Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004007.1 Hibiscus syriacus cultivar Beakdansim tig00008733_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: 54605
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2931 original size:352 final size:351
Alignment explanation
Indices: 1977--2981 Score: 1864
Period size: 348 Copynumber: 2.9 Consensus size: 351
1967 AGAGACAGAG
*
1977 ACTGCTTCGAACTTACGACGCCGA-GGGTTGGCTGTCTCATCGACTTATTTTTCTGAGGTTAGAG
1 ACTGCGTCGAACTTACGACGCCGAGGGGTTGGCTGTCTCATCGACTTATTTTTCTGAGGTTAGAG
2041 TATGAGCTCCTTGTACATCACTGCGGAGGTATATTATTCCCTAACTTGTAGAAAAAGTTAGGGTT
66 TATGAGCTCCTTGTACATCACTGCGGAGGTATATTATTCCCTAACTTGTAGAAAAAGTTAGGGTT
* * *
2106 TTGATTTCATATAAAGG-A--AAGCAAAAGAGAGCATATTACTGTAACTAATTTTAAAATTATGA
131 TTGATTTCATATAAAGGAAGTAAGCAAAAGAGAGCATATTGCTGCAACTAATTTGAAAATTATGA
*
2168 ACTGAAGGTTGATCAGTTGAACTATTGCTTTTCGGTTAAACTAGTCAGTCGGATCCGGTTTTTTA
196 ACTGAAGGTTGATCAGTTGAACTGTTGCTTTTCGGTTAAACTAGTCAGTCGGATCCGGTTTTTTA
* *
2233 TTTCATGGTTATTATGGGTAAGATAGACGAGGCTTTACGAGTTTGTTGCATTTTTAAATTTTCAA
261 TTTCATGGTTGTTATGGGTAAGATAGATGAGGCTTTACGAGTTTGTTGCATTTTTAAATTTTCAA
2298 CTAAATTTAAGTGCCTTCCAAAGATC
326 CTAAATTTAAGTGCCTTCCAAAGATC
2324 ACTGCGTCGAA-TTACGACGCCGAGGGGTTGGCTGTCTCATCGACTTATTTTTCTGAGGTTAGAG
1 ACTGCGTCGAACTTACGACGCCGAGGGGTTGGCTGTCTCATCGACTTATTTTTCTGAGGTTAGAG
2388 TATGAGCTCCTTGTACATCACTGCGGAGGTATATTATTCCCTAACTTGTAG-AAAAGTTAGGGTT
66 TATGAGCTCCTTGTACATCACTGCGGAGGTATATTATTCCCTAACTTGTAGAAAAAGTTAGGGTT
2452 TTGATTTCATAT-AAGGAAGTAAGCAAAAGAGAGCATATTGCTGCAACTAATTTGAAAATTATGA
131 TTGATTTCATATAAAGGAAGTAAGCAAAAGAGAGCATATTGCTGCAACTAATTTGAAAATTATGA
*
2516 ACTGAAGGTTGATCAGTTGAACTGTTGCTTTTCGGTTAAACTAGTCAGTCGGATCCAGTTTTTTA
196 ACTGAAGGTTGATCAGTTGAACTGTTGCTTTTCGGTTAAACTAGTCAGTCGGATCCGGTTTTTTA
2581 TTTCATGGTTGTTATGGGTAAGATAGATGAGGCTTTACGAGTTTGTTGCATTTTTAAATTTTCAA
261 TTTCATGGTTGTTATGGGTAAGATAGATGAGGCTTTACGAGTTTGTTGCATTTTTAAATTTTCAA
2646 CTAAATTTAAGTGCCTTCCAAAGATC
326 CTAAATTTAAGTGCCTTCCAAAGATC
*
2672 ACTGCGTCGAACTTAGGACGCCGAGGGGTTGGCTGTCTCATCGACTTATTTTTCTGAGGTTAGAG
1 ACTGCGTCGAACTTACGACGCCGAGGGGTTGGCTGTCTCATCGACTTATTTTTCTGAGGTTAGAG
2737 TATGAGCTCCTTGTACATCACTGCGGAGGTATATTATTCCCTAACTTGTAGAAAAAGTTAGGGTT
66 TATGAGCTCCTTGTACATCACTGCGGAGGTATATTATTCCCTAACTTGTAGAAAAAGTTAGGGTT
2802 TTGATTTCATATAAAGGAAAGTAAGCAAAAGAGAGCATATTGCTGCAACTAATTTGAAAATTATG
131 TTGATTTCATATAAAGG-AAGTAAGCAAAAGAGAGCATATTGCTGCAACTAATTTGAAAATTATG
2867 AACTGAAGGTTGATCAGTTGAACTGTTGCTTTTCGGTTAAACTAGTCAGTCGGATCCGGTTTTTT
195 AACTGAAGGTTGATCAGTTGAACTGTTGCTTTTCGGTTAAACTAGTCAGTCGGATCCGGTTTTTT
2932 ATTTCATGGTTGTTATGGGTAAGATAGATGAGGCTTTACGAG-TTGTTGCA
260 ATTTCATGGTTGTTATGGGTAAGATAGATGAGGCTTTACGAGTTTGTTGCA
2982 CCATTTCTTG
Statistics
Matches: 640, Mismatches: 10, Indels: 12
0.97 0.02 0.02
Matches are distributed among these distances:
345 4 0.01
346 38 0.06
347 101 0.16
348 204 0.32
349 103 0.16
350 25 0.04
351 12 0.02
352 153 0.24
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (351 bp):
ACTGCGTCGAACTTACGACGCCGAGGGGTTGGCTGTCTCATCGACTTATTTTTCTGAGGTTAGAG
TATGAGCTCCTTGTACATCACTGCGGAGGTATATTATTCCCTAACTTGTAGAAAAAGTTAGGGTT
TTGATTTCATATAAAGGAAGTAAGCAAAAGAGAGCATATTGCTGCAACTAATTTGAAAATTATGA
ACTGAAGGTTGATCAGTTGAACTGTTGCTTTTCGGTTAAACTAGTCAGTCGGATCCGGTTTTTTA
TTTCATGGTTGTTATGGGTAAGATAGATGAGGCTTTACGAGTTTGTTGCATTTTTAAATTTTCAA
CTAAATTTAAGTGCCTTCCAAAGATC
Found at i:14075 original size:21 final size:21
Alignment explanation
Indices: 14049--14089 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
14039 ATACGGAAGT
14049 GTTTTCTCTTTTCCA-CTTTTA
1 GTTTTC-CTTTTCCAGCTTTTA
*
14070 GTTTTCCTTTTTCAGCTTTT
1 GTTTTCCTTTTCCAGCTTTT
14090 CTTATTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.07, C:0.22, G:0.07, T:0.63
Consensus pattern (21 bp):
GTTTTCCTTTTCCAGCTTTTA
Found at i:21591 original size:2 final size:2
Alignment explanation
Indices: 21584--21635 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
21574 TATAATCATA
21584 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21626 AT AT AT AT AT
1 AT AT AT AT AT
21636 TTGTATTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29529 original size:14 final size:14
Alignment explanation
Indices: 29495--29543 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
29485 ATATAATCTT
29495 TTAATATT-AAAT-
1 TTAATATTAAAATA
*
29507 TTCATTATTAAAATA
1 TT-AATATTAAAATA
29522 TTAATATTTAAAATA
1 TTAATA-TTAAAATA
29537 -TAATATT
1 TTAATATT
29544 TTTGATGCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 2 0.06
13 7 0.23
14 12 0.39
15 10 0.32
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAATATTAAAATA
Found at i:29544 original size:14 final size:15
Alignment explanation
Indices: 29514--29544 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
29504 AATTTCATTA
29514 TTAAAATATTAATAT
1 TTAAAATATTAATAT
29529 TTAAAATA-TAATAT
1 TTAAAATATTAATAT
29543 TT
1 TT
29545 TTGATGCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAAAATATTAATAT
Found at i:37869 original size:2 final size:2
Alignment explanation
Indices: 37862--37887 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37852 GTCCAATTTA
37862 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
37888 TAAATATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37947 original size:2 final size:2
Alignment explanation
Indices: 37942--38007 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
37932 TTAACTTATT
37942 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37984 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
38008 AAATAAATAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39080 original size:21 final size:20
Alignment explanation
Indices: 39029--39080 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
39019 TTTTCTCAAT
*
39029 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* * **
39049 TCGTAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAG-AAAA
39070 TCGCAATGCGA
1 TCGCAATGCGA
39081 TACTGACTAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:39097 original size:20 final size:20
Alignment explanation
Indices: 39072--39122 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
39062 TGGAAAAATC
39072 GCAATGCGATACTGACTATA
1 GCAATGCGATACTGACTATA
* *
39092 GCAATGCGATACTTACTATC
1 GCAATGCGATACTGACTATA
39112 GCAATGCGATA
1 GCAATGCGATA
39123 ATACAAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (20 bp):
GCAATGCGATACTGACTATA
Found at i:39131 original size:61 final size:61
Alignment explanation
Indices: 39066--39182 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 61
39056 GCGAATTGGA
* * * * * *
39066 AAAATCGCAATGCGATACTGACTATAGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATAATGACTATAGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
39127 AAAATCGCAACGAGATAATGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATAATGACTATAGCAACGCGATACTGACTATCGCAACGCGAT
39183 TTACATAGCG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 46 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATAATGACTATAGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:39179 original size:20 final size:20
Alignment explanation
Indices: 39131--39183 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
39121 TAATACAAAA
* *
39131 TCGCAACGAGATAATGACTT
1 TCGCAACGCGATTATGACTT
*
39151 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTATGACTT
39171 TCGCAACGCGATT
1 TCGCAACGCGATT
39184 TACATAGCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTT
Found at i:39776 original size:19 final size:19
Alignment explanation
Indices: 39742--39781 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39732 GAGAGAATCA
**
39742 CAACGCGAAATGAAAAACG
1 CAACGCGAAACAAAAAACG
*
39761 CAACGCGAAACAAAAATCG
1 CAACGCGAAACAAAAAACG
39780 CA
1 CA
39782 TTGCGATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.25, G:0.17, T:0.05
Consensus pattern (19 bp):
CAACGCGAAACAAAAAACG
Found at i:39838 original size:36 final size:33
Alignment explanation
Indices: 39791--39881 Score: 137
Period size: 36 Copynumber: 2.6 Consensus size: 33
39781 ATTGCGATTT
39791 TCATTTCGCGTTGCGATTCTCTCGTCACGACGATAG
1 TCATTTCGCGTTGCGATTCTCTCGT--CG-CGATAG
*
39827 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
39860 TCATTTCTGCGTTGCGATTCTC
1 TCATTTC-GCGTTGCGATTCTC
39882 ATTATCTCGT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
33 13 0.25
34 15 0.28
36 25 0.47
ACGTcount: A:0.13, C:0.26, G:0.22, T:0.38
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:39874 original size:20 final size:19
Alignment explanation
Indices: 39821--39897 Score: 74
Period size: 20 Copynumber: 4.2 Consensus size: 19
39811 CTCGTCACGA
*
39821 CGATAGTCATTTCGCGTTG
1 CGATAGTCATTTCTCGTTG
39840 CGAT--TC---TCTCGTTG
1 CGATAGTCATTTCTCGTTG
39854 CGATAGTCATTTCTGCGTTG
1 CGATAGTCATTTCT-CGTTG
**
39874 CGATTCTCATTATCTCGTTG
1 CGATAGTCATT-TCTCGTTG
39894 CGAT
1 CGAT
39898 TTTCATTTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
14 11 0.23
16 2 0.04
17 2 0.04
19 7 0.15
20 23 0.48
21 3 0.06
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.40
Consensus pattern (19 bp):
CGATAGTCATTTCTCGTTG
Found at i:39898 original size:20 final size:19
Alignment explanation
Indices: 39846--39906 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
39836 GTTGCGATTC
**
39846 TCTCGTTGCGATAGTCATT
1 TCTCGTTGCGATTCTCATT
39865 TCTGCGTTGCGATTCTCATT
1 TCT-CGTTGCGATTCTCATT
*
39885 ATCTCGTTGCGATTTTCATT
1 -TCTCGTTGCGATTCTCATT
39905 TC
1 TC
39907 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 5 0.14
20 29 0.78
21 3 0.08
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (19 bp):
TCTCGTTGCGATTCTCATT
Found at i:43401 original size:14 final size:14
Alignment explanation
Indices: 43382--43417 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
43372 ATTGTTTAAT
43382 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
43396 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
43410 TGATTTGT
1 TGATTTGT
43418 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:43546 original size:19 final size:19
Alignment explanation
Indices: 43522--43588 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
43512 AAAAAGTACT
*
43522 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
43541 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
43555 ATCGCAACGCGAAATAAAA
1 ATCGCAACGCGAAATGAAA
43574 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
43589 TAAATTCGCG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:43639 original size:33 final size:32
Alignment explanation
Indices: 43597--43723 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
43587 ATTAAATTCG
*
43597 CGTTGCGATTTTCATTTCGTATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
43630 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
43663 CGTTGCGATTTTCATTTCGCATTGCAATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
43696 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
43724 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:43687 original size:66 final size:66
Alignment explanation
Indices: 43590--43722 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
43580 ACGCGAAATT
* * *
43590 AAATTCGCGTTGCGATTTTCATTTCGTATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
43655 G
66 G
*
43656 AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
43721 G
66 G
43722 A
1 A
43723 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:46228 original size:24 final size:24
Alignment explanation
Indices: 46194--46247 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
46184 CTGAAACATC
* *
46194 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
46218 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
46242 ATCAAA
1 ATCAAA
46248 TTTCAAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:47010 original size:20 final size:20
Alignment explanation
Indices: 46981--47031 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
46971 TGTATTATCT
46981 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
47001 CGTTGTGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
47021 CGTTGCGAAAG
1 CGTTGCGAAAG
47032 GCAATCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:47347 original size:20 final size:20
Alignment explanation
Indices: 47322--47399 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
47312 ATTCATTTGA
*
47322 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
47342 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
47362 CTATCGCAACGAGAAAATGG
1 CTATCGCAACGAGAAAATGG
47382 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
47400 CGCAATGCGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:47459 original size:19 final size:19
Alignment explanation
Indices: 47437--47485 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
47427 GATTTTCTCG
47437 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCACA
*
47456 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCACA
47475 TTGCGATTTTC
1 TTGCGATTTTC
47486 TCGTTGCGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.16, C:0.20, G:0.14, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCACA
Found at i:47620 original size:14 final size:14
Alignment explanation
Indices: 47601--47637 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
47591 CATCAATTAA
47601 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
47615 ACAAATCATCTTTT
1 ACAAATCAACATTT
47629 ACAAATCAA
1 ACAAATCAA
47638 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:49528 original size:20 final size:19
Alignment explanation
Indices: 49505--49572 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
49495 TAAACTTAAA
49505 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
* *
49525 ATCGCAACGTGGAAATGGCT
1 ATCGCAACG-CGAAATGACT
* **
49545 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
49564 ATCGCAACG
1 ATCGCAACG
49573 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 14 0.36
20 24 0.62
21 1 0.03
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:49567 original size:19 final size:18
Alignment explanation
Indices: 49545--49602 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 18
49535 GGAAATGGCT
49545 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
49564 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
49578 ATCGCAACGCGAAATG-AA
1 ATCGCAA-GCGAAATGAAA
49596 ATCGCAA
1 ATCGCAA
49603 CGACAAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 10 0.31
19 7 0.22
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:49580 original size:14 final size:14
Alignment explanation
Indices: 49561--49618 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
49551 ATGCGAAATG
49561 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
49575 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
49591 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
49607 AAAATCGCAACG
1 AAAATCGCAACG
49619 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:49603 original size:32 final size:33
Alignment explanation
Indices: 49545--49623 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
49535 GGAAATGGCT
*
49545 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
49578 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
49610 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
49624 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:49671 original size:14 final size:14
Alignment explanation
Indices: 49652--49708 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 14
49642 TTTCATTTCG
49652 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
49666 CGTTGCAATTTCATTT
1 CGTTGCGATTT--TGT
49682 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
49698 CGTTGCGATTT
1 CGTTGCGATTT
49709 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 19 0.54
16 8 0.23
18 8 0.23
ACGTcount: A:0.12, C:0.18, G:0.23, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:49683 original size:32 final size:32
Alignment explanation
Indices: 49642--49724 Score: 148
Period size: 32 Copynumber: 2.6 Consensus size: 32
49632 GCATTGCGAT
*
49642 TTTCATTTCGCGTTGCGATTTTGTCGTTGCAA
1 TTTCATTTCGCATTGCGATTTTGTCGTTGCAA
*
49674 TTTCATTTCGCATTGCGATTTTGTCGTTGCGA
1 TTTCATTTCGCATTGCGATTTTGTCGTTGCAA
49706 TTTCATTTCGCATTGCGAT
1 TTTCATTTCGCATTGCGAT
49725 AGCCATTTCC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.47
Consensus pattern (32 bp):
TTTCATTTCGCATTGCGATTTTGTCGTTGCAA
Found at i:49743 original size:20 final size:19
Alignment explanation
Indices: 49709--49763 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
49699 GTTGCGATTT
*
49709 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
49728 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
49748 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
49764 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:50269 original size:18 final size:18
Alignment explanation
Indices: 50243--50287 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
50233 GTCGATCAGA
*
50243 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
50261 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
50279 TGATGGCTC
1 TGATGGCTC
50288 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:51561 original size:20 final size:20
Alignment explanation
Indices: 51536--51573 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
51526 AATAGTTTCT
51536 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
51556 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
51574 GAATTTGACT
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:51598 original size:20 final size:20
Alignment explanation
Indices: 51546--51612 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
51536 GAAAATGAAA
* **
51546 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAATTTGACT
51566 ATCGCAA--CGAATTTGACT
1 ATCGCAACGCGAATTTGACT
51584 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
51604 ATCGCAACG
1 ATCGCAACG
51613 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.37
20 27 0.63
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:51905 original size:22 final size:22
Alignment explanation
Indices: 51875--51918 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
51865 GATGGAGATA
*
51875 GACGGATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
*
51897 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
51919 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:52130 original size:20 final size:20
Alignment explanation
Indices: 52105--52160 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
52095 ATTATGTATT
52105 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
52125 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
52145 ATCGCGTTGCGAAAGT
1 ATCGCGTTGCGAAAGT
52161 ATCTCGTTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:52206 original size:20 final size:19
Alignment explanation
Indices: 52084--52214 Score: 88
Period size: 20 Copynumber: 6.7 Consensus size: 19
52074 CGCTTTGAAA
* *
52084 ATCGCATTGCGATTATGTATT
1 ATCGCGTTGCGA-TA-GTAGT
* *
52105 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGATAGT-AGT
*
52125 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGT-AGT
52145 ATCGCGTTGCGA-A--AGT
1 ATCGCGTTGCGATAGTAGT
* * *
52161 ATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGA--TAGTAGT
*
52182 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGT-AGT
*
52202 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
52215 TTTCCCAATT
Statistics
Matches: 91, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
16 14 0.15
19 6 0.07
20 48 0.53
21 23 0.25
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATAGTAGT
Found at i:52232 original size:21 final size:21
Alignment explanation
Indices: 52203--52259 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
52193 ATAGTCAGTA
52203 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
52224 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
52244 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
52260 GCGTTGCGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:52247 original size:20 final size:20
Alignment explanation
Indices: 52203--52288 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
52193 ATAGTCAGTA
* **
52203 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
52224 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
52244 TCGCATTGCG----A-TT-T
1 TCGCATTGCGATTTACTTAT
*
52258 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
*
52278 TTGCATTGCGA
1 TCGCATTGCGA
52289 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
14 10 0.20
15 2 0.04
16 1 0.02
18 1 0.02
19 2 0.04
20 25 0.49
21 10 0.20
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:52266 original size:34 final size:34
Alignment explanation
Indices: 52223--52288 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
52213 ATTTTCCCAA
52223 TTCGCGTTGCGATTTACTTATTCGCATTGCGATT
1 TTCGCGTTGCGATTTACTTATTCGCATTGCGATT
*
52257 TTCGCGTTGCGATTTACTTATTTGCATTGCGA
1 TTCGCGTTGCGATTTACTTATTCGCATTGCGA
52289 ATTGGGAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.15, C:0.20, G:0.21, T:0.44
Consensus pattern (34 bp):
TTCGCGTTGCGATTTACTTATTCGCATTGCGATT
Done.