Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000701.1 Hibiscus syriacus cultivar Beakdansim tig00001363_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: 66728
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:9324 original size:13 final size:13
Alignment explanation
Indices: 9303--9365 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
9293 CATGACGCGC
9303 AATGCGCGTCATA
1 AATGCGCGTCATA
*
9316 AATGTGCGTCATA
1 AATGCGCGTCATA
* *
9329 AATACACGTCATA
1 AATGCGCGTCATA
* *
9342 AAT--GTGTTATA
1 AATGCGCGTCATA
9353 AATGCGCGTCATA
1 AATGCGCGTCATA
9366 GATTTATGAC
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
11 8 0.21
13 31 0.79
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:9329 original size:83 final size:85
Alignment explanation
Indices: 9168--9331 Score: 215
Period size: 85 Copynumber: 2.0 Consensus size: 85
9158 ATACAATCAC
* * *
9168 GACACACGAATGTGTGTCATCTTCATTTATGACGGGGGTTTCAATGACACGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGCAAGTCATA
* *
9233 CATACGTGTCATAAATTTAT
66 AATACGCGTCATAAATTTAT
* * **
9253 GACACACAAATGTGTGTCATTTTCATTTATGAC-GGGGCTTC-ATGACGCGCAATGCGCGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGCAAGTCATA
**
9316 AATGTGCGTCATAAAT
66 AATACGCGTCATAAAT
9332 ACACGTCATA
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
83 30 0.44
84 7 0.10
85 31 0.46
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGCAAGTCATA
AATACGCGTCATAAATTTAT
Found at i:11418 original size:3 final size:3
Alignment explanation
Indices: 11410--11441 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
11400 AAAAAATGTA
11410 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11442 ACACCAGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11420 original size:353 final size:356
Alignment explanation
Indices: 11004--11654 Score: 1148
Period size: 364 Copynumber: 1.8 Consensus size: 356
10994 GGTTTTGGGT
* * *
11004 TGGTTTGGTTTGGTTTTGTAATTGAGCTTCAGTTTGGGCCTGCAAAAAAT-AT-A-AATAATAAT
1 TGGTTAGGTTAGGTTTTGTAATTGAGCTTCAATTTGGGCCTGCAAAAAATAATAATAATAATAAT
11066 AATAATAATAATAAACACCAGACAAAAAATGATGTCAACAGTCATCAAATTA-TTTTTTTGAAAA
66 AATAATAATAATAAACACCAGACAAAAAATGATGTCAACAGTCATCAAATTATTTTTTTTGAAAA
*
11130 TCATATATAACAAAAATTATATAATTCTCGAAATAAACAAAAAGGAAACGAAAGATGAAACATAA
131 TCATATACAACAAAAATTATATAATTCTCGAAATAAACAAAAAGGAAACGAAAGATGAAACATAA
11195 ATCATGGATCAACTAAGCCCTTTTAAGGATTTGCTTAAGAATAAGAAAGAGGAATCTCATGTAAA
196 ATCATGGATCAACTAAGCCCTTTTAAGGATTTGCTTAAGAATAAGAAAGAGGAATCTC-TGTAAA
11260 TACCATTGAATAAGGTTTGATCCTATTCATGACGGCGGTGTGCTCTGAAAACGACGGTAGAAGCA
260 TACCATTGAATAAGGTTTGATCCTATTCATGACGGCGGTGTGCTCTGAAAACGACGGTAGAAGCA
11325 TGAAGGCTTAGGGTTAGGATTATATTAAGTTA
325 TGAAGGCTTAGGGTTAGGATTATATTAAGTTA
11357 TGGTTAGGTTAGGTTTTGTAATTGAGCTTCAATTTGGGCCTGCAAAAAATGTAAATAATAATAAT
1 TGGTTAGGTTAGGTTTTGTAATTGAGCTTCAATTTGGGCCTGC---AAA---AAATAATAATAAT
11422 AATAATAATAATAATAATAAACACCAGACAAAAAATGATGTCAACAGTCATCAAATTATTTTTTT
60 AATAATAATAATAATAATAAACACCAGACAAAAAATGATGTCAACAGTCATCAAATTA-TTTTTT
11487 TTGAAAATCATATACAACAAAAATTATATAATTCTCGAAATAAACAAAAAGGAAACGAAAGATGA
124 TTGAAAATCATATACAACAAAAATTATATAATTCTCGAAATAAACAAAAAGGAAACGAAAGATGA
* *
11552 AACATAAATCATGGATCAACTAAGCCCTTTTGAGGATTTGCTTAAGAATAAGCAAGAGGAATCTC
189 AACATAAATCATGGATCAACTAAGCCCTTTTAAGGATTTGCTTAAGAATAAGAAAGAGGAATCTC
11617 TGTAAATACCATTGAATAAGGTTTGATCCTATTCATGA
254 TGTAAATACCATTGAATAAGGTTTGATCCTATTCATGA
11655 GGATTCTGTA
Statistics
Matches: 281, Mismatches: 6, Indels: 12
0.94 0.02 0.04
Matches are distributed among these distances:
353 40 0.14
356 3 0.01
359 4 0.01
360 2 0.01
361 1 0.00
362 61 0.22
363 38 0.14
364 132 0.47
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (356 bp):
TGGTTAGGTTAGGTTTTGTAATTGAGCTTCAATTTGGGCCTGCAAAAAATAATAATAATAATAAT
AATAATAATAATAAACACCAGACAAAAAATGATGTCAACAGTCATCAAATTATTTTTTTTGAAAA
TCATATACAACAAAAATTATATAATTCTCGAAATAAACAAAAAGGAAACGAAAGATGAAACATAA
ATCATGGATCAACTAAGCCCTTTTAAGGATTTGCTTAAGAATAAGAAAGAGGAATCTCTGTAAAT
ACCATTGAATAAGGTTTGATCCTATTCATGACGGCGGTGTGCTCTGAAAACGACGGTAGAAGCAT
GAAGGCTTAGGGTTAGGATTATATTAAGTTA
Found at i:17772 original size:112 final size:112
Alignment explanation
Indices: 17367--17940 Score: 877
Period size: 112 Copynumber: 5.1 Consensus size: 112
17357 TTGTCGGTTT
* * * *
17367 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAAGTAAAAAAAATTAAAAAAC
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
*
17432 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
17480 GTGACGATACTTTATAAAAATGTATCT-ATCCATAACAATATAACAGGTAAAAAAAATGACAAAA
1 GTGTCGATACTTTATAAAAATGTAT-TGATCCATAACAATATAACAGGT-AAAAAAATGACAAAA
* * *
17544 TCGGTCTATAAATGACAAAACAGGTAAAGTGTTACCGGATATATTGAAA
64 CCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
17593 GTG--GATACTTTATAAAAATGTATCGATCTATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
17656 GGTCTATAAATGAAAAAACAGGTAAAGTGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
17703 GTGTCGATACTTTATAAAAATGTATTGATCCATAATAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
17768 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
17815 GTGTCGGTACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * * *
17879 GATCTATAAATGACAAAACAGGTAAAACGCTACTGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
17926 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
17941 TATAAGTATC
Statistics
Matches: 428, Mismatches: 29, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
110 64 0.15
111 114 0.27
112 144 0.34
113 105 0.25
114 1 0.00
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:17869 original size:223 final size:225
Alignment explanation
Indices: 17367--17940 Score: 888
Period size: 223 Copynumber: 2.6 Consensus size: 225
17357 TTGTCGGTTT
* * * * *
17367 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAAGTAAAAAAAATTAAAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
* *
17432 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAAGTGACGATACTTTATAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAA
*
17497 AAATGTATCTATCCATAACAATATAACAGGTAAAAAAAATGACAAAATCGGTCTATAAATGACAA
130 AAATGTATCTATCCATAACAATATAACAGGTAAAAAAAATGACAAAACCGGTCTATAAATGACAA
* *
17562 AACAGGTAAAGTGTTACCGGATATATTGAAA
195 AACAGGTAAAGCGCTACCGGATATATTGAAA
*
17593 GTG--GATACTTTATAAAAATGTATCGATCTATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
17656 GGTCTATAAATGAAAAAACAGGTAAAGTGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
*
17721 AATGTAT-TGATCCATAATAATATAACAGGT-AAAAAAATGACAAAACCGGTCTATAAATGACAA
131 AATGTATCT-ATCCATAACAATATAACAGGTAAAAAAAATGACAAAACCGGTCTATAAATGACAA
* *
17784 AACAGGTAAAGCGCTACCGGATATGTTGATA
195 AACAGGTAAAGCGCTACCGGATATATTGAAA
* *
17815 GTGTCGGTACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * * *
17879 GATCTATAAATGACAAAACAGGTAAAACGCTACTGGATATGTTGATAGTGTCGATACTTTAT
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAT
17941 TATAAGTATC
Statistics
Matches: 319, Mismatches: 26, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
222 63 0.20
223 174 0.55
224 79 0.25
226 3 0.01
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.26
Consensus pattern (225 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
AATGTATCTATCCATAACAATATAACAGGTAAAAAAAATGACAAAACCGGTCTATAAATGACAAA
ACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:18127 original size:182 final size:181
Alignment explanation
Indices: 17814--18266 Score: 712
Period size: 182 Copynumber: 2.5 Consensus size: 181
17804 ATATGTTGAT
* * * *
17814 AGTGTCGGTACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGTAAAAA-ATGACAAAAC
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAAT
** *
17878 CGATCTATAAATGACAAAACAGGTAAAACGCTACTGGATATGTTGATAGTGTCGATACTTTATTA
66 CGATCTCGAAATGACAAAAC-GGTAAAACGCTACCGGATATGTTGATAGTGTCGATACTTTATTA
* *
17943 TAAGTATCGACACTTTTAGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAA
130 TAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
*
17995 AGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACATGTAAAAATATGACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAAT
* * *
18060 TGGTCTCGAAATGAAAAAATCGGTAAAGA-GCTACCGGATATGTTGATAGTGTCGATACTTTATT
66 CGATCTCGAAATGACAAAA-CGGTAAA-ACGCTACCGGATATGTTGATAGTGTCGATACTTTATT
* *
18124 ATAAGTATCGACACTTTTGGAATTTAAAAGAAAATAAGTTATAGCGCCAATAA
129 ATAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
*
18177 AGTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACATGTAAAAATATGACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAAT
18242 CGATCTCGAAATGACAAAACCGGTA
66 CGATCTCGAAATGACAAAA-CGGTA
18267 GTAAAAATGT
Statistics
Matches: 248, Mismatches: 21, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
181 50 0.20
182 196 0.79
183 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (181 bp):
AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAAT
CGATCTCGAAATGACAAAACGGTAAAACGCTACCGGATATGTTGATAGTGTCGATACTTTATTAT
AAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
Found at i:18905 original size:23 final size:23
Alignment explanation
Indices: 18876--18946 Score: 106
Period size: 23 Copynumber: 3.1 Consensus size: 23
18866 AAATAGGTCA
18876 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
18899 ATATAAGCGCTTCCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* * *
18922 ATAAAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTATTACATT
18945 AT
1 AT
18947 TGTATTTGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:20262 original size:17 final size:18
Alignment explanation
Indices: 20240--20273 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20230 TCAGCCTGTC
20240 CGGTTC-GAACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
20257 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
20274 CAAATAACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Found at i:20919 original size:20 final size:19
Alignment explanation
Indices: 20894--20938 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
20884 AAATATAATT
20894 AATAAAA-TAAATATTTATAA
1 AATAAAATTAAA-ATTT-TAA
*
20914 AATAAAATTCAAATTTTAA
1 AATAAAATTAAAATTTTAA
20933 AATAAA
1 AATAAA
20939 CACATATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 11 0.48
21 3 0.13
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
AATAAAATTAAAATTTTAA
Found at i:21582 original size:2 final size:2
Alignment explanation
Indices: 21575--21620 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
21565 TATTTATAAG
21575 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
21617 AT AT
1 AT AT
21621 GAGAACCCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22130 original size:24 final size:24
Alignment explanation
Indices: 22103--22175 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
22093 CGTTCATTTA
22103 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
22127 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * *
22151 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
22175 C
1 C
22176 ATTCATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 43 0.96
25 2 0.04
ACGTcount: A:0.10, C:0.15, G:0.26, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:22132 original size:14 final size:14
Alignment explanation
Indices: 22113--22168 Score: 84
Period size: 14 Copynumber: 4.3 Consensus size: 14
22103 CGTTCGTGAA
22113 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
22127 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
22141 CG-T---TTATGTT
1 CGTTCGGTTATGTT
22151 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
22165 CGTT
1 CGTT
22169 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.07, C:0.14, G:0.27, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:22188 original size:24 final size:24
Alignment explanation
Indices: 22114--22175 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
22104 GTTCGTGAAC
*
22114 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
22138 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
22162 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
22176 ATTCATTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.08, C:0.13, G:0.26, T:0.53
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGTTAT
Found at i:23227 original size:16 final size:16
Alignment explanation
Indices: 23206--23256 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
23196 GTCTCCAACG
23206 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
23222 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
23238 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
23252 TTTAT
1 TTTAT
23257 TAAATGAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.15
15 2 0.06
16 26 0.79
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:24133 original size:23 final size:23
Alignment explanation
Indices: 24103--24181 Score: 149
Period size: 23 Copynumber: 3.4 Consensus size: 23
24093 TCTGAATATA
24103 TAAACGAACATGTTCGTAAGCGT
1 TAAACGAACATGTTCGTAAGCGT
24126 TAAACGAACATGTTCGTAAGCGT
1 TAAACGAACATGTTCGTAAGCGT
*
24149 TAAACGAACATGTTCGTAAGCAT
1 TAAACGAACATGTTCGTAAGCGT
24172 TAAACGAACA
1 TAAACGAACA
24182 CTAAATAAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (23 bp):
TAAACGAACATGTTCGTAAGCGT
Found at i:27627 original size:15 final size:16
Alignment explanation
Indices: 27603--27641 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
27593 ATTATATGGA
27603 TATT-TTATTCAT-TT
1 TATTATTATTCATGTT
*
27617 TTTTATTATTCATGTT
1 TATTATTATTCATGTT
27633 TATTATTAT
1 TATTATTAT
27642 ATGTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 3 0.14
15 8 0.38
16 10 0.48
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (16 bp):
TATTATTATTCATGTT
Found at i:30739 original size:8 final size:8
Alignment explanation
Indices: 30726--30764 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
30716 GAACATTTCA
*
30726 TGCATTCT
1 TGCATTTT
30734 TGCA-TTT
1 TGCATTTT
30741 TGCATTTT
1 TGCATTTT
*
30749 TGCCTTTT
1 TGCATTTT
30757 TGCATTTT
1 TGCATTTT
30765 CATCTACAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:31960 original size:9 final size:9
Alignment explanation
Indices: 31948--31986 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
31938 TAAAAAGGGC
31948 AAAAAGAAA
1 AAAAAGAAA
*
31957 AAAAAGCAA
1 AAAAAGAAA
*
31966 AAAAAGAAC
1 AAAAAGAAA
31975 AAAAAGAAA
1 AAAAAGAAA
31984 AAA
1 AAA
31987 GAAAAAGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:31960 original size:18 final size:17
Alignment explanation
Indices: 31934--31992 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
31924 ATATTTAATC
* *
31934 AGAATAAAAAGGGCAAAA
1 AGAA-AAAAAAGGAAAAA
*
31952 AGAAAAAAAAGCAAAAAA
1 AGAAAAAAAAG-GAAAAA
*
31970 AGAACAAAAA-GAAAAA
1 AGAAAAAAAAGGAAAAA
31986 AGAAAAA
1 AGAAAAA
31993 GGGACAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 11 0.32
17 6 0.18
18 17 0.50
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (17 bp):
AGAAAAAAAAGGAAAAA
Found at i:31965 original size:16 final size:16
Alignment explanation
Indices: 31946--31992 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
31936 AATAAAAAGG
31946 GCAAAAAGAAAAAAAA
1 GCAAAAAGAAAAAAAA
*
31962 GCAAAAAAAGAACAAAAA
1 GC--AAAAAGAAAAAAAA
*
31980 GAAAAAAGAAAAA
1 GCAAAAAGAAAAA
31993 GGGACAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (16 bp):
GCAAAAAGAAAAAAAA
Found at i:32612 original size:21 final size:21
Alignment explanation
Indices: 32586--32627 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
32576 AGCTACCCCA
32586 TCAAACC-TTGAGCATCAAATG
1 TCAAACCATT-AGCATCAAATG
32607 TCAAACCATTAGCATCAAATG
1 TCAAACCATTAGCATCAAATG
32628 AACAAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (21 bp):
TCAAACCATTAGCATCAAATG
Found at i:33695 original size:36 final size:36
Alignment explanation
Indices: 33587--33710 Score: 160
Period size: 36 Copynumber: 3.4 Consensus size: 36
33577 ATTGAAAACA
* * *
33587 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
* *
33623 TTTCCCTTGGAACTAAGTTTT-GTCTCTCTTAAGACAG
1 TTTCCCTTGAAAC-AA-TTTTCGTCTCTCTTGAGACAG
* *
33660 TTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
33696 TTTCCCTTGAAACAA
1 TTTCCCTTGAAACAA
33711 AACCTTTGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.05
36 41 0.55
37 27 0.36
38 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
Found at i:33804 original size:67 final size:68
Alignment explanation
Indices: 33686--33842 Score: 205
Period size: 68 Copynumber: 2.4 Consensus size: 68
33676 TTTCGTCTAT
* **
33686 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAACA-AATTTT-TT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
33747 CTCC
66 -TCC
* * *
33751 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
33816 TCC
66 TCC
* *
33819 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
33843 ACAGATATCT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 28 0.35
68 30 0.38
69 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
TCC
Found at i:34634 original size:105 final size:105
Alignment explanation
Indices: 34450--35173 Score: 1158
Period size: 105 Copynumber: 7.0 Consensus size: 105
34440 GAACTCGAGG
* * ** *
34450 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
34515 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
34556 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
34621 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
34661 CAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGCCTGT---CAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * *
34723 ACCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
34763 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
34828 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* **
34868 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
34933 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
34973 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
35038 GCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
35078 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * *
35138 TTCAATTTCAACTTCACGACGGAGGATATTGGACTC
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTC
35174 TGAACAATGC
Statistics
Matches: 586, Mismatches: 29, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
100 36 0.06
101 1 0.00
102 100 0.17
103 2 0.00
104 2 0.00
105 406 0.69
106 39 0.07
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:34821 original size:207 final size:207
Alignment explanation
Indices: 34450--35173 Score: 1139
Period size: 207 Copynumber: 3.5 Consensus size: 207
34440 GAACTCGAGG
* * ** *
34450 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT---C-AACAACTTCTCAATTTCAG
34515 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
62 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
34580 AAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAG
127 AAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAG
34645 GATATTGGACTTCAGA
192 GATATTGGACTTCAGA
* * *
34661 CAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACTTCTCAATTTCAGAACC
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACTTCTCAATTTCAGAGCC
* *
34726 AATTTCAACTTCACAATGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGG
66 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
34791 GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
131 GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATA
34856 TTGGACTTCAGA
196 TTGGACTTCAGA
* **
34868 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT---CAACAACTTCTCAATTTCAGA
*
34933 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGA
63 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
34998 AGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAATGAAGG
128 AGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGG
*
35063 ATATTGGACTCCAGA
193 ATATTGGACTTCAGA
* **
35078 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATT-TC-A-TTCAGATT
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACTTCTCAATTTCAGAGC
* *
35140 CAATTTCAACTTCACGACGGAGGATATTGGACTC
65 CAATTTCAACTTCACAACGAAGGATATTGGACTC
35174 TGAACAATGC
Statistics
Matches: 476, Mismatches: 33, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
205 36 0.08
206 1 0.00
207 204 0.43
208 5 0.01
210 196 0.41
211 34 0.07
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (207 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACTTCTCAATTTCAGAGCC
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATA
TTGGACTTCAGA
Found at i:36349 original size:17 final size:18
Alignment explanation
Indices: 36323--36362 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
36313 TATATATGGA
36323 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
36339 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
36357 TATTAT
1 TATTAT
36363 ATGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:46733 original size:13 final size:13
Alignment explanation
Indices: 46715--46782 Score: 91
Period size: 13 Copynumber: 5.2 Consensus size: 13
46705 TGTGTCATAA
* *
46715 ATTTATGACGCGC
1 ATTTATGACACAC
46728 ATTTATGACACAC
1 ATTTATGACACAC
46741 ATTTATGACACAC
1 ATTTATGACACAC
* *
46754 ATTTATGACGCAT
1 ATTTATGACACAC
*
46767 ATTTATGACACGC
1 ATTTATGACACAC
46780 ATT
1 ATT
46783 GCGTGTAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (13 bp):
ATTTATGACACAC
Found at i:51274 original size:13 final size:13
Alignment explanation
Indices: 51256--51289 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
51246 GTTTAAAACA
51256 AAATATAATTCCT
1 AAATATAATTCCT
51269 AAATATAATTCCT
1 AAATATAATTCCT
*
51282 AAAAATAA
1 AAATATAA
51290 AAAAAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAATTCCT
Found at i:51392 original size:23 final size:23
Alignment explanation
Indices: 51366--51411 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
51356 TGATTGAATC
*
51366 TTTTAGAAGCTGCTGACTGGGCA
1 TTTTAGAAACTGCTGACTGGGCA
*
51389 TTTTAGAAACTGTTGACTGGGCA
1 TTTTAGAAACTGCTGACTGGGCA
51412 CCACATCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (23 bp):
TTTTAGAAACTGCTGACTGGGCA
Found at i:59906 original size:22 final size:22
Alignment explanation
Indices: 59881--59930 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
59871 GGGGTTTTGG
59881 TAAAAAGAT-ATTTAAA-TAATAA
1 TAAAAA-ATGATTTAAAGTAA-AA
59903 T-AAAAATGATTTAAAGTAAAA
1 TAAAAAATGATTTAAAGTAAAA
59924 TAAAAAA
1 TAAAAAA
59931 AAAATTAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 2 0.08
21 14 0.56
22 9 0.36
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (22 bp):
TAAAAAATGATTTAAAGTAAAA
Found at i:59914 original size:21 final size:21
Alignment explanation
Indices: 59890--59929 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
59880 GTAAAAAGAT
59890 ATTTAAA-TAATAATAAAAATG
1 ATTTAAAGTAA-AATAAAAATG
59911 ATTTAAAGTAAAATAAAAA
1 ATTTAAAGTAAAATAAAAA
59930 AAAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
ATTTAAAGTAAAATAAAAATG
Done.