Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006213.1 Hibiscus syriacus cultivar Beakdansim tig00014801_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: 55744
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:2448 original size:10 final size:10
Alignment explanation
Indices: 2433--2507 Score: 57
Period size: 10 Copynumber: 8.7 Consensus size: 10
2423 CATTTAATAA
2433 ATAAACGAAC
1 ATAAACGAAC
2443 ATAAACGAAC
1 ATAAACGAAC
2453 AT----GAAC
1 ATAAACGAAC
2459 ATAAACGAAC
1 ATAAACGAAC
2469 ----ACGAAC
1 ATAAACGAAC
*
2475 ATAAATGAAC
1 ATAAACGAAC
2485 AT----GAAC
1 ATAAACGAAC
2491 ATAAACGAAC
1 ATAAACGAAC
2501 ATAAACG
1 ATAAACG
2508 TTGGATACCC
Statistics
Matches: 52, Mismatches: 1, Indels: 24
0.68 0.01 0.31
Matches are distributed among these distances:
6 18 0.35
10 34 0.65
ACGTcount: A:0.57, C:0.19, G:0.12, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:2460 original size:16 final size:16
Alignment explanation
Indices: 2439--2502 Score: 110
Period size: 16 Copynumber: 4.0 Consensus size: 16
2429 ATAAATAAAC
2439 GAACATAAACGAACAT
1 GAACATAAACGAACAT
*
2455 GAACATAAACGAACAC
1 GAACATAAACGAACAT
*
2471 GAACATAAATGAACAT
1 GAACATAAACGAACAT
2487 GAACATAAACGAACAT
1 GAACATAAACGAACAT
2503 AAACGTTGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.12
Consensus pattern (16 bp):
GAACATAAACGAACAT
Found at i:4052 original size:79 final size:78
Alignment explanation
Indices: 3956--4114 Score: 248
Period size: 79 Copynumber: 2.0 Consensus size: 78
3946 TCAGATTGAC
* *
3956 TATCAGTTACTGGAATGTAATCGAGTATCCAATGTCTCATAAAATTTTTCTT-AATCTCAAAGCG
1 TATCAGTTACTGAAATGTAATCGA-AATCCAATGTCTCATAAAA-TTTTCTTAAATCTCAAAGCG
4020 AACCTAAGGTCTCTA
64 AACCTAAGGTCTCTA
* *
4035 TATCAGTTACTGAAATGTAATCGAAATCCAATGTCTCATAAAATTTTCTTAAAATTTCGAAGCGA
1 TATCAGTTACTGAAATGTAATCGAAATCCAATGTCTCATAAAATTTTCTT-AAATCTCAAAGCGA
4100 ACCTAAGGTCTCTA
65 ACCTAAGGTCTCTA
4114 T
1 T
4115 TTAATACAAT
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
77 7 0.09
78 18 0.24
79 49 0.66
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (78 bp):
TATCAGTTACTGAAATGTAATCGAAATCCAATGTCTCATAAAATTTTCTTAAATCTCAAAGCGAA
CCTAAGGTCTCTA
Found at i:4762 original size:2 final size:2
Alignment explanation
Indices: 4757--4799 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
4747 AAAAAAAATA
4757 AT AT AT AT AT AT AT AT AT AT A- 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
4798 AT
1 AT
4800 TAAATTTGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4780 original size:21 final size:21
Alignment explanation
Indices: 4754--4798 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
4744 TTAAAAAAAA
4754 ATAATATATATATATATATAT
1 ATAATATATATATATATATAT
4775 ATAATATATATATATATATAT
1 ATAATATATATATATATATAT
4796 ATA
1 ATA
4799 TTAAATTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAATATATATATATATATAT
Found at i:8749 original size:18 final size:18
Alignment explanation
Indices: 8726--8762 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
8716 CTACCGATTC
*
8726 ATTGATTTAATCGGTCGA
1 ATTGATTCAATCGGTCGA
*
8744 ATTGATTCGATCGGTCGA
1 ATTGATTCAATCGGTCGA
8762 A
1 A
8763 AGAATCGGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (18 bp):
ATTGATTCAATCGGTCGA
Found at i:8963 original size:15 final size:15
Alignment explanation
Indices: 8945--8985 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
8935 GGTAAAACAT
8945 ATTAAATAATAAATA
1 ATTAAATAATAAATA
*
8960 ATTATATAAT--ATA
1 ATTAAATAATAAATA
8973 ATTAAA-AATAAAT
1 ATTAAATAATAAAT
8986 TTGGGGCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 3 0.14
13 8 0.36
14 2 0.09
15 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTAAATAATAAATA
Found at i:9533 original size:8 final size:9
Alignment explanation
Indices: 9513--9545 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
9503 TTAGCCGGTC
9513 CGGTTCAAA
1 CGGTTCAAA
9522 CGGTTC-AA
1 CGGTTCAAA
9530 CGGTTCAAA
1 CGGTTCAAA
9539 CGGTTCA
1 CGGTTCA
9546 CTAGTAGCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (9 bp):
CGGTTCAAA
Found at i:9535 original size:17 final size:17
Alignment explanation
Indices: 9513--9545 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9503 TTAGCCGGTC
9513 CGGTTCAAACGGTTCAA
1 CGGTTCAAACGGTTCAA
9530 CGGTTCAAACGGTTCA
1 CGGTTCAAACGGTTCA
9546 CTAGTAGCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (17 bp):
CGGTTCAAACGGTTCAA
Found at i:10254 original size:32 final size:32
Alignment explanation
Indices: 10178--10269 Score: 134
Period size: 30 Copynumber: 2.9 Consensus size: 32
10168 TTCGGGTTCA
*
10178 GGTCGGGTCGGGTTTTTTTAAGTTTGATATTC
1 GGTCGGGTCGGGTTTTTTTAAGTGTGATATTC
* *
10210 --TCGAGTCGGGTTTTTTTAAGCGTGATATTC
1 GGTCGGGTCGGGTTTTTTTAAGTGTGATATTC
*
10240 GGTCGGGTCAGGTTTTTTTAAGTGTGATAT
1 GGTCGGGTCGGGTTTTTTTAAGTGTGATAT
10270 CCGGGTCAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
30 27 0.52
32 25 0.48
ACGTcount: A:0.15, C:0.10, G:0.30, T:0.45
Consensus pattern (32 bp):
GGTCGGGTCGGGTTTTTTTAAGTGTGATATTC
Found at i:10876 original size:16 final size:18
Alignment explanation
Indices: 10855--10902 Score: 73
Period size: 16 Copynumber: 2.8 Consensus size: 18
10845 GTTTCAGATT
10855 CAGATTCCAATTCC-T-A
1 CAGATTCCAATTCCTTCA
10871 CAGATTCCAATTCCTTCA
1 CAGATTCCAATTCCTTCA
*
10889 CAGATTTCAATTCC
1 CAGATTCCAATTCC
10903 CTCAGAAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 14 0.48
17 1 0.03
18 14 0.48
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.33
Consensus pattern (18 bp):
CAGATTCCAATTCCTTCA
Found at i:17607 original size:21 final size:21
Alignment explanation
Indices: 17581--17638 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
17571 AGGCTTGATA
17581 GTATCGATACTATTGTTCAAG
1 GTATCGATACTATTGTTCAAG
* *
17602 GTATCGATACTACTGTTCATG
1 GTATCGATACTATTGTTCAAG
17623 GTATCGATACTATTGT
1 GTATCGATACTATTGT
17639 AGCACTATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.40
Consensus pattern (21 bp):
GTATCGATACTATTGTTCAAG
Found at i:19060 original size:19 final size:20
Alignment explanation
Indices: 19024--19071 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
19014 TGTAAATCAT
*
19024 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTGG
*
19044 TTTTCAAAA-TCCATTTTTG
1 TTTTCAAAATTCCATTTTGG
*
19063 CTTTCAAAA
1 TTTTCAAAA
19072 GAAAATCGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGG
Found at i:19928 original size:33 final size:33
Alignment explanation
Indices: 19886--19948 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
19876 CTTTACAAAC
19886 TCCCTAGTTTTTCACGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTTCACGGGCTAAACTAGAACCTT
19919 TCCCTAGTTTTTCACGGGCTAAACTAGAAC
1 TCCCTAGTTTTTCACGGGCTAAACTAGAAC
19949 AAAAACCCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (33 bp):
TCCCTAGTTTTTCACGGGCTAAACTAGAACCTT
Found at i:28357 original size:23 final size:23
Alignment explanation
Indices: 28310--28359 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
28300 AATAACATAT
**
28310 TAGGTAGCGCTTAGATAATGTAA
1 TAGGTAGCGCTTAGATAATAAAA
*
28333 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTAGATAATAAAA
28356 TAGG
1 TAGG
28360 CATTTAACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (23 bp):
TAGGTAGCGCTTAGATAATAAAA
Found at i:29497 original size:182 final size:182
Alignment explanation
Indices: 28848--29497 Score: 864
Period size: 182 Copynumber: 3.6 Consensus size: 182
28838 ATTAAACTAC
* *
28848 CGACACTTTCAACATA-ATCGGTAGCGTTTTACCGGTTTTGTCATTTCGATACCGGTTTTATCAT
1 CGACACTTTCAATATATA-CGGTAGCGTTTTACCGGTTTTATCATTTCGATACCGGTTTTATCAT
* * * * *
28912 ACTT-TTACCTATTATATTGTTATGGATCAATACATTTTCT-TAAAGTATCGACACTTTTTAGGC
65 A-TTATTACCTGTTATATTGCTATGAATCGATACATTTT-TATAAAGTATCGACACCTTTTAGGC
* *
28975 GCTATAATTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
128 GCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
* * * * * **
29030 CGACACTTTAAATATAT-CTGGTATCTTTTTACCGGTTTTATTATTTCGATGCCTCTTTTATCAT
1 CGACACTTTCAATATATAC-GGTAGCGTTTTACCGGTTTTATCATTTCGATACCGGTTTTATCAT
* * * * *
29094 ATTATTACCGGATATATTACTATGGATCGATACATTTGTATAAAGTATCGACA-CTTTTCAGGCG
65 ATTATTACCTGTTATATTGCTATGAATCGATACATTTTTATAAAGTATCGACACCTTTT-AGGCG
*
29158 CTATAACTTCTTCTCTTTTAAATTAAAAAAGTGTCGATACTTATATTAATTTAT
129 CTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
* * * * * * *
29212 CGACACTTTCAATATATCCGGTAACTTTTTACCGGTTTTATCATTTCAAGACCTGTTTTGTCATA
1 CGACACTTTCAATATATACGGTAGCGTTTTACCGGTTTTATCATTTCGATACCGGTTTTATCATA
* *
29277 TTATTACCTGTTATATTGCTAT-AGATCGACATATTTTTATAAAGTATCGACACCTTTTAGGCGC
66 TTATTACCTGTTATATTGCTATGA-ATCGATACATTTTTATAAAGTATCGACACCTTTTAGGCGC
*
29341 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGACACTTATATTAATTTAT
130 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
* * *
29394 CGACACTTTCAATATATACGGTAGCGCTTTACCGGTTTTATCATAAT-GACACCGGTTTTATCAT
1 CGACACTTTCAATATATACGGTAGCGTTTTACCGGTTTTATCAT-TTCGATACCGGTTTTATCAT
*
29458 ATTTTTACCTGTTATATTGCTATGAATCGATACATTTTTA
65 ATTATTACCTGTTATATTGCTATGAATCGATACATTTTTA
29498 ATTTGTATCG
Statistics
Matches: 409, Mismatches: 49, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
181 8 0.02
182 393 0.96
183 8 0.02
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (182 bp):
CGACACTTTCAATATATACGGTAGCGTTTTACCGGTTTTATCATTTCGATACCGGTTTTATCATA
TTATTACCTGTTATATTGCTATGAATCGATACATTTTTATAAAGTATCGACACCTTTTAGGCGCT
ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
Found at i:31387 original size:20 final size:20
Alignment explanation
Indices: 31362--31399 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31352 CTTAATTTTA
31362 AATTAATT-AAATCTAAAATT
1 AATTAATTCAAAT-TAAAATT
31382 AATTAATTCAAATTAAAA
1 AATTAATTCAAATTAAAA
31400 ATATTATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTAATTCAAATTAAAATT
Found at i:33715 original size:21 final size:22
Alignment explanation
Indices: 33674--33718 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
33664 TAATAATAAT
33674 AACAATAATAATTAAATATATA
1 AACAATAATAATTAAATATATA
33696 AACATATAA-AATTAAA-ATATA
1 AACA-ATAATAATTAAATATATA
33717 AA
1 AA
33719 TAAACAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (22 bp):
AACAATAATAATTAAATATATA
Found at i:33771 original size:37 final size:34
Alignment explanation
Indices: 33683--33780 Score: 90
Period size: 37 Copynumber: 2.7 Consensus size: 34
33673 TAACAATAAT
*
33683 AATTAAATATATAAACAT-ATAAAATTAAAATATA
1 AATTAAA-ATATAAAAATAATAAAATTAAAATATA
* *
33717 AATAAACAATGACAAAAATAAATAAAATTAAAACTATA
1 AATTAA-AAT-ATAAAAAT-AATAAAATTAAAA-TATA
*
33755 GTATTAAAATATAAAAAGTAATAAAA
1 -AATTAAAATATAAAAA-TAATAAAA
33781 CTTGTAAGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
34 7 0.14
35 7 0.14
37 25 0.49
38 8 0.16
39 4 0.08
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (34 bp):
AATTAAAATATAAAAATAATAAAATTAAAATATA
Found at i:34599 original size:14 final size:14
Alignment explanation
Indices: 34580--34606 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34570 GTGGTAAGTG
34580 TTTTTTTCTTTTCT
1 TTTTTTTCTTTTCT
34594 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
34607 GAATGGTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTCTTTTCT
Found at i:35104 original size:3 final size:3
Alignment explanation
Indices: 35096--35172 Score: 95
Period size: 3 Copynumber: 26.0 Consensus size: 3
35086 GGCCTGTTTG
* *
35096 TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA TAA TAG T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
35143 TAAA TAA -AA TAA TAA TAA TAT TAA AAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35173 AAAACAAATG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
2 3 0.05
3 58 0.92
4 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:35833 original size:123 final size:123
Alignment explanation
Indices: 35539--35871 Score: 458
Period size: 123 Copynumber: 2.7 Consensus size: 123
35529 GAATTAAGGC
* * * * *
35539 AAGGTTGAATAGGTTCTTCTCATTATGAACTTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTC-CTCTTCAGATAAGTTCTTCTCATTA
* * * *
35603 TGAACACTT-T-TGGAAATGTTGATGCTAAATCTATCTCCTTTTGTGATAGAGTCATGCA
65 TGAAC-TTTCTCTGGAAAAGTTGATACTAAATCTATCTCCTTCTGTGATAGAGTCATGCA
** * *
35661 AAGGTTGAACAAGTTCTTCTCATTATGATTTTTTTCTTCCTCTTCAGATAAGTTCTTCTCATAAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* *
35726 GAACTTTCTCTGGAAAAGTTTATACT-GATCTATCTCCTTCTGTGATAGAGTCATGCAA
66 GAACTTTCTCTGGAAAAGTTGATACTAAATCTATCTCCTTCTGTGATAGAGTCATGC-A
* *
35784 AAGGTTGAACAAGCTCTTCTCATTATAAACTTATTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
35849 GAACTTTCTCTGGAAAAGTTGAT
66 GAACTTTCTCTGGAAAAGTTGAT
35872 CCATCGAGTG
Statistics
Matches: 186, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
121 2 0.01
122 87 0.47
123 97 0.52
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.41
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTTTCTCTGGAAAAGTTGATACTAAATCTATCTCCTTCTGTGATAGAGTCATGCA
Found at i:35968 original size:106 final size:105
Alignment explanation
Indices: 35791--35990 Score: 312
Period size: 106 Copynumber: 1.9 Consensus size: 105
35781 CAAAAGGTTG
*
35791 AACAAGCTCTTCTCATTATAAACTTATTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTT
1 AACAAGCTCTTCTCATTATAAACTTATTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTA
*
35856 CTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCAA
66 CTCTGGAAAAGTTGATCCATCGAATGATGAATTCGAGCAA
* * *
35896 AACAAGTTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATAAACTTATTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACT-
* *
35961 TAC-CTGGAAATGTTGATCCATTGAATGATG
64 TACTCTGGAAAAGTTGATCCATCGAATGATG
35991 GATTTGAATC
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
105 31 0.36
106 53 0.62
107 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (105 bp):
AACAAGCTCTTCTCATTATAAACTTATTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTA
CTCTGGAAAAGTTGATCCATCGAATGATGAATTCGAGCAA
Found at i:36384 original size:22 final size:22
Alignment explanation
Indices: 36359--36429 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
36349 AAATCTTTCT
* *
36359 TCTTTGAAAAGATAATGTATCA
1 TCTTTGAAAAGAGAATATATCA
* *
36381 TCTTTTAAGAGAGAATATATCA
1 TCTTTGAAAAGAGAATATATCA
*
36403 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAAAGAGAATATATCA
36425 TCTTT
1 TCTTT
36430 AAAGAATGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (22 bp):
TCTTTGAAAAGAGAATATATCA
Found at i:37114 original size:22 final size:21
Alignment explanation
Indices: 37054--37106 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 21
37044 ATGTTTATAT
*
37054 AAAAGAATAAATTGAATTTTG
1 AAAAGAATAAATTGAATTTAG
37075 AAAATGAATAAATTGAATTTAG
1 AAAA-GAATAAATTGAATTTAG
37097 AAAAG-ATAAA
1 AAAAGAATAAA
37107 CTTGGAATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 5 0.17
21 5 0.17
22 20 0.67
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.28
Consensus pattern (21 bp):
AAAAGAATAAATTGAATTTAG
Found at i:47718 original size:25 final size:25
Alignment explanation
Indices: 47655--47718 Score: 58
Period size: 26 Copynumber: 2.5 Consensus size: 25
47645 AGTAATAAAG
*
47655 AAGAATATATAAAATATTATGAAAAT
1 AAGAAT-TATAAAATATTATGAAAAA
* * *
47681 AATAAGTATTAAAA-ATTTTGAAAGAA
1 AAGAATTA-TAAAATATTATGAAA-AA
47707 AAGAATTATAAA
1 AAGAATTATAAA
47719 TTAAATAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
25 14 0.47
26 16 0.53
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (25 bp):
AAGAATTATAAAATATTATGAAAAA
Found at i:48198 original size:2 final size:2
Alignment explanation
Indices: 48185--48224 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
48175 TTTTAAGAAA
48185 AT AT AT -T A- 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
48225 TTATTTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48649 original size:25 final size:22
Alignment explanation
Indices: 48602--48654 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
48592 ACATAATAAT
48602 AACAATAATAATTAAATATATA
1 AACAATAATAATTAAATATATA
48624 AACATATAA-AATATAAATATAAATA
1 AACA-ATAATAAT-TAAATAT--ATA
48649 AACAAT
1 AACAAT
48655 GACAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 7 0.26
23 11 0.41
24 2 0.07
25 7 0.26
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (22 bp):
AACAATAATAATTAAATATATA
Found at i:50038 original size:3 final size:3
Alignment explanation
Indices: 50030--50113 Score: 102
Period size: 3 Copynumber: 29.0 Consensus size: 3
50020 GGCCTGTTTG
*
50030 TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
50077 TAA TAA -AA TAG T-A TAA AAA TAA TAA TAT TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
50114 AAAATAAATG
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
2 5 0.07
3 63 0.93
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:50936 original size:51 final size:50
Alignment explanation
Indices: 50881--51008 Score: 148
Period size: 51 Copynumber: 2.5 Consensus size: 50
50871 CTAGCAGTAA
* * **
50881 AGCGCAACCCCTGCACCGCGCTATACGATGATTTGGCACCACGTGGGGTAT
1 AGCGCGACCCCTGCACCGCGCTATACGATAAGCTGGCACCACGT-GGGTAT
* * * **
50932 AGCGCGCCCCCTGCACCGCGCTATATGGTAAGCTGGCGGCACGTGGGTAT
1 AGCGCGACCCCTGCACCGCGCTATACGATAAGCTGGCACCACGTGGGTAT
* *
50982 AGCGCGGCCCCTGCAGCGCGCTATACG
1 AGCGCGACCCCTGCACCGCGCTATACG
51009 CCACGTAGGG
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
50 30 0.46
51 35 0.54
ACGTcount: A:0.18, C:0.34, G:0.31, T:0.17
Consensus pattern (50 bp):
AGCGCGACCCCTGCACCGCGCTATACGATAAGCTGGCACCACGTGGGTAT
Found at i:53831 original size:3 final size:3
Alignment explanation
Indices: 53825--53859 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
53815 ATCATCACCA
* *
53825 TCG TCG TCG TCG TCG TCA TTG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
53860 TTGCGCAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.31, G:0.29, T:0.37
Consensus pattern (3 bp):
TCG
Done.