Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_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: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 30 of 30
Found at i:6865778 original size:18 final size:19
Alignment explanation
Indices: 6865755--6865796 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
6865745 GAGTAATCCT
*
6865755 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGATAATCTTAC
6865773 ATTCCCACTGATAATCTTAC
1 ATT-CCACTGATAATCTTAC
6865793 ATTC
1 ATTC
6865797 TGTGAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 3 0.14
20 15 0.71
ACGTcount: A:0.26, C:0.29, G:0.07, T:0.38
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:6868621 original size:18 final size:19
Alignment explanation
Indices: 6868600--6868637 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
6868590 TTTGAAATGA
6868600 TTGAAATAAAT-GAAAGGT
1 TTGAAATAAATGGAAAGGT
*
6868618 TTGAATTAAATGGAAAGGT
1 TTGAAATAAATGGAAAGGT
6868637 T
1 T
6868638 GTATGAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.32
Consensus pattern (19 bp):
TTGAAATAAATGGAAAGGT
Found at i:6868705 original size:27 final size:27
Alignment explanation
Indices: 6868647--6868705 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
6868637 TGTATGAAAG
** *
6868647 GAAATGACTGAAATACCCTTGAAGTGT
1 GAAATGACCAAAATACCATTGAAGTGT
*
6868674 AAAATGACCAAAATACCATT-AATGTGT
1 GAAATGACCAAAATACCATTGAA-GTGT
6868701 GAAAT
1 GAAAT
6868706 AACATAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (27 bp):
GAAATGACCAAAATACCATTGAAGTGT
Found at i:6873352 original size:13 final size:13
Alignment explanation
Indices: 6873334--6873358 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6873324 CCTTAGTTAT
6873334 AATGTATAATTAC
1 AATGTATAATTAC
6873347 AATGTATAATTA
1 AATGTATAATTA
6873359 TATATATCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (13 bp):
AATGTATAATTAC
Found at i:6873663 original size:118 final size:119
Alignment explanation
Indices: 6873456--6873697 Score: 423
Period size: 118 Copynumber: 2.0 Consensus size: 119
6873446 AAAAAATATA
6873456 TTTTTTATTCGAAATTTGGTTTGAATCGAGTTTAAGATGATTCTATTTGATTCAAAATTTAACCT
1 TTTTTTATTCGAAATTTGGTTTGAATCGAGTTTAAGATGATTCTATTTGATTCAAAATTTAACCT
* *
6873521 ATATTTGAGATAAAATCTGAATTGGACACGATCATACACAAATATATTTATAAT
66 ATATTTGAGATAAAATCTGAATTGGACACCATCAGACACAAATATATTTATAAT
*
6873575 TTTTTTA-TCGAAATTTGGTTTGAATCGAGTTTAAGATGATTCTATTTGATTCAAAATTTAACTT
1 TTTTTTATTCGAAATTTGGTTTGAATCGAGTTTAAGATGATTCTATTTGATTCAAAATTTAACCT
* * *
6873639 ATTTTTGAGATAAATTTTGAATTGGACACCATCAGACACAAATATATTTATAAT
66 ATATTTGAGATAAAATCTGAATTGGACACCATCAGACACAAATATATTTATAAT
6873693 TTTTT
1 TTTTT
6873698 AATTTTATTC
Statistics
Matches: 117, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
118 110 0.94
119 7 0.06
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (119 bp):
TTTTTTATTCGAAATTTGGTTTGAATCGAGTTTAAGATGATTCTATTTGATTCAAAATTTAACCT
ATATTTGAGATAAAATCTGAATTGGACACCATCAGACACAAATATATTTATAAT
Found at i:6876101 original size:2 final size:2
Alignment explanation
Indices: 6876090--6876125 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6876080 AGGTGGATTC
6876090 TA TA -A TA 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 TA TA TA TA T
6876126 TATTTTAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6879930 original size:185 final size:185
Alignment explanation
Indices: 6879618--6879987 Score: 731
Period size: 185 Copynumber: 2.0 Consensus size: 185
6879608 CTTCGTGGTA
6879618 AAGAAATTGTTGTTATTTCTTGAGGGTCTGCGTTCGAACACCATAGATGTCAGAGGCGTGAGCGT
1 AAGAAATTGTTGTTATTTCTTGAGGGTCTGCGTTCGAACACCATAGATGTCAGAGGCGTGAGCGT
6879683 TTAATGTTAAAATGTTGAGAGTTTATCTTTGAACATTACTGTCTTGTACTTACCCCAAATTAATA
66 TTAATGTTAAAATGTTGAGAGTTTATCTTTGAACATTACTGTCTTGTACTTACCCCAAATTAATA
6879748 AAAATCGAGACTATCTTATGTTAGCTTTTACCTTTTGGAATGCAATTGATTTTGT
131 AAAATCGAGACTATCTTATGTTAGCTTTTACCTTTTGGAATGCAATTGATTTTGT
*
6879803 AAGAAATTGTTGTTATTTCTTGAGGGTCTGCGTTCGAATACCATAGATGTCAGAGGCGTGAGCGT
1 AAGAAATTGTTGTTATTTCTTGAGGGTCTGCGTTCGAACACCATAGATGTCAGAGGCGTGAGCGT
6879868 TTAATGTTAAAATGTTGAGAGTTTATCTTTGAACATTACTGTCTTGTACTTACCCCAAATTAATA
66 TTAATGTTAAAATGTTGAGAGTTTATCTTTGAACATTACTGTCTTGTACTTACCCCAAATTAATA
6879933 AAAATCGAGACTATCTTATGTTAGCTTTTACCTTTTGGAATGCAATTGATTTTGT
131 AAAATCGAGACTATCTTATGTTAGCTTTTACCTTTTGGAATGCAATTGATTTTGT
6879988 CATTCGTGTA
Statistics
Matches: 184, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 184 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (185 bp):
AAGAAATTGTTGTTATTTCTTGAGGGTCTGCGTTCGAACACCATAGATGTCAGAGGCGTGAGCGT
TTAATGTTAAAATGTTGAGAGTTTATCTTTGAACATTACTGTCTTGTACTTACCCCAAATTAATA
AAAATCGAGACTATCTTATGTTAGCTTTTACCTTTTGGAATGCAATTGATTTTGT
Found at i:6880273 original size:5 final size:5
Alignment explanation
Indices: 6880263--6880287 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6880253 ATTATTTTGA
6880263 TTCGG TTCGG TTCGG TTCGG TTCGG
1 TTCGG TTCGG TTCGG TTCGG TTCGG
6880288 GTTTTCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.40, T:0.40
Consensus pattern (5 bp):
TTCGG
Found at i:6880406 original size:18 final size:18
Alignment explanation
Indices: 6880379--6880442 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
6880369 TTTATTGAAA
* *
6880379 AACCGGAAAATCGAACCG
1 AACCGAAAAACCGAACCG
6880397 AACCGAAAAACCTGAACCG
1 AACCGAAAAACC-GAACCG
****
6880416 -TTTAAAAAACCGAACCG
1 AACCGAAAAACCGAACCG
6880433 AACCGAAAAA
1 AACCGAAAAA
6880443 ATCGGTTTCG
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
17 6 0.18
18 22 0.65
19 6 0.18
ACGTcount: A:0.50, C:0.27, G:0.16, T:0.08
Consensus pattern (18 bp):
AACCGAAAAACCGAACCG
Found at i:6880917 original size:19 final size:19
Alignment explanation
Indices: 6880880--6880916 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
6880870 ACATGTCCTC
6880880 AAATTATGTCCATAATTTT
1 AAATTATGTCCATAATTTT
*
6880899 AAATTA-GTCCTTAATTTT
1 AAATTATGTCCATAATTTT
6880917 TTAAACATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (19 bp):
AAATTATGTCCATAATTTT
Found at i:6881004 original size:29 final size:29
Alignment explanation
Indices: 6880915--6881004 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 29
6880905 GTCCTTAATT
6880915 TTTTAAACATTCTAATTTCATCCTCAAAC
1 TTTTAAACATTCTAATTTCATCCTCAAAC
* * ** * *
6880944 TATGACTCTCATTCTAAATTAATCCTTC-AAC
1 TTTTA--AACATTCTAATTTCATCC-TCAAAC
*
6880975 TTTTAAACATTCTAATTTCATCCCCAAAC
1 TTTTAAACATTCTAATTTCATCCTCAAAC
6881004 T
1 T
6881005 AGAAATCTTA
Statistics
Matches: 44, Mismatches: 13, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
28 1 0.02
29 21 0.48
31 20 0.45
32 2 0.05
ACGTcount: A:0.33, C:0.26, G:0.01, T:0.40
Consensus pattern (29 bp):
TTTTAAACATTCTAATTTCATCCTCAAAC
Found at i:6881037 original size:60 final size:60
Alignment explanation
Indices: 6880898--6881023 Score: 175
Period size: 60 Copynumber: 2.1 Consensus size: 60
6880888 TCCATAATTT
* * * *
6880898 TAAATTAGTCCTT-AATTTTTTAAACATTCTAATTTCATCCTCAAACTATGACTCTCATTC
1 TAAATTAATCCTTCAA-CTTTTAAACATTCTAATTTCATCCCCAAACTATGAATCTCATTC
*
6880958 TAAATTAATCCTTCAACTTTTAAACATTCTAATTTCATCCCCAAACTA-GAAATCTTATTC
1 TAAATTAATCCTTCAACTTTTAAACATTCTAATTTCATCCCCAAACTATG-AATCTCATTC
6881018 TAAATT
1 TAAATT
6881024 GGTCTCTGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
59 1 0.02
60 56 0.95
61 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.41
Consensus pattern (60 bp):
TAAATTAATCCTTCAACTTTTAAACATTCTAATTTCATCCCCAAACTATGAATCTCATTC
Found at i:6881321 original size:20 final size:20
Alignment explanation
Indices: 6881296--6881340 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
6881286 TATCCGGAAA
**
6881296 AAAAATCCGGTATGGGGTTT
1 AAAAATCCAATATGGGGTTT
*
6881316 AAAAATCCAATCTGGGGTTT
1 AAAAATCCAATATGGGGTTT
6881336 AAAAA
1 AAAAA
6881341 ATTGGATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.27
Consensus pattern (20 bp):
AAAAATCCAATATGGGGTTT
Found at i:6881722 original size:60 final size:60
Alignment explanation
Indices: 6881669--6881783 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
6881659 CATAGTTTGG
* * *
6881669 GGATGAAAATGAAATGTTTAAAAGTTT-GAGGACTAATTGAAAATTATAGTCATAGTGTAA
1 GGATGAAAATGAAATGTTTAAAAGTTTAG-GGACCAATTGAAAATAAGAGTCATAGTGTAA
** * *
6881729 GGATGCGATTGAAATGTTTAAAAGTTTAGGGACCAATTTAAAATAAGAGTCATAG
1 GGATGAAAATGAAATGTTTAAAAGTTTAGGGACCAATTGAAAATAAGAGTCATAG
6881784 ATTGTGGACA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 46 0.98
61 1 0.02
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (60 bp):
GGATGAAAATGAAATGTTTAAAAGTTTAGGGACCAATTGAAAATAAGAGTCATAGTGTAA
Found at i:6884502 original size:19 final size:20
Alignment explanation
Indices: 6884472--6884510 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
6884462 GAACGCCACC
6884472 CTAGGTGTGTCACTAAATGT
1 CTAGGTGTGTCACTAAATGT
6884492 CTAGG-GTGTCACTAAATGT
1 CTAGGTGTGTCACTAAATGT
6884511 TAAATGTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (20 bp):
CTAGGTGTGTCACTAAATGT
Found at i:6884781 original size:29 final size:29
Alignment explanation
Indices: 6884740--6884808 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
6884730 AATCGTCAAA
6884740 TTACAATAAAAAG-ACAAAATGTTTTAGAAT
1 TTACAAT-AAAAGTACAAAAT-TTTTAGAAT
* ** *
6884770 TTATAATAAAAGTTTAAACTTTTTAGAAT
1 TTACAATAAAAGTACAAAATTTTTAGAAT
6884799 TTACAATAAA
1 TTACAATAAA
6884809 GGAATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 23 0.70
30 10 0.30
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.36
Consensus pattern (29 bp):
TTACAATAAAAGTACAAAATTTTTAGAAT
Found at i:6884862 original size:29 final size:29
Alignment explanation
Indices: 6884817--6884921 Score: 106
Period size: 29 Copynumber: 3.6 Consensus size: 29
6884807 AAGGAATTTT
* * *
6884817 TTTATAAACTATAATAAAGGACAAAA-TT
1 TTTATAAATTACAATAAAGGACAAAACTA
* *
6884845 TGTTGTAAATTACAATAAAGTACAAAACTA
1 T-TTATAAATTACAATAAAGGACAAAACTA
*
6884875 TTTATAAATTACAATAAAGGATAAAAC-A
1 TTTATAAATTACAATAAAGGACAAAACTA
* *
6884903 TTTTATAAATCATAATAAA
1 -TTTATAAATTACAATAAA
6884922 AGGAGACAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
28 2 0.03
29 60 0.94
30 2 0.03
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.32
Consensus pattern (29 bp):
TTTATAAATTACAATAAAGGACAAAACTA
Found at i:6886057 original size:21 final size:21
Alignment explanation
Indices: 6886031--6886109 Score: 113
Period size: 21 Copynumber: 3.8 Consensus size: 21
6886021 TCCGAGTTAC
*
6886031 CCGCGACGGCCGCAATAGCGT
1 CCGCGACGGCCACAATAGCGT
*
6886052 CCGCGACGGCCGCAATAGCGT
1 CCGCGACGGCCACAATAGCGT
* * *
6886073 CCGCGACAGCCATAATAGCGC
1 CCGCGACGGCCACAATAGCGT
6886094 CCGCGACGGCCACAAT
1 CCGCGACGGCCACAAT
6886110 CACGATAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.23, C:0.39, G:0.29, T:0.09
Consensus pattern (21 bp):
CCGCGACGGCCACAATAGCGT
Found at i:6887614 original size:23 final size:23
Alignment explanation
Indices: 6887584--6887643 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
6887574 TTTTGATATG
6887584 TTTATCTCTATCTTTATGACACA
1 TTTATCTCTATCTTTATGACACA
* * *
6887607 TTTATCTCTGTCTTTGTGACACG
1 TTTATCTCTATCTTTATGACACA
6887630 TTTATCTCTA-CTTT
1 TTTATCTCTATCTTT
6887644 TTTATAGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 4 0.12
23 29 0.88
ACGTcount: A:0.18, C:0.22, G:0.08, T:0.52
Consensus pattern (23 bp):
TTTATCTCTATCTTTATGACACA
Found at i:6891655 original size:31 final size:32
Alignment explanation
Indices: 6891620--6891685 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
6891610 AACTATAAAT
6891620 GTTCGAT-AAATTTAATGATC-GTTTCATAATA
1 GTTCGATAAAATTTAATGATCAGTTTC-TAATA
*
6891651 GTTCGATAAAATTTAATGATCATTTTCTAATA
1 GTTCGATAAAATTTAATGATCAGTTTCTAATA
6891683 GTT
1 GTT
6891686 TGAATGAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 7 0.22
32 21 0.66
33 4 0.12
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (32 bp):
GTTCGATAAAATTTAATGATCAGTTTCTAATA
Found at i:6892825 original size:58 final size:59
Alignment explanation
Indices: 6892733--6892889 Score: 192
Period size: 58 Copynumber: 2.7 Consensus size: 59
6892723 TTCTCAGCTT
* * *
6892733 AAATTGGTCCTTAAACTTTTGATTATT-AAGATTTAATCCCTAAATTATGACTCA-TTCA
1 AAATTAGTCCTTAAACTTTTGAATATTCAA-ATTTAATCCCTAAATTATAACTCACTTCA
* * *
6892791 AAATTAGTCCTTAAACTTTTTAATATTCTAATTTAATCCCTAAATTATAACTCACTTTTA
1 AAATTAGTCCTTAAACTTTTGAATATTCAAATTTAATCCCTAAATTATAACTCAC-TTCA
* * * *
6892851 AAATTAGTCCCTAGACTTTTGAATATTCCAATTTCATCC
1 AAATTAGTCCTTAAACTTTTGAATATTCAAATTTAATCC
6892890 TCAAACTCAT
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
58 47 0.55
59 1 0.01
60 37 0.44
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (59 bp):
AAATTAGTCCTTAAACTTTTGAATATTCAAATTTAATCCCTAAATTATAACTCACTTCA
Found at i:6893253 original size:60 final size:60
Alignment explanation
Indices: 6893150--6893315 Score: 201
Period size: 60 Copynumber: 2.8 Consensus size: 60
6893140 TTCTCAACTT
* * * * * * *
6893150 AAATTGGTCCTTAAACTTTTGATTATT-AAGATTTAATCCCTAAATTATGATTCTCTTTCC
1 AAATTAGTCCTTAAACTTTTGAATATTCAA-ATTTCATCACTAAACTATAACTCTCTTTCC
*
6893210 AAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCACTAAACTATAACTCTCTTTCC
1 AAATTAGTCCTTAAACTTTTGAATATTCAAATTTCATCACTAAACTATAACTCTCTTTCC
* * *
6893270 AAATTAGTCCCTAGACTTTTGAATATTCCAATTTCATC-CTCAAACT
1 AAATTAGTCCTTAAACTTTTGAATATTCAAATTTCATCACT-AAACT
6893316 CATCTAAATA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
59 2 0.02
60 90 0.97
61 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (60 bp):
AAATTAGTCCTTAAACTTTTGAATATTCAAATTTCATCACTAAACTATAACTCTCTTTCC
Found at i:6893756 original size:60 final size:59
Alignment explanation
Indices: 6893572--6893756 Score: 187
Period size: 60 Copynumber: 3.1 Consensus size: 59
6893562 TCATATGTCT
* * * * *
6893572 CCAAACTATAATTCTCAGTTT-AAATTGGTCCTTAAACTTTTAATTATTATAATTTAATCC
1 CCAAACTATGATTCTC--TTTCAAATTAGTCCTTAAACTTTTAAATATTCTAATTTCATCC
* ** * * *
6893632 CTAATTTATGA--CTCATTCAAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCA
1 CCAAACTATGATTCTCTTTC-AAATTAGTCCTTAAACTTTTAAATATTCTAATTTCATCC
* * *
6893690 CTAAACTATGATTCTCTTTCCAAATTAGTCCCTATACTTTTAAATATTCTAATTTCATCC
1 CCAAACTATGATTCTCTTT-CAAATTAGTCCTTAAACTTTTAAATATTCTAATTTCATCC
6893750 CCAAACT
1 CCAAACT
6893757 CATCCAAATA
Statistics
Matches: 101, Mismatches: 19, Indels: 10
0.78 0.15 0.08
Matches are distributed among these distances:
56 2 0.02
58 45 0.45
60 53 0.52
61 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (59 bp):
CCAAACTATGATTCTCTTTCAAATTAGTCCTTAAACTTTTAAATATTCTAATTTCATCC
Found at i:6893888 original size:441 final size:441
Alignment explanation
Indices: 6892904--6894202 Score: 2285
Period size: 441 Copynumber: 2.9 Consensus size: 441
6892894 ACTCATCTAA
* * *
6892904 ATATATTAGAGGGTCCCTCGAGTTAACAATCCTTAGGTATGATTATAAATTTATACATCAGAACA
1 ATATATTTGAGGGTCCCTCGAGTTAACAATCCTCAGGTATGATTATAGATTTATACATCAGAACA
*
6892969 ATGAAAACAAGGAAAATTGTGATAGTAATTTAACTGGAATGGTGAATGATGTTAATCATTTGGAC
66 ATGAAAACAAGGAAAATTGTGATAGTAATTTAACTGGAATGATGAATGATGTTAATCATTTGGAC
* *
6893034 AATCTAATGATAATATAAAAGTAGAGGAACCAAAATCAAAATTTTACCTTTATGCTCTGAAAGAT
131 AATCTAATGATAATATAAAAGTAGAGGAACCAAAATCAGAAGTTTACCTTTATGCTCTGAAAGAT
* **
6893099 TTCATTAATTGTTAACTGCATCATATGTCCCCAAACTATATTTCTCAACTTAAATTGGTCCTTAA
196 TTCATTAATTGTTAACTGCATCATATGTCCCCAAACTATAATTCTCAGTTTAAATTGGTCCTTAA
* * *
6893164 ACTTTTGATTATTA-AGATTTAATCCCTAAATTATGATTCTCTTTCCAAATTAGTCCTTAAACTT
261 ACTTTTGATTATTATA-ATTTAATCCCTAATTTATGA--CTCATTCAAAATTAGTCCTTAAACTT
* * *
6893228 TTGAATATTCTAATTTCATCACTAAACTATAACTCTCTTTCCAAATTAGTCCCTAGACTTTTGAA
323 TTGAATATTCTAATTTCATCACTAAACTATGATTCTCTTTCCAAATTAGTCCCTATACTTTTGAA
* * *
6893293 TATTCCAATTTCATCCTCAAACTCATCTAAATATATAATTAGTGTCAGGCAAAT
388 TATTCTAATTTCATCCCCAAACTCATCCAAATATATAATTAGTGTCAGGCAAAT
*
6893347 ATATATTTGAGGGTCCCTCAAGTTAACAATCCTCAGGTATGATTATAGATTTATACATCAGAACA
1 ATATATTTGAGGGTCCCTCGAGTTAACAATCCTCAGGTATGATTATAGATTTATACATCAGAACA
6893412 ATGAAAACAAGGAAAATTGTGATAGTAATTTAACTGGAATGATGAATGATGTTAATCATTTGGAC
66 ATGAAAACAAGGAAAATTGTGATAGTAATTTAACTGGAATGATGAATGATGTTAATCATTTGGAC
*
6893477 AATCTAATGATAATATAAAAGTAGAGAAACCAAAATCAGAAGTTTACCTTTATGCTCTGAAAGAT
131 AATCTAATGATAATATAAAAGTAGAGGAACCAAAATCAGAAGTTTACCTTTATGCTCTGAAAGAT
*
6893542 TTCATTAATTGTTAACTGCATCATATGTCTCCAAACTATAATTCTCAGTTTAAATTGGTCCTTAA
196 TTCATTAATTGTTAACTGCATCATATGTCCCCAAACTATAATTCTCAGTTTAAATTGGTCCTTAA
*
6893607 ACTTTTAATTATTATAATTTAATCCCTAATTTATGACTCATTCAAAATTAGTCCTTAAACTTTTG
261 ACTTTTGATTATTATAATTTAATCCCTAATTTATGACTCATTCAAAATTAGTCCTTAAACTTTTG
*
6893672 AATATTCTAATTTCATCACTAAACTATGATTCTCTTTCCAAATTAGTCCCTATACTTTTAAATAT
326 AATATTCTAATTTCATCACTAAACTATGATTCTCTTTCCAAATTAGTCCCTATACTTTTGAATAT
*
6893737 TCTAATTTCATCCCCAAACTCATCCAAATATATAATTAGTTTCAGGCAAAT
391 TCTAATTTCATCCCCAAACTCATCCAAATATATAATTAGTGTCAGGCAAAT
6893788 ATATATTTGAGGGTCCCTCGAGTTAACAATCCTCAGGTATGATTATAGATTTATACATCAGAACA
1 ATATATTTGAGGGTCCCTCGAGTTAACAATCCTCAGGTATGATTATAGATTTATACATCAGAACA
6893853 ATGAAAACAAGGAAAATTGTGATAGTAATTTAACTGGAATGATGAATGATGTTAATCATTTGGAC
66 ATGAAAACAAGGAAAATTGTGATAGTAATTTAACTGGAATGATGAATGATGTTAATCATTTGGAC
6893918 AATCTAATGATAATATAAAAGTAGAGGAACCAAAATCAGAAGTTTACCTTTATGCTCTGAAAGAT
131 AATCTAATGATAATATAAAAGTAGAGGAACCAAAATCAGAAGTTTACCTTTATGCTCTGAAAGAT
* * *
6893983 TTCATTAATTTTTAACTGTATCATATGTCCCCAAACTATAATTCTTAGTTTAAATTGGTCCTTAA
196 TTCATTAATTGTTAACTGCATCATATGTCCCCAAACTATAATTCTCAGTTTAAATTGGTCCTTAA
6894048 ACTTTTGATTATTATAATTTAATCCCTAATTTATGACTCATTCAAAATTAGTCCTTAAACTTTTG
261 ACTTTTGATTATTATAATTTAATCCCTAATTTATGACTCATTCAAAATTAGTCCTTAAACTTTTG
* * **
6894113 AATATTCTAATTGCATCACTAAACTATGATTCTCTTTCTAAATTAGTCTATATACTTTTGAATAT
326 AATATTCTAATTTCATCACTAAACTATGATTCTCTTTCCAAATTAGTCCCTATACTTTTGAATAT
6894178 TCTAATTTCATCCCCAAACTCATCC
391 TCTAATTTCATCCCCAAACTCATCC
6894203 TCTAAATATA
Statistics
Matches: 819, Mismatches: 36, Indels: 4
0.95 0.04 0.00
Matches are distributed among these distances:
441 538 0.66
443 280 0.34
444 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (441 bp):
ATATATTTGAGGGTCCCTCGAGTTAACAATCCTCAGGTATGATTATAGATTTATACATCAGAACA
ATGAAAACAAGGAAAATTGTGATAGTAATTTAACTGGAATGATGAATGATGTTAATCATTTGGAC
AATCTAATGATAATATAAAAGTAGAGGAACCAAAATCAGAAGTTTACCTTTATGCTCTGAAAGAT
TTCATTAATTGTTAACTGCATCATATGTCCCCAAACTATAATTCTCAGTTTAAATTGGTCCTTAA
ACTTTTGATTATTATAATTTAATCCCTAATTTATGACTCATTCAAAATTAGTCCTTAAACTTTTG
AATATTCTAATTTCATCACTAAACTATGATTCTCTTTCCAAATTAGTCCCTATACTTTTGAATAT
TCTAATTTCATCCCCAAACTCATCCAAATATATAATTAGTGTCAGGCAAAT
Found at i:6894197 original size:60 final size:60
Alignment explanation
Indices: 6894010--6894197 Score: 188
Period size: 60 Copynumber: 3.2 Consensus size: 60
6894000 GTATCATATG
* * * * *
6894010 TCCCCAAACTATAATTCT-TAGTT-TAAATTGGTCCTTAAACTTTTGATTATTATAATTTAA
1 TCCCCAAACTATGATTCTCT--TTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCA
* ** * * *
6894070 TCCCTAATTTATGA--CTCATTCAAAATTAGTCCTTAAACTTTTGAATATTCTAATTGCA
1 TCCCCAAACTATGATTCTCTTTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCA
* * *
6894128 TCACTAAACTATGATTCTCTTTCTAAATTAGT-CTATATACTTTTGAATATTCTAATTTCA
1 TCCCCAAACTATGATTCTCTTTCTAAATTAGTCCT-TAAACTTTTGAATATTCTAATTTCA
6894188 TCCCCAAACT
1 TCCCCAAACT
6894198 CATCCTCTAA
Statistics
Matches: 103, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
57 2 0.02
58 44 0.43
59 2 0.02
60 55 0.53
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.43
Consensus pattern (60 bp):
TCCCCAAACTATGATTCTCTTTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCA
Found at i:6896435 original size:36 final size:36
Alignment explanation
Indices: 6896394--6896469 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
6896384 ATTTTCGGGA
*
6896394 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
6896430 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
6896466 TTTT
1 TTTT
6896470 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:6901429 original size:36 final size:36
Alignment explanation
Indices: 6901388--6901463 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
6901378 GATTTCGGGA
*
6901388 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
6901424 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
6901460 TTTT
1 TTTT
6901464 TAGCTATAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:6903750 original size:35 final size:36
Alignment explanation
Indices: 6903710--6903786 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 36
6903700 GTCGGGTTTA
* *
6903710 GGTCGGTGAAGG-TATATATTTTTCGGGTAAGGTCG
1 GGTCGGTGAAGGATATAGAATTTTCGGGTAAGGTCG
* **
6903745 GGTCGGTGAAGGATGTAGAATTTTCGGGTCGGGTCG
1 GGTCGGTGAAGGATATAGAATTTTCGGGTAAGGTCG
6903781 GGTCGG
1 GGTCGG
6903787 GTTGGCCCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 12 0.33
36 24 0.67
ACGTcount: A:0.17, C:0.10, G:0.43, T:0.30
Consensus pattern (36 bp):
GGTCGGTGAAGGATATAGAATTTTCGGGTAAGGTCG
Done.