Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003132.1 Hibiscus syriacus cultivar Beakdansim tig00006570_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: 1555756
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:210723 original size:78 final size:79
Alignment explanation
Indices: 210616--210811 Score: 232
Period size: 86 Copynumber: 2.4 Consensus size: 79
210606 TGGTAACAAA
*** * * * *
210616 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGT-TGCCGCAATAGGTGTTGATATTTGGC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTGTATGCCGCAATAGGTGTTGAGATTTAGC
210680 GGCATTTTTCCAAC
66 GGCATTTTTCCAAC
*
210694 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCACAAATGCCGCAATAGGTGTTGAG
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTGT-------ATGCCGCAATAGGTGTTGAG
* *
210759 ATTTAGCGGCGTTTTTCCCAC
59 ATTTAGCGGCATTTTTCCAAC
210780 AAACGCCGCAATAGGTGTTGAGATTTAGCGGC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGC
210812 CTTTTTTCCA
Statistics
Matches: 100, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
78 32 0.32
86 68 0.68
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (79 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTGTATGCCGCAATAGGTGTTGAGATTTAGC
GGCATTTTTCCAAC
Found at i:210725 original size:43 final size:43
Alignment explanation
Indices: 210655--210875 Score: 327
Period size: 43 Copynumber: 5.2 Consensus size: 43
210645 GGCGTTTGTT
* * *
210655 GCCGCAATAGGTGTTGATATTTGGCGGCATTTTTCCAACAAAC
1 GCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCCCACAAAC
* *
210698 GCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCACAAAT
1 GCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCCCACAAAC
*
210741 GCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCACAAAC
1 GCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCCCACAAAC
* *
210784 GCCGCAATAGGTGTTGAGATTTAGCGGCCTTTTTTCCACAAAC
1 GCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCCCACAAAC
* * *
210827 GCCGCAATAGGTCTTGAGATTTAGCGGC-GTTTTCCCATAAAC
1 GCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCCCACAAAC
*
210869 ACCGCAA
1 GCCGCAA
210876 AAGATCTGGT
Statistics
Matches: 165, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
42 17 0.10
43 148 0.90
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (43 bp):
GCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCCCACAAAC
Found at i:212655 original size:2 final size:2
Alignment explanation
Indices: 212648--212712 Score: 102
Period size: 2 Copynumber: 34.5 Consensus size: 2
212638 CAGTATTTGC
212648 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT A- AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
212687 AT AT AT AT AT AT AT -T AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
212713 GAAAAGTACC
Statistics
Matches: 59, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
1 4 0.07
2 55 0.93
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:212669 original size:15 final size:14
Alignment explanation
Indices: 212648--212712 Score: 102
Period size: 13 Copynumber: 4.9 Consensus size: 14
212638 CAGTATTTGC
212648 ATATATATATATAT
1 ATATATATATATAT
212662 AT-TATATATATAT
1 ATATATATATATAT
212675 ATA-ATATATAT-T
1 ATATATATATATAT
212687 ATATATATATATAT
1 ATATATATATATAT
212701 -TATATATATATA
1 ATATATATATATA
212713 GAAAAGTACC
Statistics
Matches: 48, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.08
13 41 0.85
14 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATATATATAT
Found at i:214993 original size:15 final size:16
Alignment explanation
Indices: 214964--214999 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
214954 GGTAGTTAAA
*
214964 CTTCAGATTCCTTGCT
1 CTTCAGATTCATTGCT
214980 CTTCA-ATTCATTGCT
1 CTTCAGATTCATTGCT
214995 CTTCA
1 CTTCA
215000 TTTGGATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.17, C:0.31, G:0.08, T:0.44
Consensus pattern (16 bp):
CTTCAGATTCATTGCT
Found at i:215277 original size:142 final size:142
Alignment explanation
Indices: 215014--215278 Score: 318
Period size: 142 Copynumber: 1.9 Consensus size: 142
215004 GATCTATGAT
* *
215014 TGTCAAAAGGTAGAATCACCAACCATTCATTCTTAAAAAACATGTTTTTTTATCTAAGACAAATC
1 TGTCAAAAGGTAGAATCACCAACCATTCATGCTTAAAAAACATGTTTTTTTATCCAAGACAAATC
* * ** ** *
215079 GATATCTGTTTATTTATATGTCCATCACTACAACAAAATAAAAAATTGTGGTGACCATATCAAAT
66 AATATCTGATTATTTATAAATCCATCACTACAACAAAATAAAAAATTGCAGCGACCATATCAAAT
215144 TATTTTTCTCCA
131 TATTTTTCTCCA
* * * * * * *
215156 TGTCAAAAGGTAGCATTATCAACCATTCCTGCTTAAAACACATG-TTTTTTCTCCAAGGCAAATC
1 TGTCAAAAGGTAGAATCACCAACCATTCATGCTTAAAAAACATGTTTTTTTATCCAAGACAAATC
* ***
215220 AATATCAT-ATTGTTTATAAATCCATCACTAACAACAAAATTGGAAATTGCAGCGACCAT
66 AATATC-TGATTATTTATAAATCCATCACT-ACAACAAAATAAAAAATTGCAGCGACCAT
215279 CATCGAGTAT
Statistics
Matches: 101, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
141 39 0.39
142 62 0.61
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (142 bp):
TGTCAAAAGGTAGAATCACCAACCATTCATGCTTAAAAAACATGTTTTTTTATCCAAGACAAATC
AATATCTGATTATTTATAAATCCATCACTACAACAAAATAAAAAATTGCAGCGACCATATCAAAT
TATTTTTCTCCA
Found at i:216089 original size:41 final size:41
Alignment explanation
Indices: 216015--216373 Score: 332
Period size: 41 Copynumber: 8.6 Consensus size: 41
216005 TTGTAAACTT
* * *
216015 GCGGCGTTTGTAA-ACACAAACGCCACTATAGTACAAGTGTATA
1 GCGGCGTTTG-AATA-A-AAACGCCACTAAAGTACAAGTCTTTA
* *
216058 GCGGCGTTTGAATAAAAACGCCCCTAAAGTACGAGTCTTTA
1 GCGGCGTTTGAATAAAAACGCCACTAAAGTACAAGTCTTTA
* * * *
216099 GCGGCGTTTGTATAAAAATGTCAATAAAGTACAAGTCTTTA
1 GCGGCGTTTGAATAAAAACGCCACTAAAGTACAAGTCTTTA
* * * **
216140 GCGGCGTTTGTATAAAAATGCCACTAAATTATGAGTCTTTA
1 GCGGCGTTTGAATAAAAACGCCACTAAAGTACAAGTCTTTA
* * * *
216181 GCGGCGTTTGTAA-ACACAAACGCCACTATAGTACATGTGTATA
1 GCGGCGTTTG-AATA-A-AAACGCCACTAAAGTACAAGTCTTTA
* * * *
216224 ACGGCGTTTGTATAAAAACGCCACTAAAGTACAATTCTATA
1 GCGGCGTTTGAATAAAAACGCCACTAAAGTACAAGTCTTTA
* * * *
216265 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
1 GCGGCGTTTGAATAAAAACGCCACTAAAGTACAAGTCTTTA
* *
216306 GCGGCGTTT-ATATAAAAACGCCACTAAAGTACTACTCTTTTA
1 GCGGCGTTTGA-ATAAAAACGCCACTAAAGTACAAGTC-TTTA
*
216348 -CGGCGTTTG-TTGAAAAAACGCCACTA
1 GCGGCGTTTGAAT--AAAAACGCCACTA
216374 TCGATGAACC
Statistics
Matches: 263, Mismatches: 43, Indels: 21
0.80 0.13 0.06
Matches are distributed among these distances:
40 1 0.00
41 199 0.76
42 24 0.09
43 39 0.15
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
GCGGCGTTTGAATAAAAACGCCACTAAAGTACAAGTCTTTA
Found at i:216155 original size:82 final size:82
Alignment explanation
Indices: 216015--216357 Score: 391
Period size: 82 Copynumber: 4.1 Consensus size: 82
216005 TTGTAAACTT
* * * * *
216015 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAAAAACGCC
1 GCGGCGTTTGTATA-A-AAATGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCC
*
216080 CCTAAAGTACGAGTCTTTA
64 ACTAAAGTACGAGTCTTTA
* * * *
216099 GCGGCGTTTGTATAAAAATGTCAATAAAGTACAAGTCTTTAGCGGCGTTTGTATAAAAATGCCAC
1 GCGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCAC
* *
216164 TAAATTATGAGTCTTTA
66 TAAAGTACGAGTCTTTA
* * * * * *
216181 GCGGCGTTTGTAAACACAAACGCCACTATAGTACATGTGTATAACGGCGTTTGTATAAAAACGCC
1 GCGGCGTTTGTATA-A-AAATGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCC
* * *
216246 ACTAAAGTACAATTCTATA
64 ACTAAAGTACGAGTCTTTA
* * * *
216265 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTATATAAAAACGCCAC
1 GCGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCAC
* *
216330 TAAAGTACTACTCTTTTA
66 TAAAGTACGAGTC-TTTA
216348 -CGGCGTTTGT
1 GCGGCGTTTGT
216358 TGAAAAAACG
Statistics
Matches: 216, Mismatches: 40, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
82 131 0.61
83 6 0.03
84 79 0.37
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (82 bp):
GCGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCAC
TAAAGTACGAGTCTTTA
Found at i:216237 original size:125 final size:123
Alignment explanation
Indices: 216015--216337 Score: 389
Period size: 125 Copynumber: 2.6 Consensus size: 123
216005 TTGTAAACTT
* * * * * * * *
216015 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGA-ATAAAAACGC
1 GCGGCGTTTGTATA-A-AAATGCCACTAAATTACGAGTCTTTAGCGGCGTTT-ATAAAAAAACGC
* * * * * * *
216079 CCCTAAAGTACGA-GTCTTTAGCGGCGTTTGTATAAAAATGTCAATAAAGTACAAGTCTTTA
63 CACTAAAGTAC-ATGTGTATAACGGCGTTTGTATAAAAACGCCAATAAAGTACAAGTCTATA
* *
216140 GCGGCGTTTGTATAAAAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTAAACACAAACGCC
1 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTATAAA-A-AAACGCC
* * *
216205 ACTATAGTACATGTGTATAACGGCGTTTGTATAAAAACGCCACTAAAGTACAATTCTATA
64 ACTAAAGTACATGTGTATAACGGCGTTTGTATAAAAACGCCAATAAAGTACAAGTCTATA
*
216265 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTATATAAAAACGCCAC
1 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTATAAAAAAACGCCAC
216330 TAAAGTAC
66 TAAAGTAC
216338 TACTCTTTTA
Statistics
Matches: 170, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
123 46 0.27
124 4 0.02
125 120 0.71
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (123 bp):
GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTATAAAAAAACGCCAC
TAAAGTACATGTGTATAACGGCGTTTGTATAAAAACGCCAATAAAGTACAAGTCTATA
Found at i:216304 original size:166 final size:167
Alignment explanation
Indices: 216015--216374 Score: 523
Period size: 166 Copynumber: 2.2 Consensus size: 167
216005 TTGTAAACTT
*
216015 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAAAAACGCC
1 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACGCC
* * * *
216080 CCTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGTCAATAAAGTACAAGTCTTTAGCGGC
66 ACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATGCCAATAAAGTACAAGTCTTTAGCGGC
* * * *
216145 GTTTGTATAAAAATGCCACTAAATTA-TGAGTC-TTTA
131 GTTTATATAAAAACGCCACTAAAGTACT-ACTCTTTTA
* *
216181 GCGGCGTTTGTAAACACAAACGCCACTATAGTACATGTGTATAACGGCGTTTGTATAAAAACGCC
1 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACGCC
* * * *
216246 ACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGC
66 ACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATGCCAATAAAGTACAAGTCTTTAGCGGC
216311 GTTTATATAAAAACGCCACTAAAGTACTACTCTTTTA
131 GTTTATATAAAAACGCCACTAAAGTACTACTCTTTTA
*
216348 -CGGCGTTTGTTGAA-A-AAACGCCACTAT
1 GCGGCGTTTG-TAAACACAAACGCCACTAT
216375 CGATGAACCT
Statistics
Matches: 175, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
165 12 0.07
166 155 0.89
167 8 0.05
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (167 bp):
GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACGCC
ACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATGCCAATAAAGTACAAGTCTTTAGCGGC
GTTTATATAAAAACGCCACTAAAGTACTACTCTTTTA
Found at i:216392 original size:82 final size:81
Alignment explanation
Indices: 216056--216417 Score: 238
Period size: 82 Copynumber: 4.4 Consensus size: 81
216046 TACAAGTGTA
* * * * * *
216056 TAGCGGCGTTTGA-ATAAAAACGCCCCTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGT
1 TAGCGGCGTTT-ATATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGC
* * *
216120 CAATAAAGTAC-AAGTCTT
65 CACTAATG-ACGAA-CCTT
* * * ** * * *
216138 TAGCGGCGTTTGTATAAAAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTAAACACAAACG
1 TAGCGGCGTTTATATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATA-A-AAACG
**
216203 CCACT-AT-A-GTACATGTGT
64 CCACTAATGACG-A-ACCT-T
* * * *
216221 ATAACGGCGTTTGTATAAAAACGCCACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGC
1 -TAGCGGCGTTTATATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGC
* **
216286 CACTAAATTACGAGTCTT
65 CACT-AATGACGAACCTT
* *
216304 TAGCGGCGTTTATATAAAAACGCCACTAAAGTACTACTCTTTTA-CGGCGTTTGT-TGAAAAAAC
1 TAGCGGCGTTTATATAAAAACGCCACTAAAGTACAACTC-TATAGCGGCGTTTGTAT--AAAAAC
*
216367 GCCACT-ATCGATGAACCTAT
63 GCCACTAAT-GACGAACCT-T
* **
216387 T-GCGGCGTTTTTATAAAAACGCTGCTAAAGT
1 TAGCGGCGTTTATATAAAAACGCCACTAAAGT
216418 TACCATTTTG
Statistics
Matches: 228, Mismatches: 35, Indels: 34
0.77 0.12 0.11
Matches are distributed among these distances:
81 4 0.02
82 139 0.61
83 22 0.10
84 60 0.26
85 2 0.01
86 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (81 bp):
TAGCGGCGTTTATATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGCC
ACTAATGACGAACCTT
Found at i:217738 original size:2 final size:2
Alignment explanation
Indices: 217731--217787 Score: 77
Period size: 2 Copynumber: 30.5 Consensus size: 2
217721 TGAGTTTGTT
*
217731 TA TA TA TA AA T- TA T- TA T- TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
217769 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
217788 TTAATAGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
1 4 0.08
2 45 0.92
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:220257 original size:165 final size:164
Alignment explanation
Indices: 220078--220569 Score: 525
Period size: 166 Copynumber: 3.0 Consensus size: 164
220068 CATGTGTAGG
* * ** * *
220078 TCGATAGACTCATTATAGTTTATGTTATTCATATGTACAAGAAATTATAAATTAACTTAATTATA
1 TCGATAAACTCATTA-AG-TTATGTTATTCATATATACAAGAAACGACAAATTAATTTAATTATA
* *
220143 TAAT-GGACACATATGAGTCGATAAACGTTACAAGATAATTTTAAGATTCAT-AATAGAATAAAT
64 TAATAGAACACGTATGAGTCGATAAACGTTACAAGAT-ATTTTAAGATTCATAAATAGAATAAAT
*
220206 GTTACCTTATTCAATCATATATAATGAAACGTGTAAA
128 GTTACCTTATTCAATCATATATAATGAAACATGTAAA
* * * * *
220243 TCGATAAACTCATTACGACTTATGGTGTTCATTTATACAAGAAACGACAAATTAATTTAGTTATA
1 TCGATAAACTCATTA--AGTTATGTTATTCATATATACAAGAAACGACAAATTAATTTAATTATA
* * **
220308 TAATAGAACACGTATGAGTCAATAAACTTGTAGTAGAT-TTCTTAAGATTCATAAATAGAATAAA
64 TAATAGAACACGTATGAGTCGATAAACGT-TACAAGATATT-TTAAGATTCATAAATAGAATAAA
* * *
220372 TATTACCTCATTC-ATCATATACAATGAAAACACATGTAAA
127 TGTTACCTTATTCAATCATATATAATG--AA-ACATGTAAA
* *
220412 TCAATAAACTCATTACA---AT-TTA-TCATATATACAAGAAACGACAAATTAGTTTAATTATAT
1 TCGATAAACTCATTA-AGTTATGTTATTCATATATACAAGAAACGACAAATTAATTTAATTATAT
* * *
220472 AATAGAACACGTATGAGTCGATAAACTCGTTACAAGATACTCCTAAAGATTTATAAATAGAATAA
65 AATAGAACACGTATGAGTCGATAAA--CGTTACAAGATA-T-TTTAAGATTCATAAATAGAATAA
* * *
220537 ACGCTACCTTATTCAATTATATATAATGAAACA
126 ATGTTACCTTATTCAATCATATATAATGAAACA
220570 CTTGTAGGTT
Statistics
Matches: 271, Mismatches: 42, Indels: 29
0.79 0.12 0.08
Matches are distributed among these distances:
163 59 0.22
164 10 0.04
165 63 0.23
166 75 0.28
167 39 0.14
168 3 0.01
169 22 0.08
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (164 bp):
TCGATAAACTCATTAAGTTATGTTATTCATATATACAAGAAACGACAAATTAATTTAATTATATA
ATAGAACACGTATGAGTCGATAAACGTTACAAGATATTTTAAGATTCATAAATAGAATAAATGTT
ACCTTATTCAATCATATATAATGAAACATGTAAA
Found at i:220623 original size:166 final size:161
Alignment explanation
Indices: 220126--220628 Score: 493
Period size: 166 Copynumber: 3.1 Consensus size: 161
220116 AAGAAATTAT
* * * *
220126 AAATTAACTTAATTATATAAT-GGACACATATGAGTCGATAAA--CGTTACAAGATAATTTTAAG
1 AAATTAATTTAATTATATAATAGAACACGTATGAGTCGATAAACTCGTTACAAGAT-ATCTTAAG
*
220188 ATTCAT-AATAGAATAAATGTTACCTTATTCAATCATATATAATG-AA-ACGTGTAAATCGATAA
65 ATTCATAAATAGAATAAATGTTACCTTATTCAATCATATATAATGAAACACATGTAAATCGATAA
* * *
220250 ACTCATTACGACTTATGGTGTTCATTTATACAAGAAACGAC
130 ACTCATTAC-A---A---T-TT-ATCTATTCAAGAAAAGAC
* * * ** *
220291 AAATTAATTTAGTTATATAATAGAACACGTATGAGTCAATAAACTTG-TAGTAGATTTCTTAAGA
1 AAATTAATTTAATTATATAATAGAACACGTATGAGTCGATAAACTCGTTACAAGATATCTTAAGA
* * * *
220355 TTCATAAATAGAATAAATATTACCTCATTC-ATCATATACAATGAAAACACATGTAAATCAATAA
66 TTCATAAATAGAATAAATGTTACCTTATTCAATCATATATAATG-AAACACATGTAAATCGATAA
*
220419 ACTCATTACAATTTATCATATATACAAGAAACGAC
130 ACTCATTACAATTTATC-TAT-T-CAAGAAAAGAC
* *
220454 AAATTAGTTTAATTATATAATAGAACACGTATGAGTCGATAAACTCGTTACAAGATACTCCTAAA
1 AAATTAATTTAATTATATAATAGAACACGTATGAGTCGATAAACTCGTTACAAGATA-T-CTTAA
* * * * * ** *
220519 GATTTATAAATAGAATAAACGCTACCTTATTCAATTATATATAATGAAACACTTGTAGGTTGATA
64 GATTCATAAATAGAATAAATGTTACCTTATTCAATCATATATAATGAAACACATGTAAATCGATA
*
220584 AACTCGTTACAATTTATACTATTCAA-AAATTTAGAC
129 AACTCATTACAATTTAT-CTATTCAAGAAA---AGAC
220620 AAATTAATT
1 AAATTAATT
220629 CAATAAGACA
Statistics
Matches: 280, Mismatches: 40, Indels: 35
0.79 0.11 0.10
Matches are distributed among these distances:
160 2 0.01
161 5 0.02
162 1 0.00
163 57 0.20
164 9 0.03
165 22 0.08
166 117 0.42
167 40 0.14
168 4 0.01
169 23 0.08
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (161 bp):
AAATTAATTTAATTATATAATAGAACACGTATGAGTCGATAAACTCGTTACAAGATATCTTAAGA
TTCATAAATAGAATAAATGTTACCTTATTCAATCATATATAATGAAACACATGTAAATCGATAAA
CTCATTACAATTTATCTATTCAAGAAAAGAC
Found at i:223351 original size:19 final size:19
Alignment explanation
Indices: 223327--223366 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
223317 GTTTTGAAAC
223327 AAATAATAATAATAATAAT
1 AAATAATAATAATAATAAT
223346 AAATAATAATAATAATAAT
1 AAATAATAATAATAATAAT
223365 AA
1 AA
223367 TATATGTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATAATAATAATAATAAT
Found at i:223388 original size:3 final size:3
Alignment explanation
Indices: 223328--223368 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
223318 TTTTGAAACA
223328 AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT A
223369 TATGTTAGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:223888 original size:2 final size:2
Alignment explanation
Indices: 223881--223918 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
223871 TTACTTAACA
223881 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
223919 TTAAAGCGTA
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:224333 original size:31 final size:31
Alignment explanation
Indices: 224295--224353 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
224285 ATGATACATC
* * *
224295 TATGTGTCTAAAATGGTGATGTGATACAAGT
1 TATGTGTCCAAAATGATGACGTGATACAAGT
*
224326 TATGTGTCCAAATTGATGACGTGATACA
1 TATGTGTCCAAAATGATGACGTGATACA
224354 TATCAAGTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (31 bp):
TATGTGTCCAAAATGATGACGTGATACAAGT
Found at i:227293 original size:6 final size:6
Alignment explanation
Indices: 227282--227333 Score: 95
Period size: 6 Copynumber: 8.7 Consensus size: 6
227272 TAATTCATGC
*
227282 CCATTG CCATTG CCATTG CCATTG CCATTG CCATTG CCATTG TCATTG
1 CCATTG CCATTG CCATTG CCATTG CCATTG CCATTG CCATTG CCATTG
227330 CCAT
1 CCAT
227334 GGGTCACCAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.17, C:0.33, G:0.15, T:0.35
Consensus pattern (6 bp):
CCATTG
Found at i:241247 original size:14 final size:15
Alignment explanation
Indices: 241228--241256 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
241218 AATCATATTA
241228 TCTTTACTTG-ATTC
1 TCTTTACTTGCATTC
241242 TCTTTACTTGCATTC
1 TCTTTACTTGCATTC
241257 ACAAAAGCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.24, G:0.07, T:0.55
Consensus pattern (15 bp):
TCTTTACTTGCATTC
Found at i:246204 original size:26 final size:26
Alignment explanation
Indices: 246143--246204 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
246133 CTACTTTTAG
* *
246143 TTTTAAAAATATGTTCTATTTTTATT
1 TTTTAAAAATATGTTCTATTTTAAAT
** *
246169 TTTTTTAAATA-GTTTTCATTTTAAAT
1 TTTTAAAAATATGTTCT-ATTTTAAAT
246195 TTTTAAAAAT
1 TTTTAAAAAT
246205 TAGAAAACAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (26 bp):
TTTTAAAAATATGTTCTATTTTAAAT
Found at i:250489 original size:22 final size:22
Alignment explanation
Indices: 250461--250504 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
250451 AAATTTTCAT
* *
250461 TTATTTTCTATTTTTCTAAAAA
1 TTATTTTCTAGTTTTATAAAAA
*
250483 TTATTTTTTAGTTTTATAAAAA
1 TTATTTTCTAGTTTTATAAAAA
250505 CAATATTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (22 bp):
TTATTTTCTAGTTTTATAAAAA
Found at i:257162 original size:46 final size:47
Alignment explanation
Indices: 257112--257232 Score: 151
Period size: 46 Copynumber: 2.6 Consensus size: 47
257102 ATTAGTAACG
*
257112 CACCATATTAAAATAATAATATTGTTC-AAATACATAAATAATA-TCA
1 CACCATAATAAAATAATAATATTGTTCTAAATACATAAATAATAGT-A
* * * *
257158 CACCATACTAAAACAATAATATT-ATCTAAATACATAATTAATAGTA
1 CACCATAATAAAATAATAATATTGTTCTAAATACATAAATAATAGTA
*
257204 CACCATAATAATATAATAATATTG-TCTAA
1 CACCATAATAAAATAATAATATTGTTCTAA
257233 TTGCAGAACA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
45 2 0.03
46 62 0.95
47 1 0.02
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.32
Consensus pattern (47 bp):
CACCATAATAAAATAATAATATTGTTCTAAATACATAAATAATAGTA
Found at i:260337 original size:28 final size:28
Alignment explanation
Indices: 260297--260352 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
260287 AGAAGCTAAC
*
260297 GATGTTACTGATTTTCAGACTTGTTTAT
1 GATGTTACCGATTTTCAGACTTGTTTAT
260325 GATGTTACCGATTTTCAGACTTGTTTAT
1 GATGTTACCGATTTTCAGACTTGTTTAT
260353 AATATTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.48
Consensus pattern (28 bp):
GATGTTACCGATTTTCAGACTTGTTTAT
Found at i:293428 original size:15 final size:16
Alignment explanation
Indices: 293408--293448 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
293398 GTTTACTTCA
*
293408 GAATGATT-AAGCGTT
1 GAATGATTCAAACGTT
*
293423 GAATGATTCAAATGTT
1 GAATGATTCAAACGTT
293439 GAATGATTCA
1 GAATGATTCA
293449 GAGACTCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (16 bp):
GAATGATTCAAACGTT
Found at i:293478 original size:15 final size:15
Alignment explanation
Indices: 293453--293491 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
293443 GATTCAGAGA
*
293453 CTCTAAATGAATTAG
1 CTCTGAATGAATTAG
*
293468 TTCTGAATGAATTAG
1 CTCTGAATGAATTAG
293483 CTCTGAATG
1 CTCTGAATG
293492 TGACATGCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (15 bp):
CTCTGAATGAATTAG
Found at i:303600 original size:15 final size:15
Alignment explanation
Indices: 303580--303619 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
303570 ACAGAAAATC
*
303580 TTCTTCTGATAAACA
1 TTCTTCCGATAAACA
303595 TTCTTCCGATAAACA
1 TTCTTCCGATAAACA
303610 TTCTTCCGAT
1 TTCTTCCGAT
303620 GTTTCATAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (15 bp):
TTCTTCCGATAAACA
Found at i:305995 original size:20 final size:21
Alignment explanation
Indices: 305951--306008 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
305941 ACATTGCGAT
305951 TTTCTAAATTCGCAACACTGAA
1 TTTC-AAATTCGCAACACTGAA
305973 TTTCAAATTCGCAACAC-GAA
1 TTTCAAATTCGCAACACTGAA
* *
305993 TTTTAATTTCGCAACA
1 TTTCAAATTCGCAACA
306009 GGTTTTAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 17 0.50
21 13 0.38
22 4 0.12
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (21 bp):
TTTCAAATTCGCAACACTGAA
Found at i:307007 original size:24 final size:24
Alignment explanation
Indices: 306949--306995 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
306939 AGTCAGTATT
*
306949 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
306973 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
306996 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:307954 original size:24 final size:24
Alignment explanation
Indices: 307909--307958 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
307899 ATAAAGAACC
*
307909 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
307933 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
307957 AA
1 AA
307959 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:313564 original size:24 final size:24
Alignment explanation
Indices: 313519--313568 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
313509 ATAAAGAACC
*
313519 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
313543 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
313567 AA
1 AA
313569 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:316503 original size:18 final size:18
Alignment explanation
Indices: 316480--316515 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
316470 AAACAAAAGG
*
316480 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
316498 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
316516 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:316990 original size:64 final size:64
Alignment explanation
Indices: 316889--317039 Score: 241
Period size: 64 Copynumber: 2.4 Consensus size: 64
316879 AATTTAAAAC
316889 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*** * * *
316953 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATTAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
317017 AACAAATCAAC-TTTACAAATCAA
1 AACAAATCAACTTTTACAAATCAA
317040 CTTTTACAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
63 12 0.15
64 69 0.85
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.28
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:317036 original size:13 final size:14
Alignment explanation
Indices: 317018--317050 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
317008 CATTAATTAA
317018 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
317031 ACAAATCAACTTTT
1 ACAAATCAACTTTT
317045 ACAAAT
1 ACAAAT
317051 ACATCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:318985 original size:64 final size:64
Alignment explanation
Indices: 318882--319038 Score: 210
Period size: 64 Copynumber: 2.5 Consensus size: 64
318872 TTCAGTGTGT
* * *
318882 ATCGATGCACAAGAAGTGCATCGATGCACCCATTAAAAATGAAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGGAGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATTAGTGC
* ** *
318946 ATCGATGCATAAGGAGTGCATCGATGCATCCCCTT-AAAATGAAAACATCGAAGGTGATTAGTGT
1 ATCGATGCATAAGGAGTGCATCGATGCA-CCCATTAAAAATGAAAACATCGAAGGCAATTAGTGC
*
319010 ATCGATGCAT-GGGTAGTGCATCGATGCAC
1 ATCGATGCATAAGG-AGTGCATCGATGCAC
319039 ATGTTAAAGA
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
63 3 0.04
64 75 0.90
65 5 0.06
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (64 bp):
ATCGATGCATAAGGAGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATTAGTGC
Found at i:319071 original size:20 final size:22
Alignment explanation
Indices: 319026--319083 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
319016 GCATGGGTAG
319026 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
319050 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
319070 TGTATCGATGCACT
1 TGCATCGATGCACT
319084 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:319881 original size:18 final size:18
Alignment explanation
Indices: 319860--319911 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
319850 GGGACTACGC
319860 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
*
319878 GGTCCTTTGGGACATAGT
1 GGTCCTTCGGGACATAGT
* *
319896 GGTCATTCGAGACATA
1 GGTCCTTCGGGACATA
319912 TGTGTTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:322987 original size:45 final size:45
Alignment explanation
Indices: 322917--323020 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 45
322907 ATGCACAGGA
*
322917 AGTGCATCGATGCACCCATTAAAAATGGAAA-CATCGAATGCAATT
1 AGTGCATCGATGCACCCATTAAAAAT-GAAAGCATCGAAGGCAATT
* * **
322962 AGTGCATCGATGCACCCCCTT-AAAATGAAAGTATCGAAGGTGATT
1 AGTGCATCGATGCA-CCCATTAAAAATGAAAGCATCGAAGGCAATT
*
323007 AGTGTATCGATGCA
1 AGTGCATCGATGCA
323021 TGGGTAGTGC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
44 4 0.08
45 42 0.82
46 5 0.10
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (45 bp):
AGTGCATCGATGCACCCATTAAAAATGAAAGCATCGAAGGCAATT
Found at i:323073 original size:20 final size:20
Alignment explanation
Indices: 323048--323085 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
323038 CACATGTTAA
323048 AGAATGCATCGATGCACTAT
1 AGAATGCATCGATGCACTAT
*
323068 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
323086 TCAAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTAT
Found at i:323909 original size:18 final size:18
Alignment explanation
Indices: 323860--323913 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
323850 GAGGGTCTAC
323860 GCGGTCCTTCGGGACATA
1 GCGGTCCTTCGGGACATA
* *
323878 GCGATCCTTTGGGACATA
1 GCGGTCCTTCGGGACATA
* *
323896 GTGGTCATTCGGGACATA
1 GCGGTCCTTCGGGACATA
323914 TGTGTTATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.26
Consensus pattern (18 bp):
GCGGTCCTTCGGGACATA
Found at i:324906 original size:21 final size:20
Alignment explanation
Indices: 324882--324988 Score: 83
Period size: 21 Copynumber: 5.2 Consensus size: 20
324872 GAACGGTTGG
324882 AGGGACCTCTTGAATGATGAC
1 AGGG-CCTCTTGAATGATGAC
* **
324903 AGGGCCTCTTGAA-CAGTGGG
1 AGGGCCTCTTGAATGA-TGAC
* *
324923 AGGGGCCTCTTGAAGGATGAT
1 A-GGGCCTCTTGAATGATGAC
* *
324944 AGGGGCCTCTTGAACGAT-AGG
1 A-GGGCCTCTTGAATGATGA-C
324965 AGAGGCCTCTTGAATGATGAC
1 AG-GGCCTCTTGAATGATGAC
324986 AGG
1 AGG
324989 TGCTTCGGAC
Statistics
Matches: 70, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
19 1 0.01
20 15 0.21
21 52 0.74
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (20 bp):
AGGGCCTCTTGAATGATGAC
Found at i:324972 original size:42 final size:41
Alignment explanation
Indices: 324887--324988 Score: 143
Period size: 42 Copynumber: 2.5 Consensus size: 41
324877 GTTGGAGGGA
* *
324887 CCTCTTGAATGATGACAGGGCCTCTTGAACAGTGGGAGGGG
1 CCTCTTGAATGATGACAGGGCCTCTTGAACAGTAGGAGAGG
* *
324928 CCTCTTGAAGGATGATAGGGGCCTCTTGAAC-GATAGGAGAGG
1 CCTCTTGAATGATGACA-GGGCCTCTTGAACAG-TAGGAGAGG
324970 CCTCTTGAATGATGACAGG
1 CCTCTTGAATGATGACAGG
324989 TGCTTCGGAC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
41 18 0.34
42 35 0.66
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.23
Consensus pattern (41 bp):
CCTCTTGAATGATGACAGGGCCTCTTGAACAGTAGGAGAGG
Found at i:325147 original size:12 final size:12
Alignment explanation
Indices: 325128--325169 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
325118 GGGCCGCTAA
*
325128 AAATAAATTAAT
1 AAATAAATCAAT
*
325140 ACATAAATCAAT
1 AAATAAATCAAT
325152 AAATAAA-CAAAT
1 AAATAAATC-AAT
325164 AAATAA
1 AAATAA
325170 TGTCGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 1 0.04
12 25 0.96
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAAATCAAT
Found at i:325356 original size:21 final size:21
Alignment explanation
Indices: 325332--325375 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
325322 ATTGTCATCG
325332 CGTAAA-ACCTCTACCTCACCA
1 CGTAAAGACC-CTACCTCACCA
* *
325353 CGTAAAGACCGTACCTCATCA
1 CGTAAAGACCCTACCTCACCA
325374 CG
1 CG
325376 CCATGCACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.32, C:0.39, G:0.11, T:0.18
Consensus pattern (21 bp):
CGTAAAGACCCTACCTCACCA
Found at i:325416 original size:21 final size:21
Alignment explanation
Indices: 325392--325441 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
325382 ACCATTGTCT
* *
325392 TCACGTAAAGTACCGACCTCC
1 TCACGTAAAGCACCGACCTCA
* **
325413 TCACGCAAAGCATTGACCTCA
1 TCACGTAAAGCACCGACCTCA
325434 TCACGTAA
1 TCACGTAA
325442 CTCCCCTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:327026 original size:19 final size:20
Alignment explanation
Indices: 326987--327035 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
326977 TCTGAAACTT
326987 AAAATCGCAATGCGAAAATG
1 AAAATCGCAATGCGAAAATG
*
327007 AAAATCGTAATGCG-AAATG
1 AAAATCGCAATGCGAAAATG
327026 AAAATCGCAA
1 AAAATCGCAA
327036 CCAAATAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.51, C:0.14, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAATGCGAAAATG
Found at i:327571 original size:20 final size:20
Alignment explanation
Indices: 327546--327597 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
327536 TAAACGCGCT
327546 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
*
327566 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTCTGTG
327586 TTGCGAATTTGA
1 TTGCGAATTTGA
327598 AAACTGAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.17, C:0.12, G:0.25, T:0.46
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:335280 original size:2 final size:2
Alignment explanation
Indices: 335273--335297 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
335263 TTCTTGTGTT
335273 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 T
335298 TTTCCTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:339999 original size:26 final size:26
Alignment explanation
Indices: 339961--340042 Score: 128
Period size: 26 Copynumber: 3.2 Consensus size: 26
339951 TGTACCAGAT
*
339961 GGGCGACGACCCAAGGCAACATATAG
1 GGGCGACGACCCAGGGCAACATATAG
* *
339987 GGGTGACGGCCCAGGGCAACATATAG
1 GGGCGACGACCCAGGGCAACATATAG
*
340013 GGGCGACGACCCAGGGCAGCATATAG
1 GGGCGACGACCCAGGGCAACATATAG
340039 GGGC
1 GGGC
340043 ATCAGTAGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.28, C:0.26, G:0.38, T:0.09
Consensus pattern (26 bp):
GGGCGACGACCCAGGGCAACATATAG
Found at i:343647 original size:60 final size:61
Alignment explanation
Indices: 343554--343674 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 61
343544 CTTAAAGCAG
343554 TTCATTAATGGAAGAAAGTTTACCAGTGGCAACTGATGAGTCAACTTGCTGT-AGGACGCA
1 TTCATTAATGGAAGAAAGTTTACCAGTGGCAACTGATGAGTCAACTTGCTGTAAGGACGCA
343614 TTCATTAATGGAAGAAAGTTTACCAGTGGCAACTGATGAGTCAACTTGCTGTAAGGACGCA
1 TTCATTAATGGAAGAAAGTTTACCAGTGGCAACTGATGAGTCAACTTGCTGTAAGGACGCA
343675 AAATTGCAAG
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 52 0.87
61 8 0.13
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (61 bp):
TTCATTAATGGAAGAAAGTTTACCAGTGGCAACTGATGAGTCAACTTGCTGTAAGGACGCA
Found at i:346468 original size:67 final size:67
Alignment explanation
Indices: 346360--346489 Score: 260
Period size: 67 Copynumber: 1.9 Consensus size: 67
346350 TGAAACGGCC
346360 AAATATCTCTTCCTCTTCATTTCCATTTTCATTTACAGCACTTGCTGCACGGTCATGAAGAACGA
1 AAATATCTCTTCCTCTTCATTTCCATTTTCATTTACAGCACTTGCTGCACGGTCATGAAGAACGA
346425 TG
66 TG
346427 AAATATCTCTTCCTCTTCATTTCCATTTTCATTTACAGCACTTGCTGCACGGTCATGAAGAAC
1 AAATATCTCTTCCTCTTCATTTCCATTTTCATTTACAGCACTTGCTGCACGGTCATGAAGAAC
346490 ACGATGATGC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.36
Consensus pattern (67 bp):
AAATATCTCTTCCTCTTCATTTCCATTTTCATTTACAGCACTTGCTGCACGGTCATGAAGAACGA
TG
Found at i:360908 original size:10 final size:10
Alignment explanation
Indices: 360893--360929 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
360883 AGACCGACTG
360893 AAAACCGGAA
1 AAAACCGGAA
*
360903 AAAACCGGGA
1 AAAACCGGAA
*
360913 AAAATCGGAA
1 AAAACCGGAA
360923 AAAACCG
1 AAAACCG
360930 CCAATTTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.57, C:0.19, G:0.22, T:0.03
Consensus pattern (10 bp):
AAAACCGGAA
Found at i:361616 original size:22 final size:21
Alignment explanation
Indices: 361591--361631 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
361581 TATACAAAAT
361591 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
361613 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
361632 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:372926 original size:18 final size:18
Alignment explanation
Indices: 372895--372980 Score: 75
Period size: 18 Copynumber: 4.8 Consensus size: 18
372885 CAAATGGGGT
* *
372895 AAACTTATCTAATTAGTC
1 AAACTTGTCAAATTAGTC
* *
372913 AAACCTGTCAAATTAGTG
1 AAACTTGTCAAATTAGTC
*
372931 AAACTTATCAAACTT-GTC
1 AAACTTGTCAAA-TTAGTC
* * *
372949 CAACTTGTCAAATGAATC
1 AAACTTGTCAAATTAGTC
*
372967 AAGCTTGTCAAATT
1 AAACTTGTCAAATT
372981 GTATATGTGC
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
17 1 0.02
18 49 0.94
19 2 0.04
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (18 bp):
AAACTTGTCAAATTAGTC
Found at i:373852 original size:23 final size:23
Alignment explanation
Indices: 373825--373868 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
373815 GCACTCCAAG
373825 CTCCAATATCCACCGCTCCAGAC
1 CTCCAATATCCACCGCTCCAGAC
* * *
373848 CTCCAGTCTCCATCGCTCCAG
1 CTCCAATATCCACCGCTCCAG
373869 CCAGCTCCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.48, G:0.11, T:0.20
Consensus pattern (23 bp):
CTCCAATATCCACCGCTCCAGAC
Found at i:375478 original size:21 final size:21
Alignment explanation
Indices: 375429--375486 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
375419 TTTCGTTCTA
*
375429 GGGGGTATCGATACCCAACTG
1 GGGGGTATCGGTACCCAACTG
*
375450 GGGAGTATCGGTACCCAACTG
1 GGGGGTATCGGTACCCAACTG
*
375471 GGGGGTATTGGTACCC
1 GGGGGTATCGGTACCC
375487 TTATGATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.21, C:0.22, G:0.36, T:0.21
Consensus pattern (21 bp):
GGGGGTATCGGTACCCAACTG
Found at i:379407 original size:15 final size:15
Alignment explanation
Indices: 379369--379408 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
379359 CACTACATCT
* *
379369 CGAAGGACAATGTCC
1 CGAAGGACTACGTCC
379384 CGAAGGACTACGTCC
1 CGAAGGACTACGTCC
379399 CGAAGGACTA
1 CGAAGGACTA
379409 TTATACCCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.33, C:0.28, G:0.28, T:0.12
Consensus pattern (15 bp):
CGAAGGACTACGTCC
Found at i:380012 original size:64 final size:64
Alignment explanation
Indices: 379925--380080 Score: 149
Period size: 64 Copynumber: 2.4 Consensus size: 64
379915 AATGAAGGTA
* ** * * * *
379925 TGCATCGATGAACTATTTGTGCATCGGTGCA-TAAAATGCATTCGATG-TTTTATTATT-AATGG
1 TGCATCGATGCACTACCTATGCATCGATGCACT-AAATGCATTCGATGTTTTTATT-TTAAAAGA
379987 G
64 G
* * * *
379988 ATGCATCGATGCA-TGCCTTATGCATCGATGTACTAATTGTATTCGATGTTTTTATTTTAAAAGA
1 -TGCATCGATGCACTACC-TATGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAGA
380052 G
64 G
380053 TGCATCGATGCACTACCTATGCATCGAT
1 TGCATCGATGCACTACCTATGCATCGAT
380081 ACACCTTCAA
Statistics
Matches: 75, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
63 1 0.01
64 59 0.79
65 15 0.20
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (64 bp):
TGCATCGATGCACTACCTATGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAGAG
Found at i:386242 original size:15 final size:15
Alignment explanation
Indices: 386218--386251 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
386208 CCGTAGGACC
*
386218 ACTACATCCCGAAGG
1 ACTACATCCCGAAAG
*
386233 ACTACGTCCCGAAAG
1 ACTACATCCCGAAAG
386248 ACTA
1 ACTA
386252 TTATACCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAAG
Found at i:386376 original size:29 final size:29
Alignment explanation
Indices: 386343--386416 Score: 139
Period size: 29 Copynumber: 2.5 Consensus size: 29
386333 TGTTCAAGTA
386343 CTCATGTCATTTCTCTTGTGATCATGTAG
1 CTCATGTCATTTCTCTTGTGATCATGTAG
386372 CTCATGTCATTTCTCTTGTGATCATGTAG
1 CTCATGTCATTTCTCTTGTGATCATGTAG
386401 CTCATGTCATGTTCTC
1 CTCATGTCAT-TTCTC
386417 ATATCACATA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 39 0.89
30 5 0.11
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.45
Consensus pattern (29 bp):
CTCATGTCATTTCTCTTGTGATCATGTAG
Found at i:386947 original size:64 final size:63
Alignment explanation
Indices: 386796--386951 Score: 174
Period size: 64 Copynumber: 2.5 Consensus size: 63
386786 TAATGAAGGT
* * * * *
386796 ATGCATCGATGTACTACTTATGCATCGGTGCATAAATGCATTCGATGTTTTATTATTAATGGG
1 ATGCATCGATGCACTACCTATGCATCGATGCATAAATGCATTCGATGTTTTATTATTAAAGAG
* * *
386859 ATGCATAGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTTTATT-TTAAA-A
1 ATGCATCGATGCACTACC-TATGCATCGATGCA-TAAATGCATTCGATG-TTTTATTATTAAAGA
386921 G
63 G
*
386922 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACCTATGCATCGAT
386952 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
62 2 0.03
63 26 0.34
64 39 0.51
65 10 0.13
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (63 bp):
ATGCATCGATGCACTACCTATGCATCGATGCATAAATGCATTCGATGTTTTATTATTAAAGAG
Found at i:391935 original size:24 final size:24
Alignment explanation
Indices: 391908--391957 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
391898 TGGTGGTTGA
391908 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTATTGAACTTTATT
* *
391932 TTTAATGGTGTATTTAAGTTTATT
1 TTTAATGGTGTATTGAACTTTATT
391956 TT
1 TT
391958 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTGAACTTTATT
Found at i:398780 original size:19 final size:21
Alignment explanation
Indices: 398743--398794 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
398733 TAACTTTTTC
*
398743 TTTTCTCTTTCTTTATTAA-T
1 TTTTCTCTTTCATTATTAACT
398763 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAACT
* *
398783 TTTACTTTTTCA
1 TTTTCTCTTTCA
398795 CTTTCTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Found at i:405959 original size:15 final size:15
Alignment explanation
Indices: 405935--405967 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
405925 ATGTGTCATG
*
405935 TGAATTATATGGAAA
1 TGAATGATATGGAAA
405950 TGAATGATATGGAAA
1 TGAATGATATGGAAA
405965 TGA
1 TGA
405968 TCTACGTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.30
Consensus pattern (15 bp):
TGAATGATATGGAAA
Found at i:408175 original size:20 final size:22
Alignment explanation
Indices: 408130--408187 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
408120 GCATGGGTAG
408130 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
408154 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
408174 TGCATCGATGCACT
1 TGCATCGATGCACT
408188 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:408874 original size:18 final size:18
Alignment explanation
Indices: 408847--408933 Score: 102
Period size: 18 Copynumber: 4.8 Consensus size: 18
408837 AGGGTCTATG
*
408847 TGGTTCTTCGGGACATAA
1 TGGTCCTTCGGGACATAA
*
408865 TGGTCTTTCGGGACATAA
1 TGGTCCTTCGGGACATAA
* *
408883 TGGTCCTTCGGGATATAG
1 TGGTCCTTCGGGACATAA
* *
408901 TGGTCCTTCGGGATATAG
1 TGGTCCTTCGGGACATAA
* *
408919 TGGTTCTACGGGACA
1 TGGTCCTTCGGGACA
408934 AATTCTATGT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.32
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAA
Found at i:412055 original size:45 final size:45
Alignment explanation
Indices: 411977--412079 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
411967 CACATTGAAT
* * * *
411977 GTGCATCGATGCA-CTCTTTAAAGAAGAAACATCGAATGCAATTG
1 GTGCATCGATGCATCCCCTTAAAGAAGAAACATCGAAGGAAATTG
* *
412021 GTGCATCGATGCATCCCCTTAAA-ATGAAAACATCGAAGGAAATTT
1 GTGCATCGATGCATCCCCTTAAAGAAG-AAACATCGAAGGAAATTG
*
412066 GTGTATCGATGCAT
1 GTGCATCGATGCAT
412080 GGGTAGTGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 15 0.30
45 35 0.70
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26
Consensus pattern (45 bp):
GTGCATCGATGCATCCCCTTAAAGAAGAAACATCGAAGGAAATTG
Found at i:412131 original size:20 final size:22
Alignment explanation
Indices: 412086--412143 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
412076 GCATGGGTAG
412086 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
412110 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
412130 TGCATCGATGCACT
1 TGCATCGATGCACT
412144 TCAGGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:412842 original size:18 final size:18
Alignment explanation
Indices: 412813--412907 Score: 127
Period size: 18 Copynumber: 5.3 Consensus size: 18
412803 TGATCTTTCG
412813 GGACATAGTGGTCCTTCA
1 GGACATAGTGGTCCTTCA
* * *
412831 GAACATAATGGTCCTTCG
1 GGACATAGTGGTCCTTCA
* *
412849 GGACATAATGGTCCTTCG
1 GGACATAGTGGTCCTTCA
*
412867 GGACACAGTGGTCCTTCA
1 GGACATAGTGGTCCTTCA
*
412885 GGACATAGTGGTCCTACA
1 GGACATAGTGGTCCTTCA
412903 GGACA
1 GGACA
412908 AATTCTATGC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (18 bp):
GGACATAGTGGTCCTTCA
Found at i:416667 original size:29 final size:29
Alignment explanation
Indices: 416621--416677 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
416611 TGATAATGAG
* *
416621 CTATGTGAAAGGACTATGAGATTGTGTGT
1 CTATGTGAAAGGAATATGAGAATGTGTGT
* * *
416650 CTATGTGATATGAATATGTGAATGTGTG
1 CTATGTGAAAGGAATATGAGAATGTGTG
416678 ATAACATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.28, C:0.05, G:0.30, T:0.37
Consensus pattern (29 bp):
CTATGTGAAAGGAATATGAGAATGTGTGT
Found at i:416900 original size:33 final size:33
Alignment explanation
Indices: 416862--416937 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
416852 AGGAGTGATA
*
416862 CTTCGGGACATATGTGATATGTTATATGTGGTC
1 CTTCGGGACATATGTGATATGTGATATGTGGTC
*
416895 CTTCGGGGCATATGTGATATGTGATATGTGGTC
1 CTTCGGGACATATGTGATATGTGATATGTGGTC
*
416928 TTTCGGGACA
1 CTTCGGGACA
416938 AATTTCTAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.20, C:0.13, G:0.30, T:0.37
Consensus pattern (33 bp):
CTTCGGGACATATGTGATATGTGATATGTGGTC
Found at i:429457 original size:15 final size:15
Alignment explanation
Indices: 429437--429465 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
429427 CAAAAATTTT
429437 AAGAAATTAAAATTA
1 AAGAAATTAAAATTA
429452 AAGAAATTAAAATT
1 AAGAAATTAAAATT
429466 CATGGGGTTA
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:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (15 bp):
AAGAAATTAAAATTA
Found at i:430015 original size:65 final size:64
Alignment explanation
Indices: 429946--430129 Score: 230
Period size: 65 Copynumber: 2.9 Consensus size: 64
429936 AATTAAATTG
*
429946 AACATCGAATGCATTTCATGCATCGATGCACTTACCATGCACCGATGCACTAAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACTTACCATGCACCGATGCACTAAGGATATTT-TG-
430010 A
64 A
** * ** *
430011 AACATCGAATGCATTTGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTTACCATGCACCGATGCACTAAGGATATTTTGA
* *
430075 AACATCGAATGCACTTGATGCATCGATGCACTCTTA--GTGCACCGATGCACTAAGG
1 AACATCGAATGCATTTGATGCATCGATGCA--CTTACCATGCACCGATGCACTAAGG
430130 GTCCAACGGT
Statistics
Matches: 102, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
64 45 0.44
65 52 0.51
66 5 0.05
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACTTACCATGCACCGATGCACTAAGGATATTTTGA
Found at i:430105 original size:17 final size:19
Alignment explanation
Indices: 430077--430125 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
430067 TATTTTGAAA
430077 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
430095 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
430114 CACCGATGCACT
1 CATCGATGCACT
430126 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:430127 original size:129 final size:129
Alignment explanation
Indices: 429896--430129 Score: 314
Period size: 129 Copynumber: 1.8 Consensus size: 129
429886 TTTTTCAAAG
* * *
429896 TGATGCACCGATGCACCAATCCATGCATCGGTGCACCATGAATTAAATTGAACATCGAATGCATT
1 TGATGCACCGATGCACCAATCCATGCATCGATGCACCATGAACTAAATTGAACATCGAATGCACT
429961 TCATGCATCGATGCACTTACCATGCACCGATGCACTAAGGATTTTATGAAAACATCGAATGCATT
66 TCATGCATCGATGCACTTA-CATGCACCGATGCACTAAGGATTTTATGAAAACATCGAATGCATT
* * **
430026 TGATGCATCGATGCACCAA-CCATGCATCGATGCACTC-TG-GCTATTTTGAAACATCGAATGCA
1 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGAACTAAATTG-AACATCGAATGCA
* *
430088 CTTGATGCATCGATGCACTCTTA-GTGCACCGATGCACTAAGG
64 CTTCATGCATCGATGCA--CTTACATGCACCGATGCACTAAGG
430130 GTCCAACGGT
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
128 5 0.05
129 63 0.69
130 19 0.21
131 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (129 bp):
TGATGCACCGATGCACCAATCCATGCATCGATGCACCATGAACTAAATTGAACATCGAATGCACT
TCATGCATCGATGCACTTACATGCACCGATGCACTAAGGATTTTATGAAAACATCGAATGCATT
Found at i:437088 original size:21 final size:21
Alignment explanation
Indices: 437062--437103 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
437052 CCAGAATGGG
* *
437062 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACACCTTCATA
*
437083 GGGAATTGATACACCTTCATA
1 GGGAATCGATACACCTTCATA
437104 ATATTCAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (21 bp):
GGGAATCGATACACCTTCATA
Found at i:437237 original size:15 final size:15
Alignment explanation
Indices: 437217--437305 Score: 65
Period size: 15 Copynumber: 5.5 Consensus size: 15
437207 ACCATGCATG
437217 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
437232 GGGGAATC-GATACCC
1 GGGGAATCTG-TACCC
*
437247 ATGGGGGGAATATGTACCC
1 ----GGGGAATCTGTACCC
**
437266 AAGGAATC-GATACCC
1 GGGGAATCTG-TACCC
437281 TGGGGGAATCTGTACCC
1 --GGGGAATCTGTACCC
437298 GGGGAATC
1 GGGGAATC
437306 GATATCCCCT
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 2 0.03
15 31 0.53
17 11 0.19
18 1 0.02
19 12 0.21
20 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.34, T:0.18
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:437263 original size:34 final size:33
Alignment explanation
Indices: 437216--437328 Score: 165
Period size: 34 Copynumber: 3.4 Consensus size: 33
437206 AACCATGCAT
437216 GGGGGAATCTGTACCCGGGGAATCGATACCCATG
1 GGGGGAATCTGTACCCGGGGAATCGATACCC-TG
* **
437250 GGGGGAATATGTACCCAAGGAATCGATACCCT-
1 GGGGGAATCTGTACCCGGGGAATCGATACCCTG
437282 GGGGGAATCTGTACCCGGGGAATCGATATCCCCTG
1 GGGGGAATCTGTACCCGGGGAATCGATA--CCCTG
437317 GGGGGAATCTGT
1 GGGGGAATCTGT
437329 TCCCTCTGGG
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
32 25 0.36
33 1 0.01
34 32 0.46
35 12 0.17
ACGTcount: A:0.24, C:0.22, G:0.35, T:0.19
Consensus pattern (33 bp):
GGGGGAATCTGTACCCGGGGAATCGATACCCTG
Found at i:438762 original size:19 final size:20
Alignment explanation
Indices: 438732--438769 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
438722 CAAAATTTCA
438732 TTTTGACTTTCAAAATCAAC
1 TTTTGACTTTCAAAATCAAC
438752 TTTTG-CTTTCAAAATCAA
1 TTTTGACTTTCAAAATCAA
438770 ATTATCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.42
Consensus pattern (20 bp):
TTTTGACTTTCAAAATCAAC
Found at i:440312 original size:32 final size:33
Alignment explanation
Indices: 440268--440337 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
440258 CCTTACAAAC
* *
440268 TCCCTAG-TTTTTACGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTAACGGGATAAACTAGAACCTT
* *
440300 TCCCTAGCTTTTACACGGGATTATCTAGAACCTT
1 TCCCTAGCTTTTA-ACGGGATAAACTAGAACCTT
440334 TCCC
1 TCCC
440338 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 4 0.12
34 21 0.66
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (33 bp):
TCCCTAGCTTTTAACGGGATAAACTAGAACCTT
Found at i:440626 original size:21 final size:21
Alignment explanation
Indices: 440600--440641 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
440590 CCAGAATGGG
*
440600 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
440621 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
440642 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:440793 original size:19 final size:18
Alignment explanation
Indices: 440769--440827 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
440759 ATCTGTACCC
440769 GGGGAATCGATACCCCTAG
1 GGGGAATCGATACCCCT-G
440788 GGGGAATCTG-TA-CCC--
1 GGGGAATC-GATACCCCTG
440803 GGGGAATCGATACCCCCTG
1 GGGGAATCGATA-CCCCTG
440822 GGGGAA
1 GGGGAA
440828 ATCTGTTCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
14 1 0.03
15 10 0.29
17 3 0.09
18 3 0.09
19 16 0.47
20 1 0.03
ACGTcount: A:0.24, C:0.25, G:0.36, T:0.15
Consensus pattern (18 bp):
GGGGAATCGATACCCCTG
Found at i:440793 original size:34 final size:34
Alignment explanation
Indices: 440753--440833 Score: 137
Period size: 34 Copynumber: 2.4 Consensus size: 34
440743 AACCATGCAG
440753 GGGGGAATCTGTACCCGGGGAATCGATA-CCCCT
1 GGGGGAATCTGTACCCGGGGAATCGATACCCCCT
440786 AGGGGGAATCTGTACCCGGGGAATCGATACCCCCT
1 -GGGGGAATCTGTACCCGGGGAATCGATACCCCCT
440821 GGGGGAAATCTGT
1 GGGGG-AATCTGT
440834 TCCCTCTGGG
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
34 33 0.73
35 12 0.27
ACGTcount: A:0.22, C:0.25, G:0.35, T:0.19
Consensus pattern (34 bp):
GGGGGAATCTGTACCCGGGGAATCGATACCCCCT
Found at i:440817 original size:15 final size:15
Alignment explanation
Indices: 440754--440810 Score: 62
Period size: 15 Copynumber: 3.5 Consensus size: 15
440744 ACCATGCAGG
440754 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
440769 GGGGAATC-GATACCCC
1 GGGGAATCTG-TA-CCC
440785 TAGGGGGAATCTGTACCC
1 ---GGGGAATCTGTACCC
440803 GGGGAATC
1 GGGGAATC
440811 GATACCCCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
14 1 0.03
15 18 0.50
16 3 0.08
18 3 0.08
19 10 0.28
20 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.35, T:0.18
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:442333 original size:65 final size:64
Alignment explanation
Indices: 442203--442386 Score: 185
Period size: 65 Copynumber: 2.9 Consensus size: 64
442193 AATTAAATTG
* * * *
442203 AACATAGAATGCATTTCATGCATCGATGAACTTACCATGCACCGATGCACTAAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACTCACCATGCACCGATGCACTAAGGATTTTATG-A
* * ** *
442268 AACATCGAATGCATTTGATGCATTGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCACTCA-CCATGCACCGATGCACTAAGGAT-TTTATG
442331 A
64 A
* * * **
442332 AACATCAAATGCACTTGATACATCGATGCACTC-TTAGTGCACCGATGCACTAAGG
1 AACATCGAATGCATTTGATGCATCGATGCACTCACCA-TGCACCGATGCACTAAGG
442387 GTCCAACGGT
Statistics
Matches: 97, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
63 1 0.01
64 44 0.45
65 49 0.51
66 3 0.03
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCACCATGCACCGATGCACTAAGGATTTTATGA
Found at i:444081 original size:5 final size:5
Alignment explanation
Indices: 444053--444414 Score: 112
Period size: 5 Copynumber: 74.8 Consensus size: 5
444043 AATAACGTTA
* * *
444053 ATAAT ATAGT ATAAT AGAACAT ATAAT AT-AT ATAAT ATAAT AT-AT GCT-AT
1 ATAAT ATAAT ATAAT A-TA-AT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT
* * * *
444103 GTAAT ACAA- AT-AT ATAAT A-AAT A-AAT AATACT AT-AT ATTAT ATAA-
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT
* * * * * *
444148 AT-AT ATTAT ATAAC ATAA- AT-AT ATAAC GTAAT ATAAC ATATT AT-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* * * * *
444194 ATACT ATAAT AT--T ATAAT AT-AT ATTAT GTAAA AT-AT ACTATAT ATACT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TA-AT ATAAT
* * * *
444242 ACAAT ATTAT ATAA- AT-AT ACAAT ATAAGT ATAAT A-AAT ATATAT ATTAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAA-T ATAAT ATAAT ATA-AT ATAAT
* * * * **
444291 ATGATT GTACTAT ATAAT AT-AT AT-AT ATATAT GTAAT ATAAC ATGTT
1 AT-AAT ATA--AT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT
* * *
444338 AT-AT ATTAT ATAAT ATAA- AT-AT ATATAT ATATAT GTAAT ATAAT ATAGT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATA-AT ATAAT ATAAT ATAAT
*
444387 AT--T ATAAT ATAAAT ATTAT ATAAT ATAA
1 ATAAT ATAAT AT-AAT ATAAT ATAAT ATAA
444415 AGATATACTA
Statistics
Matches: 263, Mismatches: 56, Indels: 76
0.67 0.14 0.19
Matches are distributed among these distances:
3 11 0.04
4 59 0.22
5 148 0.56
6 36 0.14
7 9 0.03
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:444085 original size:2 final size:2
Alignment explanation
Indices: 444073--444473 Score: 135
Period size: 2 Copynumber: 213.5 Consensus size: 2
444063 ATAATAGAAC
* * * *
444073 AT AT A- AT AT AT AT A- AT AT A- AT AT AT GCT AT GT A- AT AC AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
* * *
444112 AT AT AT A- AT AA AT AA AT A- AT ACT AT AT AT -T AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * * * *
444152 AT -T AT AT A- AC AT AA AT AT AT A- AC GT A- AT AT A- AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
444189 -T AT AT AT ACT AT A- AT AT -T AT A- AT AT AT AT -T AT GT A- AA
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
444226 AT AT ACT AT AT AT ACT AC A- AT AT -T AT AT AA AT AT AC A- AT AT
1 AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
444267 A- AGT AT A- AT AA AT AT AT AT AT -T AT AT GAT -T GT ACT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A-T AT AT
* * *
444306 A- AT AT AT AT AT AT AT AT GT A- AT AT A- AC AT GT -T 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
* *
444344 -T AT AT A- AT AT AA AT AT AT AT AT AT AT AT GT A- AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
444382 AT AGT AT -T AT A- AT AT AA AT AT -T AT AT A- AT AT AA AG AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
**
444421 ACT AT ACT AT ACT AT GC AT ACT AT ACT AT AT AT AT -T AT AT A- AT
1 A-T AT A-T AT A-T AT AT AT A-T AT A-T AT AT AT AT AT AT AT AT AT
444464 AT AT AT -T AT A
1 AT AT AT AT AT A
444474 ACTACACCTT
Statistics
Matches: 298, Mismatches: 47, Indels: 108
0.66 0.10 0.24
Matches are distributed among these distances:
1 40 0.13
2 232 0.78
3 26 0.09
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (2 bp):
AT
Found at i:444132 original size:18 final size:18
Alignment explanation
Indices: 444073--444415 Score: 90
Period size: 19 Copynumber: 17.8 Consensus size: 18
444063 ATAATAGAAC
444073 ATATA-ATATATATAATATA
1 ATATATATATATA-AATA-A
* *
444092 ATATATGCTATGT-AATACA
1 ATATAT-ATATATAAATA-A
444111 A-ATATATA-ATAAATAA
1 ATATATATATATAAATAA
*
444127 ATAATACTATATATTATATAA
1 AT-ATA-TATATA-TAAATAA
444148 ATATAT-TATATAACATAA
1 ATATATATATATAA-ATAA
444166 ATATATAACGTAATATAACAT-A
1 ATATAT-A--T-ATATAA-ATAA
*
444188 TTATATATACTATAATATTATA
1 ATATATATA-TATAA-A-TA-A
**
444210 ATATATAT-TATGTA-AA
1 ATATATATATATAAATAA
*
444226 ATATACTATATAT-ACTACA
1 ATATA-TATATATAAATA-A
444245 ATAT-TATATA-AATATACA
1 ATATATATATATAA-ATA-A
*
444263 ATATA-A-GTAT-AATAA
1 ATATATATATATAAATAA
* *
444278 ATATATATAT-TATAT-G
1 ATATATATATATAAATAA
* *
444294 AT-TGTACTATATAATATAT
1 ATATATA-TATATAA-ATAA
*
444313 ATATATATATGTAATATAA
1 ATATATATATATAA-ATAA
444332 CATGTTATATATTATATAATATAA
1 -A---TATATA-TATATAA-ATAA
*
444356 ATATATATATATATATGTAA
1 ATATATATATATA-A-ATAA
444376 TATAATATAGTATTATAATATAA
1 -AT-ATATA-TA-TATAA-ATAA
444399 ATATTATATAATATAAA
1 ATA-TATAT-ATATAAA
444416 GATATACTAT
Statistics
Matches: 250, Mismatches: 28, Indels: 91
0.68 0.08 0.25
Matches are distributed among these distances:
15 9 0.04
16 19 0.08
17 27 0.11
18 37 0.15
19 47 0.19
20 24 0.10
21 22 0.09
22 27 0.11
23 23 0.09
24 15 0.06
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (18 bp):
ATATATATATATAAATAA
Found at i:444306 original size:39 final size:38
Alignment explanation
Indices: 444245--444409 Score: 126
Period size: 39 Copynumber: 4.3 Consensus size: 38
444235 ATATACTACA
* *
444245 ATATTATATAAATATACAATATAAGTATAATAAATATAT
1 ATATTATATAAATGTACTATATAA-TATAATAAATATAT
* * *
444284 ATATTATATGATTGTACTATATAATAT-ATATATATAT
1 ATATTATATAAATGTACTATATAATATAATAAATATAT
* * *
444321 ATGTAATATAACATGTTA-TATATTATATAATATAA-ATAT
1 ATATTATATAA-ATG-TACTATATAATATAATA-AATATAT
* *
444360 ATA-TATATATATGTA--ATATAATATAGTATTATAATATAA
1 ATATTATATAAATGTACTATATAATATA--A-TA-AATATAT
444399 ATATTATATAA
1 ATATTATATAA
444410 TATAAAGATA
Statistics
Matches: 100, Mismatches: 17, Indels: 17
0.75 0.13 0.13
Matches are distributed among these distances:
35 9 0.09
36 2 0.02
37 21 0.21
38 24 0.24
39 37 0.37
40 7 0.07
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (38 bp):
ATATTATATAAATGTACTATATAATATAATAAATATAT
Found at i:444402 original size:49 final size:50
Alignment explanation
Indices: 444301--444413 Score: 149
Period size: 49 Copynumber: 2.2 Consensus size: 50
444291 ATGATTGTAC
*
444301 TATATAATATATATATATATATGTAATATAACATGTTATATATTATATAA
1 TATATAATATATATATATATATGTAATATAACATGTTATATAATATATAA
* *
444351 TATA-AATATATATATATATATGTAATATAATATAG-TATTATAATATAAATAT
1 TATATAATATATATATATATATGTAATATAACAT-GTTA-TATAATAT--ATAA
444403 TATATAATATA
1 TATATAATATA
444414 AAGATATACT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
49 30 0.55
50 12 0.22
52 7 0.13
53 6 0.11
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (50 bp):
TATATAATATATATATATATATGTAATATAACATGTTATATAATATATAA
Found at i:444426 original size:5 final size:5
Alignment explanation
Indices: 444418--444459 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
444408 AATATAAAGA
* *
444418 TATAC TATAC TATAC TATGC -ATAC TATAC TATA- TATAT TATA
1 TATAC TATAC TATAC TATAC TATAC TATAC TATAC TATAC TATA
444460 TAATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 7 0.21
5 26 0.79
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.43
Consensus pattern (5 bp):
TATAC
Found at i:444728 original size:36 final size:33
Alignment explanation
Indices: 444646--444734 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 33
444636 TCGATTACGA
* *
444646 TTTGGAAGAGATATTCAGACCACAAAACAACTT
1 TTTGGAAGAGATGTTCAGACCACAAAACAACAT
* *
444679 TTTGGAATG-GATGTTCAGACCCCCAAACAATGTCAT
1 TTTGGAA-GAGATGTTCAGACCACAAAACAA---CAT
*
444715 TTTGGAAGAGATGTTTAGAC
1 TTTGGAAGAGATGTTCAGAC
444735 TCCAAAATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
33 25 0.54
34 1 0.02
35 1 0.02
36 19 0.41
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (33 bp):
TTTGGAAGAGATGTTCAGACCACAAAACAACAT
Found at i:445337 original size:18 final size:20
Alignment explanation
Indices: 445289--445337 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 20
445279 TTCTTTTTCA
445289 ATTCAATATTTTAACTATGTTT
1 ATTC-ATATTTTAACTA-GTTT
445311 ATT-AT-TTTT-ACTA-TTT
1 ATTCATATTTTAACTAGTTT
445327 ATTCATATTTT
1 ATTCATATTTT
445338 TACTGGCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 6 0.24
17 2 0.08
18 8 0.32
19 4 0.16
20 2 0.08
22 3 0.12
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTCATATTTTAACTAGTTT
Found at i:457577 original size:16 final size:18
Alignment explanation
Indices: 457553--457594 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
457543 ACTTTTTGTA
*
457553 ATAAAATAAGA-TTA-TT
1 ATAATATAAGATTTATTT
*
457569 ATAATATAATATTTATTT
1 ATAATATAAGATTTATTT
457587 ATAATATA
1 ATAATATA
457595 TTTTAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 9 0.41
17 3 0.14
18 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
ATAATATAAGATTTATTT
Found at i:463390 original size:20 final size:21
Alignment explanation
Indices: 463365--463406 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
463355 ACGAAAGTTA
463365 CTGTAGCA-GGGAATCGATAC
1 CTGTAGCAGGGGAATCGATAC
*
463385 CTGTAGCAGGGGTATCGATAC
1 CTGTAGCAGGGGAATCGATAC
463406 C
1 C
463407 CCTAAAGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.21
Consensus pattern (21 bp):
CTGTAGCAGGGGAATCGATAC
Found at i:463455 original size:12 final size:12
Alignment explanation
Indices: 463438--463462 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
463428 TTTTAACATT
463438 CGGTATTGTTCA
1 CGGTATTGTTCA
463450 CGGTATTGTTCA
1 CGGTATTGTTCA
463462 C
1 C
463463 TACTGTTCAT
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:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (12 bp):
CGGTATTGTTCA
Found at i:463487 original size:19 final size:20
Alignment explanation
Indices: 463453--463491 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
463443 TTGTTCACGG
463453 TATTGTTCACTACTGTTCAT
1 TATTGTTCACTACTGTTCAT
*
463473 TATTGTTC-GTACTGTTCAT
1 TATTGTTCACTACTGTTCAT
463492 ACCGTATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.51
Consensus pattern (20 bp):
TATTGTTCACTACTGTTCAT
Found at i:467564 original size:23 final size:23
Alignment explanation
Indices: 467531--467591 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
467521 CTCGCATAAA
467531 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
467554 TGCACCAAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
467577 TACACCGAAGTGCCA
1 TGCACCGAAGTGCCA
467592 TATAAGATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.16
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:468321 original size:63 final size:64
Alignment explanation
Indices: 468232--468393 Score: 168
Period size: 63 Copynumber: 2.5 Consensus size: 64
468222 ATCCCTTGAC
* * * *
468232 GGGTGGATCGATGCACTA-TCTATGCATCGATACAGAAAT-CCTATTCGATATTTGTA-TTTAAG
1 GGGTGCATCGATGCACTACT-TGTGCATCGATACACAAATGCC-ATTCGATATTTGTATTTTAAA
468294 G
64 G
* ** * * *
468295 GGGTGCATCGATGCACTACTTGTGCATTGATACACTGATGGCATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACTACTTGTGCATCGATACACAAATGCCATTCGATATTTGTATTTTAAAG
* * *
468359 GAGTGCATCGATGCACTTCATGTGCATCGATACAC
1 GGGTGCATCGATGCACTACTTGTGCATCGATACAC
468394 CTTGAACAAT
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
63 43 0.52
64 39 0.48
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (64 bp):
GGGTGCATCGATGCACTACTTGTGCATCGATACACAAATGCCATTCGATATTTGTATTTTAAAG
Found at i:468383 original size:64 final size:63
Alignment explanation
Indices: 468274--468393 Score: 168
Period size: 64 Copynumber: 1.9 Consensus size: 63
468264 CAGAAATCCT
* * * *
468274 ATTCGATATTTGTATTTAAGGGGGTGCATCGATGCACTACTTGTGCATTGATACACTGATGGC
1 ATTCGATATTTGTATTTAAAGGAGTGCATCGATGCACTACATGTGCATCGATACACTGATGGC
* * *
468337 ATTCGATGTTTTTATTTTAAAGGAGTGCATCGATGCACTTCATGTGCATCGATACAC
1 ATTCGATATTTGTA-TTTAAAGGAGTGCATCGATGCACTACATGTGCATCGATACAC
468394 CTTGAACAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 12 0.24
64 37 0.76
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.36
Consensus pattern (63 bp):
ATTCGATATTTGTATTTAAAGGAGTGCATCGATGCACTACATGTGCATCGATACACTGATGGC
Found at i:474510 original size:20 final size:23
Alignment explanation
Indices: 474487--474540 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
474477 CTCGTATAAA
474487 TGCACCGAAGTG-C-C-TAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
474507 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
474530 TGCACCGAAGT
1 TGCACCGAAGT
474541 ACCATATAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.39
21 1 0.03
22 1 0.03
23 17 0.55
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:475316 original size:61 final size:61
Alignment explanation
Indices: 475184--475335 Score: 173
Period size: 61 Copynumber: 2.5 Consensus size: 61
475174 TTGACGGGTA
* * *** * *
475184 CATCGATGCACTATC-TATGCATCGATACATAAATCTTATTCGATGTTTTTATTTAAGGGGTG
1 CATCGATGCACTA-CATGTGCATCGATACAT-GATGGCATTCGATGTTTTTATTAAAGGAGTG
* *
475246 CATCGATGCACTACTTGTTCATCGATACATGATGGCATTCGATGTTTATT-TTAAAGGAGTG
1 CATCGATGCACTACATGTGCATCGATACATGATGGCATTCGATGTTT-TTATTAAAGGAGTG
*
475307 CATCGATGCACTTCATGTGCATCGATACA
1 CATCGATGCACTACATGTGCATCGATACA
475336 CCTTGAACAA
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
61 49 0.64
62 28 0.36
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (61 bp):
CATCGATGCACTACATGTGCATCGATACATGATGGCATTCGATGTTTTTATTAAAGGAGTG
Found at i:483707 original size:218 final size:218
Alignment explanation
Indices: 483329--483764 Score: 824
Period size: 218 Copynumber: 2.0 Consensus size: 218
483319 GTATATAAAA
483329 AACTAGGCCAATGCATTGGTCACCTATTTTTTTTTTAGCCACTGAATTTTGAAATAATAATAAAT
1 AACTAGGCCAATGCATTGGTCACCTATTTTTTTTTTAGCCACTGAATTTTGAAATAATAATAAAT
483394 TAAAATAGAGTGAGTAAAATTTAAATTTTTAACGTATTAAAGGGACTAAAATATAACTGAACTTA
66 TAAAATAGAGTGAGTAAAATTTAAATTTTTAACGTATTAAAGGGACTAAAATATAACTGAACTTA
483459 AAACAAAGTGTTCGAGGCTTAATATACTATAGCATGTAAACTCATCATGAAGATTTGACTATAT-
131 AAACAAAGTGTTCGAGGCTTAATATACTATAGCATGTAAACTCATCATGAAGATTTGACTATATA
483523 ATTTAAATATTTTCTTTGTATTTT
196 ATTTAAATATTTTC-TTGTATTTT
483547 AACTAGGCCAATGCATTGGTCACCTATTTTTTTTTTAGCCACTTGAATTTTGAAAATAATAATAA
1 AACTAGGCCAATGCATTGGTCACCTATTTTTTTTTTAGCCAC-TGAATTTTG-AAATAATAATAA
483612 ATTAAAATAGAGTGAGTAAAATTTAAA-TTTTAACGTATTAAAGGGACTAAAATAT-ACTGAACT
64 ATTAAAATAGAGTGAGTAAAATTTAAATTTTTAACGTATTAAAGGGACTAAAATATAACTGAACT
483675 TAAAACAAAGTGTTCGAGGCTTAATATACTATAGCATGTAAACTCATCATGAAGATTTGACTATA
129 TAAAACAAAGTGTTCGAGGCTTAATATACTATAGCATGTAAACTCATCATGAAGATTTGACTATA
483740 TAATTTAAATATTTTCTTGTATTTT
194 TAATTTAAATATTTTCTTGTATTTT
483765 TTTGTTATTA
Statistics
Matches: 215, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
218 125 0.58
219 51 0.24
220 39 0.18
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (218 bp):
AACTAGGCCAATGCATTGGTCACCTATTTTTTTTTTAGCCACTGAATTTTGAAATAATAATAAAT
TAAAATAGAGTGAGTAAAATTTAAATTTTTAACGTATTAAAGGGACTAAAATATAACTGAACTTA
AAACAAAGTGTTCGAGGCTTAATATACTATAGCATGTAAACTCATCATGAAGATTTGACTATATA
ATTTAAATATTTTCTTGTATTTT
Found at i:495897 original size:21 final size:22
Alignment explanation
Indices: 495873--495916 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
495863 ACTAAACTCA
*
495873 AATTTAAAAAATTT-TGAGTCG
1 AATTTAAAAAATTTATGAATCG
**
495894 AATTTGTAAAATTTATGAATCG
1 AATTTAAAAAATTTATGAATCG
495916 A
1 A
495917 GTTGAGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.39
Consensus pattern (22 bp):
AATTTAAAAAATTTATGAATCG
Found at i:501696 original size:10 final size:10
Alignment explanation
Indices: 501681--501727 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
501671 ATAATCATAC
501681 TAATTTTTTG
1 TAATTTTTTG
501691 TAATTTTTCTG
1 TAATTTTT-TG
501702 --ATTTTTTG
1 TAATTTTTTG
*
501710 T-ATTTTTTC
1 TAATTTTTTG
501719 TAATTTTTT
1 TAATTTTTT
501728 TAAATTAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 2 0.06
9 14 0.42
10 15 0.45
11 2 0.06
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.72
Consensus pattern (10 bp):
TAATTTTTTG
Found at i:501705 original size:19 final size:19
Alignment explanation
Indices: 501680--501727 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
501670 AATAATCATA
501680 CTAATTTTTTGTAATTTTT
1 CTAATTTTTTGTAATTTTT
* *
501699 CTGATTTTTTGTATTTTTT
1 CTAATTTTTTGTAATTTTT
501718 CTAATTTTTT
1 CTAATTTTTT
501728 TAAATTAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (19 bp):
CTAATTTTTTGTAATTTTT
Found at i:501732 original size:110 final size:112
Alignment explanation
Indices: 501612--501821 Score: 361
Period size: 110 Copynumber: 1.9 Consensus size: 112
501602 ACTACATTTG
* * *
501612 TTTTTTTAAATTAAAGTATATTAAATTATAATATAGATAAAAAT-ATTGAAATTAGATAAATAAT
1 TTTTTTTAAATTAAAGTAGATTAAATTATAAGATAGATAAAAATAATTGAAATTAGATAAATAAA
501676 CATACTAA-TTTTTTGTAATTTTTCTGATTTTTTGTATTTTTTCTAA
66 CATACTAATTTTTTTGTAATTTTTCTGATTTTTTGTATTTTTTCTAA
*
501722 TTTTTTTAAATTAAAGTAGATTAAATTGTAAGATAGATAAAAATACATTGAAATTAGATAAATAA
1 TTTTTTTAAATTAAAGTAGATTAAATTATAAGATAGATAAAAATA-ATTGAAATTAGATAAATAA
501787 ACATACTAATTTTTTTGTAATTTTTCTGATTTTTT
65 ACATACTAATTTTTTTGTAATTTTTCTGATTTTTT
501822 TAAATTCAAA
Statistics
Matches: 93, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
110 41 0.44
112 27 0.29
113 25 0.27
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (112 bp):
TTTTTTTAAATTAAAGTAGATTAAATTATAAGATAGATAAAAATAATTGAAATTAGATAAATAAA
CATACTAATTTTTTTGTAATTTTTCTGATTTTTTGTATTTTTTCTAA
Found at i:504271 original size:2 final size:2
Alignment explanation
Indices: 504264--504294 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
504254 ATAAAGGAAT
504264 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 T
504295 GTCTGTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:505365 original size:16 final size:17
Alignment explanation
Indices: 505336--505373 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
505326 AAAAAAATTC
505336 AAAAATTATCAAAAAGA
1 AAAAATTATCAAAAAGA
*
505353 AAAAATT-TTAAAAAGA
1 AAAAATTATCAAAAAGA
505369 AAAAA
1 AAAAA
505374 GGCTAAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAAATTATCAAAAAGA
Found at i:505758 original size:16 final size:17
Alignment explanation
Indices: 505732--505763 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
505722 GCCCAAATAT
505732 TTTATGTAAAATTTATA
1 TTTATGTAAAATTTATA
505749 TTTA-GTAAAATTTAT
1 TTTATGTAAAATTTAT
505764 TCATCTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TTTATGTAAAATTTATA
Found at i:506127 original size:25 final size:26
Alignment explanation
Indices: 506075--506129 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
506065 CATACACAAA
* * *
506075 AAATTATATAAATATAAATATAAAAT
1 AAATTATATAAAAATAAAAACAAAAT
*
506101 AAATTAT-TAAAAATAAAAACAATAT
1 AAATTATATAAAAATAAAAACAAAAT
506126 AAAT
1 AAAT
506130 ACAAAACACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATTATATAAAAATAAAAACAAAAT
Found at i:506511 original size:51 final size:50
Alignment explanation
Indices: 506418--506538 Score: 136
Period size: 51 Copynumber: 2.4 Consensus size: 50
506408 CAAAGCGCGC
* *
506418 CCCCTGCACCGCGCTATACGATGATTTGGCGCCACGTGGGGTATAACACG
1 CCCCTGCACCGCGCTATACGATGATCTGGCGACACGTGGGGTATAACACG
* * * *
506468 CCTCCTGCACCGCGCTATACGGTGATCTGTCATACACGT-GGGTATAGCACG
1 CC-CCTGCACCGCGCTATACGATGATCTGGC-GACACGTGGGGTATAACACG
**
506519 ACCCCTGCAGTGCGCTATAC
1 -CCCCTGCACCGCGCTATAC
506539 CTAGATATCT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
50 2 0.03
51 51 0.85
52 7 0.12
ACGTcount: A:0.20, C:0.33, G:0.26, T:0.21
Consensus pattern (50 bp):
CCCCTGCACCGCGCTATACGATGATCTGGCGACACGTGGGGTATAACACG
Found at i:512789 original size:24 final size:24
Alignment explanation
Indices: 512738--512789 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
512728 GTATTTAAAT
*
512738 TATTTACGTTTATTTTAATTATTT
1 TATTTACGTTTATTTTAATTATTA
512762 TATTT-CGTTATATTTTAATTCA-TA
1 TATTTACGTT-TATTTTAATT-ATTA
512786 TATT
1 TATT
512790 ATTTATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 4 0.16
24 20 0.80
25 1 0.04
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (24 bp):
TATTTACGTTTATTTTAATTATTA
Found at i:514895 original size:25 final size:26
Alignment explanation
Indices: 514846--514896 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
514836 ACTACAAGTG
*
514846 CAAACAAAACTTCAGAAACTACATATC
1 CAAAAAAAACTTCAGAAAC-ACATATC
514873 CAAAAAAAACTTCAGAAAC-CATAT
1 CAAAAAAAACTTCAGAAACACATAT
514897 AACTGTACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.22
27 18 0.78
ACGTcount: A:0.55, C:0.24, G:0.04, T:0.18
Consensus pattern (26 bp):
CAAAAAAAACTTCAGAAACACATATC
Found at i:515883 original size:2 final size:2
Alignment explanation
Indices: 515876--515916 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
515866 TAATAAAATT
515876 TA TA TA TA 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 TA TA TA TA T
515917 TTTATAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:520832 original size:22 final size:22
Alignment explanation
Indices: 520807--520850 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
520797 TCCGATTTAC
*
520807 TTGAAATGAATATATTTT-CAAA
1 TTGAAATAAATAT-TTTTACAAA
*
520829 TTGAATTAAATATTTTTACAAA
1 TTGAAATAAATATTTTTACAAA
520851 AATTATTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (22 bp):
TTGAAATAAATATTTTTACAAA
Found at i:522315 original size:2 final size:2
Alignment explanation
Indices: 522308--522356 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
522298 AAGAACCCAT
522308 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
522350 TA TA TA T
1 TA TA TA T
522357 GAAGATTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:523091 original size:183 final size:184
Alignment explanation
Indices: 522750--523101 Score: 487
Period size: 183 Copynumber: 1.9 Consensus size: 184
522740 AAATTGAAAC
* * * * *
522750 ATATGGCTAGTGTGGTATGATATATTAATATTTTTAATCTTTAAAACATGTATATTTTATTAATT
1 ATATGGCTAATGTGATATGATATATTAATATTTTTAATCTTTAAAACATGTACATTCTATCAATT
* * * * *
522815 TTGTCTTAATTTAAAATAATCTTATAAATTTAACATTTTATATTTAGAAATTTCATCAATTTAGT
66 TTGTCCTAATTTAAAATAATCTAATAAATTTAACATTTTATATTTAAAAATCTCATCAATTTAAT
**
522880 CTTTTTTACGTATTAATAAACCAAGTGAG-TCTATCGGATTAATGCAGTACTTGG
131 CTTTTTTAAATATTAATAAACCAAGTGAGTTC-ATCGGATTAATGCAGTACTTGG
* *
522934 ATATGTCTAATGTGATATGATATAATT-GTATTTTTAATCTTTAAAACATGTACATTCTATCAAT
1 ATATGGCTAATGTGATATGATAT-ATTAATATTTTTAATCTTTAAAACATGTACATTCTATCAAT
* *
522998 TTTGTCCTAA-TTGAAATAATCTAATAAATTTAACTTTTTATATTTAAAAAATCT-ATCAATTTA
65 TTTGTCCTAATTTAAAATAATCTAATAAATTTAACATTTTATATTT-AAAAATCTCATCAATTTA
* *
523061 ATCTTTTTTAAATATTGATAAACTAAGTGAGTTCATCGGAT
129 ATCTTTTTTAAATATTAATAAACCAAGTGAGTTCATCGGAT
523102 CAAAGTAGTA
Statistics
Matches: 147, Mismatches: 18, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
183 74 0.50
184 70 0.48
185 3 0.02
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (184 bp):
ATATGGCTAATGTGATATGATATATTAATATTTTTAATCTTTAAAACATGTACATTCTATCAATT
TTGTCCTAATTTAAAATAATCTAATAAATTTAACATTTTATATTTAAAAATCTCATCAATTTAAT
CTTTTTTAAATATTAATAAACCAAGTGAGTTCATCGGATTAATGCAGTACTTGG
Found at i:524078 original size:18 final size:18
Alignment explanation
Indices: 524055--524100 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
524045 AGCATTCCCA
*
524055 GTAATCTTATTCCCGCCG
1 GTAATCTTATTCCCACCG
*
524073 GTAATCCTATTCCCACCG
1 GTAATCTTATTCCCACCG
*
524091 GTAATATTAT
1 GTAATCTTAT
524101 ATTTCGTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (18 bp):
GTAATCTTATTCCCACCG
Found at i:544265 original size:259 final size:251
Alignment explanation
Indices: 543778--544375 Score: 839
Period size: 259 Copynumber: 2.4 Consensus size: 251
543768 CATATTCATA
* *
543778 TATTGAATAAAAATATTTTTTAATTATTTCGGGTCGGGTTTCTTATTCATATA-T----TCGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGT
*
543838 CGGGTGAAATTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTTAAGTGTGATATTCGGGTCGGGTC
66 CGGGTGAAATTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTTAAGTGTGATATTCAGGTC-GG-C
*
543903 GAGTTCGGGTTTAGGGTGAAAAATACCTGACCCGAAAATATATATAAATTTACCTTATATATTTA
129 GAGTTCGGGTTTAGGGTGAAAAATACCTGACCCGAAAAAATATATAAATTTACCTTATATATTTA
* * *
543968 GGAATAATTACAATAATAGCCCTCTATATATAATTTTTTTCAATTAAGTCACTGTTTT
194 GGAATAATTACAATAATACCCCTCTATATATAATTTTTTCCAATTAAGTAACTGTTTT
544026 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGG
1 TATTGAATAAAAAT-ATTTTTTTATTATTTCGGGTC--G--GG-TTTCTAATTCATATATTCGGG
544091 TCGGGTCGGGTGAAATTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTTAAGTGTGATATTCAGGT
60 TCGGGTCGGGTGAAATTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTTAAGTGTGATATTCAGGT
* *
544156 C-G-G-GTTCGGGTTTAGGGTGAAATATACCCGACTCGACCC-AAAAAATATATAATTTTACCTT
125 CGGCGAGTTCGGGTTTAGGGTGAAAAATA--C--CT-GACCCGAAAAAATATATAAATTTACCTT
* * *
544217 ATATATTTAGGAATAATTACAATAATACCCCTCTCTCTATATATTTTTTCCAATTAAGTAATTGT
185 ATATATTTAGGAATAATTACAATAATACCCCTCTATATATA-ATTTTTTCCAATTAAGTAACTGT
544282 TTT
249 TTT
* *
544285 TATTAAATAAAAATATTTTTTTATTA--T----TCGAGTTTCTAATTCATATATTCGGGTCGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGT
544344 CGGGTGAAATTTTATTTTGGTCGGGTCGGGTC
66 CGGGTGAAATTTTATTTTGGTCGGGTCGGGTC
544376 TCGGATGGAG
Statistics
Matches: 319, Mismatches: 14, Indels: 35
0.87 0.04 0.10
Matches are distributed among these distances:
247 59 0.18
248 15 0.05
249 20 0.06
250 1 0.00
251 1 0.00
252 2 0.01
253 2 0.01
254 36 0.11
255 2 0.01
256 2 0.01
257 1 0.00
258 72 0.23
259 106 0.33
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.42
Consensus pattern (251 bp):
TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGT
CGGGTGAAATTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTTAAGTGTGATATTCAGGTCGGCGA
GTTCGGGTTTAGGGTGAAAAATACCTGACCCGAAAAAATATATAAATTTACCTTATATATTTAGG
AATAATTACAATAATACCCCTCTATATATAATTTTTTCCAATTAAGTAACTGTTTT
Done.