Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004280.1 Hibiscus syriacus cultivar Beakdansim tig00009384_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: 77905
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5210 original size:34 final size:34
Alignment explanation
Indices: 5172--5258 Score: 111
Period size: 34 Copynumber: 2.6 Consensus size: 34
5162 TGTATATTAT
*
5172 ATGATTGCATTTGGAGTGTATATTTTTGTATCTG
1 ATGATTGCATTTGGAGTGCATATTTTTGTATCTG
* ** * *
5206 ATGATTTCAACTGGAATGCATATTTTTGTTTCTG
1 ATGATTGCATTTGGAGTGCATATTTTTGTATCTG
*
5240 ATGATAGCATTTGGAGTGC
1 ATGATTGCATTTGGAGTGC
5259 TCATTACACA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (34 bp):
ATGATTGCATTTGGAGTGCATATTTTTGTATCTG
Found at i:5394 original size:20 final size:20
Alignment explanation
Indices: 5366--5407 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5356 ATTAAATTTC
*
5366 AAAATGAGTTATGAATATGA
1 AAAAAGAGTTATGAATATGA
* *
5386 AAAAAGAGTTGTGAATCTGA
1 AAAAAGAGTTATGAATATGA
5406 AA
1 AA
5408 TGTGAAAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.21, T:0.26
Consensus pattern (20 bp):
AAAAAGAGTTATGAATATGA
Found at i:19094 original size:2 final size:2
Alignment explanation
Indices: 19087--19146 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
19077 TTATTATTAC
19087 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
19129 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
19147 TTTATTATTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19213 original size:3 final size:3
Alignment explanation
Indices: 19195--19244 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
19185 ATTACTCTTT
* * * *
19195 TTA TTA CTA GTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19243 TT
1 TT
19245 TACTTATTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:19329 original size:19 final size:18
Alignment explanation
Indices: 19306--19351 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
19296 ATTTTCTTTA
*
19306 TATTTTCTTATTTTTTTC
1 TATTTTCTTATTTATTTC
19324 TCATTTAT-TTATTTATTTC
1 T-ATTT-TCTTATTTATTTC
19343 TATTTTCTT
1 TATTTTCTT
19352 CTAGTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 1 0.04
18 7 0.29
19 15 0.62
20 1 0.04
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTTCTTATTTATTTC
Found at i:19348 original size:48 final size:47
Alignment explanation
Indices: 19251--19351 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 47
19241 TATTTACTTA
* *
19251 TTTCTATATATTTTTTATATTTTTCCTTTTATTTTATTTTAATTCAT
1 TTTCTTTATATTTTTTATATTTTTCCATTTATTTTATTTTAATTCAT
* *
19298 TTTCTTTATATTTTCTTATTTTTTTCTCATTTA-TTTA-TTTATTTCTAT
1 TTTCTTTATATTTT-TTATATTTTTC-CATTTATTTTATTTTAATTC-AT
19346 TTTCTT
1 TTTCTT
19352 CTAGTTTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
47 20 0.43
48 22 0.47
49 5 0.11
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (47 bp):
TTTCTTTATATTTTTTATATTTTTCCATTTATTTTATTTTAATTCAT
Found at i:19382 original size:23 final size:23
Alignment explanation
Indices: 19356--19400 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
19346 TTTCTTCTAG
*
19356 TTTTTATTTATTTA-TTTATTTAA
1 TTTTT-TTTAGTTATTTTATTTAA
*
19379 TTTTTTTTCGTTATTTTATTTA
1 TTTTTTTTAGTTATTTTATTTA
19401 CTTTCATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTTTTTTAGTTATTTTATTTAA
Found at i:19396 original size:35 final size:35
Alignment explanation
Indices: 19306--19400 Score: 95
Period size: 39 Copynumber: 2.5 Consensus size: 35
19296 ATTTTCTTTA
*
19306 TATTTTCTTATTTTTTTCTCATTTATTTATTTATTTC
1 TATTTTCTTATTTTATT-T-ATTTATTTATTTATTTC
19343 TATTTTCTTCTAGTTTTTATTTATTTATTTATTTAATTT-
1 TATTTTC-T-TA--TTTTATTTATTTATTTATTT-ATTTC
19382 T-TTTTCGTTATTTTATTTA
1 TATTTTC-TTATTTTATTTA
19401 CTTTCATTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
35 9 0.18
37 9 0.18
38 7 0.14
39 15 0.29
40 5 0.10
41 6 0.12
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (35 bp):
TATTTTCTTATTTTATTTATTTATTTATTTATTTC
Found at i:24242 original size:157 final size:156
Alignment explanation
Indices: 23943--24377 Score: 563
Period size: 157 Copynumber: 2.8 Consensus size: 156
23933 CTCAATAAAT
* * * *
23943 AACTTTCCAGTTTCATTCATAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGATACAAC
1 AACTTTCCAGTTTCATTCA-AATCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAAACAAC
* * * *
24008 GCAACTTACACAAGATTGGATTTCAACTTCCCAACG-ATGAATATCCAATTCAAAGCTTAACTTC
65 ACAATTTACACAAGATTGGATTTCAACTTCACAACGAATG-ATATCCAATTCAAAGCTCAACTTC
* *
24072 ACAGCGAATGAGCGACAGTCGACAAA-A
129 ACAGCGAAGGAGCGACAGTCAACAAACA
* *
24099 AACTTTCCAAGTTTCATTCAGAATCAATTTCAACTTCACAGCAAAGGATATTGTACTCGAAACAA
1 AACTTTCC-AGTTTCATTCA-AATCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAAACAA
24164 CACAATTTACACAAGATTGGATTTCAACTTCACAACGAATGATATCCAATTCAAAGCTCAACTTC
64 CACAATTTACACAAGATTGGATTTCAACTTCACAACGAATGATATCCAATTCAAAGCTCAACTTC
* *
24229 ACAGCGAAGGAGCGACTGTCAACAAACC
129 ACAGCGAAGGAGCGACAGTCAACAAACA
* * * * **
24257 AACTTTCTAGTTTCTTTCAAAGTCAATTTCAACTTCATAGTGAAGGATATTGAACTC-AAAGTGA
1 AACTTTCCAGTTTCATTCAAA-TCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAAA-CAA
* * * *
24321 CACAATTTACTCGAGATTGGATTT-AGACTTCACAACGAAGGATATCCAACTCAAAGC
64 CACAATTTACACAAGATTGGATTTCA-ACTTCACAACGAATGATATCCAATTCAAAGC
24378 CAATATGGTG
Statistics
Matches: 247, Mismatches: 26, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
156 14 0.06
157 223 0.90
158 10 0.04
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (156 bp):
AACTTTCCAGTTTCATTCAAATCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAAACAACA
CAATTTACACAAGATTGGATTTCAACTTCACAACGAATGATATCCAATTCAAAGCTCAACTTCAC
AGCGAAGGAGCGACAGTCAACAAACA
Found at i:24423 original size:60 final size:60
Alignment explanation
Indices: 24336--24497 Score: 231
Period size: 60 Copynumber: 2.7 Consensus size: 60
24326 TTTACTCGAG
24336 ATTGGATTT-AGACTTCACAACGAAGGATATCCAACTCAAAGCCAA-TATGGTGAAACAACC
1 ATTGGATTTCA-ACTTCACAACGAAGGATATCCAACTCAAAGCCAAGT-TGGTGAAACAACC
* * *
24396 ATTGGATTTCAACTTCCCGAC-AGAGGATATCCAACTCAAAACCAAGTTGGTGAAACAACC
1 ATTGGATTTCAACTTCACAACGA-AGGATATCCAACTCAAAGCCAAGTTGGTGAAACAACC
* *
24456 CTTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGC
1 ATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGC
24498 TCAACTTCAT
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
59 1 0.01
60 86 0.96
61 3 0.03
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (60 bp):
ATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAAGTTGGTGAAACAACC
Found at i:24623 original size:124 final size:124
Alignment explanation
Indices: 24457--24807 Score: 488
Period size: 124 Copynumber: 2.8 Consensus size: 124
24447 GAAACAACCC
* *
24457 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCATGACCAAGGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCAAGACAAAGGAGCCAT
* * *
24522 CCACAATTTCAACTTCACGAAGAAGGATACCGTGCCCACAAGCAACATCTATCTCTAGA
66 CCACGATTTCAACTTCACGAAGAAGGATATCGTGCCCACAAGCAACATCCATCTCTAGA
* *
24581 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTTAAGACAAAGAAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCAAGACAAAGGAGCCAT
* * * * * * * *
24646 CCATGATTT-AACCTTCAAGACGAATGATATCATGCCCACCAGCAGCATCCATCTCTAGG
66 CCACGATTTCAA-CTTCACGAAGAAGGATATCGTGCCCACAAGCAACATCCATCTCTAGA
* *** *
24705 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGAGAAACTTCACGACAAAGGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCAAGACAAAGGAGCCAT
* *
24770 CAACGATTTCAACTTCACGATGAAGGATATCGTGCCCA
66 CCACGATTTCAACTTCACGAAGAAGGATATCGTGCCCA
24808 ACGGATCAAC
Statistics
Matches: 197, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
123 2 0.01
124 193 0.98
125 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (124 bp):
TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCAAGACAAAGGAGCCAT
CCACGATTTCAACTTCACGAAGAAGGATATCGTGCCCACAAGCAACATCCATCTCTAGA
Found at i:25103 original size:86 final size:85
Alignment explanation
Indices: 24898--25190 Score: 331
Period size: 85 Copynumber: 3.4 Consensus size: 85
24888 TATGTCAACC
* *
24898 AAGACCTTCGAGTTCGATTACATTCAGCTCAGAGGTACATCAAATTTACAGCATA-ACTCAAGGC
1 AAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACATCAAATTTACAGCATAGA-TCAAGGC
* * *
24962 GGGAAAGGTTATATGTCAAC-C
65 -GGAAGGGTTATATGTTAACAA
** * *
24983 AAGACCTTCGAGTTTTATTACACTCAGCTCAAAGGCACATCAAATTTACAACATAGATCAAGGCA
1 AAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACATCAAATTTACAGCATAGATCAAGGC-
25048 GGAAGGGTTATATGTTAACAA
65 GGAAGGGTTATATGTTAACAA
* * * * * * * *
25069 AAGACCTTAGAGTTTGATTACTTTCAGCTCAAAGGCATATCAAATTTATAGTATAGGTCACGGCG
1 AAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACATCAAATTTACAGCATAGATCAAGGCG
* **
25134 AGAAGGGTTATCTGTTAGTAA
66 -GAAGGGTTATATGTTAACAA
* *
25155 AA-ACCTTCGAGTTCAATTACATTCAGCTCAAGGGCA
1 AAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCA
25191 TGTCAAAATC
Statistics
Matches: 177, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
85 103 0.58
86 74 0.42
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (85 bp):
AAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACATCAAATTTACAGCATAGATCAAGGCG
GAAGGGTTATATGTTAACAA
Found at i:25197 original size:85 final size:85
Alignment explanation
Indices: 24871--25268 Score: 325
Period size: 85 Copynumber: 4.7 Consensus size: 85
24861 TAGCATATCA
* * * * * * * * *
24871 CAAGGCGATAATGGCTATATGTCAACCAAGACCTTCGAGTTCGATTACATTCAGCTCAGAGGTAC
1 CAAGGCGAGAAGGGTTATATGTTAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
24936 ATCAAATTTACAGCATA-ACT
66 ATCAAATTTACAGCATAGA-T
* * * * * ** * *
24956 CAAGGCGGGAAAGGTTATATGTCAACCAAGACCTTCGAGTTTTATTACACTCAGCTCAAAGGCAC
1 CAAGGCGAGAAGGGTTATATGTTAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
*
25021 ATCAAATTTACAACATAGAT
66 ATCAAATTTACAGCATAGAT
* * *
25041 CAAGGC-AGGAAGGGTTATATGTTAACAAAAGACCTTAGAGTTTGATTACTTTCAGCTCAAAGGC
1 CAAGGCGA-GAAGGGTTATATGTTAACAAAA-ACCTTCGAGTTCGATTACATTCAGCTCAAAGGC
* * *
25105 ATATCAAATTTATAGTATAGGT
64 ATATCAAATTTACAGCATAGAT
* * ** * *
25127 CACGGCGAGAAGGGTTATCTGTTAGTAAAAACCTTCGAGTTCAATTACATTCAGCTCAAGGGCAT
1 CAAGGCGAGAAGGGTTATATGTTAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
* * * * *
25192 GTCAAAATCACAGAATAGCT
66 ATCAAATTTACAGCATAGAT
* * ** * * * * * *
25212 TAAGTCGAGAAACGCTATTTATTTACAAAAA-CTGTCGAGTTTGATTCCATTCAGCTC
1 CAAGGCGAGAAGGGTTATATGTTAACAAAAACCT-TCGAGTTCGATTACATTCAGCTC
25269 TACAACACAT
Statistics
Matches: 255, Mismatches: 53, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
84 2 0.01
85 181 0.71
86 71 0.28
87 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (85 bp):
CAAGGCGAGAAGGGTTATATGTTAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
ATCAAATTTACAGCATAGAT
Found at i:27351 original size:18 final size:18
Alignment explanation
Indices: 27330--27365 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
27320 TTATATTCAA
27330 ATATCATAT-TTTATTATT
1 ATAT-ATATATTTATTATT
27348 ATATATATATTTATTATT
1 ATATATATATTTATTATT
27366 CTTATACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATATATATTTATTATT
Found at i:27435 original size:9 final size:9
Alignment explanation
Indices: 27403--27513 Score: 51
Period size: 11 Copynumber: 10.9 Consensus size: 9
27393 TTTTTATTAC
27403 TATTTTTTT
1 TATTTTTTT
*
27412 TATTATTATCAT
1 TATT-TT-T-TT
27424 TATTTTTTT
1 TATTTTTTT
27433 TATTTTTTT
1 TATTTTTTT
27442 TACTTATTTTT
1 TA-TT-TTTTT
27453 ATATATTTTTGCT
1 -TAT-TTTTT--T
*
27466 AATTTTCCTTT
1 TATTTT--TTT
27477 TATTTTATGTT
1 TATTTT-T-TT
*
27488 TATTCTTTT
1 TATTTTTTT
* * *
27497 TCTTTATCT
1 TATTTTTTT
27506 TATTTTTT
1 TATTTTTT
27514 CTCCCTTGTT
Statistics
Matches: 77, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
9 28 0.36
10 7 0.09
11 29 0.38
12 10 0.13
13 3 0.04
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (9 bp):
TATTTTTTT
Found at i:27451 original size:21 final size:22
Alignment explanation
Indices: 27393--27462 Score: 81
Period size: 21 Copynumber: 3.2 Consensus size: 22
27383 TATTTCGTTC
27393 TTTTTATTAC-TATTTTTTTTA
1 TTTTTATTACTTATTTTTTTTA
* *
27414 TTATTATCA-TTATTTTTTTTA
1 TTTTTATTACTTATTTTTTTTA
* *
27435 TTTTTTTTACTTATTTTTATATA
1 TTTTTATTACTTATTTTT-TTTA
27458 TTTTT
1 TTTTT
27463 GCTAATTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 24 0.60
22 8 0.20
23 8 0.20
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTTATTACTTATTTTTTTTA
Found at i:27745 original size:14 final size:14
Alignment explanation
Indices: 27726--27766 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
27716 TTTCATTTGT
27726 TTTTATTTTCTTTA
1 TTTTATTTTCTTTA
* *
27740 TTTTATTTCCGTTA
1 TTTTATTTTCTTTA
*
27754 TTTTCTTTTCTTT
1 TTTTATTTTCTTT
27767 CATTATTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTTATTTTCTTTA
Found at i:29447 original size:66 final size:66
Alignment explanation
Indices: 29376--29567 Score: 185
Period size: 66 Copynumber: 2.9 Consensus size: 66
29366 GATTCACATG
* *
29376 GAAGCTGTGGAGAAGATAAAGTATGTTGTAATGGAACAGAGGTGGGTGTTGGTAATGATGGAGAT
1 GAAGCTGTGGAGAAGATAAAGTATGTTGTAATGGATCGGAGGTGGGTGTTGGTAATGATGGAGAT
29441 -
66 A
** * * ** * * *
29441 GTAAGCTGTAAAGATGA-AGAAATATGTTACAATGGATTGGAAGTGGGTGTTGTTAGA-GATGGA
1 G-AAGCTGTGGAGAAGATA-AAGTATGTTGTAATGGATCGGAGGTGGGTGTTGGTA-ATGATGGA
29504 GATA
63 GATA
* * *
29508 GAAG-TCGTGGAGAAGATGAAGTATGTTGTAATGGTATGGGGGGTGGGTGTTGGTAATGAT
1 GAAGCT-GTGGAGAAGATAAAGTATGTTGTAATGG-ATCGGAGGTGGGTGTTGGTAATGAT
29568 AGACATGGAA
Statistics
Matches: 97, Mismatches: 22, Indels: 14
0.73 0.17 0.11
Matches are distributed among these distances:
65 3 0.03
66 73 0.75
67 21 0.22
ACGTcount: A:0.31, C:0.03, G:0.38, T:0.28
Consensus pattern (66 bp):
GAAGCTGTGGAGAAGATAAAGTATGTTGTAATGGATCGGAGGTGGGTGTTGGTAATGATGGAGAT
A
Found at i:29521 original size:132 final size:133
Alignment explanation
Indices: 29317--29567 Score: 344
Period size: 132 Copynumber: 1.9 Consensus size: 133
29307 ATGAAAGTCA
** * *
29317 TAAAGATGAAGAAATATATTGGAATGGAATGAAAGTGGGTATTGTTAGAGATTCACATGGAAGCT
1 TAAAGATGAAGAAATATATTACAATGGAATGAAAGTGGGTATTGTTAGAGATGCACATAGAAGCT
29382 GTGGAGAAGATAAAGTATGTTGTAATGG-AACAGAGGTGGGTGTTGGTAATGATGGAGATGTAAG
66 GTGGAGAAGATAAAGTATGTTGTAATGGTAACAGAGGTGGGTGTTGGTAATGATGGAGATGTAAG
29446 CTG
131 CTG
* * * * * *
29449 TAAAGATGAAGAAATATGTTACAATGGATTGGAAGTGGGTGTTGTTAGAGATGGAGATAGAAG-T
1 TAAAGATGAAGAAATATATTACAATGGAATGAAAGTGGGTATTGTTAGAGATGCACATAGAAGCT
* *** *
29513 CGTGGAGAAGATGAAGTATGTTGTAATGGTATGGGGGGTGGGTGTTGGTAATGAT
66 -GTGGAGAAGATAAAGTATGTTGTAATGGTAACAGAGGTGGGTGTTGGTAATGAT
29568 AGACATGGAA
Statistics
Matches: 102, Mismatches: 15, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
131 1 0.01
132 80 0.78
133 21 0.21
ACGTcount: A:0.33, C:0.03, G:0.35, T:0.28
Consensus pattern (133 bp):
TAAAGATGAAGAAATATATTACAATGGAATGAAAGTGGGTATTGTTAGAGATGCACATAGAAGCT
GTGGAGAAGATAAAGTATGTTGTAATGGTAACAGAGGTGGGTGTTGGTAATGATGGAGATGTAAG
CTG
Found at i:31062 original size:13 final size:13
Alignment explanation
Indices: 31019--31073 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
31009 TTCTGATTAC
* *
31019 TAATAAAAATAGT
1 TAATAATAATAAT
* *
31032 TATTAATAACAAT
1 TAATAATAATAAT
31045 T-ATAATAATAAT
1 TAATAATAATAAT
*
31057 TAATAATAATAAA
1 TAATAATAATAAT
31070 TAAT
1 TAAT
31074 TAAAACCCAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
12 10 0.29
13 24 0.71
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (13 bp):
TAATAATAATAAT
Found at i:32282 original size:98 final size:102
Alignment explanation
Indices: 32045--32303 Score: 357
Period size: 102 Copynumber: 2.6 Consensus size: 102
32035 GCTATCTTAG
* * * * * *
32045 GTGAGATAAACTATTGTTTCGAGT-AAATAATTTCAAAATTTGTGTTTCAATGGAAAATTAACTC
1 GTGAGATAAA-TTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCGAGGGAAAACTAACTC
*
32109 AAGCGAGACAAAATATGTTCTGAGGAAAACAATCTCAA
65 AAGAGAGACAAAATATGTTCTGAGGAAAACAATCTCAA
* *
32147 GTGAGATAAATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTCCGAGGGAAAACTATCTCA
1 GTGAGATAAATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCGAGGGAAAACTAACTCA
** * *
32212 AGAGAGA-TGAAT-T-TTTTTAGGAAAACAATCTCAA
66 AGAGAGACAAAATATGTTCTGAGGAAAACAATCTCAA
32246 GTGAGAT-AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCGAGGGAAAACT
1 GTGAGATAAATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCGAGGGAAAACT
32304 GTCTTAAGCG
Statistics
Matches: 142, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
98 50 0.35
99 26 0.18
100 1 0.01
101 14 0.10
102 51 0.36
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (102 bp):
GTGAGATAAATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCGAGGGAAAACTAACTCA
AGAGAGACAAAATATGTTCTGAGGAAAACAATCTCAA
Found at i:32407 original size:67 final size:66
Alignment explanation
Indices: 32297--32458 Score: 189
Period size: 67 Copynumber: 2.4 Consensus size: 66
32287 TGTTTCGAGG
* * * * * * * *
32297 GAAAACTGTCTTAAGCGAAAAAAAATTTGTTTTGAGATAAACAATCTCAATGGTTTATGTTTTAA
1 GAAAA-TGTCTCAAGCGAGACAAAATTTGATTGGAGAGAAACAATCTAAAAGGTTTATGTTTTAA
32362 AA
65 AA
* * *
32364 TAAATTGTCTCAAGCGAGACGAAACTTTGATTGGAGAGAAACAATCTAAAAGGTTTATGTTTTAA
1 GAAAATGTCTCAAGCGAGAC-AAAATTTGATTGGAGAGAAACAATCTAAAAGGTTTATGTTTTAA
*
32429 GA
65 AA
*
32431 GAAAATGTCTCAAGTGAGACAAAATTTG
1 GAAAATGTCTCAAGCGAGACAAAATTTG
32459 TTTCAAGAGA
Statistics
Matches: 78, Mismatches: 16, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
66 19 0.24
67 59 0.76
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.31
Consensus pattern (66 bp):
GAAAATGTCTCAAGCGAGACAAAATTTGATTGGAGAGAAACAATCTAAAAGGTTTATGTTTTAAA
A
Found at i:32468 original size:36 final size:35
Alignment explanation
Indices: 32421--32553 Score: 126
Period size: 37 Copynumber: 3.7 Consensus size: 35
32411 AAAAGGTTTA
* *
32421 TGTTTTAAGAGAAAATGTCTCAAGTGAGACAAAATT
1 TGTTTCAAGAGAAAATATCTCAAGTGAGA-AAAATT
* *
32457 TGTTTCAAGAGAAAATAATCTCAAGTGAGATTAATTT
1 TGTTTCAAGAGAAAAT-ATCTCAAGTGAGA-AAAATT
* *
32494 TGCTTCAAGA-AAAACTATCTCAAATGAGAAGAAACTT
1 TGTTTCAAGAGAAAA-TATCTCAAGTGAGAA-AAA-TT
*
32531 TGTTTCGAGAGAAACA-ATCTCAA
1 TGTTTCAAGAGAAA-ATATCTCAA
32554 AGGTGATAGA
Statistics
Matches: 80, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
36 33 0.41
37 43 0.54
38 3 0.04
39 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (35 bp):
TGTTTCAAGAGAAAATATCTCAAGTGAGAAAAATT
Found at i:32477 original size:67 final size:66
Alignment explanation
Indices: 32318--32477 Score: 178
Period size: 67 Copynumber: 2.4 Consensus size: 66
32308 TAAGCGAAAA
* * * * *
32318 AAAATTTGTTTTGAGATAAACAATCTCAATGGTTTATGTTTTAAAATAAATTGTCTCAAGCGAGA
1 AAAATTTGTTTAGAGA-AAACAATCTAAAAGGTTTATGTTTTAAAAGAAAATGTCTCAAGCGAGA
32383 CG
65 CG
* * * * *
32385 AAACTTTGATTGGAGAGAAACAATCTAAAAGGTTTATGTTTTAAGAGAAAATGTCTCAAGTGAGA
1 AAAATTTGTTTAGAGA-AAACAATCTAAAAGGTTTATGTTTTAAAAGAAAATGTCTCAAGCGAGA
32450 C-
65 CG
*
32451 AAAATTTGTTTCAAGAGAAAATAATCT
1 AAAATTTGTTT--AGAGAAAACAATCT
32478 CAAGTGAGAT
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
66 9 0.12
67 64 0.83
68 4 0.05
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (66 bp):
AAAATTTGTTTAGAGAAAACAATCTAAAAGGTTTATGTTTTAAAAGAAAATGTCTCAAGCGAGAC
G
Found at i:37458 original size:23 final size:23
Alignment explanation
Indices: 37416--37481 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
37406 CACGGAAGTG
* *
37416 CCACATAAATTTGTCCCGAAAAA
1 CCACATAAAATTATCCCGAAAAA
* * * *
37439 CCATATAGAATTATCGCGAAATA
1 CCACATAAAATTATCCCGAAAAA
37462 CCACATAAAATTATCCCGAA
1 CCACATAAAATTATCCCGAA
37482 GGACTGCATA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.23
Consensus pattern (23 bp):
CCACATAAAATTATCCCGAAAAA
Found at i:44145 original size:28 final size:28
Alignment explanation
Indices: 44104--44167 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
44094 ATTGTTCAAT
*
44104 TCATATCAATTTGTTTAACTAGCCCAAC
1 TCATATCAACTTGTTTAACTAGCCCAAC
*
44132 TCATATTAACTTGTTTAACTAGCCCAAC
1 TCATATCAACTTGTTTAACTAGCCCAAC
*
44160 TTATATCA
1 TCATATCA
44168 CTGAGAACTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (28 bp):
TCATATCAACTTGTTTAACTAGCCCAAC
Found at i:44315 original size:23 final size:23
Alignment explanation
Indices: 44289--44342 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
44279 CATAGATTTA
*
44289 TCCCGAAAGACCACATAAAATTG
1 TCCCGAAAGACCACATAAAAGTG
* * *
44312 TCCCGAATGACCATATAGAAGTG
1 TCCCGAAAGACCACATAAAAGTG
44335 TCCC-AAAG
1 TCCCGAAAG
44343 GACCGCGTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.19
Consensus pattern (23 bp):
TCCCGAAAGACCACATAAAAGTG
Found at i:45924 original size:20 final size:20
Alignment explanation
Indices: 45899--45936 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
45889 TTACATAGTT
45899 GTATCGGTACCCTCTGGGGG
1 GTATCGGTACCCTCTGGGGG
45919 GTATCGGTACCCTCTGGG
1 GTATCGGTACCCTCTGGG
45937 CAATCTGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
GTATCGGTACCCTCTGGGGG
Found at i:46600 original size:16 final size:16
Alignment explanation
Indices: 46565--46615 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
46555 AGCATTTAAG
46565 TTCAAACATCCAAAACAAA
1 TTCAAACATCC---ACAAA
46584 TTCAAACATCCACAAA
1 TTCAAACATCCACAAA
* *
46600 TTTAAACATTCACAAA
1 TTCAAACATCCACAAA
46616 CTTCCAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 19 0.63
19 11 0.37
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (16 bp):
TTCAAACATCCACAAA
Found at i:48561 original size:21 final size:22
Alignment explanation
Indices: 48537--48578 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
48527 AACCAGAACC
48537 CATGT-AGGGTATCAATACCCT
1 CATGTGAGGGTATCAATACCCT
* *
48558 CATGTGGGGGTATCGATACCC
1 CATGTGAGGGTATCAATACCC
48579 ATTCAAAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (22 bp):
CATGTGAGGGTATCAATACCCT
Found at i:48593 original size:23 final size:23
Alignment explanation
Indices: 48565--48623 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
48555 CCTCATGTGG
*
48565 GGGTATCGATACCCATTCAAAGA
1 GGGTATCGATACCCATGCAAAGA
*
48588 GGGTATC-AGTACCCATGCAAAGG
1 GGGTATCGA-TACCCATGCAAAGA
48611 GGGTATCGATACC
1 GGGTATCGATACC
48624 TAGCGCTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 1 0.03
23 30 0.94
24 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (23 bp):
GGGTATCGATACCCATGCAAAGA
Found at i:52472 original size:22 final size:21
Alignment explanation
Indices: 52430--52469 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
52420 AAGACTATTT
52430 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
52451 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
52470 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:57959 original size:90 final size:90
Alignment explanation
Indices: 57831--58008 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
57821 TAATCCCGAA
* * *
57831 TATTTAATTTCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
57896 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
* *
57921 TATTAAATTCCAATTAATTTAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
* *
57986 TAGGGTAACTTGGCTATGAAAGG
66 TAGGGTAACTTGGATATAAAAGG
58009 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:64372 original size:90 final size:90
Alignment explanation
Indices: 64254--64421 Score: 266
Period size: 90 Copynumber: 1.9 Consensus size: 90
64244 TAATCCCGAA
* * * *
64254 TATTTAATTTCAATTCATTAAATATAGATTTAATTAATTTGAAAT-ATTAAAATCCCTAATATGA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAT-CCTAATATGA
*
64318 TTAGGGTAGCTTGGATATAAATGGAT
65 TTAGGGTAACTTGGATATAAATGGAT
*
64344 TATTAAATTCCAATTAATTAAATATAGATTTAGTTAATTTGAAATAATAAAAATCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAATCCTAATATGAT
64409 TAGGGTAACTTGG
66 TAGGGTAACTTGG
64422 CCATAAAAGT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
90 64 0.90
91 7 0.10
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.40
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAATCCTAATATGAT
TAGGGTAACTTGGATATAAATGGAT
Found at i:66242 original size:6 final size:6
Alignment explanation
Indices: 66224--66262 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
66214 TCTAATTTAC
*
66224 TTTGAT TTCGAT TTTGAT TTTGAT TTTGAT TTTGAT TTT
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTT
66263 TATCAAGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.15, C:0.03, G:0.15, T:0.67
Consensus pattern (6 bp):
TTTGAT
Found at i:66291 original size:15 final size:15
Alignment explanation
Indices: 66271--66299 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
66261 TTTATCAAGT
66271 ATTTATTTTTATTTC
1 ATTTATTTTTATTTC
66286 ATTTATTTTTATTT
1 ATTTATTTTTATTT
66300 TTTAGTACCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTATTTTTATTTC
Done.