Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009219.1 Hibiscus syriacus cultivar Beakdansim tig00112808_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: 109438
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:7927 original size:19 final size:20
Alignment explanation
Indices: 7890--7927 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7880 TTTTTTTATA
*
7890 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
7910 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
7928 TCTATCATTC
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:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:14716 original size:19 final size:20
Alignment explanation
Indices: 14679--14716 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
14669 TTTTTTTATA
*
14679 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
14699 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
14717 TCTAGCATTC
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:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:14767 original size:21 final size:21
Alignment explanation
Indices: 14743--14785 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
14733 TTCATATTCG
* *
14743 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
14764 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
14785 T
1 T
14786 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:17235 original size:17 final size:18
Alignment explanation
Indices: 17205--17241 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
17195 TATTTTTTAA
17205 TATTTTTAAT-AAAATAT
1 TATTTTTAATAAAAATAT
17222 TATTTTT-ATCAAAAATAT
1 TATTTTTAAT-AAAAATAT
17240 TA
1 TA
17242 ATATTAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 7 0.39
18 9 0.50
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTTTAATAAAAATAT
Found at i:18185 original size:27 final size:27
Alignment explanation
Indices: 18155--18220 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 27
18145 TTTGTTCGGG
18155 TCGGGTCGGGTTTTTAAAGTGTGATAT
1 TCGGGTCGGGTTTTTAAAGTGTGATAT
* * *
18182 TCGGGTCTAGTTTTTTTAAGTGTGATAT
1 TCGGGTC-GGGTTTTTAAAGTGTGATAT
18210 TCGGGTCGGGT
1 TCGGGTCGGGT
18221 CGGGTTAGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 9 0.27
28 24 0.73
ACGTcount: A:0.15, C:0.09, G:0.33, T:0.42
Consensus pattern (27 bp):
TCGGGTCGGGTTTTTAAAGTGTGATAT
Found at i:31512 original size:20 final size:19
Alignment explanation
Indices: 31471--31517 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
31461 CCTCTAAAAT
31471 TAAAAAAATAAATTTCAAC
1 TAAAAAAATAAATTTCAAC
*
31490 TAAAATAAATAAATTGT-ATC
1 TAAAA-AAATAAATT-TCAAC
31510 TAAAAAAA
1 TAAAAAAA
31518 CCCACCCCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 8 0.32
20 16 0.64
21 1 0.04
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (19 bp):
TAAAAAAATAAATTTCAAC
Found at i:39230 original size:108 final size:108
Alignment explanation
Indices: 39041--39253 Score: 390
Period size: 108 Copynumber: 2.0 Consensus size: 108
39031 GTGTGGCCGA
*
39041 TGCCACGTGGGAACGGTGGTCCATGCAGACATCAAAGAGTTTAAAAGTAATACGTGTTAGATAAA
1 TGCCACGTGGGAACGGTGGTCCATGCAGACATCAAAGAGTTTAAAAGTAACACGTGTTAGATAAA
* *
39106 GAGAGGTGACAGGCTGTTTATTAAGACGCATATGTGATTTCGG
66 GAGAGGTGACAGGCTGTTTATCAAGACGCATATGCGATTTCGG
39149 TGCCACGTGGGAACGGTGGTCCATGCAGACATCAAAGAGTTTAAAAGTAACACGTGTTAGATAAA
1 TGCCACGTGGGAACGGTGGTCCATGCAGACATCAAAGAGTTTAAAAGTAACACGTGTTAGATAAA
*
39214 GAGATGTGACAGGCTGTTTATCAAGACGCATATGCGATTT
66 GAGAGGTGACAGGCTGTTTATCAAGACGCATATGCGATTT
39254 TTGTTTATTT
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 101 1.00
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (108 bp):
TGCCACGTGGGAACGGTGGTCCATGCAGACATCAAAGAGTTTAAAAGTAACACGTGTTAGATAAA
GAGAGGTGACAGGCTGTTTATCAAGACGCATATGCGATTTCGG
Found at i:41845 original size:35 final size:35
Alignment explanation
Indices: 41792--41867 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 35
41782 TTACATTTAT
* * * *
41792 TAAACTATTATAATATAATCACTACAATCTTATAA
1 TAAATTATCATAAAATAATCACTACAATATTATAA
* * *
41827 TAAATTATCATAAAATAATTATTATAATATTATAA
1 TAAATTATCATAAAATAATCACTACAATATTATAA
41862 TAAATT
1 TAAATT
41868 TTAAAAGTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (35 bp):
TAAATTATCATAAAATAATCACTACAATATTATAA
Found at i:42448 original size:13 final size:13
Alignment explanation
Indices: 42430--42457 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42420 CTAGAAAACT
42430 AAAAATCATTATA
1 AAAAATCATTATA
42443 AAAAATCATTATA
1 AAAAATCATTATA
42456 AA
1 AA
42458 CGACCCTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAAATCATTATA
Found at i:46039 original size:22 final size:19
Alignment explanation
Indices: 46016--46105 Score: 108
Period size: 19 Copynumber: 4.4 Consensus size: 19
46006 AACGCGATTT
*
46016 TGAAAAATGTGTTGCGAGAG
1 TGAAAAA-GTGTTGCGATAG
46036 TTTGAAAAACGTGTTGTTGCGATAG
1 --TGAAAAA-GTG-T--TGCGATAG
46061 TGAAAAAGTGTTGCGATAG
1 TGAAAAAGTGTTGCGATAG
46080 TGAAAAAGTGTTGCGATAG
1 TGAAAAAGTGTTGCGATAG
46099 TGAAAAA
1 TGAAAAA
46106 TCCAAAATAA
Statistics
Matches: 63, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
19 34 0.54
21 1 0.02
22 13 0.21
23 8 0.13
25 7 0.11
ACGTcount: A:0.37, C:0.06, G:0.30, T:0.28
Consensus pattern (19 bp):
TGAAAAAGTGTTGCGATAG
Found at i:46074 original size:19 final size:19
Alignment explanation
Indices: 46050--46105 Score: 112
Period size: 19 Copynumber: 2.9 Consensus size: 19
46040 AAAAACGTGT
46050 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAGTGAAAAAG
46069 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAGTGAAAAAG
46088 TGTTGCGATAGTGAAAAA
1 TGTTGCGATAGTGAAAAA
46106 TCCAAAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAAAG
Found at i:46555 original size:21 final size:21
Alignment explanation
Indices: 46528--46698 Score: 109
Period size: 21 Copynumber: 8.3 Consensus size: 21
46518 AATTTGGAAA
46528 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* ** * **
46549 ATTGCAA--CGAGTTTGGAAA
1 ATCGCAACGCGAACTTCGACT
46568 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
46589 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
* * **
46610 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
* *
46629 ATCGCAACGCGAACTTCCATT
1 ATCGCAACGCGAACTTCGACT
* * **
46650 ATCGCAACGTGAA-TTTGAAAA
1 ATCGCAACGCGAACTTCG-ACT
** *
46671 ATCGCAACGTAAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
46692 ATCGCAA
1 ATCGCAA
46699 AATCGCGTTG
Statistics
Matches: 112, Mismatches: 32, Indels: 12
0.72 0.21 0.08
Matches are distributed among these distances:
19 28 0.25
20 2 0.02
21 79 0.71
22 3 0.03
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:46569 original size:40 final size:40
Alignment explanation
Indices: 46509--46597 Score: 151
Period size: 40 Copynumber: 2.2 Consensus size: 40
46499 ATTTTGGAAA
*
46509 ATCGTAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
* *
46549 ATTGCAACGAGTTTGGAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
46589 ATCGCAACG
1 ATCGCAACG
46598 TGAACTTGGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (40 bp):
ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
Found at i:46576 original size:19 final size:19
Alignment explanation
Indices: 46501--46637 Score: 94
Period size: 21 Copynumber: 6.9 Consensus size: 19
46491 TCGTTGCGAT
*
46501 TTTGGAAAATCGTAACGAA
1 TTTGGAAAATCGCAACGAA
46520 TTTGGAAAATCGCAACGCGAA
1 TTTGGAAAATCGCAA--CGAA
* * ** * *
46541 CTTCGACTATTGCAACGAG
1 TTTGGAAAATCGCAACGAA
46560 TTTGGAAAATCGCAACGCGAA
1 TTTGGAAAATCGCAA--CGAA
* * **
46581 CTTCGACTATCGCAACGTGAA
1 TTTGGAAAATCGCAAC--GAA
* **
46602 CTTGGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGAA
46621 TTTGGAAAATCGCAACG
1 TTTGGAAAATCGCAACG
46638 CGAACTTCCA
Statistics
Matches: 91, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
19 45 0.49
21 46 0.51
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (19 bp):
TTTGGAAAATCGCAACGAA
Found at i:46603 original size:61 final size:61
Alignment explanation
Indices: 46528--46662 Score: 216
Period size: 61 Copynumber: 2.2 Consensus size: 61
46518 AATTTGGAAA
* * * *
46528 ATCGCAACGCGAACTTCGACTATTGCAACGAGTTTGGAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGTGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCCACT
* *
46589 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCCATT
1 ATCGCAACGTGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCCACT
46650 ATCGCAACGTGAA
1 ATCGCAACGTGAA
46663 TTTGAAAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (61 bp):
ATCGCAACGTGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCCACT
Found at i:46675 original size:61 final size:61
Alignment explanation
Indices: 46552--46679 Score: 193
Period size: 61 Copynumber: 2.1 Consensus size: 61
46542 TTCGACTATT
* * * **
46552 GCAACGAGTTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATC
1 GCAACGAATTTGGAAAATCGCAACGCGAACTTCCACTATCGCAACGTGAACTTGAAAAATC
* *
46613 GCAACGAATTTGGAAAATCGCAACGCGAACTTCCATTATCGCAACGTGAATTTGAAAAATC
1 GCAACGAATTTGGAAAATCGCAACGCGAACTTCCACTATCGCAACGTGAACTTGAAAAATC
46674 GCAACG
1 GCAACG
46680 TAAACTTGGA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (61 bp):
GCAACGAATTTGGAAAATCGCAACGCGAACTTCCACTATCGCAACGTGAACTTGAAAAATC
Found at i:46695 original size:42 final size:40
Alignment explanation
Indices: 46589--46698 Score: 148
Period size: 42 Copynumber: 2.7 Consensus size: 40
46579 AACTTCGACT
*
46589 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGAAAA
* ** *
46629 ATCGCAACGCGAACTTCCATTATCGCAACGTGAATTTGAAAA
1 ATCGCAACGTGAACTTGGACTATCGCAAC--GAATTTGAAAA
*
46671 ATCGCAACGTAAACTTGGACTATCGCAA
1 ATCGCAACGTGAACTTGGACTATCGCAA
46699 AATCGCGTTG
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 25 0.43
42 33 0.57
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (40 bp):
ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGAAAA
Found at i:48288 original size:15 final size:15
Alignment explanation
Indices: 48268--48301 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
48258 AGTGATGCAG
48268 CTTCATCTTCATCCT
1 CTTCATCTTCATCCT
*
48283 CTTCATCTTCGTCCT
1 CTTCATCTTCATCCT
48298 CTTC
1 CTTC
48302 GCCATCATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.41, G:0.03, T:0.47
Consensus pattern (15 bp):
CTTCATCTTCATCCT
Found at i:48997 original size:27 final size:27
Alignment explanation
Indices: 48967--49025 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
48957 TAGGCGCGTC
48967 TTTGGAAGATTAAGCAAAGCTCTGACT
1 TTTGGAAGATTAAGCAAAGCTCTGACT
48994 TTTGGAAGATTAAGCAAAGCTCTGACT
1 TTTGGAAGATTAAGCAAAGCTCTGACT
49021 TTTGG
1 TTTGG
49026 GTTTTGAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.32
Consensus pattern (27 bp):
TTTGGAAGATTAAGCAAAGCTCTGACT
Found at i:50250 original size:18 final size:18
Alignment explanation
Indices: 50229--50268 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
50219 AATGATGAAT
50229 ATGAAGATGACGATGAGG
1 ATGAAGATGACGATGAGG
* * *
50247 ATGACGATGAGGATGGGG
1 ATGAAGATGACGATGAGG
50265 ATGA
1 ATGA
50269 TAATGTGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.42, T:0.17
Consensus pattern (18 bp):
ATGAAGATGACGATGAGG
Found at i:50268 original size:12 final size:12
Alignment explanation
Indices: 50229--50261 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
50219 AATGATGAAT
*
50229 ATGAAGATGACG
1 ATGAGGATGACG
50241 ATGAGGATGACG
1 ATGAGGATGACG
50253 ATGAGGATG
1 ATGAGGATG
50262 GGGATGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.06, G:0.39, T:0.18
Consensus pattern (12 bp):
ATGAGGATGACG
Found at i:64924 original size:21 final size:21
Alignment explanation
Indices: 64898--64937 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
64888 CCCCCTTTGA
*
64898 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
64919 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
64938 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:73614 original size:223 final size:223
Alignment explanation
Indices: 73226--73670 Score: 845
Period size: 223 Copynumber: 2.0 Consensus size: 223
73216 GTGATTGTTC
73226 TTGGTGTGAGAATTCTGAAATCCTTAAGCATGAAGCAGTTGGGTATTTTAGGTGCCTATTTATAA
1 TTGGTGTGAGAATTCTGAAATCCTTAAGCATGAAGCAGTTGGGTATTTTAGGTGCCTATTTATAA
73291 AGAACTTCGGTGGCATCCTCTCCTCTTTGTGGGAAGTTTCATAGATTCTTGGAGATCGAGATTGG
66 AGAACTTCGGTGGCATCCTCTCCTCTTTGTGGGAAGTTTCATAGATTCTTGGAGATCGAGATTGG
* *
73356 TGGCATCTGACATGCAACATCTAAAGGTCCCAACTCCCAAGTAGTGATGACTTTCATGTTCTTTT
131 TGGCATCTGACATGCAACATCTAAAGGTCCCAACTCCCAAGTAGCGATGACTTCCATGTTCTTTT
*
73421 TTATCAGAAGAATTAGAGCATTGTGGAA
196 TTATCAGAAGAATTAGAACATTGTGGAA
* *
73449 TTGGTGTGAGAATTCTGAAATCCTTAAGCATGAAGCAGTTGGGTATTTTCGGTTCCTATTTATAA
1 TTGGTGTGAGAATTCTGAAATCCTTAAGCATGAAGCAGTTGGGTATTTTAGGTGCCTATTTATAA
73514 AGAACTTCGGTGGCATCCTCTCCTCTTTGTGGGAAGTTTCATAGATTCTTGGAGATCGAGATTGG
66 AGAACTTCGGTGGCATCCTCTCCTCTTTGTGGGAAGTTTCATAGATTCTTGGAGATCGAGATTGG
73579 TGGCATCTGACATGCAACATCTAAAGGTCCCAACTCCCAAGTAGCGATGACTTCCATGTTCTTTT
131 TGGCATCTGACATGCAACATCTAAAGGTCCCAACTCCCAAGTAGCGATGACTTCCATGTTCTTTT
73644 TTATCAGAAGAATTAGAACATTGTGGA
196 TTATCAGAAGAATTAGAACATTGTGGA
73671 TTTAATCTTT
Statistics
Matches: 217, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
223 217 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.33
Consensus pattern (223 bp):
TTGGTGTGAGAATTCTGAAATCCTTAAGCATGAAGCAGTTGGGTATTTTAGGTGCCTATTTATAA
AGAACTTCGGTGGCATCCTCTCCTCTTTGTGGGAAGTTTCATAGATTCTTGGAGATCGAGATTGG
TGGCATCTGACATGCAACATCTAAAGGTCCCAACTCCCAAGTAGCGATGACTTCCATGTTCTTTT
TTATCAGAAGAATTAGAACATTGTGGAA
Found at i:81215 original size:11 final size:11
Alignment explanation
Indices: 81199--81226 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
81189 GTGAGTAATT
81199 AAATATAATAG
1 AAATATAATAG
81210 AAATATAATAG
1 AAATATAATAG
81221 AAATAT
1 AAATAT
81227 CAAATAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (11 bp):
AAATATAATAG
Found at i:83205 original size:9 final size:9
Alignment explanation
Indices: 83187--83266 Score: 70
Period size: 9 Copynumber: 8.3 Consensus size: 9
83177 GGTCGGGTCG
*
83187 GGTCAGACC
1 GGTCAAACC
83196 GGTCAAACC
1 GGTCAAACC
*
83205 GGTTCGAACC
1 GG-TCAAACC
*
83215 GGTTGAAACC
1 GG-TCAAACC
83225 GGTCAAACC
1 GGTCAAACC
83234 GGTCAGAACC
1 GGTCA-AACC
*
83244 GGTTGAAAACC
1 GG-T-CAAACC
*
83255 GGTTAAACC
1 GGTCAAACC
83264 GGT
1 GGT
83267 TTCCAGCAGC
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
9 29 0.48
10 23 0.38
11 7 0.12
12 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:83227 original size:29 final size:31
Alignment explanation
Indices: 83193--83267 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
83183 GTCGGGTCAG
83193 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
83222 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
83252 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
83268 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:90406 original size:17 final size:17
Alignment explanation
Indices: 90384--90439 Score: 112
Period size: 17 Copynumber: 3.3 Consensus size: 17
90374 AACGGTCAAC
90384 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
90401 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
90418 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
90435 GGTCA
1 GGTCA
90440 GACCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.12, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:90453 original size:9 final size:9
Alignment explanation
Indices: 90435--90503 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
90425 GGTCGGGTCG
*
90435 GGTCAGACC
1 GGTCAAACC
90444 GGTCAAACC
1 GGTCAAACC
* *
90453 GATTCAGACC
1 G-GTCAAACC
90463 GGTCAAACC
1 GGTCAAACC
*
90472 GGTTGAAACC
1 GG-TCAAACC
90482 GGTCAAACC
1 GGTCAAACC
90491 GGTCAGAACC
1 GGTCA-AACC
90501 GGT
1 GGT
90504 TGAAAACCAG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
9 28 0.56
10 22 0.44
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:90472 original size:28 final size:27
Alignment explanation
Indices: 90435--90503 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
90425 GGTCGGGTCG
* * *
90435 GGTCAGACCGGTCAAACCGATTCAGACC
1 GGTCAAACCGGTCAAACCG-GTCAAACC
*
90463 GGTCAAACCGGTTGAAACCGGTCAAACC
1 GGTCAAACCGG-TCAAACCGGTCAAACC
90491 GGTCAGAACCGGT
1 GGTCA-AACCGGT
90504 TGAAAACCAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 22 0.63
29 13 0.37
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.14
Consensus pattern (27 bp):
GGTCAAACCGGTCAAACCGGTCAAACC
Found at i:90492 original size:19 final size:19
Alignment explanation
Indices: 90441--90503 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
90431 GTCGGGTCAG
* *
90441 ACCGGTCAAACCGATTCAG
1 ACCGGTCAAACCGGTTCAA
*
90460 ACCGGTCAAACCGGTTGAA
1 ACCGGTCAAACCGGTTCAA
90479 ACCGGTCAAACCGG-TCAGA
1 ACCGGTCAAACCGGTTCA-A
90498 ACCGGT
1 ACCGGT
90504 TGAAAACCAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 2 0.05
19 37 0.95
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.14
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAA
Found at i:92260 original size:12 final size:12
Alignment explanation
Indices: 92235--92304 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
92225 ACGAAGATAT
* *
92235 CAGAAATCAAAA
1 CAGAATTCAGAA
92247 CAGAATTCAGAA
1 CAGAATTCAGAA
*
92259 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* * *
92271 CAGAATCCATAT
1 CAGAATTCAGAA
*
92283 CAGAAATCAGAA
1 CAGAATTCAGAA
92295 CAGAATTCAG
1 CAGAATTCAG
92305 GTCATTTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.13, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:92302 original size:48 final size:48
Alignment explanation
Indices: 92231--92341 Score: 143
Period size: 48 Copynumber: 2.3 Consensus size: 48
92221 TTAAACGAAG
*
92231 ATATCAGAAATCAAAACAGAATTCAGAACAGATATCATAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTCAGAACAGATATCATAACAGAATCC
** ** *
92279 ATATCAGAAATCAGAACAGAATTCAGGTCATTTATCATAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTCAGAACAGATATCATAACAGAATCC
*
92327 A-AGTCGGAAATCAGA
1 ATA-TCAGAAATCAGA
92342 TAAAATTTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 54 0.98
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.22
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATTCAGAACAGATATCATAACAGAATCC
Found at i:92339 original size:24 final size:24
Alignment explanation
Indices: 92234--92339 Score: 90
Period size: 24 Copynumber: 4.4 Consensus size: 24
92224 AACGAAGATA
*
92234 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCATAACAGAATTCAAG
* * *
92257 AACAGATATCATAACAGAATCCATA-
1 -TCAGAAATCATAACAGAATTCA-AG
* *
92282 TCAGAAATCAGAACAGAATTCAGG
1 TCAGAAATCATAACAGAATTCAAG
***
92306 TCATTTATCATAACAGAATTCAAG
1 TCAGAAATCATAACAGAATTCAAG
*
92330 TCGGAAATCA
1 TCAGAAATCA
92340 GATAAAATTT
Statistics
Matches: 61, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
24 60 0.98
26 1 0.02
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (24 bp):
TCAGAAATCATAACAGAATTCAAG
Found at i:94752 original size:13 final size:13
Alignment explanation
Indices: 94734--94773 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
94724 GGGTCAACGA
94734 TCAACGGGTCGGG
1 TCAACGGGTCGGG
94747 TCAACGGGTCGGG
1 TCAACGGGTCGGG
94760 TCAACGGGTCGGG
1 TCAACGGGTCGGG
94773 T
1 T
94774 TGTGACCGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.15, C:0.23, G:0.45, T:0.17
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:101592 original size:29 final size:28
Alignment explanation
Indices: 101551--101607 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
101541 ATCAACGAAG
*
101551 AAGATGACAGCAAGAAGGGGTATGCCAA
1 AAGATGACAGCAAGAAGGGGTATACCAA
*
101579 AAGATGAACAGCAAGGAGGGGTATACCAA
1 AAGATG-ACAGCAAGAAGGGGTATACCAA
101608 GGCAAGATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.44, C:0.14, G:0.32, T:0.11
Consensus pattern (28 bp):
AAGATGACAGCAAGAAGGGGTATACCAA
Found at i:106516 original size:18 final size:19
Alignment explanation
Indices: 106481--106520 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
106471 ATTTAAAAAT
*
106481 TAAATTAATATGAATGAAA
1 TAAAATAATATGAATGAAA
106500 TAAAATAATAT-AATGAAA
1 TAAAATAATATGAATGAAA
106518 TAA
1 TAA
106521 GCAATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (19 bp):
TAAAATAATATGAATGAAA
Found at i:106575 original size:2 final size:2
Alignment explanation
Indices: 106570--106614 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
106560 ACACACATAA
** * *
106570 AT AT AT AT AT GC AT AA AT AT AT AT AC 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
106612 AT A
1 AT A
106615 ATAAAATCTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:106591 original size:14 final size:14
Alignment explanation
Indices: 106564--106608 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
106554 AATTAAACAC
106564 ACATAAATATATAT
1 ACATAAATATATAT
106578 ATGCATAAATATATAT
1 A--CATAAATATATAT
*
106594 ACATATATATATAT
1 ACATAAATATATAT
106608 A
1 A
106609 TATATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 14 0.50
16 14 0.50
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (14 bp):
ACATAAATATATAT
Found at i:106610 original size:16 final size:15
Alignment explanation
Indices: 106564--106617 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
106554 AATTAAACAC
106564 ACATAAATATATATAT
1 ACAT-AATATATATAT
*
106580 GCATAA-ATATATAT
1 ACATAATATATATAT
106594 ACATATATATATATAT
1 ACATA-ATATATATAT
*
106610 ATATAATA
1 ACATAATA
106618 AAATCTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 12 0.36
15 6 0.18
16 15 0.45
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.39
Consensus pattern (15 bp):
ACATAATATATATAT
Found at i:106707 original size:16 final size:16
Alignment explanation
Indices: 106688--106721 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
106678 CTTTAAAAAC
* *
106688 AAAGGACTAAATTATA
1 AAAGGACAAAATGATA
106704 AAAGGACAAAATGATA
1 AAAGGACAAAATGATA
106720 AA
1 AA
106722 GCATAAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.15, T:0.18
Consensus pattern (16 bp):
AAAGGACAAAATGATA
Found at i:108319 original size:43 final size:42
Alignment explanation
Indices: 108175--108499 Score: 156
Period size: 43 Copynumber: 7.7 Consensus size: 42
108165 AGATTGTCTG
* * *
108175 AGGGTGACACTGCTCCTATGTGATGAAGAGGTCTGG---TC-G
1 AGGGTGACACGGCTCCTACGTGATGAAGAGG-CTGGTTATCTA
* * * ** *
108214 AGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCAT-AA
1 AGG-GTGACACGGCTCCTACGTGATGAAGAG-GCTGGTTATCTA
* * *
108257 AGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
1 AGG-G-TGACACGGCTCCTACGTGATGAAGA-GGCTGGTTATCTA
* *
108302 AGGGTGACACGGCTCCTACGTGATGAAGAGGTATGG---TCGA
1 AGGGTGACACGGCTCCTACGTGATGAAGAGG-CTGGTTATCTA
* * * * **
108342 A-TG-GACACGACTCATACGTGATGAAGAGTTCTGGCCATCTAA
1 AGGGTGACACGGCTCCTACGTGATGAAGAG-GCTGGTTATCT-A
* * *
108384 AGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
1 AGG-G-TGACACGGCTCCTACGTGATGAAGA-GGCTGGTTATCTA
* * * *
108429 TGGTTGACACGGCTCATACGTGATGAAGAGATCTGG-TA--T-
1 AGGGTGACACGGCTCCTACGTGATGAAGAG-GCTGGTTATCTA
* *
108468 GGGGAATGACACGGCTCATACGTGATGAAGAG
1 AGGG--TGACACGGCTCCTACGTGATGAAGAG
108500 TTATGGCCAT
Statistics
Matches: 218, Mismatches: 45, Indels: 44
0.71 0.15 0.14
Matches are distributed among these distances:
38 26 0.12
39 6 0.03
40 32 0.15
41 28 0.13
42 7 0.03
43 54 0.25
44 29 0.13
45 8 0.04
46 27 0.12
47 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.24
Consensus pattern (42 bp):
AGGGTGACACGGCTCCTACGTGATGAAGAGGCTGGTTATCTA
Found at i:108319 original size:127 final size:127
Alignment explanation
Indices: 108175--108551 Score: 589
Period size: 127 Copynumber: 2.9 Consensus size: 127
108165 AGATTGTCTG
* *
108175 AGGGTGACACTGCTCCTATGTGATGAAGAGGTCTGGTCGAGGAATGACACGGCTCATACGTGATG
1 AGGGTGACACGGCTCCTACGTGATGAAGAGGTCTGGTCG-GGAATGACACGGCTCATACGTGATG
108240 AAGAGTTCTGGCCA-TAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
65 AAGAGTTCTGGCCACTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
* *
108302 AGGGTGACACGGCTCCTACGTGATGAAGAGGTATGGTC--GAATGGACACGACTCATACGTGATG
1 AGGGTGACACGGCTCCTACGTGATGAAGAGGTCTGGTCGGGAAT-GACACGGCTCATACGTGATG
108365 AAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
65 AAGAGTTCTGGCCA-CTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
* * * * *
108429 TGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTATGGGGAATGACACGGCTCATACGTGAT
1 AGGGTGACACGGCTCCTACGTGATGAAGAGGTCTGG--TCGGGAATGACACGGCTCATACGTGAT
*
108494 GAAGAGTTATGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGG
64 GAAGAGTTCTGGCCA-CTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGG
108552 CCATCTTTAG
Statistics
Matches: 231, Mismatches: 12, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
124 4 0.02
125 33 0.14
127 114 0.49
129 1 0.00
130 75 0.32
131 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.24
Consensus pattern (127 bp):
AGGGTGACACGGCTCCTACGTGATGAAGAGGTCTGGTCGGGAATGACACGGCTCATACGTGATGA
AGAGTTCTGGCCACTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
Found at i:108428 original size:46 final size:44
Alignment explanation
Indices: 108221--108541 Score: 147
Period size: 43 Copynumber: 7.5 Consensus size: 44
108211 TCGAGGAATG
** * *
108221 ACACGGCTCATACGTGATGAAGAGTTCTGGCCAT-AAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGG-TATCTAAGGTGATA
* * * *
108265 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAAGG-G-TG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGG-TATCTAAGGTGATA
* * * *
108308 ACACGGCTCCTACGTGATGAAGAG-GTATGG--TCGAA--TG--G
1 ACACGGCTCATACGTGATGAAGAGAG-CTGGTATCTAAGGTGATA
* ** *
108346 ACACGACTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGG-TATCT-AAGGTGATA
* * * * *
108392 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT--TG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGG-TATCTAAGGTGATA
* * *
108435 ACACGGCTCATACGTGATGAAGAGATCTGGTA--T--GGGGAATG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTATCTAAGGTG-ATA
*** *
108476 ACACGGCTCATACGTGATGAAGAGTTATGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGG-TATCT-AAGGTGATA
* *
108522 ACACGGTTCCTACGTGATGA
1 ACACGGCTCATACGTGATGA
108542 GGACGGCTGG
Statistics
Matches: 214, Mismatches: 39, Indels: 46
0.72 0.13 0.15
Matches are distributed among these distances:
38 28 0.13
39 1 0.00
40 5 0.02
41 32 0.15
42 8 0.04
43 50 0.23
44 30 0.14
45 9 0.04
46 47 0.22
47 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (44 bp):
ACACGGCTCATACGTGATGAAGAGAGCTGGTATCTAAGGTGATA
Found at i:108553 original size:46 final size:45
Alignment explanation
Indices: 108346--108557 Score: 136
Period size: 46 Copynumber: 4.8 Consensus size: 45
108336 GGTCGAATGG
* **
108346 ACACGACTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGGCCATCT-AAGGTGATA
* * * ** * *
108392 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT--TG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGCCATCTAAGGTGATA
* * * *
108435 ACACGGCTCATACGTGATGAAGAGATCTGG-----TATGGGGAATG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGCCATCTAAGGTG-ATA
***
108476 ACACGGCTCATACGTGATGAAGAGTTATGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGGCCATCT-AAGGTGATA
* * *
108522 ACACGGTTCCTACGTGATGAGGACG-GCTGGCCATCT
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGCCATCT
108558 TTAGGAGTTA
Statistics
Matches: 130, Mismatches: 24, Indels: 24
0.73 0.13 0.13
Matches are distributed among these distances:
38 5 0.04
41 30 0.23
42 1 0.01
43 25 0.19
45 4 0.03
46 59 0.45
47 6 0.05
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (45 bp):
ACACGGCTCATACGTGATGAAGAGAGCTGGCCATCTAAGGTGATA
Found at i:108622 original size:27 final size:28
Alignment explanation
Indices: 108570--108657 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 28
108560 AGGAGTTATG
* *
108570 GTTTCAAGAGAAACCAAA-TTAAAGATTT
1 GTTTCAAGA-AAAACAAACTCAAAGATTT
*
108598 GTTTCAA-AAGAAACAAAC-CCAAGATTT
1 GTTTCAAGAA-AAACAAACTCAAAGATTT
*
108625 GTTTCAAGAAAAACATACTCAAAGACTTT
1 GTTTCAAGAAAAACAAACTCAAAGA-TTT
108654 GTTT
1 GTTT
108658 GTTTTGTTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.02
27 28 0.56
28 14 0.28
29 7 0.14
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.28
Consensus pattern (28 bp):
GTTTCAAGAAAAACAAACTCAAAGATTT
Found at i:109205 original size:27 final size:27
Alignment explanation
Indices: 109171--109227 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
109161 TAAAATTTTG
*
109171 TTTCAAAAGAAATAGACTCAAAGAT-TT
1 TTTCAAAAGAAACA-ACTCAAAGATATT
109198 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTCAAAAGAAACAACTCAAAGATATT
109225 TTT
1 TTT
109228 TAATTAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (27 bp):
TTTCAAAAGAAACAACTCAAAGATATT
Found at i:109226 original size:26 final size:27
Alignment explanation
Indices: 109171--109226 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
109161 TAAAATTTTG
* *
109171 TTTCAAAAGAAATAGACTCAAAGATTT
1 TTTCAAAAGAAACAGACTCAAAGATAT
109198 TTTCAAAAGAAACA-ACTCAAAGATAT
1 TTTCAAAAGAAACAGACTCAAAGATAT
109224 TTT
1 TTT
109227 TTAATTAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.30
Consensus pattern (27 bp):
TTTCAAAAGAAACAGACTCAAAGATAT
Found at i:109252 original size:92 final size:89
Alignment explanation
Indices: 109102--109317 Score: 217
Period size: 92 Copynumber: 2.4 Consensus size: 89
109092 TCGAGAAAAT
* * ** *
109102 TTTTTTCAAAGGAAACAAACTCAAAGATTTTCTTCTCAAGAGAAATTGTCTTTAAGAGATAAAAT
1 TTTTTTCAAAAGAAACAAACTCAAAGATTTTCTTCTCAAGAGAAACTGTCTCAAAGAGACAAAAT
109167 T-TTGTTTCAAAAGAAATAGACTCAAAGA
66 TGTT-TTT---AA-AAATAGACTCAAAGA
*
109195 TTTTTTCAAAAGAAAC-AACTCAAAGATATTT-TT-T-AATTAGAAACTGTCTCAAGAGAGACAA
1 TTTTTTCAAAAGAAACAAACTCAAAGAT-TTTCTTCTCAA-GAGAAACTGTCTCAA-AGAGACAA
*
109256 CATTGTTTTTAAAAATAGACTCAAAGA
63 AATTGTTTTTAAAAATAGACTCAAAGA
* *
109283 TGATTTTGTTAAGAGAAACAAACTCAAAGATTTTC
1 T--TTTT-TCAAAAGAAACAAACTCAAAGATTTTC
109318 AAAATGAACA
Statistics
Matches: 105, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
88 16 0.15
89 2 0.02
90 6 0.06
91 24 0.23
92 37 0.35
93 20 0.19
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (89 bp):
TTTTTTCAAAAGAAACAAACTCAAAGATTTTCTTCTCAAGAGAAACTGTCTCAAAGAGACAAAAT
TGTTTTTAAAAATAGACTCAAAGA
Done.