Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009337.1 Hibiscus syriacus cultivar Beakdansim tig00113105_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: 64564
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:11187 original size:45 final size:45
Alignment explanation
Indices: 11114--11376 Score: 214
Period size: 45 Copynumber: 5.9 Consensus size: 45
11104 TTGAAGGAAT
* *
11114 AGTCAATC-TTTAGTGATGTCATTATTGACTTTCTCGTGAAAAGA
1 AGTCAATCTTTTAGTGATGTTATTCTTGACTTTCTCGTGAAAAGA
* * * * *
11158 AGTCAACCTTTTAGTGGTGTTGTTCTTGACTTTCTCGTGGAGAGA
1 AGTCAATCTTTTAGTGATGTTATTCTTGACTTTCTCGTGAAAAGA
* * ** * * *
11203 AGTAAATCTTTCAGTTTTG-TCTTCATTGACTTTCTCGAGAAGATG-
1 AGTCAATCTTTTAGTGATGTTATTC-TTGACTTTCTCGTGAA-AAGA
* * * *
11248 AGTCAATCTTTTAGTGATGTCATTTTTGACTTTCTCGTGAAGAGG
1 AGTCAATCTTTTAGTGATGTTATTCTTGACTTTCTCGTGAAAAGA
* * * * *
11293 AGTCAATCTTTTAGTGCTATCATTCTTTACTTTCTGGT-AAAGAGA
1 AGTCAATCTTTTAGTGATGTTATTCTTGACTTTCTCGTGAAA-AGA
* *
11338 AATCAATCTTTCT-GT-ATTGTGATTCTTGACTTTCTCGTG
1 AGTCAATCTTT-TAGTGA-TGTTATTCTTGACTTTCTCGTG
11377 TAGATGAGTT
Statistics
Matches: 170, Mismatches: 40, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
44 14 0.08
45 152 0.89
46 4 0.02
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.42
Consensus pattern (45 bp):
AGTCAATCTTTTAGTGATGTTATTCTTGACTTTCTCGTGAAAAGA
Found at i:11301 original size:90 final size:89
Alignment explanation
Indices: 11114--11376 Score: 241
Period size: 90 Copynumber: 2.9 Consensus size: 89
11104 TTGAAGGAAT
* * *
11114 AGTCAATCTTTAGTGATGTCATTATTGACTTTCTCGTGAAAAGAAGTCAACCTTTTAGTGGTGTT
1 AGTCAATCTTTAGTGATGTCATTATTGACTTTCTCGAGAAAAGAAGTCAACCTTTTAGTGATGTC
* *
11179 GTTCTTGACTTTCTCGTGGAGAGA
66 ATTCTTGACTTTCTCGTGAAGAGA
* ** * *
11203 AGTAAATCTTTCAGTTTTGTC-TTCATTGACTTTCTCGAGAAGATG-AGTCAATCTTTTAGTGAT
1 AGTCAATCTTT-AGTGATGTCATT-ATTGACTTTCTCGAGAA-AAGAAGTCAACCTTTTAGTGAT
* *
11266 GTCATTTTTGACTTTCTCGTGAAGAGG
63 GTCATTCTTGACTTTCTCGTGAAGAGA
* * * * * *
11293 AGTCAATCTTTTAGTGCTATCATTCTTTACTTTCT-G-GTAAAGAGAAATCAATCTTTCT-GT-A
1 AGTCAATC-TTTAGTGATGTCATTATTGACTTTCTCGAG-AAA-AGAAGTCAACCTTT-TAGTGA
*
11354 TTGTGATTCTTGACTTTCTCGTG
62 -TGTCATTCTTGACTTTCTCGTG
11377 TAGATGAGTT
Statistics
Matches: 142, Mismatches: 22, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
88 2 0.01
89 17 0.12
90 115 0.81
91 8 0.06
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.42
Consensus pattern (89 bp):
AGTCAATCTTTAGTGATGTCATTATTGACTTTCTCGAGAAAAGAAGTCAACCTTTTAGTGATGTC
ATTCTTGACTTTCTCGTGAAGAGA
Found at i:11367 original size:135 final size:134
Alignment explanation
Indices: 11114--11385 Score: 348
Period size: 135 Copynumber: 2.0 Consensus size: 134
11104 TTGAAGGAAT
* * *
11114 AGTCAATCTTTAGTGATGTCATTATTGACTTTCTCGTGAAAAGAAGTCAACCTTTTAGTGGTGTT
1 AGTCAATCTTTAGTGATGTCATTATTGACTTTCTCGTGAAAAGAAGTCAACCTTTTAGTGCTATC
* ** * * *
11179 GTTCTTGACTTTCTCGTGGAGAGAAGTAAATCTTTCAGTTTTGTCTTCATTGACTTTCTCGAGAA
66 ATTCTTGACTTTCTCGTAAAGAGAAATAAATCTTTCAGTATTGTATTCATTGACTTTCTCGAGAA
11244 GATG
131 GATG
* * * *
11248 AGTCAATCTTTTAGTGATGTCATTTTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGCTAT
1 AGTCAATC-TTTAGTGATGTCATTATTGACTTTCTCGTGAAAAGAAGTCAACCTTTTAGTGCTAT
* * * * *
11313 CATTCTTTACTTTCTGGTAAAGAGAAATCAATCTTTCTGTATTGTGATTC-TTGACTTTCTCGTG
65 CATTCTTGACTTTCTCGTAAAGAGAAATAAATCTTTCAGTATTGT-ATTCATTGACTTTCTCGAG
*
11377 TAGATG
129 AAGATG
11383 AGT
1 AGT
11386 TAACCTGTCT
Statistics
Matches: 117, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
134 8 0.07
135 106 0.91
136 3 0.03
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.42
Consensus pattern (134 bp):
AGTCAATCTTTAGTGATGTCATTATTGACTTTCTCGTGAAAAGAAGTCAACCTTTTAGTGCTATC
ATTCTTGACTTTCTCGTAAAGAGAAATAAATCTTTCAGTATTGTATTCATTGACTTTCTCGAGAA
GATG
Found at i:12191 original size:55 final size:55
Alignment explanation
Indices: 12103--12758 Score: 741
Period size: 55 Copynumber: 12.0 Consensus size: 55
12093 GTAAATCACA
* *
12103 TTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCACCTTCTAAAGATTT
1 TTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTT
** * * * * *
12158 TTTTAGTCTTATCTCCCTAAAAGAAAAGTGGAGCACACCTATCTTCCAAATATTT
1 TTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTT
* **** *
12213 TTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGAAGATTTGTCTACCAAAGATTT
1 TTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTT
* * * *
12268 TT-TA-TCTTATCTCCCTAAAAGAAAAGTGGAGCAGACCTATCTTCCAAAGATTT
1 TTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTT
* ** * *
12321 ATCGAGTCTTATCTCATTGAAAGAAGAGTGGAGCAGACCCGTCTTACAAAGATTT
1 TTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTT
* ** * * *
12376 TTCGAGTCTTATATCTTTCAAAGAAGAGTGGAGCAGACCCTTCTTACAAAGATTT
1 TTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTT
* * * * * * *
12431 TT-GAGTCTTATCTCCCGGAAAGAATAGTGGAGTAGGCTCGTCTTCCAAATATTT
1 TTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTT
* * *
12485 TTCGAGGCTTATCTCCCTGAAAGAAGAGTGGAGCATG-CCCACCTTTCAAAGAATTT
1 TTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCA-GACCCATCTTCCAAAG-ATTT
* * * **
12541 TT-GAGTCTTATCTCCCTGAAAGAAGAGTGGATCATAGCTTTCTTCCAAAGATTT
1 TTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTT
* * *
12595 TTTGAGTCTTATCTCCCTGAAAGAAGAGTCGAGCAGACCCATCTTCCAAATATTT
1 TTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTT
* * * ** *
12650 TTCAAGTCTTATCTCCCTGAAAGTAGAGTGGAGCATACTTATCTTCCATAGATTT
1 TTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTT
*
12705 TTCTAGT-TTCATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAA-ATTT
1 TTCGAGTCTT-ATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTT
12759 ATCTGACTAC
Statistics
Matches: 500, Mismatches: 93, Indels: 17
0.82 0.15 0.03
Matches are distributed among these distances:
53 43 0.09
54 56 0.11
55 394 0.79
56 7 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (55 bp):
TTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTT
Found at i:16420 original size:19 final size:20
Alignment explanation
Indices: 16396--16433 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16386 CTGTAATTTT
*
16396 GTCACTTAT-TTATACTTTA
1 GTCACTGATCTTATACTTTA
16415 GTCACTGATCTTATACTTT
1 GTCACTGATCTTATACTTT
16434 TTATGTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.24, C:0.18, G:0.08, T:0.50
Consensus pattern (20 bp):
GTCACTGATCTTATACTTTA
Found at i:25594 original size:21 final size:20
Alignment explanation
Indices: 25554--25596 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
25544 TAATTCCTTA
*
25554 TTTTTCATTATTTTTGTTAT
1 TTTTTCATTATGTTTGTTAT
25574 TTTTTACATGTATGTTT-TTAT
1 TTTTT-CAT-TATGTTTGTTAT
25595 TT
1 TT
25597 CGATCATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 9 0.45
22 6 0.30
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.72
Consensus pattern (20 bp):
TTTTTCATTATGTTTGTTAT
Found at i:26482 original size:19 final size:19
Alignment explanation
Indices: 26458--26503 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
26448 TATTGGATGA
26458 CTTGATGCAGCTAGCCATG
1 CTTGATGCAGCTAGCCATG
26477 CTTGATGCAGCTAGCCATG
1 CTTGATGCAGCTAGCCATG
26496 CTTGATGC
1 CTTGATGC
26504 TGGTTATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (19 bp):
CTTGATGCAGCTAGCCATG
Found at i:27594 original size:45 final size:45
Alignment explanation
Indices: 27545--27679 Score: 171
Period size: 45 Copynumber: 3.0 Consensus size: 45
27535 TTAAAAAAAG
*
27545 GTCTTAGGGAATAAGTTGGGTAATGCTGGTAATAACTCCAACATA
1 GTCTTAGGGAATAAGTTGGGTAATGCTGGTAATAGCTCCAACATA
* ** ** * * *
27590 GTCTTAAGTTATAAGTTGGGTAATGCTAATAAGAGTTCCAATATA
1 GTCTTAGGGAATAAGTTGGGTAATGCTGGTAATAGCTCCAACATA
* *
27635 CTCTTAGGGAATAAGATGGGTAATGCTGGTAATAGCTCCAACATA
1 GTCTTAGGGAATAAGTTGGGTAATGCTGGTAATAGCTCCAACATA
27680 ATGAGAGAAA
Statistics
Matches: 71, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (45 bp):
GTCTTAGGGAATAAGTTGGGTAATGCTGGTAATAGCTCCAACATA
Found at i:38414 original size:41 final size:41
Alignment explanation
Indices: 38369--38536 Score: 178
Period size: 41 Copynumber: 4.1 Consensus size: 41
38359 TTATATCTTT
*
38369 ACAATTCTATTCAATTCAATCATAGCAGCATGCAATAATTC
1 ACAATTCTATTCAATTCAATCATGGCAGCATGCAATAATTC
* *
38410 ACAATTCGATTCAATTCAATCATGGCAGCATACAATAATTC
1 ACAATTCTATTCAATTCAATCATGGCAGCATGCAATAATTC
* * * *
38451 ACAATTCAACTT-AATTCGATCATGGTAGCATGCAATAATCC
1 ACAATTCTA-TTCAATTCAATCATGGCAGCATGCAATAATTC
* ** * * * *
38492 ATAATT-TAATTCAATTCGGTCATGGAAACATGCATTTATTC
1 ACAATTCT-ATTCAATTCAATCATGGCAGCATGCAATAATTC
38533 ACAA
1 ACAA
38537 ACCAATTCAA
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
40 2 0.02
41 103 0.96
42 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (41 bp):
ACAATTCTATTCAATTCAATCATGGCAGCATGCAATAATTC
Found at i:41173 original size:34 final size:34
Alignment explanation
Indices: 41134--41239 Score: 99
Period size: 41 Copynumber: 2.9 Consensus size: 34
41124 AAAAGGAATT
41134 TTATCTTTTGAATATTTCAAATTAAAAGATAGTA
1 TTATCTTTTGAATATTTCAAATTAAAAGATAGTA
41168 TTATCTATTTAAAGTTGAATATTTCAAATTAAAAGATAGTA
1 TTATC---TT----TTGAATATTTCAAATTAAAAGATAGTA
* *
41209 TTATCTGTTT-AA-AGTTGAATATTAAAAGATA
1 TTATCT-TTTGAATATTTCAA-ATTAAAAGATA
41240 TTTGGTTAGA
Statistics
Matches: 61, Mismatches: 2, Indels: 18
0.75 0.02 0.22
Matches are distributed among these distances:
33 5 0.08
34 18 0.30
35 2 0.03
37 2 0.03
38 1 0.02
39 1 0.02
41 32 0.52
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (34 bp):
TTATCTTTTGAATATTTCAAATTAAAAGATAGTA
Found at i:41179 original size:21 final size:21
Alignment explanation
Indices: 41155--41221 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
41145 ATATTTCAAA
41155 TTAAAAGATAGTATTATCTAT
1 TTAAAAGATAGTATTATCTAT
* * * *
41176 TT-AAAGTTGAATATT-TCAAA
1 TTAAAAGAT-AGTATTATCTAT
*
41196 TTAAAAGATAGTATTATCTGT
1 TTAAAAGATAGTATTATCTAT
41217 TTAAA
1 TTAAA
41222 GTTGAATATT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.42
Consensus pattern (21 bp):
TTAAAAGATAGTATTATCTAT
Found at i:41181 original size:20 final size:20
Alignment explanation
Indices: 41158--41222 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
41148 TTTCAAATTA
41158 AAAGATAGTATTATCTATTT
1 AAAGATAGTATTATCTATTT
* * * *
41178 AAAGTTGAATATT-TCAAATTA
1 AAAGAT-AGTATTATC-TATTT
*
41199 AAAGATAGTATTATCTGTTT
1 AAAGATAGTATTATCTATTT
41219 AAAG
1 AAAG
41223 TTGAATATTA
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (20 bp):
AAAGATAGTATTATCTATTT
Found at i:41187 original size:41 final size:41
Alignment explanation
Indices: 41141--41231 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
41131 ATTTTATCTT
41141 TTGAATATTTCAAATTAAAAGATAGTATTATCTATTTAAAG
1 TTGAATATTTCAAATTAAAAGATAGTATTATCTATTTAAAG
*
41182 TTGAATATTTCAAATTAAAAGATAGTATTATCTGTTTAAAG
1 TTGAATATTTCAAATTAAAAGATAGTATTATCTATTTAAAG
41223 TTGAATATT
1 TTGAATATT
41232 AAAAGATATT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (41 bp):
TTGAATATTTCAAATTAAAAGATAGTATTATCTATTTAAAG
Found at i:41231 original size:21 final size:21
Alignment explanation
Indices: 41166--41232 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
41156 TAAAAGATAG
41166 TATTATCTATTTAAAGTTGAA
1 TATTATCTATTTAAAGTTGAA
* * * *
41187 TATT-TCAAATTAAAAGAT-AG
1 TATTATC-TATTTAAAGTTGAA
*
41207 TATTATCTGTTTAAAGTTGAA
1 TATTATCTATTTAAAGTTGAA
41228 TATTA
1 TATTA
41233 AAAGATATTT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.45
Consensus pattern (21 bp):
TATTATCTATTTAAAGTTGAA
Found at i:41359 original size:19 final size:21
Alignment explanation
Indices: 41330--41379 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
41320 AATTGAAGAA
*
41330 ATTTTCTTCT-CTTGAAAAAT
1 ATTTTCTTCTCCTTAAAAAAT
41350 ATTTTC-TCTCCTTAAAAAAT
1 ATTTTCTTCTCCTTAAAAAAT
* *
41370 ACTCTCTTCT
1 ATTTTCTTCT
41380 ACTAGTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 3 0.12
20 19 0.76
21 3 0.12
ACGTcount: A:0.28, C:0.22, G:0.02, T:0.48
Consensus pattern (21 bp):
ATTTTCTTCTCCTTAAAAAAT
Found at i:45795 original size:32 final size:32
Alignment explanation
Indices: 45758--45821 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
45748 AATCTCAATC
45758 CTTTTTCGAAATATGAGAAGTTCAAGAACCTT
1 CTTTTTCGAAATATGAGAAGTTCAAGAACCTT
*
45790 CTTTTTTGAAATATGAGAAGTTCAAGAACCTT
1 CTTTTTCGAAATATGAGAAGTTCAAGAACCTT
45822 TAAGGTGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (32 bp):
CTTTTTCGAAATATGAGAAGTTCAAGAACCTT
Found at i:46354 original size:25 final size:25
Alignment explanation
Indices: 46293--46355 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
46283 AATTTTCGAG
* *
46293 TCGAGTCAAGCCCTTTTCAAAATTT
1 TCGAGTCAAACTCTTTTCAAAATTT
*
46318 TCGAGTCAAACTCTTTTTAAAATTT
1 TCGAGTCAAACTCTTTTCAAAATTT
46343 TCGAGTCAAACTC
1 TCGAGTCAAACTC
46356 AACAACACTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (25 bp):
TCGAGTCAAACTCTTTTCAAAATTT
Found at i:51513 original size:34 final size:31
Alignment explanation
Indices: 51425--51516 Score: 87
Period size: 34 Copynumber: 2.8 Consensus size: 31
51415 AATTAAAATA
**
51425 TATTTTTT-AATTTGAATATTAGTAGGATAAT
1 TATTTTTTAAATTTGAA-ATTAAAAGGATAAT
* *
51456 TATTTTTTAAATATGTCAAATTAAAAGGTATTAT
1 TATTTTTTAAAT-T-TGAAATTAAAAGG-ATAAT
51490 TATTTGTTTAAATTTGAAGATTAAAAG
1 TATTT-TTTAAATTTGAA-ATTAAAAG
51517 ATATATGATT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
31 8 0.16
32 3 0.06
33 11 0.22
34 21 0.42
35 7 0.14
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.48
Consensus pattern (31 bp):
TATTTTTTAAATTTGAAATTAAAAGGATAAT
Found at i:55014 original size:21 final size:21
Alignment explanation
Indices: 54956--55017 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
54946 TGCCTAAAAC
* *
54956 AGGGAGTATTAGTACTGCCTA
1 AGGGAGTATCAGTACTTCCTA
54977 AGGGAGTATCAGTACTTCCTA
1 AGGGAGTATCAGTACTTCCTA
54998 AGGGAGTATCAGTACTTCCT
1 AGGGAGTATCAGTACTTCCT
55018 TTATAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (21 bp):
AGGGAGTATCAGTACTTCCTA
Found at i:57303 original size:63 final size:65
Alignment explanation
Indices: 57163--57337 Score: 221
Period size: 63 Copynumber: 2.7 Consensus size: 65
57153 TTTTATCTAT
* * * * *
57163 GTATTTTAGTTTAAATAAGTTTTTAGTATTTTAAGTTTTAGGATTTTGTATATTTTATCTTTGTT
1 GTATTTTAGTTTAAATAAG-TTTTAGTGTTTTAA---TTAGGATTTAGAATATTATATCTATGTT
57228 TTAG
62 TTAG
* *
57232 GTAATTTAGTTGAAATAAGTTTTAGTGTTTTAATTAGGATTTAGAATATTATAT-TAT-TTTTAG
1 GTATTTTAGTTTAAATAAGTTTTAGTGTTTTAATTAGGATTTAGAATATTATATCTATGTTTTAG
57295 GTATTTTAGTTTAAAT-AGTTTTAAGTGTTTTAATTAGGATTTA
1 GTATTTTAGTTTAAATAAGTTTT-AGTGTTTTAATTAGGATTTA
57338 AGATGTTTTA
Statistics
Matches: 96, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
62 6 0.06
63 40 0.42
64 2 0.02
65 18 0.19
68 13 0.14
69 17 0.18
ACGTcount: A:0.29, C:0.01, G:0.15, T:0.55
Consensus pattern (65 bp):
GTATTTTAGTTTAAATAAGTTTTAGTGTTTTAATTAGGATTTAGAATATTATATCTATGTTTTAG
Found at i:57939 original size:17 final size:17
Alignment explanation
Indices: 57917--57952 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
57907 CTCATTCTCT
57917 TTAATTTGTTTATTTAA
1 TTAATTTGTTTATTTAA
*
57934 TTAATTTTTTTATTTAA
1 TTAATTTGTTTATTTAA
57951 TT
1 TT
57953 CTTATCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
TTAATTTGTTTATTTAA
Found at i:58884 original size:16 final size:15
Alignment explanation
Indices: 58865--58898 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
58855 AATTTACTTA
58865 AATATAATTGACCATT
1 AATATAATTGACC-TT
*
58881 AATATAATTTACCTT
1 AATATAATTGACCTT
58896 AAT
1 AAT
58899 GGTTAACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (15 bp):
AATATAATTGACCTT
Found at i:59446 original size:77 final size:79
Alignment explanation
Indices: 59361--59505 Score: 188
Period size: 77 Copynumber: 1.9 Consensus size: 79
59351 GAATTAATTA
* **
59361 ATTTAATTAATT-TAAATTAAATATCCCTT-AAAGACTTATAATCTGAATTACACTC-TTTAATG
1 ATTTAATT-ATTCTAAATTAAATATCCATTAAAAGACTTATAATAAGAATTACACTCTTTTAATG
59423 TTTATTTAAACTCTT
65 TTTATTTAAACTCTT
* * * * *
59438 ATTTAATTATTCTGAATTAAATATCCATTAAAAGAGTTGTAATAAGAATTGCATTCTTTTAATGT
1 ATTTAATTATTCTAAATTAAATATCCATTAAAAGACTTATAATAAGAATTACACTCTTTTAATGT
59503 TTA
66 TTA
59506 CTTACTATAC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
76 3 0.05
77 23 0.40
78 20 0.35
79 11 0.19
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (79 bp):
ATTTAATTATTCTAAATTAAATATCCATTAAAAGACTTATAATAAGAATTACACTCTTTTAATGT
TTATTTAAACTCTT
Done.