Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005129.1 Hibiscus syriacus cultivar Beakdansim tig00011547_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: 545926
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 3 of 3
Found at i:451312 original size:21 final size:21
Alignment explanation
Indices: 451256--451325 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
451246 TTCTTTGATG
** * *
451256 AAAAGGTTAAGCCCTTTCATC
1 AAAAGGTTAAATCTTTTAATC
** *
451277 AAAAGGAGAATTCTTTTAATC
1 AAAAGGTTAAATCTTTTAATC
*
451298 AAAAGGTTAAATCTTTTTATC
1 AAAAGGTTAAATCTTTTAATC
*
451319 TAAAGGT
1 AAAAGGT
451326 CTTAACCTCT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (21 bp):
AAAAGGTTAAATCTTTTAATC
Found at i:455077 original size:18 final size:18
Alignment explanation
Indices: 455054--455090 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
455044 AGTTTTGATC
* *
455054 AAAATAATTTCTTTAATA
1 AAAATAATTACTTGAATA
455072 AAAATAATTACTTGAATA
1 AAAATAATTACTTGAATA
455090 A
1 A
455091 TGATCAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (18 bp):
AAAATAATTACTTGAATA
Found at i:456558 original size:251 final size:253
Alignment explanation
Indices: 456046--456727 Score: 932
Period size: 251 Copynumber: 2.7 Consensus size: 253
456036 CAGGGTTTTT
* *
456046 TTGCCTTATTGTGAACTAGGCTCTCGTAAACTTCAGGGAAATTACTTGTGCATTGTTCTTGGGTG
1 TTGCCTT-TTGTGAACTAGGTTCTCGTAAACTTCAGGAAAATTACTTGTGCATTGTTCTTGGGTG
*
456111 AACCTCTGGATTTTATTGGTGCTTGAAGGTTCAGTAAATGATGCTACATTTTGTAATCCTCTATA
65 AACCTCTGGATTTTATTGGTGCCTGAAGGTTCAGTAAATGATGCTACATTTTGTAATCCTCTATA
* ** *
456176 AGGAATTAAGTTTTCGGG-TTG----ATATGAGTTCAATTGTTTATTGAGTTGTTCTGCTGTTGT
130 AGGAATTAAGTTTT-GGGATTGATATATATGAGTTCAATTGTTTCTTGAGGCGTTCTGATGTTGT
* * * * *
456236 CTGATCCTCTTTTTGGCTGAGATTTTGGGTTCTTAAACCTGACGTAAAAAAGCAGGGCCTTG
194 CTGATCCTATTTTTGGCTGAGATTTTGGATTCCTAAACCTGACGTAAAAAAGCA--GACATG
456298 TTGCCTTTTGTGAACTAGGTTCTCGTAAACTTCAGGAAAATTACTTGTGCATTGTTCTTGGGTGA
1 TTGCCTTTTGTGAACTAGGTTCTCGTAAACTTCAGGAAAATTACTTGTGCATTGTTCTTGGGTGA
*
456363 ACCTCTGGA-TTTATTGGTGCCTGAAGGTTCAGTAAATGATGCTACATTTTGTATTCCTCTATAA
66 ACCTCTGGATTTTATTGGTGCCTGAAGGTTCAGTAAATGATGCTACATTTTGTAATCCTCTATAA
* * *
456427 GGAATTAAGTTTTGGGATTGATACATATATGAGTTAAATTGTTTCTTGAGGCGTTTTGAT-TTTT
131 GGAATTAAGTTTTGGGATTGAT--ATATATGAGTTCAATTGTTTCTTGAGGCGTTCTGATGTTGT
* * * *
456491 TTGGTCCTATTTTTGGTTGAGATTTTGGATTCCTAAACCTGATGTAAAAAAG-A-ACATG
194 CTGATCCTATTTTTGGCTGAGATTTTGGATTCCTAAACCTGACGTAAAAAAGCAGACATG
* * * * **
456549 TTTCCTTTTGTGAACTAGATTCTCTTAAACTTCAGCAAAATTACCCGTGCATTGTTCTTGGGTGA
1 TTGCCTTTTGTGAACTAGGTTCTCGTAAACTTCAGGAAAATTACTTGTGCATTGTTCTTGGGTGA
* * * * *
456614 ACCTCTGTATTTTATTGGTACCTGAAGGCTCAGTAAATGATGCTACATTTTGTAATCCTATGTAA
66 ACCTCTGGATTTTATTGGTGCCTGAAGGTTCAGTAAATGATGCTACATTTTGTAATCCTCTATAA
* * *
456679 GGAATTTAGTTTTTGGATTGATATGATATGATTTCAATTGTTTCTTGAG
131 GGAATTAAGTTTTGGGATTGATAT-ATATGAGTTCAATTGTTTCTTGAG
456728 AAATTTTAAT
Statistics
Matches: 385, Mismatches: 36, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
249 3 0.01
250 71 0.18
251 157 0.41
252 77 0.20
254 1 0.00
255 48 0.12
256 28 0.07
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (253 bp):
TTGCCTTTTGTGAACTAGGTTCTCGTAAACTTCAGGAAAATTACTTGTGCATTGTTCTTGGGTGA
ACCTCTGGATTTTATTGGTGCCTGAAGGTTCAGTAAATGATGCTACATTTTGTAATCCTCTATAA
GGAATTAAGTTTTGGGATTGATATATATGAGTTCAATTGTTTCTTGAGGCGTTCTGATGTTGTCT
GATCCTATTTTTGGCTGAGATTTTGGATTCCTAAACCTGACGTAAAAAAGCAGACATG
Found at i:461879 original size:21 final size:19
Alignment explanation
Indices: 461855--461894 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
461845 TAAATTAAAA
*
461855 CATAATGGATGTAAATATTTT
1 CATAAT-GATGCAAA-ATTTT
461876 CATAATGATGCAAAATTTT
1 CATAATGATGCAAAATTTT
461895 ACCATGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 7 0.39
21 6 0.33
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (19 bp):
CATAATGATGCAAAATTTT
Found at i:464015 original size:3 final size:3
Alignment explanation
Indices: 464001--464034 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
463991 ATATAGGAAA
464001 AAG AAGG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG
464035 CTAACCTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:466100 original size:26 final size:26
Alignment explanation
Indices: 466063--466142 Score: 151
Period size: 26 Copynumber: 3.1 Consensus size: 26
466053 CGAATGAGGG
*
466063 TATGTTCGTATTCGTTTATTTAATTT
1 TATGTTCATATTCGTTTATTTAATTT
466089 TATGTTCATATTCGTTTATTTAATTT
1 TATGTTCATATTCGTTTATTTAATTT
466115 TATGTTCATATTCGTTTATTTAATTT
1 TATGTTCATATTCGTTTATTTAATTT
466141 TA
1 TA
466143 ACCAAACAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.61
Consensus pattern (26 bp):
TATGTTCATATTCGTTTATTTAATTT
Found at i:469557 original size:14 final size:14
Alignment explanation
Indices: 469538--469565 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
469528 CATAAACAAT
469538 GAACATAAATGAAC
1 GAACATAAATGAAC
469552 GAACATAAATGAAC
1 GAACATAAATGAAC
469566 AGATTATCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:478153 original size:16 final size:16
Alignment explanation
Indices: 478134--478164 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
478124 TTTAGGTCCT
*
478134 ATAAATTTAAATATTA
1 ATAAAATTAAATATTA
478150 ATAAAATTAAATATT
1 ATAAAATTAAATATT
478165 TGTTTTCATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTAAATATTA
Found at i:482226 original size:34 final size:34
Alignment explanation
Indices: 482177--482254 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
482167 TTCTAAATTA
* * * *
482177 TTACAGTTATTAGATGGTTTCAGTTATCAAATAT
1 TTACAGATATAAGATGATTACAGTTATCAAATAT
* *
482211 TTACATATATAAGATGATTACAGTTATCAGATAT
1 TTACAGATATAAGATGATTACAGTTATCAAATAT
482245 TTACAGATAT
1 TTACAGATAT
482255 CAGACCTTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (34 bp):
TTACAGATATAAGATGATTACAGTTATCAAATAT
Found at i:482242 original size:17 final size:16
Alignment explanation
Indices: 482175--482258 Score: 62
Period size: 17 Copynumber: 5.0 Consensus size: 16
482165 AATTCTAAAT
*
482175 TATTACAGTTATTAGA
1 TATTACAGTTATCAGA
* * *
482191 TGGTTTCAGTTATCAAA
1 T-ATTACAGTTATCAGA
*
482208 TATTTACA-TATATAAGA
1 TA-TTACAGT-TATCAGA
482225 TGATTACAGTTATCAGA
1 T-ATTACAGTTATCAGA
*
482242 TATTTACAGATATCAGA
1 TA-TTACAGTTATCAGA
482259 CCTTTCACAA
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
16 3 0.06
17 47 0.90
18 2 0.04
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (16 bp):
TATTACAGTTATCAGA
Found at i:483856 original size:17 final size:17
Alignment explanation
Indices: 483816--483855 Score: 66
Period size: 15 Copynumber: 2.5 Consensus size: 17
483806 AAGTATCTAG
483816 TAAATATAATACTATTT
1 TAAATATAATACTATTT
483833 TAAATATAATA-T-TTT
1 TAAATATAATACTATTT
483848 TAAATATA
1 TAAATATA
483856 TTCAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 11 0.48
16 1 0.04
17 11 0.48
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATATAATACTATTT
Found at i:484818 original size:8 final size:8
Alignment explanation
Indices: 484802--484835 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
484792 TGTGGATAAG
484802 TAATTAAA
1 TAATTAAA
*
484810 TAGTTAAA
1 TAATTAAA
484818 TAATTAAA
1 TAATTAAA
484826 TAATTAAA
1 TAATTAAA
484834 TA
1 TA
484836 TATAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
TAATTAAA
Found at i:488858 original size:21 final size:21
Alignment explanation
Indices: 488834--488951 Score: 132
Period size: 21 Copynumber: 5.6 Consensus size: 21
488824 TCGTACCAAG
* *
488834 GACGTGAAGAACATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
488855 GACGAGAATG-TCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
488876 GACGAGAATG-CCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
**
488897 GACGAGAAGGTCATTCATCAA
1 GACGAGAAGACCATTCATCAA
* * *
488918 AACGAGAAGACCCTTCATAAA
1 GACGAGAAGACCATTCATCAA
488939 GACGAGAAGACCA
1 GACGAGAAGACCA
488952 CATCGCATGG
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
20 1 0.01
21 82 0.98
22 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (21 bp):
GACGAGAAGACCATTCATCAA
Found at i:488892 original size:42 final size:42
Alignment explanation
Indices: 488839--488947 Score: 157
Period size: 42 Copynumber: 2.6 Consensus size: 42
488829 CCAAGGACGT
* * *
488839 GAAGAACATTCATCAAGACGAGAATGTCATTCATCAAGACGA
1 GAAGACCATTCATCAAGACGAGAAGGTCATTCATCAAAACGA
488881 GAATG-CCATTCATCAAGACGAGAAGGTCATTCATCAAAACGA
1 GAA-GACCATTCATCAAGACGAGAAGGTCATTCATCAAAACGA
* *
488923 GAAGACCCTTCATAAAGACGAGAAG
1 GAAGACCATTCATCAAGACGAGAAG
488948 ACCACATCGC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
41 1 0.02
42 58 0.97
43 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.17
Consensus pattern (42 bp):
GAAGACCATTCATCAAGACGAGAAGGTCATTCATCAAAACGA
Found at i:491555 original size:17 final size:16
Alignment explanation
Indices: 491535--491580 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
491525 AGAGAAATGT
*
491535 AGAAAGAGAAAAGGAAA
1 AGAAA-AGAAAAAGAAA
491552 AGAAAAGAAGAAAGAAA
1 AGAAAAGAA-AAAGAAA
491569 AGAAAAGAAAAA
1 AGAAAAGAAAAA
491581 ATTGAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 7 0.26
17 20 0.74
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AGAAAAGAAAAAGAAA
Found at i:491558 original size:5 final size:5
Alignment explanation
Indices: 491535--491579 Score: 54
Period size: 5 Copynumber: 8.2 Consensus size: 5
491525 AGAGAAATGT
491535 AGAAA GAGAAA AGGAAA AGAAA AGAAGAA AGAAA AGAAA AGAAA A
1 AGAAA -AGAAA A-GAAA AGAAA AG-A-AA AGAAA AGAAA AGAAA A
491580 AATTGAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
5 20 0.56
6 12 0.33
7 4 0.11
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:491565 original size:12 final size:11
Alignment explanation
Indices: 491535--491579 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
491525 AGAGAAATGT
*
491535 AGAAAGAGAAA
1 AGAAAAAGAAA
*
491546 AGGAAAAGAAA
1 AGAAAAAGAAA
491557 AGAAGAAAGAAA
1 AGAA-AAAGAAA
491569 AG-AAAAGAAA
1 AGAAAAAGAAA
491579 A
1 A
491580 AATTGAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
10 8 0.27
11 13 0.43
12 9 0.30
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:493127 original size:123 final size:120
Alignment explanation
Indices: 492884--493113 Score: 266
Period size: 123 Copynumber: 1.9 Consensus size: 120
492874 AATACCCATA
* * ** * *
492884 TTGGGGCATGACTGAACCCCCATCATTTTGAGATGACAAAATATTCAGACCAAGAAGGCATTGAG
1 TTGGGGCACGACTGAACCCACATCATGATGAGACGAC-AAAGATTCAGACCAAGAAGGCATTGAG
** * * *
492949 AATGAGCCTTACATTTTGAGGTGGGCATTTTGAAGGCTCGTAATTGCAAAAGATAAAG
65 -ATGAGCCTTACAAATTGAGGTGGGCATTTTGAAGACCCGTAAAT-CAAAAGATAAAG
*
493007 TTGGGGCACGACTGAACCCACATCATGATGAGACGAC-AAGATTCAGACCAAGAAGGCGTTGAG-
1 TTGGGGCACGACTGAACCCACATCATGATGAGACGACAAAGATTCAGACCAAGAAGGCATTGAGA
*
493070 TGAGCCTTACAAATTGATGTTTTGGGGCATTTTGAAGACCCGTA
66 TGAGCCTTACAAATTGA-G--GT-GGGCATTTTGAAGACCCGTA
493114 CCAATATAAG
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
119 15 0.16
120 1 0.01
121 24 0.26
122 1 0.01
123 50 0.55
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (120 bp):
TTGGGGCACGACTGAACCCACATCATGATGAGACGACAAAGATTCAGACCAAGAAGGCATTGAGA
TGAGCCTTACAAATTGAGGTGGGCATTTTGAAGACCCGTAAATCAAAAGATAAAG
Found at i:495028 original size:218 final size:218
Alignment explanation
Indices: 494590--495658 Score: 1768
Period size: 218 Copynumber: 4.9 Consensus size: 218
494580 TGAAGCAAAA
* * * *
494590 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT-GGGGAGAAGACGCGATTGATGAAGATTGT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGG-GCAGACGCGATCGTTGAAGATTGT
*
494654 TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTG-T-GGGTCTTA
65 TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTTCGAGTCTTA
*
494717 TACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTGGGTCTTATACTCTCTGAAG
130 TACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTGGGTCTTATACTCTCTGAAG
494782 AAATAGGGGGCAGACGCGATCGTT
195 AAATAGGGGGCAGACGCGATCGTT
* * *
494806 GAAGATTGTTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
*
494871 CGAGTATTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTTCGAGTCTTAT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTTCGAGTCTTAT
* *
494936 ACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGAGTCTTATACTCTCTGAAGA
131 ACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTGGGTCTTATACTCTCTGAAGA
*
495001 AATAGGGGGCAGACGCGATCATT
196 AATAGGGGGCAGACGCGATCGTT
*
495024 GAAGATTGTTCGAGTCTTATATTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
* * *
495089 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATTGCTGAAGATTGTTCGAGTCTGAT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTTCGAGTCTTAT
* * *
495154 ACTCTCTGAAGAAATGGGGGGCAGACGCGATTGATGAAGATTGTGGGTCTTATACTCTTTGAAGA
131 ACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTGGGTCTTATACTCTCTGAAGA
495219 AATAGGGGGCAGACGCGATCGTT
196 AATAGGGGGCAGACGCGATCGTT
495242 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
*
495307 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTCGAGTCTTAT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTTCGAGTCTTAT
* *
495372 ACTCTCTGAAGAAATAGGGGGGCAGACACGATTGTTGAAGATTGTTCGGGTTTTATACTCTCTGA
131 ACTCTCTGAAGAAATA-GGGGGCAGACGCGATTGTTGAAGATTG-T-GGGTCTTATACTCTCTGA
* *
495437 AGAAATAGGGGACGGACGCGATCGTT
193 AGAAATAGGGGGCAGACGCGATCGTT
* *
495463 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGTAGACGCGATCGATGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
*
495528 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA-TCAGTGAAGATTGTTCGAGTCTTA
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA-TGAAGATTGTTCGAGTCTTA
* * *
495592 TACTCTCTGAAGAAATAGGGGGCAGATGCGATTGTTAAAGATTGTTCGAGTCTTATACTCTCTGA
130 TACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTG-T-GGGTCTTATACTCTCTGA
495657 AG
193 AG
495659 GACTAGAGAA
Statistics
Matches: 801, Mismatches: 45, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
216 105 0.13
217 5 0.01
218 439 0.55
219 25 0.03
220 47 0.06
221 180 0.22
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (218 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTTCGAGTCTTAT
ACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTGGGTCTTATACTCTCTGAAGA
AATAGGGGGCAGACGCGATCGTT
Found at i:495688 original size:55 final size:55
Alignment explanation
Indices: 494590--495658 Score: 1690
Period size: 55 Copynumber: 19.6 Consensus size: 55
494580 TGAAGCAAAA
* * * *
494590 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT-GGGGAGAAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGG-GCAGACGCGATCGTT
* *
494645 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
494700 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
494753 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
494806 GAAGATTGTTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
494861 GAAGATTGTTCGAGTATTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
494916 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
494971 GAAGATTG-T-GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
495024 GAAGATTGTTCGAGTCTTATATTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
495079 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATTGCT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * * *
495134 GAAGATTGTTCGAGTCTGATACTCTCTGAAGAAATGGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
495189 GAAGATTG-T-GGGTCTTATACTCTTTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
495242 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
495297 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
495352 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATA-GGGGGCAGACGCGATCGTT
* * * *
495408 GAAGATTGTTCGGGTTTTATACTCTCTGAAGAAATAGGGGACGGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
495463 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGTAGACGCGATCGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
495518 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCAG-T
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATC-GTT
* *
495573 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
495628 AAAGATTGTTCGAGTCTTATACTCTCTGAAG
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAG
495659 GACTAGAGAA
Statistics
Matches: 952, Mismatches: 52, Indels: 20
0.93 0.05 0.02
Matches are distributed among these distances:
53 197 0.21
54 7 0.01
55 691 0.73
56 57 0.06
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:496034 original size:16 final size:17
Alignment explanation
Indices: 495998--496034 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
495988 ATATATGCGG
*
495998 ATAAGTAATTAAATAGT
1 ATAAATAATTAAATAGT
496015 -TAAATAATTAAATA-T
1 ATAAATAATTAAATAGT
496030 ATAAA
1 ATAAA
496035 ATATGCACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 1 0.06
16 17 0.94
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (17 bp):
ATAAATAATTAAATAGT
Found at i:497568 original size:18 final size:16
Alignment explanation
Indices: 497540--497617 Score: 61
Period size: 18 Copynumber: 4.6 Consensus size: 16
497530 TCTGGACAAT
497540 AATTAAAATTAAAATA
1 AATTAAAATTAAAATA
*
497556 GAATTTTAAATT-AAATA
1 -AA-TTAAAATTAAAATA
*
497573 AATAAAATATTAACAAT-
1 AATTAAA-ATTAA-AATA
*
497590 AATTTAAATTAAAATA
1 AATTAAAATTAAAATA
497606 GAATTTAAAATT
1 -AA-TTAAAATT
497618 CTTACCGTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
15 6 0.12
16 10 0.21
17 15 0.31
18 17 0.35
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (16 bp):
AATTAAAATTAAAATA
Found at i:498821 original size:22 final size:23
Alignment explanation
Indices: 498796--498838 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
498786 GCTCTCGAAG
498796 TTTAAATCGTT-ATTTTATTTGT
1 TTTAAATCGTTAATTTTATTTGT
* *
498818 TTTAATTTGTTAATTTTATTT
1 TTTAAATCGTTAATTTTATTT
498839 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.67
Consensus pattern (23 bp):
TTTAAATCGTTAATTTTATTTGT
Found at i:511540 original size:10 final size:10
Alignment explanation
Indices: 511495--511544 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
511485 ATTAATTAAT
*
511495 TATATATATA
1 TATATATTTA
*
511505 TATATATTAA
1 TATATATTTA
*
511515 TTTATATTTA
1 TATATATTTA
*
511525 -GT-TATTTA
1 TATATATTTA
511533 TATATATTTA
1 TATATATTTA
511543 TA
1 TA
511545 AAAATATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 24 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (10 bp):
TATATATTTA
Found at i:511543 original size:14 final size:14
Alignment explanation
Indices: 511503--511543 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
511493 ATTATATATA
*
511503 TATATATATTAATT
1 TATATATATTTATT
* *
511517 TATATTTAGTTATT
1 TATATATATTTATT
511531 TATATATATTTAT
1 TATATATATTTAT
511544 AAAAATATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (14 bp):
TATATATATTTATT
Found at i:512684 original size:21 final size:21
Alignment explanation
Indices: 512658--512702 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
512648 AAATTACGTG
*
512658 TTTAGTAACTAAACTATCAGT
1 TTTAGTAACTAAACTATCAAT
* *
512679 TTTAGTACCTAAACTTTCAAT
1 TTTAGTAACTAAACTATCAAT
512700 TTT
1 TTT
512703 TTTCAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (21 bp):
TTTAGTAACTAAACTATCAAT
Found at i:513090 original size:28 final size:28
Alignment explanation
Indices: 513050--513109 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
513040 CCTCCTATAA
513050 TAATGTGATTATCAATTATGATATTTTT
1 TAATGTGATTATCAATTATGATATTTTT
513078 TAATGTGATTATCAATTATGATATTTTT
1 TAATGTGATTATCAATTATGATATTTTT
513106 TAAT
1 TAAT
513110 AGTACAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.53
Consensus pattern (28 bp):
TAATGTGATTATCAATTATGATATTTTT
Found at i:517664 original size:21 final size:21
Alignment explanation
Indices: 517640--517679 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
517630 GATAGTTTGT
517640 GTACTAAACGCGTTAAGTTGG
1 GTACTAAACGCGTTAAGTTGG
517661 GTACTAAACGCGTTAAGTT
1 GTACTAAACGCGTTAAGTT
517680 TTTAACATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (21 bp):
GTACTAAACGCGTTAAGTTGG
Found at i:518621 original size:12 final size:12
Alignment explanation
Indices: 518604--518635 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
518594 AATGATCTTG
518604 GCATGACACGTA
1 GCATGACACGTA
518616 GCATGACACGTA
1 GCATGACACGTA
518628 GCATGACA
1 GCATGACA
518636 TGAGACATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.16
Consensus pattern (12 bp):
GCATGACACGTA
Found at i:519441 original size:29 final size:29
Alignment explanation
Indices: 519408--519489 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 29
519398 CAAAATATAT
* *
519408 AACTTTTAAAAATTATATTTTTGTCTCTA
1 AACTTTTAAAAATTATATTTTGGCCTCTA
* *
519437 AACTTTTACAAAGTTTATACTTTGGCCTCTA
1 AACTTTTA-AAA-ATTATATTTTGGCCTCTA
* * *
519468 AACTTTCAAAACTTACATTTTG
1 AACTTTTAAAAATTATATTTTG
519490 ACTTCACTAG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 16 0.37
30 6 0.14
31 21 0.49
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (29 bp):
AACTTTTAAAAATTATATTTTGGCCTCTA
Found at i:520483 original size:21 final size:21
Alignment explanation
Indices: 520457--520510 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
520447 GGGCAGGTGC
520457 ATCGATGCACTATGAGTGTGT
1 ATCGATGCACTATGAGTGTGT
520478 ATCGATGCACTATGAGTGTGT
1 ATCGATGCACTATGAGTGTGT
*
520499 ACCGATGCACTA
1 ATCGATGCACTA
520511 AGACAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (21 bp):
ATCGATGCACTATGAGTGTGT
Found at i:524412 original size:20 final size:21
Alignment explanation
Indices: 524387--524433 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
524377 CCAAGAGTGG
*
524387 GTATCGATAATAAAG-GGTTA
1 GTATCGATAATAAAGTGCTTA
*
524407 GTATCGATACTAAAGTGCTTA
1 GTATCGATAATAAAGTGCTTA
524428 GTATCG
1 GTATCG
524434 GTACCATCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (21 bp):
GTATCGATAATAAAGTGCTTA
Found at i:527284 original size:28 final size:30
Alignment explanation
Indices: 527233--527288 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 30
527223 CTACTTAGTT
* *
527233 TTTTTTAAATATTTATAACGTTTAAATATA
1 TTTTATAAATATTTAAAACGTTTAAATATA
527263 TTTTATAAA-ATTTAAAAC-TTTAAATA
1 TTTTATAAATATTTAAAACGTTTAAATA
527289 ATTATGATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.33
29 8 0.33
30 8 0.33
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (30 bp):
TTTTATAAATATTTAAAACGTTTAAATATA
Found at i:527303 original size:28 final size:29
Alignment explanation
Indices: 527240--527303 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
527230 GTTTTTTTTA
* *
527240 AATATTTATAACGTTTAAATATATTTTAT
1 AATATTTAAAACGTTTAAATATATTTGAT
*
527269 AAAATTTAAAAC-TTTAAATA-ATTATGAT
1 AATATTTAAAACGTTTAAATATATT-TGAT
*
527297 CATATTT
1 AATATTT
527304 TTAAAAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 16 0.55
29 10 0.34
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (29 bp):
AATATTTAAAACGTTTAAATATATTTGAT
Found at i:527943 original size:17 final size:18
Alignment explanation
Indices: 527921--527954 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
527911 GATTTGCATG
527921 ATTTTAAAAC-AAAATAA
1 ATTTTAAAACTAAAATAA
*
527938 ATTTTAAGACTAAAATA
1 ATTTTAAAACTAAAATA
527955 TAATAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (18 bp):
ATTTTAAAACTAAAATAA
Found at i:529435 original size:20 final size:19
Alignment explanation
Indices: 529412--529458 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
529402 CGATATACCA
529412 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
529432 GGTAACAAAATGATAAAACT
1 GGTAA-AAAATGATAAAACC
529452 GGTAAAA
1 GGTAAAA
529459 CGTTACCGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:529546 original size:181 final size:181
Alignment explanation
Indices: 529200--529668 Score: 660
Period size: 182 Copynumber: 2.6 Consensus size: 181
529190 GATCCAAATT
* * * *
529200 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATA-GAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAAATGAT
* * * * * *
529264 AAAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* *
529329 CGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
130 CGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATAC-TTTA
*
529382 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* * *
529447 AAACTGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
529511 GTGAATTTAAAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATACTTTA
131 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTA
* * * *
529562 AAAAA-ATATCGATCCACAACGATATAACATGT-AAAA-ATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
529624 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
529669 CGTAAGTACG
Statistics
Matches: 259, Mismatches: 27, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
177 66 0.25
178 4 0.02
179 23 0.09
180 9 0.03
181 61 0.24
182 96 0.37
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (181 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTA
Found at i:529620 original size:20 final size:20
Alignment explanation
Indices: 529595--529632 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
529585 ATAACATGTA
529595 AAAATGATAAAACCGGTATC
1 AAAATGATAAAACCGGTATC
529615 AAAATGATAAAACCGGTA
1 AAAATGATAAAACCGGTA
529633 AAATGATACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAATGATAAAACCGGTATC
Found at i:531888 original size:21 final size:21
Alignment explanation
Indices: 531861--531925 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
531851 AAGACAATCA
*
531861 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
* * *
531882 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
531903 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
531924 AG
1 AG
531926 GCATAAGGGG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:532000 original size:32 final size:32
Alignment explanation
Indices: 531959--532019 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
531949 AAATAGATGG
*
531959 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
*
531991 AGTGGTGAAAGAAGTTGAGGTGTTAAGGG
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGG
532020 GTGATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.46, T:0.23
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
Found at i:533829 original size:19 final size:19
Alignment explanation
Indices: 533805--533853 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
533795 AATGTAGGGT
533805 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
533824 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
533843 TATTTTTGTAT
1 TAATTTTGTAT
533854 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:535033 original size:199 final size:200
Alignment explanation
Indices: 533972--535739 Score: 3238
Period size: 200 Copynumber: 8.9 Consensus size: 200
533962 CAATATGGCC
* * *
533972 AACAGGGTGCAACCATAAATTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
*
534037 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
*
534102 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCTAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
534167 TGGAA
196 TGGAA
*
534172 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAATGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
*
534237 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
*
534302 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTT-TCCCCAGAATGA
131 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGT-TCCAGAATGA
534366 ATGGAA
195 ATGGAA
*
534372 AACAGGGTTCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
*
534437 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
534502 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
534567 TGGAA
196 TGGAA
534572 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
534637 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
534702 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
534767 TGGAA
196 TGGAA
534772 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
534837 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGG-TTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
534901 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
534966 TGGAA
196 TGGAA
534971 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
535036 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGG--CAAGTTTACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
535099 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
535164 TGGAA
196 TGGAA
* *
535169 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
535233 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAA-TTATACCGGTTTTATGAG
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTT-TACCGGTTTTATGAG
535297 AGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGA
130 AGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGA
535362 ATGGAA
195 ATGGAA
* *
535368 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
535432 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA-CGGTACAA-TTATACCGGTTTTATGAG
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTT-TACCGGTTTTATGAG
535495 A-AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGA
130 AGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGA
535559 ATGGAA
195 ATGGAA
* *
535565 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
* * *
535629 CCAAAAGTATAATGTAATATGTAATTTTTCAATATAACCGGTACAAGTATAACGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
535694 GAATATGTCTAAATAATGTGTCGACACGT--TTTAGTTTGTGTCGATA
131 GAATATGTCTAAATAATGTGTCGACAC-TAATTTAGTTTGTGTCGATA
535740 CTAATTTAAA
Statistics
Matches: 1542, Mismatches: 16, Indels: 22
0.98 0.01 0.01
Matches are distributed among these distances:
197 224 0.15
198 208 0.13
199 403 0.26
200 706 0.46
201 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (200 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
TGGAA
Found at i:537221 original size:12 final size:12
Alignment explanation
Indices: 537204--537292 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
537194 GGTCGCAGAA
*
537204 GATGAAGCTGAC
1 GATGAAGATGAC
537216 GATGAAGATGAC
1 GATGAAGATGAC
*
537228 GATGATGATGAC
1 GATGAAGATGAC
* *
537240 GATGAAGTTGGC
1 GATGAAGATGAC
*
537252 GATGAAGATGAT
1 GATGAAGATGAC
* * *
537264 GACGATGATGAT
1 GATGAAGATGAC
* *
537276 GATGATGATGAT
1 GATGAAGATGAC
537288 GATGA
1 GATGA
537293 TCCAAACAAG
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 66 1.00
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:537222 original size:18 final size:18
Alignment explanation
Indices: 537201--537289 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
537191 AGCGGTCGCA
*
537201 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGACGAT
* *
537219 GAAGATGACGATGATGAT
1 GAAGATGAAGATGACGAT
* * *
537237 GACGATGAAGTTGGCGAT
1 GAAGATGAAGATGACGAT
537255 GAAGAT---GATGACGAT
1 GAAGATGAAGATGACGAT
* * *
537270 GATGATGATGATGATGAT
1 GAAGATGAAGATGACGAT
537288 GA
1 GA
537290 TGATCCAAAC
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
15 12 0.22
18 43 0.78
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.22
Consensus pattern (18 bp):
GAAGATGAAGATGACGAT
Found at i:537236 original size:3 final size:3
Alignment explanation
Indices: 537216--537293 Score: 75
Period size: 3 Copynumber: 26.0 Consensus size: 3
537206 TGAAGCTGAC
* * * * * ** *
537216 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GTT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
537264 GAC GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
537294 CCAAACAAGT
Statistics
Matches: 58, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.35, C:0.05, G:0.35, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:537255 original size:36 final size:36
Alignment explanation
Indices: 537204--537280 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
537194 GGTCGCAGAA
*
537204 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * * *
537240 GATGAAGTTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
537276 GATGA
1 GATGA
537281 TGATGATGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:538323 original size:15 final size:15
Alignment explanation
Indices: 538303--538340 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
538293 TTGAACATTC
538303 TTGTGTATTTATATT
1 TTGTGTATTTATATT
538318 TTGTGTGA-TTATATT
1 TTGTGT-ATTTATATT
*
538333 GTGTGTAT
1 TTGTGTAT
538341 ATTTCATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 1 0.05
15 18 0.90
16 1 0.05
ACGTcount: A:0.18, C:0.00, G:0.21, T:0.61
Consensus pattern (15 bp):
TTGTGTATTTATATT
Found at i:538440 original size:20 final size:20
Alignment explanation
Indices: 538415--538453 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
538405 TAATATATTG
*
538415 TAAAGTATCTATCCTTTTTA
1 TAAAGTATCTATACTTTTTA
*
538435 TAAAGTGTCTATACTTTTT
1 TAAAGTATCTATACTTTTT
538454 CCACTGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (20 bp):
TAAAGTATCTATACTTTTTA
Found at i:539066 original size:182 final size:182
Alignment explanation
Indices: 538759--539099 Score: 542
Period size: 182 Copynumber: 1.9 Consensus size: 182
538749 CTTTCAACAT
* * * * *
538759 ATTATAATAAAATAGGTAAATTTGCAATGTTATCGGTATAAATATACTGGTTTTATGCGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAATCGGTATAAATATACCGGTTTTATGAGCGAATA
* * *
538824 GGTCTACAACCTATATCGACACTTTTTAATCTTGTGTCGGTACTTTATGTCCATATTGGAA-AAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
*
538888 AATGTTTCGATA-CATTGTTAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACCA-T-TTAAAAAGTGTCGACATTTACACATCGGAACCCATA
** *
538941 ATTATAATGTAATAGATAAATTTGTAATATAATCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAATCGGTATAAATATACCGGTTTTATGAGCGAATA
539006 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
539071 AATGTGTCGATACCATTTAAAAAGTGTCG
131 AATGTGTCGATACCATTTAAAAAGTGTCG
539100 GTAATTTTAA
Statistics
Matches: 145, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
182 128 0.88
183 15 0.10
184 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (182 bp):
ATTATAATAAAATAGATAAATTTGCAATATAATCGGTATAAATATACCGGTTTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
AATGTGTCGATACCATTTAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:541591 original size:25 final size:25
Alignment explanation
Indices: 541563--541621 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
541553 TTATCATTAA
541563 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
541588 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
541613 ATTTAGGTA
1 ATTTAGGTA
541622 AGGTTATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Done.