Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008296.1 Hibiscus syriacus cultivar Beakdansim tig00110963_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: 1205179
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:179978 original size:400 final size:399
Alignment explanation
Indices: 179265--180163 Score: 1480
Period size: 400 Copynumber: 2.3 Consensus size: 399
179255 AAAATATTGC
* * * *
179265 TACATGTTGTAGACCTATTCTCTAATAAAAGTGGTATATTTATACCGGTTATATTACACAATTAC
1 TACATGTTGTAGACCTATTTTCTCATAAAACTGGTATATTTATACCGGTTATATTACAAAATTAC
* * *
179330 CTATTATATTATAATTATGGGTTTTGATGTTTATGGGATAGACACTTTTTAAAATGTATCGACAC
66 CTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATAGACACTTTTTAAAATGTATCGACAC
* *
179395 TTTGTGCGTTCACCCTTTTTGGCGTCCATTCTGGACATAAAGTATCGACACAATATTAACAAGTG
131 TTTGTGCGTTCACCCTTTTTGGCGTCCATTCTGAACATAAAGTATCGACACAATATTAACAAGGG
*
179460 TCGATACATGTTATAGACCTATTCTCTCATGAAACCAGTATATTTATACCGGTTACATTGTAAAT
196 TCGATACATGTTATAGACATATTCTCTCATGAAACCAGTATATTTATACCGGTTACATTGTAAAT
* * *
179525 TTACCTATTACATTATAATTATAGGTTTCGATGTTTTTCGGATTGACACTTTTTGAAAATGTATC
261 TTACCTATTACATTATAATTATAGGTTTCGATATTTTTCGGATCGACACTTTTTCAAAATGTATC
179590 GACACTTTGTGCGTTCACAATTTTTGGCATCCATTCTGGACAAAAAATATCGACACAATATTAAT
326 GACACTTTGTGCGTTCACAATTTTTGGCATCCATTCTGGACAAAAAATATCGACACAATATTAAT
179655 AAGTGTCGA
391 AAGTGTCGA
* *
179664 TACATGTTGTAGACATATTTTCTCATAAAACTGGTATATGTATACCGGTTATATTACAAAATTAC
1 TACATGTTGTAGACCTATTTTCTCATAAAACTGGTATATTTATACCGGTTATATTACAAAATTAC
*
179729 CTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACAC-TTTTAGTAAATGTATCGAC
66 CTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATAGACACTTTTTA--AAATGTATCGAC
179793 ACTTTGTGCGTTCACCCTTTTTGGCGTCCATTCTGAACATAAAGTATCGACACAATATTAACAAG
129 ACTTTGTGCGTTCACCCTTTTTGGCGTCCATTCTGAACATAAAGTATCGACACAATATTAACAAG
*
179858 GGTCGATACATGTTATAGACATATTCTCTCATGAAACCAGTATATTTATATCGGTTACATTGTAA
194 GGTCGATACATGTTATAGACATATTCTCTCATGAAACCAGTATATTTATACCGGTTACATTGTAA
* *
179923 ATTTACCTATTACATTATAATTATAGGTTTCGATATTTTTTGGATCGATACTTTTTCAAAATGTA
259 ATTTACCTATTACATTATAATTATAGGTTTCGATATTTTTCGGATCGACACTTTTTCAAAATGTA
* ** * * *
179988 TCGACACTTTGTGCTTTCACCCTTTTTGGCATCTATTTTGGACAAAAAGTATCGACACAATATTA
324 TCGACACTTTGTGCGTTCACAATTTTTGGCATCCATTCTGGACAAAAAATATCGACACAATATTA
180053 ATAAGTGTCGA
389 ATAAGTGTCGA
* * *
180064 TACATGTTGTAGACCTATTTT-TCATAAAACTGGTATATTTATATCAGTTACATTGA-AAAATTA
1 TACATGTTGTAGACCTATTTTCTCATAAAACTGGTATATTTATACCGGTTATATT-ACAAAATTA
**
180127 CCTATTACATTATAATTATCAGTTTCGATGTTTTTGG
65 CCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
180164 AGTCGTTACT
Statistics
Matches: 465, Mismatches: 32, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
398 5 0.01
399 171 0.37
400 289 0.62
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (399 bp):
TACATGTTGTAGACCTATTTTCTCATAAAACTGGTATATTTATACCGGTTATATTACAAAATTAC
CTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATAGACACTTTTTAAAATGTATCGACAC
TTTGTGCGTTCACCCTTTTTGGCGTCCATTCTGAACATAAAGTATCGACACAATATTAACAAGGG
TCGATACATGTTATAGACATATTCTCTCATGAAACCAGTATATTTATACCGGTTACATTGTAAAT
TTACCTATTACATTATAATTATAGGTTTCGATATTTTTCGGATCGACACTTTTTCAAAATGTATC
GACACTTTGTGCGTTCACAATTTTTGGCATCCATTCTGGACAAAAAATATCGACACAATATTAAT
AAGTGTCGA
Found at i:183631 original size:198 final size:200
Alignment explanation
Indices: 183045--183846 Score: 1315
Period size: 200 Copynumber: 4.0 Consensus size: 200
183035 CGATACATTT
*
183045 ACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTAGACCAAAAGTATCGACACAAAATTAAAG
1 ACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGACCAAAAGTATCGACACAAAATTAAAG
*
183110 AGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTATATTTATACTGGTTACATTGA
66 AGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTGA
*
183175 AAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATA
131 AAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATG
*
183240 TATCG
196 GATCG
* *
183245 ACACTTCATGGTTGCACCCTTTTTGGCATTCATTCTGGACCAAAAGTATCGACACAAAATTAAAA
1 ACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGACCAAAAGTATCGACACAAAATTAAAG
*
183310 AGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCAGTTACATTGA
66 AGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTGA
*
183375 AAATTTACCTATTAGATTATACTTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATG
131 AAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATG
*
183440 TATCG
196 GATCG
*
183445 ACACTTTATGGTTGCACCCTTTTTGGCATTCATTATGGACCAAAAGTATCGACACAAAATT-AA-
1 ACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGACCAAAAGTATCGACACAAAATTAAAG
* *
183508 AGTGTCGATATATGTTGTAGATCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTGC
66 AGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTG-
*
183573 AAAA-TTACCTATTACATTATACTTATGAGTTTCGATGTTTCTGGGATCGATACTTTTTATAAAT
130 AAAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAAT
183637 GGATCG
195 GGATCG
* * * * * * * * *
183643 ACACTTTATAGATACACGCTTTTTAGTATTCATTCTGGACCAAAAGTATCAACTCAAAATTAAAT
1 ACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGACCAAAAGTATCGACACAAAATTAAAG
* * *
183708 AGTATCGATACATGTTATAGACTTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTGT
66 AGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTG-
* *
183773 AAAA-TTACCTATTACTTTATACTTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATATAT
130 AAAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAAT
183837 GGATCG
195 GGATCG
183843 ACAC
1 ACAC
183847 ATATGCTTAC
Statistics
Matches: 566, Mismatches: 33, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
198 176 0.31
199 8 0.01
200 382 0.67
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (200 bp):
ACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGACCAAAAGTATCGACACAAAATTAAAG
AGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTGA
AAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATG
GATCG
Found at i:183676 original size:398 final size:399
Alignment explanation
Indices: 182902--183846 Score: 1499
Period size: 398 Copynumber: 2.4 Consensus size: 399
182892 TATTTAAATT
* *
182902 AGTATCGACACAAAATTAAAAAGTGTCGATACATATTGTAGACCTATTCTCTCATAAAACCGATA
1 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
182967 TATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGG
66 TATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGG
*
183032 GATCGATAC--------AT-T-T--ACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTAGAC
131 GATCGATACTTTTTATAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTATAGAC
183085 CAAAAGTATCGACACAAAATTAAAGAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACC
196 CAAAAGTATCGACACAAAATTAAAGAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACC
* *
183150 GGTATATTTATACTGGTTACATTGAAAATTTACCTATTACATTATACTTATGGGTTTCGATGTTT
261 GGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGAGTTTCGATGTTT
* * * * *
183215 CTGGGATCGATACTTTTTATAAATATATCGACACTTCATGGTTGCACCCTTTTTGGCATTCATTC
326 CTGGGATCGATACTTTTTATAAATAGATCGACACTTCATAGATACACCCTTTTTAGCATTCATTC
183280 TGGACCAAA
391 TGGACCAAA
183289 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
* *
183354 TATTTATACCAGTTACATTGAAAATTTACCTATTAGATTATACTTATGGGTTTCGATGTTTCTGG
66 TATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGG
*
183419 GATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTATGGA
131 GATCGATACTTTTTAT-AATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTATAGA
* *
183484 CCAAAAGTATCGACACAAAATT-AA-AGTGTCGATATATGTTGTAGATCTATTCTCTCATAAAAC
195 CCAAAAGTATCGACACAAAATTAAAGAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAAC
183547 CGGTATATTTATACCGGTTACATTGCAAAA-TTACCTATTACATTATACTTATGAGTTTCGATGT
260 CGGTATATTTATACCGGTTACATTG-AAAATTTACCTATTACATTATACTTATGAGTTTCGATGT
* * * *
183611 TTCTGGGATCGATACTTTTTATAAATGGATCGACACTTTATAGATACACGCTTTTTAGTATTCAT
324 TTCTGGGATCGATACTTTTTATAAATAGATCGACACTTCATAGATACACCCTTTTTAGCATTCAT
183676 TCTGGACCAAA
389 TCTGGACCAAA
* * * * * *
183687 AGTATCAACTCAAAATTAAATAGTATCGATACATGTTATAGACTTATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
*
183752 TATTTATACCGGTTACATTGTAAAA-TTACCTATTACTTTATACTTATGGGTTTCGATGTTTCTG
66 TATTTATACCGGTTACATTG-AAAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
*
183816 GGATCGATACTTTTTATATATGGATCGACAC
130 GGATCGATACTTTTTATA-ATGTATCGACAC
183847 ATATGCTTAC
Statistics
Matches: 513, Mismatches: 29, Indels: 21
0.91 0.05 0.04
Matches are distributed among these distances:
387 135 0.26
396 2 0.00
397 2 0.00
398 305 0.59
399 10 0.02
400 59 0.12
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (399 bp):
AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
TATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGG
GATCGATACTTTTTATAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTATAGAC
CAAAAGTATCGACACAAAATTAAAGAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACC
GGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGAGTTTCGATGTTT
CTGGGATCGATACTTTTTATAAATAGATCGACACTTCATAGATACACCCTTTTTAGCATTCATTC
TGGACCAAA
Found at i:184101 original size:19 final size:19
Alignment explanation
Indices: 184077--184125 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
184067 TTACATTCAC
*
184077 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATAGT
* *
184096 ATACAAATTTATAAATATT
1 ATACAAAATTATAAATAGT
184115 ATACAAAATTA
1 ATACAAAATTA
184126 ACCCTACATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATAGT
Found at i:185706 original size:21 final size:21
Alignment explanation
Indices: 185680--185719 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
185670 CCTCCTCATT
*
185680 TCCTCCATCTTTTCTTCTTCC
1 TCCTCCATATTTTCTTCTTCC
*
185701 TCCTCCCTATTTTCTTCTT
1 TCCTCCATATTTTCTTCTT
185720 TATATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.40, G:0.00, T:0.55
Consensus pattern (21 bp):
TCCTCCATATTTTCTTCTTCC
Found at i:185942 original size:33 final size:33
Alignment explanation
Indices: 185905--185970 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
185895 CATCTTAAGA
*
185905 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
* *
185938 TCACCTCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
185971 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.45, G:0.00, T:0.32
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:186067 original size:21 final size:21
Alignment explanation
Indices: 186004--186068 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
185994 CCCCTTATGC
*
186004 CTCTCAAGTGTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
186025 ATCTCAAGTTTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
186046 CTCTCAAATTTCTCTTTGACT
1 CTCTCAAGTTTCTCTTCGACT
186067 CT
1 CT
186069 TGATTGTCTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.18, C:0.29, G:0.09, T:0.43
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:186883 original size:18 final size:19
Alignment explanation
Indices: 186860--186896 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
186850 ATTTTACACT
186860 TAGGGA-ACCGATTCCCCA
1 TAGGGAGACCGATTCCCCA
186878 TAGGGAGTACCGATTCCCC
1 TAGGGAG-ACCGATTCCCC
186897 CCATGCTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.19
Consensus pattern (19 bp):
TAGGGAGACCGATTCCCCA
Found at i:192643 original size:23 final size:20
Alignment explanation
Indices: 192592--192651 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 20
192582 TTTTGGTGCA
*
192592 GAGGGAATCGA-TCCCCCTT
1 GAGGGAACCGATTCCCCCTT
192611 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-TT
192632 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
192652 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 10 0.28
20 6 0.17
21 3 0.08
22 1 0.03
23 16 0.44
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:192678 original size:20 final size:21
Alignment explanation
Indices: 192634--192673 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
192624 CCCCCTTTGA
*
192634 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
192655 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
192674 TAGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:197445 original size:182 final size:182
Alignment explanation
Indices: 197217--197631 Score: 652
Period size: 182 Copynumber: 2.3 Consensus size: 182
197207 CGTACTTATG
** ** *
197217 AAAGTATTTACACTTTCAATATATCCGGTAGCGCTTTATAGGTTTTATCATTTTGATACCAATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGATACCAATTT
* *
197282 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTT-TAAAAGTATCAATACTTTA
66 TATCATATTTTTACATGTTATATCGTTGTGGATCGATACATTTTTAT-AAAGTATCAACACTTTA
*
197346 TAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
130 TAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATACTTATATT
* *
197399 AAAGTATCGACACTTTAAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGATACCAGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGATACCAATTT
* * * *
197464 TGTCATATTTTTATATGTTATATTGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
66 TATCATATTTTTACATGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCAACACTTTAT
197529 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATACTTATATT
131 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATACTTATATT
* * * *
197581 AAAGTATCGACACGTTCAATATATACGGTAGGGCTTTACCGGTATTATCAT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCAT
197632 ATTTTTACAT
Statistics
Matches: 213, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
182 212 1.00
183 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGATACCAATTT
TATCATATTTTTACATGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCAACACTTTAT
AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATACTTATATT
Found at i:199162 original size:3 final size:3
Alignment explanation
Indices: 199156--199203 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
199146 ATTATTGTAA
* * * *
199156 TAT TAT TAT TAT TAT TATT TGT TGT TGT TGT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
199202 TA
1 TA
199204 ACATTACAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.95
4 2 0.05
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:200605 original size:60 final size:59
Alignment explanation
Indices: 200515--200688 Score: 190
Period size: 60 Copynumber: 2.9 Consensus size: 59
200505 TCTGATTTAT
* * * *
200515 TTGTATTTACT-GTTTAGTCTTTTAATTTTCTGTTTTTGCTGTTTAACCCTTTTAGTT-
1 TTGTATTTGCTAGTTTAGTCCTTTAACTTTCTGTTTTTGCTGTTTAACCCTTTAAGTTG
* * * *
200572 TATGTTTTTGGCTAGTTTAGTCCTTTAACTTTCTGTTTTAGCTATTTTAATCCTTTAAGTTG
1 T-TGTATTT-GCTAGTTTAGTCCTTTAACTTTCTGTTTTTGCT-GTTTAACCCTTTAAGTTG
* * * * *
200634 TTGTATTTGCTATTTTGGTCCTTTAACTTTCTGTATTTACTGTTTAGCCCTTTAA
1 TTGTATTTGCTAGTTTAGTCCTTTAACTTTCTGTTTTTGCTGTTTAACCCTTTAA
200689 ATTTCTGTTA
Statistics
Matches: 95, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
57 1 0.01
58 6 0.06
59 13 0.14
60 54 0.57
61 20 0.21
62 1 0.01
ACGTcount: A:0.16, C:0.14, G:0.13, T:0.57
Consensus pattern (59 bp):
TTGTATTTGCTAGTTTAGTCCTTTAACTTTCTGTTTTTGCTGTTTAACCCTTTAAGTTG
Found at i:200628 original size:30 final size:30
Alignment explanation
Indices: 200526--200697 Score: 111
Period size: 30 Copynumber: 5.8 Consensus size: 30
200516 TGTATTTACT
* * * *
200526 GTTTAGTCTTTTAATTTTCTGTTTTTGCT-
1 GTTTAATCCTTTAACTTTCTGTTTTAGCTA
* * * * *
200555 GTTTAACCCTTTTAGTTTATGTTTTTGGCTA
1 GTTTAATCCTTTAACTTTCTG-TTTTAGCTA
*
200586 GTTTAGTCCTTTAACTTTCTGTTTTAGCTA
1 GTTTAATCCTTTAACTTTCTGTTTTAGCTA
* *
200616 TTTTAATCCTTTAAGTTGT-TGTATTT-GCTA
1 GTTTAATCCTTTAACTT-TCTGT-TTTAGCTA
* **
200646 TTTTGGTCCTTTAACTTTCTGTATTTA-CT-
1 GTTTAATCCTTTAACTTTCTGT-TTTAGCTA
** *
200675 GTTTAGCCCTTTAAATTTCTGTT
1 GTTTAATCCTTTAACTTTCTGTT
200698 AATTATATTT
Statistics
Matches: 114, Mismatches: 23, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
28 1 0.01
29 34 0.30
30 59 0.52
31 20 0.18
ACGTcount: A:0.16, C:0.14, G:0.13, T:0.57
Consensus pattern (30 bp):
GTTTAATCCTTTAACTTTCTGTTTTAGCTA
Found at i:200992 original size:10 final size:10
Alignment explanation
Indices: 200974--201054 Score: 65
Period size: 11 Copynumber: 7.8 Consensus size: 10
200964 AAATGTATGT
200974 TTTTA-TTTA
1 TTTTATTTTA
200983 TTTTATTTTA
1 TTTTATTTTA
*
200993 TTTCATTTGTA
1 TTTTATTT-TA
* * *
201004 TGTTGTTATTG
1 TTTTATT-TTA
*
201015 TTTTGTTTTA
1 TTTTATTTTA
201025 TTTTATTTTA
1 TTTTATTTTA
*
201035 TTTTTATTTAA
1 -TTTTATTTTA
201046 TATTTATTT
1 T-TTTATTT
201055 CCCTTATGTT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
9 5 0.09
10 23 0.40
11 29 0.50
12 1 0.02
ACGTcount: A:0.19, C:0.01, G:0.06, T:0.74
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:201041 original size:6 final size:5
Alignment explanation
Indices: 200974--201054 Score: 65
Period size: 5 Copynumber: 15.6 Consensus size: 5
200964 AAATGTATGT
* * * * *
200974 TTTTA -TTTA TTTTA TTTTA TTTCA TTTGTA TGTTG TTATTG TTTTG TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA TTTTA TT-TTA TTTTA TTTTA
*
201025 TTTTA TTTTA TTTTTA TTTAA TATTTA TTT
1 TTTTA TTTTA -TTTTA TTTTA T-TTTA TTT
201055 CCCTTATGTT
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
4 4 0.06
5 42 0.67
6 17 0.27
ACGTcount: A:0.19, C:0.01, G:0.06, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:201823 original size:25 final size:25
Alignment explanation
Indices: 201793--201841 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
201783 AATCAATTCC
201793 AAATCACCAATT-TTTTCAAAATAAA
1 AAATCA-CAATTGTTTTCAAAATAAA
* *
201818 AAATCATAATTGTTTTTAAAATAA
1 AAATCACAATTGTTTTCAAAATAA
201842 TATTTAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (25 bp):
AAATCACAATTGTTTTCAAAATAAA
Found at i:204042 original size:17 final size:17
Alignment explanation
Indices: 204020--204052 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
204010 TAGCTATCTC
*
204020 TTTTAATTTTATTTTTA
1 TTTTAATATTATTTTTA
204037 TTTTAATATTATTTTT
1 TTTTAATATTATTTTT
204053 CATTGACTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTAATATTATTTTTA
Found at i:207851 original size:15 final size:16
Alignment explanation
Indices: 207819--207851 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
207809 AAAATCTTTC
207819 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
207835 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
207850 TT
1 TT
207852 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:208628 original size:16 final size:17
Alignment explanation
Indices: 208601--208635 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
208591 TATCGCTGAC
208601 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
208618 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
208634 CG
1 CG
208636 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:211981 original size:29 final size:29
Alignment explanation
Indices: 211938--212018 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
211928 CTCACCTAAC
*
211938 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
211968 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
211997 TAAATGATGTAAGTAATGACAT
1 TAAATGATGTAAGCAATGACAT
212019 TAATTTAGTC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:215272 original size:15 final size:15
Alignment explanation
Indices: 215252--215281 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
215242 CTTTCTCATA
215252 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
215267 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
215282 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:216616 original size:29 final size:29
Alignment explanation
Indices: 216574--216651 Score: 129
Period size: 29 Copynumber: 2.7 Consensus size: 29
216564 CTAACTAATT
*
216574 TGATGTAAGCAATGACATCATTACTTAAA
1 TGATGTAAGCAATGACATCATTAATTAAA
*
216603 TGATGTAAGCAATGACATCTTTAATTAAA
1 TGATGTAAGCAATGACATCATTAATTAAA
*
216632 TGATGTAAGTAATGACATCA
1 TGATGTAAGCAATGACATCA
216652 ATTTAGTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (29 bp):
TGATGTAAGCAATGACATCATTAATTAAA
Found at i:217879 original size:20 final size:20
Alignment explanation
Indices: 217850--217905 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
217840 ATTCGCGTTG
*
217850 CATTTTGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
217870 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
217890 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
217906 AGTCTACAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:217925 original size:22 final size:22
Alignment explanation
Indices: 217897--217968 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
217887 TTCCATTTCG
217897 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * *
217919 CGTTGCGAT--TTTTCAAATT-T
1 CGTTGCGATAGTCTAC-AGTTGT
217939 -GTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
217960 CGTTGCGAT
1 CGTTGCGAT
217969 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 8 0.21
20 7 0.18
21 7 0.18
22 17 0.44
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:217950 original size:41 final size:41
Alignment explanation
Indices: 217877--217990 Score: 176
Period size: 41 Copynumber: 2.8 Consensus size: 41
217867 TTCCATTTCG
*
217877 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
* *
217919 CGTTGCGATTTTTCAAATTTGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
217960 CGTTGCGATTTTCCAAATTCGTTGCGATAGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGT
217991 TAAAAAAAAG
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 50 0.76
42 13 0.20
43 3 0.05
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:217983 original size:19 final size:19
Alignment explanation
Indices: 217918--217987 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
217908 TCTACAGTTG
*
217918 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTACAAAT
* * **
217937 TTGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTACAAAT
*
217958 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTACAAAT
217978 TCGTTGCGAT
1 TCGTTGCGAT
217988 AGTTAAAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 19 0.50
20 5 0.13
21 5 0.13
22 9 0.24
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGTTGCGATTTTACAAAT
Found at i:219011 original size:2 final size:2
Alignment explanation
Indices: 219006--219059 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
218996 GCAGAGAGCT
219006 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
219048 TA TA TA TA TA TA
1 TA TA TA TA TA TA
219060 ATTGGGAGGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:220816 original size:45 final size:45
Alignment explanation
Indices: 220766--220855 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
220756 GTCCAATGTG
*
220766 ACTTTCGGTCCTGCAATTGCCGTGGGGGCCAATGAATTATCAATT
1 ACTTTCGGTCCTGAAATTGCCGTGGGGGCCAATGAATTATCAATT
* * * * * *
220811 ACTTTCGGTGCTGAAATTGTCGTGGGGTCCAGTGCATTTTCAATT
1 ACTTTCGGTCCTGAAATTGCCGTGGGGGCCAATGAATTATCAATT
220856 GTTGCATTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (45 bp):
ACTTTCGGTCCTGAAATTGCCGTGGGGGCCAATGAATTATCAATT
Found at i:226170 original size:45 final size:45
Alignment explanation
Indices: 226120--226209 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
226110 GTCCAATGTG
*
226120 ACTTTCGGTCCTGCAATTGCCGTGGGGGCCAATGAATTATCAATT
1 ACTTTCGGTCCTGAAATTGCCGTGGGGGCCAATGAATTATCAATT
* * * * * *
226165 ACTTTCGGTGCTGAAATTGTCGTGGGGTCCAGTGCATTTTCAATT
1 ACTTTCGGTCCTGAAATTGCCGTGGGGGCCAATGAATTATCAATT
226210 GTTGCATTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (45 bp):
ACTTTCGGTCCTGAAATTGCCGTGGGGGCCAATGAATTATCAATT
Found at i:230478 original size:29 final size:29
Alignment explanation
Indices: 230435--230517 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
230425 CTCACCTAAC
*
230435 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
230465 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
230494 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
230518 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:233583 original size:20 final size:20
Alignment explanation
Indices: 233558--233609 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
233548 TAGTTGAAAA
233558 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
233578 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
233598 TCGCGTTGCGAT
1 TCGCGTTGCGAT
233610 AATCTACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:233645 original size:19 final size:20
Alignment explanation
Indices: 233601--233691 Score: 78
Period size: 19 Copynumber: 4.5 Consensus size: 20
233591 TTCCATTTCG
* *
233601 CGTTGCGATAATCTACAATGT
1 CGTTGCGATATTCCA-AATGT
233622 CGTTGCGATATTCCAAAT-T
1 CGTTGCGATATTCCAAATGT
* * **
233641 CGTTGTGATAGTCTACAGTTGT
1 CGTTGCGATA-T-TCCAAATGT
*
233663 CGTTGCGATTTTCCAAAT-T
1 CGTTGCGATATTCCAAATGT
233682 CGTTGCGATA
1 CGTTGCGATA
233692 GTTAAAAAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
19 20 0.36
20 8 0.15
21 18 0.33
22 9 0.16
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
CGTTGCGATATTCCAAATGT
Found at i:233692 original size:41 final size:40
Alignment explanation
Indices: 233581--233693 Score: 147
Period size: 41 Copynumber: 2.8 Consensus size: 40
233571 TTCCATTTCG
* *
233581 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAATCTACAATGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAATGT
* * *
233622 CGTTGCGATATTCCAAATTCGTTGTGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACA-ATGT
233663 CGTTGCGATTTTCCAAATTCGTTGCGATAGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGT
233694 TAAAAAAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
40 15 0.24
41 45 0.71
42 3 0.05
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.39
Consensus pattern (40 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAATGT
Found at i:234458 original size:21 final size:21
Alignment explanation
Indices: 234432--234488 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
234422 ACAACTGTAG
234432 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
*
234453 ACTATCGCAACGTGATTTTCA
1 ACTATCGCAACGCGATTTTCA
*
234474 ATTATCGCAACGCGA
1 ACTATCGCAACGCGA
234489 AATGCAACGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTTCA
Found at i:235154 original size:15 final size:15
Alignment explanation
Indices: 235134--235163 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
235124 CTTTCTCATA
235134 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
235149 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
235164 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:236482 original size:29 final size:29
Alignment explanation
Indices: 236439--236550 Score: 188
Period size: 29 Copynumber: 3.8 Consensus size: 29
236429 CTCACCTAAC
236439 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
236469 TAAATGATGTAAGCAATGACATCATTACT
1 TAAATGATGTAAGCAATGACATCATTACT
* *
236498 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTACT
*
236527 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
236551 ATTTAGTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 74 0.95
30 4 0.05
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:239847 original size:48 final size:48
Alignment explanation
Indices: 239790--239900 Score: 177
Period size: 48 Copynumber: 2.3 Consensus size: 48
239780 AAAAAAGTCA
*
239790 TTATAATATTATAATAAATTATAAAAATTTAAAAGTATAATAATTATT
1 TTATAATATTATAATAAATTATAAAAAATTAAAAGTATAATAATTATT
** *
239838 TTATAATATTACGATAAATTATAAAAAATTATAAGTATAATAATTATT
1 TTATAATATTATAATAAATTATAAAAAATTAAAAGTATAATAATTATT
*
239886 TTATAATATTTTAAT
1 TTATAATATTATAAT
239901 TCAATTTAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (48 bp):
TTATAATATTATAATAAATTATAAAAAATTAAAAGTATAATAATTATT
Found at i:240948 original size:21 final size:21
Alignment explanation
Indices: 240897--240949 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
240887 ATTATTACTA
240897 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
240918 TCGCGTTGCGATTTTCTCAA-T
1 TCGCAATGCGATTTTC-CAATT
240939 TCGCAATGCGA
1 TCGCAATGCGA
240950 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:241013 original size:21 final size:21
Alignment explanation
Indices: 240989--241051 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
240979 TCGCAATGTA
*
240989 ATTTTCCTAATTCGCATTGCG
1 ATTTTCATAATTCGCATTGCG
* * *
241010 ATTTACGT-ATTCGCGTTGCG
1 ATTTTCATAATTCGCATTGCG
*
241030 ATTTTCATAATTCGCAATGCG
1 ATTTTCATAATTCGCATTGCG
241051 A
1 A
241052 ATACGTAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (21 bp):
ATTTTCATAATTCGCATTGCG
Found at i:241066 original size:20 final size:20
Alignment explanation
Indices: 241041--241134 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
241031 TTTTCATAAT
241041 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
241061 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
241081 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
241102 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
241122 TCGCAATGCGAAT
1 TCGCAATGCGAAT
241135 CTGACTATCG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 46 0.72
21 18 0.28
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:241072 original size:41 final size:39
Alignment explanation
Indices: 241033--241134 Score: 114
Period size: 41 Copynumber: 2.5 Consensus size: 39
241023 CGTTGCGATT
* *
241033 TTCATAATTCGCAATGCGAATACGTAAATCGCAACGCGA
1 TTCATAAATCGCAATGCGAATACGAAAATCGCAACGCGA
* * *
241072 TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGAA
1 TTCA-TAAATCGCAATGCGAA-TACGAAAATCGCAACGCG-A
* *
241114 TACGTAAATCGCAATGCGAAT
1 TTCATAAATCGCAATGCGAAT
241135 CTGACTATCG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
39 3 0.06
40 16 0.31
41 31 0.60
42 2 0.04
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.23
Consensus pattern (39 bp):
TTCATAAATCGCAATGCGAATACGAAAATCGCAACGCGA
Found at i:241106 original size:102 final size:101
Alignment explanation
Indices: 240896--241112 Score: 242
Period size: 102 Copynumber: 2.1 Consensus size: 101
240886 GATTATTACT
* **
240896 ATCGCAATGCGATTTTCCAATTTCGCGTTGCGATTTTCTCAATTCGCAATGCGAATAAGTAAATC
1 ATCGCAATGCGATTTACGTA-TTCGCGTTGCGATTTTCTCAATTCGCAATGCGAATAAGTAAATC
* * * *
240961 GCAATGCGATACTAACTATCGCAATGTAATTTTCCTAA
65 GCAACGCGATACTAAC-ATCGCAATGGAATTTACCAAA
* * *
240999 TTCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCAT-AATTCGCAATGCGAATACGTAAATC
1 ATCGCAATGCGATTTACGTATTCGCGTTGCGATTTTC-TCAATTCGCAATGCGAATAAGTAAATC
* **
241063 GCAACGCGATTAAGTAA-ATCGCAATGCGAA-TTAGGAAA
65 GCAACGCGA-T-ACTAACATCGCAATG-GAATTTACCAAA
241101 ATCGCAATGCGA
1 ATCGCAATGCGA
241113 ATACGTAAAT
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
102 72 0.76
103 19 0.20
104 4 0.04
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (101 bp):
ATCGCAATGCGATTTACGTATTCGCGTTGCGATTTTCTCAATTCGCAATGCGAATAAGTAAATCG
CAACGCGATACTAACATCGCAATGGAATTTACCAAA
Found at i:241742 original size:19 final size:19
Alignment explanation
Indices: 241678--241762 Score: 81
Period size: 19 Copynumber: 4.7 Consensus size: 19
241668 TAGTTTCGAG
*
241678 AATGAAAATCGCATCGCGGA
1 AATGAAAATCGCAACGC-GA
241698 AATGAAAATCGCAA--CG-
1 AATGAAAATCGCAACGCGA
* *
241714 -A-GAGAATCGCAAGGCGA
1 AATGAAAATCGCAACGCGA
241731 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
**
241750 AACCAAAATCGCA
1 AATGAAAATCGCA
241763 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 1 0.02
18 2 0.04
19 25 0.46
20 13 0.24
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:241847 original size:20 final size:19
Alignment explanation
Indices: 241758--241870 Score: 128
Period size: 19 Copynumber: 6.1 Consensus size: 19
241748 GAAACCAAAA
*
241758 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
241777 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
241796 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
241810 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
241829 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
241849 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
241869 TC
1 TC
241871 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.12
16 2 0.03
17 3 0.04
19 32 0.40
20 32 0.40
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:244186 original size:18 final size:18
Alignment explanation
Indices: 244163--244210 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
244153 CGGGTCGATT
244163 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
244181 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
244199 AGGTGATGGCTC
1 AGGTGATGGCTC
244211 CCAAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:245554 original size:20 final size:20
Alignment explanation
Indices: 245529--245566 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
245519 AATAGTTTCT
245529 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
245549 GAAAATGACAATCGCAAC
1 GAAAATGAAAATCGCAAC
245567 GCAAATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.21, G:0.16, T:0.11
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:245877 original size:22 final size:22
Alignment explanation
Indices: 245850--245893 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
245840 GATGGAGATA
245850 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
245872 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
245894 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:246109 original size:20 final size:20
Alignment explanation
Indices: 246080--246152 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
246070 GATTATGTAT
* *
246080 TATCTCGTTGTGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
246100 TATCGTGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
246120 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
246140 TATCGCATTGCGA
1 TATCGCGTTGCGA
246153 TTTTGTATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:246256 original size:21 final size:22
Alignment explanation
Indices: 246204--246256 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
246194 ATTTACTTAT
246204 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
246225 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
246246 TCGCATTGCGA
1 TCGCATTGCGA
246257 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:247964 original size:3 final size:3
Alignment explanation
Indices: 247956--247987 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
247946 ATTAACATTT
*
247956 TTC TTC TTC TTC TTC TTC TTC TTC TTA TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
247988 TATCATTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:248273 original size:6 final size:6
Alignment explanation
Indices: 248262--248287 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
248252 AGATCGAATA
248262 AAAATG AAAATG AAAATG AAAATG AA
1 AAAATG AAAATG AAAATG AAAATG AA
248288 TGATAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:248482 original size:18 final size:17
Alignment explanation
Indices: 248437--248483 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
248427 CAAAATAAGG
248437 AATAAA-AATAAAACAA
1 AATAAATAATAAAACAA
248453 AATAAATAAATAAATA-AA
1 AATAAAT-AATAAA-ACAA
248471 ATATAAATAATAA
1 A-ATAAATAATAA
248484 TAATGATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.22
18 14 0.52
19 7 0.26
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (17 bp):
AATAAATAATAAAACAA
Found at i:248529 original size:3 final size:3
Alignment explanation
Indices: 248476--248515 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
248466 ATAAAATATA
* *
248476 AAT AAT AAT AAT GAT AAT GAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
248516 GAAAGAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:248534 original size:2 final size:2
Alignment explanation
Indices: 248527--248562 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
248517 AAAGAAAATA
248527 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
248563 GTAATAACGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:264463 original size:20 final size:21
Alignment explanation
Indices: 264438--264477 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
264428 AAATTCAGTG
264438 CAAAAAAATCA-TTATATACT
1 CAAAAAAATCATTTATATACT
*
264458 CAAAAAAATTATTTATATAC
1 CAAAAAAATCATTTATATAC
264478 AAACTTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (21 bp):
CAAAAAAATCATTTATATACT
Found at i:270482 original size:17 final size:18
Alignment explanation
Indices: 270449--270482 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
270439 CCGCTACTAG
270449 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
270467 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
270483 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:271314 original size:12 final size:12
Alignment explanation
Indices: 271299--271328 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
271289 CGATAGCATG
271299 ACCGGTTCGCTA
1 ACCGGTTCGCTA
271311 ACCGGTTCGCTA
1 ACCGGTTCGCTA
271323 ACCGGT
1 ACCGGT
271329 CCGGTTCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.17, C:0.33, G:0.27, T:0.23
Consensus pattern (12 bp):
ACCGGTTCGCTA
Found at i:276136 original size:29 final size:30
Alignment explanation
Indices: 276094--276151 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
276084 ATTATTTATT
* *
276094 TTTAAAGATGTTAATATTTATATTTTTTAG
1 TTTAAAGATGTTAATATTGAAATTTTTTAG
*
276124 TTTAAA-ATTTTAATATTGAAATTTTTTA
1 TTTAAAGATGTTAATATTGAAATTTTTTA
276152 ATTTGTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (30 bp):
TTTAAAGATGTTAATATTGAAATTTTTTAG
Found at i:276543 original size:20 final size:20
Alignment explanation
Indices: 276449--276817 Score: 431
Period size: 20 Copynumber: 18.4 Consensus size: 20
276439 GATTTTCCAT
* ** *
276449 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
276469 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
276489 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
276509 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
276529 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
276549 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
276569 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
276589 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
276609 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
276629 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
276649 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
276669 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
276689 AATCGCAACG-ATAATTCGTA
1 AATCGCAACGCGT-ATCCGTA
*
276709 AATCGCAACGCGTATCCATA
1 AATCGCAACGCGTATCCGTA
*
276729 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
276749 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
276769 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
276789 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
276809 AATCACAAC
1 AATCGCAAC
276818 ACTGAAATTT
Statistics
Matches: 301, Mismatches: 40, Indels: 16
0.84 0.11 0.04
Matches are distributed among these distances:
19 3 0.01
20 295 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:277538 original size:24 final size:24
Alignment explanation
Indices: 277499--277545 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
277489 AAATTTGGTC
277499 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
277523 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
277546 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:277737 original size:12 final size:12
Alignment explanation
Indices: 277720--277744 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
277710 ATATAATCCT
277720 GAAGAAGAAAAA
1 GAAGAAGAAAAA
277732 GAAGAAGAAAAA
1 GAAGAAGAAAAA
277744 G
1 G
277745 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:280081 original size:53 final size:52
Alignment explanation
Indices: 280020--280159 Score: 167
Period size: 52 Copynumber: 2.7 Consensus size: 52
280010 CGGAAAATAC
*
280020 AATCGCAACGCGA-AAT-GAAAATCCCAACATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGAGAGAATCG-AAATCCCAA-ATGAAAATCGCAATGC-GAAATGAA
* * *
280073 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGAAATCCCAAATGAAAATCGCAATGCGAAATGAA
* * * *
280125 AATCGCAACGAAAGAATCGCAATGCGAAATGAAAA
1 AATCGCAACGAGAGAATCGAAATCCCAAATGAAAA
280160 ATATAAGAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
52 42 0.52
53 28 0.35
54 9 0.11
55 1 0.01
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.13
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGAAATCCCAAATGAAAATCGCAATGCGAAATGAA
Found at i:280107 original size:33 final size:33
Alignment explanation
Indices: 280020--280113 Score: 136
Period size: 34 Copynumber: 2.8 Consensus size: 33
280010 CGGAAAATAC
* *
280020 AATCGCAACGCGAAATGAAAATCCCAACATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACATGAA
*
280053 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAAC-ATGAA
280087 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
280114 TGCGAAATGA
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
33 26 0.46
34 29 0.52
35 1 0.02
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACATGAA
Found at i:280135 original size:52 final size:53
Alignment explanation
Indices: 280048--280159 Score: 208
Period size: 52 Copynumber: 2.1 Consensus size: 53
280038 AAATCCCAAC
*
280048 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
280101 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
280153 ATGAAAA
1 ATGAAAA
280160 ATATAAGAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 42 0.72
53 16 0.28
ACGTcount: A:0.48, C:0.16, G:0.22, T:0.13
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:280144 original size:14 final size:17
Alignment explanation
Indices: 280052--280158 Score: 91
Period size: 19 Copynumber: 6.2 Consensus size: 17
280042 CCCAACATGA
280052 AAATCGCAATGCGGAAATG
1 AAATCGCAA-GC-GAAATG
*
280071 AAAATCGCAA-CGAGA-G
1 -AAATCGCAAGCGAAATG
280087 -AATCGCAATGCGAAATG
1 AAATCGCAA-GCGAAATG
280104 AAAATCGCAATGCGAAATG
1 -AAATCGCAA-GCGAAATG
280123 AAAATCGCAA-CGAAA-G
1 -AAATCGCAAGCGAAATG
280139 -AATCGCAATGCGAAATG
1 AAATCGCAA-GCGAAATG
280156 AAA
1 AAA
280159 AATATAAGAA
Statistics
Matches: 76, Mismatches: 2, Indels: 20
0.78 0.02 0.20
Matches are distributed among these distances:
14 16 0.21
16 11 0.14
17 10 0.13
18 3 0.04
19 27 0.36
20 9 0.12
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (17 bp):
AAATCGCAAGCGAAATG
Found at i:280181 original size:11 final size:11
Alignment explanation
Indices: 280155--280187 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
280145 AATGCGAAAT
280155 GAAAAATATAA
1 GAAAAATATAA
280166 G--AAATATAA
1 GAAAAATATAA
280175 GAAAAATATAA
1 GAAAAATATAA
280186 GA
1 GA
280188 CTTACCCCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.45
11 11 0.55
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (11 bp):
GAAAAATATAA
Found at i:281102 original size:14 final size:14
Alignment explanation
Indices: 281083--281139 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
281073 GCGAAATTAA
*
281083 AATCGCAACGACAG
1 AATCGCAACGAAAG
281097 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
281114 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
281130 AATCGCAACG
1 AATCGCAACG
281140 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:281110 original size:33 final size:33
Alignment explanation
Indices: 281064--281156 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
281054 GCGAAACCAA
* *
281064 AATCGCAACGCGAAATTAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
281097 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
281130 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
281157 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:281121 original size:19 final size:19
Alignment explanation
Indices: 281027--281161 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
281017 TAGTTTACTT
* *
281027 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
281047 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
281066 TCGCAACGCGAAATTAAAA
1 TCGCAACGCGAAATGAAAA
*
281085 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
281099 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
281118 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
281132 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
281151 TCGCAATGCGA
1 TCGCAACGCGA
281162 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.17
16 10 0.10
17 11 0.11
19 47 0.49
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:281179 original size:19 final size:19
Alignment explanation
Indices: 281157--281285 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
281147 AAAATCGCAA
281157 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
281176 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
281190 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
281209 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
281223 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
281242 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
281261 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
281281 TGCGA
1 TGCGA
281286 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:281199 original size:33 final size:33
Alignment explanation
Indices: 281157--281248 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
281147 AAAATCGCAA
281157 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
281190 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
281223 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
281249 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:281551 original size:92 final size:93
Alignment explanation
Indices: 281329--281890 Score: 1071
Period size: 92 Copynumber: 6.1 Consensus size: 93
281319 TTGAATGGAT
281329 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
281394 AGTTTAGCATAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
281422 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
281485 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
281513 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
281577 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
281605 AAA-TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
281669 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
281697 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
281761 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
281789 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
281854 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
281882 AAATTTACT
1 AAATTTACT
281891 AAGCAATCTA
Statistics
Matches: 462, Mismatches: 2, Indels: 10
0.97 0.00 0.02
Matches are distributed among these distances:
91 109 0.24
92 234 0.51
93 119 0.26
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:283608 original size:14 final size:14
Alignment explanation
Indices: 283589--283678 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
283579 TTGAAATGAA
283589 AATCGCAACGAGAG
1 AATCGCAACGAGAG
283603 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
283620 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
283636 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
283655 AATCGCAACGAGAG
1 AATCGCAACGAGAG
283669 AATCGCAACG
1 AATCGCAACG
283679 CGAAACCAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:283626 original size:33 final size:33
Alignment explanation
Indices: 283581--283694 Score: 192
Period size: 33 Copynumber: 3.5 Consensus size: 33
283571 TCTTTTGGTT
283581 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
283614 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
283647 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
283680 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
283695 TTGCGATTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.45, C:0.23, G:0.24, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:283712 original size:19 final size:19
Alignment explanation
Indices: 283690--283754 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
283680 GAAACCAAAA
*
283690 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
283709 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
283723 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
283742 TCGCGTTGCGATT
1 TCGCGTTGCGATT
283755 CTCTCGTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 22 0.58
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:283731 original size:14 final size:14
Alignment explanation
Indices: 283712--283766 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
283702 TTTCATTTCG
283712 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
283726 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
283745 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
283759 CGTTGCGA
1 CGTTGCGA
283767 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:283737 original size:33 final size:33
Alignment explanation
Indices: 283695--283766 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
283685 CAAAATCGCA
283695 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
283728 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
283761 TTGCGA
1 TTGCGA
283767 CAGTCATTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:283774 original size:33 final size:33
Alignment explanation
Indices: 283704--283788 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
283694 ATTGCGATTT
***
283704 TCATTTCGCGTTGCGATTCTCTCGTTGCGATTT
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGACAG
283737 TCATTTCGCGTTGCGATTCTCTCGTTGCGACAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGACAG
*
283770 TCATTCTCTCGTTGCGATT
1 TCATT-TCGCGTTGCGATT
283789 TTCATTTATC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 35 0.74
34 12 0.26
ACGTcount: A:0.11, C:0.26, G:0.21, T:0.42
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTTGCGACAG
Found at i:283793 original size:20 final size:20
Alignment explanation
Indices: 283719--283807 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
283709 TCGCGTTGCG
283719 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
283739 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
283752 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
283772 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
283792 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
283808 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:283929 original size:33 final size:33
Alignment explanation
Indices: 283887--283957 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
283877 AATACTAACT
*
283887 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
283920 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
283953 TGAAA
1 TGAAA
283958 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:284191 original size:22 final size:22
Alignment explanation
Indices: 284139--284193 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
284129 TGGTTGTGAG
**
284139 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
284161 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
284183 GGATTTCTTCG
1 GGATTTCTTCG
284194 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:284362 original size:20 final size:20
Alignment explanation
Indices: 284337--284529 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
284327 CTTTAAATAT
284337 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
284357 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
284379 -TCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
284398 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
284418 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
284438 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
284458 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
284478 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
284498 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
284518 CGCGTTGCGATT
1 CGCGTTGCGATT
284530 ATGGAAAATC
Statistics
Matches: 144, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.88
21 14 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:284524 original size:60 final size:60
Alignment explanation
Indices: 284337--284529 Score: 242
Period size: 60 Copynumber: 3.2 Consensus size: 60
284327 CTTTAAATAT
** *
284337 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
284398 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
284458 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
284518 CGCGTTGCGATT
1 CGCGTTGCGATT
284530 ATGGAAAATC
Statistics
Matches: 110, Mismatches: 22, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
60 82 0.75
61 28 0.25
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:284610 original size:20 final size:20
Alignment explanation
Indices: 284585--284636 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
284575 AAGAATCGCG
*
284585 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
284605 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
284625 TTGCGATTCTGG
1 TTGCGATTCTGG
284637 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:285362 original size:16 final size:16
Alignment explanation
Indices: 285337--285373 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
285327 GTTTATGAAC
* *
285337 ATAAATGAACTAGTCG
1 ATAAACGAACAAGTCG
285353 ATAAACGAACAAGTCG
1 ATAAACGAACAAGTCG
285369 ATAAA
1 ATAAA
285374 TAATCTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (16 bp):
ATAAACGAACAAGTCG
Found at i:294796 original size:2 final size:2
Alignment explanation
Indices: 294789--294822 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
294779 ATAAAACCAA
294789 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
294823 CAAAAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:311813 original size:24 final size:23
Alignment explanation
Indices: 311779--311828 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
311769 TTTTGATCAA
*
311779 TTTTAATATTT-TAATATTTATT
1 TTTTAATATTTCAAATATTTATT
*
311801 TTTTAAATCATTTCAAATGTTTATT
1 TTTT-AAT-ATTTCAAATATTTATT
311826 TTT
1 TTT
311829 GTTTCATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.17
23 3 0.13
24 4 0.17
25 12 0.52
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTTAATATTTCAAATATTTATT
Found at i:312862 original size:16 final size:16
Alignment explanation
Indices: 312841--312893 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
312831 ATCTTTTGGA
312841 TTATTTTTAAGATATT
1 TTATTTTTAAGATATT
* * *
312857 TTATTTTGAATATTTCT
1 TTATTTTTAAGATAT-T
*
312874 TCTATCTTTAAGATATT
1 T-TATTTTTAAGATATT
312891 TTA
1 TTA
312894 GACTATAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
16 14 0.50
17 4 0.14
18 10 0.36
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (16 bp):
TTATTTTTAAGATATT
Found at i:316078 original size:23 final size:22
Alignment explanation
Indices: 316040--316090 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
316030 TAAAATATAA
316040 AAAAATTGTTAATTTTTTTATC
1 AAAAATTGTTAATTTTTTTATC
316062 AAAAATTGTTAATTTTTTTATC
1 AAAAATTGTTAATTTTTTTATC
316084 AAAAATT
1 AAAAATT
316091 TAAATACTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (22 bp):
AAAAATTGTTAATTTTTTTATC
Found at i:316997 original size:23 final size:26
Alignment explanation
Indices: 316954--317003 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
316944 ATTATGAGAA
*
316954 AAAATAATTTATATATATTTATAAAT
1 AAAATAATTTATATATATTTAGAAAT
316980 AAAAT-ATTTAT-T-TATTTAGAAAT
1 AAAATAATTTATATATATTTAGAAAT
317003 A
1 A
317004 TCAGAAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 6 0.26
26 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AAAATAATTTATATATATTTAGAAAT
Found at i:317077 original size:23 final size:22
Alignment explanation
Indices: 317053--317097 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
317043 CTTCGATATT
317053 AATAAATATTAATATAATAATTTA
1 AATAAA-ATTAA-ATAATAATTTA
*
317077 AATAAAATTAAATTATAATTT
1 AATAAAATTAAATAATAATTT
317098 TTTATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATAAAATTAAATAATAATTTA
Found at i:318688 original size:3 final size:3
Alignment explanation
Indices: 318682--318744 Score: 92
Period size: 3 Copynumber: 21.0 Consensus size: 3
318672 TTTATTTTTT
* *
318682 TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
318727 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
318745 AATGGGTAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.91
4 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:319102 original size:124 final size:118
Alignment explanation
Indices: 318881--319169 Score: 350
Period size: 124 Copynumber: 2.4 Consensus size: 118
318871 ATGTTGAATA
* * * *
318881 AATTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGAGATGATGTTGACC
1 AATTCTTCTTTTTCTTCAGATGAGTTCTTCTCATTATGAAC-TT-CTCTGGAGATGATGCTAACC
* * * ** *
318946 TATTTTCTTCTGTGATAGAGTCATTTAAAAGGTTGAATAAGCTCTTCTTATTATG
64 TATCTGCTTCTGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATG
*
319001 AACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACATTCTCTGGAAAGGTTGATGCT
1 AA-TTCTTCTTT-TTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGG--A-GATGATGCT
* * *
319066 AATCTATCTGCTTCTGTGATAGAATTATGCAAAAGGTTGAATAAGCTCTTCTCATTGTG
60 AACCTATCTGCTTCTGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATG
319125 AA--CTT-TTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCT
1 AATTCTTCTTT-TTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCT
319170 AAAAAAGCTG
Statistics
Matches: 148, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
119 6 0.04
120 35 0.24
121 16 0.11
122 32 0.22
123 1 0.01
124 58 0.39
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.43
Consensus pattern (118 bp):
AATTCTTCTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAGATGATGCTAACCTA
TCTGCTTCTGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATG
Found at i:319429 original size:113 final size:113
Alignment explanation
Indices: 319094--320899 Score: 2756
Period size: 113 Copynumber: 16.0 Consensus size: 113
319084 ATAGAATTAT
* * * * *
319094 GCAAAAGGTTGAATAAGCTCTTCTCATTGTGAAC-T-TT-TT-ATTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* ** * * * * *
319155 ATTATGAACTTC--TCTAAAAAAGCTGATCCA-TCAAGTGATGGATTTGA
66 ATTATGAAC-TCGAACTGGAAATGTTGATCCATTGAA-TGATGAATTTAA
* *
319202 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTT
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
* * * * **
319263 CTTATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTTAA
63 CTCATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
*
319314 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
319379 ATTATGAGCTCGAACTGGAAATGCTGATCCATTGAATCATGAATTCAA
66 ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
*
319427 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
319492 ATTACGAACTCGAACTGGAAATGTTGATCCATTGAATGATGGATTTAA
66 ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
*
319540 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
319605 ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATCATGAATTCAA
66 ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
*
319653 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
319718 ATTATGAGCTCGAACTGGAAATGATGATCCATTGAATCATGAATTCAA
66 ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
319766 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
319831 ATTACGAACTCGAACTGGAAATGTTGATCCATTGAATGATGGATTTAA
66 ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
319879 GCAAAAAGTTGAACAAGTTCTTCTCATTATCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
1 GCAAAAAGTTGAACAAGTTC-T-TC----TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
* * * *
319944 CTTCTCATTATGAACTCGAACTGGAAATGCTGATCAATTGAATCATGAATTCAA
60 CTTCTCATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
* *
319998 GCAAAAACTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
320063 ATTATGAACTCGAACTGGTAATGTTGATCCATTGAATGATGAATTTAA
66 ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
320111 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
320176 ATTATGAACTAGAACTGGAAATGTTGATCCATTGAATCATGAATTCAA
66 ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
320224 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
320289 ATTACGAACTCGAACTGGAAATGTTGACCCATTGAATGATGGATTTAA
66 ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
320337 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
320402 ATTACGAACTCAAACTGGAAATGTTGATCCATTGAATGAT-AGGTTTAA
66 ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGA-ATTTAA
320450 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * *
320515 ATTACAAACTCGAACTGGAAATGTTGACCCATTGAATGATGGATTTAA
66 ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
320563 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
320628 ATTACGAACTCAAACTGGAAATGTTGATCCATTGAATGAT-AGATTTAA
66 ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGA-ATTTAA
320676 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
320741 ATTATGAACTCGAACTGGAAATGCTGATCCATTAAATCATGAATTCAA
66 ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
*
320789 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * ** *
320854 ATTATGAACTCGAACTGGTAATGCTGGTCCATCAAATGATGGATTT
66 ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTT
320900 GAATCTTTGC
Statistics
Matches: 1573, Mismatches: 104, Indels: 37
0.92 0.06 0.02
Matches are distributed among these distances:
107 3 0.00
108 41 0.03
110 2 0.00
111 19 0.01
112 53 0.03
113 1328 0.84
114 3 0.00
115 7 0.00
116 11 0.01
117 2 0.00
118 1 0.00
119 103 0.07
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
Found at i:321848 original size:93 final size:92
Alignment explanation
Indices: 321689--322175 Score: 758
Period size: 93 Copynumber: 5.2 Consensus size: 92
321679 TTTATTTGTA
* * * *
321689 CTATGAGCACATTCATCTTTCAAATCCAATGATTAGTTCTGTAGTTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTT-TTTGGGTTCATACCAAACCAGATCAG
321754 ATAACTCAAAGAACACTTCCAGAAGATG
65 ATAACTCAAAGAACACTTCCAGAAGATG
* *
321782 CTATGAGCACCTTCATCTTTCAAATTCAATGATTGGTTTTTCGGGTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTT-GGGTTCATACCAAACCAGATCAG
321847 ATAACTCAAAGAACACTTCCAGAAGATG
65 ATAACTCAAAGAACACTTCCAGAAGATG
* * * *
321875 CTATGAGCACCTTCATCTTTTAAATTCAATGATTGGTTTTTCGGGTTCATACCAAACCGGATCAG
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTT-GGGTTCATACCAAACCAGATCAG
321940 ATAACTCAAAGAACACTTCCAGAAGATG
65 ATAACTCAAAGAACACTTCCAGAAGATG
* * * *
321968 TTATGAGCACATTCATCTTTCAAGTCCAATGATGGGGTTTTGGGGTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTTCAAATCCAATGAT-TGGTTTTTGGGTTCATACCAAACCAGATCAG
322033 ATAACTCAAAGAACACTTCCAGAAGATG
65 ATAACTCAAAGAACACTTCCAGAAGATG
* * * *
322061 CTATGAGCACATTCATTTTTCAAGTCCAATGATGGGGTTTTGGAGTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTTGG-GTTCATACCAAACCAGATCAG
*
322126 ATAACTCAAAGAATACTTCCAGAAGATG
65 ATAACTCAAAGAACACTTCCAGAAGATG
322154 CTATGAGCACATTCATCTTTCA
1 CTATGAGCACATTCATCTTTCA
322176 CTTGAATCTG
Statistics
Matches: 369, Mismatches: 22, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
92 10 0.03
93 353 0.96
94 6 0.02
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.29
Consensus pattern (92 bp):
CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTTGGGTTCATACCAAACCAGATCAGA
TAACTCAAAGAACACTTCCAGAAGATG
Found at i:323162 original size:8 final size:7
Alignment explanation
Indices: 323142--323195 Score: 58
Period size: 7 Copynumber: 7.4 Consensus size: 7
323132 TCTTGACACC
323142 CTTTTTT
1 CTTTTTT
323149 CTTTTTT
1 CTTTTTT
323156 CTCTTTTT
1 CT-TTTTT
323164 CTTTTCTT
1 CTTTT-TT
323172 -TTTTTT
1 CTTTTTT
323178 CTTTCTATT
1 CTTT-T-TT
323187 -TTTTTT
1 CTTTTTT
323193 CTT
1 CTT
323196 CAAGCATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
6 4 0.10
7 22 0.54
8 13 0.32
9 2 0.05
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (7 bp):
CTTTTTT
Found at i:323188 original size:20 final size:20
Alignment explanation
Indices: 323145--323192 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
323135 TGACACCCTT
* *
323145 TTTTCTTTTTTCTCTTTTTC
1 TTTTCTTTTTTCTCTTTCTA
*
323165 TTTTCTTTTTTTTCTTTCTA
1 TTTTCTTTTTTCTCTTTCTA
323185 TTTT-TTTT
1 TTTTCTTTT
323193 CTTCAAGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTCTTTTTTCTCTTTCTA
Found at i:323190 original size:14 final size:14
Alignment explanation
Indices: 323143--323195 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
323133 CTTGACACCC
323143 TTTTTTCTTTT-TT
1 TTTTTTCTTTTCTT
323156 CTCTTTTTCTTTTCTT
1 -T-TTTTTCTTTTCTT
*
323172 TTTTTTCTTTCTATT
1 TTTTTTCTTT-TCTT
323187 TTTTTTCTT
1 TTTTTTCTT
323196 CAAGCATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
14 10 0.29
15 23 0.66
16 2 0.06
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTCTTTTCTT
Found at i:334440 original size:23 final size:26
Alignment explanation
Indices: 334397--334446 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
334387 ATTATGAGAA
*
334397 AAAATAATTTATATATATTTATAAAT
1 AAAATAATTTATATATATTTAGAAAT
334423 AAAAT-ATTTAT-T-TATTTAGAAAT
1 AAAATAATTTATATATATTTAGAAAT
334446 A
1 A
334447 TCAGAAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 6 0.26
26 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AAAATAATTTATATATATTTAGAAAT
Found at i:334520 original size:23 final size:22
Alignment explanation
Indices: 334496--334540 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
334486 CTTCGATATT
334496 AATAAATATTAATATAATAATTTA
1 AATAAA-ATTAA-ATAATAATTTA
*
334520 AATAAAATTAAATTATAATTT
1 AATAAAATTAAATAATAATTT
334541 TTTATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATAAAATTAAATAATAATTTA
Found at i:336137 original size:3 final size:3
Alignment explanation
Indices: 336129--336190 Score: 81
Period size: 3 Copynumber: 20.7 Consensus size: 3
336119 TTATTTATTT
* *
336129 TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
336174 TAA TTA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
336191 TAAAATGGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:336151 original size:12 final size:12
Alignment explanation
Indices: 336131--336193 Score: 103
Period size: 12 Copynumber: 5.3 Consensus size: 12
336121 ATTTATTTTA
336131 ATAATAATAA-T
1 ATAATAATAATT
336142 ATATATAATAATT
1 ATA-ATAATAATT
336155 ATAATAATAATT
1 ATAATAATAATT
336167 ATAATAATAATT
1 ATAATAATAATT
336179 ATAATAATAA-T
1 ATAATAATAATT
336190 ATAA
1 ATAA
336194 AATGGGTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
11 8 0.16
12 38 0.76
13 4 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:341237 original size:21 final size:21
Alignment explanation
Indices: 341205--341252 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
341195 TAATTTTCAA
*
341205 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
* *
341226 ATATTGTTGCACTTAATTTTG
1 ACATTGTTGCACCTAATTTTG
341247 ACATTG
1 ACATTG
341253 CAATATTAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:341753 original size:2 final size:2
Alignment explanation
Indices: 341746--341816 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
341736 TTCCTATTGT
341746 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
341788 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
341817 GTGTGTGTGT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:343357 original size:3 final size:3
Alignment explanation
Indices: 343349--343401 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
343339 ATCAATCGGA
343349 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
343397 AAT AA
1 AAT AA
343402 GCTGGGTGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:349790 original size:34 final size:34
Alignment explanation
Indices: 349751--349833 Score: 123
Period size: 34 Copynumber: 2.4 Consensus size: 34
349741 ATCATGGTAA
349751 GGGTATCGATACCAAGAAACATCGAA-TGTAAAAT
1 GGGTATCGATACCAAGAAACATCGAACT-TAAAAT
* * *
349785 TGGTATCGATACCAGGTAACATCGAACTTAAAAT
1 GGGTATCGATACCAAGAAACATCGAACTTAAAAT
349819 GGGTATCGATACCAA
1 GGGTATCGATACCAA
349834 AAGGGGTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 42 0.98
35 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (34 bp):
GGGTATCGATACCAAGAAACATCGAACTTAAAAT
Found at i:350232 original size:56 final size:56
Alignment explanation
Indices: 350142--350477 Score: 516
Period size: 56 Copynumber: 6.0 Consensus size: 56
350132 TGTTATACTA
* *
350142 GTACAGGGTACTATGTGTGCAAAACCACAGAATTCATCATGAGTTGATGAATAACT
1 GTACAGGGCACTATGTGTGCAAAACCACAGAATTCATCATGAGTTGATGAATAACC
* *
350198 GTACAGGGCATTATATGTGCAAAACCAC-GAAATTCATCATGAGTTGATGAATAACC
1 GTACAGGGCACTATGTGTGCAAAACCACAG-AATTCATCATGAGTTGATGAATAACC
*
350254 GTACAGGGCACTATGTATGCAAAACCACAGAATTCATCATGAGTTGATGAATAACC
1 GTACAGGGCACTATGTGTGCAAAACCACAGAATTCATCATGAGTTGATGAATAACC
*
350310 GTACAGGGCACTATGTGTGTAAAACCA-AGGAATTCATCATGAGTTGATGAATAACC
1 GTACAGGGCACTATGTGTGCAAAACCACA-GAATTCATCATGAGTTGATGAATAACC
* * *
350366 GTACATGGCACTATGTGTACAAAACCACAGAATTCGTCATGAGTTGATGAATAACC
1 GTACAGGGCACTATGTGTGCAAAACCACAGAATTCATCATGAGTTGATGAATAACC
* * *
350422 GTACATGGCACTATGTGTGCAAATCCAC-GAAATTCATCACGAGTTGATGAATAACC
1 GTACAGGGCACTATGTGTGCAAAACCACAG-AATTCATCATGAGTTGATGAATAACC
350478 ATATAAGAAC
Statistics
Matches: 258, Mismatches: 17, Indels: 10
0.91 0.06 0.04
Matches are distributed among these distances:
55 3 0.01
56 253 0.98
57 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (56 bp):
GTACAGGGCACTATGTGTGCAAAACCACAGAATTCATCATGAGTTGATGAATAACC
Found at i:353042 original size:16 final size:16
Alignment explanation
Indices: 353021--353052 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
353011 ATATAACGTT
353021 TATGGTTAATGGGATA
1 TATGGTTAATGGGATA
353037 TATGGTTAATGGGATA
1 TATGGTTAATGGGATA
353053 GAGGCTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (16 bp):
TATGGTTAATGGGATA
Found at i:355236 original size:17 final size:18
Alignment explanation
Indices: 355214--355255 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
355204 GTACCAGAGT
355214 ATGGTA-GTATCGATACC
1 ATGGTAGGTATCGATACC
355231 ATGGTAAGGGTATCGATACC
1 ATGGT-A-GGTATCGATACC
355251 A-GGTA
1 ATGGTA
355256 ACATCGAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.23
18 2 0.09
19 3 0.14
20 12 0.55
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (18 bp):
ATGGTAGGTATCGATACC
Found at i:355250 original size:93 final size:93
Alignment explanation
Indices: 355108--355343 Score: 261
Period size: 93 Copynumber: 2.5 Consensus size: 93
355098 ATTAAATCAA
* *
355108 TATCGATACCA-ACG-A-GGTAGTATCGATACCATGGTAAGAGTATCAATACCAGGAAACGTCGA
1 TATCGATACCAGA-GTATGGTAGTATCGATACCATGGTAAGAGTATCGATACCAGGAAACATCGA
**
355170 A-TCTAAAATTG-GTATCGATACTGGAAA-GG
65 ACT-TAAAA-TGAGTATCGATA-TCAAAAGGG
* * * *
355199 TATTGGTACCAGAGTATGGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGTAACATCGAA
1 TATCGATACCAGAGTATGGTAGTATCGATACCATGGTAAGAGTATCGATACCAGGAAACATCGAA
355264 CTTAAAATGAGTATCGATATCAAAAGGGG
66 CTTAAAATGAGTATCGATATCAAAA-GGG
* * * *
355293 TATCGATACCATAGTATAGAAGTATCGGTACCATGGT-AGTAGTATCGATAC
1 TATCGATACCAGAGTATGGTAGTATCGATACCATGGTAAG-AGTATCGATAC
355344 TATTTAACTT
Statistics
Matches: 122, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
91 10 0.08
92 8 0.07
93 60 0.49
94 44 0.36
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (93 bp):
TATCGATACCAGAGTATGGTAGTATCGATACCATGGTAAGAGTATCGATACCAGGAAACATCGAA
CTTAAAATGAGTATCGATATCAAAAGGG
Found at i:355753 original size:56 final size:56
Alignment explanation
Indices: 355667--356126 Score: 652
Period size: 56 Copynumber: 8.2 Consensus size: 56
355657 ACAAAACAGA
* * *
355667 CACTAAGTGTGCAAAATCACGGAATTCATCATGAGTTGCTGAATAACCGTACAGGG
1 CACTATGTGTGCAAAACCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGG
* **
355723 CACTATGTGTGCAAAACCATGGAATTCATCATGAGTTGATGAATAACCGTACATAG
1 CACTATGTGTGCAAAACCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGG
* * * * *
355779 AACTATGTGTACAAAACCATGGAATTCATAATGAGTTGATGAATAACCGTACAGAG
1 CACTATGTGTGCAAAACCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGG
* *
355835 CACTATGTGTGCAAAACCACAGAATTCATCATGAGTTGATGAATAACCGTATAGGG
1 CACTATGTGTGCAAAACCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGG
* * * * *
355891 CACTATGTATACAAAACCACAGAATTCATCATGAGTTGATGAATAACTGTACAGAG
1 CACTATGTGTGCAAAACCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGG
*
355947 CACTAAGTGTGCAAAACCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGG
1 CACTATGTGTGCAAAACCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGG
* *
356003 TACTATGTGTGCAAAACCACGGAATTCATCATGAGTTGATGAATAACCTTACAGGG
1 CACTATGTGTGCAAAACCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGG
* * * * * *
356059 TATTATGTGTGCAAATCCACGTAATTCATCATAAGTTGATGAATAACCGTATA-GG
1 CACTATGTGTGCAAAACCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGG
* *
356114 AACTATGGGTGCA
1 CACTATGTGTGCA
356127 TCTTAATAAA
Statistics
Matches: 364, Mismatches: 40, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
55 12 0.03
56 352 0.97
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (56 bp):
CACTATGTGTGCAAAACCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGG
Found at i:356638 original size:83 final size:81
Alignment explanation
Indices: 356498--356685 Score: 216
Period size: 83 Copynumber: 2.3 Consensus size: 81
356488 TAGATTAATG
* ** * * * * * *
356498 GCCTAGTTGTGCA-TTGACAGAAAGGTGTCAATCCTGCCAGTTAGATGAAGGGCTAAATGCTTTT
1 GCCTAGTTGTGTATTTGGTAGAAAGGTGTCAATCATACCAGTTAGATGAAAGACTAAATACCTTT
*
356562 GGGTTAAAAGAACTAAAT
66 GGG-TAAAAG-ACGAAAT
*
356580 GCCTAGTTGTGTATTTGGTAGAAAGGTGTCAATCATACCAGTTAGATGAAAGATTAAATACCTTT
1 GCCTAGTTGTGTATTTGGTAGAAAGGTGTCAATCATACCAGTTAGATGAAAGACTAAATACCTTT
356645 GGGTAAAAGACGAAAT
66 GGGTAAAAGACGAAAT
* ***
356661 GTCTAACGGTGTATTTGGTAGAAAG
1 GCCTAGTTGTGTATTTGGTAGAAAG
356686 ATGCCAATAA
Statistics
Matches: 90, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 27 0.30
82 18 0.20
83 45 0.50
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (81 bp):
GCCTAGTTGTGTATTTGGTAGAAAGGTGTCAATCATACCAGTTAGATGAAAGACTAAATACCTTT
GGGTAAAAGACGAAAT
Found at i:361222 original size:24 final size:22
Alignment explanation
Indices: 361187--361231 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
361177 ATTCATGTGA
361187 TTTAAATAACTACAT-GATCATT
1 TTTAAATAACTAC-TGGATCATT
361209 TTTACAATAAACTACTGGATCAT
1 TTTA-AAT-AACTACTGGATCAT
361232 GATTTTGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 4 0.20
24 12 0.60
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.38
Consensus pattern (22 bp):
TTTAAATAACTACTGGATCATT
Found at i:362700 original size:20 final size:20
Alignment explanation
Indices: 362658--362731 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
362648 GCTCTTTATC
* ** *
362658 GGTTTTCTCAAATTGAAACT
1 GGTTTTGTCAAATTTCAATT
362678 GGTTTTGTCAAATTTCAATT
1 GGTTTTGTCAAATTTCAATT
*
362698 GGTTTTGTC-AATTTCCAATC
1 GGTTTTGTCAAATTT-CAATT
362718 GGTTTTGTCAAATT
1 GGTTTTGTCAAATT
362732 CGTTACCTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
19 5 0.11
20 38 0.81
21 4 0.09
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (20 bp):
GGTTTTGTCAAATTTCAATT
Found at i:366371 original size:2 final size:2
Alignment explanation
Indices: 366364--366400 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
366354 TGATTTGTGC
366364 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
366401 CGTGGATTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:368605 original size:21 final size:21
Alignment explanation
Indices: 368581--368645 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
368571 TTTTTCTCAC
368581 CAGCATCCTTGTGTGGTGGTT
1 CAGCATCCTTGTGTGGTGGTT
* ** ***
368602 CAGCAGCCTT-T-TTCT-CAC
1 CAGCATCCTTGTGTGGTGGTT
368620 CAGCATCCTTGTGTGGTGGTT
1 CAGCATCCTTGTGTGGTGGTT
368641 CAGCA
1 CAGCA
368646 GCTGGTTTTA
Statistics
Matches: 29, Mismatches: 12, Indels: 6
0.62 0.26 0.13
Matches are distributed among these distances:
18 9 0.31
19 3 0.10
20 3 0.10
21 14 0.48
ACGTcount: A:0.14, C:0.26, G:0.26, T:0.34
Consensus pattern (21 bp):
CAGCATCCTTGTGTGGTGGTT
Found at i:368614 original size:39 final size:39
Alignment explanation
Indices: 368560--368647 Score: 176
Period size: 39 Copynumber: 2.3 Consensus size: 39
368550 TTGGCACTCT
368560 GTTCAGCAGCCTTTTTCTCACCAGCATCCTTGTGTGGTG
1 GTTCAGCAGCCTTTTTCTCACCAGCATCCTTGTGTGGTG
368599 GTTCAGCAGCCTTTTTCTCACCAGCATCCTTGTGTGGTG
1 GTTCAGCAGCCTTTTTCTCACCAGCATCCTTGTGTGGTG
368638 GTTCAGCAGC
1 GTTCAGCAGC
368648 TGGTTTTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.14, C:0.28, G:0.24, T:0.34
Consensus pattern (39 bp):
GTTCAGCAGCCTTTTTCTCACCAGCATCCTTGTGTGGTG
Found at i:382483 original size:19 final size:19
Alignment explanation
Indices: 382443--382480 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
382433 AATAACTTTT
382443 TTATTATATTATATTGTAA
1 TTATTATATTATATTGTAA
*
382462 TTATTGTATTCATATTGTA
1 TTATTATATT-ATATTGTA
382481 TTAACAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.58
Consensus pattern (19 bp):
TTATTATATTATATTGTAA
Found at i:384495 original size:46 final size:46
Alignment explanation
Indices: 384445--384554 Score: 136
Period size: 46 Copynumber: 2.4 Consensus size: 46
384435 TGTACGTTGT
*
384445 TAATTATTAAAA-AATATTTTAAACAGATAAT-ACTTTATAATCGCTC
1 TAATTATTAAAAGAATA--TTAAACAGAAAATGACTTTATAATCGCTC
* **
384491 TAATTATTAAAAGAATA-TAAATAGAAAATGGGTTTATAATCGCTC
1 TAATTATTAAAAGAATATTAAACAGAAAATGACTTTATAATCGCTC
384536 TAAATTATTAAAAGAATAT
1 T-AATTATTAAAAGAATAT
384555 AAAGAGGAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
44 10 0.18
45 14 0.25
46 28 0.50
47 4 0.07
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.36
Consensus pattern (46 bp):
TAATTATTAAAAGAATATTAAACAGAAAATGACTTTATAATCGCTC
Done.