Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001224.1 Hibiscus syriacus cultivar Beakdansim tig00002413_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: 46405
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2584 original size:2 final size:2
Alignment explanation
Indices: 2577--2609 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2567 GAATACAAAC
2577 TA TA 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 TA TA T
2610 GTATGCATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3900 original size:20 final size:19
Alignment explanation
Indices: 3877--3922 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
3867 CGATATAACA
3877 GATAAAAATATGATAAAACC
1 GATAAAAA-ATGATAAAACC
*
3897 GATATCAAAATGATAAAACC
1 GATA-AAAAATGATAAAACC
*
3917 GGTAAA
1 GATAAA
3923 GAGCTACCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.57, C:0.11, G:0.13, T:0.20
Consensus pattern (19 bp):
GATAAAAAATGATAAAACC
Found at i:6059 original size:15 final size:15
Alignment explanation
Indices: 6039--6071 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
6029 TGGTTGTATT
6039 GGGGGATGACGGTGA
1 GGGGGATGACGGTGA
6054 GGGGGATGACGGTGA
1 GGGGGATGACGGTGA
6069 GGG
1 GGG
6072 AAAACAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.64, T:0.12
Consensus pattern (15 bp):
GGGGGATGACGGTGA
Found at i:6217 original size:21 final size:21
Alignment explanation
Indices: 6153--6205 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
6143 AAGACAATCA
6153 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
6174 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
*
6195 AGAGTTGAAGA
1 AGAGTCGAAGA
6206 TACTCTTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.43, C:0.08, G:0.34, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:6511 original size:18 final size:18
Alignment explanation
Indices: 6474--6512 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6464 TATGTAGATC
* *
6474 AAAAATATGATGAACTAA
1 AAAAATATGAAGAACAAA
*
6492 AAAAATATGAAGAAGAAA
1 AAAAATATGAAGAACAAA
6510 AAA
1 AAA
6513 GGGAGGAGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.69, C:0.03, G:0.13, T:0.15
Consensus pattern (18 bp):
AAAAATATGAAGAACAAA
Found at i:9108 original size:200 final size:201
Alignment explanation
Indices: 8396--9735 Score: 2258
Period size: 200 Copynumber: 6.7 Consensus size: 201
8386 GTAAAATTTA
8396 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
*
8461 TAAATATACTGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
* *
8526 CGATACTTTTAGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCACAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTC-A
8591 AAAAGTG
195 AAAAGTG
* ** *
8598 TCGATCACAGAAACATACACATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGATA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
*
8663 TAAATATACTGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
*
8728 CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCACAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
8793 AAAGTG
196 AAAGTG
*
8799 TCGATCACAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
* *
8864 TAAATATATCGGTTTTATGAGAGAATAGGTTTACAACATGTATCGACACTTGTTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
*
8929 TGATACTTTTGGTCCACAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTT-AA
131 CGATACTTTTGGTCCACAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
*
8993 AAAGCG
196 AAAGTG
8999 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
* *
9064 TAAATATACCGGTTTTATGAGAGAATAGATCTACAACGTGTATCGACACTTGTTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
*
9129 CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCACAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
9194 AAAGTG
196 AAAGTG
*
9200 TCGATCCCAGAAACATATGCATCCATAAGTATAATGAAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
*
9265 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGATACTTGTTTAATTTTG-GT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
* * * *
9329 CG-TAGTTTTGGTCCACAATGGATGGCAAAAAGGATGAACGTATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCACAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
9393 AAAGTG
196 AAAGTG
* * * *
9399 TCTATCCCATAAACATATGCATCCATAAGTATAATATAATAGGTAAATTTACAATGTAACCAGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
* ** * *
9464 TAACTATACCAATTTTATGAGAGAATAGGTCAACAATATGTATCGACACTTGTTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
9529 CGATACTTTTGGTCCACAATGGATGCC-AAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCACAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
9593 AAAGTG
196 AAAGTG
* * * *
9599 TCGATCCCAGAAACAT-TGAAACCCACAAGTATAATGTAATAGGTAAATTTACAATGTAACAGGT
1 TCGATCCCAGAAACATATG-CATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGT
* * * * *
9663 GTAAATATACCAGTTTTATGAGAGAATATGTCTACAACATGTATCGATACTTTTTTAATTTTGTG
65 ATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTG
9728 TCGATACT
130 TCGATACT
9736 AATTTAAATA
Statistics
Matches: 1072, Mismatches: 62, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
199 181 0.17
200 359 0.33
201 344 0.32
202 188 0.18
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (201 bp):
TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
CGATACTTTTGGTCCACAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
AAAGTG
Found at i:9178 original size:401 final size:402
Alignment explanation
Indices: 8396--9735 Score: 2267
Period size: 401 Copynumber: 3.3 Consensus size: 402
8386 GTAAAATTTA
8396 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
*
8461 TAAATATACTGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
* *
8526 CGATACTTTTAGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCACAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTC-A
* **
8591 AAAAGTGTCGATCACAGAAACATACACATCCATAAGTATAATGTAATAGGTAAATTTACAATGTA
195 AAAAGTGTCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTA
* *
8656 ACCGATATAAATATACTGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAAT
260 ACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAAT
8721 TTTGTGTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACA
325 TTTGTGTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACA
8786 TTTTCAAAAAGTG
390 TTTTCAAAAAGTG
*
8799 TCGATCACAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
* *
8864 TAAATATATCGGTTTTATGAGAGAATAGGTTTACAACATGTATCGACACTTGTTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
*
8929 TGATACTTTTGGTCCACAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTT-AA
131 CGATACTTTTGGTCCACAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
*
8993 AAAGCGTCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAA
196 AAAGTGTCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAA
* *
9058 CCGGTATAAATATACCGGTTTTATGAGAGAATAGATCTACAACGTGTATCGACACTTGTTTAATT
261 CCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATT
9123 TTGTGTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACAT
326 TTGTGTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACAT
9188 TTTCAAAAAGTG
391 TTTCAAAAAGTG
*
9200 TCGATCCCAGAAACATATGCATCCATAAGTATAATGAAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
*
9265 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGATACTTGTTTAATTTTG-GT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
* * * *
9329 CG-TAGTTTTGGTCCACAATGGATGGCAAAAAGGATGAACGTATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCACAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
* * *
9393 AAAGTGTCTATCCCATAAACATATGCATCCATAAGTATAATATAATAGGTAAATTTACAATGTAA
196 AAAGTGTCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAA
* * ** * *
9458 CCAGTATAACTATACCAATTTTATGAGAGAATAGGTCAACAATATGTATCGACACTTGTTTAATT
261 CCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATT
*
9523 TTGTGTCGATACTTTTGGTCCACAATGGATGCC-AAAAGGGTGAACGCATAAAGTGTCGATACAT
326 TTGTGTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACAT
9587 TTTCAAAAAGTG
391 TTTCAAAAAGTG
* * * *
9599 TCGATCCCAGAAACAT-TGAAACCCACAAGTATAATGTAATAGGTAAATTTACAATGTAACAGGT
1 TCGATCCCAGAAACATATG-CATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGT
* * * * *
9663 GTAAATATACCAGTTTTATGAGAGAATATGTCTACAACATGTATCGATACTTTTTTAATTTTGTG
65 ATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTG
9728 TCGATACT
130 TCGATACT
9736 AATTTAAATA
Statistics
Matches: 885, Mismatches: 48, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
398 2 0.00
399 213 0.24
400 159 0.18
401 326 0.37
403 185 0.21
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (402 bp):
TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
CGATACTTTTGGTCCACAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
AAAGTGTCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAA
CCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATT
TTGTGTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACAT
TTTCAAAAAGTG
Found at i:16302 original size:74 final size:74
Alignment explanation
Indices: 16213--16354 Score: 257
Period size: 74 Copynumber: 1.9 Consensus size: 74
16203 CAATATAAGC
*
16213 GCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAA
1 GCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCCAGTTAA
16278 ATGCCTAGT
66 ATGCCTAGT
* *
16287 GCTACCTATTACATTATATAAGTGCTACCTAATATGTTATTGTACTTGATAATATTTTCAGTTAA
1 GCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCCAGTTAA
16352 ATG
66 ATG
16355 ATATAACATT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.41
Consensus pattern (74 bp):
GCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCCAGTTAA
ATGCCTAGT
Found at i:17478 original size:16 final size:16
Alignment explanation
Indices: 17457--17501 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
17447 TTAATATTCA
17457 CGTGAATAGTGAATTT
1 CGTGAATAGTGAATTT
17473 CGTGAATAGTGAATTT
1 CGTGAATAGTGAATTT
*
17489 TGTGAATAGTGAA
1 CGTGAATAGTGAA
17502 ATTTTATCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (16 bp):
CGTGAATAGTGAATTT
Found at i:21549 original size:36 final size:35
Alignment explanation
Indices: 21503--21573 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
21493 TGGCAACCAA
21503 CTTTGAAAAATGTTTTTCAAAGTTTAGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTAGTAAA-GTTT
*
21539 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTAGTAAAGTTT
21574 GATAGATGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.46
Consensus pattern (35 bp):
CTTTGAAAAATGTTTTTCAAAGTTTAGTAAAGTTT
Found at i:27559 original size:23 final size:23
Alignment explanation
Indices: 27533--27580 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
27523 ATAAAGTACA
*
27533 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
27556 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
27579 AT
1 AT
27581 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:30760 original size:182 final size:184
Alignment explanation
Indices: 30196--30901 Score: 1323
Period size: 184 Copynumber: 3.9 Consensus size: 184
30186 TTTTAAATGG
* *
30196 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
30261 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
30326 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
30380 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
30445 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
30510 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
*
30564 TATGGATA-AAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
30628 TAAAACC-GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
30692 GATGTGTAAAATGTCGACAC-TTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
*
30745 TATGGATATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
30810 TAAGACCGGTATATTTATACCGGTTATATTAC-AAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
30874 GATGTGT-AAATGTCGACACTTTTGTAAA
131 GATGTGTAAAATGTCGACACTTTTTTAAA
30902 AAGTGTCCAT
Statistics
Matches: 514, Mismatches: 5, Indels: 8
0.98 0.01 0.02
Matches are distributed among these distances:
181 53 0.10
182 185 0.36
183 87 0.17
184 189 0.37
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:30923 original size:22 final size:22
Alignment explanation
Indices: 30893--30945 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
30883 ATGTCGACAC
*
30893 TTTTGTAAAAAGTG-TCCATACT
1 TTTTATAAAAAG-GATCCATACT
*
30915 TTTTATAAAAAGGATCGATACT
1 TTTTATAAAAAGGATCCATACT
*
30937 TTTTTTAAA
1 TTTTATAAA
30946 GATATGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (22 bp):
TTTTATAAAAAGGATCCATACT
Found at i:32365 original size:3 final size:3
Alignment explanation
Indices: 32357--32430 Score: 76
Period size: 3 Copynumber: 24.7 Consensus size: 3
32347 ACTTGTTTGG
* * * **
32357 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
32405 AGC TTC ATC GTC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
32431 TGTCATCTTC
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.26, C:0.34, G:0.05, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:32424 original size:42 final size:42
Alignment explanation
Indices: 32365--32455 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
32355 GGATCATCAT
*
32365 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* ** * *
32407 CTTCATCGTCATCATCATCATCATTGTCATCTTCATTGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
32449 CTTCATC
1 CTTCATC
32456 TTCTGCGACC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.22, C:0.33, G:0.08, T:0.37
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:32436 original size:9 final size:9
Alignment explanation
Indices: 32370--32437 Score: 57
Period size: 9 Copynumber: 7.6 Consensus size: 9
32360 ATCATCTTCA
*
32370 TCATCATCA
1 TCATCATCG
32379 TCATCATCG
1 TCATCATCG
*
32388 TCATCATCT
1 TCATCATCG
**
32397 TCATCGCCAG
1 TCATCATC-G
*
32407 -CTTCATCG
1 TCATCATCG
*
32415 TCATCATCA
1 TCATCATCG
*
32424 TCATCATTG
1 TCATCATCG
32433 TCATC
1 TCATC
32438 TTCATTGTCA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
8 1 0.02
9 44 0.98
ACGTcount: A:0.24, C:0.34, G:0.07, T:0.35
Consensus pattern (9 bp):
TCATCATCG
Found at i:32458 original size:6 final size:6
Alignment explanation
Indices: 32361--32458 Score: 56
Period size: 6 Copynumber: 16.3 Consensus size: 6
32351 GTTTGGATCA
* * * * * * * *
32361 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
32409 TCATCG TCATCA TCATCA TCAT-T GTCATCT TCAT-T GTCAGCT TCATCT
1 TCATCT TCATCT TCATCT TCATCT -TCATCT TCATCT -TCATCT TCATCT
32457 TC
1 TC
32459 TGCGACCGAT
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
5 1 0.01
6 70 0.96
7 2 0.03
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:34275 original size:198 final size:198
Alignment explanation
Indices: 33897--35304 Score: 2536
Period size: 198 Copynumber: 7.1 Consensus size: 198
33887 TTTAAATTAG
33897 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
33962 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
34026 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTTAATTCATTCTGTAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TTTTTAATTCATTCTGGAAA
34091 AAAA
195 AAAA
34095 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
34160 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTT-GGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *
34224 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAA
34289 AAAA
195 AAAA
*
34293 TATCGACACAGAC--TA-TAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
34355 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
34420 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGTAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
34485 AAA
196 AAA
34488 -ATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
34552 ATTGTACCGGTTAGA-TAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
34615 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCT-GGAA
34680 AAAAA
194 AAAAA
34685 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
* *
34750 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATTCTTTTGGGTTCGATGATTTT-GGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
34814 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCT-GGAAA
34879 AAAA
195 AAAA
34883 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
* *
34948 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATTCTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
35013 CGACAC-TTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
35077 AAA
196 AAA
35080 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
35145 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
35210 CGACAC-TTTT-TATATGGATCGACACTTTATTGATGCACCTTG-TTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGG-AAA
35272 AAAA
195 AAAA
*
35276 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
35305 TGACCCTTAA
Statistics
Matches: 1176, Mismatches: 21, Indels: 28
0.96 0.02 0.02
Matches are distributed among these distances:
194 11 0.01
195 180 0.15
196 186 0.16
197 227 0.19
198 475 0.40
199 94 0.08
200 3 0.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
AAA
Found at i:35413 original size:19 final size:19
Alignment explanation
Indices: 35386--35426 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
35376 ATTCACATAA
35386 AAAAATATAAATCGTATAC
1 AAAAATATAAATCGTATAC
* *
35405 AAAATTATAAATCTTATAC
1 AAAAATATAAATCGTATAC
35424 AAA
1 AAA
35427 TTAACTCGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAATATAAATCGTATAC
Found at i:37252 original size:33 final size:33
Alignment explanation
Indices: 37215--37280 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
37205 CATCTTAATA
*
37215 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
37248 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
37281 CCTTCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:39592 original size:17 final size:18
Alignment explanation
Indices: 39570--39612 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
39560 ATATATCCGG
39570 TATCATT-TTACCGGTTT
1 TATCATTATTACCGGTTT
39587 TATCATTTTATTACCGGTTT
1 TATCA--TTATTACCGGTTT
39607 TATCAT
1 TATCAT
39613 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 1 0.04
19 2 0.09
20 15 0.65
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.53
Consensus pattern (18 bp):
TATCATTATTACCGGTTT
Found at i:39602 original size:20 final size:20
Alignment explanation
Indices: 39575--39621 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
39565 TCCGGTATCA
39575 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
39594 TTATTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
39615 TTTTACC
1 TTTTACC
39622 TGTTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:39768 original size:20 final size:20
Alignment explanation
Indices: 39742--39787 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
39732 CACTTTTAAA
39742 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
39761 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
39782 TTTACC
1 TTTACC
39788 TGGTATATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:40251 original size:227 final size:221
Alignment explanation
Indices: 39854--40294 Score: 715
Period size: 227 Copynumber: 2.0 Consensus size: 221
39844 TAAAAACTGC
39854 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTCATGTTTTCCACCTACAATAT
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTCATGTTTTCCACCTACAATAT
**
39919 TAATTAATAATTTAATTTACACAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTATTAG
66 TAATTAATAATTTAATTTACACAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTAG
*
39984 AATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAGTAT
131 AATTTAAATTTAACAATATTAACCAAAGATAATAATAAATA--TTTTC-ACAGTGAAATAAGTAT
*
40049 GGACACTTTTATAAAAATGATATATACTT
193 GGACACTTTTATAAAAAGGATATATACTT
*
40078 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTG-TTCATGTTTTCCACCTACAAT
*
40143 ATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTAT-AAA-ATTA
64 ATTAA-TTAATAATTTAATTTACAC-AAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
* *
40206 TTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATTTTCACAGTGAAATAAGT
127 -TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATTTTCACAGTGAAATAAGT
*
40271 ATGGATACTTTTATAAAAAGGATA
191 ATGGACACTTTTATAAAAAGGATA
40295 GATAATTTAC
Statistics
Matches: 203, Mismatches: 9, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
224 40 0.20
225 42 0.21
226 30 0.15
227 63 0.31
228 28 0.14
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (221 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTCATGTTTTCCACCTACAATAT
TAATTAATAATTTAATTTACACAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTAG
AATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATTTTCACAGTGAAATAAGTATGGA
CACTTTTATAAAAAGGATATATACTT
Found at i:41296 original size:21 final size:21
Alignment explanation
Indices: 41270--41316 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
41260 ACCTCGACCT
*
41270 TAAACTTTAAATCTCATATCA
1 TAAACTTTAAACCTCATATCA
41291 TAAACTTTAAACCTCATATCA
1 TAAACTTTAAACCTCATATCA
41312 TAAAC
1 TAAAC
41317 CATGAATCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAACTTTAAACCTCATATCA
Done.