36801 TATTAAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 2 0.06
27 16 0.48
28 15 0.45
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
TATTATATATTAAATATACAAATAAAAT
Found at i:36850 original size:23 final size:23
Alignment explanation
Indices: 36811--36863 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
36801 TATTAAAACA
*
36811 AAAATATAATATCTTATATTATT
1 AAAATATAATATATTATATTATT
*
36834 AAAATATAAT-TGATTATTTTATT
1 AAAATATAATAT-ATTATATTATT
*
36857 ATAATAT
1 AAAATAT
36864 TACAAATAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
AAAATATAATATATTATATTATT
Found at i:36865 original size:31 final size:29
Alignment explanation
Indices: 36824--36897 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 29
36814 ATATAATATC
* * *
36824 TTATATTATTAAAATATAATTGATTATTTTA
1 TTATAATATTAAAATAGAA-T-ATTATATTA
36855 TTATAATATTACAAATAGAATATTATATTA
1 TTATAATATTA-AAATAGAATATTATATTA
*
36885 TAATAAATATTAA
1 TTAT-AATATTAA
36898 TAAATATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 12 0.32
31 18 0.49
32 7 0.19
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (29 bp):
TTATAATATTAAAATAGAATATTATATTA
Found at i:37177 original size:42 final size:42
Alignment explanation
Indices: 37116--37210 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
37106 TTCCTCCAAC
* * ***
37116 CAAACACTGGAAAACATTTTCCGGAAAACGAATTGTGTGAAA
1 CAAACACGGGAAAACATTTTCCGAAAAACGAATTACATGAAA
*
37158 CAAACACGGGAAAATATTTTCCGAAAAACGAATTACATGAAA
1 CAAACACGGGAAAACATTTTCCGAAAAACGAATTACATGAAA
*
37200 CAAACATGGGA
1 CAAACACGGGA
37211 TTTCGAGAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.46, C:0.17, G:0.18, T:0.19
Consensus pattern (42 bp):
CAAACACGGGAAAACATTTTCCGAAAAACGAATTACATGAAA
Found at i:38522 original size:21 final size:21
Alignment explanation
Indices: 38498--38562 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
38488 CTCAGTTTCA
38498 AAATTCGCAACGCGAATATGT
1 AAATTCGCAACGCGAATATGT
** * * **
38519 AAA-TCGCATTGCGATTTTCC
1 AAATTCGCAACGCGAATATGT
*
38539 AATTTCGCAACGCGAATATGT
1 AAATTCGCAACGCGAATATGT
38560 AAA
1 AAA
38563 ATTTGTAATT
Statistics
Matches: 29, Mismatches: 14, Indels: 2
0.64 0.31 0.04
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (21 bp):
AAATTCGCAACGCGAATATGT
Found at i:38594 original size:20 final size:20
Alignment explanation
Indices: 38569--38617 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
38559 TAAAATTTGT
38569 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
38589 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
38609 AATTCGCAA
1 AATTCGCAA
38618 AGCGCGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.24, G:0.14, T:0.16
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:38649 original size:20 final size:19
Alignment explanation
Indices: 38624--38719 Score: 102
Period size: 19 Copynumber: 4.9 Consensus size: 19
38614 GCAAAGCGCG
*
38624 TTTATTTTCGCAACGCGAAT
1 TTTATTTTCGCAACAC-AAT
*
38644 TTTATTTTCGAAACACAAT
1 TTTATTTTCGCAACACAAT
* * *
38663 ATTAATTTCGCAACGCGAAT
1 TTTATTTTCGCAACAC-AAT
*
38683 TTTATTTTCGAAACACAAT
1 TTTATTTTCGCAACACAAT
* *
38702 ATTAATTTCGCAACACAA
1 TTTATTTTCGCAACACAA
38720 ATGTAAACAA
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
19 33 0.53
20 29 0.47
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (19 bp):
TTTATTTTCGCAACACAAT
Found at i:38672 original size:39 final size:39
Alignment explanation
Indices: 38629--38715 Score: 174
Period size: 39 Copynumber: 2.2 Consensus size: 39
38619 GCGCGTTTAT
38629 TTTCGCAACGCGAATTTTATTTTCGAAACACAATATTAA
1 TTTCGCAACGCGAATTTTATTTTCGAAACACAATATTAA
38668 TTTCGCAACGCGAATTTTATTTTCGAAACACAATATTAA
1 TTTCGCAACGCGAATTTTATTTTCGAAACACAATATTAA
38707 TTTCGCAAC
1 TTTCGCAAC
38716 ACAAATGTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (39 bp):
TTTCGCAACGCGAATTTTATTTTCGAAACACAATATTAA
Found at i:39175 original size:20 final size:20
Alignment explanation
Indices: 39138--39175 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39128 ATTCATTCAA
* *
39138 GTTGCGATTTTCATTTTCGC
1 GTTGCGATTTTAAGTTTCGC
39158 GTTGCGATTTTAAGTTTC
1 GTTGCGATTTTAAGTTTC
39176 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATTTTAAGTTTCGC
Found at i:40888 original size:21 final size:21
Alignment explanation
Indices: 40845--40894 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
40835 GTTAGGGGAG
* *
40845 TTACGTGATGAGGTCAATTCT
1 TTACGTGAGGAGGTCAATACT
* *
40866 TTGCGTGAGGAGGTCAGTACT
1 TTACGTGAGGAGGTCAATACT
40887 TTACGTGA
1 TTACGTGA
40895 CGACAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACT
Found at i:40991 original size:21 final size:21
Alignment explanation
Indices: 40967--41006 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40957 ATGACAATGG
*
40967 TACTTTACGTGGTGAGGTATC
1 TACTTTACGTGATGAGGTATC
40988 TACTTTACGTGATGAGGTA
1 TACTTTACGTGATGAGGTA
41007 GCCGCTCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.38
Consensus pattern (21 bp):
TACTTTACGTGATGAGGTATC
Found at i:41345 original size:42 final size:42
Alignment explanation
Indices: 41298--41405 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 42
41288 GCTCGATTCA
* *
41298 CCTATCATCATTCAAGAGGCCTC-GCCTATCGTTCAAAAGGCC
1 CCTATCATCATTCAAGAGGCCCCTGCC-ACCGTTCAAAAGGCC
* * * *
41340 CCTATCATCCTTCAAGACGCCCCTTCCACCGTTCAAGAGGCC
1 CCTATCATCATTCAAGAGGCCCCTGCCACCGTTCAAAAGGCC
* * *
41382 CCTGTCATCGTTCAAGAGGTCCCT
1 CCTATCATCATTCAAGAGGCCCCT
41406 CTCACCATTC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 53 0.96
43 2 0.04
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATCATTCAAGAGGCCCCTGCCACCGTTCAAAAGGCC
Found at i:41353 original size:21 final size:20
Alignment explanation
Indices: 41302--41420 Score: 82
Period size: 21 Copynumber: 5.7 Consensus size: 20
41292 GATTCACCTA
* *
41302 TCATCATTCAAGAGGCCTCGCC
1 TCATCCTTCAAGAGGCC-C-CT
* *
41324 T-ATCGTTCAAAAGGCCCCT
1 TCATCCTTCAAGAGGCCCCT
*
41343 ATCATCCTTCAAGACGCCCCT
1 -TCATCCTTCAAGAGGCCCCT
41364 TCCA-CCGTTCAAGAGGCCCCT
1 T-CATCC-TTCAAGAGGCCCCT
* *
41385 GTCATCGTTCAAGAGGTCCCT
1 -TCATCCTTCAAGAGGCCCCT
41406 CTCA-CCATTCAAGAG
1 -TCATCC-TTCAAGAG
41421 CCCGATTCAC
Statistics
Matches: 79, Mismatches: 11, Indels: 15
0.75 0.10 0.14
Matches are distributed among these distances:
19 1 0.01
20 6 0.08
21 69 0.87
22 3 0.04
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.24
Consensus pattern (20 bp):
TCATCCTTCAAGAGGCCCCT
Found at i:41417 original size:42 final size:42
Alignment explanation
Indices: 41329--41420 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
41319 TCGCCTATCG
* *
41329 TTCAAAAGGCCCCTATCATCCTTCAAGACGCCCCTTCCACCG
1 TTCAAGAGGCCCCTATCATCCTTCAAGACGCCCCTTCCACCA
* * * *
41371 TTCAAGAGGCCCCTGTCATCGTTCAAGAGGTCCC-TCTCACCA
1 TTCAAGAGGCCCCTATCATCCTTCAAGACGCCCCTTC-CACCA
41413 TTCAAGAG
1 TTCAAGAG
41421 CCCGATTCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 2 0.05
42 41 0.95
ACGTcount: A:0.24, C:0.37, G:0.16, T:0.23
Consensus pattern (42 bp):
TTCAAGAGGCCCCTATCATCCTTCAAGACGCCCCTTCCACCA
Found at i:42805 original size:63 final size:63
Alignment explanation
Indices: 42731--42895 Score: 258
Period size: 63 Copynumber: 2.6 Consensus size: 63
42721 CGGGGTACAC
* *
42731 TTTTTTCTTGTTTAATTGATTTATAAAAGTTTATTTGTTTAATTGATGAGGAAATAAGAATTA
1 TTTTTTCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
* * * ***
42794 TTTTTTGTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTA
1 TTTTTTCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
42857 TTTTTTCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
42896 GTTTTAAATT
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 93 1.00
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.55
Consensus pattern (63 bp):
TTTTTTCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
Found at i:43017 original size:20 final size:20
Alignment explanation
Indices: 42989--43068 Score: 106
Period size: 20 Copynumber: 4.0 Consensus size: 20
42979 GTTGCGATGG
* **
42989 TTGCAAAAGTCAAATTCATG
1 TTGCGAAAGTCAAATTCACA
*
43009 TTGCGAAAGTCAAATTCGCA
1 TTGCGAAAGTCAAATTCACA
*
43029 TTGCGAAAGTCAAATTCGCA
1 TTGCGAAAGTCAAATTCACA
*
43049 TTGCGATAGTCAAATTCACA
1 TTGCGAAAGTCAAATTCACA
43069 ACACGAAAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (20 bp):
TTGCGAAAGTCAAATTCACA
Found at i:43095 original size:40 final size:40
Alignment explanation
Indices: 42994--43095 Score: 123
Period size: 40 Copynumber: 2.5 Consensus size: 40
42984 GATGGTTGCA
** * * ***
42994 AAAGTCAAATTCATGTTGCGAAAGTCAAATTCGCATTGCG
1 AAAGTCAAATTCGCGTTGCGATAGTCAAATTCACAACACG
*
43034 AAAGTCAAATTCGCATTGCGATAGTCAAATTCACAACACG
1 AAAGTCAAATTCGCGTTGCGATAGTCAAATTCACAACACG
*
43074 AAAGTTAAATTCGCGTTGCGAT
1 AAAGTCAAATTCGCGTTGCGAT
43096 TTCGCATTTC
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (40 bp):
AAAGTCAAATTCGCGTTGCGATAGTCAAATTCACAACACG
Found at i:43130 original size:29 final size:29
Alignment explanation
Indices: 43105--43160 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
43095 TTTCGCATTT
*
43105 CGAATTTGACTTTCGTAACAATCGCAATG
1 CGAATTTGACTTTCGCAACAATCGCAATG
43134 CGAATTTGACTTTCGCAACAATCGCAA
1 CGAATTTGACTTTCGCAACAATCGCAA
43161 CAACAAATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (29 bp):
CGAATTTGACTTTCGCAACAATCGCAATG
Found at i:45730 original size:24 final size:24
Alignment explanation
Indices: 45696--45749 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
45686 CTGAAACATT
45696 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
45720 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
45744 ATCAAA
1 ATCAAA
45750 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:45763 original size:24 final size:24
Alignment explanation
Indices: 45696--45763 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
45686 CTGAAACATT
* * *
45696 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
45720 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
45744 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
45764 TAGTACTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:46512 original size:16 final size:15
Alignment explanation
Indices: 46490--46528 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
46480 GAAATCATTG
46490 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
46506 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
46521 AAAAATTA
1 AAAAATTA
46529 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:46731 original size:40 final size:40
Alignment explanation
Indices: 46686--46782 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
46676 CTAAAACCTA
** **
46686 TTGCGAAATTAAAATTCGTTTTGTGAATTCAAAAATCGAG
1 TTGCGAAATTAAAATTCGCGTTACGAATTCAAAAATCGAG
** *
46726 TTGCGAAAACAAAATTCGCGTTACGAATTCAGAAATCGAG
1 TTGCGAAATTAAAATTCGCGTTACGAATTCAAAAATCGAG
* *
46766 TTGCGAATTTGAAATTC
1 TTGCGAAATTAAAATTC
46783 AGTGTTGCGA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (40 bp):
TTGCGAAATTAAAATTCGCGTTACGAATTCAAAAATCGAG
Found at i:46774 original size:20 final size:20
Alignment explanation
Indices: 46710--46815 Score: 81
Period size: 20 Copynumber: 5.2 Consensus size: 20
46700 TTCGTTTTGT
*
46710 GAATTCAAAAATCGAGTTGC
1 GAATTCAGAAATCGAGTTGC
** * *
46730 GAAAACA-AAATTCGCGTTAC
1 GAATTCAGAAA-TCGAGTTGC
46750 GAATTCAGAAATCGAGTTGC
1 GAATTCAGAAATCGAGTTGC
* *
46770 GAATT-TGAAATTCAGTGTTGC
1 GAATTCAGAAA-TC-GAGTTGC
** *
46791 GAATTTGGAAATCGCGTTGC
1 GAATTCAGAAATCGAGTTGC
46811 GAATT
1 GAATT
46816 TGGAAAATCG
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
19 7 0.10
20 42 0.61
21 16 0.23
22 4 0.06
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (20 bp):
GAATTCAGAAATCGAGTTGC
Found at i:46816 original size:20 final size:20
Alignment explanation
Indices: 46741--46898 Score: 124
Period size: 20 Copynumber: 7.8 Consensus size: 20
46731 AAAACAAAAT
* **
46741 TCGCGTTACGAATTCAGAAA
1 TCGCGTTGCGAATTTGGAAA
*
46761 TCGAGTTGCGAATTT-GAAA
1 TCGCGTTGCGAATTTGGAAA
*
46780 TTCAGTGTTGCGAATTTGGAAA
1 -TC-GCGTTGCGAATTTGGAAA
46802 TCGCGTTGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGG-AAA
** ** *
46823 TCGCAATGCG-ATTTACATAT
1 TCGCGTTGCGAATTTGGA-AA
46843 TCGCGTTGCGAATTTGGAAA
1 TCGCGTTGCGAATTTGGAAA
* * **
46863 -CTGAGTTGCGAAATTGGAGT
1 TC-GCGTTGCGAATTTGGAAA
46883 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
46899 TTGGTCATTT
Statistics
Matches: 109, Mismatches: 21, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
19 6 0.06
20 68 0.62
21 31 0.28
22 4 0.04
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGGAAA
Found at i:46833 original size:41 final size:40
Alignment explanation
Indices: 46757--46898 Score: 119
Period size: 41 Copynumber: 3.5 Consensus size: 40
46747 TACGAATTCA
* * *
46757 GAAATCGAGTTGCGAATTT-GAAATTCAGTGTTGCGAATTTG
1 GAAATCGCGTTGCGAATTTGGAAAATC-G-ATTGCGAATTTG
* *
46798 GAAATCGCGTTGCGAATTTGGAAAATCGCAATGCG-ATTTA
1 GAAATCGCGTTGCGAATTTGGAAAATCG-ATTGCGAATTTG
* * * *
46838 CATATTCGCGTTGCGAATTTGGAAACT-GAGTTGCGAAATTG
1 GA-AATCGCGTTGCGAATTTGGAAAATCGA-TTGCGAATTTG
**
46879 GAGTTCGCGTTGCGAATTTG
1 GAAATCGCGTTGCGAATTTG
46899 TTGGTCATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 9
0.78 0.13 0.08
Matches are distributed among these distances:
39 1 0.01
40 27 0.33
41 49 0.59
42 6 0.07
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.32
Consensus pattern (40 bp):
GAAATCGCGTTGCGAATTTGGAAAATCGATTGCGAATTTG
Found at i:47339 original size:15 final size:15
Alignment explanation
Indices: 47319--47348 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
47309 TAAGCAAAAA
47319 AAAGAAAAAAAAAGG
1 AAAGAAAAAAAAAGG
47334 AAAGAAAAAAAAAGG
1 AAAGAAAAAAAAAGG
47349 CTTTAACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAAAGG
Found at i:49614 original size:3 final size:3
Alignment explanation
Indices: 49606--49637 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
49596 TTTTTCGTCA
49606 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
49638 TATTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:49644 original size:3 final size:3
Alignment explanation
Indices: 49638--49744 Score: 160
Period size: 3 Copynumber: 35.7 Consensus size: 3
49628 ACTACTACTA
*
49638 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
49686 TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TGT TGT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
49734 TGT TAT TAT TA
1 TAT TAT TAT TA
49745 AATTTCATTT
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 98 1.00
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:52100 original size:131 final size:131
Alignment explanation
Indices: 51844--52201 Score: 361
Period size: 131 Copynumber: 2.8 Consensus size: 131
51834 TGAGAATAAT
* * * * *
51844 AATATCTTTTCATTTCGGTCGGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTC----ATTCT
1 AATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGTTATGAAAGGTCATTTATTCT
* * * * * * *
51905 -TGATTGGAAATGATTTGATATTATCGTTTTCTCTCGAATTAATATTGATTTTTAAGGTGGAATA
66 CT-ATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGCTGAAATA
*
51969 GT
130 GC
* * * * *
51971 GATATCTCTTCATTTCGATTGGATTAATAAATGAATGCTTTAAGTTATGATAGATCATTTATTCT
1 AATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGTTATGAAAGGTCATTTATTCT
* * *
52036 CTATTGGAAATCATTAGATATTATCGTTTTCACTTGAATCGATATTGAATTTTAAGACT-AAATA
66 CTATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAG-CTGAAATA
52100 GC
130 GC
* * * * * * *
52102 AATATCTCTTTATTTCTATTGGGGTATTAAATGATTGTTTTAA-TGCACGAAAGGTCATTTATTC
1 AATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGT-TATGAAAGGTCATTTATTC
* * *
52166 TCGATCGGAAGTAATTAGATATTATCGTTTTCACTC
65 TCTATTGGAAATAATTAGATATTATCGTTTTCACTC
52202 TTAAAATAAT
Statistics
Matches: 188, Mismatches: 36, Indels: 10
0.80 0.15 0.04
Matches are distributed among these distances:
127 47 0.25
130 1 0.01
131 138 0.73
132 2 0.01
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (131 bp):
AATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGTTATGAAAGGTCATTTATTCT
CTATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGCTGAAATAG
C
Found at i:53109 original size:17 final size:17
Alignment explanation
Indices: 53087--53124 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
53077 TCCATAGGGT
53087 CCTCATGATGGTTTTCA
1 CCTCATGATGGTTTTCA
53104 CCTCATGATGGTTTTCA
1 CCTCATGATGGTTTTCA
53121 CCTC
1 CCTC
53125 CGTATAGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.16, C:0.29, G:0.16, T:0.39
Consensus pattern (17 bp):
CCTCATGATGGTTTTCA
Done.