Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003345.1 Hibiscus syriacus cultivar Beakdansim tig00007043_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: 605145
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:215406 original size:34 final size:34
Alignment explanation
Indices: 215364--215448 Score: 143
Period size: 34 Copynumber: 2.5 Consensus size: 34
215354 CGATTTTATA
*
215364 TATATATATAATGTTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
*
215398 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
*
215432 TATATATAAAATATTTT
1 TATATATATAATATTTT
215449 TGGGTTCGGG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:215436 original size:25 final size:25
Alignment explanation
Indices: 215382--215436 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
215372 TAATGTTTTA
215382 TATATTTTATATTAATTATATATAT
1 TATATTTTATATTAATTATATATAT
* **
215407 AATATTTTATATTTTTTATAT-TAAT
1 TATATTTTATATTAATTATATAT-AT
215432 TATAT
1 TATAT
215437 ATAAAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TATATTTTATATTAATTATATATAT
Found at i:217328 original size:6 final size:6
Alignment explanation
Indices: 217073--217327 Score: 321
Period size: 6 Copynumber: 42.5 Consensus size: 6
217063 ATGCATATGC
217073 ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT
1 ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT
* * * * *
217121 ATAGGT ATAGGT ATAGGT ATAGGC ATAGGC ATAGGC ATAGGC ATAGGC
1 ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT
* * * * * * * *
217169 ATAGGC ATAGGC ATAGGC ATAGGC ATAGGC ATAGGC ATAGGC ATAGGC
1 ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT
* * *
217217 ATAGGT ATAGGT ATAGGT ATAGGT ATAGGC ATAGGC ATAGGC ATAGGT
1 ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT
* * *
217265 ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGC ATAGGG ATAGGC
1 ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT ATAGGT
* *
217313 ATATGT ATATGT ATA
1 ATAGGT ATAGGT ATA
217328 TATACCTTGA
Statistics
Matches: 240, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 240 1.00
ACGTcount: A:0.34, C:0.07, G:0.33, T:0.27
Consensus pattern (6 bp):
ATAGGT
Found at i:220785 original size:101 final size:101
Alignment explanation
Indices: 220610--220845 Score: 436
Period size: 101 Copynumber: 2.3 Consensus size: 101
220600 GCGTTATGTT
* * *
220610 ATTCGAATTCTTAAATTTCTTCTATATAAACATCGTATATTTACCACGAATCAAGTAATCTCGGT
1 ATTCGAATTCTTCATTTTCTTCTATATAAACATCGTATATTTACCACGAATCAAATAATCTCGGT
220675 AATAAAGAAATTATTATTATTCTCGGAGGTTTCGGG
66 AATAAAGAAATTATTATTATTCTCGGAGGTTTCGGG
*
220711 ATTCGAATTCTTCATTTTCTTCTATATAAACATCGTATATTTAGCACGAATCAAATAATCTCGGT
1 ATTCGAATTCTTCATTTTCTTCTATATAAACATCGTATATTTACCACGAATCAAATAATCTCGGT
220776 AATAAAGAAATTATTATTATTCTCGGAGGTTTCGGG
66 AATAAAGAAATTATTATTATTCTCGGAGGTTTCGGG
220812 ATTCGAATTCTTCATTTTCTTCTATATAAACATC
1 ATTCGAATTCTTCATTTTCTTCTATATAAACATC
220846 ATTTTCTTTG
Statistics
Matches: 131, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 131 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (101 bp):
ATTCGAATTCTTCATTTTCTTCTATATAAACATCGTATATTTACCACGAATCAAATAATCTCGGT
AATAAAGAAATTATTATTATTCTCGGAGGTTTCGGG
Found at i:221200 original size:2 final size:2
Alignment explanation
Indices: 221193--221219 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
221183 TCAAACTTCC
221193 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
221220 AACCCACTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:226856 original size:13 final size:13
Alignment explanation
Indices: 226838--226862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
226828 AGTGTTAATA
226838 AATTTTAAGATTG
1 AATTTTAAGATTG
226851 AATTTTAAGATT
1 AATTTTAAGATT
226863 TTATATTCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
AATTTTAAGATTG
Found at i:226898 original size:17 final size:18
Alignment explanation
Indices: 226864--226900 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
226854 TTTAAGATTT
226864 TATATTCGATTCAAAATTA
1 TATATTCGATTC-AAATTA
226883 TATATTCGATTC-AATTA
1 TATATTCGATTCAAATTA
226900 T
1 T
226901 TCGAATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATTCGATTCAAATTA
Found at i:229061 original size:12 final size:12
Alignment explanation
Indices: 229046--229070 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
229036 TTAAATATAA
229046 AAAATCTAATTT
1 AAAATCTAATTT
229058 AAAATCTAATTT
1 AAAATCTAATTT
229070 A
1 A
229071 TACACATAGA
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATCTAATTT
Found at i:232090 original size:19 final size:19
Alignment explanation
Indices: 232048--232112 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
232038 TTTGAAATTA
232048 TTAATAA-TTATTAATGAA-
1 TTAATAATTTATTAAT-AAT
* * *
232066 TTAATATTTTCTTATTAAT
1 TTAATAATTTATTAATAAT
232085 TTAATAATTTATTAATAAT
1 TTAATAATTTATTAATAAT
232104 TTAAATAAT
1 TT-AATAAT
232113 CAAATAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
18 8 0.21
19 24 0.63
20 6 0.16
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TTAATAATTTATTAATAAT
Found at i:235726 original size:2 final size:2
Alignment explanation
Indices: 235719--235770 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
235709 TACATATAAG
235719 TA TA TA TA TA TA TA TA TA TA TA TA TA -A T- 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
*
235759 TA TT TA TA TA TA
1 TA TA TA TA TA TA
235771 AACTTAGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:237257 original size:54 final size:54
Alignment explanation
Indices: 237132--237296 Score: 235
Period size: 54 Copynumber: 3.1 Consensus size: 54
237122 ACTAAGGTAA
* * *
237132 CGAAATGGTAATTCACAAACTCATTATGAATATCATGGGTTG--TACATAGTGC
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGGTTGCACACATAGTGT
* * *
237184 CAAAATTGTAATTCACAAACTCATTATGAATACCATGGGTTGCACACATAGTAT
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGGTTGCACACATAGTGT
* * *
237238 CGAAATGGTAATTTACAAACTCATTATAAATACTATGGGTTGCACACATAGTGT
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGGTTGCACACATAGTGT
237292 CGAAA
1 CGAAA
237297 GTACACATAA
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
52 39 0.39
54 60 0.61
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (54 bp):
CGAAATGGTAATTCACAAACTCATTATGAATACCATGGGTTGCACACATAGTGT
Found at i:243293 original size:20 final size:19
Alignment explanation
Indices: 243270--243334 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 19
243260 GAACACAAGC
243270 TTCGCAACACAGTTTTCAAA
1 TTCGCAACAC-GTTTTCAAA
* *
243290 TTCGTAACACGATTCTCCAAA
1 TTCGCAACACG-TT-TTCAAA
*
243311 ATCGCAACACGGTTTTCAAA
1 TTCGCAACAC-GTTTTCAAA
243331 TTCG
1 TTCG
243335 TAACGTGAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
19 1 0.03
20 19 0.53
21 15 0.42
22 1 0.03
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.29
Consensus pattern (19 bp):
TTCGCAACACGTTTTCAAA
Found at i:243828 original size:20 final size:20
Alignment explanation
Indices: 243800--243846 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
243790 GGTAATTAGA
*
243800 GTTGCGAATTTAAATATCAC
1 GTTGCGAATTTAAAAATCAC
* *
243820 GTTGTGAATTTAAAAATCGC
1 GTTGCGAATTTAAAAATCAC
243840 GTTGCGA
1 GTTGCGA
243847 TTTTGGAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTTAAAAATCAC
Found at i:244668 original size:60 final size:60
Alignment explanation
Indices: 244496--244668 Score: 204
Period size: 60 Copynumber: 2.9 Consensus size: 60
244486 ACCATAACCT
* * * ** * *
244496 TCATTTTAAATTTATCCTTAAACTTTTGAATA-TTCTAATGTCATCTTTAAACTATGACCC
1 TCATTCTAAATTAATCCTTAAACTTTTGAATATTTC-AATTTCATCCCTAAATTATGACCA
* * **
244556 TCATTCTAAATTAGTCTTTAAACTTTTGAATATTTCAATTTCATCCCTAAATTATGATTA
1 TCATTCTAAATTAATCCTTAAACTTTTGAATATTTCAATTTCATCCCTAAATTATGACCA
* * *
244616 TCTTTCTAAGTTAATCCTTAAACTTTTGAATATTTCAATTTCATCCCCAAATT
1 TCATTCTAAATTAATCCTTAAACTTTTGAATATTTCAATTTCATCCCTAAATT
244669 CATCCATATA
Statistics
Matches: 96, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 93 0.97
61 3 0.03
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.46
Consensus pattern (60 bp):
TCATTCTAAATTAATCCTTAAACTTTTGAATATTTCAATTTCATCCCTAAATTATGACCA
Found at i:246365 original size:22 final size:23
Alignment explanation
Indices: 246335--246380 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
246325 TGAAAATAAG
* *
246335 TTAACAAAATTATATTTATTTAA
1 TTAACAAAATAATATTTAATTAA
246358 TTAA-AAAATAATATTTAATTAA
1 TTAACAAAATAATATTTAATTAA
246380 T
1 T
246381 GTAGAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TTAACAAAATAATATTTAATTAA
Found at i:248094 original size:22 final size:20
Alignment explanation
Indices: 248062--248108 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
248052 ATTAAATACT
*
248062 TATATTAATAAAATTATTTA
1 TATATTAATAAAATTATATA
*
248082 TATACTTACATAAATTTATATA
1 TATA-TTA-ATAAAATTATATA
248104 TATAT
1 TATAT
248109 ATATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 15 0.65
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
TATATTAATAAAATTATATA
Found at i:248103 original size:2 final size:2
Alignment explanation
Indices: 248098--248126 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
248088 TACATAAATT
248098 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
248127 GAAATAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:252373 original size:60 final size:58
Alignment explanation
Indices: 252308--252445 Score: 134
Period size: 60 Copynumber: 2.3 Consensus size: 58
252298 TTTAAATATT
* ** * * *
252308 TTAATTTCATCCTTAAATTATGACTTTTATTCTAAATTA-ATACCTAAACTTTTGAACC
1 TTAATTTCATCCATAAATTATGACCCTCATTCTAAATTAGACA-CTAAACTTTTGAACA
* * ** *
252366 TCCTAATTTTATCCCTAAAACATGACCCTCATTCTAAATTAGCCACTAAACTTTTGAACA
1 T--TAATTTCATCCATAAATTATGACCCTCATTCTAAATTAGACACTAAACTTTTGAACA
252426 TTAAGTTTCATCCATAAATT
1 TTAA-TTTCATCCATAAATT
252446 CATCCAAATA
Statistics
Matches: 62, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
58 4 0.06
59 11 0.18
60 46 0.74
61 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (58 bp):
TTAATTTCATCCATAAATTATGACCCTCATTCTAAATTAGACACTAAACTTTTGAACA
Found at i:253781 original size:3 final size:3
Alignment explanation
Indices: 253773--253801 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
253763 TCAATGCACA
253773 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
253802 AACTTCAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:254167 original size:3 final size:3
Alignment explanation
Indices: 254159--254184 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
254149 TTTGATTGAT
254159 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
254185 GTTGCAGAAT
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:261499 original size:27 final size:27
Alignment explanation
Indices: 261464--261650 Score: 230
Period size: 27 Copynumber: 6.9 Consensus size: 27
261454 TTATAAAGCC
* ** *
261464 AACTTCACTCTCCTATTCATCTTCAGA
1 AACTTCATTCTCAGATTCAGCTTCAGA
* * * *
261491 AACCTCACTCTCAGGTTCAGTTTCAGA
1 AACTTCATTCTCAGATTCAGCTTCAGA
261518 AACTTCATTCTCAGATTCAGCTTCAGA
1 AACTTCATTCTCAGATTCAGCTTCAGA
261545 AACTTCATTCTCAGATTCAGCTTCAGA
1 AACTTCATTCTCAGATTCAGCTTCAGA
261572 AACTTCATTCTCAGATTCAGCTTCAGA
1 AACTTCATTCTCAGATTCAGCTTCAGA
* * * *
261599 AACTTCATTCTTAAATTCATCTTTAGA
1 AACTTCATTCTCAGATTCAGCTTCAGA
* * * *
261626 GATTTTACTCTCAGATTCAGCTTCA
1 AACTTCATTCTCAGATTCAGCTTCA
261651 AATGGGCACG
Statistics
Matches: 138, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 138 1.00
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (27 bp):
AACTTCATTCTCAGATTCAGCTTCAGA
Found at i:271640 original size:17 final size:17
Alignment explanation
Indices: 271611--271643 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
271601 TTCTTCTTCA
271611 ATCTCTCCCCCCAAATG
1 ATCTCTCCCCCCAAATG
271628 ATCTC-CCCTCCCAAAT
1 ATCTCTCCC-CCCAAAT
271644 TACACAAGCT
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:0.24, C:0.48, G:0.03, T:0.24
Consensus pattern (17 bp):
ATCTCTCCCCCCAAATG
Found at i:281348 original size:231 final size:231
Alignment explanation
Indices: 280699--281545 Score: 1172
Period size: 231 Copynumber: 3.7 Consensus size: 231
280689 ATCATCTCTA
* *
280699 TCACCTATATGTATTTTTTTCAAACCCATAATTCATATAAATTTCAAATGATTTAAAAGCATAAA
1 TCACCTATATGTATTTTTTTCAAACTCATAATTCACATAAATTTCAAATGA-TTAAAAGCATAAA
* * *
280764 TAAC---CAATACTAAAATATTAAGTG----GAAATCAAAGATTGAGATAAACATACCACGAAAA
65 TAACTAATAATACTAAAATATTAAGCGAAAAAAAATCAAAGATTGAGATAAACATACCACGAAAA
* * **
280822 GGAGAATCAGGAAACTGACAATCAAATTCATCTTCAATTGGGACATTGTTATCATCTACAGGAAC
130 GGAGAATCGGGAAACTGAGAATCAAATTCATCTTCAATTGAAACATTGTTATCATCTACAGGAAC
* *
280887 CGTATCTTGAAGAAAGTTTAATTCATTTTCACACCCG
195 CGTATCTTGAAGAAAGTTTAATTCATTATCACAACCG
* *
280924 TCACCTATATGTATTTTTTTCAAACTCATAATTCACATAAATTTCAAATAATTGAAAGCATAAAT
1 TCACCTATATGTATTTTTTTCAAACTCATAATTCACATAAATTTCAAATGATTAAAAGCATAAAT
* * * *
280989 AACTAATAATACTAAAATATTAAGCGAAAGAATAATCAAAGATTGTGATAAACATACCACGATAT
66 AACTAATAATACTAAAATATTAAGCGAAA-AAAAATCAAAGATTGAGATAAACATACCACGAAAA
* * * * *
281054 GGAGAATCGGGTAACTGAGAGTCAAATTCATCTTCAATTGTAGCATTGTTATCATCCACAGGAAC
130 GGAGAATCGGGAAACTGAGAATCAAATTCATCTTCAATTGAAACATTGTTATCATCTACAGGAAC
281119 CGTATCTTGAAGAAAGTTTAATTCATTATCACAACCG
195 CGTATCTTGAAGAAAGTTTAATTCATTATCACAACCG
* *
281156 TCACCTATATGT-TTTTTTTCCAAACTCGTAATTCACATAAATTTCAAATGATTCAAAGCATAAA
1 TCACCTATATGTATTTTTTT-CAAACTCATAATTCACATAAATTTCAAATGATTAAAAGCATAAA
* * * *
281220 TAACTAATAATTCTACAATATTAATCCAAAAAAAATCAAAGATTGAGATAAACATACCACGAAAA
65 TAACTAATAATACTAAAATATTAAGCGAAAAAAAATCAAAGATTGAGATAAACATACCACGAAAA
* * * ** *
281285 GGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATAGAAACATTGTTGTTGTCTACAGGAAT
130 GGAGAATCGGGAAACTGAGAATCAAATTCATCTTCAATTGAAACATTGTTATCATCTACAGGAAC
* * *
281350 AGTATCTTGTAGAAAGTTCAATTCATTATCACAACCG
195 CGTATCTTGAAGAAAGTTTAATTCATTATCACAACCG
* * * * *
281387 TCACCTCTATGAATTTTTTT-AAAGCTCGTAATTCACATAAATTTCAAATGATTTAAAGCGTAAA
1 TCACCTATATGTATTTTTTTCAAA-CTCATAATTCACATAAATTTCAAATGATTAAAAGCATAAA
* * * * *
281451 TAACTAATAATACTAAAATATTAAGGGGAAAAGAATCAAAGATTGAGATAAATATACCAGGAAAA
65 TAACTAATAATACTAAAATATTAAGCGAAAAAAAATCAAAGATTGAGATAAACATACCACGAAAA
281516 GGAGAATCGGGAAACTGAGAATCAAATTCA
130 GGAGAATCGGGAAACTGAGAATCAAATTCA
281546 AAGGGCTGGG
Statistics
Matches: 553, Mismatches: 58, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
224 16 0.03
225 48 0.09
227 18 0.03
230 3 0.01
231 261 0.47
232 207 0.37
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.30
Consensus pattern (231 bp):
TCACCTATATGTATTTTTTTCAAACTCATAATTCACATAAATTTCAAATGATTAAAAGCATAAAT
AACTAATAATACTAAAATATTAAGCGAAAAAAAATCAAAGATTGAGATAAACATACCACGAAAAG
GAGAATCGGGAAACTGAGAATCAAATTCATCTTCAATTGAAACATTGTTATCATCTACAGGAACC
GTATCTTGAAGAAAGTTTAATTCATTATCACAACCG
Found at i:282059 original size:30 final size:30
Alignment explanation
Indices: 281999--282059 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
281989 AATAAGGTTA
**
281999 TATTCATGTTCGTTTGTTTATTTTTGAAAT
1 TATTCATGTTCGTTTGTTTACGTTTGAAAT
282029 TATTCATGTTCGATTTGTGTT-CGTTT-AAAT
1 TATTCATGTTCG-TTTGT-TTACGTTTGAAAT
282059 T
1 T
282060 TTTAGTATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 17 0.63
31 8 0.30
32 2 0.07
ACGTcount: A:0.20, C:0.08, G:0.15, T:0.57
Consensus pattern (30 bp):
TATTCATGTTCGTTTGTTTACGTTTGAAAT
Found at i:282219 original size:23 final size:24
Alignment explanation
Indices: 282122--282217 Score: 97
Period size: 24 Copynumber: 4.0 Consensus size: 24
282112 TTCTTCACGA
** *
282122 ATATGTTCGTAAATATGTTCGTTT
1 ATATGTTCACAAATATGTTCATTT
282146 ATATGTTCACAAA-AGTGTTCATTT
1 ATATGTTCACAAATA-TGTTCATTT
* *
282170 ATATGTTTACGAATATGTTCATTT
1 ATATGTTCACAAATATGTTCATTT
* * *
282194 A-GTGTTCACAAATATATTCGTTT
1 ATATGTTCACAAATATGTTCATTT
282217 A
1 A
282218 GTATTATTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
23 19 0.32
24 40 0.67
25 1 0.02
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (24 bp):
ATATGTTCACAAATATGTTCATTT
Found at i:282483 original size:24 final size:24
Alignment explanation
Indices: 282439--282484 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
282429 TGAACATAAA
*
282439 TAAACAAGTTGATGAACGAGCTCC
1 TAAACAAGTTGATAAACGAGCTCC
*
282463 TAAACAAGCTT-ATAAATGAGCT
1 TAAACAAG-TTGATAAACGAGCT
282485 TGTTCATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (24 bp):
TAAACAAGTTGATAAACGAGCTCC
Found at i:282766 original size:34 final size:34
Alignment explanation
Indices: 282710--282790 Score: 110
Period size: 34 Copynumber: 2.4 Consensus size: 34
282700 AAATAAATTT
* * * *
282710 ATTC-AATAGTAAATTTTTATATTGTAAAAGATC
1 ATTCTAATAATAAATCTTGATATTGTAAAAAATC
*
282743 ATTCTAATAATAAATCTTGATATTGTAAAAAATT
1 ATTCTAATAATAAATCTTGATATTGTAAAAAATC
282777 ATTCTAATAATAAA
1 ATTCTAATAATAAA
282791 AATCTTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 4 0.10
34 38 0.90
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (34 bp):
ATTCTAATAATAAATCTTGATATTGTAAAAAATC
Found at i:285210 original size:39 final size:39
Alignment explanation
Indices: 285156--285233 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
285146 ATGCTACTTT
285156 CACTGTCACAGCTTTCACTGGATTCAACAGTTTGTTTCC
1 CACTGTCACAGCTTTCACTGGATTCAACAGTTTGTTTCC
285195 CACTGTCACAGCTTTCACTGGATTCAACAGTTTGTTTCC
1 CACTGTCACAGCTTTCACTGGATTCAACAGTTTGTTTCC
285234 TTCCTCTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (39 bp):
CACTGTCACAGCTTTCACTGGATTCAACAGTTTGTTTCC
Found at i:289984 original size:14 final size:14
Alignment explanation
Indices: 289948--290010 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
289938 TATAAATTTT
289948 TTAA-ATAATTA-A
1 TTAATATAATTATA
* *
289960 TAAATATTAATTATT
1 TTAATA-TAATTATA
289975 TTAATATAA-TATA
1 TTAATATAATTATA
289988 TT-ATATATATTATA
1 TTAATATA-ATTATA
290002 TTATATATA
1 TTA-ATATA
290011 TTAAGTACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
12 8 0.20
13 7 0.17
14 15 0.38
15 5 0.12
16 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAATATAATTATA
Found at i:290011 original size:14 final size:14
Alignment explanation
Indices: 289969--290013 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
289959 ATAAATATTA
*
289969 ATTATTTTA-ATAT
1 ATTATATTATATAT
*
289982 AATATATTATATAT
1 ATTATATTATATAT
289996 ATTATATTATATAT
1 ATTATATTATATAT
290010 ATTA
1 ATTA
290014 AGTACAAGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 7 0.25
14 21 0.75
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTATATTATATAT
Found at i:290169 original size:22 final size:22
Alignment explanation
Indices: 290144--290187 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
290134 AAGACCACTC
290144 GGTTCATGCTTAAATAATATAT
1 GGTTCATGCTTAAATAATATAT
290166 GGTTCATGCTTAAATAATATAT
1 GGTTCATGCTTAAATAATATAT
290188 TTGAATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (22 bp):
GGTTCATGCTTAAATAATATAT
Found at i:296499 original size:60 final size:60
Alignment explanation
Indices: 296377--296500 Score: 149
Period size: 60 Copynumber: 2.1 Consensus size: 60
296367 ACGGGTAATC
* * * * * * *
296377 ATTTTGTAATTTTTAATAGTCAATGGATTTAATGAAGCAACACCCTATAGTTGGAGGACT
1 ATTTTATAATTTTTAATAGTCAATGAACTCAATAAAGCAACACCCTATAGGTGGAGCACT
* * * *
296437 ATTTTATAATTTTTAATAGTCGATGAACTCAATAAAGCAATACCCTATAGGTGGTGCTCT
1 ATTTTATAATTTTTAATAGTCAATGAACTCAATAAAGCAACACCCTATAGGTGGAGCACT
296497 ATTT
1 ATTT
296501 GTGTACTTTA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (60 bp):
ATTTTATAATTTTTAATAGTCAATGAACTCAATAAAGCAACACCCTATAGGTGGAGCACT
Found at i:298903 original size:3 final size:3
Alignment explanation
Indices: 298895--298978 Score: 152
Period size: 3 Copynumber: 28.3 Consensus size: 3
298885 TTTTACCCAC
298895 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
298942 ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
298979 AATATATATT
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 2 0.03
3 76 0.97
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:299005 original size:14 final size:15
Alignment explanation
Indices: 298977--299011 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
298967 TTATTATTAT
298977 TAAATATATATTAAA
1 TAAATATATATTAAA
*
298992 TAAATCTATA-TAAA
1 TAAATATATATTAAA
299006 TAAATA
1 TAAATA
299012 ATTACAGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:311804 original size:8 final size:7
Alignment explanation
Indices: 311787--311833 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
311777 ATTATGCTTG
311787 AAAAA-A
1 AAAAAGA
*
311793 AAAAGGA
1 AAAAAGA
311800 AAAAA-A
1 AAAAAGA
311806 GAAAAAGA
1 -AAAAAGA
311814 AAAAAGA
1 AAAAAGA
311821 AAGAAAGA
1 AA-AAAGA
311829 AAAAA
1 AAAAA
311834 AAAGGGGGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
6 5 0.14
7 22 0.63
8 8 0.23
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:311804 original size:9 final size:8
Alignment explanation
Indices: 311790--311834 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
311780 ATGCTTGAAA
311790 AAAAAAAGG
1 AAAAAAA-G
311799 AAAAAAAG
1 AAAAAAAG
311807 --AAAAAG
1 AAAAAAAG
311813 -AAAAAAG
1 AAAAAAAG
*
311820 AAAGAAAG
1 AAAAAAAG
311828 AAAAAAA
1 AAAAAAA
311835 AAGGGGGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 6 0.19
7 6 0.19
8 13 0.41
9 7 0.22
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:311810 original size:15 final size:14
Alignment explanation
Indices: 311787--311834 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
311777 ATTATGCTTG
*
311787 AAAAAA-AAAAGGA
1 AAAAAAGAAAAAGA
311800 AAAAAAGAAAAAG-
1 AAAAAAGAAAAAGA
311813 AAAAAAGAAAGAAAGA
1 AAAAAAG-AA-AAAGA
311829 AAAAAA
1 AAAAAA
311835 AAGGGGGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 13 0.43
14 7 0.23
15 4 0.13
16 6 0.20
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAGA
Found at i:311816 original size:21 final size:20
Alignment explanation
Indices: 311786--311836 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
311776 TATTATGCTT
*
311786 GAAAAAAAAAAGGAAAAAAA
1 GAAAAAAAAAAAGAAAAAAA
*
311806 GAAAAAGAAAAAAGAAAGAAA
1 GAAAAA-AAAAAAGAAAAAAA
311827 GAAAAAAAAA
1 GAAAAAAAAA
311837 GGGGGGGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (20 bp):
GAAAAAAAAAAAGAAAAAAA
Found at i:312174 original size:16 final size:16
Alignment explanation
Indices: 312148--312192 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
312138 TTTGAATACA
*
312148 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
312165 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
312180 ATTCAATTTATTT
1 ATTCAATTTATTT
312193 TTGGAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:313088 original size:83 final size:83
Alignment explanation
Indices: 312943--313653 Score: 1157
Period size: 83 Copynumber: 8.6 Consensus size: 83
312933 AAATATAATG
312943 TGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCAT
1 TGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCAT
313008 TGAATTTAGAAGATGAATT
65 TGAATTTAGAAGATGAATT
*
313027 TGCTCATAGCATCTTCTTGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATT
313092 GAATTTAGAAGATGAATT
66 GAATTTAGAAGATGAATT
* * *
313110 TGCTCATAGCATCTTCTTGAAGTGTTCTTTGAGTGATCTGATCTGGTTTGACAGAA-CAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATT
313174 GAATTTAGAAGATGAATT
66 GAATTTAGAAGATGAATT
* *
313192 TG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTGATCTGATCTGGTTTGACAGAA-CAATCAT
1 TGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCAT
313255 TGAATTTAGAAGATGAATT
65 TGAATTTAGAAGATGAATT
* *
313274 TGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAG-CAGAACCAATCAT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTAGACAGAACCAATCAT
313338 TGAATTTAGAAGATGAATT
65 TGAATTTAGAAGATGAATT
* *
313357 TGCTCATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATT
313422 GAATTTAGAAGATGAATT
66 GAATTTAGAAGATGAATT
* *
313440 TGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAG-CAGAACCAATCAT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTAGACAGAACCAATCAT
*
313504 TGAATTTGGAAGAAT-AATT
65 TGAATTTAGAAG-ATGAATT
* * *
313523 TGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCAT
1 TGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCAT
* *
313587 TGAATTTGGAAGATGAATG
65 TGAATTTAGAAGATGAATT
313606 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
313654 TGGTAAGAAC
Statistics
Matches: 595, Mismatches: 21, Indels: 23
0.93 0.03 0.04
Matches are distributed among these distances:
81 2 0.00
82 159 0.27
83 423 0.71
84 11 0.02
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (83 bp):
TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATT
GAATTTAGAAGATGAATT
Found at i:314502 original size:113 final size:113
Alignment explanation
Indices: 314307--315059 Score: 1055
Period size: 113 Copynumber: 6.6 Consensus size: 113
314297 ATTCAAATCT
* * * *
314307 ATCATTTGATGGATTGA-CATTTCAAGAGAAGGTTCATGATGAGAAGAACTCATCTGAAGAAAGA
1 ATCATTTGATGGA-TCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
314371 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTCTGCCT-AATTC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATTC
* * *
314419 TATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 -ATCATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
314484 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATTC
* * * *
314533 ATTAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* **
314598 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATTC
* * *
314646 ATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATC-ATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* **
314711 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGATTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATTC
* * *
314760 ATCATTTGATGGATCAACATTTCCAGAGAAGGTTCATAATTAGAAGAACTCATCTGAAGAATGAA
1 ATCATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
314825 GAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATTC
* * *
314873 ATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCATTTGATGGATCATCATTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* *
314937 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
62 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATTC
** * *
314989 ATCATTTGATGGATCATCATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-
1 ATCATTTGATGGATCATCATTTCCAG-AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
315053 AGAAGAA
65 AGAAGAA
315060 TTTATTCAAT
Statistics
Matches: 594, Mismatches: 37, Indels: 18
0.92 0.06 0.03
Matches are distributed among these distances:
112 5 0.01
113 356 0.60
114 126 0.21
115 2 0.00
116 86 0.14
117 17 0.03
118 2 0.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (113 bp):
ATCATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATTC
Found at i:314742 original size:227 final size:226
Alignment explanation
Indices: 314307--315059 Score: 1091
Period size: 227 Copynumber: 3.3 Consensus size: 226
314297 ATTCAAATCT
* * *
314307 ATCATTTGATGGATTGA-CATTTCAAGAGAAGGTTCATGATGAGAAGAACTCATCTGAAGAAAGA
1 ATCATTTGATGGA-TCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* * * *
314371 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTCTGCCT-AATTCTATCACTTGATGGATC
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTC-ATCAATTGATGGATC
*
314435 AGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
129 AACTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * * *
314500 GAGAAGAATTTGTTCAACCTTTTTCCTGAATTC
194 GAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
* * * * *
314533 ATTAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAAGAA
* *
314598 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCAAATTGATGGATTA
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATC-AATTGATGGATCA
*
314663 TCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
130 ACTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
314728 AGAAGAACTTGTTCAATCTTTTGATTGAATTC
195 AGAAGAACTTGTTCAATCTTTTGCTTGAATTC
* * *
314760 ATCATTTGATGGATCAACATTTCCAGAGAAGGTTCATAATTAGAAGAACTCATCTGAAGAATGAA
1 ATCATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAAGAA
* * * * *
314825 GAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGATGGATCAA
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAATTGATGGATCAA
* * *
314890 CATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATA
131 CTTTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATA
314954 ATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
192 ATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
** *
314989 ATCATTTGATGGATCATCATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-
1 ATCATTTGATGGATCATCATTTCCAG-AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
315053 AGAAGAA
65 AGAAGAA
315060 TTTATTCAAT
Statistics
Matches: 475, Mismatches: 44, Indels: 13
0.89 0.08 0.02
Matches are distributed among these distances:
225 5 0.01
226 131 0.28
227 211 0.44
228 1 0.00
229 93 0.20
230 34 0.07
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (226 bp):
ATCATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAAGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAATTGATGGATCAA
CTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAATCTTTTGCTTGAATTC
Found at i:314944 original size:340 final size:338
Alignment explanation
Indices: 314307--315059 Score: 1057
Period size: 340 Copynumber: 2.2 Consensus size: 338
314297 ATTCAAATCT
* * *
314307 ATCATTTGATGGATTGA-CATTTCAAGAGAAGGTTCATGATGAGAAGAACTCATCTGAAGAAAGA
1 ATCAATTGATGGATT-ATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* *
314371 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTCTGCCTAATTCTATCACTTGATGGATCA
65 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTCTGACTAATTCTATCACTTGATGGATCA
* *
314436 GCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
130 ACATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * * * *
314501 AGAAGAATTTGTTCAACCTTTTTCCTGAATTCATTAATTGATGGATTATCTTTTCCAGAGAAGGT
195 AGAAGAACTTGTTCAACCTTTTGCCTGAATTCATCAATTGATGGATCAACATTGCCAGAGAAGGT
*
314566 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAC
260 TCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
*
314631 CTTTT-TTCTGAATTC
324 CTTTTGCT-TGAATTC
* *
314646 ATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATC-AATTGATGGATTATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* * * * *
314711 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGATTGAATTC-ATCATTTGATGGATC
65 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTCTGACT-AATTCTATCACTTGATGGATC
* *
314775 AACATTTCCAGAGAAGGTTCATAATTAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAAT
129 AACATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * * *
314840 GAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGA
194 GAGAAGAACTTGTTCAACCTTTTGCCTGAATTCATCAATTGATGGATCAACATTGCCAGAGAAG-
314904 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
258 GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGT
*
314969 TCAATCTTTTGCTTGAATTC
319 TCAACCTTTTGCTTGAATTC
* * ** *
314989 ATCATTTGATGGATCATCATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-
1 ATCAATTGATGGATTATCATTTCCAG-AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
315053 AGAAGAA
65 AGAAGAA
315060 TTTATTCAAT
Statistics
Matches: 368, Mismatches: 37, Indels: 15
0.88 0.09 0.04
Matches are distributed among these distances:
339 7 0.02
340 232 0.63
341 5 0.01
342 26 0.07
343 97 0.26
344 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (338 bp):
ATCAATTGATGGATTATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAAGAA
GAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTCTGACTAATTCTATCACTTGATGGATCAA
CATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACCTTTTGCCTGAATTCATCAATTGATGGATCAACATTGCCAGAGAAGGTT
CATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
TTTGCTTGAATTC
Found at i:315205 original size:3 final size:3
Alignment explanation
Indices: 315197--315314 Score: 209
Period size: 3 Copynumber: 39.3 Consensus size: 3
315187 TTTTACCCAC
315197 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
315245 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATC ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
315293 ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
315315 AATATATATT
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 113 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:315341 original size:14 final size:15
Alignment explanation
Indices: 315313--315347 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
315303 TTATTATTAT
315313 TAAATATATATTAAA
1 TAAATATATATTAAA
*
315328 TAAATCTATA-TAAA
1 TAAATATATATTAAA
315342 TAAATA
1 TAAATA
315348 ATTACAGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:315822 original size:19 final size:19
Alignment explanation
Indices: 315798--315835 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
315788 TAAAGAACCG
315798 GAGAAAGAAAAAAAAAACA
1 GAGAAAGAAAAAAAAAACA
315817 GAGAAAGAAAAAAAAAACA
1 GAGAAAGAAAAAAAAAACA
315836 ACTACTAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (19 bp):
GAGAAAGAAAAAAAAAACA
Found at i:318307 original size:28 final size:28
Alignment explanation
Indices: 318276--318332 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
318266 GTATATTATT
318276 TTTTAAAAACTATATATA-ATATATACTA
1 TTTTAAAAACTATATATATA-ATATACTA
* * *
318304 TTTTTAAAATTATTTATATAATATACTA
1 TTTTAAAAACTATATATATAATATACTA
318332 T
1 T
318333 ATATATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (28 bp):
TTTTAAAAACTATATATATAATATACTA
Found at i:320696 original size:2 final size:2
Alignment explanation
Indices: 320689--320778 Score: 153
Period size: 2 Copynumber: 45.0 Consensus size: 2
320679 GAACAAGATG
320689 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
** *
320731 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GG GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
320773 AT AT AT
1 AT AT AT
320779 GGGGGACTCA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:321904 original size:31 final size:30
Alignment explanation
Indices: 321864--321931 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
321854 GGAAATTATT
*
321864 AAATTTTAATATGACCCTTAAATTTTAGATA
1 AAATATTAATATGA-CCTTAAATTTTAGATA
* **
321895 AAATATTAATTTGATTTTAAATTTTAGATA
1 AAATATTAATATGACCTTAAATTTTAGATA
321925 AAATATT
1 AAATATT
321932 GATTTAATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 21 0.64
31 12 0.36
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (30 bp):
AAATATTAATATGACCTTAAATTTTAGATA
Found at i:321915 original size:30 final size:31
Alignment explanation
Indices: 321881--321969 Score: 126
Period size: 30 Copynumber: 2.9 Consensus size: 31
321871 AATATGACCC
*
321881 TTAAATTTTAGATAAAATATTAATTTGAT-T
1 TTAAATTTTAGATAAAATATTAATTTAATCT
*
321911 TTAAATTTTAGATAAAATATTGATTTAATCT
1 TTAAATTTTAGATAAAATATTAATTTAATCT
* **
321942 TTGAACCTTAGATAAAATATTAATTTAA
1 TTAAATTTTAGATAAAATATTAATTTAA
321970 CCTTCCAATC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 27 0.52
31 25 0.48
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (31 bp):
TTAAATTTTAGATAAAATATTAATTTAATCT
Found at i:321956 original size:31 final size:30
Alignment explanation
Indices: 321888--321969 Score: 110
Period size: 31 Copynumber: 2.7 Consensus size: 30
321878 CCCTTAAATT
* **
321888 TTAGATAAAATATTAATTTGATTTTAAATT
1 TTAGATAAAATATTAATTTAATTTTAAACC
* *
321918 TTAGATAAAATATTGATTTAATCTTTGAACC
1 TTAGATAAAATATTAATTTAAT-TTTAAACC
321949 TTAGATAAAATATTAATTTAA
1 TTAGATAAAATATTAATTTAA
321970 CCTTCCAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
30 20 0.44
31 25 0.56
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (30 bp):
TTAGATAAAATATTAATTTAATTTTAAACC
Found at i:326698 original size:15 final size:16
Alignment explanation
Indices: 326675--326707 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
326665 TAAATTTAAA
326675 AATATTAAAATATTTT
1 AATATTAAAATATTTT
326691 AATA-TAAAATATTTT
1 AATATTAAAATATTTT
326706 AA
1 AA
326708 ATTTTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATTAAAATATTTT
Found at i:328475 original size:59 final size:59
Alignment explanation
Indices: 328379--328490 Score: 199
Period size: 59 Copynumber: 1.9 Consensus size: 59
328369 AACTATGAAT
*
328379 CTCATTCTAAATTGGTCTCATAACTTTTGAATCTTCCAATTTTCATCCCAAATTGTGACC
1 CTCATTCTAAATTGGTCTCACAACTTTTGAATCTTCCAA-TTTCATCCCAAATTGTGACC
328439 CTCATTCTAAATTGGTC-CACAACTTTTGAATCTTCCAATTTCATCCCAAATT
1 CTCATTCTAAATTGGTCTCACAACTTTTGAATCTTCCAATTTCATCCCAAATT
328491 CATCCAAATA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
58 14 0.27
59 20 0.39
60 17 0.33
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.39
Consensus pattern (59 bp):
CTCATTCTAAATTGGTCTCACAACTTTTGAATCTTCCAATTTCATCCCAAATTGTGACC
Found at i:333726 original size:11 final size:11
Alignment explanation
Indices: 333710--333741 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
333700 GGGATGGCAA
333710 CGGGCCGGGTT
1 CGGGCCGGGTT
333721 CGGGCCGGGTT
1 CGGGCCGGGTT
333732 CGGGCCGGGT
1 CGGGCCGGGT
333742 ATTGGTCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.28, G:0.56, T:0.16
Consensus pattern (11 bp):
CGGGCCGGGTT
Found at i:333909 original size:12 final size:11
Alignment explanation
Indices: 333894--333944 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 11
333884 TATTTAAACG
333894 GGTATTGGGCC
1 GGTATTGGGCC
*
333905 AGGTATTGGGTC
1 -GGTATTGGGCC
333917 GGTATTGGGCC
1 GGTATTGGGCC
* *
333928 GAGAATCGGGCC
1 G-GTATTGGGCC
333940 GGTAT
1 GGTAT
333945 ATATATATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
11 14 0.42
12 19 0.58
ACGTcount: A:0.16, C:0.16, G:0.43, T:0.25
Consensus pattern (11 bp):
GGTATTGGGCC
Found at i:333922 original size:11 final size:12
Alignment explanation
Indices: 333894--333927 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
333884 TATTTAAACG
333894 GGTATTGGGCCA
1 GGTATTGGGCCA
*
333906 GGTATTGGGTC-
1 GGTATTGGGCCA
333917 GGTATTGGGCC
1 GGTATTGGGCC
333928 GAGAATCGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.12, C:0.15, G:0.44, T:0.29
Consensus pattern (12 bp):
GGTATTGGGCCA
Found at i:333942 original size:23 final size:23
Alignment explanation
Indices: 333894--333944 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
333884 TATTTAAACG
* * *
333894 GGTATTGGGCCAGGTATTGGGTC
1 GGTATTGGGCCAGGAATCGGGCC
333917 GGTATTGGGCC-GAGAATCGGGCC
1 GGTATTGGGCCAG-GAATCGGGCC
333940 GGTAT
1 GGTAT
333945 ATATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.16, C:0.16, G:0.43, T:0.25
Consensus pattern (23 bp):
GGTATTGGGCCAGGAATCGGGCC
Found at i:334006 original size:24 final size:24
Alignment explanation
Indices: 333943--334006 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
333933 TCGGGCCGGT
*
333943 ATATATATATATATATTTAAATTAA
1 ATATATAGATAT-TATTTAAATTAA
* *
333968 ATATATAGTTTTTATTTAAATTAA
1 ATATATAGATATTATTTAAATTAA
*
333992 ATTTATTA-ATATTAT
1 ATATA-TAGATATTAT
334007 ATATATATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 21 0.66
25 11 0.34
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
ATATATAGATATTATTTAAATTAA
Found at i:334068 original size:13 final size:12
Alignment explanation
Indices: 334037--334073 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
334027 TTTTAATATT
*
334037 TATCGGGTCGGG
1 TATCGGGGCGGG
334049 TATCGGGGCGGG
1 TATCGGGGCGGG
334061 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
334074 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:339860 original size:18 final size:18
Alignment explanation
Indices: 339839--339877 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
339829 AATAAAGCAA
339839 CATCCTGTAATAGGAGAT
1 CATCCTGTAATAGGAGAT
339857 CATCCTGTAATAGGAGAT
1 CATCCTGTAATAGGAGAT
339875 CAT
1 CAT
339878 TTGTGTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (18 bp):
CATCCTGTAATAGGAGAT
Found at i:340459 original size:31 final size:32
Alignment explanation
Indices: 340415--340475 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
340405 TACATTAAAT
340415 TATATATTTAGTATTTAAATTGCTAATTTTGA
1 TATATATTTAGTATTTAAATTGCTAATTTTGA
**
340447 TATAT-TTTAGTATTTAAATTTTTAATTTT
1 TATATATTTAGTATTTAAATTGCTAATTTT
340476 TTTAAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (32 bp):
TATATATTTAGTATTTAAATTGCTAATTTTGA
Found at i:347689 original size:3 final size:3
Alignment explanation
Indices: 347681--347802 Score: 181
Period size: 3 Copynumber: 40.3 Consensus size: 3
347671 TTTTTATCCA
* * *
347681 TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT GAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
347729 TAT TAT TAT TAT TAT CAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
347777 TAT TAT TAG TATT TAT TAT TAT TAT T
1 TAT TAT TAT TA-T TAT TAT TAT TAT T
347803 TAATAAATAA
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
3 104 0.98
4 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:348527 original size:13 final size:13
Alignment explanation
Indices: 348509--348537 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
348499 ACCACCGTTA
348509 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
348522 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
348535 CGG
1 CGG
348538 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:349117 original size:19 final size:19
Alignment explanation
Indices: 349079--349114 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
349069 CAATTTAGTC
349079 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
349098 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
349115 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:349901 original size:17 final size:17
Alignment explanation
Indices: 349879--349920 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
349869 TTCAAATTTT
349879 TTTTTAT-ATATTTATTA
1 TTTTTATAATATTTA-TA
349896 TTTTTATAATATTTATA
1 TTTTTATAATATTTATA
349913 TGTTTTAT
1 T-TTTTAT
349921 TTGCAAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTTATAATATTTATA
Found at i:360533 original size:7 final size:7
Alignment explanation
Indices: 360521--360573 Score: 65
Period size: 7 Copynumber: 7.7 Consensus size: 7
360511 GAAAAGAAAG
360521 AAAAGAA
1 AAAAGAA
360528 AAAAGAA
1 AAAAGAA
360535 AAAA-AA
1 AAAAGAA
*
360541 AATAGAA
1 AAAAGAA
*
360548 AATAGAA
1 AAAAGAA
360555 AAAAGAGA
1 AAAAGA-A
360563 AAAA-AA
1 AAAAGAA
360569 AAAAG
1 AAAAG
360574 GAGGGTCAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
6 10 0.24
7 26 0.63
8 5 0.12
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (7 bp):
AAAAGAA
Found at i:360549 original size:20 final size:20
Alignment explanation
Indices: 360509--360573 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 20
360499 ATTATGCTTG
360509 AAGAAAAGAAAGAAAAGAAAA
1 AAGAAAA-AAAGAAAAGAAAA
360530 AAGAAAAAAA-AAATAGAAAA
1 AAGAAAAAAAGAAA-AGAAAA
* *
360550 TAGAAAAAAGAGAAAAAAAAA
1 AAGAAAAAA-AGAAAAGAAAA
360571 AAG
1 AAG
360574 GAGGGTCAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
19 3 0.08
20 17 0.45
21 15 0.39
22 3 0.08
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (20 bp):
AAGAAAAAAAGAAAAGAAAA
Found at i:361734 original size:52 final size:51
Alignment explanation
Indices: 361691--362237 Score: 992
Period size: 52 Copynumber: 10.7 Consensus size: 51
361681 GACTCAATAA
361691 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
*
361741 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTGAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
*
361792 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAAAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
361843 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
361893 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
*
361945 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
*
361997 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
362049 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
*
362099 CATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTAGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
362151 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
362202 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
362238 ATTGGACAGA
Statistics
Matches: 485, Mismatches: 7, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
50 133 0.27
51 151 0.31
52 201 0.41
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (51 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
Found at i:361868 original size:102 final size:102
Alignment explanation
Indices: 361691--362256 Score: 987
Period size: 102 Copynumber: 5.5 Consensus size: 102
361681 GACTCAATAA
361691 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TAGA-AGAACATAGCATCTTCTGGAAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
361754 TGTTCTTTGAGTTATCTGATCTGGTGAGAAGAACATAG
66 TGTTCTTTGAGTTATCTGATCTGGT-AGAAGAACATAG
*
361792 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AAAACATAGCATCTTCTGGAAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
*
361856 TGTTCTTTGAGTTATCTGATCTGGTTGAAGAACATAG
66 TGTTCTTTGAGTTATCTGATCTGGTAGAAGAACATAG
361893 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
*
361958 TGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
66 TGTTCTTTGAGTTATCTGATCTGG-TAGA-AGAACATAG
*
361997 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
*
362062 TGTTCTTTGAGTTATCTGATCTGGTTGAAGAACATAG
66 TGTTCTTTGAGTTATCTGATCTGGTAGAAGAACATAG
*
362099 CATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
362164 TGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
66 TGTTCTTTGAGTTATCTGATCTGG-TAGAAGAACATAG
* *
362202 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA-AGCAT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAA-CATAGCAT
362257 TTAATTTGGA
Statistics
Matches: 447, Mismatches: 12, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
101 90 0.20
102 191 0.43
103 67 0.15
104 99 0.22
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (102 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
TGTTCTTTGAGTTATCTGATCTGGTAGAAGAACATAG
Found at i:362089 original size:206 final size:205
Alignment explanation
Indices: 361691--362256 Score: 1025
Period size: 206 Copynumber: 2.8 Consensus size: 205
361681 GACTCAATAA
361691 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TAGA-AGAACATAGCATCTTCTGGAAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
361754 TGTTCTTTGAGTTATCTGATCTGG-TGAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTT
66 TGTTCTTTGAGTTATCTGATCTGGTTG-GAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTT
* *
361818 ATCTGATCTGGTTAGA-AAAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
130 ATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
361882 GAAGAACATAG
195 GAAGAACATAG
361893 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
361958 TGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTT
66 TGTTCTTTGAGTTATCTGATCTGGTTGGA-AGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTT
362023 ATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
130 ATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
362088 GAAGAACATAG
195 GAAGAACATAG
*
362099 CATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
*
362164 TGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
66 TGTTCTTTGAGTTATCTGATCTGGTTGGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
*
362229 TCTGATCTGATTGGACAGAATCA-AGCAT
131 TCTGATCTGGTTGGACAGAA-CATAGCAT
362257 TTAATTTGGA
Statistics
Matches: 353, Mismatches: 5, Indels: 9
0.96 0.01 0.02
Matches are distributed among these distances:
202 37 0.10
203 4 0.01
204 48 0.14
205 112 0.32
206 152 0.43
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (205 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAG
TGTTCTTTGAGTTATCTGATCTGGTTGGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
TCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTG
AAGAACATAG
Found at i:363440 original size:113 final size:114
Alignment explanation
Indices: 362874--363541 Score: 1216
Period size: 114 Copynumber: 5.9 Consensus size: 114
362864 TTAGCAAAGA
362874 CTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
1 CTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
362939 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
362988 CTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
1 CTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
363053 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
363102 CTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
1 CTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
363167 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
*
363216 CTTGAATTCATCACTTGATAGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
1 CTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
363281 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
*
363330 CTTGAATTCATCACTTGATGGATCA-TCTTTTCCCGAGAAAGTTCATAATGAGAAGAACTCATCT
1 CTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
*
363394 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
* * * * * *
363443 CGTGAATTCATCATTTGATGGATCA-ACATTACCAG-GTAAAGTTCATAATGAGAAGAACTCATT
1 CTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATC
*
363506 TGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACT
65 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
363542 CATCAAGAGC
Statistics
Matches: 540, Mismatches: 13, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
112 1 0.00
113 174 0.32
114 365 0.68
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (114 bp):
CTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
Found at i:363795 original size:3 final size:3
Alignment explanation
Indices: 363787--363917 Score: 199
Period size: 3 Copynumber: 43.3 Consensus size: 3
363777 TTTTTATCCA
* * *
363787 TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT GAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
363835 TAT TAT TAT TAT TAT CAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
363883 TAT TAT TAT TAT TAT TAG TATT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT T
363918 TAATAAATAA
Statistics
Matches: 115, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
3 113 0.98
4 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:365220 original size:19 final size:19
Alignment explanation
Indices: 365182--365217 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
365172 CAATTTAGTC
365182 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
365201 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
365218 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:370668 original size:20 final size:20
Alignment explanation
Indices: 370620--370716 Score: 121
Period size: 20 Copynumber: 5.0 Consensus size: 20
370610 CACTGAATAT
*
370620 TTGTCCCGAATGACCACT-A
1 TTGTCCCGAAGGACCACTGA
370639 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
370658 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
* *
370677 -TGTCCCAAAGGACCACTGT
1 TTGTCCCGAAGGACCACTGA
370696 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
370716 T
1 T
370717 CATCCCTCGA
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
18 30 0.46
19 2 0.03
20 33 0.51
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.23
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:370674 original size:38 final size:38
Alignment explanation
Indices: 370620--370713 Score: 136
Period size: 38 Copynumber: 2.5 Consensus size: 38
370610 CACTGAATAT
*
370620 TTGTCCCGAATG-ACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAA-GAACCACTATGTCCCAAAGGACCACTGA
* *
370658 TTGTTCCGAAGAACCACTATGTCCCAAAGGACCACTGT
1 TTGTCCCGAAGAACCACTATGTCCCAAAGGACCACTGA
*
370696 TTGTCCCGAAGGACCACT
1 TTGTCCCGAAGAACCACT
370714 GATCATCCCT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
37 1 0.02
38 49 0.98
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCAAAGGACCACTGA
Found at i:371187 original size:2 final size:2
Alignment explanation
Indices: 371141--371171 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
371131 ATGTAGTTCA
371141 AT AT CAT 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
371172 TTCCTCTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:371831 original size:20 final size:20
Alignment explanation
Indices: 371806--371843 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
371796 TTTCCCTTGA
371806 AGTGCATAGATACATTCTAC
1 AGTGCATAGATACATTCTAC
* *
371826 AGTGCATTGATGCATTCT
1 AGTGCATAGATACATTCT
371844 TTAACATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (20 bp):
AGTGCATAGATACATTCTAC
Found at i:371938 original size:64 final size:63
Alignment explanation
Indices: 371851--372007 Score: 163
Period size: 64 Copynumber: 2.4 Consensus size: 63
371841 TCTTTAACAT
* * ** *
371851 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTTATTTT-AAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAAGGA
* * **
371914 GATGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTAAAGGA
1 G-TGCATCGATGCACTCC-TATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAAGGA
* * *
371979 GTGCATCGATACACTTCATGTGCATCGAT
1 GTGCATCGATGCAC-TCCTATGCATCGAT
372008 GCACCTTCAA
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
63 3 0.04
64 68 0.87
65 7 0.09
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAAGGA
Found at i:379410 original size:45 final size:45
Alignment explanation
Indices: 379346--379446 Score: 202
Period size: 45 Copynumber: 2.2 Consensus size: 45
379336 CTTGGACTTG
379346 TTGAATGTTTCAAGTTGTTAAAGAAGTAAGGTAACCCAACCCACA
1 TTGAATGTTTCAAGTTGTTAAAGAAGTAAGGTAACCCAACCCACA
379391 TTGAATGTTTCAAGTTGTTAAAGAAGTAAGGTAACCCAACCCACA
1 TTGAATGTTTCAAGTTGTTAAAGAAGTAAGGTAACCCAACCCACA
379436 TTGAATGTTTC
1 TTGAATGTTTC
379447 CTAAGGGGCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Consensus pattern (45 bp):
TTGAATGTTTCAAGTTGTTAAAGAAGTAAGGTAACCCAACCCACA
Found at i:387919 original size:21 final size:18
Alignment explanation
Indices: 387893--387931 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 18
387883 TTCAAAATAT
387893 ATTATAATTATAATATTATTA
1 ATTAT-ATT-TAATA-TATTA
387914 ATTATATTTAATATATTA
1 ATTATATTTAATATATTA
387932 TATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 3 0.17
21 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTATATTTAATATATTA
Found at i:388007 original size:27 final size:25
Alignment explanation
Indices: 387957--388010 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
387947 TTATTTCAAA
387957 ATTTACAAAATATATTATAATTATT
1 ATTTACAAAATATATTATAATTATT
* *
387982 ATTTATAAAATATCTATTTTAATTATT
1 ATTTACAAAATA--TATTATAATTATT
388009 AT
1 AT
388011 ATTTATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 11 0.44
27 14 0.56
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTACAAAATATATTATAATTATT
Found at i:388033 original size:17 final size:16
Alignment explanation
Indices: 388013--388056 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 16
388003 ATTATTATAT
388013 TTATTATTATATTTCAA
1 TTATTATTATATTT-AA
*
388030 TTATTTATTGTATTTAA
1 TTA-TTATTATATTTAA
388047 TTATTATTAT
1 TTATTATTAT
388057 TATTATTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.25
17 8 0.33
18 10 0.42
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (16 bp):
TTATTATTATATTTAA
Found at i:388051 original size:26 final size:26
Alignment explanation
Indices: 387996--388051 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
387986 ATAAAATATC
* *
387996 TATTTTAATTATTATATTTATTATTA
1 TATTTCAATTATTATATTTATTAATA
388022 TATTTCAATTATT-TATTGTATTTAAT-
1 TATTTCAATTATTATATT-TA-TTAATA
388048 TATT
1 TATT
388052 ATTATTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 4 0.15
26 18 0.69
27 4 0.15
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (26 bp):
TATTTCAATTATTATATTTATTAATA
Found at i:388725 original size:23 final size:24
Alignment explanation
Indices: 388698--388746 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
388688 TCGAGACTGC
388698 CATATAGAAT-TGCACCAAAGTGA
1 CATATAGAATATGCACCAAAGTGA
*
388721 CATATAGAATATGCACCGAAGTGA
1 CATATAGAATATGCACCAAAGTGA
388745 CA
1 CA
388747 CGTAGAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (24 bp):
CATATAGAATATGCACCAAAGTGA
Found at i:388752 original size:24 final size:23
Alignment explanation
Indices: 388701--388753 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
388691 AGACTGCCAT
*
388701 ATAGAATTGCACCAAAGTGACAT
1 ATAGAATTGCACCAAAGTGACAC
*
388724 ATAGAATATGCACCGAAGTGACAC
1 ATAGAAT-TGCACCAAAGTGACAC
*
388748 GTAGAA
1 ATAGAA
388754 ATGTCCCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (23 bp):
ATAGAATTGCACCAAAGTGACAC
Found at i:388775 original size:23 final size:23
Alignment explanation
Indices: 388747--388845 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
388737 CGAAGTGACA
* *
388747 CGTAGAAATGTCCCGAAGAACCA
1 CGTAGAAATGTCCCGAAGGACCG
* *
388770 CATAGATATGTCCCGAAGGACCG
1 CGTAGAAATGTCCCGAAGGACCG
388793 CGTAGAAATGTCCCGAAGGACCG
1 CGTAGAAATGTCCCGAAGGACCG
*
388816 CGTAGAAATGTCCCGAAGGATCG
1 CGTAGAAATGTCCCGAAGGACCG
388839 CGTAGAA
1 CGTAGAA
388846 CCCTCGACTC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.33, C:0.24, G:0.27, T:0.15
Consensus pattern (23 bp):
CGTAGAAATGTCCCGAAGGACCG
Found at i:390315 original size:3 final size:3
Alignment explanation
Indices: 390307--390379 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
390297 GGATGTTACA
390307 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
390355 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
390380 CTACTACTAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:395166 original size:41 final size:40
Alignment explanation
Indices: 395092--395368 Score: 187
Period size: 40 Copynumber: 6.8 Consensus size: 40
395082 TAGTGGCATT
* * **
395092 TTTAGCGGCGTTTTT-TGAACAAATGCCGGTAAATACTCGCAC
1 TTTAGCGGCGTTTTTAT--ACAAACGCCGCTAAATACT-ATAC
* * *
395134 TTTAGCGGTGTTTTTATATAAACGCCGCTAAATACTATAA
1 TTTAGCGGCGTTTTTATACAAACGCCGCTAAATACTATAC
* * * * * *
395174 TTTAGTGACGTTTTCATATAAACGCGGCTAATTACTATAC
1 TTTAGCGGCGTTTTTATACAAACGCCGCTAAATACTATAC
* * *
395214 TTTAGGGGCGTTTTTGTACAAACGCCGCTAAAAACTCATAC
1 TTTAGCGGCGTTTTTATACAAACGCCGCTAAATACT-ATAC
* * * ** **
395255 TCTAGCGGCGTTTTAAGCACAAACGCCGCTAAAGGCCCCTAC
1 TTTAGCGGCGTTTTTA-TACAAACGCCGCTAAA-TACTATAC
* ** * * * *
395297 ATTAGTAGCGTTTTCATATAAACGCCACTAATTACTATAC
1 TTTAGCGGCGTTTTTATACAAACGCCGCTAAATACTATAC
* * * *
395337 TTTAGCAGCGTTTTTGTGCAAACGCCTCTAAA
1 TTTAGCGGCGTTTTTATACAAACGCCGCTAAA
395369 AGCTCTTATT
Statistics
Matches: 179, Mismatches: 52, Indels: 10
0.74 0.22 0.04
Matches are distributed among these distances:
40 90 0.50
41 44 0.25
42 43 0.24
43 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTATACAAACGCCGCTAAATACTATAC
Found at i:398470 original size:43 final size:43
Alignment explanation
Indices: 398405--398665 Score: 229
Period size: 43 Copynumber: 6.1 Consensus size: 43
398395 AATACACTGC
* * *
398405 AATACACAGTTAATAACGGCGTTTGTAAAGAAAAATGTCGCTA
1 AATACACAGTCAATAACGGCGTTTGTAAAGAAAAACGCCGCTA
* ** ** *
398448 AATGCACAGTCAATAGTGGCGTTTGT--CTACAAACGCCGCTA
1 AATACACAGTCAATAACGGCGTTTGTAAAGAAAAACGCCGCTA
* * * * *
398489 AATACACAGTCAATAGCGGCATTTATAAAGACAAACGCCGTTA
1 AATACACAGTCAATAACGGCGTTTGTAAAGAAAAACGCCGCTA
* * *
398532 AATACATAGTTAATAACGGCGTTTGTAAAGAAAAATGCCGCTA
1 AATACACAGTCAATAACGGCGTTTGTAAAGAAAAACGCCGCTA
* * **** * *
398575 AATGCACAATCAATAACGGCGTTTGTCTTTACAAACACCGCTA
1 AATACACAGTCAATAACGGCGTTTGTAAAGAAAAACGCCGCTA
* * * ** *
398618 AATACATAGTCAATAGCGGCCTTTAAAAAGACAAACGCCGCTA
1 AATACACAGTCAATAACGGCGTTTGTAAAGAAAAACGCCGCTA
398661 AATAC
1 AATAC
398666 CAATACCTAT
Statistics
Matches: 169, Mismatches: 47, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
41 32 0.19
43 137 0.81
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.23
Consensus pattern (43 bp):
AATACACAGTCAATAACGGCGTTTGTAAAGAAAAACGCCGCTA
Found at i:398697 original size:129 final size:127
Alignment explanation
Indices: 398415--398706 Score: 372
Period size: 129 Copynumber: 2.3 Consensus size: 127
398405 AATACACAGT
* * * **
398415 TAATAACGGCGTTTGTAAAGAAAAATGTCGCTAAATGCACAGTCAATAGTGGCGTTTGTCTACAA
1 TAATAACGGCGTTTGTAAACAAAAATGCCGCTAAATGCACAATCAATAACGGCGTTTGTCTACAA
* * * **
398480 ACGCCGCTAAATACACAGTCAATAGCGGCATTTATAAAGACAAACGCCGTTAAATACATAGT
66 ACACCGCTAAATACACAGTCAATAGCGGCATTTAAAAAGACAAACGCCGCTAAATACATACC
*
398542 TAATAACGGCGTTTGTAAAGAAAAATGCCGCTAAATGCACAATCAATAACGGCGTTTGTCTTTAC
1 TAATAACGGCGTTTGTAAACAAAAATGCCGCTAAATGCACAATCAATAACGGCGTTTGTC--TAC
* *
398607 AAACACCGCTAAATACATAGTCAATAGCGGCCTTTAAAAAGACAAACGCCGCTAAATACCAATAC
64 AAACACCGCTAAATACACAGTCAATAGCGGCATTTAAAAAGACAAACGCCGCTAAATA-C-ATAC
398672 C
127 C
** ** *
398673 T-ATTGCGGCGTTTG-GCACACAAATGCCGCTAAAT
1 TAATAACGGCGTTTGTAAACAAAAATGCCGCTAAAT
398707 ATCAATACCT
Statistics
Matches: 144, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
127 56 0.39
129 72 0.50
130 12 0.08
131 4 0.03
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (127 bp):
TAATAACGGCGTTTGTAAACAAAAATGCCGCTAAATGCACAATCAATAACGGCGTTTGTCTACAA
ACACCGCTAAATACACAGTCAATAGCGGCATTTAAAAAGACAAACGCCGCTAAATACATACC
Found at i:406619 original size:30 final size:29
Alignment explanation
Indices: 406562--406619 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
406552 GTGGATGAAC
*
406562 TTGAACTTACAAAATTTCGAGGGACGAAT
1 TTGAACTTACAAAATTTCAAGGGACGAAT
* *
406591 TTGAACTTATAAAATTTTAAGAGGACGAA
1 TTGAACTTACAAAATTTCAAG-GGACGAA
406620 AACAGATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.29
Consensus pattern (29 bp):
TTGAACTTACAAAATTTCAAGGGACGAAT
Found at i:408302 original size:30 final size:31
Alignment explanation
Indices: 408268--408352 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 31
408258 CATAACGTTT
408268 ACTTTTTGCTTCATTTTAGT-CCCC-TTGTTA
1 ACTTTTTG-TTCATTTTAGTACCCCGTTGTTA
408298 ACTTTTTGTTCCATTTTAGTACCCCGTTGTTA
1 ACTTTTTGTT-CATTTTAGTACCCCGTTGTTA
*
408330 AATTTTTGTTTCATTTTAGTACC
1 ACTTTTTG-TTCATTTTAGTACC
408353 TCAATTTTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
29 2 0.04
30 17 0.34
31 4 0.08
32 25 0.50
33 2 0.04
ACGTcount: A:0.16, C:0.20, G:0.11, T:0.53
Consensus pattern (31 bp):
ACTTTTTGTTCATTTTAGTACCCCGTTGTTA
Found at i:413412 original size:26 final size:27
Alignment explanation
Indices: 413353--413412 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 27
413343 CATAAGACCT
413353 TATAATACCATTAATGCTTATTATGAAA
1 TATAATACCATTAATGCTTATTAT-AAA
*
413381 TCATAATACTATTAATGCTTATTAT-AA
1 T-ATAATACCATTAATGCTTATTATAAA
413408 TATAA
1 TATAA
413413 AATTTATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 4 0.13
27 3 0.10
28 1 0.03
29 22 0.73
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (27 bp):
TATAATACCATTAATGCTTATTATAAA
Found at i:415075 original size:16 final size:17
Alignment explanation
Indices: 415041--415076 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
415031 TAAAACATTA
415041 ATATTTAAAATATAATT
1 ATATTTAAAATATAATT
*
415058 ATATTTAAGATA-AATT
1 ATATTTAAAATATAATT
415074 ATA
1 ATA
415077 CCCGTGATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATATTTAAAATATAATT
Found at i:415886 original size:3 final size:3
Alignment explanation
Indices: 415874--415935 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
415864 CTACGAAAAC
*
415874 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
415921 AAT -TT ATAT ATT ATT
1 ATT ATT AT-T ATT ATT
415936 TTGCAGTCAC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
2 3 0.06
3 46 0.88
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:417056 original size:8 final size:8
Alignment explanation
Indices: 417043--417080 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
417033 ATAAAGGTCC
417043 TTTTTATT
1 TTTTTATT
417051 TTTTTA-T
1 TTTTTATT
417058 TTTTTATT
1 TTTTTATT
*
417066 ATTTTTCTT
1 -TTTTTATT
417075 TTTTTA
1 TTTTTA
417081 CTAACTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 7 0.27
8 12 0.46
9 7 0.27
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTATT
Found at i:420848 original size:65 final size:66
Alignment explanation
Indices: 420698--420856 Score: 223
Period size: 65 Copynumber: 2.4 Consensus size: 66
420688 CTTTTAGAGT
* * *
420698 CAATTTCAACTTCACA-ACGAAGGATATTCAATTCAAAGCTCAACTTCACAACGAATGAGCCATC
1 CAATTTCAACTTCA-AGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCAACC
*
420762 TA
65 CA
* * *
420764 CAATTTCAACTTCACGACGAAGGATATCCAATTCAATGCTTAAC-TCACAACGAATGAGCAACCC
1 CAATTTCAACTTCAAGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCAACCC
420828 A
66 A
*
420829 CGATTTCAACTTCAAGACGAAGGATATC
1 CAATTTCAACTTCAAGACGAAGGATATC
420857 GTGCCCACAA
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
65 44 0.53
66 39 0.47
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (66 bp):
CAATTTCAACTTCAAGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCAACCC
A
Found at i:421253 original size:65 final size:63
Alignment explanation
Indices: 421143--421315 Score: 235
Period size: 65 Copynumber: 2.7 Consensus size: 63
421133 GTAGCAATAC
* *
421143 AACTCGAGATTGGATTTCAACTTCACAATGAAGGATATCCAACTCAAAACCAATTTGGTGAAACT
1 AACTC-AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGT-AAAAT
* *
421208 TACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATTTGGTAAAAT
1 AACTC-AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTAAAAT
* * *
421272 AATTC---TTAGATTTCAACTTCACAACGAAGGATATCCAATTCAAA
1 AACTCAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAA
421316 GATCAACTTC
Statistics
Matches: 98, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
60 36 0.37
64 7 0.07
65 55 0.56
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.27
Consensus pattern (63 bp):
AACTCAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTAAAAT
Found at i:421602 original size:86 final size:86
Alignment explanation
Indices: 421451--421658 Score: 296
Period size: 86 Copynumber: 2.4 Consensus size: 86
421441 CCCAGTGCAT
* * *
421451 CATAACTCAAGGCGAGAAGGGTTATTTGTCATC-AAAGACCTTCGATTTCGATTACATTCAACTC
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGATTTCGATTACATTCAACTC
421515 AAAGGCAC-ATCAAATTTACAG
66 AAAGGC-CTATCAAATTTACAG
* * *
421536 CATAGCTCAAGGCGAGAAGGGTTATCTGTTAACAAAAGACTTTCGAGTTT-GATTACATTCAGCT
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGA-TTTCGATTACATTCAACT
421600 CAAAGGCCTATCAAATTTACAG
65 CAAAGGCCTATCAAATTTACAG
* * *
421622 TATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAA
421659 AATGTCGAGC
Statistics
Matches: 110, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
85 30 0.27
86 77 0.70
87 3 0.03
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (86 bp):
CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGATTTCGATTACATTCAACTC
AAAGGCCTATCAAATTTACAG
Found at i:422002 original size:17 final size:17
Alignment explanation
Indices: 421980--422013 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
421970 TAGAGACAAT
421980 TTTCGA-TTCACATACGA
1 TTTCGACTTCACA-ACGA
421997 TTTCGACTTCACAACGA
1 TTTCGACTTCACAACGA
422014 AAGATATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (17 bp):
TTTCGACTTCACAACGA
Found at i:423678 original size:13 final size:14
Alignment explanation
Indices: 423660--423719 Score: 72
Period size: 14 Copynumber: 4.4 Consensus size: 14
423650 TAAAGGTCCT
423660 TTTTA-TTTTTTTA
1 TTTTATTTTTTTTA
423673 TTTTATTTTTTTTA
1 TTTTATTTTTTTTA
*
423687 TTCTATTATTTTTTA
1 TTTTATT-TTTTTTA
423702 --TTATTTTTCTTTA
1 TTTTATTTTT-TTTA
423715 TTTTA
1 TTTTA
423720 CTAACTTTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 3 0.08
13 13 0.32
14 14 0.35
15 10 0.25
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTATTTTTTTTA
Found at i:423745 original size:9 final size:9
Alignment explanation
Indices: 423730--423779 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
423720 CTAACTTTCA
423730 TTTATCT-T
1 TTTATCTAT
423738 TGTTATCTAT
1 T-TTATCTAT
423748 TTTATCTAT
1 TTTATCTAT
423757 TTTAT-TAT
1 TTTATCTAT
423765 TATTAT-TAT
1 T-TTATCTAT
423774 TATTAT
1 T-TTAT
423780 ATTAATATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
8 5 0.13
9 32 0.82
10 2 0.05
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTATCTAT
Found at i:423766 original size:3 final size:3
Alignment explanation
Indices: 423740--423788 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
423730 TTTATCTTTG
423740 TTA TCTA TT- TTA TCTA TT- TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA T-TA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
423784 ATA TT
1 TTA TT
423789 TTTTTCATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 6 0.15
3 27 0.69
4 6 0.15
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:424616 original size:27 final size:27
Alignment explanation
Indices: 424544--424616 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
424534 AAAATAAAAA
* *
424544 TAAATTTAAGATTTTAATAATTTTAAAC
1 TAAATTTAAGATTTT-TTTATTTTAAAC
* * *
424572 TAAATTT-AGTATTATTTTCTTTTAATC
1 TAAATTTAAG-ATTTTTTTATTTTAAAC
424599 TAAATTTAAGATTTTTTT
1 TAAATTTAAGATTTTTTT
424617 TTAAAAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
27 24 0.65
28 13 0.35
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (27 bp):
TAAATTTAAGATTTTTTTATTTTAAAC
Found at i:428465 original size:2 final size:2
Alignment explanation
Indices: 428458--428510 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
428448 TGGGTCTGGT
428458 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
428500 TC TC TC TC TC T
1 TC TC TC TC TC T
428511 GCTTCAGTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:431524 original size:21 final size:22
Alignment explanation
Indices: 431499--431543 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
431489 TTTATGTTTA
*
431499 TATGGCATG-TTTCTTTGCCTT
1 TATGGCATGATTTCTCTGCCTT
*
431520 TATGGTATGATTTTCTCTGCCTT
1 TATGGCATGA-TTTCTCTGCCTT
431543 T
1 T
431544 TAGTAGCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
23 12 0.60
ACGTcount: A:0.11, C:0.18, G:0.18, T:0.53
Consensus pattern (22 bp):
TATGGCATGATTTCTCTGCCTT
Found at i:433065 original size:17 final size:17
Alignment explanation
Indices: 433045--433089 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
433035 TTATTATATA
433045 TATATATTTTACCTTCT
1 TATATATTTTACCTTCT
* * *
433062 TATATTTTTTTCTTTCT
1 TATATATTTTACCTTCT
*
433079 TTTATATTTTA
1 TATATATTTTA
433090 TTTCGTCATT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (17 bp):
TATATATTTTACCTTCT
Found at i:433197 original size:25 final size:20
Alignment explanation
Indices: 433169--433227 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 20
433159 CTTTCCTTTG
433169 TTTTATTTATTTTATCTATGTTAT
1 TTTTATTT-TTTTAT-T-TG-TAT
*
433193 TTTTTTTTCTCTTTATTTGTAT
1 TTTTATTT-T-TTTATTTGTAT
433215 TTTTATTTTTTTA
1 TTTTATTTTTTTA
433228 CATTCTTCCG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.13
21 1 0.03
22 10 0.32
23 2 0.06
24 9 0.29
25 5 0.16
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTATTTTTTTATTTGTAT
Found at i:436548 original size:60 final size:60
Alignment explanation
Indices: 436418--436548 Score: 135
Period size: 60 Copynumber: 2.2 Consensus size: 60
436408 AAGTGATCAT
* *
436418 TTTAT-TACTTTTAATAGTTAAGGGACTCAACAAAACAACACTCTATAGTTAAAAAACTA
1 TTTATGTACTTTTAATAGTTAAGAGACTCAACAAAACAACACTCTATAGTGAAAAAACTA
* * * * * *
436477 TTT-TGTAACTTTTAATAGTTGATAGACTTAATAAAACAATA-TCTTATAGTCGAAAGAAC-A
1 TTTATGT-ACTTTTAATAGTTAAGAGACTCAACAAAACAACACTC-TATAGT-GAAAAAACTA
436537 TTTATGTACTTT
1 TTTATGTACTTT
436549 ACCCTAAATT
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
58 1 0.02
59 6 0.10
60 43 0.73
61 9 0.15
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.37
Consensus pattern (60 bp):
TTTATGTACTTTTAATAGTTAAGAGACTCAACAAAACAACACTCTATAGTGAAAAAACTA
Found at i:451502 original size:29 final size:29
Alignment explanation
Indices: 451452--451507 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
451442 TTAGTTTTCA
* *
451452 TTTCATTTTAGTATCCTGTCATTAAAAAC
1 TTTCATTTTAATATCCTATCATTAAAAAC
451481 TTTCATTTTAATAT-CTCATCATTAAAA
1 TTTCATTTTAATATCCT-ATCATTAAAA
451508 GCTTAACGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.34, C:0.16, G:0.04, T:0.46
Consensus pattern (29 bp):
TTTCATTTTAATATCCTATCATTAAAAAC
Found at i:452439 original size:3 final size:3
Alignment explanation
Indices: 452420--452470 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
452410 CAAAGGCAAC
* *
452420 CTT CTT CATT -TT GTT CTT CTT CTT CTT C-T CTTT CTT CTT TTT CTT
1 CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT
452465 CTT CTT
1 CTT CTT
452471 TTTGTTCTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
2 4 0.10
3 33 0.80
4 4 0.10
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:452446 original size:21 final size:20
Alignment explanation
Indices: 452420--452479 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
452410 CAAAGGCAAC
452420 CTTCTTCATTTTGTTCTTCTT
1 CTTCTTC-TTTTGTTCTTCTT
* *
452441 CTTCTTCTCTTTCTTCTTTTT
1 CTTCTTCT-TTTGTTCTTCTT
452462 CTTCTTCTTTTTGTTCTT
1 CTTCTTC-TTTTGTTCTT
452480 ATCCTGTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.02, C:0.25, G:0.03, T:0.70
Consensus pattern (20 bp):
CTTCTTCTTTTGTTCTTCTT
Found at i:452471 original size:12 final size:12
Alignment explanation
Indices: 452433--452479 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
452423 CTTCATTTTG
452433 TTCTTCTTCTTCT
1 TTCTTCTTCTT-T
452446 TCTCTTTCTTCTTT
1 T-TC-TTCTTCTTT
452460 TTCTTCTTCTTT
1 TTCTTCTTCTTT
*
452472 TTGTTCTT
1 TTCTTCTT
452480 ATCCTGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 16 0.52
13 3 0.10
14 4 0.13
15 8 0.26
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:453139 original size:71 final size:71
Alignment explanation
Indices: 453018--453160 Score: 214
Period size: 71 Copynumber: 2.0 Consensus size: 71
453008 CTTCTTCTAA
* * *
453018 TGTACCCGCATTTATGTCTAACACCTATTCGTATATAATCCTCAAAATATGTAACAGATCTCGGG
1 TGTACCCGCATTTATGTCTAACACATATTCATATATAATCCTCAAAATATGTAACAGAACTCGGG
453083 AAATCT
66 AAATCT
* * * * *
453089 TGTACCGGCATTTGTGTCTAACACATATTCATATATGATCCTCTAGATATGTAACAGAACTCGGG
1 TGTACCCGCATTTATGTCTAACACATATTCATATATAATCCTCAAAATATGTAACAGAACTCGGG
453154 AAATCT
66 AAATCT
453160 T
1 T
453161 TGAGTATACT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (71 bp):
TGTACCCGCATTTATGTCTAACACATATTCATATATAATCCTCAAAATATGTAACAGAACTCGGG
AAATCT
Found at i:455034 original size:24 final size:24
Alignment explanation
Indices: 455007--455059 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
454997 GCTAAGGTAG
455007 GCATCATGATGCGGCTTAGGGGTC
1 GCATCATGATGCGGCTTAGGGGTC
455031 GCATCATGATGCGGCTTAGGGGTC
1 GCATCATGATGCGGCTTAGGGGTC
455055 GCATC
1 GCATC
455060 TCGGAGCTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.17, C:0.23, G:0.36, T:0.25
Consensus pattern (24 bp):
GCATCATGATGCGGCTTAGGGGTC
Found at i:458084 original size:15 final size:13
Alignment explanation
Indices: 458063--458103 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
458053 TTTTACCGGA
458063 TAAAAAACCGGTT
1 TAAAAAACCGGTT
458076 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
458090 TAAAAAACCGGTT
1 TAAAAAACCGGTT
458103 T
1 T
458104 TTATCCGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:458094 original size:12 final size:12
Alignment explanation
Indices: 458057--458102 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
458047 CCGGTTTTTT
*
458057 ACCGGATAAAAA
1 ACCGGTTAAAAA
458069 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
458084 ACCGGTTAAAAA
1 ACCGGTTAAAAA
458096 ACCGGTT
1 ACCGGTT
458103 TTTATCCGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:460370 original size:21 final size:21
Alignment explanation
Indices: 460346--460385 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
460336 TTTATTTTAT
460346 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
460367 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
460386 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:460433 original size:33 final size:33
Alignment explanation
Indices: 460380--460478 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
460370 TTTGTTTCAA
460380 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
460412 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
460445 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
460478 T
1 T
460479 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:460507 original size:13 final size:13
Alignment explanation
Indices: 460464--460518 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
460454 TTGGAAGTAT
460464 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
460477 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
460491 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
460504 TTAAGTATTTGAA
1 TTAAGTATTTCAA
460517 TT
1 TT
460519 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Done.