Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002649.1 Hibiscus syriacus cultivar Beakdansim tig00005415_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: 92033
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2910 original size:20 final size:20
Alignment explanation
Indices: 2887--2929 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2877 AATCCACCAT
*
2887 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGATTCTAA
* *
2907 ATGCATCTATATGATTCTAA
1 ATGCAACTAAATGATTCTAA
2927 ATG
1 ATG
2930 GTCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGATTCTAA
Found at i:12060 original size:16 final size:16
Alignment explanation
Indices: 12039--12088 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
12029 TGCACTGATA
*
12039 TACATGAGCTATGTGT
1 TACATGACCTATGTGT
*
12055 TACATGTCATCCTAGGTGT
1 TACATG--A-CCTATGTGT
12074 TACATGACCTATGTG
1 TACATGACCTATGTG
12089 GATATATGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 13 0.46
17 1 0.04
18 1 0.04
19 13 0.46
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (16 bp):
TACATGACCTATGTGT
Found at i:12276 original size:23 final size:23
Alignment explanation
Indices: 12250--12341 Score: 94
Period size: 23 Copynumber: 4.0 Consensus size: 23
12240 TTTTACGTAA
*
12250 TCCTTCGGGACAATTCTACGTGG
1 TCCTTCGGGACAATTCTATGTGG
* * **
12273 TCCTTCGGGACATTTATATACGG
1 TCCTTCGGGACAATTCTATGTGG
* * *
12296 TCCTTTGGGATAATACTATGTGG
1 TCCTTCGGGACAATTCTATGTGG
* *
12319 TCCTTCGAGACATTTCTATGTGG
1 TCCTTCGGGACAATTCTATGTGG
12342 CACTTCGATG
Statistics
Matches: 52, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.36
Consensus pattern (23 bp):
TCCTTCGGGACAATTCTATGTGG
Found at i:17938 original size:108 final size:109
Alignment explanation
Indices: 17805--18092 Score: 400
Period size: 108 Copynumber: 2.7 Consensus size: 109
17795 TAATATACAA
* * * *
17805 GAAAAAAGGTAAATAACAATTTTGGTCCTTGCAGGTGACCAACATGCACAAACACGCTAAACTAT
1 GAAAAATGGTAAATAACAACTTTGGTCCTCGCAGGTGACCAACATGCAAAAACACGCTAAACTAT
17870 GGGGGACTAAACAGCAAATATCCCAAA-AATATATAACATGCAT
66 GGGGGACTAAACAGCAAATATCCCAAAGAATATATAACATGCAT
* * *
17913 GAAAAATGGTAAATAACAACCTTGGTCATCGCAGGTGACCAACATGCAAAAACATGCTAAACTAT
1 GAAAAATGGTAAATAACAACTTTGGTCCTCGCAGGTGACCAACATGCAAAAACACGCTAAACTAT
* * * *
17978 -GGGGAGTAAATAGCAAATATCCCAAAGAATATATAGCATTCAT
66 GGGGGACTAAACAGCAAATATCCCAAAGAATATATAACATGCAT
* * * ** **
18021 GAAAATTGGTAAATAACAACTTTGGTCCTCACAGATGATTAACATGCAAAAATGCGCTAAACTAT
1 GAAAAATGGTAAATAACAACTTTGGTCCTCGCAGGTGACCAACATGCAAAAACACGCTAAACTAT
18086 GGGGGAC
66 GGGGGAC
18093 CTATGCATGA
Statistics
Matches: 156, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
107 24 0.15
108 127 0.81
109 5 0.03
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (109 bp):
GAAAAATGGTAAATAACAACTTTGGTCCTCGCAGGTGACCAACATGCAAAAACACGCTAAACTAT
GGGGGACTAAACAGCAAATATCCCAAAGAATATATAACATGCAT
Found at i:19022 original size:7 final size:6
Alignment explanation
Indices: 19009--19065 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
18999 AATAATAATA
* * * *
19009 AAAATT AAACATT AAAATT ATAATT ATAATTT AAAATT ATAATT ATAATT
1 AAAATT AAA-ATT AAAATT AAAATT A-AAATT AAAATT AAAATT AAAATT
*
19059 ATAATT A
1 AAAATT A
19066 GATAATAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
6 34 0.77
7 10 0.23
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (6 bp):
AAAATT
Found at i:19031 original size:25 final size:24
Alignment explanation
Indices: 19003--19057 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
18993 ACAAATAATA
19003 ATAATAAAAATTAAACATTAAAATT
1 ATAATAAAAATTAAA-ATTAAAATT
* * *
19028 ATAATTATAATTTAAAATTATAATT
1 ATAA-TAAAAATTAAAATTAAAATT
19053 ATAAT
1 ATAAT
19058 TATAATTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 16 0.62
26 9 0.35
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
ATAATAAAAATTAAAATTAAAATT
Found at i:19042 original size:19 final size:19
Alignment explanation
Indices: 19020--19058 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
19010 AAATTAAACA
19020 TTAAAATTATAATTATAAT
1 TTAAAATTATAATTATAAT
19039 TTAAAATTATAATTATAAT
1 TTAAAATTATAATTATAAT
19058 T
1 T
19059 ATAATTAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAAAATTATAATTATAAT
Found at i:26794 original size:18 final size:18
Alignment explanation
Indices: 26771--26805 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
26761 CATTTCAAAA
26771 TAGATATCAACTCTTCGC
1 TAGATATCAACTCTTCGC
**
26789 TAGATATTTACTCTTCG
1 TAGATATCAACTCTTCG
26806 TGTAAAGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (18 bp):
TAGATATCAACTCTTCGC
Found at i:28227 original size:30 final size:30
Alignment explanation
Indices: 28183--28254 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
28173 AAACATTTTT
*
28183 TAATTTTTTAATAGTAGGAGACTTAACAAAG
1 TAATATTTT-ATAGTAGGAGACTTAACAAAG
* * *
28214 TAATATTTTATAGTCGGGGATTTAACAAAG
1 TAATATTTTATAGTAGGAGACTTAACAAAG
*
28244 TAATATCTTAT
1 TAATATTTTAT
28255 TGTTGGGGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 28 0.78
31 8 0.22
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (30 bp):
TAATATTTTATAGTAGGAGACTTAACAAAG
Found at i:28263 original size:30 final size:30
Alignment explanation
Indices: 28205--28263 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
28195 AGTAGGAGAC
*
28205 TTAACAAAGTAATATTTTATAGTCGGGGAT
1 TTAACAAAGTAATATCTTATAGTCGGGGAT
* *
28235 TTAACAAAGTAATATCTTATTGTTGGGGA
1 TTAACAAAGTAATATCTTATAGTCGGGGA
28264 CCATTTGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.37
Consensus pattern (30 bp):
TTAACAAAGTAATATCTTATAGTCGGGGAT
Found at i:29370 original size:16 final size:17
Alignment explanation
Indices: 29342--29376 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
29332 TATTTTTATT
29342 TTTCATGTTTTTGA-TA
1 TTTCATGTTTTTGAGTA
*
29358 TTTCATTTTTTTGAGTA
1 TTTCATGTTTTTGAGTA
29375 TT
1 TT
29377 CTTTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.66
Consensus pattern (17 bp):
TTTCATGTTTTTGAGTA
Found at i:31127 original size:18 final size:19
Alignment explanation
Indices: 31092--31128 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
31082 CACGGAATGT
31092 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
31112 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
31129 GGATTATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:37562 original size:44 final size:44
Alignment explanation
Indices: 37514--37640 Score: 184
Period size: 44 Copynumber: 2.9 Consensus size: 44
37504 TCTCTTATTG
* *
37514 TTAATTACATTATGTTCGTTACTTTCCATGCATTTACTTCATCT
1 TTAATTACTTTATGTTCTTTACTTTCCATGCATTTACTTCATCT
* * *
37558 TTAATTATTTTATGTTCTTTACTTTCCTTGCATTTACATCATCT
1 TTAATTACTTTATGTTCTTTACTTTCCATGCATTTACTTCATCT
*
37602 TTAATTACTTTATGTTATTTACTTT-CATTGCATTTACTT
1 TTAATTACTTTATGTTCTTTACTTTCCA-TGCATTTACTT
37641 TTATGCATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
43 1 0.01
44 72 0.99
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.55
Consensus pattern (44 bp):
TTAATTACTTTATGTTCTTTACTTTCCATGCATTTACTTCATCT
Found at i:37649 original size:14 final size:14
Alignment explanation
Indices: 37618--37658 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
37608 ACTTTATGTT
*
37618 ATTTACTTTCATTGC
1 ATTTACTTTTA-TGC
37633 ATTTACTTTTATGC
1 ATTTACTTTTATGC
*
37647 ATTTACTATTAT
1 ATTTACTTTTAT
37659 TTTACTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (14 bp):
ATTTACTTTTATGC
Found at i:38186 original size:79 final size:79
Alignment explanation
Indices: 38055--38204 Score: 273
Period size: 79 Copynumber: 1.9 Consensus size: 79
38045 CAACACTCTT
*
38055 TGGATGATTACTTAAGCTACAGTAGCTAGAGTGAAATGCAACTTGACACCATTAGAGAAGTATTG
1 TGGATGATTACTTAAGCTACAGTAGCTAGAGTGAAATGCAACTTGACACCATTAGACAAGTATTG
38120 CAAAATGAACACCG
66 CAAAATGAACACCG
* *
38134 TGGATGATTACTTAAGCTACAGTAGCTAGAGTGAGATGCAACTTGACACCATTAGACAAGTATTT
1 TGGATGATTACTTAAGCTACAGTAGCTAGAGTGAAATGCAACTTGACACCATTAGACAAGTATTG
38199 CAAAAT
66 CAAAAT
38205 AAGTAAAGGC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 68 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (79 bp):
TGGATGATTACTTAAGCTACAGTAGCTAGAGTGAAATGCAACTTGACACCATTAGACAAGTATTG
CAAAATGAACACCG
Found at i:39059 original size:22 final size:22
Alignment explanation
Indices: 39031--39077 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
39021 TGTTTGGGTG
39031 CATTAGAAATGCTTTAGTGCTA
1 CATTAGAAATGCTTTAGTGCTA
39053 CATTAGAAATGCTTTAGTGCTA
1 CATTAGAAATGCTTTAGTGCTA
39075 CAT
1 CAT
39078 AATATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (22 bp):
CATTAGAAATGCTTTAGTGCTA
Found at i:40160 original size:27 final size:27
Alignment explanation
Indices: 40130--40187 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
40120 AGTCTCTTAG
40130 AAGCTTGCTAGGTCTTTGAGTCCCGAT
1 AAGCTTGCTAGGTCTTTGAGTCCCGAT
* *
40157 AAGCTTGCTAGTTCTTTGAGTCCCGCT
1 AAGCTTGCTAGGTCTTTGAGTCCCGAT
40184 AAGC
1 AAGC
40188 ATACTAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (27 bp):
AAGCTTGCTAGGTCTTTGAGTCCCGAT
Found at i:40194 original size:27 final size:27
Alignment explanation
Indices: 40137--40203 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
40127 TAGAAGCTTG
* * *
40137 CTAGGTCTTTGAGTCCCGATAAGCTTG
1 CTAGTTCTTTGAGTCCCGATAAGCATA
*
40164 CTAGTTCTTTGAGTCCCGCTAAGCATA
1 CTAGTTCTTTGAGTCCCGATAAGCATA
40191 CTAGTT-TTTGAGT
1 CTAGTTCTTTGAGT
40204 AGAGGATAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 7 0.19
27 29 0.81
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (27 bp):
CTAGTTCTTTGAGTCCCGATAAGCATA
Found at i:44210 original size:13 final size:14
Alignment explanation
Indices: 44186--44215 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
44176 AGTTAACTAA
44186 ATTATTTAAGTTAT
1 ATTATTTAAGTTAT
44200 ATTATTT-AGTTAT
1 ATTATTTAAGTTAT
44213 ATT
1 ATT
44216 GTACATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (14 bp):
ATTATTTAAGTTAT
Found at i:46524 original size:24 final size:27
Alignment explanation
Indices: 46479--46537 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 27
46469 TAAGATTTAA
46479 ATATTAATATATTCTTATTAAA-AAATAT
1 ATATTAATATATTC-TATTAAATAAA-AT
46507 ATATTAATATA-TC-A-TAAATAAAAT
1 ATATTAATATATTCTATTAAATAAAAT
*
46531 AAATTAA
1 ATATTAA
46538 AATAATAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 12 0.41
25 4 0.14
27 2 0.07
28 11 0.38
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (27 bp):
ATATTAATATATTCTATTAAATAAAAT
Found at i:46859 original size:23 final size:23
Alignment explanation
Indices: 46828--46874 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
46818 AATTTGTTTG
46828 TATGATACGTTTTCATATGTCTT
1 TATGATACGTTTTCATATGTCTT
* * *
46851 TATGGTACGTTTTCTTCTGTCTT
1 TATGATACGTTTTCATATGTCTT
46874 T
1 T
46875 TGGCATGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (23 bp):
TATGATACGTTTTCATATGTCTT
Found at i:54100 original size:23 final size:23
Alignment explanation
Indices: 54074--54139 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 23
54064 TATTTCTAAA
54074 ATTTATAAATAAAAATATTAATT
1 ATTTATAAATAAAAATATTAATT
* *
54097 ATTT-TCTAATACTAAAATATTATTT
1 ATTTAT-AAATA--AAAATATTAATT
*
54122 A-TTA-AAATAAGAATATTA
1 ATTTATAAATAAAAATATTA
54140 TACTATTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
21 8 0.23
22 1 0.03
23 12 0.34
24 2 0.06
25 12 0.34
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTTATAAATAAAAATATTAATT
Found at i:54202 original size:15 final size:16
Alignment explanation
Indices: 54182--54211 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54172 TAAGAATATT
54182 ATTATAATA-TAAAAA
1 ATTATAATATTAAAAA
54197 ATTATAATATTAAAA
1 ATTATAATATTAAAA
54212 TGATACTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTATAATATTAAAAA
Found at i:56607 original size:17 final size:17
Alignment explanation
Indices: 56585--56625 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
56575 CCTCTTTCTT
56585 CTCTCATCGTCTCTCAA
1 CTCTCATCGTCTCTCAA
56602 CTCTCATCGTCTCTCAA
1 CTCTCATCGTCTCTCAA
56619 CTCTCAT
1 CTCTCAT
56626 AACCAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.17, C:0.41, G:0.05, T:0.37
Consensus pattern (17 bp):
CTCTCATCGTCTCTCAA
Found at i:61695 original size:35 final size:35
Alignment explanation
Indices: 61649--61715 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
61639 TATTCTAGAG
61649 TTAATATTGTGGTTTGAATCTTGAA-ATTTGACATT
1 TTAATATTGTGGTTTGAATCTT-AATATTTGACATT
*
61684 TTAATATTGTGGTTTGAGTCTTAATATTTGAC
1 TTAATATTGTGGTTTGAATCTTAATATTTGAC
61716 TTTATTTACG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 2 0.07
35 28 0.93
ACGTcount: A:0.27, C:0.06, G:0.18, T:0.49
Consensus pattern (35 bp):
TTAATATTGTGGTTTGAATCTTAATATTTGACATT
Found at i:62409 original size:74 final size:75
Alignment explanation
Indices: 62310--62495 Score: 202
Period size: 74 Copynumber: 2.5 Consensus size: 75
62300 TAATAAAGTT
* * * *
62310 AAATATTAATATTCAAACCACAATATTAAGTTTAGAACATTAAAATCCATAA-ACAAA-CAACAA
1 AAATCTTAAGATTCAAACCATAATATTAAGTTTAGAACAATAAAATCCATAATA-AAATC-ACAA
*
62373 TGTTAAAATGTC
64 TATTAAAATGTC
* *
62385 -AAT-TTCAAGATTCAAACCATAATATTAA-TTCTAGAATAATAAAATCCATAATAAAATCATAA
1 AAATCTT-AAGATTCAAACCATAATATTAAGTT-TAGAACAATAAAATCCATAATAAAATCACAA
*
62447 TATTAAAGTGTC
64 TATTAAAATGTC
* * *
62459 AAATCTTAAGACTCGAACCATAATATTAAGTCTAGAA
1 AAATCTTAAGATTCAAACCATAATATTAAGTTTAGAA
62496 AAGTATTAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
73 4 0.04
74 57 0.61
75 30 0.32
76 3 0.03
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.30
Consensus pattern (75 bp):
AAATCTTAAGATTCAAACCATAATATTAAGTTTAGAACAATAAAATCCATAATAAAATCACAATA
TTAAAATGTC
Found at i:62447 original size:11 final size:12
Alignment explanation
Indices: 62420--62448 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
62410 TAATTCTAGA
62420 ATAATAAAATCC
1 ATAATAAAATCC
62432 ATAATAAAAT-C
1 ATAATAAAATCC
62443 ATAATA
1 ATAATA
62449 TTAAAGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (12 bp):
ATAATAAAATCC
Found at i:64765 original size:22 final size:23
Alignment explanation
Indices: 64720--64768 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
64710 ATTCAGTAAT
** *
64720 GAAAAAAATTTGAAAAGGGTAGA
1 GAAAAAAATTTGAAAAACGCAGA
64743 GAAAAAAA-TTGAAAAACGCAGA
1 GAAAAAAATTTGAAAAACGCAGA
64765 GAAA
1 GAAA
64769 TTGAGAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.61, C:0.04, G:0.22, T:0.12
Consensus pattern (23 bp):
GAAAAAAATTTGAAAAACGCAGA
Found at i:69878 original size:10 final size:9
Alignment explanation
Indices: 69843--69941 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
69833 GCTACTGGAA
*
69843 ACCGGTTTA
1 ACCGGTTTG
*
69852 ACCGGTTTTTA
1 ACCGG--TTTG
69863 ACCGGTTCTG
1 ACCGGTT-TG
69873 ACCGGTTTG
1 ACCGGTTTG
* *
69882 ACCAGTTTCA
1 ACCGGTTT-G
*
69892 ACCGGTTCG
1 ACCGGTTTG
69901 AACCGGTTTG
1 -ACCGGTTTG
*
69911 ACCGGTCTG
1 ACCGGTTTG
69920 AACCGGTTTG
1 -ACCGGTTTG
*
69930 ACCGGTCTG
1 ACCGGTTTG
69939 ACC
1 ACC
69942 CGACCCGACC
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
9 35 0.47
10 30 0.41
11 9 0.12
ACGTcount: A:0.17, C:0.27, G:0.26, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:69898 original size:29 final size:29
Alignment explanation
Indices: 69843--69941 Score: 112
Period size: 29 Copynumber: 3.4 Consensus size: 29
69833 GCTACTGGAA
* *
69843 ACCGGTTTAACCGGTTTTTAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTCTG
*
69873 ACCGGTTTGACCAGTTTCAACCGGTTC-G
1 ACCGGTTTGACCGGTTTCAACCGGTTCTG
* *
69901 AACCGGTTTGACCGGTCTGAACCGGTT-TG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCTG
*
69930 ACCGGTCTGACC
1 ACCGGTTTGACC
69942 CGACCCGACC
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
28 12 0.20
29 36 0.60
30 12 0.20
ACGTcount: A:0.17, C:0.27, G:0.26, T:0.29
Consensus pattern (29 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:69936 original size:19 final size:19
Alignment explanation
Indices: 69842--69939 Score: 92
Period size: 19 Copynumber: 5.1 Consensus size: 19
69832 GGCTACTGGA
* * *
69842 AACCGGTTTAACCGGTTTTT
1 AACCGGTTTGACCGG-TCTG
*
69862 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTCTG
* *
69882 -ACCAGTTTCAACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
69901 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
69920 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
69939 A
1 A
69940 CCCGACCCGA
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
18 2 0.03
19 40 0.60
20 19 0.28
21 6 0.09
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.30
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:69959 original size:17 final size:17
Alignment explanation
Indices: 69937--69997 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 17
69927 TTGACCGGTC
69937 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
69954 TGACCCGACCCGACCCGACCGT
1 T-----GACCCGACCCGACCGT
*
69976 TGACCCGACCCGATCGT
1 TGACCCGACCCGACCGT
69993 TGACC
1 TGACC
69998 GTTGACCGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 21 0.55
22 17 0.45
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:69964 original size:22 final size:22
Alignment explanation
Indices: 69938--69988 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
69928 TGACCGGTCT
69938 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
69960 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
69982 GACCCGA
1 GACCCGA
69989 TCGTTGACCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.49, G:0.24, T:0.08
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:72207 original size:82 final size:81
Alignment explanation
Indices: 72103--72324 Score: 218
Period size: 82 Copynumber: 2.7 Consensus size: 81
72093 TATAGCAACG
* * * * * *
72103 TTTTTGGGAAAATGCCGTTAAAAACACGTACTTTAGTGGTGTTTGTGAAACAAACGCTGCTATAG
1 TTTTTGAGAAAACGCTGCTAAAAACACGTACTTTAGTGGCGTTTGTGAAACAAACGCCGCTATAG
72168 ACTGATA-TAAGGTAGCA
66 ACTGATAGTAA--TAGCA
* ** *
72185 TTTTTGAGAAAACGCTGCTAAAAACATGTACTTTAGTGGCGTTTGAT-ACCCAAAAGCCGCTATA
1 TTTTTGAGAAAACGCTGCTAAAAACACGTACTTTAGTGGCGTTTG-TGAAACAAACGCCGCTATA
* *
72249 GACTTATATGTAATGGCA
65 GACTGATA-GTAATAGCA
* * * *
72267 TTTTTGA-ACAAACG-TCGCTATATACACGTACTTTAGTGGCGTTTGTGTAGCAAACGCC
1 TTTTTGAGA-AAACGCT-GCTAAAAACACGTACTTTAGTGGCGTTTGTGAAACAAACGCC
72325 ATAAATTGTT
Statistics
Matches: 115, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
81 3 0.03
82 108 0.94
83 1 0.01
84 3 0.03
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (81 bp):
TTTTTGAGAAAACGCTGCTAAAAACACGTACTTTAGTGGCGTTTGTGAAACAAACGCCGCTATAG
ACTGATAGTAATAGCA
Found at i:82043 original size:13 final size:13
Alignment explanation
Indices: 82025--82071 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
82015 TACATTTTGA
82025 TTTTCAAACATTG
1 TTTTCAAACATTG
*
82038 TTTTCAAATATTG
1 TTTTCAAACATTG
*
82051 TTTTCAAACATAG
1 TTTTCAAACATTG
82064 TTTTCAAA
1 TTTTCAAA
82072 GTTTGCCCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (13 bp):
TTTTCAAACATTG
Found at i:82570 original size:29 final size:29
Alignment explanation
Indices: 82532--82587 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 29
82522 TATTTGGATT
82532 TGTTTAAATTTGTGTT-TTTGGAT-TTTAGA
1 TGTTTAAA-TTGT-TTGTTTGGATGTTTAGA
*
82561 TGTTTCAATTGTTTGTTTGGATGTTTA
1 TGTTTAAATTGTTTGTTTGGATGTTTA
82588 TTTTGGTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 2 0.08
28 11 0.46
29 11 0.46
ACGTcount: A:0.18, C:0.02, G:0.21, T:0.59
Consensus pattern (29 bp):
TGTTTAAATTGTTTGTTTGGATGTTTAGA
Found at i:89354 original size:19 final size:20
Alignment explanation
Indices: 89327--89368 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
89317 AAAAAAATTG
89327 TTTTGATTTAAAT-TGTTGT
1 TTTTGATTTAAATATGTTGT
* * *
89346 TTTTTATTTGATTATGTTGT
1 TTTTGATTTAAATATGTTGT
89366 TTT
1 TTT
89369 GAAAACTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (20 bp):
TTTTGATTTAAATATGTTGT
Found at i:89403 original size:13 final size:13
Alignment explanation
Indices: 89385--89432 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
89375 TACATTTTGA
89385 TTTTCAAACATTG
1 TTTTCAAACATTG
*
89398 TTTTCAAATATTG
1 TTTTCAAACATTG
**
89411 TTTTCAAAACATAC
1 TTTTC-AAACATTG
89425 TTTTCAAA
1 TTTTCAAA
89433 GTTTGCCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 20 0.67
14 10 0.33
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (13 bp):
TTTTCAAACATTG
Found at i:89918 original size:29 final size:30
Alignment explanation
Indices: 89876--89957 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 30
89866 CTTTAAAACA
*
89876 TTTTGAATATTTGGATTTGTTTGAATTTGT
1 TTTTGGATATTTGGATTTGTTTGAATTTGT
*
89906 TTTTGGAT-TTTGGA--TGTTTCAA-TTGT
1 TTTTGGATATTTGGATTTGTTTGAATTTGT
*
89932 TTGTTGGATGTTT--ATTTGGTTTGAAT
1 TT-TTGGATATTTGGATTT-GTTTGAAT
89958 GATATTTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
26 7 0.16
27 13 0.30
28 4 0.09
29 12 0.28
30 7 0.16
ACGTcount: A:0.17, C:0.01, G:0.23, T:0.59
Consensus pattern (30 bp):
TTTTGGATATTTGGATTTGTTTGAATTTGT
Done.