Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009035.1 Hibiscus syriacus cultivar Beakdansim tig00112442_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: 74957
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:1477 original size:21 final size:21
Alignment explanation
Indices: 1451--1490 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1441 CAGAACCCCA
*
1451 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1472 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1491 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1519 original size:20 final size:21
Alignment explanation
Indices: 1473--1533 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
1463 TTCCCCTGTG
1473 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
1496 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
1516 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1534 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:7911 original size:19 final size:19
Alignment explanation
Indices: 7887--7925 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
7877 CAGGTTGAAA
*
7887 TTGTAATCGGGCCTCTGGG
1 TTGTAATCGGGCCTCCGGG
*
7906 TTGTAATTGGGCCTCCGGG
1 TTGTAATCGGGCCTCCGGG
7925 T
1 T
7926 ATGGGCCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.10, C:0.21, G:0.36, T:0.33
Consensus pattern (19 bp):
TTGTAATCGGGCCTCCGGG
Found at i:7964 original size:3 final size:3
Alignment explanation
Indices: 7958--8080 Score: 212
Period size: 3 Copynumber: 41.0 Consensus size: 3
7948 TAGTATTATT
7958 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
8006 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
8054 TAA TAA TAA TAA TAA -AGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA
8081 AACAGAATGG
Statistics
Matches: 114, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
2 1 0.01
3 112 0.98
4 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:8310 original size:23 final size:22
Alignment explanation
Indices: 8267--8311 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
8257 TATCAAGAGC
* *
8267 GTAACTTTTTAGGTTGGATCGA
1 GTAACATTTTAGGTTGAATCGA
8289 GTAACATTTTAGGTTGAAATCGA
1 GTAACATTTTAGGTTG-AATCGA
8312 AAATGTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
GTAACATTTTAGGTTGAATCGA
Found at i:8584 original size:30 final size:31
Alignment explanation
Indices: 8518--8584 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
8508 ATTTATAAAT
*
8518 ATTTTG-AGTGGTCAAATTGAATTTTTTTAA
1 ATTTTGAAGTGGTCAAATTGAAATTTTTTAA
* *
8548 AATTTGAAG-GGTCAAAATT-AAATTTTTTGA
1 ATTTTGAAGTGGTC-AAATTGAAATTTTTTAA
8578 ATTTTGA
1 ATTTTGA
8585 GGGGCCCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
30 24 0.77
31 7 0.23
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.46
Consensus pattern (31 bp):
ATTTTGAAGTGGTCAAATTGAAATTTTTTAA
Found at i:15099 original size:13 final size:13
Alignment explanation
Indices: 15083--15128 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
15073 AGTAAAATTG
*
15083 ATATATAAATTTA
1 ATATATATATTTA
15096 ATATA-ATATTTA
1 ATATATATATTTA
15108 ATA-ATATTATTTA
1 ATATATA-TATTTA
15121 AT-TATATA
1 ATATATATA
15129 CCATTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
11 1 0.03
12 12 0.41
13 16 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATATATATATTTA
Found at i:15284 original size:16 final size:16
Alignment explanation
Indices: 15263--15304 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
15253 ACATGCACAA
15263 TAAGAAATAAACAT-TT
1 TAAGAAATAAA-ATATT
15279 TAAGAAATAAAATATT
1 TAAGAAATAAAATATT
*
15295 TAAAAAATAA
1 TAAGAAATAA
15305 GTACATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 2 0.08
16 22 0.92
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (16 bp):
TAAGAAATAAAATATT
Found at i:17294 original size:3 final size:3
Alignment explanation
Indices: 17286--17316 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
17276 ATCACCATTT
17286 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
17317 AAATCAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:22599 original size:95 final size:96
Alignment explanation
Indices: 22432--22712 Score: 435
Period size: 95 Copynumber: 3.0 Consensus size: 96
22422 TATAATATTA
* *
22432 TATA-TATACAATAAAGCTTGAGTTGTCCCTCTAGAGA-AATTGGTTAAACGCACCGACTTTATA
1 TATACTATACAATAAAGCTTGAGTTGTCCCTCTAGAGACAATTGGTTAAACGCCCCGACTTTATG
22495 GATAATATTCAGCTAGCCTGATAAAGGTGAT
66 GATAATATTCAGCTAGCCTGATAAAGGTGAT
22526 TATACTATACAATAAAGCTTGAGTTGTCCCTCTAGA-ACAATTGGTTAAACGCCCCGACTTTATG
1 TATACTATACAATAAAGCTTGAGTTGTCCCTCTAGAGACAATTGGTTAAACGCCCCGACTTTATG
*
22590 GATAATATTCAGCTAGCCTGATAAATGTGAT
66 GATAATATTCAGCTAGCCTGATAAAGGTGAT
* * * * *
22621 TATACTATACAATAAAGCTTGAGCTATCCCTCTA-AGGCAATTGGTTAAATGCCCCGGCTTTATG
1 TATACTATACAATAAAGCTTGAGTTGTCCCTCTAGAGACAATTGGTTAAACGCCCCGACTTTATG
* * *
22685 GATAAGATTCAGCTAACCCGATAAAGGT
66 GATAATATTCAGCTAGCCTGATAAAGGT
22713 ATTTACAGAT
Statistics
Matches: 172, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
94 6 0.03
95 166 0.97
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (96 bp):
TATACTATACAATAAAGCTTGAGTTGTCCCTCTAGAGACAATTGGTTAAACGCCCCGACTTTATG
GATAATATTCAGCTAGCCTGATAAAGGTGAT
Found at i:24020 original size:84 final size:83
Alignment explanation
Indices: 23883--24861 Score: 821
Period size: 84 Copynumber: 11.8 Consensus size: 83
23873 ATATCGGCAA
* * * * * * * * * * *
23883 CATAACTCAAGGCGAGAAAGGTTGTCTGTCAGCTAAGACCTTTGAGTTTGACTATGCTTAGCTCC
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
* * *
23948 GAGGTACATCATTTGCAA
66 AAGGCACATCATTTGCAG
* * * * *
23966 CATAGCTCAAGGCTAGAAGGGTTATCTGCCACTAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCAC-CAAAGACCTTCGAGTTCGACTACGCTCAGCTC
*
24031 CAAGGCATATCATTTGCAG
65 CAAGGCACATCATTTGCAG
* * * * *
24050 CATAACTTAAGTGGAGAAGGGTTATCTGTCAACCAAAGACCTTTGAGTTTGATTACGCTCAGCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTG-CCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
*
24115 CAAGGCACATCATTTGTAG
65 CAAGGCACATCATTTGCAG
* * * * * * * * * *
24134 CATAGCTTAAGTCGAGAAGAGCTATCTG---CTAAAGACCCTCGAGTTCAATTACACTCAACTTT
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TC
* * *
24196 GAGGGCACATCATTTACAG
65 CAAGGCACATCATTTGCAG
* * * * * *
24215 CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCAACTACGCTCAGCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * *
24280 TAAGGCATATCATTTTCAG
65 CAAGGCACATCATTTGCAG
* * * *
24299 TATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTTAACTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
**
24364 CAAGG-AGCATCATTTATAG
65 CAAGGCA-CATCATTTGCAG
* * * * * *
24383 CATAACTTAAGTCGAGAAGGGCTGTCT---ACCAAAGACCCTCGAGTGT-GATTACACTCAGCTT
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGT-TCGACTACGCTCAGCTC
* * * *
24444 CGAGAGCATATCATTTACTG
65 CAAG-GCACATCATTTGCAG
* * * * *
24464 CATAACTCAAGACTAGAAGGGTTATCTGTCACTAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCAC-CAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
24529 TAAGGCATATCATTTGCAG
65 CAAGGCACATCATTTGCAG
* * * * *
24548 CATAACTTAAGTCGA-ATAGGGTTATCTGCTAACCAATGACCTTCGAGTTTGACTACACTCAACT
1 CATAACTTAAGTCGAGA-AGGGTTATCTGC-CACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
*
24612 CCAAGACACATCATTTGCAG
64 CCAAGGCACATCATTTGCAG
* * * * * *
24632 CATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCTCGAGTTCGATTACACTCAGCTTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
**
24694 AAGGGCACATCATTTATAG
66 AA-GGCACATCATTTGCAG
* * * ** * * * *
24713 CATAACTCAAGGCTAGAAGGGTTATCTATCACCAAAAGACCTTCGAGTCCGACTCCGCTTAGCTT
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
24778 AAAGGCACATTATTTGCAG
65 CAAGGCACATCATTTGCAG
* * * * * * *
24797 CATAGCTTAAATCGAGGAGGGCTATCTGCCATCCAAAGACCTTCAAGTTCGATTACACTCAGCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCA-CCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
24862 AGAGGCAAAC
Statistics
Matches: 713, Mismatches: 157, Indels: 51
0.77 0.17 0.06
Matches are distributed among these distances:
80 84 0.12
81 106 0.15
82 1 0.00
83 28 0.04
84 405 0.57
85 89 0.12
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (83 bp):
CATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
AAGGCACATCATTTGCAG
Found at i:24394 original size:249 final size:248
Alignment explanation
Indices: 23953--24857 Score: 1267
Period size: 249 Copynumber: 3.6 Consensus size: 248
23943 GCTCCGAGGT
* * * * *
23953 ACATCATTTGCAACATAGCTCAAGGCTAGAAGGGTTATCTGCCACTAAAAGACCTTCGAGTTCGA
1 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGA
* * *
24018 CTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTGGAGAAGGGTTATCTGTCAAC
66 CTACGCTCAGCTCTAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC
* * * * *
24083 CAAAGACCTTTGAGTTTGATTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCG
131 CAAAGACCTTCGAGTTCGACTACACTCAACTCCAAGG-ACATCATTTGTAGCATAGCTTAAGTCG
* * * * *
24148 AGAAGAGCTATCTGCTAAAGACCCTCGAGTTCAATTACACTCAACTTTGAGGGC
195 AGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* *
24202 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCAA
1 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGA
* *
24267 CTACGCTCAGCTCTAAGGCATATCATTTTCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAAC
66 CTACGCTCAGCTCTAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC
* * *
24332 CAAAGACCTTCGAGTTCGACTACACTTAACTCCAAGGAGCATCATTTATAGCATAACTTAAGTCG
131 CAAAGACCTTCGAGTTCGACTACACTCAACTCCAAGGA-CATCATTTGTAGCATAGCTTAAGTCG
* * *
24397 AGAAGGGCTGTCTACCAAAGACCCTCGAGTGT-GATTACACTCAGCTTCGAGAGC
195 AGAAGGGCTATCTGCCAAAGACCCTCGAGT-TCGATTACACTCAGCTTCGAGGGC
* * * *
24451 ATATCATTTACTGCATAACTCAAGACTAGAAGGGTTATCTGTCACTAAAAGACCTTCGAGTTCGA
1 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGA
*
24516 CTACGCTCAGCTCTAAGGCATATCATTTGCAGCATAACTTAAGTCGA-ATAGGGTTATCTGCTAA
66 CTACGCTCAGCTCTAAGGCATATCATTTGCAGCATAACTTAAGTCGAGA-AGGGTTATCTGCCAA
* * * *
24580 CCAATGACCTTCGAGTTTGACTACACTCAACTCCAAGACACATCATTTGCAGCATAGCTTAAGTC
130 CCAAAGACCTTCGAGTTCGACTACACTCAACTCCAAG-GACATCATTTGTAGCATAGCTTAAGTC
*
24645 GAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCAAGGGC
194 GAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* * *
24700 ACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTATCACCAAAAGACCTTCGAGTCCGA
1 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGA
* * * * * * * * *
24765 CTCCGCTTAGCT-TAAAGGCACATTATTTGCAGCATAGCTTAAATCGAGGAGGGCTATCTGCCAT
66 CTACGCTCAGCTCT-AAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
* *
24829 CCAAAGACCTTCAAGTTCGATTACACTCA
130 CCAAAGACCTTCGAGTTCGACTACACTCA
24858 GCTCAGAGGC
Statistics
Matches: 580, Mismatches: 69, Indels: 14
0.87 0.10 0.02
Matches are distributed among these distances:
248 4 0.01
249 574 0.99
250 2 0.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (248 bp):
ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGA
CTACGCTCAGCTCTAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC
CAAAGACCTTCGAGTTCGACTACACTCAACTCCAAGGACATCATTTGTAGCATAGCTTAAGTCGA
GAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
Found at i:27848 original size:22 final size:26
Alignment explanation
Indices: 27790--27848 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
27780 TATTTGTTTT
*
27790 TTAACAAATTGAATTCTACTATATTA
1 TTAAAAAATTGAATTCTACTATATTA
*
27816 TTAATATAATT-AATT-TA-TATA-TA
1 TTAA-AAAATTGAATTCTACTATATTA
27839 TTAAAAAATT
1 TTAAAAAATT
27849 TTAAATTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 5 0.17
23 6 0.21
24 4 0.14
25 2 0.07
26 8 0.28
27 4 0.14
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (26 bp):
TTAAAAAATTGAATTCTACTATATTA
Found at i:31172 original size:28 final size:28
Alignment explanation
Indices: 31140--31205 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
31130 TTTTATAAGG
*
31140 TTGAATCAAAGTTGATTTCATGCTTGAA
1 TTGAATCAAAGTTGATTTCATGCTTAAA
31168 TTGAATCAAAGTTGATTTCATGCTTAAA
1 TTGAATCAAAGTTGATTTCATGCTTAAA
31196 TTGAATCAAA
1 TTGAATCAAA
31206 ATCGAGTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (28 bp):
TTGAATCAAAGTTGATTTCATGCTTAAA
Found at i:34000 original size:21 final size:22
Alignment explanation
Indices: 33969--34009 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
33959 AAGACTCTAT
33969 TTTCAAAAATTCAAAAATGATA
1 TTTCAAAAATTCAAAAATGATA
*
33991 TTTC-AAAATTGAAAAATGA
1 TTTCAAAAATTCAAAAATGA
34010 AAACAGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (22 bp):
TTTCAAAAATTCAAAAATGATA
Found at i:37822 original size:23 final size:23
Alignment explanation
Indices: 37786--37841 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
37776 TAGGAGAAAT
*
37786 CGATACCCCC-TTGAAGGGGAAC
1 CGATTCCCCCTTTGAAGGGGAAC
* *
37808 TGATTCCCCCTTTGAATGGGAAC
1 CGATTCCCCCTTTGAAGGGGAAC
37831 CGATTCCCCCT
1 CGATTCCCCCT
37842 GTAGGGAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 8 0.28
23 21 0.72
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.23
Consensus pattern (23 bp):
CGATTCCCCCTTTGAAGGGGAAC
Found at i:38347 original size:13 final size:13
Alignment explanation
Indices: 38329--38361 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
38319 ATATATTGAC
38329 TTTCAAACCTT-GT
1 TTTCAAA-CTTAGT
38342 TTTCAAACTTAGT
1 TTTCAAACTTAGT
38355 TTTCAAA
1 TTTCAAA
38362 ATTTCCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 3 0.16
13 16 0.84
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTCAAACTTAGT
Found at i:40098 original size:13 final size:13
Alignment explanation
Indices: 40080--40104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40070 AGGGGGAGTA
40080 ATTTCAAAATTTG
1 ATTTCAAAATTTG
40093 ATTTCAAAATTT
1 ATTTCAAAATTT
40105 ATTATTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
ATTTCAAAATTTG
Found at i:44315 original size:64 final size:64
Alignment explanation
Indices: 44247--44367 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 64
44237 ATTGTTCAAG
* * * * * *
44247 GTGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAATATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCAATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
* * *
44311 GTGTATCGATGCACAAGTAGTGCATCAATGTACCCCCTTAAAATACAAACATCGAAT
1 GTGTATCGATGCACAAGAAGTGCATCAATGCACCCCCTTAAAATAAAAACATCGAAT
44368 TTGATTTATG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 48 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCACAAGAAGTGCATCAATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
Found at i:45087 original size:22 final size:23
Alignment explanation
Indices: 45062--45104 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
45052 GGCACTACTG
45062 TGCAATT-TACGCGACACTTCAT
1 TGCAATTCTACGCGACACTTCAT
* *
45084 TGCAATTCTACGTGGCACTTC
1 TGCAATTCTACGCGACACTTC
45105 GGTGCATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (23 bp):
TGCAATTCTACGCGACACTTCAT
Found at i:45110 original size:23 final size:22
Alignment explanation
Indices: 45051--45114 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
45041 AAATCTTATA
* *
45051 TGGCACTACTGTGCAATTTACG
1 TGGCACTTCAGTGCAATTTACG
* * *
45073 CGACACTTCATTGCAATTCTACG
1 TGGCACTTCAGTGCAATT-TACG
*
45096 TGGCACTTCGGTGC-ATTTA
1 TGGCACTTCAGTGCAATTTA
45115 TACGAGCTGT
Statistics
Matches: 32, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
21 2 0.06
22 16 0.50
23 14 0.44
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (22 bp):
TGGCACTTCAGTGCAATTTACG
Found at i:51299 original size:64 final size:64
Alignment explanation
Indices: 51231--51352 Score: 181
Period size: 64 Copynumber: 1.9 Consensus size: 64
51221 ATTGTTCAAG
* * * * *
51231 GTGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAATATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
* *
51295 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATATAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATG
51353 AGATTTATGC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
Found at i:51369 original size:64 final size:64
Alignment explanation
Indices: 51237--51393 Score: 163
Period size: 64 Copynumber: 2.5 Consensus size: 64
51227 CAAGGTGTAT
* * * * * * * * *
51237 CGATGCACATGAAGTGTATCGATGCACTCCTTTAATATAAAAACATCGAATGCCATCAGTGTAT
1 CGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATCAGTGCAC
* * *
51301 CGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATATAAACATCGAATGAGATTTA-TGCAC
1 CGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGACA-TCAGTGCAC
* * *
51365 CGATGCATAAATAGTGCATCGGTGCACCC
1 CGATGCACAAGTAGTGCATCGATGCACCC
51394 GTCAAGGGAT
Statistics
Matches: 77, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
64 75 0.97
65 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (64 bp):
CGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATCAGTGCAC
Found at i:52078 original size:23 final size:23
Alignment explanation
Indices: 52010--52070 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
52000 CAATCTTATA
*
52010 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
52033 GGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
52056 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
52071 TTTATACGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.26
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:56814 original size:2 final size:2
Alignment explanation
Indices: 56807--56834 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
56797 GTTCAATTTC
56807 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
56835 GAAATTGGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58395 original size:61 final size:63
Alignment explanation
Indices: 58260--58404 Score: 170
Period size: 61 Copynumber: 2.3 Consensus size: 63
58250 GTAGGTTTAT
* *
58260 ATTAGCACTAGTGTGTAAGGACACTAGGTCCAGGTGGTGGGCACAACCTTATGTGTCATATCCGG
1 ATTAGCACTAGAGTGTAA-GACACTAGGT-CAGGTGGTGGGCACAACCTTATGTATCATATCCGG
* * * **
58325 ATCAACACTAGAGTGTAA-AC-CTAGTGT-AGGTGGTGGGCACGACCTTATGTATCATATTTGG
1 ATTAGCACTAGAGTGTAAGACACTAG-GTCAGGTGGTGGGCACAACCTTATGTATCATATCCGG
*
58386 ATTAGCACTAGAGCGTAAG
1 ATTAGCACTAGAGTGTAAG
58405 CTTAGTGCAG
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
61 45 0.66
62 4 0.06
63 4 0.06
65 15 0.22
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.27
Consensus pattern (63 bp):
ATTAGCACTAGAGTGTAAGACACTAGGTCAGGTGGTGGGCACAACCTTATGTATCATATCCGG
Found at i:67194 original size:34 final size:34
Alignment explanation
Indices: 67148--67225 Score: 115
Period size: 34 Copynumber: 2.3 Consensus size: 34
67138 ATCGAATTAA
*
67148 ACGGGGACGGGAAACACTG-TTATGTTGAACGGGG
1 ACGGGGACGGGAAA-ACTGTTTATGTTAAACGGGG
*
67182 ACGGGGATGGGAAAACTGTTTATGTTAAACGGGG
1 ACGGGGACGGGAAAACTGTTTATGTTAAACGGGG
67216 AC-GGGACGGG
1 ACGGGGACGGG
67226 TTTAGTAATC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
33 11 0.28
34 29 0.73
ACGTcount: A:0.27, C:0.13, G:0.42, T:0.18
Consensus pattern (34 bp):
ACGGGGACGGGAAAACTGTTTATGTTAAACGGGG
Found at i:70147 original size:39 final size:39
Alignment explanation
Indices: 70086--70169 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 39
70076 TTGTAAGACC
* * *
70086 TTACCACAGGCTCATCTGCTTTGTGCTCATGGTAAGTCA
1 TTACCACAGCCTCATCTACTTTGTGCTCAGGGTAAGTCA
* * *
70125 TTACCGCAGCCTCCTCTACTTTGTGCTCAGGGTAAGTCC
1 TTACCACAGCCTCATCTACTTTGTGCTCAGGGTAAGTCA
70164 TTACCA
1 TTACCA
70170 AAGGTCCTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.32
Consensus pattern (39 bp):
TTACCACAGCCTCATCTACTTTGTGCTCAGGGTAAGTCA
Done.