Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008252.1 Hibiscus syriacus cultivar Beakdansim tig00110904_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: 2928487
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 13
Found at i:2887491 original size:55 final size:55
Alignment explanation
Indices: 2886739--2887483 Score: 649
Period size: 55 Copynumber: 13.5 Consensus size: 55
2886729 GAAGGTTTTG
* ** ** * * *
2886739 CAAGTCCTATACTCCCTGAAAGAAGATAGAGGGGACACATTTGTCGACGATTGTT
1 CAAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGACCCATTTTTCGAAGATTGTT
* * * * * * * *
2886794 CGAGTCCTATACTCCTTGAAAGAAGAAGGAGCAAACCTATTTTCCAAAAATTATT
1 CAAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGACCCATTTTTCGAAGATTGTT
* * * * * * ** *
2886849 CGAGTCCTATACTCCCTGAAATAAGAGGGAGTAGACACGTTTGCCGAATATTGTT
1 CAAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGACCCATTTTTCGAAGATTGTT
2886904 CAAGTCCTATACTCCTTGAAAGAAG-GAGGAGCAGACCCATTTTTCGAAGAATT-TT
1 CAAGTCCTATACTCCTTGAAAGAAGAG-GGAGCAGACCCATTTTTCGAAG-ATTGTT
* * * * * *
2886959 AAAGTCATATACTCCCTAAAAGAAAATGGAGCAGACCCATTTTAT-GAAGATTGTT
1 CAAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGACCCATTTT-TCGAAGATTGTT
* * * * * * * * *
2887014 CGAGTCCTATACTCCTTGATAGAAGAAGTAGCGGACCCGTTCTCCGAAGATTTTT
1 CAAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGACCCATTTTTCGAAGATTGTT
* * *
2887069 CAAGTCCTATACTCCTTGAAAGAAGAGGGAGCAAACACATTTTCCGAAGATTGTT
1 CAAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGACCCATTTTTCGAAGATTGTT
** * * ** * *
2887124 TGAGTCCTATATTCCTTGAAAGAAGAAGGAGCAGACCTGTTTTTCAAAAATTGTT
1 CAAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGACCCATTTTTCGAAGATTGTT
* * * * * * * * *
2887179 CGAGTCCTATACTCCCTAAAAGAAGAGGAAGCAGACACATTTGTCGAGGAGTCTT
1 CAAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGACCCATTTTTCGAAGATTGTT
* * *
2887234 CAAGTCCTATACTCCTTGAAGGAAGAAGGAGCAGACCCA-TTTTCTGAAGAGTGTT
1 CAAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGACCCATTTTTC-GAAGATTGTT
* * * * *
2887289 CAAGTCCTATACTCCTTGATAGAAGAAGAAGCGGACCCA-TTTTCTGAAGATTATT
1 CAAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGACCCATTTTTC-GAAGATTGTT
** * * * *
2887344 TGAGTCCTATACTCCTTGAAAGAAGAGGGAGTAGACCCGTTTTTTGAAAAAATT-TT
1 CAAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGACCCATTTTTCG--AAGATTGTT
* * ** * *
2887400 -GAGTCTTATACTCCCCGAAAGAAAAGGGAGCGGACCCATTTTTCGAAGATTGTT
1 CAAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGACCCATTTTTCGAAGATTGTT
*
2887454 CAAGTCCTATACTCCTTGAAAGAAGTGGGA
1 CAAGTCCTATACTCCTTGAAAGAAGAGGGA
2887484 ATGGACCCGT
Statistics
Matches: 545, Mismatches: 133, Indels: 24
0.78 0.19 0.03
Matches are distributed among these distances:
53 5 0.01
54 10 0.02
55 515 0.94
56 10 0.02
57 5 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (55 bp):
CAAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGACCCATTTTTCGAAGATTGTT
Found at i:2887493 original size:110 final size:110
Alignment explanation
Indices: 2886734--2887478 Score: 728
Period size: 110 Copynumber: 6.8 Consensus size: 110
2886724 TTTTTGAAGG
** ** * *
2886734 TTTTGCAAGTCCTATACTCCCTGAAAGAAGATAGAGGGGACACATTTGTCGACGATTGTTCGAGT
1 TTTT-CAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACATTTTTCGAAGATTGTTCGAGT
* **
2886799 CCTATACTCCTTGAAAGAAGAAGGAGCA-AACC-TATTTTCCAAAAA
65 CCTATACTCCTTGAAAGAAGAAGGAGCAGACCCGT-TTTTTGAAAAA
* * * * ** * *
2886844 TTATTCGAGTCCTATACTCCCTGAAATAAGAGGGAGTAGACACGTTTGCCGAATATTGTTCAAGT
1 TT-TTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACATTTTTCGAAGATTGTTCGAGT
* * * *
2886909 CCTATACTCCTTGAAAGAAGGAGGAGCAGACCCATTTTTCGAAGAA
65 CCTATACTCCTTGAAAGAAGAAGGAGCAGACCCGTTTTTTGAAAAA
* * * * * *
2886955 TTTTAAAGTCATATACTCCCTAAAAGAAAATGGAGCAGACCCATTTTAT-GAAGATTGTTCGAGT
1 TTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACATTTT-TCGAAGATTGTTCGAGT
* * * * ** * *
2887019 CCTATACTCCTTGATAGAAGAAGTAGCGGACCCGTTCTCCGAAGAT
65 CCTATACTCCTTGAAAGAAGAAGGAGCAGACCCGTTTTTTGAAAAA
* * * *
2887065 TTTTCAAGTCCTATACTCCTTGAAAGAAGAGGGAGCAAACACATTTTCCGAAGATTGTTTGAGTC
1 TTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACATTTTTCGAAGATTGTTCGAGTC
* * *
2887130 CTATATTCCTTGAAAGAAGAAGGAGCAGACCTG-TTTTTCAAAAA
66 CTATACTCCTTGAAAGAAGAAGGAGCAGACCCGTTTTTTGAAAAA
* * * * * * * *
2887174 TTGTTCGAGTCCTATACTCCCTAAAAGAAGAGGAAGCAGACACATTTGTCGAGGAGTCTTCAAGT
1 TT-TTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACATTTTTCGAAGATTGTTCGAGT
* * * * *
2887239 CCTATACTCCTTGAAGGAAGAAGGAGCAGACCCATTTTCTGAAGAG
65 CCTATACTCCTTGAAAGAAGAAGGAGCAGACCCGTTTTTTGAAAAA
* * * * * * * * *
2887285 TGTTCAAGTCCTATACTCCTTGATAGAAGAAGAAGCGGACCCA-TTTTCTGAAGATTATTTGAGT
1 TTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACATTTTTC-GAAGATTGTTCGAGT
* *
2887349 CCTATACTCCTTGAAAGAAGAGGGAGTAGACCCGTTTTTTGAAAAAA
65 CCTATACTCCTTGAAAGAAGAAGGAGCAGACCCGTTTTTTG-AAAAA
* * * * * * *
2887396 TTTT-GAGTCTTATACTCCCCGAAAGAAAAGGGAGCGGACCCATTTTTCGAAGATTGTTCAAGTC
1 TTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACATTTTTCGAAGATTGTTCGAGTC
2887460 CTATACTCCTTGAAAGAAG
66 CTATACTCCTTGAAAGAAG
2887479 TGGGAATGGA
Statistics
Matches: 514, Mismatches: 111, Indels: 20
0.80 0.17 0.03
Matches are distributed among these distances:
109 11 0.02
110 467 0.91
111 35 0.07
112 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (110 bp):
TTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACATTTTTCGAAGATTGTTCGAGTC
CTATACTCCTTGAAAGAAGAAGGAGCAGACCCGTTTTTTGAAAAA
Found at i:2890588 original size:21 final size:21
Alignment explanation
Indices: 2890535--2890588 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
2890525 GCAAATTTTG
* * * *
2890535 GTATCGATTCTCTAGTTTAGA
1 GTATAGATACTCTAGCTAAGA
2890556 GATATAGATACTCTAGCTAAGA
1 G-TATAGATACTCTAGCTAAGA
*
2890578 GTATTGATACT
1 GTATAGATACT
2890589 ACCTAATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (21 bp):
GTATAGATACTCTAGCTAAGA
Found at i:2891628 original size:2 final size:2
Alignment explanation
Indices: 2891621--2891658 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2891611 GAGTGTTACA
2891621 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
2891659 TCTCTTTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2891766 original size:17 final size:17
Alignment explanation
Indices: 2891744--2891776 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2891734 TATACAATAC
2891744 TATAAATATTT-ATTATT
1 TATAAAT-TTTCATTATT
2891761 TATAAATTTTCATTAT
1 TATAAATTTTCATTAT
2891777 GATTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TATAAATTTTCATTATT
Found at i:2892228 original size:33 final size:33
Alignment explanation
Indices: 2892191--2892289 Score: 123
Period size: 33 Copynumber: 3.1 Consensus size: 33
2892181 CACCTCCGCA
2892191 ACCCCCGCCGCCACCTCCGCCACCGTCTCCTCC
1 ACCCCCGCCGCCACCTCCGCCACCGTCTCCTCC
* *
2892224 ACCCCCGCCACCACCTCCGTCACCGTCTCCTCC
1 ACCCCCGCCGCCACCTCCGCCACCGTCTCCTCC
* * * *
2892257 A---CCTCCGCAACCCCCGCCACCGTCTCCTAC
1 ACCCCCGCCGCCACCTCCGCCACCGTCTCCTCC
2892287 ACC
1 ACC
2892290 TCCACAACCT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
30 24 0.43
33 32 0.57
ACGTcount: A:0.13, C:0.64, G:0.10, T:0.13
Consensus pattern (33 bp):
ACCCCCGCCGCCACCTCCGCCACCGTCTCCTCC
Found at i:2892232 original size:30 final size:30
Alignment explanation
Indices: 2892198--2892313 Score: 133
Period size: 30 Copynumber: 3.8 Consensus size: 30
2892188 GCAACCCCCG
* *
2892198 CCGCCACCTCCGCCACCGTCTCCTCCACCC
1 CCGCAACCTCCGCCACCGTCTCCTCCACCT
*
2892228 CCGCCACCACCTCCGTCACCGTCTCCTCCACCT
1 CCG-CA--ACCTCCGCCACCGTCTCCTCCACCT
* *
2892261 CCGCAACCCCCGCCACCGTCTCCTACACCT
1 CCGCAACCTCCGCCACCGTCTCCTCCACCT
* * *
2892291 CCACAACCTCCGCCGCCGCCTCC
1 CCGCAACCTCCGCCACCGTCTCC
2892314 ACCTGCAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
30 44 0.60
31 1 0.01
32 2 0.03
33 26 0.36
ACGTcount: A:0.13, C:0.63, G:0.10, T:0.14
Consensus pattern (30 bp):
CCGCAACCTCCGCCACCGTCTCCTCCACCT
Found at i:2892241 original size:21 final size:21
Alignment explanation
Indices: 2892201--2892277 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 21
2892191 ACCCCCGCCG
* **
2892201 CCACCTCCGCCACCGTCTCCT
1 CCACCCCCGCCACCACCTCCT
2892222 CCACCCCCGCCACCACCTCCGT
1 CCACCCCCGCCACCACCTCC-T
** * * *
2892244 -CACCGTCTCCTCCACCTCCG
1 CCACCCCCGCCACCACCTCCT
*
2892264 CAACCCCCGCCACC
1 CCACCCCCGCCACC
2892278 GTCTCCTACA
Statistics
Matches: 41, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
21 40 0.98
22 1 0.02
ACGTcount: A:0.13, C:0.65, G:0.09, T:0.13
Consensus pattern (21 bp):
CCACCCCCGCCACCACCTCCT
Found at i:2895479 original size:49 final size:50
Alignment explanation
Indices: 2895381--2895482 Score: 179
Period size: 49 Copynumber: 2.1 Consensus size: 50
2895371 AAAAGTTCTT
*
2895381 CTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTTTGAA
1 CTCATTATGAACTTCTTCTTCCTCATTGGATGAGTACTTCTCATTTTGAA
*
2895431 CTCATTATGAACTTTTTCTTCCTCA-TGGATGAGTACTTCTCATTTTGAA
1 CTCATTATGAACTTCTTCTTCCTCATTGGATGAGTACTTCTCATTTTGAA
2895480 CTC
1 CTC
2895483 TCCACTGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 26 0.52
50 24 0.48
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.45
Consensus pattern (50 bp):
CTCATTATGAACTTCTTCTTCCTCATTGGATGAGTACTTCTCATTTTGAA
Found at i:2895718 original size:105 final size:107
Alignment explanation
Indices: 2895461--2895708 Score: 331
Period size: 105 Copynumber: 2.3 Consensus size: 107
2895451 CCTCATGGAT
* * * * * * *
2895461 GAGTACTTCTCATTTTGAACTCTCCACTGAAAATGTTGAGTCACCTCCTTCTGCGGTGGACTTGA
1 GAGTTCTTCTCATTATGAACTCTCCATTAAAAATGTTGAATCACCTCATTCTGCGGTGAACTTGA
* *
2895526 AAGGAATAAGTTTTTCTCATTATGAACTTTCTCCTTTAAGAC
66 AAGGAACAAGTTATTCTCATTATGAACTTTCTCCTTTAAGAC
* ** * *
2895568 GAGTTCTTCTTATTATGAACTCT---TTAAGAAATGTTGGTTCACCTCATTCTGTGGTGAATTTG
1 GAGTTCTTCTCATTATGAACTCTCCATTAA-AAATGTTGAATCACCTCATTCTGCGGTGAACTTG
*
2895630 AAAGGAACAAGTTATTCTCATTATGAACTTTCTCCTTTAGGAC
65 AAAGGAACAAGTTATTCTCATTATGAACTTTCTCCTTTAAGAC
2895673 GAGTTCTTCTCATTATGAACTCTCCATTAAAAATGT
1 GAGTTCTTCTCATTATGAACTCTCCATTAAAAATGT
2895709 CAATCCCTCA
Statistics
Matches: 122, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
104 2 0.02
105 90 0.74
107 26 0.21
108 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (107 bp):
GAGTTCTTCTCATTATGAACTCTCCATTAAAAATGTTGAATCACCTCATTCTGCGGTGAACTTGA
AAGGAACAAGTTATTCTCATTATGAACTTTCTCCTTTAAGAC
Found at i:2896321 original size:76 final size:76
Alignment explanation
Indices: 2896231--2896373 Score: 171
Period size: 76 Copynumber: 1.9 Consensus size: 76
2896221 GAGTTAAATT
* * * *
2896231 TTGTTTCGAAGGAAAATTGTCTCAAGCAAGACGAACTAAGTTTTTAGAAAAACCATCTCAAGTGA
1 TTGTTTCGAAGGAAAACTATCTCAAGCAAGACGAACTAAGTTTTAAGAAAAACCATCTCAAGAGA
2896296 GATTCAATTTC
66 GATTCAATTTC
* * ** * **
2896307 TTGTTTC-AAGGGAAAGCTATCTTAAGTGAGACGAATTTGGTTTTAAGAAAAACCATCTCAAGAG
1 TTGTTTCGAA-GGAAAACTATCTCAAGCAAGACGAACTAAGTTTTAAGAAAAACCATCTCAAGAG
2896371 AGA
65 AGA
2896374 CAAAATGTTG
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
75 2 0.04
76 53 0.96
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (76 bp):
TTGTTTCGAAGGAAAACTATCTCAAGCAAGACGAACTAAGTTTTAAGAAAAACCATCTCAAGAGA
GATTCAATTTC
Found at i:2896439 original size:36 final size:37
Alignment explanation
Indices: 2896362--2896440 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 37
2896352 AGAAAAACCA
* *
2896362 TCTCAAGAGAGACAAAATGTTGTTTCAAGTGAAACTG
1 TCTCAAGAGAGACAAAATGTCGTTTCAAGGGAAACTG
*
2896399 TCTCAAGGGAGACAAAAT-TCGTTTCAAGGGAAA-TG
1 TCTCAAGAGAGACAAAATGTCGTTTCAAGGGAAACTG
2896434 TTCTCAA
1 -TCTCAA
2896441 AATTTTGTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 2 0.05
36 19 0.50
37 17 0.45
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.27
Consensus pattern (37 bp):
TCTCAAGAGAGACAAAATGTCGTTTCAAGGGAAACTG
Found at i:2896491 original size:36 final size:36
Alignment explanation
Indices: 2896448--2896529 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
2896438 CAAAATTTTG
*
2896448 TGTTTCAAGAGAAACTAT-TTCAAGGGAGGCAAAATT
1 TGTTTCAAGAGAAACTATCTT-AAGGGAGACAAAATT
* * *
2896484 TGTTTCAATG-GAAATTGTCTTAAGTGAGACAAAATT
1 TGTTTCAA-GAGAAACTATCTTAAGGGAGACAAAATT
2896520 TGTTTCAAGA
1 TGTTTCAAGA
2896530 AAAAAAAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 1 0.03
36 35 0.90
37 3 0.08
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.33
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTATCTTAAGGGAGACAAAATT
Found at i:2896848 original size:40 final size:40
Alignment explanation
Indices: 2896534--2896839 Score: 479
Period size: 40 Copynumber: 7.7 Consensus size: 40
2896524 TCAAGAAAAA
* * *
2896534 AAAAACAATCTTGAGCGAGATAAAATCTTTTGTTTGAAGG
1 AAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGG
*
2896574 AAAAACAATCTTGAGCGAGATAAAATCTTCTGTTTCAAGG
1 AAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGG
*
2896614 AAAAACAATCTTGAGCGAGATAAAATCTTCTGTTTCAAGG
1 AAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGG
* * * *
2896654 AAAAAAAATCTTGAGTGAGATGAAATCTTATGTTTCTAGG
1 AAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGG
*
2896694 AAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAAG
1 AAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGG
*
2896734 AAAAATAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGG
1 AAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGG
*
2896774 AAAAACAATCTTGAGTGAAATAAAATCTTCTGTTTCAAGTG
1 AAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAG-G
*
2896815 -AAAACAATCTTGAGTGAAATAAAAT
1 AAAAACAATCTTGAGTGAGATAAAAT
2896840 GTCTTGTTTT
Statistics
Matches: 249, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 248 1.00
41 1 0.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (40 bp):
AAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGG
Found at i:2896911 original size:76 final size:77
Alignment explanation
Indices: 2896815--2897051 Score: 290
Period size: 76 Copynumber: 3.1 Consensus size: 77
2896805 GTTTCAAGTG
* *
2896815 AAAACAATCTTGAGTGAAATAAAATGTCTTGTTTTAAATAAAACCTGTCTCCAACGAGA-CAAGT
1 AAAACAATCTTGAGTCAAATAAAATGTCTTGTTTTAAATAAAACCTGTCTCCAACGAGAGAAAGT
2896879 CATGTTTTGAAA
66 CATGTTTTGAAA
* * *
2896891 AAAACAATCTTGAGTCAAATAAAATGTCTTGTTTTGAATAAAACATGTCTCCAGCGAGATG-AA-
1 AAAACAATCTTGAGTCAAATAAAATGTCTTGTTTTAAATAAAACCTGTCTCCAACGAGA-GAAAG
* *
2896954 TCTTGTTTTGAGA
65 TCATGTTTTGAAA
* * * * *
2896967 AAAACAATCTTGAGTCAAATAAAATGTCTTCTTTCAAGTAAAA-CAGTCT-CAAGTGAGAGAAAG
1 AAAACAATCTTGAGTCAAATAAAATGTCTTGTTTTAAATAAAACCTGTCTCCAA-CGAGAGAAAG
2897030 T-ATGTTTT-AAGA
65 TCATGTTTTGAA-A
2897042 AAAACAATCT
1 AAAACAATCT
2897052 CCAGTGAGAT
Statistics
Matches: 139, Mismatches: 16, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
74 4 0.03
75 27 0.19
76 106 0.76
77 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (77 bp):
AAAACAATCTTGAGTCAAATAAAATGTCTTGTTTTAAATAAAACCTGTCTCCAACGAGAGAAAGT
CATGTTTTGAAA
Found at i:2898290 original size:32 final size:32
Alignment explanation
Indices: 2898249--2898315 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
2898239 AGCCTTCAAA
2898249 ATGCCTCAACATGAGCTTTCAAAATGACCCAT
1 ATGCCTCAACATGAGCTTTCAAAATGACCCAT
2898281 ATGCCTCAACATGAGCTTTCAAAATGACCCAT
1 ATGCCTCAACATGAGCTTTCAAAATGACCCAT
2898313 ATG
1 ATG
2898316 GATCATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.27, G:0.13, T:0.25
Consensus pattern (32 bp):
ATGCCTCAACATGAGCTTTCAAAATGACCCAT
Found at i:2899164 original size:11 final size:10
Alignment explanation
Indices: 2899148--2899222 Score: 51
Period size: 11 Copynumber: 6.6 Consensus size: 10
2899138 TCTTTATAAC
2899148 TTTTTTTCTAT
1 TTTTTTTCT-T
*
2899159 TTTTTTCACTTT
1 TTTTTT-TC-TT
2899171 TTTTTCTTGCTAT
1 TTTTT-TT-CT-T
*
2899184 TTTTTTCCTTT
1 TTTTTTTC-TT
2899195 TTTTTGTTCTT
1 TTTTT-TTCTT
2899206 TTTTTGTTCTT
1 TTTTT-TTCTT
2899217 TTTTTT
1 TTTTTT
2899223 ATTTGAAACT
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
10 1 0.02
11 31 0.58
12 12 0.23
13 9 0.17
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.80
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:2899185 original size:25 final size:22
Alignment explanation
Indices: 2899148--2899222 Score: 89
Period size: 23 Copynumber: 3.2 Consensus size: 22
2899138 TCTTTATAAC
2899148 TTTTTTTCTATTTTTTTCACTTT
1 TTTTTTTCTATTTTTTTC-CTTT
2899171 TTTTTCTTGCTATTTTTTTCCTTT
1 TTTTT-TT-CTATTTTTTTCCTTT
*
2899195 TTTTTGTTCT-TTTTTTGTTCTTT
1 TTTTT-TTCTATTTTTT-TCCTTT
2899218 TTTTT
1 TTTTT
2899223 ATTTGAAACT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.13
23 17 0.36
24 13 0.28
25 11 0.23
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.80
Consensus pattern (22 bp):
TTTTTTTCTATTTTTTTCCTTT
Found at i:2905995 original size:3 final size:3
Alignment explanation
Indices: 2905987--2906012 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2905977 GACTTTTCCG
2905987 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2906013 CAAACAAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2907211 original size:20 final size:20
Alignment explanation
Indices: 2907186--2907225 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2907176 GTATTGATAC
*
2907186 TCATTCATACGGTATCAATA
1 TCATTCATACAGTATCAATA
*
2907206 TCATTCATTCAGTATCAATA
1 TCATTCATACAGTATCAATA
2907226 CTAATTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (20 bp):
TCATTCATACAGTATCAATA
Found at i:2907589 original size:14 final size:15
Alignment explanation
Indices: 2907560--2907591 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2907550 AATAAATAAA
2907560 AATAATATAGTTTAT
1 AATAATATAGTTTAT
2907575 AATAATATA-TTTAT
1 AATAATATAGTTTAT
2907589 AAT
1 AAT
2907592 TATTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AATAATATAGTTTAT
Found at i:2907657 original size:41 final size:40
Alignment explanation
Indices: 2907577--2907676 Score: 103
Period size: 41 Copynumber: 2.4 Consensus size: 40
2907567 TAGTTTATAA
* *
2907577 TAATATATTTATAATTATTTATTATATTTAAACTGTTAAAT
1 TAATATTTTTATAA-TATTTATTATATTTAAACTATTAAAT
* *
2907618 TAATATTTTTATAATATTTTTTATATTCTTAA-TAATTAAAT
1 TAATATTTTTATAATATTTATTATATT-TAAACT-ATTAAAT
* *
2907659 TATATATTGTAATAATAT
1 TA-ATATTTTTATAATAT
2907677 AAAAATAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
40 13 0.26
41 24 0.48
42 13 0.26
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (40 bp):
TAATATTTTTATAATATTTATTATATTTAAACTATTAAAT
Found at i:2909408 original size:4 final size:4
Alignment explanation
Indices: 2909394--2909467 Score: 116
Period size: 4 Copynumber: 18.8 Consensus size: 4
2909384 ACTTGATTTA
*
2909394 TATG ATATG TATG TATG TATG TATG TATG TATG TATG TATA TATG TATG
1 TATG -TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2909443 TATG TATG TATG TA-- TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
2909468 ATGTATATGT
Statistics
Matches: 65, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
2 2 0.03
4 59 0.91
5 4 0.06
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:2909462 original size:6 final size:6
Alignment explanation
Indices: 2909427--2909518 Score: 71
Period size: 6 Copynumber: 15.3 Consensus size: 6
2909417 TGTATGTATG
* * * * *
2909427 TATGTA TATATG TATGTA TGTATG TATGTA TATG-- TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
* * * *
2909473 TATGTA TATGTATA TATATA TATATA TATCTA TATGTA TATATA TA
1 TATGTA TATG--TA TATGTA TATGTA TATGTA TATGTA TATGTA TA
2909519 ATATAGATAT
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
4 4 0.06
6 59 0.87
8 5 0.07
ACGTcount: A:0.36, C:0.01, G:0.13, T:0.50
Consensus pattern (6 bp):
TATGTA
Found at i:2909470 original size:16 final size:16
Alignment explanation
Indices: 2909392--2909513 Score: 101
Period size: 16 Copynumber: 7.7 Consensus size: 16
2909382 ACACTTGATT
2909392 TATATG-ATATGTATG
1 TATATGTATATGTATG
2909407 TATGTATGTATGTATGTATG
1 TA--TATGTA--TATGTATG
* *
2909427 TATGTATATATGTATG
1 TATATGTATATGTATG
2909443 --TATG--TATGTATG
1 TATATGTATATGTATG
* *
2909455 TATATGTATGTATATG
1 TATATGTATATGTATG
*
2909471 TATATGTATATGTATA
1 TATATGTATATGTATG
* * *
2909487 TATATATATATATATC
1 TATATGTATATGTATG
2909503 TATATGTATAT
1 TATATGTATAT
2909514 ATATAATATA
Statistics
Matches: 85, Mismatches: 13, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
12 8 0.09
14 6 0.07
15 2 0.02
16 50 0.59
17 4 0.05
18 5 0.06
20 10 0.12
ACGTcount: A:0.33, C:0.01, G:0.16, T:0.50
Consensus pattern (16 bp):
TATATGTATATGTATG
Found at i:2909492 original size:4 final size:4
Alignment explanation
Indices: 2909431--2909534 Score: 75
Period size: 4 Copynumber: 26.0 Consensus size: 4
2909421 TGTATGTATG
* * * * * * * * *
2909431 TATA TATG TATG TATG TATG TATG TATA TGTA TGTA TATG TATA TGTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
2909479 TATG TATA TATA TATA TATA TATC TATA TGTA TATA TATA -ATA TAGA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
2909526 TATCA TATA
1 TAT-A TATA
2909535 AAATTCAAAT
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
3 3 0.04
4 75 0.91
5 4 0.05
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (4 bp):
TATA
Found at i:2909512 original size:22 final size:22
Alignment explanation
Indices: 2909393--2909518 Score: 76
Period size: 22 Copynumber: 5.6 Consensus size: 22
2909383 CACTTGATTT
*
2909393 ATATGATATGTATGTATGTATGTAT
1 ATAT-ATATGTA--TATGTATATAT
* *
2909418 GTATGTATG--TATGTATATAT
1 ATATATATGTATATGTATATAT
* * *
2909438 GTATGTATGTATGTATGTATATGT
1 ATATATATGTA--TATGTATATAT
* *
2909462 ATGTATATGTATATGTATATGT
1 ATATATATGTATATGTATATAT
* * *
2909484 ATATATATATATATATATCTAT
1 ATATATATGTATATGTATATAT
* *
2909506 ATGTATATATATA
1 ATATATATGTATA
2909519 ATATAGATAT
Statistics
Matches: 84, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
20 19 0.23
22 40 0.48
24 22 0.26
25 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (22 bp):
ATATATATGTATATGTATATAT
Found at i:2909768 original size:33 final size:33
Alignment explanation
Indices: 2909722--2909798 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
2909712 TCAGCAACCT
*
2909722 CCGCCGCCGCCTCCACCTCCACAACCTCCGCCG
1 CCGCCGCCACCTCCACCTCCACAACCTCCGCCG
2909755 CCGCCGCCACCTCCACCTCCACAACCTCCGCCG
1 CCGCCGCCACCTCCACCTCCACAACCTCCGCCG
* *
2909788 CCTCCTCCACC
1 CCGCCGCCACC
2909799 ACCGCCACCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.65, G:0.12, T:0.10
Consensus pattern (33 bp):
CCGCCGCCACCTCCACCTCCACAACCTCCGCCG
Found at i:2909808 original size:27 final size:27
Alignment explanation
Indices: 2909728--2909808 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 27
2909718 ACCTCCGCCG
* * * * *
2909728 CCGCCTCCACCTCCACAACCTCCGCCG
1 CCGCCGCCACCTCCACCACCACCACCT
* *
2909755 CCGCCGCCACCTCCACCTCCACAACCT
1 CCGCCGCCACCTCCACCACCACCACCT
* *
2909782 CCGCCGCCTCCTCCACCACCGCCACCT
1 CCGCCGCCACCTCCACCACCACCACCT
2909809 ACATAGCCAC
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.15, C:0.64, G:0.10, T:0.11
Consensus pattern (27 bp):
CCGCCGCCACCTCCACCACCACCACCT
Found at i:2910900 original size:87 final size:86
Alignment explanation
Indices: 2910754--2910919 Score: 296
Period size: 87 Copynumber: 1.9 Consensus size: 86
2910744 GATATCAAAG
*
2910754 AACTTGTAAGGCTGACATTTACTTGGTCCATGTGGGCCACAATGTTTTTATTTATTTTAATTTTT
1 AACTTGTAAGGCTGACATTTACTTGGTCCATCTGGGCCACAATGTTTTTATTTATTTTAA-TTTT
2910819 ATTTTAGACTTTTCATAAATAA
65 ATTTTAGACTTTTCATAAATAA
* *
2910841 AACTTGTAAGGTTGACATTTACTTTGTCCATCTGGGCCACAATGTTTTTATTTATTTTAATTTTA
1 AACTTGTAAGGCTGACATTTACTTGGTCCATCTGGGCCACAATGTTTTTATTTATTTTAATTTTA
2910906 TTTTAGACTTTTCA
66 TTTTAGACTTTTCA
2910920 AATTTTATTT
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
86 19 0.25
87 57 0.75
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (86 bp):
AACTTGTAAGGCTGACATTTACTTGGTCCATCTGGGCCACAATGTTTTTATTTATTTTAATTTTA
TTTTAGACTTTTCATAAATAA
Found at i:2914065 original size:12 final size:13
Alignment explanation
Indices: 2914042--2914079 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
2914032 TCATTTGGAT
*
2914042 TAGGATTAGGAGG
1 TAGGATTTGGAGG
2914055 T-GGATTTGGAGG
1 TAGGATTTGGAGG
2914067 TAGG-TTTGGAGG
1 TAGGATTTGGAGG
2914079 T
1 T
2914080 CGGTTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 20 0.87
13 3 0.13
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.32
Consensus pattern (13 bp):
TAGGATTTGGAGG
Found at i:2914346 original size:20 final size:20
Alignment explanation
Indices: 2914305--2914347 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2914295 ATTTTTCATT
*
2914305 AAAACAACATAATTAAATCA
1 AAAACAACATAATTAAAACA
*
2914325 AAAACAACA-ATTTAAAAACA
1 AAAACAACATAATT-AAAACA
2914345 AAA
1 AAA
2914348 CATTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.70, C:0.14, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAACAACATAATTAAAACA
Found at i:2916878 original size:12 final size:12
Alignment explanation
Indices: 2916861--2916885 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2916851 ATGATGGTTC
2916861 TCCAACGTCATG
1 TCCAACGTCATG
2916873 TCCAACGTCATG
1 TCCAACGTCATG
2916885 T
1 T
2916886 GCTTTTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (12 bp):
TCCAACGTCATG
Found at i:2919253 original size:18 final size:17
Alignment explanation
Indices: 2919226--2919263 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2919216 TACCTCTTTG
2919226 CCTAGGGGTA-TCGGTAC
1 CCTAGGGGTATTC-GTAC
2919243 CCTATGGGGTATTCGTAC
1 CCTA-GGGGTATTCGTAC
2919261 CCT
1 CCT
2919264 TATTGCATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 13 0.68
19 2 0.11
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (17 bp):
CCTAGGGGTATTCGTAC
Done.