Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009064.1 Hibiscus syriacus cultivar Beakdansim tig00112487_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: 748991
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 4
Found at i:228789 original size:400 final size:398
Alignment explanation
Indices: 227988--229221 Score: 1609
Period size: 400 Copynumber: 3.1 Consensus size: 398
227978 AAATATCCAA
* * * ** * * * *
227988 TTTTGATACTTTTTATACAAGTATCGCTACTTTTATTCCAATGTACATCTGAAACAATTTGCACG
1 TTTTGATACTTTTTGTATAAGTATCGATACTTTTGGTCCAATATACTTCTCAAACAATATGCACG
* * *
228053 CAAAAATGTATCGATACACATATAACAAGTATCAGTACTT-CTATTTTCGAAACCTATTACTTTA
66 CAGAAA-GTATCGATACACATATAACAAGTATCAATACTTAC-AATTTCGAAACCTATTACTTTA
* * * * * *
228117 AAGTTATAGGTAAATTTACAATGTTAAGGGTAAAAGTCTACCAGTTTAATGATATTAGGCCTAAA
129 AAGTAATAGGTAAATTTAAAATG-TAAGGGTAAAAATCTACCGGTTTAATGATAATAGGCGTAAA
* * *
228182 CATAAAGTATCGATACTCTTTGTATATGTATCGATACTTTTAGTCCAGTATGC-TATCAAACAAC
193 CATAAAGTATCGATACTATTTGTATAGGTATCGATACTTTTAGTCCAGTATGCTTCTCAAACAAC
* ** * * * *
228246 ATGCA-TAAAAAGAGTATCGATACATGTATAACAAGTATCAATACTTGTAACTTCGAAATTGATT
258 ATGCACGAAAAA-AGTATCGATACATGTATAACAAGTATTGATTCTTATAACTTTGAAACTGATT
* * * *
228310 ACTTTAAAGTAATAGGTAAATTTAAAATGTAACCGGTAAAAATATATCGACTTAATGATAATAGG
322 ACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTAT-GGCTTAATGATAATAGG
*
228375 CGTAAAAAATAAAG
386 CGT-AAACATAAAG
* * * *
228389 TTTTGATACTTTTTGTATATGTATCGATACTTTTGGTCCAATATACTTCTTAATCAATATGCATG
1 TTTTGATACTTTTTGTATAAGTATCGATACTTTTGGTCCAATATACTTCTCAAACAATATGCACG
* * *
228454 CAGAAAGTATCGATACACGTATAACAAGTATCAATACTTACCATTTCAAAACCTATTACTTTAAA
66 CAGAAAGTATCGATACACATATAACAAGTATCAATACTTACAATTTCGAAACCTATTACTTTAAA
* *
228519 GTAATAGGCAAATTTAGAATGTAAGCGGTAAAAATCTACCGGTTTAATGATAATAGGCGTAAACA
131 GTAATAGGTAAATTTAAAATGTAAG-GGTAAAAATCTACCGGTTTAATGATAATAGGCGTAAACA
* * *
228584 TAAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTGCAGTATGCTTCTCACACAACAT
195 TAAAGTATCGATACTATTTGTATAGGTATCGATACTTTTAGTCCAGTATGCTTCTCAAACAACAT
* *
228649 GCACGCAAAAAGTATCGATACATGTATAACAAGTATTGATTCTTATAACTTTGAAACTAATTACT
260 GCACGAAAAAAGTATCGATACATGTATAACAAGTATTGATTCTTATAACTTTGAAACTGATTACT
* ** * *
228714 TTAAAGTAATAAGTAAATTTACAATGTAAGTGGTAAAAATCTAGTGGCTTAATGATAAAAGACGT
325 TTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTA-TGGCTTAATGATAATAGGCGT
228779 AAACATAAAG
389 AAACATAAAG
* * *
228789 TTTCT-ATACTTTTTGTATATGTATCGATACTTTTGGTCCAATATGCTTCTCAAACAACATGCAC
1 TTT-TGATACTTTTTGTATAAGTATCGATACTTTTGGTCCAATATACTTCTCAAACAATATGCAC
* * *
228853 GCAGAAAGTATCGATACACATATAACAAGTATCGATACTTATAATTTTGAAACCTATTACTTTAA
65 GCAGAAAGTATCGATACACATATAACAAGTATCAATACTTACAATTTCGAAACCTATTACTTTAA
* * * *
228918 AGTAATAGGTAAATTCAAAATGTAAGAGGTAAAAATCTGCTGATTTAATGATAATAGGCGTAAAC
130 AGTAATAGGTAAATTTAAAATGTAAG-GGTAAAAATCTACCGGTTTAATGATAATAGGCGTAAAC
* * * ** *
228983 ATAAAGAACCGATACTATGTGTATAGGTATATATACTTTTAGTCCAATATG-TTACTCAAACAAC
194 ATAAAGTATCGATACTATTTGTATAGGTATCGATACTTTTAGTCCAGTATGCTT-CTCAAACAAC
* * * * *
229047 ATGCACGTAGAAAGTATCGATACATGTATCACAAGT-TTCG-TTACTTATAATTTTGAAACCGAT
258 ATGCACGAAAAAAGTATCGATACATGTATAACAAGTATT-GATT-CTTATAACTTTGAAACTGAT
* *
229110 TACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAG
321 TACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTA-TGGCTTAATGATAATAG
229175 GCGTAAACATAAAG
385 GCGTAAACATAAAG
*
229189 TTTTGATACTTCTTGTATAAGTATCGATACTTT
1 TTTTGATACTTTTTGTATAAGTATCGATACTTT
229222 CGATCTAAAC
Statistics
Matches: 732, Mismatches: 91, Indels: 21
0.87 0.11 0.02
Matches are distributed among these distances:
399 11 0.02
400 539 0.74
401 177 0.24
402 5 0.01
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (398 bp):
TTTTGATACTTTTTGTATAAGTATCGATACTTTTGGTCCAATATACTTCTCAAACAATATGCACG
CAGAAAGTATCGATACACATATAACAAGTATCAATACTTACAATTTCGAAACCTATTACTTTAAA
GTAATAGGTAAATTTAAAATGTAAGGGTAAAAATCTACCGGTTTAATGATAATAGGCGTAAACAT
AAAGTATCGATACTATTTGTATAGGTATCGATACTTTTAGTCCAGTATGCTTCTCAAACAACATG
CACGAAAAAAGTATCGATACATGTATAACAAGTATTGATTCTTATAACTTTGAAACTGATTACTT
TAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTATGGCTTAATGATAATAGGCGTAA
ACATAAAG
Found at i:233779 original size:21 final size:20
Alignment explanation
Indices: 233753--233791 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
233743 GTAAACATAA
233753 AGTATCGATACTTATTATTTC
1 AGTATCGATACTT-TTATTTC
233774 AGTATCGATACTTTTATT
1 AGTATCGATACTTTTATT
233792 CCAATATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (20 bp):
AGTATCGATACTTTTATTTC
Found at i:234126 original size:199 final size:201
Alignment explanation
Indices: 233661--234189 Score: 651
Period size: 202 Copynumber: 2.6 Consensus size: 201
233651 CGATACTTAG
* *
233661 AATTTCGAAACCTATTTCTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACC-
1 AATTTCGAAACCTATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCG
* * *
233725 AGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACT-TATTATTTCAGTATCGATACTTTT
66 A-TTTAATGATAATAGGCGTAAACATCAAGTATCGATACTGT-TTGTAT-AGTATCGATACTTTT
* * * * *
233789 ATTCCAATATGCATCTCAAATAATTTTCACACAAAAAAGTATTGATACACATGTATAAAGTATCG
128 AGTCCAATATGCATATCAAACAATTTGCACACAAAAAAGTATCGATACACATGTATAAAGTATCG
233854 ATACGCAAA
193 ATACGCAAA
* * * * * **
233863 AAGTTCAAAATCGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGATAAAGGTCTACCG
1 AATTTCGAAACCTATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCG
*
233928 ATTTAATAATAATAGGCGTAAACATCAAGTATCGATA-TGTTTTGTATAGATATCGATACTTTTA
66 ATTTAATGATAATAGGCGTAAACATCAAGTATCGATACTG-TTTGTATAG-TATCGATACTTTTA
* * * *
233992 GTCCAGTATGCTTATC-AACAATTTGCACGC-ACAAAGTATCGATACACATGTATAAAGTATCGA
129 GTCCAATATGCATATCAAACAATTTGCACACAAAAAAGTATCGATACACATGTATAAAGTATCGA
* *
234055 TTCGC-GA
194 TACGCAAA
* *
234062 AATTTTGAAACCTATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAACATCTACCG
1 AATTTCGAAACCTATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCG
* * ** * *
234127 ATATATTGATAATAGGCACAAATA-CAAGTATCGATACTG-TCGATATAGGTATCGATACTTTTA
66 ATTTAATGATAATAGGCGTAAACATCAAGTATCGATACTGTTTG-TATA-GTATCGATACTTTTA
234190 TACAGTTAAC
Statistics
Matches: 281, Mismatches: 39, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
197 2 0.01
198 30 0.11
199 79 0.28
200 35 0.12
201 14 0.05
202 119 0.42
203 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (201 bp):
AATTTCGAAACCTATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCG
ATTTAATGATAATAGGCGTAAACATCAAGTATCGATACTGTTTGTATAGTATCGATACTTTTAGT
CCAATATGCATATCAAACAATTTGCACACAAAAAAGTATCGATACACATGTATAAAGTATCGATA
CGCAAA
Found at i:234229 original size:20 final size:20
Alignment explanation
Indices: 234201--234265 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
234191 ACAGTTAACG
* *
234201 AATTTGACAAAACTGATTGGA
1 AATTTGACAAAACCGATT-AA
*
234222 AA-TTGACAAATCCGATTAA
1 AATTTGACAAAACCGATTAA
*
234241 AATTTGACAAAACCGGTTGAA
1 AATTTGACAAAACCGATT-AA
234262 AATT
1 AATT
234266 AAAAAAACCA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.08
20 26 0.70
21 8 0.22
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (20 bp):
AATTTGACAAAACCGATTAA
Found at i:237938 original size:220 final size:221
Alignment explanation
Indices: 237421--238337 Score: 1198
Period size: 220 Copynumber: 4.1 Consensus size: 221
237411 TAACAAATCG
*
237421 AGTAATTAATCGATTATGTTATCGTCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
1 AGTAATTAATCGGTTATGTTATCGTCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
** * * * *
237486 TTTAAACGTTACCTACTATGTTGATAATAGTGATAGCAAATTAAGTAATTAACCTTTTTTGTTAT
66 TTTAGTCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * *
237551 CGTCGGATTTCTAAGGCCCCATCTGCTCTTTAAAAAGGGGCTACCTATTACGTTACATAAGTGCT
131 CGTCGGATTTCTAAGGCCCCATCAG--CTTTAAAAA---G-T-GCTATTACATTACATAAGCGCT
*
237616 ACCTAATATGTTATTATGGTTAATAATGTTTCC
189 ACCTAATATGTTATTATGGTTGATAATGTTTCC
* * *
237649 AGTAATTAA-CTGGGTATGTTATCGTCGGATTTCTAAGGTTCCATCAGCTTAAACTTTGGTAACA
1 AGTAATTAATC-GGTTATGTTATCGTCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACA
*
237713 TTTTAGTTGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTA
65 TTTTAGTCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTA
* * *
237778 TCATCGGATTTCTAAGGCCCCGTCAGCTTTAAAAA-TGCTATTACATTACATAAGCGTTACCTAA
130 TCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGTGCTATTACATTACATAAGCGCTACCTAA
237842 TATGTTATTATGGTTGATAATGTTTCC
195 TATGTTATTATGGTTGATAATGTTTCC
* * ** *
237869 AGTAATTAATCGGTTATGTTATCGTAGAATTTCTAAGGCTCTATCAGCGCAAACTTTGATAACAT
1 AGTAATTAATCGGTTATGTTATCGTCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* * *
237934 TTTAGTTGTTACCTAATATGTTGACAATACTGATAACAAATTAAGTAATTAACCTATTTTATTAT
66 TTTAGTCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * *
237999 CGTCGGATTTCTAAAGCCCCATAAGCTTTAAAAAGGCGCTACCAATTACGTTACATAAGCGCTAC
131 CGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAA-GTGCT----ATTACATTACATAAGCGCTAC
* * *
238064 CTAATATATTATTATGGTTGATAACGTTTAC
191 CTAATATGTTATTATGGTTGATAATGTTTCC
* * * *
238095 AGTAATTAACCAGTTATGTTAT-G--GGATTTATAAGGCTCCATCAGCTTAAACTTTGGTAACAT
1 AGTAATTAATCGGTTATGTTATCGTCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* * *
238157 TTTAGGCATTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTATCCTATTTTGTTAT
66 TTTAGTCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * *
238222 CGTCGAATTTCTAAGGCCCCTTCAGCTTTAAAAAGGGC-ACTACCTATTACGTTATAAGCGCTAC
131 CGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGTGCTATTA-C-ATTAC---ATAAGCGCTAC
* *
238286 CTAATATGTTATTATGGTTGATAGTTTTTCC
191 CTAATATGTTATTATGGTTGATAATGTTTCC
*
238317 AGTAATTAATCGATTATGTTA
1 AGTAATTAATCGGTTATGTTA
238338 AAGTTAATAT
Statistics
Matches: 608, Mismatches: 68, Indels: 32
0.86 0.10 0.05
Matches are distributed among these distances:
217 3 0.00
218 1 0.00
219 4 0.01
220 198 0.33
221 2 0.00
222 61 0.10
223 122 0.20
225 1 0.00
226 76 0.12
227 1 0.00
228 139 0.23
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (221 bp):
AGTAATTAATCGGTTATGTTATCGTCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
TTTAGTCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
CGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGTGCTATTACATTACATAAGCGCTACCTAAT
ATGTTATTATGGTTGATAATGTTTCC
Found at i:238281 original size:448 final size:446
Alignment explanation
Indices: 237421--238337 Score: 1356
Period size: 448 Copynumber: 2.0 Consensus size: 446
237411 TAACAAATCG
* ** *
237421 AGTAATTAATCGATTATGTTATCGTCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
1 AGTAATTAATCGATTATGTTATCGTAGAATTTCTAAGGCTCCATCAGCGCAAACTTTGATAACAT
* * * * * *
237486 TTTAAACGTTACCTACTATGTTGATAATAGTGATAGCAAATTAAGTAATTAACCTTTTTTGTTAT
66 TTTAAACGTTACCTAATATGTTGACAATACTGATAACAAATTAAGTAATTAACCTATTTTATTAT
* ** * * *
237551 CGTCGGATTTCTAAGGCCCCATCTGCTCTTTAAAAAGGGGCTACCTATTACGTTACATAAGTGCT
131 CGTCGGATTTCTAAAGCCCCATAAGC-CTTTAAAAAGGCGCTACCAATTACGTTACATAAGCGCT
* * * **
237616 ACCTAATATGTTATTATGGTTAATAATGTTTCCAGTAATTAACTGGGTATGTTATCGTCGGATTT
195 ACCTAATATATTATTATGGTTAATAACGTTTACAGTAATTAACCAGGTATGTTATCG-CGGATTT
* * ***
237681 CTAAGGTTCCATCAGCTTAAACTTTGGTAACATTTTAGTTGTTACCTAATATGTTGATAATACTG
259 ATAAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGGCATTACCTAATATGTTGATAATACTG
*
237746 ATAACAAATTAAGTAATTAACCTATTTTGTTATCATCGGATTTCTAAGGCCCCGTCAGCTTTAAA
324 ATAACAAATTAAGTAATTAACCTATTTTGTTATCATCGAATTTCTAAGGCCCCGTCAGCTTTAAA
* * *
237811 AATGCTATTACATTACATAAGCGTTACCTAATATGTTATTATGGTTGATAATGTTTCC
389 AAGGCTACTACATTACATAAGCGCTACCTAATATGTTATTATGGTTGATAATGTTTCC
* *
237869 AGTAATTAATCGGTTATGTTATCGTAGAATTTCTAAGGCTCTATCAGCGCAAACTTTGATAACAT
1 AGTAATTAATCGATTATGTTATCGTAGAATTTCTAAGGCTCCATCAGCGCAAACTTTGATAACAT
***
237934 TTTAGTTGTTACCTAATATGTTGACAATACTGATAACAAATTAAGTAATTAACCTATTTTATTAT
66 TTTAAACGTTACCTAATATGTTGACAATACTGATAACAAATTAAGTAATTAACCTATTTTATTAT
237999 CGTCGGATTTCTAAAGCCCCATAAG-CTTTAAAAAGGCGCTACCAATTACGTTACATAAGCGCTA
131 CGTCGGATTTCTAAAGCCCCATAAGCCTTTAAAAAGGCGCTACCAATTACGTTACATAAGCGCTA
* *
238063 CCTAATATATTATTATGGTTGATAACGTTTACAGTAATTAACCAGTTATGTTAT-G-GGATTTAT
196 CCTAATATATTATTATGGTTAATAACGTTTACAGTAATTAACCAGGTATGTTATCGCGGATTTAT
238126 AAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGGCATTACCTAATATGTTGATAATACTGAT
261 AAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGGCATTACCTAATATGTTGATAATACTGAT
* * *
238191 AACAAATTAAGTAATTATCCTATTTTGTTATCGTCGAATTTCTAAGGCCCCTTCAGCTTTAAAAA
326 AACAAATTAAGTAATTAACCTATTTTGTTATCATCGAATTTCTAAGGCCCCGTCAGCTTTAAAAA
* *
238256 GGGC-ACTACCTATTACGTTATAAGCGCTACCTAATATGTTATTATGGTTGATAGTTTTTCC
391 -GGCTACTA-C-ATTAC---ATAAGCGCTACCTAATATGTTATTATGGTTGATAATGTTTCC
238317 AGTAATTAATCGATTATGTTA
1 AGTAATTAATCGATTATGTTA
238338 AAGTTAATAT
Statistics
Matches: 420, Mismatches: 43, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
443 132 0.31
444 3 0.01
445 6 0.01
446 83 0.20
448 196 0.47
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (446 bp):
AGTAATTAATCGATTATGTTATCGTAGAATTTCTAAGGCTCCATCAGCGCAAACTTTGATAACAT
TTTAAACGTTACCTAATATGTTGACAATACTGATAACAAATTAAGTAATTAACCTATTTTATTAT
CGTCGGATTTCTAAAGCCCCATAAGCCTTTAAAAAGGCGCTACCAATTACGTTACATAAGCGCTA
CCTAATATATTATTATGGTTAATAACGTTTACAGTAATTAACCAGGTATGTTATCGCGGATTTAT
AAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGGCATTACCTAATATGTTGATAATACTGAT
AACAAATTAAGTAATTAACCTATTTTGTTATCATCGAATTTCTAAGGCCCCGTCAGCTTTAAAAA
GGCTACTACATTACATAAGCGCTACCTAATATGTTATTATGGTTGATAATGTTTCC
Found at i:239172 original size:65 final size:65
Alignment explanation
Indices: 239092--239228 Score: 229
Period size: 65 Copynumber: 2.1 Consensus size: 65
239082 CCATAAATGA
* * * *
239092 ATATACCCATGTTTAGCTATTTACAGTAACTATACTATGTACGACTTAAATGAACCCATCAACAT
1 ATATACACATGTTTAGCTATTTACAGTAACTATACTATGTACAACTTAAACGAACCCATAAACAT
*
239157 ATATACACATTTTTAGCTATTTACAGTAACTATACTATGTACAACTTAAACGAACCCATAAACAT
1 ATATACACATGTTTAGCTATTTACAGTAACTATACTATGTACAACTTAAACGAACCCATAAACAT
239222 ATATACA
1 ATATACA
239229 TATTACCTAT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.32
Consensus pattern (65 bp):
ATATACACATGTTTAGCTATTTACAGTAACTATACTATGTACAACTTAAACGAACCCATAAACAT
Found at i:239598 original size:44 final size:44
Alignment explanation
Indices: 239543--239875 Score: 375
Period size: 44 Copynumber: 7.6 Consensus size: 44
239533 GTGAAATAAC
* *
239543 GTTGATCCAACTACTTATGTGATGGAATCGAGTGAAATAGTGAT
1 GTTGATCCAACTCCTTATGTGATGGAATCGAGCGAAATAGTGAT
** *
239587 GTTGATCCAACTCCTTAAATGATGGAATCGAGTGAAATAGTGAT
1 GTTGATCCAACTCCTTATGTGATGGAATCGAGCGAAATAGTGAT
* * * *
239631 GTTGATCTAACTCCTTTTGTGATGGAATCAAGCGAAATGGTGAT
1 GTTGATCCAACTCCTTATGTGATGGAATCGAGCGAAATAGTGAT
239675 GTT-ATCCAACTCCTTATGTGATGGAATCGAGCGAAATAGTGAT
1 GTTGATCCAACTCCTTATGTGATGGAATCGAGCGAAATAGTGAT
* * * ** * * **
239718 GTCGATCCAACTGCTTTTGTGATATAATCGAGCGAAGTGGCAAT
1 GTTGATCCAACTCCTTATGTGATGGAATCGAGCGAAATAGTGAT
* *
239762 GTTGATTCAACTCCTTATATGATGGAATCGAG-GAAAATAGTGAT
1 GTTGATCCAACTCCTTATGTGATGGAATCGAGCG-AAATAGTGAT
* * * * *
239806 GTTGATCCAACTACCTTATATGAAGGAATGGA-CAAAATAATGAT
1 GTTGATCCAACT-CCTTATGTGATGGAATCGAGCGAAATAGTGAT
* * *
239850 GATGATCTAACTCCTTTTGTGATGGA
1 GTTGATCCAACTCCTTATGTGATGGA
239876 TGAGCCAAAG
Statistics
Matches: 241, Mismatches: 44, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
43 50 0.21
44 174 0.72
45 17 0.07
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (44 bp):
GTTGATCCAACTCCTTATGTGATGGAATCGAGCGAAATAGTGAT
Found at i:239711 original size:131 final size:132
Alignment explanation
Indices: 239543--239865 Score: 366
Period size: 131 Copynumber: 2.5 Consensus size: 132
239533 GTGAAATAAC
* *
239543 GTTGATCCAACTACTTATGTGATGGAATCGAGTGAAATAGTGATGTTGATCCAACTCCTTAAATG
1 GTTGATCCAACTCCTTATGTGATGGAATCGAGCGAAATAGTGATGTTGATCCAACTCCTTAAATG
* * ** * * *
239608 ATGGAATCGAGTGAAATAGTGATGTTGA-TCTAACTCCTTTTGTGATGGAATCAAGCG-AAATGG
66 ATAGAATCGAGCGAAATAGCAATGTTGATTC-AACTCCTTATATGATGGAATCAAG-GAAAATAG
239671 TGAT
129 TGAT
* * ***
239675 GTT-ATCCAACTCCTTATGTGATGGAATCGAGCGAAATAGTGATGTCGATCCAACTGCTTTTGTG
1 GTTGATCCAACTCCTTATGTGATGGAATCGAGCGAAATAGTGATGTTGATCCAACTCCTTAAATG
* * * *
239739 ATATAATCGAGCGAAGTGGCAATGTTGATTCAACTCCTTATATGATGGAATCGAGGAAAATAGTG
66 ATAGAATCGAGCGAAATAGCAATGTTGATTCAACTCCTTATATGATGGAATCAAGGAAAATAGTG
239804 AT
131 AT
* * * * * * *
239806 GTTGATCCAACTACCTTATATGAAGGAATGGA-CAAAATAATGATGATGATCTAACTCCTT
1 GTTGATCCAACT-CCTTATGTGATGGAATCGAGCGAAATAGTGATGTTGATCCAACTCCTT
239866 TTGTGATGGA
Statistics
Matches: 160, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
130 1 0.01
131 108 0.68
132 35 0.22
133 16 0.10
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31
Consensus pattern (132 bp):
GTTGATCCAACTCCTTATGTGATGGAATCGAGCGAAATAGTGATGTTGATCCAACTCCTTAAATG
ATAGAATCGAGCGAAATAGCAATGTTGATTCAACTCCTTATATGATGGAATCAAGGAAAATAGTG
AT
Found at i:240517 original size:18 final size:18
Alignment explanation
Indices: 240466--240523 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 18
240456 GCTATTCGAG
*
240466 TTTTCACTTTCGTTCTTT-T
1 TTTTC-CTTTCCTT-TTTCT
*
240485 TTTT-CTGTTCTTTTTTCT
1 TTTTCCT-TTCCTTTTTCT
240503 TTTTCCTTTCC-TTTTCT
1 TTTTCCTTTCCTTTTTCT
240520 TTTT
1 TTTT
240524 ATTACAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
17 15 0.44
18 13 0.38
19 6 0.18
ACGTcount: A:0.02, C:0.21, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTCCTTTCCTTTTTCT
Found at i:243232 original size:12 final size:13
Alignment explanation
Indices: 243209--243248 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
243199 TTTATGTGAT
243209 ATTTTATAAAATG
1 ATTTTATAAAATG
243222 ATTTTAT-AAATG
1 ATTTTATAAAATG
* *
243234 ATTATAAAAAATG
1 ATTTTATAAAATG
243247 AT
1 AT
243249 ATTTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (13 bp):
ATTTTATAAAATG
Found at i:252333 original size:15 final size:15
Alignment explanation
Indices: 252313--252342 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
252303 GTAAGTTTTT
252313 CATTATCTAACCCTA
1 CATTATCTAACCCTA
*
252328 CATTATCTAATCCTA
1 CATTATCTAACCCTA
252343 ATGCTTTGGC
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:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (15 bp):
CATTATCTAACCCTA
Found at i:258858 original size:22 final size:22
Alignment explanation
Indices: 258832--258905 Score: 132
Period size: 22 Copynumber: 3.4 Consensus size: 22
258822 AAACCATTCA
258832 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTACCCCCTTGG
*
258854 GGGGGAATAGGTA-CCCCTTGG
1 GGGGGAATCGGTACCCCCTTGG
258875 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTACCCCCTTGG
258897 GGGGGAATC
1 GGGGGAATC
258906 AGTTCCCTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.41
22 29 0.59
ACGTcount: A:0.16, C:0.23, G:0.43, T:0.18
Consensus pattern (22 bp):
GGGGGAATCGGTACCCCCTTGG
Found at i:260507 original size:29 final size:28
Alignment explanation
Indices: 260461--260515 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
260451 TCCATACCTA
*
260461 CAATTGATATCATATTTTTTTTCAAATAT
1 CAATTGACATCATATTTTTTTT-AAATAT
260490 CAATTGACATCA-ATTTTTTTTTAAAT
1 CAATTGACATCATA-TTTTTTTTAAAT
260516 TAGTATCCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.51
Consensus pattern (28 bp):
CAATTGACATCATATTTTTTTTAAATAT
Found at i:260515 original size:28 final size:29
Alignment explanation
Indices: 260461--260515 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
260451 TCCATACCTA
*
260461 CAATTGATATCATATTTTTTTTCAAATAT
1 CAATTGACATCATATTTTTTTTCAAATAT
*
260490 CAATTGACATCA-ATTTTTTTTTAAAT
1 CAATTGACATCATATTTTTTTTCAAAT
260516 TAGTATCCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.51
Consensus pattern (29 bp):
CAATTGACATCATATTTTTTTTCAAATAT
Found at i:261413 original size:31 final size:30
Alignment explanation
Indices: 261364--261453 Score: 94
Period size: 31 Copynumber: 3.0 Consensus size: 30
261354 AGTTTCGAAA
*
261364 GTAACAAATCGGTCACTAACAATATCGATTT
1 GTAAAAAAT-GGTCACTAACAATATCGATTT
* **
261395 GTAATAAAATTGTCACTAACGTTATCGATTT
1 GTAA-AAAATGGTCACTAACAATATCGATTT
* *
261426 GTAACAAATGGTCACT-CCAATATC-ATTT
1 GTAAAAAATGGTCACTAACAATATCGATTT
261454 TCGTTAAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
28 4 0.08
29 5 0.10
30 10 0.20
31 26 0.53
32 4 0.08
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (30 bp):
GTAAAAAATGGTCACTAACAATATCGATTT
Found at i:268604 original size:3 final size:3
Alignment explanation
Indices: 268596--268626 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
268586 CCGGGTTTAT
268596 TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
268627 ATAATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:269490 original size:31 final size:31
Alignment explanation
Indices: 269455--269516 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
269445 TCTTATAAAA
** *
269455 TAAAACAAGTTGAAATCACATTAA-TTGAAAC
1 TAAAACAAACTGAAATAACA-TAAGTTGAAAC
*
269486 TAAAAGAAACTGAAATAACATAAGTTGAAAC
1 TAAAACAAACTGAAATAACATAAGTTGAAAC
269517 ATTAGAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.23
Consensus pattern (31 bp):
TAAAACAAACTGAAATAACATAAGTTGAAAC
Found at i:272599 original size:83 final size:83
Alignment explanation
Indices: 272460--272979 Score: 588
Period size: 83 Copynumber: 6.3 Consensus size: 83
272450 GTGAAATAAT
* * * *
272460 AGAGATTCTTTGAATAATAATGGAAAATGCTTCCTCTCGAACGCGCCTTTCATTTCGGATGGGAT
1 AGAGATTCTCTGAATAATAATGGAAAAAGCTTCCCCTGGAACGCGCCTTTCATTTCGGATGGGAT
*
272525 AGAACACTATGACATGAC
66 GGAACACTATGACATGAC
* * * *
272543 AGAGACTCTCTAAATAGTAATGGAAAAAGCTTCCCCTGGAACGCGCCTTTCATTTCGAATGGGAT
1 AGAGATTCTCTGAATAATAATGGAAAAAGCTTCCCCTGGAACGCGCCTTTCATTTCGGATGGGAT
*
272608 TGAACACTATGACATGAC
66 GGAACACTATGACATGAC
* * * *
272626 AGAGATTCTCTGAATAATAATGGAAAATGCTTCCCCTGGAACGCACCTTTTATTTCGGATAGGAT
1 AGAGATTCTCTGAATAATAATGGAAAAAGCTTCCCCTGGAACGCGCCTTTCATTTCGGATGGGAT
* * *
272691 TGAACACTATAACATGAT
66 GGAACACTATGACATGAC
* * * * *
272709 AGAGATTCTCTAAATAATAATGGAAAATGTTTCCCCTAGAATGCGCCTTTCATTTCGGATGGGAT
1 AGAGATTCTCTGAATAATAATGGAAAAAGCTTCCCCTGGAACGCGCCTTTCATTTCGGATGGGAT
* *
272774 GGAACACTATAACATTG-T
66 GGAACACTATGACA-TGAC
* * * * * * *
272792 AGAGATTCTATGAATAATAACGGAAAACA-CTTTCCCTGGAATGTGCCTTTTATTTTGGATGGGA
1 AGAGATTCTCTGAATAATAATGGAAAA-AGCTTCCCCTGGAACGCGCCTTTCATTTCGGATGGGA
* **
272856 TGTAACACTATGACATGGT
65 TGGAACACTATGACATGAC
* * * ** *
272875 AGAGATTCTCTGAATAATAATGG-AAAA----CCCCTGAAATGTGCCTTTCATTTCAAATAGGAT
1 AGAGATTCTCTGAATAATAATGGAAAAAGCTTCCCCTGGAACGCGCCTTTCATTTCGGATGGGAT
*
272935 GGAATACTATGACATGAC
66 GGAACACTATGACATGAC
*
272953 AAAGATTCTCTGAATAATAAT-GAAAAA
1 AGAGATTCTCTGAATAATAATGGAAAAA
272980 CACTATGACA
Statistics
Matches: 380, Mismatches: 53, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
77 1 0.00
78 64 0.17
81 1 0.00
82 5 0.01
83 307 0.81
84 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (83 bp):
AGAGATTCTCTGAATAATAATGGAAAAAGCTTCCCCTGGAACGCGCCTTTCATTTCGGATGGGAT
GGAACACTATGACATGAC
Found at i:272734 original size:166 final size:165
Alignment explanation
Indices: 272460--272979 Score: 647
Period size: 166 Copynumber: 3.2 Consensus size: 165
272450 GTGAAATAAT
* * * *
272460 AGAGATTCTTTGAATAATAATGGAAAATGCTTCCTCTCGAACGCGCCTTTCATTTCGGATGGGAT
1 AGAGATTCTCTGAATAATAATGGAAAATGCTTCCCCTGGAACGCGCCTTTTATTTCGGATGGGAT
* * * * *
272525 AGAACACTATGACATGACAGAGACTCTCTAAATAGTAATGGAAAAAGCTTCCCCTGGAACGCGCC
66 TGAACACTATGACATGATAGAGATTCTCTAAATAATAATGGAAAAAG-TTCCCCTGGAATGCGCC
*
272590 TTTCATTTCGAATGGGATTGAACACTATGACATGAC
130 TTTCATTTCGAATGGGATGGAACACTATGACATGAC
* *
272626 AGAGATTCTCTGAATAATAATGGAAAATGCTTCCCCTGGAACGCACCTTTTATTTCGGATAGGAT
1 AGAGATTCTCTGAATAATAATGGAAAATGCTTCCCCTGGAACGCGCCTTTTATTTCGGATGGGAT
* * *
272691 TGAACACTATAACATGATAGAGATTCTCTAAATAATAATGGAAAATGTTTCCCCTAGAATGCGCC
66 TGAACACTATGACATGATAGAGATTCTCTAAATAATAATGGAAAAAG-TTCCCCTGGAATGCGCC
* * *
272756 TTTCATTTCGGATGGGATGGAACACTATAACATTG-T
130 TTTCATTTCGAATGGGATGGAACACTATGACA-TGAC
* * ** * * * *
272792 AGAGATTCTATGAATAATAACGGAAAACACTTTCCCTGGAATGTGCCTTTTATTTTGGATGGGA-
1 AGAGATTCTCTGAATAATAATGGAAAATGCTTCCCCTGGAACGCGCCTTTTATTTCGGATGGGAT
* * * *
272856 TGTAACACTATGACATGGTAGAGATTCTCTGAATAATAATGG-AAAA---CCCCTGAAATGTGCC
66 TG-AACACTATGACATGATAGAGATTCTCTAAATAATAATGGAAAAAGTTCCCCTGGAATGCGCC
* * *
272917 TTTCATTTCAAATAGGATGGAATACTATGACATGAC
130 TTTCATTTCGAATGGGATGGAACACTATGACATGAC
* *
272953 AAAGATTCTCTGAATAATAATGAAAAA
1 AGAGATTCTCTGAATAATAATGGAAAA
272980 CACTATGACA
Statistics
Matches: 305, Mismatches: 46, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
160 2 0.01
161 62 0.20
165 5 0.02
166 234 0.77
167 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (165 bp):
AGAGATTCTCTGAATAATAATGGAAAATGCTTCCCCTGGAACGCGCCTTTTATTTCGGATGGGAT
TGAACACTATGACATGATAGAGATTCTCTAAATAATAATGGAAAAAGTTCCCCTGGAATGCGCCT
TTCATTTCGAATGGGATGGAACACTATGACATGAC
Found at i:273136 original size:16 final size:16
Alignment explanation
Indices: 273112--273150 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
273102 ATGGTCCTTA
*
273112 GTATTTTTCCTATTAT
1 GTATCTTTCCTATTAT
*
273128 GTATCTTTCTTATTAT
1 GTATCTTTCCTATTAT
273144 GTTATCT
1 G-TATCT
273151 ATCATTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.18, C:0.13, G:0.08, T:0.62
Consensus pattern (16 bp):
GTATCTTTCCTATTAT
Found at i:273991 original size:31 final size:31
Alignment explanation
Indices: 273956--274021 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
273946 TCTCAGACCT
* *
273956 TAAACAATAAATAAAATCGTACAAATACACC
1 TAAACAATAAATAAAAGCATACAAATACACC
* *
273987 TAAACAGTAAATAAAAGCATACACATACACC
1 TAAACAATAAATAAAAGCATACAAATACACC
274018 TAAA
1 TAAA
274022 ACAAACTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.58, C:0.20, G:0.05, T:0.18
Consensus pattern (31 bp):
TAAACAATAAATAAAAGCATACAAATACACC
Found at i:274827 original size:6 final size:6
Alignment explanation
Indices: 274813--274882 Score: 50
Period size: 6 Copynumber: 11.7 Consensus size: 6
274803 TACTTCTCAC
* * * * * **
274813 CATCCT CATCGT CATCCT CCTCCT CCTCCT TATCGT CATTAT CATCCT
1 CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT
* * *
274861 CATCCT CGTCGT CATCAT CATC
1 CATCCT CATCCT CATCCT CATC
274883 ATCACTCTCA
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.16, C:0.43, G:0.06, T:0.36
Consensus pattern (6 bp):
CATCCT
Found at i:274860 original size:24 final size:24
Alignment explanation
Indices: 274813--274882 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
274803 TACTTCTCAC
* *
274813 CATCCTCATCGTCATCCTCCTCCT
1 CATCCTCATCGTCATCATCATCCT
* * *
274837 CCTCCTTATCGTCATTATCATCCT
1 CATCCTCATCGTCATCATCATCCT
*
274861 CATCCTCGTCGTCATCATCATC
1 CATCCTCATCGTCATCATCATC
274883 ATCACTCTCA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.16, C:0.43, G:0.06, T:0.36
Consensus pattern (24 bp):
CATCCTCATCGTCATCATCATCCT
Found at i:274869 original size:21 final size:21
Alignment explanation
Indices: 274845--274885 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
274835 CTCCTCCTTA
* *
274845 TCGTCATTATCATCCTCATCC
1 TCGTCATCATCATCATCATCC
*
274866 TCGTCGTCATCATCATCATC
1 TCGTCATCATCATCATCATC
274886 ACTCTCAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.37, G:0.07, T:0.37
Consensus pattern (21 bp):
TCGTCATCATCATCATCATCC
Found at i:289695 original size:19 final size:20
Alignment explanation
Indices: 289671--289726 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
289661 AGTTTACAAT
*
289671 TAAATAATCAAATAAAA-AA
1 TAAATAATAAAATAAAATAA
*
289690 TAAATACTAAAATAAAATAA
1 TAAATAATAAAATAAAATAA
289710 TAATAATAATAAAATAA
1 T-A-AATAATAAAATAA
289727 TTAATTACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.48
20 3 0.10
21 1 0.03
22 12 0.39
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (20 bp):
TAAATAATAAAATAAAATAA
Found at i:289707 original size:13 final size:13
Alignment explanation
Indices: 289672--289726 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 13
289662 GTTTACAATT
*
289672 AAATAATCAAATA
1 AAATAATAAAATA
289685 AAA-AATAAATACTA
1 AAATAATAAA-A-TA
289699 AAATAA-AATAATA
1 AAATAATAA-AATA
289712 ATAATAATAAAATA
1 A-AATAATAAAATA
289726 A
1 A
289727 TTAATTACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
12 5 0.14
13 7 0.20
14 18 0.51
15 5 0.14
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAATAAAATA
Found at i:289708 original size:17 final size:18
Alignment explanation
Indices: 289671--289731 Score: 65
Period size: 17 Copynumber: 3.4 Consensus size: 18
289661 AGTTTACAAT
289671 TAAATAATCAAATAA-AAAA
1 TAAATAAT--AATAATAAAA
*
289690 TAAATACTAA-AATAAAA
1 TAAATAATAATAATAAAA
289707 T-AATAATAATAATAAAA
1 TAAATAATAATAATAAAA
*
289724 TAATTAAT
1 TAAATAAT
289732 TACTTAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 9 0.25
17 15 0.42
18 5 0.14
19 7 0.19
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAATAATAATAATAAAA
Found at i:289731 original size:12 final size:11
Alignment explanation
Indices: 289681--289727 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
289671 TAAATAATCA
289681 AATAA-AAAAT
1 AATAATAAAAT
*
289691 AAATACTAAAAT
1 -AATAATAAAAT
289703 AA-AATAATAAT
1 AATAATAA-AAT
289714 AATAATAAAAT
1 AATAATAAAAT
289725 AAT
1 AAT
289728 TAATTACTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 4 0.13
11 17 0.55
12 10 0.32
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:290553 original size:14 final size:14
Alignment explanation
Indices: 290534--290561 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
290524 TAAAAATATC
290534 GACCAGATCTTAGA
1 GACCAGATCTTAGA
290548 GACCAGATCTTAGA
1 GACCAGATCTTAGA
290562 TGAGTTCAAA
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:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (14 bp):
GACCAGATCTTAGA
Found at i:291075 original size:20 final size:20
Alignment explanation
Indices: 291052--291089 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
291042 AAATAAACAT
291052 AAAATTAAACATATAAATCG
1 AAAATTAAACATATAAATCG
291072 AAAATTAAACATATAAAT
1 AAAATTAAACATATAAAT
291090 TTAAATAAAA
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:0.63, C:0.08, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAATTAAACATATAAATCG
Found at i:302457 original size:45 final size:45
Alignment explanation
Indices: 302387--302651 Score: 334
Period size: 45 Copynumber: 5.9 Consensus size: 45
302377 GAAACCTAAA
* * ***
302387 CTTGACTTTTTCACGAAGATA-AGTCAACCTTTAAGTGGCATCATT
1 CTTGACTTTCTCACGAAGA-AGAGTCAACCTTTCAGTGATGTCATT
* *
302432 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTCAGTGATGTCATT
1 CTTGACTTTCTCACGAAGAAGAGTCAACCTTTCAGTGATGTCATT
* **
302477 CTTGACTTTCTCGCGAAGAAGAGTCAATATTTCAGTGATGTCATT
1 CTTGACTTTCTCACGAAGAAGAGTCAACCTTTCAGTGATGTCATT
* ** *
302522 CTTGACTTTCTCACGAAGATGAGTCAATATTTCAGTGATATCATT
1 CTTGACTTTCTCACGAAGAAGAGTCAACCTTTCAGTGATGTCATT
* * * *
302567 CTTGACTTTCTCGCGAAGAGGAGTCAACTTTTCAGTGATGTCTTT
1 CTTGACTTTCTCACGAAGAAGAGTCAACCTTTCAGTGATGTCATT
* *
302612 CTTGACTTTGTCACGAAGAAGAGTCAACCTTTCTGTGATG
1 CTTGACTTTCTCACGAAGAAGAGTCAACCTTTCAGTGATG
302652 AGTCAAATTT
Statistics
Matches: 195, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 195 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (45 bp):
CTTGACTTTCTCACGAAGAAGAGTCAACCTTTCAGTGATGTCATT
Found at i:302629 original size:135 final size:135
Alignment explanation
Indices: 302387--302638 Score: 405
Period size: 135 Copynumber: 1.9 Consensus size: 135
302377 GAAACCTAAA
* * *
302387 CTTGACTTTTTCACGAAGATAAGTCAACCTTTAAGTGGCATCATTCTTGACTTTCTCGCGAAGAG
1 CTTGACTTTCTCACGAAGATAAGTCAACATTTAAGTGACATCATTCTTGACTTTCTCGCGAAGAG
*
302452 GAGTCAACCTTTCAGTGATGTCATTCTTGACTTTCTCGCGAAGAAGAGTCAATATTTCAGTGATG
66 GAGTCAACCTTTCAGTGATGTCATTCTTGACTTTCTCACGAAGAAGAGTCAATATTTCAGTGATG
302517 TCATT
131 TCATT
* * * *
302522 CTTGACTTTCTCACGAAGATGAGTCAATATTTCAGTGATATCATTCTTGACTTTCTCGCGAAGAG
1 CTTGACTTTCTCACGAAGATAAGTCAACATTTAAGTGACATCATTCTTGACTTTCTCGCGAAGAG
* * *
302587 GAGTCAACTTTTCAGTGATGTCTTTCTTGACTTTGTCACGAAGAAGAGTCAA
66 GAGTCAACCTTTCAGTGATGTCATTCTTGACTTTCTCACGAAGAAGAGTCAA
302639 CCTTTCTGTG
Statistics
Matches: 106, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
135 106 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (135 bp):
CTTGACTTTCTCACGAAGATAAGTCAACATTTAAGTGACATCATTCTTGACTTTCTCGCGAAGAG
GAGTCAACCTTTCAGTGATGTCATTCTTGACTTTCTCACGAAGAAGAGTCAATATTTCAGTGATG
TCATT
Found at i:302709 original size:64 final size:64
Alignment explanation
Indices: 302587--302715 Score: 161
Period size: 64 Copynumber: 2.0 Consensus size: 64
302577 TCGCGAAGAG
* * * *
302587 GAGTCAACTTTTCAGTGATGTCTTTCTTGACTTTGTCACGAAGAAGAGTCAACCTTTCTGTGAT
1 GAGTCAAATTTTCAGTGATGTCATTATTGACTTTCTCACGAAGAAGAGTCAACCTTTCTGTGAT
* * * * *
302651 GAGTCAAATTTTTAGTGATGTCATTATTGACTTTCTCGCTAAG-AGTAGTCTACTTTTCTGTGAT
1 GAGTCAAATTTTCAGTGATGTCATTATTGACTTTCTCACGAAGAAG-AGTCAACCTTTCTGTGAT
302715 G
1 G
302716 TCATTCTCAA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 2 0.04
64 53 0.96
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.40
Consensus pattern (64 bp):
GAGTCAAATTTTCAGTGATGTCATTATTGACTTTCTCACGAAGAAGAGTCAACCTTTCTGTGAT
Found at i:302823 original size:50 final size:50
Alignment explanation
Indices: 302677--302825 Score: 192
Period size: 50 Copynumber: 3.0 Consensus size: 50
302667 GATGTCATTA
* * * *
302677 TTGACTTTCTCGCT-AAGAGTAGTCTACTTTTCTGTGATGTCATTCTCAAC
1 TTGACTTTCTC-ATGAAGAGGAGTCAACTTTTCTGTGATGTCATTCTTAAC
* * * *
302727 TTGACTTTCTCATGGAGAGGAGTCAACTTTCCGGTTATGTCATTCTTAAC
1 TTGACTTTCTCATGAAGAGGAGTCAACTTTTCTGTGATGTCATTCTTAAC
* *
302777 TTGACTTTCTCATGAAGATGAGTCAACTTTTCTGCGATGTCATTCTTAA
1 TTGACTTTCTCATGAAGAGGAGTCAACTTTTCTGTGATGTCATTCTTAA
302826 ACAAATAATT
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 1 0.01
50 83 0.99
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.40
Consensus pattern (50 bp):
TTGACTTTCTCATGAAGAGGAGTCAACTTTTCTGTGATGTCATTCTTAAC
Found at i:305596 original size:75 final size:75
Alignment explanation
Indices: 305497--305635 Score: 215
Period size: 75 Copynumber: 1.9 Consensus size: 75
305487 GTAGCGCTTA
* * *
305497 TTTAACGTATTAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACTTTTAAACAAAT
1 TTTAACGTAATAGGTAACGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAT
305562 CAGTATATAT
66 CAGTATATAT
* * * *
305572 TTTAACGTAATATGTAACGTCTATTTTATTTTACTGTTTACATTATTATTAACCTTTAAACAAA
1 TTTAACGTAATAGGTAACGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAA
305636 CCAAATAGCT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 57 1.00
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (75 bp):
TTTAACGTAATAGGTAACGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAT
CAGTATATAT
Found at i:305697 original size:23 final size:23
Alignment explanation
Indices: 305648--305719 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
305638 AAATAGCTAG
* * * *
305648 TTTAACGTAATAAGTATCGTTTG
1 TTTAACGTAATAGGTAGCGTATA
* *
305671 TTTAACGTAATAGGAAGCGTCTA
1 TTTAACGTAATAGGTAGCGTATA
*
305694 TTTAACATAATAGGTAGCGTATA
1 TTTAACGTAATAGGTAGCGTATA
305717 TTT
1 TTT
305720 TATTTTACCG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (23 bp):
TTTAACGTAATAGGTAGCGTATA
Found at i:308024 original size:27 final size:27
Alignment explanation
Indices: 307994--308045 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
307984 TAACATTATT
*
307994 ATTAATAATAA-TAATACTAATAAAAAC
1 ATTAATAATAATTAAAACT-ATAAAAAC
308021 ATTAATAATAATTAAAACTATAAAA
1 ATTAATAATAATTAAAACTATAAAA
308046 TATCATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (27 bp):
ATTAATAATAATTAAAACTATAAAAAC
Found at i:311423 original size:23 final size:23
Alignment explanation
Indices: 311397--311457 Score: 122
Period size: 23 Copynumber: 2.7 Consensus size: 23
311387 TTTTACGATT
311397 TAAAATTTAGGACTTTTTTGACA
1 TAAAATTTAGGACTTTTTTGACA
311420 TAAAATTTAGGACTTTTTTGACA
1 TAAAATTTAGGACTTTTTTGACA
311443 TAAAATTTAGGACTT
1 TAAAATTTAGGACTT
311458 AAGGTCATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (23 bp):
TAAAATTTAGGACTTTTTTGACA
Found at i:312622 original size:46 final size:46
Alignment explanation
Indices: 312547--312635 Score: 121
Period size: 46 Copynumber: 1.9 Consensus size: 46
312537 GTCGAAACTG
*
312547 CCGCATAGAATTTGCACCGAAGTGCCACATAGATTTGTCCCGAAGGA
1 CCGCATAGAATTTGCACCGAAGTGCCACATAGAATTG-CCCGAAGGA
312594 CCGCATAGAA-TTGTC-CCGAAG-GACCACATAGAATTGCCCGAA
1 CCGCATAGAATTTG-CACCGAAGTG-CCACATAGAATTGCCCGAA
312636 TGACTGCGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
45 7 0.18
46 21 0.54
47 11 0.28
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (46 bp):
CCGCATAGAATTTGCACCGAAGTGCCACATAGAATTGCCCGAAGGA
Found at i:312648 original size:22 final size:23
Alignment explanation
Indices: 312547--312635 Score: 103
Period size: 23 Copynumber: 3.9 Consensus size: 23
312537 GTCGAAACTG
312547 CCGCATAGAATT-TGCACCGAAGTG-
1 CCGCATAGAATTGT-C-CCGAAG-GA
* *
312571 CCACATAGATTTGTCCCGAAGGA
1 CCGCATAGAATTGTCCCGAAGGA
312594 CCGCATAGAATTGTCCCGAAGGA
1 CCGCATAGAATTGTCCCGAAGGA
*
312617 CCACATAGAATTG-CCCGAA
1 CCGCATAGAATTGTCCCGAA
312636 TGACTGCGTA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
22 7 0.12
23 39 0.67
24 11 0.19
25 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (23 bp):
CCGCATAGAATTGTCCCGAAGGA
Found at i:314816 original size:86 final size:87
Alignment explanation
Indices: 314669--314851 Score: 352
Period size: 86 Copynumber: 2.1 Consensus size: 87
314659 GGTGTTCGAC
314669 ACTTTCTTCCATATAAAGCTTCGTATGGCGCCATCTTGATACTAGATTGATAACTATTATTATCA
1 ACTTTCTTCCATATAAAGCTTCGTATGGCGCCATCTTGATACTAGATTGATAACTATTATTATCA
314734 GCGAATTCTGCCAAAGGAAAAT
66 GCGAATTCTGCCAAAGGAAAAT
314756 A-TTTCTTCCATATAAAGCTTCGTATGGCGCCATCTTGATACTAGATTGATAACTATTATTATCA
1 ACTTTCTTCCATATAAAGCTTCGTATGGCGCCATCTTGATACTAGATTGATAACTATTATTATCA
314820 GCGAATTCTGCCAAAGGAAAAT
66 GCGAATTCTGCCAAAGGAAAAT
314842 ACTTT-TTCCA
1 ACTTTCTTCCA
314852 AGATCCCTTG
Statistics
Matches: 95, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
86 91 0.96
87 4 0.04
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (87 bp):
ACTTTCTTCCATATAAAGCTTCGTATGGCGCCATCTTGATACTAGATTGATAACTATTATTATCA
GCGAATTCTGCCAAAGGAAAAT
Found at i:315649 original size:15 final size:15
Alignment explanation
Indices: 315629--315658 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
315619 TACCACTATC
315629 CTTTAAAGAAAATCG
1 CTTTAAAGAAAATCG
315644 CTTTAAAGAAAATCG
1 CTTTAAAGAAAATCG
315659 GGCATCTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (15 bp):
CTTTAAAGAAAATCG
Found at i:322803 original size:21 final size:21
Alignment explanation
Indices: 322779--322820 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
322769 AGTTTATTTT
322779 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
322800 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
322821 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:322856 original size:32 final size:33
Alignment explanation
Indices: 322815--322913 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
322805 TTTGTTTCAA
322815 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTAGAAGTTTTTAAGTATTTGAAT
*
322847 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTAGAAGTTTTTAAGTATTTGAAT
* * *
322880 TTATCAAACTTAGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTAGAAGTTTTTAAGTATTTGAAT
322913 T
1 T
322914 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 11 0.18
33 51 0.82
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTAGAAGTTTTTAAGTATTTGAAT
Found at i:322942 original size:13 final size:13
Alignment explanation
Indices: 322899--322953 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
322889 TTAGAAGTAT
322899 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
322912 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
322926 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
322939 TTAAGTATTTGAA
1 TTAAGTATTTCAA
322952 TT
1 TT
322954 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:323654 original size:15 final size:15
Alignment explanation
Indices: 323627--323683 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
323617 TTTAATAATA
*
323627 TTAAAATCGATTTTT
1 TTAAAACCGATTTTT
*
323642 TTATAACCGATTTTT
1 TTAAAACCGATTTTT
*
323657 TAAAAAAACCGATTTTT
1 T--TAAAACCGATTTTT
323674 TTAAAACCGA
1 TTAAAACCGA
323684 AACCGGTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 22 0.63
17 13 0.37
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (15 bp):
TTAAAACCGATTTTT
Found at i:323666 original size:17 final size:18
Alignment explanation
Indices: 323646--323679 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
323636 ATTTTTTTAT
323646 AACCGA-TTTTTTAAAAA
1 AACCGATTTTTTTAAAAA
323663 AACCGATTTTTTTAAAA
1 AACCGATTTTTTTAAAA
323680 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (18 bp):
AACCGATTTTTTTAAAAA
Found at i:334305 original size:6 final size:6
Alignment explanation
Indices: 334247--334298 Score: 86
Period size: 6 Copynumber: 8.5 Consensus size: 6
334237 AGAAAGAAAG
*
334247 AAAGAA AAATGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAATAA
1 AAAGAA AAA-GAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
334296 AAA
1 AAA
334299 ATAAAAAACT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
6 38 0.86
7 6 0.14
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:341489 original size:18 final size:19
Alignment explanation
Indices: 341466--341513 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
341456 GATGCAATTA
**
341466 GTATCGATAC-TGAGGTGG
1 GTATCGATACATGAGGAAG
341484 GTATCGATACTATGAGGAAG
1 GTATCGATAC-ATGAGGAAG
341504 GTATCGATAC
1 GTATCGATAC
341514 CATTGATTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 10 0.38
20 16 0.62
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.27
Consensus pattern (19 bp):
GTATCGATACATGAGGAAG
Found at i:342313 original size:161 final size:165
Alignment explanation
Indices: 342037--342401 Score: 621
Period size: 161 Copynumber: 2.2 Consensus size: 165
342027 CTATATGTGT
*
342037 AAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGAACTTTGTGTGCAAAACTAAGAA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGAACTTTGTGTGCAAAACTAAGAA
* * *
342102 ATTCATAATAAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCAAAACTAAGAAATT-ATAATA
66 ATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGAAAAACTAAGAAATTCACAATA
342166 AGTTTATGAA-TTCCGTATGGGCACT-TGTGTCCA
131 AGTTTATGAATTTCCGTATGGGCACTGTGTGTCCA
* *
342199 AAA-TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGTAAAACTAAGAA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGAACTTTGTGTGCAAAACTAAGAA
*
342263 ATTCATAATAAGTTTATGAATTTCCGTATGGGCTCTTTGTGTGAAAAACTAAGAAATTCACAATA
66 ATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGAAAAACTAAGAAATTCACAATA
*
342328 AGTTTATGAATTTCCGTATGGGCACTGTGTGTGCA
131 AGTTTATGAATTTCCGTATGGGCACTGTGTGTCCA
*
342363 AAACTTAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
342402 TGGTAGTGGG
Statistics
Matches: 190, Mismatches: 9, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
161 113 0.59
162 18 0.09
163 15 0.08
164 10 0.05
165 34 0.18
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (165 bp):
AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGAACTTTGTGTGCAAAACTAAGAA
ATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGAAAAACTAAGAAATTCACAATA
AGTTTATGAATTTCCGTATGGGCACTGTGTGTCCA
Found at i:342418 original size:55 final size:55
Alignment explanation
Indices: 342037--342401 Score: 612
Period size: 55 Copynumber: 6.7 Consensus size: 55
342027 CTATATGTGT
* *
342037 AAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGAACTTTGTGTGCA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
*
342092 AAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
*
342147 AAACTAAGAAATT-ATAATAAGTTTATGAA-TTCCGTATGGGCAC-TTGTGTCCA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
*
342199 AAA-TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGTA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* *
342253 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCTCTTTGTGTGAA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* *
342308 AAACTAAGAAATTCACAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGCA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
*
342363 AAACTTAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
342402 TGGTAGTGGG
Statistics
Matches: 291, Mismatches: 15, Indels: 8
0.93 0.05 0.03
Matches are distributed among these distances:
51 9 0.03
52 27 0.09
53 27 0.09
54 26 0.09
55 202 0.69
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (55 bp):
AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
Found at i:344123 original size:30 final size:28
Alignment explanation
Indices: 344109--344183 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
344099 ATTGTCTCCT
344109 TTTATTATAATTTATAAAAACTTTATCC
1 TTTATTATAATTTATAAAAACTTTATCC
* ** * *
344137 TTTATTTTAATTTATAAATAGTTTTGTAC
1 TTTATTATAATTTATAAA-AACTTTATCC
*
344166 TTTATTGTAATTTATAAA
1 TTTATTATAATTTATAAA
344184 TTGTTTGTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 17 0.43
29 23 0.57
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (28 bp):
TTTATTATAATTTATAAAAACTTTATCC
Found at i:344147 original size:28 final size:29
Alignment explanation
Indices: 344109--344311 Score: 104
Period size: 28 Copynumber: 7.3 Consensus size: 29
344099 ATTGTCTCCT
*
344109 TTTATTATAATTTATAAA-AACTTTATCC
1 TTTATTATAATTTATAAATAACTTTATAC
* ** *
344137 TTTATTTTAATTTATAAATAGTTTTGTAC
1 TTTATTATAATTTATAAATAACTTTATAC
* ** *
344166 TTTATTGTAATTTATAAAT-TGTTTGTAC
1 TTTATTATAATTTATAAATAACTTTATAC
* *** *
344194 --T-TTGTAA--TATAAATTGTTTTGTAC
1 TTTATTATAATTTATAAATAACTTTATAC
* ** *
344218 TTTATTGTAATTTATAAA-AAAATTATCC
1 TTTATTATAATTTATAAATAACTTTATAC
*
344246 TTTATTATAATTTATAAA-ATA-TTTTTAC
1 TTTATTATAATTTATAAATA-ACTTTATAC
* * * * *
344274 TTTATTGTAAATTCTAAA-AAGTTTAAAC
1 TTTATTATAATTTATAAATAACTTTATAC
344302 TTTATTATAA
1 TTTATTATAA
344312 ATTCTAAAGC
Statistics
Matches: 140, Mismatches: 26, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
23 7 0.05
24 7 0.05
25 6 0.04
26 2 0.01
27 7 0.05
28 80 0.57
29 31 0.22
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (29 bp):
TTTATTATAATTTATAAATAACTTTATAC
Found at i:344219 original size:24 final size:25
Alignment explanation
Indices: 344148--344220 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 25
344138 TTATTTTAAT
*
344148 TTATAAATAGTTTTGTACTTTATTGTAA
1 TTATAAATTGTTTTGTAC--T-TTGTAA
344176 TTTATAAATTG-TTTGTACTTTGTAA
1 -TTATAAATTGTTTTGTACTTTGTAA
344201 -TATAAATTGTTTTGTACTTT
1 TTATAAATTGTTTTGTACTTT
344221 ATTGTAATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
23 9 0.21
24 10 0.24
25 6 0.14
26 1 0.02
28 7 0.17
29 9 0.21
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.56
Consensus pattern (25 bp):
TTATAAATTGTTTTGTACTTTGTAA
Found at i:344312 original size:28 final size:28
Alignment explanation
Indices: 344245--344319 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
344235 AAAAATTATC
* * **
344245 CTTTATTATAATTTATAAAATATTTTTA
1 CTTTATTATAAATTCTAAAATATTTAAA
*
344273 CTTTATTGTAAATTCTAAAA-AGTTTAAA
1 CTTTATTATAAATTCTAAAATA-TTTAAA
344301 CTTTATTATAAATTCTAAA
1 CTTTATTATAAATTCTAAA
344320 GCATTTTGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
27 1 0.03
28 39 0.98
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (28 bp):
CTTTATTATAAATTCTAAAATATTTAAA
Found at i:355060 original size:47 final size:49
Alignment explanation
Indices: 355007--355102 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 49
354997 ATGGTATTTC
355007 TTATGCCTAACCTT-CCGACAGAGTCTACAGAGG-CCCTATGCTATCTT
1 TTATGCCTAACCTTCCCGACAGAGTCTACAGAGGACCCTATGCTATCTT
355054 TTATGCCTAACCTTCCCGACAGAGTCTACAGAGGTACCCTATGCTATCT
1 TTATGCCTAACCTTCCCGACAGAGTCTACAGAGG-ACCCTATGCTATCT
355103 CTAGTAAGGG
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
47 14 0.30
48 19 0.41
50 13 0.28
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (49 bp):
TTATGCCTAACCTTCCCGACAGAGTCTACAGAGGACCCTATGCTATCTT
Found at i:362682 original size:15 final size:14
Alignment explanation
Indices: 362650--362692 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 14
362640 ATTGATTAAA
*
362650 AAGAAAAAAGAAT-
1 AAGAAAAAAAAATG
362663 AAGAAAAAAAAATG
1 AAGAAAAAAAAATG
362677 AGAGAAAAAAAAATG
1 A-AGAAAAAAAAATG
362692 A
1 A
362693 TAGGAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 12 0.44
14 1 0.04
15 14 0.52
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (14 bp):
AAGAAAAAAAAATG
Found at i:365453 original size:14 final size:15
Alignment explanation
Indices: 365420--365453 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
365410 AAGGGTTTGG
365420 TATTTTCTTTAATTT
1 TATTTTCTTTAATTT
*
365435 AATTTTCTTT-ATTT
1 TATTTTCTTTAATTT
365449 TATTT
1 TATTT
365454 CATGCATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTTCTTTAATTT
Found at i:366205 original size:20 final size:20
Alignment explanation
Indices: 366169--366210 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
366159 AGATAAACAA
*
366169 AAACAACACAAAAAAATTGT
1 AAACAACACAAAAAAATCGT
*
366189 AAACAACGAC-AAGAAATCGT
1 AAACAAC-ACAAAAAAATCGT
366209 AA
1 AA
366211 GCTACCAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.62, C:0.17, G:0.10, T:0.12
Consensus pattern (20 bp):
AAACAACACAAAAAAATCGT
Found at i:368554 original size:2 final size:2
Alignment explanation
Indices: 368547--368587 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
368537 CACAATTATG
368547 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
368588 CCATAGGCCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:381243 original size:20 final size:20
Alignment explanation
Indices: 381199--381250 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
381189 TATAGCAGTA
*
381199 GAGTATCGATACCCTAGGAG
1 GAGTATCGATACCCAAGGAG
*
381219 GAGTATCGATACTCAAGG-G
1 GAGTATCGATACCCAAGGAG
*
381238 GTAGTATCAATAC
1 G-AGTATCGATAC
381251 GAGAGGATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (20 bp):
GAGTATCGATACCCAAGGAG
Found at i:384154 original size:29 final size:29
Alignment explanation
Indices: 384112--384167 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
384102 TCTCTAAGCT
* *
384112 TTTCTAAATTTATACTTTGATCACTAAAC
1 TTTCAAAAGTTATACTTTGATCACTAAAC
* *
384141 TTTCAAAAGTTATATTTTGGTCACTAA
1 TTTCAAAAGTTATACTTTGATCACTAA
384168 CCAAAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (29 bp):
TTTCAAAAGTTATACTTTGATCACTAAAC
Found at i:386516 original size:83 final size:83
Alignment explanation
Indices: 386377--386538 Score: 297
Period size: 83 Copynumber: 2.0 Consensus size: 83
386367 AGGGGGGATC
*
386377 TATATGATGCTGAGAGCAAGTGAAGATGCCGAGAATTTGGCTTGAGGAACTTATTTTTATCCCTT
1 TATATGATGCTGAGAGCAAGTGAAGATGCCGAGAATTTGGCTTGAGGAACTTATTTTGATCCCTT
386442 CAATAATTATTCTTCTTT
66 CAATAATTATTCTTCTTT
*
386460 TATATGATGCTGAGAGCAAGTGAAGATGCCGAGAATTTGGCTTGAGGAACTTATTTTGGTCCCTT
1 TATATGATGCTGAGAGCAAGTGAAGATGCCGAGAATTTGGCTTGAGGAACTTATTTTGATCCCTT
*
386525 CAATAATTCTTCTT
66 CAATAATTATTCTT
386539 TTATGTCTTA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (83 bp):
TATATGATGCTGAGAGCAAGTGAAGATGCCGAGAATTTGGCTTGAGGAACTTATTTTGATCCCTT
CAATAATTATTCTTCTTT
Found at i:387654 original size:3 final size:3
Alignment explanation
Indices: 387646--387670 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
387636 GTCAACTGAG
387646 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
387671 AAAATGGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:388678 original size:21 final size:21
Alignment explanation
Indices: 388621--388707 Score: 90
Period size: 20 Copynumber: 4.3 Consensus size: 21
388611 GTGAAATTAA
*
388621 TTTT-TAAATTTTAAATTTA-
1 TTTTATAAATATTAAATTTAT
* *
388640 TTTCAAAAATATTAAATTTAT
1 TTTTATAAATATTAAATTTAT
* * *
388661 TTTTATACATATTCAATTTAA
1 TTTTATAAATATTAAATTTAT
388682 TTTTA-AAATATTAAATTTAT
1 TTTTATAAATATTAAATTTAT
*
388702 TATTAT
1 TTTTAT
388708 TTTAAATCTC
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 3 0.06
20 29 0.55
21 21 0.40
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATAAATATTAAATTTAT
Found at i:388744 original size:23 final size:23
Alignment explanation
Indices: 388705--388753 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
388695 AATTTATTAT
* * *
388705 TATTTTAAATCTCATATTAACTG
1 TATTTTAAATATCATATGAAATG
388728 TATTTTAAAATAT-ATATGAAATG
1 TATTTT-AAATATCATATGAAATG
388751 TAT
1 TAT
388754 ATATTTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (23 bp):
TATTTTAAATATCATATGAAATG
Found at i:394743 original size:75 final size:76
Alignment explanation
Indices: 394635--394843 Score: 262
Period size: 75 Copynumber: 2.8 Consensus size: 76
394625 CCGTTGTACA
* * *
394635 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
** *
394699 CAAAACTGTTT
66 CAAAACCATTC
* * * *
394710 AGGGGGGAATCGGTTCCTCCTAT-TGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
*
394774 CCAAACCATTC
66 CAAAACCATTC
**
394785 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTATGAGCA-ATCTGGAATT
1 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATA-CTGGAATT
394844 TTTGGCTTTG
Statistics
Matches: 114, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
75 85 0.75
76 1 0.01
77 28 0.25
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
CAAAACCATTC
Found at i:400315 original size:76 final size:76
Alignment explanation
Indices: 400112--400317 Score: 256
Period size: 75 Copynumber: 2.7 Consensus size: 76
400102 CCGTTGTACA
* * * *
400112 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGC-ATACTGGAATTCTCGGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAAT-CTGGAAATCTCGGA
** *
400175 ACAAAACTGTTT
65 ACAAAACCATTC
* * *
400187 AGGGGGGAATCAGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGAA
*
400251 CCAAACCATTC
66 CAAAACCATTC
* **
400262 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATTGGTTCCCTATGAGCAATCTGGAA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAA
400318 TTTTTGGCTT
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
75 82 0.73
76 30 0.27
ACGTcount: A:0.22, C:0.23, G:0.32, T:0.23
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGAA
CAAAACCATTC
Found at i:401623 original size:25 final size:25
Alignment explanation
Indices: 401589--401637 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
401579 AACCTTTCTA
**
401589 CACTTTTAAGAGACGTGATGAGTTG
1 CACTTTTAAGAGACACGATGAGTTG
401614 CACTTTTAAGAGACACGATGAGTT
1 CACTTTTAAGAGACACGATGAGTT
401638 ATCTTCTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (25 bp):
CACTTTTAAGAGACACGATGAGTTG
Found at i:406373 original size:25 final size:25
Alignment explanation
Indices: 406345--406405 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
406335 TTATACACTT
406345 TTAAATATTTTTATCAAATTTTAAA
1 TTAAATATTTTTATCAAATTTTAAA
*
406370 TTAAATATTTTTATCAATTTTTAAA
1 TTAAATATTTTTATCAAATTTTAAA
406395 TTAAATATTTT
1 TTAAATATTTT
406406 CAAAAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (25 bp):
TTAAATATTTTTATCAAATTTTAAA
Found at i:406461 original size:32 final size:32
Alignment explanation
Indices: 406425--406572 Score: 188
Period size: 32 Copynumber: 4.5 Consensus size: 32
406415 AATTTTAATT
* *
406425 TATATATATATTTTTAAAAATGAATATATATATA
1 TATATATATATATATAAAAAT--ATATATATATA
* *
406459 TATATATATATTTAAAAACGAATATATATATATA
1 TATATATATATATATAAA--AATATATATATATA
* *
406493 TATATATATATATATATATATATATATATATA
1 TATATATATATATATAAAAATATATATATATA
* *
406525 TATATATATATATATATATATATATATATATA
1 TATATATATATATATAAAAATATATATATATA
406557 TATATATATATATATA
1 TATATATATATATATA
406573 TTTAAAAACG
Statistics
Matches: 106, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
32 61 0.58
34 42 0.40
36 3 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (32 bp):
TATATATATATATATAAAAATATATATATATA
Found at i:406486 original size:22 final size:20
Alignment explanation
Indices: 406448--406597 Score: 167
Period size: 20 Copynumber: 7.5 Consensus size: 20
406438 TTAAAAATGA
*
406448 ATATATATATATATATATAT
1 ATATATATATAAATATATAT
* * * **
406468 ATTTAAAAACGAATATATAT
1 ATATATATATAAATATATAT
*
406488 ATATATATATATATATATAT
1 ATATATATATAAATATATAT
*
406508 ATATATATATATATATATAT
1 ATATATATATAAATATATAT
*
406528 ATATATATATATATATATAT
1 ATATATATATAAATATATAT
*
406548 ATATATATATATATATATAT
1 ATATATATATAAATATATAT
* * *
406568 ATATATTTAAAAACGA-ATAT
1 ATATATATATAAA-TATATAT
406588 ATATATATAT
1 ATATATATAT
406598 GAATGACCTA
Statistics
Matches: 111, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
20 110 0.99
21 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (20 bp):
ATATATATATAAATATATAT
Found at i:406593 original size:2 final size:2
Alignment explanation
Indices: 406448--406573 Score: 200
Period size: 2 Copynumber: 63.0 Consensus size: 2
406438 TTAAAAATGA
* * * *
406448 AT AT AT AT AT AT AT AT AT AT AT TT AA AA ACG A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
406490 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
406532 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
406574 TTAAAAACGA
Statistics
Matches: 118, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 116 0.98
3 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:414218 original size:32 final size:32
Alignment explanation
Indices: 414182--414271 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 32
414172 AATTTAAGCT
*
414182 TTATTTTATAATTTTTCTATAAGTTTTAGTGA
1 TTATTTTGTAATTTTTCTATAAGTTTTAGTGA
** * * *
414214 TTATTTTGTAATAATTCAATAAG-TTTAATGG
1 TTATTTTGTAATTTTTCTATAAGTTTTAGTGA
*
414245 TCATTTTGTAATTTTT-TA-AA-TTTTAGT
1 TTATTTTGTAATTTTTCTATAAGTTTTAGT
414272 TACCAAAAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
29 7 0.15
30 1 0.02
31 19 0.41
32 19 0.41
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (32 bp):
TTATTTTGTAATTTTTCTATAAGTTTTAGTGA
Found at i:425582 original size:8 final size:8
Alignment explanation
Indices: 425565--425606 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
425555 TGAAGAGTTG
*
425565 GATATGTT
1 GATATATT
425573 GATATATT
1 GATATATT
425581 GATATATT
1 GATATATT
*
425589 GATATCTT
1 GATATATT
425597 AGATA-ATT
1 -GATATATT
425605 GA
1 GA
425607 ATAATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
7 2 0.07
8 24 0.80
9 4 0.13
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (8 bp):
GATATATT
Found at i:425906 original size:38 final size:38
Alignment explanation
Indices: 425864--425957 Score: 134
Period size: 38 Copynumber: 2.5 Consensus size: 38
425854 TGCATTGGGC
* *
425864 TATGAATTTGAAAATAAGCTATGAATTTGAAAATAAGT
1 TATGAATATGAAAATAAGCTATGAATCTGAAAATAAGT
* * *
425902 TATGAATATGACAGTAAGCTATGAGTCTGAAAATAAGT
1 TATGAATATGAAAATAAGCTATGAATCTGAAAATAAGT
*
425940 TATGAATATGGAAATAAG
1 TATGAATATGAAAATAAG
425958 TTCTGATTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.31
Consensus pattern (38 bp):
TATGAATATGAAAATAAGCTATGAATCTGAAAATAAGT
Found at i:425958 original size:19 final size:19
Alignment explanation
Indices: 425864--425959 Score: 111
Period size: 19 Copynumber: 5.1 Consensus size: 19
425854 TGCATTGGGC
* *
425864 TATGAATTTGAAAATAAGC
1 TATGAATATGAAAATAAGT
*
425883 TATGAATTTGAAAATAAGT
1 TATGAATATGAAAATAAGT
* * *
425902 TATGAATATGACAGTAAGC
1 TATGAATATGAAAATAAGT
* *
425921 TATGAGTCTGAAAATAAGT
1 TATGAATATGAAAATAAGT
*
425940 TATGAATATGGAAATAAGT
1 TATGAATATGAAAATAAGT
425959 T
1 T
425960 CTGATTCAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 64 1.00
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (19 bp):
TATGAATATGAAAATAAGT
Found at i:425973 original size:38 final size:38
Alignment explanation
Indices: 425864--425975 Score: 100
Period size: 38 Copynumber: 2.9 Consensus size: 38
425854 TGCATTGGGC
* * * ***
425864 TATGAATTTGAAAATAAGCTATGAATTTGAAAATAAGT
1 TATGAATATGACAATAAGCTATGAGTCAAAAAATAAGT
* **
425902 TATGAATATGACAGTAAGCTATGAGTCTGAAAATAAGT
1 TATGAATATGACAATAAGCTATGAGTCAAAAAATAAGT
* * *
425940 TATGAATATGGA-AATAAGTTCTGATTCAAAAAATAA
1 TATGAATAT-GACAATAAGCTATGAGTCAAAAAATAA
425976 ATTCTTAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
38 60 0.97
39 2 0.03
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.31
Consensus pattern (38 bp):
TATGAATATGACAATAAGCTATGAGTCAAAAAATAAGT
Found at i:429749 original size:47 final size:47
Alignment explanation
Indices: 429684--429987 Score: 446
Period size: 47 Copynumber: 6.5 Consensus size: 47
429674 AATAAACCCT
* * * *
429684 TTTCAAGCATTTCCAATTATGGCATCCGTTCATGCCTTAATGCATCC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
* * *
429731 TTTCATGTATTTTAAATTATGGCATCCGTTCATGCCTTTATGCATCC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
* * * *
429778 TTTTATTCATTTTCAATTATGGCATCTGTTCATGCCTTTATGCATCC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
* * * *
429825 TTTCATTCATTTTCGATTATGACATCTGTTCATGCCTTTATGGATCC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
*
429872 TTTCATGCATTTTCAATTATGACATCAGTTCATGCCTTTATGCATCC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
* *
429919 TTTCATGCATTGTCAATTATGACATCCGTTCATGCCTTTATGCATCA
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
429966 TTTCATGCATTTTCAATTATGA
1 TTTCATGCATTTTCAATTATGA
429988 AATTGATTTA
Statistics
Matches: 235, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 235 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (47 bp):
TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
Found at i:429923 original size:20 final size:20
Alignment explanation
Indices: 429900--429973 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 20
429890 ATGACATCAG
429900 TTCATGCCTTTATGCATCCT
1 TTCATGCCTTTATGCATCCT
* *
429920 TTCATGCATTGTCAATTATGACATCCG
1 TTCATGC-----C-TTTATG-CATCCT
*
429947 TTCATGCCTTTATGCATCAT
1 TTCATGCCTTTATGCATCCT
429967 TTCATGC
1 TTCATGC
429974 ATTTTCAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
20 18 0.43
21 5 0.12
22 1 0.02
25 1 0.02
26 5 0.12
27 12 0.29
ACGTcount: A:0.20, C:0.26, G:0.12, T:0.42
Consensus pattern (20 bp):
TTCATGCCTTTATGCATCCT
Found at i:430544 original size:72 final size:73
Alignment explanation
Indices: 430434--430572 Score: 183
Period size: 72 Copynumber: 1.9 Consensus size: 73
430424 TACCCCTTCG
* *
430434 GGTATCGATACCAAAAATAGGTTCGATATTACCTGGTATCGATACAAC-CTATATGGTATCGATA
1 GGTATCGATACCAAAAATAGATTCGATATTACCTGGTATCAATACAACTCTATATGGTATCGATA
430498 CCCCCTAC
66 CCCCCTAC
* * * ** *
430506 GGTATTGATACCAAAAATAGATTCGATGTT-TCTAGGTATCAATACCCCTCTTTATGGTATCGAT
1 GGTATCGATACCAAAAATAGATTCGATATTACCT-GGTATCAATACAACTCTATATGGTATCGAT
430570 ACC
65 ACC
430573 ACCTCTTCAT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
71 2 0.04
72 38 0.67
73 17 0.30
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (73 bp):
GGTATCGATACCAAAAATAGATTCGATATTACCTGGTATCAATACAACTCTATATGGTATCGATA
CCCCCTAC
Found at i:430566 original size:21 final size:22
Alignment explanation
Indices: 430540--430593 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
430530 GATGTTTCTA
* *
430540 GGTATCAATACC-CCTCTTTAT
1 GGTATCGATACCACCTCTTCAT
430561 GGTATCGATACCACCTCTTCAT
1 GGTATCGATACCACCTCTTCAT
*
430583 TGTATCGATAC
1 GGTATCGATAC
430594 ACAATAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (22 bp):
GGTATCGATACCACCTCTTCAT
Found at i:436768 original size:47 final size:47
Alignment explanation
Indices: 436694--436997 Score: 428
Period size: 47 Copynumber: 6.5 Consensus size: 47
436684 AATAAACCCT
* * *
436694 TTTCAAGCATTTCCAATTATGACATCCGTTCATGCCTTAATGCATCC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
* * * **
436741 TTTCATGTATTTTAAATTAAGGGATCCGTTCATGCCTTTATGCATCC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
* * * *
436788 TTTCATTCATTTTCAATTATGGCATCCGTTCATGCCTCTATGCAACC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
* ** *
436835 TTTCATTCATTTTTGATTATGACATCCGTTCATGCCTTTATGGATCC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
* *
436882 TTTCATGCATTTTCAATTATGACATTCGTTCGTGCCTTTATGCATCC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
*
436929 TTTAATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
*
436976 TTTCATGCATTTTCTATTATGA
1 TTTCATGCATTTTCAATTATGA
436998 AATTGATTTA
Statistics
Matches: 225, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 225 1.00
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (47 bp):
TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
Found at i:436963 original size:27 final size:27
Alignment explanation
Indices: 436878--436963 Score: 69
Period size: 27 Copynumber: 3.4 Consensus size: 27
436868 GCCTTTATGG
*
436878 ATCCTTTCATGCATTTTCAATTATGAC
1 ATCCGTTCATGCATTTTCAATTATGAC
* * *
436905 ATTCGTTCGTGC-----C-TTTATG-C
1 ATCCGTTCATGCATTTTCAATTATGAC
* *
436925 ATCCTTTAATGCATTTTCAATTATGAC
1 ATCCGTTCATGCATTTTCAATTATGAC
436952 ATCCGTTCATGC
1 ATCCGTTCATGC
436964 CTTTATGCAT
Statistics
Matches: 41, Mismatches: 11, Indels: 14
0.62 0.17 0.21
Matches are distributed among these distances:
20 9 0.22
21 5 0.12
22 1 0.02
25 1 0.02
26 5 0.12
27 20 0.49
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (27 bp):
ATCCGTTCATGCATTTTCAATTATGAC
Found at i:436980 original size:20 final size:21
Alignment explanation
Indices: 436945--436983 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
436935 GCATTTTCAA
436945 TTATGACATCCGTTCATGCCT
1 TTATGACATCCGTTCATGCCT
*
436966 TTATG-CATCCTTTCATGC
1 TTATGACATCCGTTCATGC
436984 ATTTTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.18, C:0.28, G:0.13, T:0.41
Consensus pattern (21 bp):
TTATGACATCCGTTCATGCCT
Found at i:437605 original size:23 final size:24
Alignment explanation
Indices: 437575--437627 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
437565 TGTTTCTAGG
*
437575 TATCGATATACC-TCTCTTCATGA
1 TATCGATATACCACCTCTTCATGA
*
437598 TATCG--ATACCACCTCTTCATGG
1 TATCGATATACCACCTCTTCATGA
437620 TATCGATA
1 TATCGATA
437628 CACATTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 5 0.20
22 14 0.56
23 5 0.20
24 1 0.04
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.36
Consensus pattern (24 bp):
TATCGATATACCACCTCTTCATGA
Found at i:438239 original size:2 final size:2
Alignment explanation
Indices: 438232--438276 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
438222 GCTTTATCCT
438232 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
438274 TA T
1 TA T
438277 CTATTTCAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:443734 original size:17 final size:18
Alignment explanation
Indices: 443707--443744 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
443697 TTTTTAGGGA
443707 CATCATTTATA-AA-TTT
1 CATCATTTATAGAAGTTT
443723 CATCAGTTTATAGAAGTTT
1 CATCA-TTTATAGAAGTTT
443742 CAT
1 CAT
443745 GGCTCCTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 6 0.32
18 2 0.11
19 6 0.32
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (18 bp):
CATCATTTATAGAAGTTT
Found at i:453411 original size:51 final size:51
Alignment explanation
Indices: 453354--453453 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 51
453344 CGAGTGTCGT
* *
453354 TTTAATATAATATATATAATATTATTATATTATTTTTATTTACAAGACCAG
1 TTTAATATAATATATATAATATCATTATATTATTATTATTTACAAGACCAG
453405 TTTAATATAATATATATAATATCATTATATTATTATTATTTACAAGACC
1 TTTAATATAATATATATAATATCATTATATTATTATTATTTACAAGACC
453454 CGAAGGCCTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (51 bp):
TTTAATATAATATATATAATATCATTATATTATTATTATTTACAAGACCAG
Found at i:465109 original size:36 final size:36
Alignment explanation
Indices: 465059--465373 Score: 388
Period size: 36 Copynumber: 8.8 Consensus size: 36
465049 AAATCAAAAG
*
465059 TTCAACCTTCACAGAAGAGTAGTGAAGTCAGTCATT
1 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATT
* * * * * **
465095 TTTAACCTTCACAGAAGAGTAATGGAGT-AATGCAAG
1 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGT-CATT
465131 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATT
1 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATT
* * **
465167 TTCAACCTTCACAGAAGAGTAGT-AGAGT-AATGCAAA
1 TTCAACCTTCACGGAAGAGTAGTGA-AGTCAGT-CATT
465203 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATT
1 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATT
*
465239 TTCAACCTTCACGGAAGAATAGTGAAGTCAGTCATT
1 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATT
465275 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATT
1 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATT
* * **
465311 TTCAACCTTCACGAAAGAGTAGTTG-AGT-AATGCAAA
1 TTCAACCTTCACGGAAGAGTAG-TGAAGTCAGT-CATT
*
465347 TTCAGCCTTCACGGAAGAGTAGTGAAG
1 TTCAACCTTCACGGAAGAGTAGTGAAG
465374 CAAATCATTG
Statistics
Matches: 241, Mismatches: 29, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
35 9 0.04
36 225 0.93
37 7 0.03
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (36 bp):
TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATT
Found at i:465174 original size:72 final size:72
Alignment explanation
Indices: 465059--465373 Score: 481
Period size: 72 Copynumber: 4.4 Consensus size: 72
465049 AAATCAAAAG
* * *
465059 TTCAACCTTCACAGAAGAGTAGTGAAGTCAGTCATTTTTAACCTTCACAGAAGAGTAATGGAGTA
1 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATTTTCAACCTTCACAGAAGAGTAGTGGAGTA
*
465124 ATGCAAG
66 ATGCAAA
*
465131 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATTTTCAACCTTCACAGAAGAGTAGTAGAGTA
1 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATTTTCAACCTTCACAGAAGAGTAGTGGAGTA
465196 ATGCAAA
66 ATGCAAA
* * * *
465203 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATTTTCAACCTTCACGGAAGAATAGTGAAGTC
1 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATTTTCAACCTTCACAGAAGAGTAGTGGAGTA
**
465268 A-GTCATT
66 ATG-CAAA
*
465275 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATTTTCAACCTTCAC-GAAAGAGTAGTTGAGT
1 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATTTTCAACCTTCACAG-AAGAGTAGTGGAGT
465339 AATGCAAA
65 AATGCAAA
*
465347 TTCAGCCTTCACGGAAGAGTAGTGAAG
1 TTCAACCTTCACGGAAGAGTAGTGAAG
465374 CAAATCATTG
Statistics
Matches: 221, Mismatches: 19, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
71 2 0.01
72 218 0.99
73 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (72 bp):
TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATTTTCAACCTTCACAGAAGAGTAGTGGAGTA
ATGCAAA
Found at i:465248 original size:108 final size:107
Alignment explanation
Indices: 465059--465373 Score: 429
Period size: 108 Copynumber: 2.9 Consensus size: 107
465049 AAATCAAAAG
* * *
465059 TTCAACCTTCACAGAAGAGTAGTGAAGTCAGTCATTTTTAACCTTCACAGAAGAGTAATGGAGTA
1 TTCAACCTTCACAGAAGAGTAGTGAAGTCAGTCATTTTCAACCTTCACGGAAGAGTAGT-GAGTA
*
465124 ATGCAAGTTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATT
65 ATGCAAATTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATT
* **
465167 TTCAACCTTCACAGAAGAGTAGT-AGAGT-AATGCAAATTCAACCTTCACGGAAGAGTAGTGAAG
1 TTCAACCTTCACAGAAGAGTAGTGA-AGTCAGT-CATTTTCAACCTTCACGGAAGAGTAGTG-AG
* ** *
465230 TCA-GTCATTTTCAACCTTCACGGAAGAATAGTGAAGTCAGTCATT
63 TAATG-CAAATTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATT
* *
465275 TTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATTTTCAACCTTCACGAAAGAGTAGTTGAGTA
1 TTCAACCTTCACAGAAGAGTAGTGAAGTCAGTCATTTTCAACCTTCACGGAAGAGTAG-TGAGTA
*
465340 ATGCAAATTCAGCCTTCACGGAAGAGTAGTGAAG
65 ATGCAAATTCAACCTTCACGGAAGAGTAGTGAAG
465374 CAAATCATTG
Statistics
Matches: 179, Mismatches: 20, Indels: 16
0.83 0.09 0.07
Matches are distributed among these distances:
107 5 0.03
108 168 0.94
109 6 0.03
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (107 bp):
TTCAACCTTCACAGAAGAGTAGTGAAGTCAGTCATTTTCAACCTTCACGGAAGAGTAGTGAGTAA
TGCAAATTCAACCTTCACGGAAGAGTAGTGAAGTCAGTCATT
Found at i:470944 original size:14 final size:14
Alignment explanation
Indices: 470925--470952 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
470915 TTGCATGAAC
470925 TATTTAGATTTCAT
1 TATTTAGATTTCAT
470939 TATTTAGATTTCAT
1 TATTTAGATTTCAT
470953 GTTTAATTAT
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:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (14 bp):
TATTTAGATTTCAT
Found at i:471031 original size:19 final size:19
Alignment explanation
Indices: 471007--471074 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
470997 TACATGGTAG
*
471007 TTCATTAAATCATGTTTAA
1 TTCATTAAAGCATGTTTAA
471026 TTCATTAAAGCATGTTTAA
1 TTCATTAAAGCATGTTTAA
* *
471045 TTCAAT-AAGCATG-TT-G
1 TTCATTAAAGCATGTTTAA
471061 TTCATTAAAGCATG
1 TTCATTAAAGCATG
471075 CATTTCATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
16 5 0.11
17 9 0.20
18 7 0.16
19 23 0.52
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (19 bp):
TTCATTAAAGCATGTTTAA
Found at i:471183 original size:18 final size:18
Alignment explanation
Indices: 471162--471211 Score: 75
Period size: 17 Copynumber: 2.8 Consensus size: 18
471152 CAATTCAGCA
471162 AGTTCATTAATCAAAACT
1 AGTTCATTAATCAAAACT
*
471180 AGTTCATTAAT-TAAACT
1 AGTTCATTAATCAAAACT
*
471197 AGTGCATTAATCAAA
1 AGTTCATTAATCAAA
471212 TTAACTCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (18 bp):
AGTTCATTAATCAAAACT
Found at i:471197 original size:17 final size:17
Alignment explanation
Indices: 471126--471207 Score: 67
Period size: 17 Copynumber: 4.7 Consensus size: 17
471116 TTTATGCATT
*
471126 TAGTTCATTCAA-TAAGC
1 TAGTTCATT-AATTAAAC
* * *
471143 TACTTCATTCAATTCAGC
1 TAGTTCATT-AATTAAAC
* *
471161 AAGTTCATTAATCAAAAC
1 TAGTTCATTAAT-TAAAC
471179 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
471196 TAGTGCATTAAT
1 TAGTTCATTAAT
471208 CAAATTAACT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
17 29 0.55
18 24 0.45
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.37
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:475262 original size:22 final size:22
Alignment explanation
Indices: 475236--475288 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
475226 CATTGGCGTG
475236 GGAACAATTGAAGATGTATGAT
1 GGAACAATTGAAGATGTATGAT
475258 GGAACAATTGAAGATGTATGAT
1 GGAACAATTGAAGATGTATGAT
475280 GGAACAATT
1 GGAACAATT
475289 AAAGTTGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (22 bp):
GGAACAATTGAAGATGTATGAT
Found at i:482802 original size:15 final size:15
Alignment explanation
Indices: 482763--482804 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
482753 ATTGCAGAGG
482763 CAGCAGCAGCAACAA
1 CAGCAGCAGCAACAA
* * *
482778 CAACAACAGCAACAC
1 CAGCAGCAGCAACAA
482793 CAGCAGCAGCAA
1 CAGCAGCAGCAA
482805 AGGGAAGGGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.48, C:0.36, G:0.17, T:0.00
Consensus pattern (15 bp):
CAGCAGCAGCAACAA
Found at i:488829 original size:16 final size:16
Alignment explanation
Indices: 488808--488839 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
488798 CACCTTACTT
488808 CTGTTGAATATCAACC
1 CTGTTGAATATCAACC
488824 CTGTTGAATATCAACC
1 CTGTTGAATATCAACC
488840 TCTAACTTCG
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:0.25, G:0.12, T:0.31
Consensus pattern (16 bp):
CTGTTGAATATCAACC
Found at i:500620 original size:36 final size:36
Alignment explanation
Indices: 500570--500676 Score: 135
Period size: 36 Copynumber: 2.9 Consensus size: 36
500560 TCAGAGTCGG
* * *
500570 AACAGATAAGCACACACAGTGC-TATCACATCGGAAAT
1 AACA-ATATGCACACAAAGTGCAT-TCACATCAGAAAT
* *
500607 AATAATATGCACACAAAGTGCATTCATATCAGAAAT
1 AACAATATGCACACAAAGTGCATTCACATCAGAAAT
*
500643 AACAATATGCACACAAAGTGCATTCATATCAGAA
1 AACAATATGCACACAAAGTGCATTCACATCAGAA
500677 TATATATATT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
36 59 0.94
37 4 0.06
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.21
Consensus pattern (36 bp):
AACAATATGCACACAAAGTGCATTCACATCAGAAAT
Found at i:510946 original size:3 final size:3
Alignment explanation
Indices: 510938--511006 Score: 72
Period size: 3 Copynumber: 23.3 Consensus size: 3
510928 TTTTACTTAA
** *
510938 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT AAAT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
510983 ATT A-T ATAT ATT A-T ATT ATT ATT A
1 ATT ATT AT-T ATT ATT ATT ATT ATT A
511007 AATAATTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
2 6 0.11
3 44 0.80
4 5 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:510998 original size:25 final size:22
Alignment explanation
Indices: 510938--511006 Score: 101
Period size: 21 Copynumber: 3.3 Consensus size: 22
510928 TTTTACTTAA
510938 ATTATTATTAAA-ATTATTATT
1 ATTATTATTAAATATTATTATT
510959 ATTATTATTAAATATTATTATT
1 ATTATTATTAAATATTATTATT
*
510981 A-TATTA-TATATATTA-TATT
1 ATTATTATTAAATATTATTATT
511000 ATTATTA
1 ATTATTA
511007 AATAATTTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
19 5 0.11
20 13 0.29
21 17 0.38
22 10 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTATTATTAAATATTATTATT
Found at i:519532 original size:92 final size:92
Alignment explanation
Indices: 519375--519652 Score: 484
Period size: 92 Copynumber: 3.0 Consensus size: 92
519365 ATAGTAGAAA
*
519375 TTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTTGG
1 TTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
519440 TATGAACCACAGAACCAATCATTGAAT
66 TATGAACCACAGAACCAATCATTGAAT
*
519467 TTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGGTTTGG
1 TTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
*
519532 TATGAACCACAGAACCAATTATTGAAT
66 TATGAACCACAGAACCAATCATTGAAT
* * *
519559 TTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTTGG
1 TTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
*
519624 TAGGAACCACAGAACCAATCATTGGAAT
66 TATGAACCACAGAACCAATCATT-GAAT
519652 T
1 T
519653 AAAAGATGAA
Statistics
Matches: 176, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
92 171 0.97
93 5 0.03
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (92 bp):
TTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
TATGAACCACAGAACCAATCATTGAAT
Found at i:522255 original size:22 final size:22
Alignment explanation
Indices: 522224--522278 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
522214 ATCTACACTA
522224 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
522246 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
522268 TTCAAAAATGA
1 TTCAAAGATGA
522279 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:522822 original size:75 final size:75
Alignment explanation
Indices: 522725--523391 Score: 1223
Period size: 75 Copynumber: 8.9 Consensus size: 75
522715 CTATTTCCCA
*
522725 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
522790 GCCTTAGGGT
66 GCCTTAGGGT
522800 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
522865 GCCTTAGGGT
66 GCCTTAGGGT
522875 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
522940 GCCTTAGGGT
66 GCCTTAGGGT
522950 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATG-TTTAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
523013 GCCTTAGGGT
66 GCCTTAGGGT
523023 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
523087 GCCTTAGGGT
66 GCCTTAGGGT
*
523097 CATATGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
523162 GCCTTAGGGT
66 GCCTTAGGGT
*
523172 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGTTGTTTTAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
523237 GCCTTAGGGT
66 GCCTTAGGGT
* *
523247 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT-AA
523312 AGCCTTAGGGT
65 AGCCTTAGGGT
* * *
523323 CATCTGTAAGTCCTACAGTGCATGATGGTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT-AA
523388 AGCC
65 AGCC
523392 CTTCAGTGCA
Statistics
Matches: 579, Mismatches: 10, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
73 48 0.08
74 123 0.21
75 329 0.57
76 79 0.14
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (75 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
GCCTTAGGGT
Found at i:523260 original size:297 final size:300
Alignment explanation
Indices: 522725--523383 Score: 1216
Period size: 297 Copynumber: 2.2 Consensus size: 300
522715 CTATTTCCCA
*
522725 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTAAA
*
522790 GCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
65 GCCTTAGGGTCATATGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
522855 ATGTTTTAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
130 ATGTTTTAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
*
522920 GAGCTTTTTGATGTTTTAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AA
195 GAGCTTTTTGATGTTTTAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAA
522984 AAGCCTTCGGGAGCTTTTTGATG-TTT-AAAGCCTTAGGGT
260 AAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
523023 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTAAAG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTAAAG
523088 CCTTAGGGTCATATGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGA
66 CCTTAGGGTCATATGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGA
523153 TGTTTTAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
131 TGTTTTAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
*
523218 AGCTTTTTGTTGTTTTAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAA
196 AGCTTTTTGATGTTTTAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAA
*
523283 AGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTAGGGT
261 AGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
* * *
523323 CATCTGTAAGTCCTACAGTGCATGATGGTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTT
523384 TCAAAGCCCT
Statistics
Matches: 350, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
297 195 0.56
298 81 0.23
299 3 0.01
300 71 0.20
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (300 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTAAAG
CCTTAGGGTCATATGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGA
TGTTTTAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
AGCTTTTTGATGTTTTAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAA
AGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
Found at i:523572 original size:3 final size:3
Alignment explanation
Indices: 523564--523632 Score: 72
Period size: 3 Copynumber: 23.3 Consensus size: 3
523554 TTTTACTTAA
** *
523564 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT AAAT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
523609 ATT A-T ATAT ATT A-T ATT ATT ATT A
1 ATT ATT AT-T ATT ATT ATT ATT ATT A
523633 AATAATTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
2 6 0.11
3 44 0.80
4 5 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:523624 original size:25 final size:22
Alignment explanation
Indices: 523564--523632 Score: 101
Period size: 21 Copynumber: 3.3 Consensus size: 22
523554 TTTTACTTAA
523564 ATTATTATTAAA-ATTATTATT
1 ATTATTATTAAATATTATTATT
523585 ATTATTATTAAATATTATTATT
1 ATTATTATTAAATATTATTATT
*
523607 A-TATTA-TATATATTA-TATT
1 ATTATTATTAAATATTATTATT
523626 ATTATTA
1 ATTATTA
523633 AATAATTTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
19 5 0.11
20 13 0.29
21 17 0.38
22 10 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTATTATTAAATATTATTATT
Found at i:526888 original size:28 final size:29
Alignment explanation
Indices: 526856--526912 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
526846 ACGGCTATCA
* *
526856 GAAAATAGCTTTATATGTTC-TTTAAAAG
1 GAAAATAGCATTATATGTGCTTTTAAAAG
526884 GAAAATAGCATTATATGTGCTTTTAAAAG
1 GAAAATAGCATTATATGTGCTTTTAAAAG
526913 AGATTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (29 bp):
GAAAATAGCATTATATGTGCTTTTAAAAG
Found at i:537445 original size:20 final size:21
Alignment explanation
Indices: 537408--537448 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
537398 AGTATGTCCA
537408 GGGGGTATCGATTCCCCCCTG
1 GGGGGTATCGATTCCCCCCTG
537429 GGGGGTATCGATTCCCCCCT
1 GGGGGTATCGATTCCCCCCT
537449 AAAGGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.34, G:0.32, T:0.24
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCCCTG
Found at i:538089 original size:15 final size:15
Alignment explanation
Indices: 538071--538105 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
538061 CGAGGGTATT
538071 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
538086 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
538101 GTAGT
1 GTAGT
538106 GGTTCTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:544339 original size:22 final size:22
Alignment explanation
Indices: 544313--544354 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
544303 AGTATGTCCA
*
544313 GGGGGTATCTATTCCCCCCTTG
1 GGGGGTATCGATTCCCCCCTTG
544335 GGGGGTATCGATTCCCCCCT
1 GGGGGTATCGATTCCCCCCT
544355 AAAGGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (22 bp):
GGGGGTATCGATTCCCCCCTTG
Found at i:545004 original size:15 final size:15
Alignment explanation
Indices: 544984--545012 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
544974 TATTGTGGTC
544984 CTTCGGGACGTAGTT
1 CTTCGGGACGTAGTT
544999 CTTCGGGACGTAGT
1 CTTCGGGACGTAGT
545013 GGTGCTACGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.34, T:0.31
Consensus pattern (15 bp):
CTTCGGGACGTAGTT
Found at i:547158 original size:95 final size:95
Alignment explanation
Indices: 546961--547221 Score: 346
Period size: 95 Copynumber: 2.7 Consensus size: 95
546951 AACCACCTGG
* * * * *
546961 ATCCATAAAGCTGGGGCATTTAACCAATTGCTCTAGAGGGATAACTGAATATCATTGTATAG-AT
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAACT-CAT-GC-TT-TATTGTAT
* *
547025 ATTATAATCGCCTTTATCAGGCTAGCTGAATATT
62 ATTATAATCACCTTTATCAGACTAGCTGAATATT
**
547059 ATCCATAAAGCCAAGGCATTTAACCAATTGCTCTAGAGGGACAACTCATGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCATGCTTTATTGTATATTA
*
547124 TAATCACCTTTATCAGACTAGCTGAATCTT
66 TAATCACCTTTATCAGACTAGCTGAATATT
* * * *
547154 ATCCATAAAGACGGGGCGTTTAACCAATTGCTCTAGAGGGACATCTCAAGCTTTATTGTATA-TA
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCATGCTTTATTGTATATTA
547218 TAAT
66 TAAT
547222 ATGGGTATAC
Statistics
Matches: 146, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
94 10 0.07
95 91 0.62
96 1 0.01
97 2 0.01
98 42 0.29
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCATGCTTTATTGTATATTA
TAATCACCTTTATCAGACTAGCTGAATATT
Found at i:553609 original size:83 final size:83
Alignment explanation
Indices: 553106--554259 Score: 1199
Period size: 83 Copynumber: 13.8 Consensus size: 83
553096 TGACATGCTC
* * * * * * * *
553106 TTGAGCTTAGTGAAATCGAACTCGAAGGTATTTGTTGACAGATAGCCTTTCTCGCCTCGAGTTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
*
553171 GCTGCAGATTCGATGTGCCT
66 GCTGCA-AAT-GATGTGCCT
* * * * * *
553191 TTGAGTTGAGTATAATCGAACTCGAAGGTCTTTCTTGACAGATAACTCTTCTCGCCTTGAGTTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
* * * * *
553256 GTTGTAAATTAAATATTCCT
66 GCTGCAAA-T-GATGTGCCT
* * * * * * * *
553276 TTTAGCTGAATGCAATCGAACTC-AGAGGTCTTTTGTTGACAGATAGCCCTTATCGCCTTGAGCT
1 TTGAGCTGAGTGTAATCGAACTCGA-AGGTC-TTTGTTGGCAGATAACCCTTCTAGCCTTGAGTT
* *
553340 ATGCTGTAAATTTGATGTTCCT
64 ATGCTGCAAA--TGATGTGCCT
* * * **
553362 TTGAGCTGAGTATAGTCGAACTCGAAGGTATTTTGTTGGCAGATAACCCTTCTCCCCTTGAGTTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGT-CTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTA
** *
553427 TGCTATAAATGTTGTGCCT
65 TGCTGCAAATGATGTGCCT
* * * * * * *
553446 TTGAGCTGAGTGTAATCAAACTTGAAGGTCTTTTATTAGCAGATAGCCTTTCTTGCCTTGAGTTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTA
* *
553511 TTCTACAAATGATGTGCCT
65 TGCTGCAAATGATGTGCCT
* * *
553530 TTAAGTTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAATCCTTCTAGCCTTGAGTTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
*
553595 GCTGCAAATGATGTGCTT
66 GCTGCAAATGATGTGCCT
* * **
553613 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATATCCCTTCTTGCCTTGAACTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
* *
553678 GCTGGAAATGACGTGCCT
66 GCTGCAAATGATGTGCCT
* * * * * * *
553696 TTGATCTGAGTGTAATCGAACTCAAATGTCTTTGTTGGAAAATAACCCTTCTTGCCTTGAGCTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
* * *
553761 GTTGCAAAAGATATGCCT
66 GCTGCAAATGATGTGCCT
* * * *
553779 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTATTGGCAGATAGCCCTTCTTGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTA
*
553844 TGCTGCAAATGATGTGTCT
65 TGCTGCAAATGATGTGCCT
* *
553863 TTGAGCTGAGTGTAATTGAACTCGAAGGTTTTTGTTGGCAGATAACCCTTCTAGCCTTGAG-TAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
* * ***
553927 GTTGTAAATGATACACCT
66 GCTGCAAATGATGTGCCT
* * * *
553945 TTGAACTGAGTGTAATCGAACTCGAAGGTTTTTTGTTGGCAGATAACCCTTTTTA-CCATGAGTT
1 TTGAGCTGAGTGTAATCGAACTCGAAGG-TCTTTGTTGGCAGATAACCC-TTCTAGCCTTGAGTT
**
554009 ATGCTGCAAATGACATGCCT
64 ATGCTGCAAATGATGTGCCT
* * * *
554029 TTGAGCTGAGTATAATTGAACTCGAAGGTC--T-TTGGCAGATAGCCCTTCTTGCCTTGA-TCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGT-TA
*
554090 TGCTACAAATGATGTGCCT
65 TGCTGCAAATGATGTGCCT
* * *
554109 TTGAGCTGAGTGTAATCGAACTTGAAGGTCTTTGTTGACATATAACCCTTCTAGCCTTGAGTTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
* ** *
554174 GCTGTAAATGATACGTCT
66 GCTGCAAATGATGTGCCT
* * * *
554192 TTGAGTTGAGTGTAATCGAACTCGAAGGTCTTGCGTTGGCAGATAGCCCTTCTCA-CCTTGAGCT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTT-TGTTGGCAGATAACCCTTCT-AGCCTTGAGTT
554256 ATGC
64 ATGC
554260 GACAAATAAA
Statistics
Matches: 896, Mismatches: 154, Indels: 39
0.82 0.14 0.04
Matches are distributed among these distances:
79 4 0.00
80 63 0.07
81 1 0.00
82 42 0.05
83 338 0.38
84 252 0.28
85 90 0.10
86 103 0.11
87 3 0.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (83 bp):
TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
GCTGCAAATGATGTGCCT
Found at i:553696 original size:250 final size:250
Alignment explanation
Indices: 553101--554236 Score: 1218
Period size: 250 Copynumber: 4.5 Consensus size: 250
553091 GAATTTGACA
* * * * * * * * *
553101 TGCTCTTGAGCTTAGTGAAATCGAACTCGAAGGTATTTGTTGACAGATAGCCTTTCTCGCCTCGA
1 TGCTTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGA
* * * * * *
553166 GTTATGCTGCAGATTCGATGTGCCTTTGAGTTGAGTATAATCGAACTCGAAGGTC-TTTCTTGAC
66 GTTATGCTGTA-AAT-GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGC
* * * * * * * * *
553230 AGATAACTCTTCTCGCCTTGAGTTATGTTGTA-AATTAAATATTCCTTTTAGCTGAATGCAATCG
129 AGATACCT-TTCTTGCCTTGAGTTA--TTCTACAAAT-GATATGCCTTTGAGCTGAGTGTAATCG
* * * *
553294 AACTC-AGAGGTCTTTTGTTGACAGATAGCCCTTATCGCCTTGAGCTATGCTGTAAATTTGATG
190 AACTCGA-AGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAA--TGATG
* * * * * **
553357 TTCCTTTGAGCTGAGTATAGTCGAACTCGAAGGTATTTTGTTGGCAGATAACCCTTCTCCCCTTG
1 TGCTTTTGAGCTGAGTGTAATCGAACTCGAAGGT-CTTTGTTGGCAGATAACCCTTCTAGCCTTG
* * * * * *
553422 AGTTATGCTATAAATGTTGTGCCTTTGAGCTGAGTGTAATCAAACTTGAAGGTCTTTTATTAGCA
65 AGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCA
* * *
553487 GATAGCCTTTCTTGCCTTGAGTTATTCTACAAATGATGTGCCTTTAAGTTGAGTGTAATCGAACT
130 GATA-CCTTTCTTGCCTTGAGTTATTCTACAAATGATATGCCTTTGAGCTGAGTGTAATCGAACT
** * *
553552 CGAAGGTC-TTTGTTGGCAGATAATCCTTCTAGCCTTGAGTTATGCTGCAAATGATG
194 CGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
* *
553608 TGCTTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATATCCCTTCTTGCCTTGA
1 TGCTTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGA
** * * * * * * *
553673 ACTATGCTGGAAATGACGTGCCTTTGATCTGAGTGTAATCGAACTCAAATGTC-TTTGTTGGAAA
66 GTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAG
* * * *
553737 ATAACCCTTCTTGCCTTGAGCTATGT-TGCAAAAGATATGCCTTTGAGCTGAGTGTAATCGAACT
131 AT-ACCTTTCTTGCCTTGAGTTAT-TCTACAAATGATATGCCTTTGAGCTGAGTGTAATCGAACT
*
553801 CGAAGGTCTTTTATTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
194 CGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
* *
553858 TG-TCTTTGAGCTGAGTGTAATTGAACTCGAAGGTTTTTGTTGGCAGATAACCCTTCTAGCCTTG
1 TGCT-TTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTG
* *** * *
553922 AG-TATGTTGTAAATGATACACCTTTGAACTGAGTGTAATCGAACTCGAAGGTTTTTTGTTGGCA
65 AGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCA
* * * * * * *
553986 GATAACCCTTT-TTACCATGAGTTATGCTGCAAATGACATGCCTTTGAGCTGAGTATAATTGAAC
130 GAT-A-CCTTTCTTGCCTTGAGTTATTCTACAAATGATATGCCTTTGAGCTGAGTGTAATCGAAC
* *
554050 TCGAAGGTC---T-TTGGCAGATAGCCCTTCTTGCCTTGATCTATGCTACAAATGATG
193 TCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
* * * *
554104 TGCCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTTGTTGACATATAACCCTTCTAGCCTTGA
1 TGCTTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGA
** * * **
554169 GTTATGCTGTAAATGATACGTCTTTGAGTTGAGTGTAATCGAACTCGAAGGTCTTGCGTTGGCAG
66 GTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAG
554234 ATA
131 ATA
554237 GCCCTTCTCA
Statistics
Matches: 747, Mismatches: 119, Indels: 38
0.83 0.13 0.04
Matches are distributed among these distances:
246 102 0.14
247 58 0.08
249 110 0.15
250 239 0.32
251 39 0.05
253 36 0.05
254 34 0.05
255 38 0.05
256 55 0.07
257 36 0.05
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (250 bp):
TGCTTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGA
GTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAG
ATACCTTTCTTGCCTTGAGTTATTCTACAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCG
AAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
Found at i:555462 original size:95 final size:95
Alignment explanation
Indices: 555214--555470 Score: 367
Period size: 94 Copynumber: 2.7 Consensus size: 95
555204 ACCTGGATCT
* * *
555214 ATAAAACTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATATCATTGTATAG-ATATTA
1 ATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTC-A-AGC-TT-TATTGTATATTA
*
555278 TAATCGCCTTTATCAGGCTAGCTGAATATTATCC
62 TAATCACCTTTATCAGGCTAGCTGAATATTATCC
* * *
555312 ATAAAG-TCGGGCGTTTAACCAATTGCTCTAGAGGGGCAACTCATGCTTTATTGTATATTATAAT
1 ATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAAT
*
555376 CACCTTTATCAGGCTAGCTGAATCTTATCC
66 CACCTTTATCAGGCTAGCTGAATATTATCC
* *
555406 ATAAAGCTGGGGCGTTTAACCAATTTCTCTAGAGGGATAACTCAAGCTTTATTGTATA-TATAAT
1 ATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAAT
555470 C
66 C
555471 TGGGTATACG
Statistics
Matches: 144, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
93 4 0.03
94 53 0.37
95 47 0.33
96 1 0.01
97 34 0.24
98 5 0.03
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (95 bp):
ATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAAT
CACCTTTATCAGGCTAGCTGAATATTATCC
Found at i:558584 original size:19 final size:20
Alignment explanation
Indices: 558555--558592 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
558545 AGAAATTTGT
558555 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
558575 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
558593 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:558635 original size:63 final size:62
Alignment explanation
Indices: 558560--558715 Score: 197
Period size: 63 Copynumber: 2.5 Consensus size: 62
558550 TTTGTTGAAG
* * * *
558560 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCA
** **
558623 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
558686 GTGCATCGATGCATCAGGAGTGCATCGATG
1 GTGCATCGATGCAT-AGGAGTGCATCGATG
558716 AATGCCTCCA
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
63 77 0.94
64 5 0.06
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Done.