Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002939.1 Hibiscus syriacus cultivar Beakdansim tig00006069_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: 49970
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:889 original size:12 final size:12
Alignment explanation
Indices: 872--963 Score: 76
Period size: 12 Copynumber: 7.4 Consensus size: 12
862 AGTCGCAGAA
*
872 GATGAAGCTGAC
1 GATGAAGATGAC
884 GATGAAGATGAC
1 GATGAAGATGAC
896 GATGATGATGATGAC
1 GATGA--A-GATGAC
* *
911 GATGAAGCTGGC
1 GATGAAGATGAC
*
923 GATGAAGATGAT
1 GATGAAGATGAC
* * *
935 GACGATGATGAT
1 GATGAAGATGAC
* *
947 GATGATGATGAA
1 GATGAAGATGAC
959 GATGA
1 GATGA
964 TGATCCAAAC
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
12 54 0.81
13 1 0.01
14 1 0.01
15 11 0.16
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.22
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:893 original size:6 final size:6
Alignment explanation
Indices: 869--963 Score: 55
Period size: 6 Copynumber: 15.3 Consensus size: 6
859 ATCAGTCGCA
* * * * *
869 GAAGAT GAAGCT GACGAT GAAGAT GACGATGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GA--A-GAT GAAGAT GAAGAT GAAGAT
** * * * * *
920 GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
964 TGATCCAAAC
Statistics
Matches: 69, Mismatches: 17, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
6 63 0.91
8 1 0.01
9 5 0.07
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:908 original size:15 final size:15
Alignment explanation
Indices: 884--966 Score: 91
Period size: 15 Copynumber: 5.7 Consensus size: 15
874 TGAAGCTGAC
*
884 GATGAAGATGACGAT
1 GATGATGATGACGAT
899 GATGATGATGACGAT
1 GATGATGATGACGAT
* *
914 GA--A-GCTGGCGAT
1 GATGATGATGACGAT
*
926 GAAGATGATGACGAT
1 GATGATGATGACGAT
*
941 GATGATGATGATGAT
1 GATGATGATGACGAT
*
956 GAAGATGATGA
1 GATGATGATGA
967 TCCAAACAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
12 9 0.16
13 1 0.02
14 1 0.02
15 46 0.81
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (15 bp):
GATGATGATGACGAT
Found at i:910 original size:27 final size:27
Alignment explanation
Indices: 880--963 Score: 114
Period size: 27 Copynumber: 3.1 Consensus size: 27
870 AAGATGAAGC
880 TGACGATGAAGATGACGATGATGATGA
1 TGACGATGAAGATGACGATGATGATGA
* * *
907 TGACGATGAAGCTGGCGATGAAGATGA
1 TGACGATGAAGATGACGATGATGATGA
* * *
934 TGACGATGATGATGATGATGATGAAGA
1 TGACGATGAAGATGACGATGATGATGA
961 TGA
1 TGA
964 TGATCCAAAC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.23
Consensus pattern (27 bp):
TGACGATGAAGATGACGATGATGATGA
Found at i:2747 original size:179 final size:181
Alignment explanation
Indices: 2415--3244 Score: 1407
Period size: 179 Copynumber: 4.6 Consensus size: 181
2405 TTTCAAACAT
** * *
2415 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAATATACCGGTCTTATGCGCGAATAG
1 ATTATAATGTAATAGATAA-TTTGTAATATAACCGGTATAAAATACCGGTTTTATGCGCGAATAG
2480 GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCA-ATTGGAAGAAAA
65 GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
2544 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
130 ATGTGTCGATACGATTT-AAAAAGTGTCGACATTTTACACATCGGAACCCATA
* * *
2597 ATTATAA-GTAATAGATAATTTATAATATAACCGGTA-AAAATACCGGTTTTATGAGCCAATAGG
1 ATTATAATGTAATAGATAATTTGTAATATAACCGGTATAAAATACCGGTTTTATGCGCGAATAGG
2660 TCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAA
66 TCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAA
*
2725 TGTGTCGATACAATTTAAAAAGTGTCGACATTTTACACATC-GAACCCATA
131 TGTGTCGATACGATTTAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
2775 ATTATAATGTAATAGATAATTTGTAATATAACCGGTATAATATACCGG-TATATGCGCGAATAGG
1 ATTATAATGTAATAGATAATTTGTAATATAACCGGTATAAAATACCGGTTTTATGCGCGAATAGG
2839 TCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAA
66 TCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAA
2904 TGTGTCGATACGATTTAAAAAGTGTCGACA-TTTACACATCGGAACCCAT-
131 TGTGTCGATACGATTTAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
2953 ATTATAATGTAATAGATAATTTTGT-A-ATAACCGGTAT-AAATACCGGTCTTATGCGCGAATAG
1 ATTATAATGTAATAGATAA-TTTGTAATATAACCGGTATAAAATACCGGTTTTATGCGCGAATAG
3015 GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AAA
65 GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
3079 ATGTGTCGATACGATTT-AAAAGTGTCGACATTTTACACATCGGAACCC-TA
130 ATGTGTCGATACGATTTAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
3129 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAA-TTTGTAATATAACCGGTATAAA-ATACCGGTTTTATGCGCGAATA
*
3194 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTC
64 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTC
3245 TATACCATTT
Statistics
Matches: 616, Mismatches: 20, Indels: 26
0.93 0.03 0.04
Matches are distributed among these distances:
175 14 0.02
176 70 0.11
177 86 0.14
178 57 0.09
179 249 0.40
180 124 0.20
181 9 0.01
182 7 0.01
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (181 bp):
ATTATAATGTAATAGATAATTTGTAATATAACCGGTATAAAATACCGGTTTTATGCGCGAATAGG
TCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAA
TGTGTCGATACGATTTAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:2823 original size:13 final size:14
Alignment explanation
Indices: 2798--2826 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2788 AGATAATTTG
2798 TAATATAACCGGTA
1 TAATATAACCGGTA
2812 TAATAT-ACCGGTA
1 TAATATAACCGGTA
2825 TA
1 TA
2827 TGCGCGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (14 bp):
TAATATAACCGGTA
Found at i:3175 original size:356 final size:359
Alignment explanation
Indices: 2415--3244 Score: 1435
Period size: 356 Copynumber: 2.3 Consensus size: 359
2405 TTTCAAACAT
**
2415 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAATATACCGGTCTTATGCGCGAATAG
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAATATACCGGT-TTATGCGCGAATAG
2480 GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAATTGGAAGAAAAA
65 GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAATTGGAAGAAAAA
2545 TGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAAGTAATA
130 TGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAAGTAATA
*
2610 GATAATTTATAATATAACCGGTAAAAATACCGGTTTTATGAGCCAATAGGTCTACAACCTATATC
195 GATAATTTATAATATAACCGGTAAAAATACCGGTCTTATGAGCCAATAGGTCTACAACCTATATC
2675 GACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACAATT
260 GACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACAATT
2740 TAAAAAGTGTCGACATTTTACACATCGAACCCATA
325 TAAAAAGTGTCGACATTTTACACATCGAACCCATA
*
2775 ATTATAATGTAATAGATAA-TTTGTAATATAACCGGTATAATATACCGGTATATGCGCGAATAGG
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAATATACCGGTTTATGCGCGAATAGG
2839 TCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAA
66 TCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCA-ATTGGAAGAAAAA
2904 TGTGTCGATACGATTT-AAAAAGTGTCGACA-TTTACACATCGGAACCCAT-ATTATAATGTAAT
130 TGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAA-GTAAT
* * * *
2966 AGATAATTT-T-GTAATAACCGGTATAAATACCGGTCTTATGCGCGAATAGGTCTACAACCTATA
194 AGATAATTTATAAT-ATAACCGGTAAAAATACCGGTCTTATGAGCCAATAGGTCTACAACCTATA
*
3029 TCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AAAATGTGTCGATACGA
258 TCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACAA
3093 TTT-AAAAGTGTCGACATTTTACACATCGGAACCC-TA
323 TTTAAAAAGTGTCGACATTTTACACATC-GAACCCATA
*
3129 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTAT-AATATACCGG-TTTATGCGCGAATA
*
3194 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTC
64 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTC
3245 TATACCATTT
Statistics
Matches: 451, Mismatches: 12, Indels: 17
0.94 0.03 0.04
Matches are distributed among these distances:
354 45 0.10
355 45 0.10
356 111 0.25
357 95 0.21
358 79 0.18
359 59 0.13
360 17 0.04
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (359 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAATATACCGGTTTATGCGCGAATAGG
TCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAATTGGAAGAAAAAT
GTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAAGTAATAG
ATAATTTATAATATAACCGGTAAAAATACCGGTCTTATGAGCCAATAGGTCTACAACCTATATCG
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACAATTT
AAAAAGTGTCGACATTTTACACATCGAACCCATA
Found at i:5827 original size:21 final size:23
Alignment explanation
Indices: 5796--5857 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 23
5786 ATAGGTAAAC
*
5796 ATATGATGTAATAGGTAGC-CCT
1 ATATAATGTAATAGGTAGCGCCT
* **
5818 -TATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCCT
5840 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
5858 TGGTTATATG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 16 0.48
22 1 0.03
23 16 0.48
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCCT
Found at i:5864 original size:23 final size:23
Alignment explanation
Indices: 5818--5866 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
5808 AGGTAGCCCT
*
5818 TATAATGTAATAGGTATCGTTTA
1 TATAATGTAATAGGTATCGGTTA
5841 TATAATGTAATAGGTAGT-GGTTA
1 TATAATGTAATAGGTA-TCGGTTA
5864 TAT
1 TAT
5867 GTAAAGTGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.20, T:0.43
Consensus pattern (23 bp):
TATAATGTAATAGGTATCGGTTA
Found at i:6246 original size:23 final size:23
Alignment explanation
Indices: 6215--6277 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
6205 ATAGGTAAAC
*
6215 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
6238 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
6261 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
6278 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:6285 original size:23 final size:23
Alignment explanation
Indices: 6215--6287 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
6205 ATAGGTAAAC
* * **
6215 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
6238 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
6261 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
6284 ATAT
1 ATAT
6288 TGTAAGTGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:6670 original size:427 final size:422
Alignment explanation
Indices: 5697--6703 Score: 1880
Period size: 427 Copynumber: 2.4 Consensus size: 422
5687 AATTCGCAGT
5697 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
*
5762 AAAAGTATGGACACTTTCAATAAAATAGGTAAACATATGATGTAATAGGTAGCCC-T-TATAATG
65 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
*
5825 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATGTAAAGTGTCTATCCTTTTTATA
130 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATGTAAAGTGTCTATCCTTTTTATA
5890 AAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
195 AAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
*
5955 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTTTTTTTTACGTTACGGTATATATTATTAA
260 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTAA
6020 ATTAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTGTGCAATGAAAT
325 ATTAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTGTGCAATGAAAT
6085 TATTAAATCAATATTGTAGGTGGAAAACATGAA
390 TATTAAATCAATATTGTAGGTGGAAAACATGAA
6118 ACACTGTTAAAAAATTG-AACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAA
1 ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAA
6182 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
66 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
6247 AATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGT-AAGTGTCTATCCTTTTTATA
131 AATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATA-TGTAAAGTGTCTATCCTTTTTATA
6311 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
195 AAAGTGTCCATAC-TTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
6376 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATTTATTAT
259 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATA--TATTAT
6441 TAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTGTGCAAAT
322 TAAATT-AAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTGTGC-AAT
6506 GAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
385 GAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
6544 ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAA
1 ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAA
*
6609 AAAATATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
66 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
6674 AATAGGTATCG-TTATATAATGTAATAGGTA
131 AATAGGTATCGTTTATATAATGTAATAGGTA
6704 TCTATCTCGC
Statistics
Matches: 573, Mismatches: 4, Indels: 13
0.97 0.01 0.02
Matches are distributed among these distances:
419 100 0.17
420 10 0.02
421 88 0.15
422 110 0.19
424 12 0.02
425 54 0.09
426 77 0.13
427 122 0.21
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (422 bp):
ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAA
AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
AATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATGTAAAGTGTCTATCCTTTTTATAA
AAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAG
ATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTAAA
TTAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTGTGCAATGAAATT
ATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:6691 original size:22 final size:22
Alignment explanation
Indices: 6642--6705 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
6632 ATAGGTAAAC
* *
6642 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTA-TCCTT
*
6665 ATATAATGTAATAGGTATCGTT
1 ATATAATGTAATAGGTATCCTT
6687 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
6706 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
22 22 0.58
23 16 0.42
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (22 bp):
ATATAATGTAATAGGTATCCTT
Found at i:14619 original size:3 final size:3
Alignment explanation
Indices: 14611--14648 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
14601 TTCAAATGTG
14611 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
14649 GAATTAGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:14923 original size:23 final size:23
Alignment explanation
Indices: 14880--14923 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
14870 AATTTGGGTT
*
14880 TTAAAATATTAATGAGTTTAAGA
1 TTAAAATATTAATAAGTTTAAGA
*
14903 TTAAAAT-TTATTAAGTCTTAA
1 TTAAAATATTAATAAGT-TTAA
14924 TATTTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (23 bp):
TTAAAATATTAATAAGTTTAAGA
Found at i:18640 original size:15 final size:15
Alignment explanation
Indices: 18601--18642 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
18591 TACAGAGCCT
18601 CTTAATCATTCAGCA
1 CTTAATCATTCAGCA
* *
18616 TTTGAATCATTCAGCG
1 CTT-AATCATTCAGCA
18632 CTTAATCATTC
1 CTTAATCATTC
18643 TGAAATAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.38
Consensus pattern (15 bp):
CTTAATCATTCAGCA
Found at i:20061 original size:42 final size:43
Alignment explanation
Indices: 20014--20103 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 43
20004 GCTGAAAAAT
*
20014 ATTTTACGTAAAA-TATTTTCCAGTGTTTGATAGTTGCAATTG
1 ATTTTACGAAAAATTATTTTCCAGTGTTTGATAGTTGCAATTG
* * *
20056 GTTTTACGAAAAATTATTTTTCAGTGTTTGATAGTTGTAATTG
1 ATTTTACGAAAAATTATTTTCCAGTGTTTGATAGTTGCAATTG
20099 ATTTT
1 ATTTT
20104 CTCAATATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 11 0.26
43 31 0.74
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.49
Consensus pattern (43 bp):
ATTTTACGAAAAATTATTTTCCAGTGTTTGATAGTTGCAATTG
Found at i:20320 original size:42 final size:41
Alignment explanation
Indices: 20274--20367 Score: 100
Period size: 42 Copynumber: 2.3 Consensus size: 41
20264 GTTAGAAAAT
* *
20274 ATTTTCTGAAAAATGGTTTCCAGTGTTTAATAGCTACAATTG
1 ATTTTC-GAAAAATAGTTTACAGTGTTTAATAGCTACAATTG
* * * **
20316 ATTTTACGAAAAATATTTTACAGTGTTTGATAGTTGTAATTG
1 ATTTT-CGAAAAATAGTTTACAGTGTTTAATAGCTACAATTG
20358 ATTTTC-AAAA
1 ATTTTCGAAAA
20368 TGTAATTCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
40 4 0.09
41 1 0.02
42 38 0.86
43 1 0.02
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.43
Consensus pattern (41 bp):
ATTTTCGAAAAATAGTTTACAGTGTTTAATAGCTACAATTG
Found at i:20736 original size:19 final size:19
Alignment explanation
Indices: 20699--20743 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
20689 AATAATGAGG
*
20699 AATATTAATTTATATATTT
1 AATATTAATTAATATATTT
20718 AATATTAATATAATA-ATTT
1 AATATTAAT-TAATATATTT
*
20737 AGTATTA
1 AATATTA
20744 TGTTAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
AATATTAATTAATATATTT
Found at i:20762 original size:30 final size:27
Alignment explanation
Indices: 20704--20765 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 27
20694 TGAGGAATAT
*
20704 TAATTTATATATTTAATATTAATATAA
1 TAATTTATATATTTAATATAAATATAA
20731 TAATTTAGTATTATGTTAATA-AAATACTAA
1 TAATTTA-TA-TAT-TTAATATAAATA-TAA
20761 TAATT
1 TAATT
20766 AAAATTAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.23
28 2 0.07
29 7 0.23
30 14 0.47
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (27 bp):
TAATTTATATATTTAATATAAATATAA
Found at i:23859 original size:2 final size:2
Alignment explanation
Indices: 23852--23880 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23842 TATTCGTCTT
23852 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23881 TGCAGTTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25953 original size:24 final size:24
Alignment explanation
Indices: 25890--25966 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
25880 CATTTAAATG
* * *
25890 ATAAACGAACACAAAGGAAAGAAC
1 ATAAACAAACACAAATGAACGAAC
* * *
25914 GTAAATAGACACAAATGAACGAAC
1 ATAAACAAACACAAATGAACGAAC
* *
25938 ATAAACAAACATAAATGAGCGAAC
1 ATAAACAAACACAAATGAACGAAC
25962 ATAAA
1 ATAAA
25967 ATTAATTAGG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.60, C:0.16, G:0.14, T:0.10
Consensus pattern (24 bp):
ATAAACAAACACAAATGAACGAAC
Found at i:27150 original size:14 final size:14
Alignment explanation
Indices: 27131--27161 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
27121 ATCATTATTC
27131 TAATTATATAAAGA
1 TAATTATATAAAGA
27145 TAATTATATAAAGA
1 TAATTATATAAAGA
27159 TAA
1 TAA
27162 GTGTTGGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (14 bp):
TAATTATATAAAGA
Found at i:31737 original size:19 final size:19
Alignment explanation
Indices: 31713--31769 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
31703 AAATAGAGAT
31713 ATCAGAAC-GAAAATCAGAG
1 ATCAGAACAG-AAATCAGAG
* *
31732 ATCAGAACAGATATCAAAG
1 ATCAGAACAGAAATCAGAG
* *
31751 TTCAGAACATAAATCAGAG
1 ATCAGAACAGAAATCAGAG
31770 GCCAAACTGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 30 0.97
20 1 0.03
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.16
Consensus pattern (19 bp):
ATCAGAACAGAAATCAGAG
Found at i:34116 original size:30 final size:31
Alignment explanation
Indices: 34082--34145 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
34072 CTGTTAAAAA
34082 TTTAATAT-TTTTAGTAATTAAATTATTAAT
1 TTTAATATGTTTTAGTAATTAAATTATTAAT
** *
34112 TTTAATATGTTTTAGTGCTTAAATTTTTAAT
1 TTTAATATGTTTTAGTAATTAAATTATTAAT
34143 TTT
1 TTT
34146 CTCAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (31 bp):
TTTAATATGTTTTAGTAATTAAATTATTAAT
Found at i:34293 original size:31 final size:30
Alignment explanation
Indices: 34246--34304 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
34236 TAATTTTTTA
34246 AAAAATAAAAATTTAAATACTAAAACAAATT
1 AAAAATAAAAATTTAAATA-TAAAACAAATT
* * *
34277 AAAATTAATAATTTAAATATTAAACAAA
1 AAAAATAAAAATTTAAATATAAAACAAA
34305 AAATTTAGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (30 bp):
AAAAATAAAAATTTAAATATAAAACAAATT
Found at i:37238 original size:17 final size:18
Alignment explanation
Indices: 37218--37252 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
37208 TGTCTAATAA
37218 TTTTAA-TAATTAAATTT
1 TTTTAAGTAATTAAATTT
*
37235 TTTTAAGTAATTATATTT
1 TTTTAAGTAATTAAATTT
37253 ATACGTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTAAGTAATTAAATTT
Found at i:40275 original size:20 final size:20
Alignment explanation
Indices: 40230--40343 Score: 70
Period size: 20 Copynumber: 5.5 Consensus size: 20
40220 CCCAAACCCC
* *
40230 AAACCCATAATCTCAAACCATT
1 AAACCC-TAAACTCAAA-TATT
* * * *
40252 AAACCTTTACCTCAAATCTT
1 AAACCCTAAACTCAAATATT
40272 AAACCCTAAACTCAAATATT
1 AAACCCTAAACTCAAATATT
*
40292 AAACCCCAAAC-CATAA-ACTTT
1 AAACCCTAAACTCA-AATA--TT
* * *
40313 GAACCTTAAAGCTTAAATATT
1 AAACCCTAAA-CTCAAATATT
40334 AAACCCTAAA
1 AAACCCTAAA
40344 TTCCAAACCT
Statistics
Matches: 70, Mismatches: 16, Indels: 13
0.71 0.16 0.13
Matches are distributed among these distances:
19 3 0.04
20 30 0.43
21 27 0.39
22 8 0.11
23 2 0.03
ACGTcount: A:0.46, C:0.27, G:0.02, T:0.25
Consensus pattern (20 bp):
AAACCCTAAACTCAAATATT
Found at i:41053 original size:44 final size:43
Alignment explanation
Indices: 40981--41140 Score: 160
Period size: 43 Copynumber: 3.7 Consensus size: 43
40971 TTTTGGAAAA
* * * *
40981 AAAAAAGCCTCTAATTATCCTGTATTTAGTGGCGTTTTTTTTCC
1 AAAAACGCCGCTAATTATCTTGTCTTTAGTGGCG-TTTTTTTCC
* * *
41025 AAAAACGCCGCTAATTCTCTTGTCTTTAGTGGTGCTTTTTGT-C
1 AAAAACGCCGCTAATTATCTTGTCTTTAGTGGCG-TTTTTTTCC
* * ** * * *
41068 ACAAATGATGCTAATTCTCTTGTCTTTAGTGGCGTTTATTGCC
1 AAAAACGCCGCTAATTATCTTGTCTTTAGTGGCGTTTTTTTCC
*
41111 ACAAACGCCGCTAATTATCTTGTCTTTAGT
1 AAAAACGCCGCTAATTATCTTGTCTTTAGT
41141 CACATGTTTG
Statistics
Matches: 95, Mismatches: 20, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
42 4 0.04
43 57 0.60
44 34 0.36
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (43 bp):
AAAAACGCCGCTAATTATCTTGTCTTTAGTGGCGTTTTTTTCC
Found at i:41155 original size:43 final size:43
Alignment explanation
Indices: 41077--41161 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
41067 CACAAATGAT
* ** * *
41077 GCTAATTCTCTTGTCTTTAGTGGCGTTTATTGCCACAAACGCC
1 GCTAATTATCTTGTCTTTAGTCACATTTATGGCCACAAACGCC
41120 GCTAATTATCTTGTCTTTAGTCACATGTT-TGGCCACAAACGC
1 GCTAATTATCTTGTCTTTAGTCACAT-TTATGGCCACAAACGC
41162 TCTGCTTGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 34 0.94
44 2 0.06
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (43 bp):
GCTAATTATCTTGTCTTTAGTCACATTTATGGCCACAAACGCC
Found at i:41157 original size:86 final size:86
Alignment explanation
Indices: 40991--41158 Score: 196
Period size: 86 Copynumber: 1.9 Consensus size: 86
40981 AAAAAAGCCT
* * * *
40991 CTAATTATCCTGTATTTAGTGGCGTTTTTTTTCCAAAAACGCCGCTAATTCTCTTGTCTTTAGTG
1 CTAATTATCCTGTATTTAGTGGCGTTTTATTGCCAAAAACGCCGCTAATTATCTTGTCTTTAGTC
* * *
41056 GTGCTTTTTGTCACAAATGATG
66 ATGC-TTTGGCCACAAATGATG
* * * *
41078 CTAATTCTCTTGTCTTTAGTGGCG-TTTATTGCCACAAACGCCGCTAATTATCTTGTCTTTAGTC
1 CTAATTATCCTGTATTTAGTGGCGTTTTATTGCCAAAAACGCCGCTAATTATCTTGTCTTTAGT-
41142 ACATG-TTTGGCCACAAA
65 -CATGCTTTGGCCACAAA
41159 CGCTCTGCTT
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
86 45 0.66
87 21 0.31
88 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (86 bp):
CTAATTATCCTGTATTTAGTGGCGTTTTATTGCCAAAAACGCCGCTAATTATCTTGTCTTTAGTC
ATGCTTTGGCCACAAATGATG
Done.