Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000731.1 Hibiscus syriacus cultivar Beakdansim tig00001418_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: 166303
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:141654 original size:16 final size:15
Alignment explanation
Indices: 141614--141703 Score: 55
Period size: 16 Copynumber: 5.9 Consensus size: 15
141604 CAACTATTTT
*
141614 AAATCATT-AGTATC
1 AAATCATTAAATATC
* *
141628 AAATAACTAAATCATC
1 AAATCATTAAAT-ATC
*
141644 AAATCATTAAATATTT
1 AAATCATTAAATA-TC
141660 AAATCA-T---TATC
1 AAATCATTAAATATC
141671 AAATCATTACTAAATCATC
1 AAATCA-T--TAAAT-ATC
141690 AAATCATTAAATAT
1 AAATCATTAAATAT
141704 TTAATTCATT
Statistics
Matches: 58, Mismatches: 7, Indels: 21
0.67 0.08 0.24
Matches are distributed among these distances:
11 7 0.12
12 2 0.03
14 6 0.10
15 7 0.12
16 25 0.43
18 2 0.03
19 9 0.16
ACGTcount: A:0.50, C:0.14, G:0.01, T:0.34
Consensus pattern (15 bp):
AAATCATTAAATATC
Found at i:141683 original size:46 final size:46
Alignment explanation
Indices: 141633--141724 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
141623 GTATCAAATA
141633 ACTAAATCATCAAATCATTAAATATTTAAATCATTATCAAATCATT
1 ACTAAATCATCAAATCATTAAATATTTAAATCATTATCAAATCATT
* *
141679 ACTAAATCATCAAATCATTAAATATTTAATTCATTATTAAATCATT
1 ACTAAATCATCAAATCATTAAATATTTAAATCATTATCAAATCATT
141725 TTTATAATGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (46 bp):
ACTAAATCATCAAATCATTAAATATTTAAATCATTATCAAATCATT
Found at i:141745 original size:26 final size:26
Alignment explanation
Indices: 141711--141900 Score: 202
Period size: 26 Copynumber: 7.6 Consensus size: 26
141701 TATTTAATTC
* *
141711 ATTATTAAATCATTTTTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
141737 ATTAAT-AAATCATTATTATAATGATT
1 ATT-ATCAAATCATTATTATAATGATT
*
141763 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
*
141789 ATTATCAAATCATTACTA-AAT-ATTT
1 ATTATCAAATCATTATTATAATGA-TT
* * * *
141814 GTTCATTAAAT-A--GTTA-AATCATT
1 ATT-ATCAAATCATTATTATAATGATT
141837 A-T-T-AAATCATTATTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
*
141860 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
141886 ATTATCAAATCATTA
1 ATTATCAAATCATTA
141901 CTAAATCATC
Statistics
Matches: 142, Mismatches: 10, Indels: 24
0.81 0.06 0.14
Matches are distributed among these distances:
19 4 0.03
20 2 0.01
22 4 0.03
23 14 0.10
24 3 0.02
25 11 0.08
26 102 0.72
27 2 0.01
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (26 bp):
ATTATCAAATCATTATTATAATGATT
Found at i:141842 original size:123 final size:124
Alignment explanation
Indices: 141665--141903 Score: 383
Period size: 123 Copynumber: 1.9 Consensus size: 124
141655 TATTTAAATC
* * *
141665 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAATTCATTATTAAATCATTTTTAT
1 ATTATCAAATCATTACTAAATCATCAAATCATTAAATAGTTAAATCATTATTAAATCATTATTAT
*
141730 AATGATTATTAAT-AAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATT
66 AATGATTATT-ATCAAATCATTACTATAATGATTATTATCAAATCATTACTATAATGATT
****
141789 ATTATCAAATCATTACTAAAT-ATTTGTTCATTAAATAGTTAAATCATTATTAAATCATTATTAT
1 ATTATCAAATCATTACTAAATCATCAAATCATTAAATAGTTAAATCATTATTAAATCATTATTAT
141853 AATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTA
66 AATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTA
141904 AATCATCAAA
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
122 2 0.02
123 83 0.78
124 21 0.20
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (124 bp):
ATTATCAAATCATTACTAAATCATCAAATCATTAAATAGTTAAATCATTATTAAATCATTATTAT
AATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTATAATGATT
Found at i:141856 original size:97 final size:98
Alignment explanation
Indices: 141737--141958 Score: 374
Period size: 97 Copynumber: 2.3 Consensus size: 98
141727 TATAATGATT
*
141737 ATTAATAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
1 ATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
****
141802 TACTAAAT-ATTTGTTCATTAAATAGTTAAATC
66 TACTAAATCATCAAATCATTAAATAGTTAAATC
141834 ATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
1 ATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
*
141899 TACTAAATCATCAAATCATTAAATATTTAAATC
66 TACTAAATCATCAAATCATTAAATAGTTAAATC
*
141932 ATTATTAAATCATTTTTATAATGATTA
1 ATTATTAAATCATTATTATAATGATTA
141959 ATAAATACAT
Statistics
Matches: 117, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
97 72 0.62
98 45 0.38
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (98 bp):
ATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
TACTAAATCATCAAATCATTAAATAGTTAAATC
Found at i:141915 original size:71 final size:70
Alignment explanation
Indices: 141766--141919 Score: 181
Period size: 71 Copynumber: 2.2 Consensus size: 70
141756 AATGATTATT
* *
141766 ATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATATTTGTTCATTAAATAGTTAA
1 ATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATATTTATTCATCAAATAGTTAA
*
141831 ATCATT
66 A-CATC
* *
141837 ATTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGA-TTATT-ATCAAATCA-T
1 ATCAAATCATTACTATAATGATTATTATCAAATCATTACTA-AAT-ATTTATTCATCAAAT-AGT
141899 TACTAA-ATC
63 TA--AACATC
141908 ATCAAATCATTA
1 ATCAAATCATTA
141920 AATATTTAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
71 61 0.85
72 8 0.11
73 3 0.04
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.42
Consensus pattern (70 bp):
ATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATATTTATTCATCAAATAGTTAA
ACATC
Found at i:144840 original size:26 final size:24
Alignment explanation
Indices: 144782--144840 Score: 57
Period size: 26 Copynumber: 2.3 Consensus size: 24
144772 CTAATAAACC
*
144782 TAATAATGATTTGATCATTACTAT
1 TAATAATGATTTGATCATTAATAT
144806 TAATCTAATGATTTGAT-ATTTAATGATT
1 TAA--TAATGATTTGATCA-TTAAT-A-T
144834 TAATAAT
1 TAATAAT
144841 AATATGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
24 3 0.10
25 1 0.03
26 20 0.69
27 1 0.03
28 4 0.14
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATCATTAATAT
Found at i:145620 original size:41 final size:44
Alignment explanation
Indices: 145575--145683 Score: 134
Period size: 47 Copynumber: 2.5 Consensus size: 44
145565 GTTTAAAGAC
*
145575 ACTAACAAATTAATTAATATTTTTTATAT-T-TA-ATAACTTAA
1 ACTAACAAACTAATTAATATTTTTTATATATATATATAACTTAA
*
145616 ACTAAGAAACTAATTAACTAATTTTTTATATATAATATATAACTTAA
1 ACTAACAAACTAATTAA-T-ATTTTTTATATAT-ATATATAACTTAA
*
145663 ACTAATAAACTAATATAATAT
1 ACTAACAAACTAAT-TAATAT
145684 AACTTAAACT
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
41 15 0.26
42 1 0.02
43 11 0.19
44 1 0.02
46 4 0.07
47 23 0.40
48 3 0.05
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.41
Consensus pattern (44 bp):
ACTAACAAACTAATTAATATTTTTTATATATATATATAACTTAA
Found at i:145689 original size:28 final size:28
Alignment explanation
Indices: 145652--145705 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
145642 TATATATAAT
*
145652 ATATAACTTAAACTAATAAACTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
*
145680 ATATAACTTAAACTTACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
145706 ATTTATACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:145712 original size:28 final size:28
Alignment explanation
Indices: 145647--145712 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
145637 TTTTTTATAT
*
145647 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
*
145675 AT-ATAATATAACTTAAACTTACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
145703 ATAATTTATA
1 ATAATATATA
145713 CTAACAAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.35
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:146072 original size:32 final size:32
Alignment explanation
Indices: 146036--146099 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
146026 GGAATCTCTG
146036 AGCTATGAGCTATGATGCAACGCATGCATGCA
1 AGCTATGAGCTATGATGCAACGCATGCATGCA
146068 AGCTATGAGCTATGATGCAACGCATGCATGCA
1 AGCTATGAGCTATGATGCAACGCATGCATGCA
146100 GCAGGACCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (32 bp):
AGCTATGAGCTATGATGCAACGCATGCATGCA
Found at i:146219 original size:15 final size:15
Alignment explanation
Indices: 146199--146378 Score: 137
Period size: 15 Copynumber: 11.1 Consensus size: 15
146189 CATCCCCTCC
146199 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
146214 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* * *
146229 CGTCCAATGCACCATCCCCTC
1 C--CCCATG---CATTCCC-A
146250 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
146265 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
146280 CGTCCCATGCATCCCCTC
1 C--CCCATGCATTCCC-A
146298 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
146313 CATCCCATG-TTGATCCCTC
1 C--CCCATGCAT--TCCC-A
146332 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
146347 CCCCATGCATCCCCTC
1 CCCCATGCATTCCC-A
146363 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
146378 C
1 C
146379 GTCCCATGTT
Statistics
Matches: 131, Mismatches: 18, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
15 47 0.36
16 36 0.27
17 29 0.22
18 6 0.05
19 6 0.05
20 6 0.05
21 1 0.01
ACGTcount: A:0.18, C:0.53, G:0.08, T:0.21
Consensus pattern (15 bp):
CCCCATGCATTCCCA
Found at i:146274 original size:51 final size:51
Alignment explanation
Indices: 146174--146313 Score: 241
Period size: 51 Copynumber: 2.8 Consensus size: 51
146164 ATGCACAGTT
146174 CCACGTCCAATGCACCATCCCCTCCCCCCATGCATTCCCACCCCATGCATTC
1 CCACGTCCAATGCACCATCCCCT-CCCCCATGCATTCCCACCCCATGCATTC
146226 CCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCACCCCATGCATTC
1 CCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCACCCCATGCATTC
*
146277 CCACGTCCCATG---CATCCCCTCCCCCATGCATTCCCAC
1 CCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCAC
146314 ATCCCATGTT
Statistics
Matches: 87, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
48 25 0.29
51 39 0.45
52 23 0.26
ACGTcount: A:0.19, C:0.54, G:0.08, T:0.19
Consensus pattern (51 bp):
CCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCACCCCATGCATTC
Found at i:146342 original size:82 final size:83
Alignment explanation
Indices: 146200--146378 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 83
146190 ATCCCCTCCC
* *
146200 CCCATGCATTCCCACCCCATGCATTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCA
1 CCCATGCATCCCCACCCCATGCATTCCCACATCCAATGCACCATCCCCTCCCCCATGCATTCCCA
146265 CCCCATGCATTCCCACGT
66 CCCCATGCATTCCCACGT
* * ***
146283 CCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATG-TTGAT-CCCTCCCCCATGCATTCCC
1 CCCATGCATCCCC-ACCCCATGCATTCCCACATCCAATGCACCATCCCCTCCCCCATGCATTCCC
* * *
146346 ACCCCATGCATCCCCTC-C
65 ACCCCATGCATTCCCACGT
*
146364 CCCATGCATTCCCAC
1 CCCATGCATCCCCAC
146379 GTCCCATGTT
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
80 1 0.01
81 12 0.14
82 34 0.41
83 14 0.17
84 22 0.27
ACGTcount: A:0.18, C:0.53, G:0.08, T:0.21
Consensus pattern (83 bp):
CCCATGCATCCCCACCCCATGCATTCCCACATCCAATGCACCATCCCCTCCCCCATGCATTCCCA
CCCCATGCATTCCCACGT
Found at i:146362 original size:65 final size:66
Alignment explanation
Indices: 146265--146391 Score: 229
Period size: 65 Copynumber: 1.9 Consensus size: 66
146255 TGCATTCCCA
146265 CCCCATGCATTCCCACGTCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGATCCC
1 CCCCATGCATTCCCACG-CCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGATCCC
146330 TC
65 TC
*
146332 CCCCATGCATTCCCAC-CCCATGCATCCCCTCCCCCATGCATTCCCACGTCCCATGTTGAT
1 CCCCATGCATTCCCACGCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGAT
146392 TGCATGGCAT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 43 0.73
67 16 0.27
ACGTcount: A:0.17, C:0.50, G:0.09, T:0.24
Consensus pattern (66 bp):
CCCCATGCATTCCCACGCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGATCCCT
C
Found at i:146409 original size:45 final size:45
Alignment explanation
Indices: 146353--146442 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
146343 CCCACCCCAT
146353 GCATCCCCTCCCCCATGCATTCCCACGTCCCATGTTGATTGCATG
1 GCATCCCCTCCCCCATGCATTCCCACGTCCCATGTTGATTGCATG
146398 GCATCCCCTCCCCCATGCATTCCCACGTCCCATGTTGATTGCATG
1 GCATCCCCTCCCCCATGCATTCCCACGTCCCATGTTGATTGCATG
146443 TCCCATGTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.16, C:0.42, G:0.16, T:0.27
Consensus pattern (45 bp):
GCATCCCCTCCCCCATGCATTCCCACGTCCCATGTTGATTGCATG
Found at i:146467 original size:17 final size:18
Alignment explanation
Indices: 146424--146477 Score: 101
Period size: 18 Copynumber: 3.1 Consensus size: 18
146414 GCATTCCCAC
146424 GTCCCATGTTGATTGCAT
1 GTCCCATGTTGATTGCAT
146442 GTCCCATGTTGATTGCAT
1 GTCCCATGTTGATTGCAT
146460 GT-CCATGTTGATTGCAT
1 GTCCCATGTTGATTGCAT
146477 G
1 G
146478 GCCCTATTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 16 0.44
18 20 0.56
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (18 bp):
GTCCCATGTTGATTGCAT
Found at i:146532 original size:29 final size:29
Alignment explanation
Indices: 146499--146566 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
146489 TAATACACAC
146499 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
146528 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
146557 AGGTCGCCCG
1 AGGTCGCCCG
146567 CCAAGACCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.16, C:0.38, G:0.32, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:151407 original size:2 final size:2
Alignment explanation
Indices: 151400--151442 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
151390 ATCTCTTCTG
151400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
151442 A
1 A
151443 AGCACACACG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:161151 original size:23 final size:23
Alignment explanation
Indices: 161125--161170 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
161115 TGAGGTGTTA
*
161125 ATGATTCAACTCCATATGTGATG
1 ATGATCCAACTCCATATGTGATG
*
161148 ATGATCCAACTCCTTATGTGATG
1 ATGATCCAACTCCATATGTGATG
161171 GACGAGCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (23 bp):
ATGATCCAACTCCATATGTGATG
Found at i:161325 original size:245 final size:245
Alignment explanation
Indices: 160895--161393 Score: 980
Period size: 245 Copynumber: 2.0 Consensus size: 245
160885 GGTTTACCCA
*
160895 ATGTGATGTTGATCCAACTCCTTATGTGATGGACGAGCAAAATGATGAGACTGATTCAACGCCTT
1 ATGTGATGATGATCCAACTCCTTATGTGATGGACGAGCAAAATGATGAGACTGATTCAACGCCTT
160960 ATATGATGGACGAGCAAAAGTCAGTGTTTTCCAACTCCTTATACGATGAAAACAAGCTAAGGTTG
66 ATATGATGGACGAGCAAAAGTCAGTGTTTTCCAACTCCTTATACGATGAAAACAAGCTAAGGTTG
*
161025 AACAAGTTCTTTTCATTATGAACTTCTTCTTCCTTATTGGATGAGTTCTTCTCATTACAAACTCT
131 AACAAGTTCTTTTCATTATGAACTTCTTCTTCCTTATCGGATGAGTTCTTCTCATTACAAACTCT
161090 CCACTGGAAATTTTGATCCCTCGAGTGAGGTGTTAATGATTCAACTCCAT
196 CCACTGGAAATTTTGATCCCTCGAGTGAGGTGTTAATGATTCAACTCCAT
161140 ATGTGATGATGATCCAACTCCTTATGTGATGGACGAGCAAAATGATGAGACTGATTCAACGCCTT
1 ATGTGATGATGATCCAACTCCTTATGTGATGGACGAGCAAAATGATGAGACTGATTCAACGCCTT
161205 ATATGATGGACGAGCAAAAGTCAGTGTTTTCCAACTCCTTATACGATGAAAACAAGCTAAGGTTG
66 ATATGATGGACGAGCAAAAGTCAGTGTTTTCCAACTCCTTATACGATGAAAACAAGCTAAGGTTG
161270 AACAAGTTCTTTTCATTATGAACTTCTTCTTCCTTATCGGATGAGTTCTTCTCATTACAAACTCT
131 AACAAGTTCTTTTCATTATGAACTTCTTCTTCCTTATCGGATGAGTTCTTCTCATTACAAACTCT
161335 CCACTGGAAATTTTGATCCCTCGAGTGAGGTGTTAATGATTCAACTCCAT
196 CCACTGGAAATTTTGATCCCTCGAGTGAGGTGTTAATGATTCAACTCCAT
161385 ATGTGATGA
1 ATGTGATGA
161394 ATCAAGTTAA
Statistics
Matches: 252, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
245 252 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (245 bp):
ATGTGATGATGATCCAACTCCTTATGTGATGGACGAGCAAAATGATGAGACTGATTCAACGCCTT
ATATGATGGACGAGCAAAAGTCAGTGTTTTCCAACTCCTTATACGATGAAAACAAGCTAAGGTTG
AACAAGTTCTTTTCATTATGAACTTCTTCTTCCTTATCGGATGAGTTCTTCTCATTACAAACTCT
CCACTGGAAATTTTGATCCCTCGAGTGAGGTGTTAATGATTCAACTCCAT
Found at i:161514 original size:139 final size:138
Alignment explanation
Indices: 161257--161904 Score: 842
Period size: 139 Copynumber: 4.7 Consensus size: 138
161247 ACGATGAAAA
* * *
161257 CAAGCTAAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCTTCCTTATCGGATGAGTTCTTCT
1 CAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCT
** * *
161322 CATTACAAACTCTCCACTGGAAATTTTGATCCCTCGAGTGAGGTGTTAATGATTCAACTCCATAT
66 CATTATGAACTCTTCACTGGAAATGTTGATCCCTCGAGTGAGGTGTT-ATGATTCAACTCCATAT
161387 GTGATGAAT
130 GTGATGAAT
* * * * * *
161396 CAAGTTAAGGTTGAACAAGTTCATATCATTATGAACTTTTTCTCCCTCATTGGATAAGTTCTTCT
1 CAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCT
161461 CATTATGAACTCTTCACTGGAAATGTTGATCCCTCGAGTGAGGTGTTACTGATTCAACTCCATAT
66 CATTATGAACTCTTCACTGGAAATGTTGATCCCTCGAGTGAGGTGTTA-TGATTCAACTCCATAT
161526 GTGATGAA-
130 GTGATGAAT
* * * *
161534 CTGAGCTAAGGGTGAACAAGTTCTTCTCATTATGAATTTATTCTCCCTCATCGGATGAGTTCTTC
1 C-AAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTC
* * * * *
161599 TCATTATGAATTCTTCACTGGAAATGTTGATCCTTCGAGTGAGGTGTTGTTGATTTAACTCTATA
65 TCATTATGAACTCTTCACTGGAAATGTTGATCCCTCGAGTGAGGTGTT-ATGATTCAACTCCATA
*
161664 TGCGATGAAT
129 TGTGATGAAT
* *
161674 CGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTC-T-T
1 CAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCT
* * * *
161737 CATTATGAACTCTCCATTGGAAATGTTGATCCCTCTAGTGAGGTGTTGATAATTCAACT-C-TAT
66 CATTATGAACTCTTCACTGGAAATGTTGATCCCTCGAGTGAGGTGTT-ATGATTCAACTCCATAT
161800 GTG-TGAAT
130 GTGATGAAT
* * * * * *
161808 CATGGTAAGG-TGAACAAGTTCTTCTCATTATGAACTTATTCTCCTTCTTTGGATGAGTTCTTCT
1 CAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCT
* * * *
161872 CATTATGAACCCTTCCATTGGAAACGATGATCC
66 CATTATGAACTCTT-CACTGGAAATGTTGATCC
161905 ACCTCTTTTT
Statistics
Matches: 450, Mismatches: 52, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
133 46 0.10
134 13 0.03
135 18 0.04
136 16 0.04
137 52 0.12
138 3 0.01
139 301 0.67
140 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (138 bp):
CAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCT
CATTATGAACTCTTCACTGGAAATGTTGATCCCTCGAGTGAGGTGTTATGATTCAACTCCATATG
TGATGAAT
Found at i:162846 original size:40 final size:39
Alignment explanation
Indices: 162802--162897 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 39
162792 GGAAGGCCCG
*
162802 AAGGACTTATCATCTTACTCGAAAGACTTATGATGACCCA
1 AAGGACTTATCATCATACTC-AAAGACTTATGATGACCCA
* * * * * *
162842 AAGGATTTAAGCACCATGCTCAAAGACTTATGATGGCCCG
1 AAGGACTT-ATCATCATACTCAAAGACTTATGATGACCCA
162882 AAGGACTTACTCATCA
1 AAGGACTTA-TCATCA
162898 AAAAACCCTT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
39 1 0.02
40 35 0.80
41 8 0.18
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (39 bp):
AAGGACTTATCATCATACTCAAAGACTTATGATGACCCA
Found at i:163086 original size:55 final size:55
Alignment explanation
Indices: 163002--163330 Score: 337
Period size: 54 Copynumber: 6.2 Consensus size: 55
162992 ATTCATCATG
* * * *
163002 TCAAGAAAGCTT-TGAAAATCATACTTAGTTTTTTTGAAAGCTCATTTAAAAATTA
1 TCAAGAAA-CTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATTA
* * * **
163057 TCAAGAAACTTCTAAAAATCAAAGTTAGTTTCTTT-AAAA---A-TTAATCATGT-
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAAT-TA
* * *
163107 T-AAGAAACCTT-TGGAAATCAGACTTAGTTTC-TTATAAAGCTC-GTTAAAAATTA
1 TCAAGAAA-CTTCTGAAAATCAGACTTAGTTTCTTTA-AAAACTCATTTAAAAATTA
* * * *
163160 TCAAGAAACTTCTG-AAATTAGACTTAGTTTCTTTAAAAAATCATTTGAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATTA
*
163214 TCAAGAAACTTCTGAAAATCA-ACTTGGTTTCTTTAAAAAACTCATTT-AAAATTA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAAACTCATTTAAAAATTA
* *
163268 TCAGGAAACTTCTGAAAATTAGACTTAGTTTCTTTAAAAACTCATTTAAAAA-TA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATTA
163322 TCAAGAAAC
1 TCAAGAAAC
163331 CCTTGAAAAT
Statistics
Matches: 228, Mismatches: 28, Indels: 37
0.78 0.10 0.13
Matches are distributed among these distances:
48 2 0.01
49 22 0.10
50 13 0.06
51 2 0.01
52 1 0.00
53 31 0.14
54 98 0.43
55 59 0.26
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (55 bp):
TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATTA
Found at i:163360 original size:108 final size:108
Alignment explanation
Indices: 163108--163361 Score: 282
Period size: 108 Copynumber: 2.4 Consensus size: 108
163098 TAATCATGTT
* * ** * * * *
163108 AAGAAACCTTTGGAAATCAGACTTAGTTTCTT-ATAAAGCTCGTTAAAAATTATCAAGAAACTTC
1 AAGAAACCTCTGAAAATCA-ACTTAACTTCTTAAAAAAACTCATTTAAAATTATCAAGAAACTTC
*
163172 TGAAATTAGACTTAGTTTCTTTAAAAAATCATTTGAAAATCATC
65 TGAAATTAGACTTAGTTTCTTTAAAAAATCATTTAAAAATCATC
* *** * *
163216 AAGAAACTTCTGAAAATCAACTTGGTTTCTTTAAAAAACTCATTTAAAATTATCAGGAAACTTCT
1 AAGAAACCTCTGAAAATCAACTTAACTTCTTAAAAAAACTCATTTAAAATTATCAAGAAACTTCT
*
163281 GAAAATTAGACTTAGTTTCTTTAAAAACTCATTTAAAAAT-ATC
66 G-AAATTAGACTTAGTTTCTTTAAAAAATCATTTAAAAATCATC
* *
163324 AAGAAACC-CTTGAAAATTATGCTTAACTTC-TAAAAAAA
1 AAGAAACCTC-TGAAAATCA-ACTTAACTTCTTAAAAAAA
163362 TCGTGTTACT
Statistics
Matches: 124, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
107 12 0.10
108 70 0.56
109 42 0.34
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.33
Consensus pattern (108 bp):
AAGAAACCTCTGAAAATCAACTTAACTTCTTAAAAAAACTCATTTAAAATTATCAAGAAACTTCT
GAAATTAGACTTAGTTTCTTTAAAAAATCATTTAAAAATCATC
Found at i:163361 original size:54 final size:54
Alignment explanation
Indices: 163150--163361 Score: 173
Period size: 54 Copynumber: 3.9 Consensus size: 54
163140 ATAAAGCTCG
* ** *
163150 TTAAAAATTATCAAGAAACTTCTG-AAATTAGACTTAGTTTCTTTAAAAAA-TCAT
1 TTAAAAA-TATCAAGAAACCTCTGAAAATTAGACTTAACTTC-TAAAAAAACTCAT
* * * *** *
163204 TTGAAAATCATCAAGAAACTTCTGAAAATCA-ACTTGGTTTCTTTAAAAAACTCAT
1 TTAAAAAT-ATCAAGAAACCTCTGAAAATTAGACTTAACTTC-TAAAAAAACTCAT
* * * ** **
163259 TTAAAATTATCAGGAAACTTCTGAAAATTAGACTTAGTTTCTTTAAAAACTCAT
1 TTAAAAATATCAAGAAACCTCTGAAAATTAGACTTAACTTCTAAAAAAACTCAT
163313 TTAAAAATATCAAGAAACC-CTTGAAAATTATG-CTTAACTTCTAAAAAAA
1 TTAAAAATATCAAGAAACCTC-TGAAAATTA-GACTTAACTTCTAAAAAAA
163362 TCGTGTTACT
Statistics
Matches: 136, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
53 2 0.01
54 109 0.80
55 25 0.18
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (54 bp):
TTAAAAATATCAAGAAACCTCTGAAAATTAGACTTAACTTCTAAAAAAACTCAT
Found at i:163361 original size:109 final size:108
Alignment explanation
Indices: 163153--163361 Score: 278
Period size: 109 Copynumber: 1.9 Consensus size: 108
163143 AAGCTCGTTA
*
163153 AAAATTATCAAGAAACTTCTGAAATTAGACTTAGTTTCTTTAAAAAATCATTTGAAAATCATCAA
1 AAAATTATCAAGAAACTTCTGAAATTAGACTTAGTTTCTTTAAAAAATCATTTAAAAATCATCAA
* *** **
163218 GAAACTTCTGAAAATCAACTTGGTTTCTTTAAAAAACTCATTT
66 GAAACCTCTGAAAATCAACTTAACTTCTAAAAAAAACTCATTT
* *
163261 AAAATTATCAGGAAACTTCTGAAAATTAGACTTAGTTTCTTTAAAAACTCATTTAAAAAT-ATCA
1 AAAATTATCAAGAAACTTCTG-AAATTAGACTTAGTTTCTTTAAAAAATCATTTAAAAATCATCA
* *
163325 AGAAACC-CTTGAAAATTATGCTTAACTTCTAAAAAAA
65 AGAAACCTC-TGAAAATCA-ACTTAACTTCTAAAAAAA
163362 TCGTGTTACT
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
107 1 0.01
108 38 0.44
109 48 0.55
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.33
Consensus pattern (108 bp):
AAAATTATCAAGAAACTTCTGAAATTAGACTTAGTTTCTTTAAAAAATCATTTAAAAATCATCAA
GAAACCTCTGAAAATCAACTTAACTTCTAAAAAAAACTCATTT
Found at i:164683 original size:28 final size:28
Alignment explanation
Indices: 164651--164704 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
164641 TTTTAGATTA
** *
164651 ATTTGAGGAGGTAATGTGTTTCAGGTCG
1 ATTTGAGGAGACAATGTGTTCCAGGTCG
*
164679 ATTTGGGGAGACAATGTGTTCCAGGT
1 ATTTGAGGAGACAATGTGTTCCAGGT
164705 TGGCTTCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.22, C:0.09, G:0.35, T:0.33
Consensus pattern (28 bp):
ATTTGAGGAGACAATGTGTTCCAGGTCG
Found at i:165461 original size:3 final size:3
Alignment explanation
Indices: 165455--165486 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
165445 TTTTTTTTTC
165455 TCT TCT TCT TCT TCT TCT TCT TCT TCT T-T TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
165487 CACTTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:165508 original size:49 final size:49
Alignment explanation
Indices: 165440--165536 Score: 119
Period size: 49 Copynumber: 2.0 Consensus size: 49
165430 TTTCTTTTTT
* * *
165440 CTTTTTTTTTTTTTCTCTTCTTCTTCTTCTTCT-TCT-TCTTCTTTTCTCA
1 CTTTTTTATTTTTTCTCTTCTTATT-TT-TTCTATATCTCTTCTTTTCTCA
165489 CTTTTTATATTTTTT-TCTTCTTATTTTTTCTATATCTCTTCTTTTCTC
1 CTTTTT-TATTTTTTCTCTTCTTATTTTTTCTATATCTCTTCTTTTCTC
165537 TCTCTGTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
47 4 0.10
48 4 0.10
49 27 0.64
50 7 0.17
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (49 bp):
CTTTTTTATTTTTTCTCTTCTTATTTTTTCTATATCTCTTCTTTTCTCA
Done.