Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold80
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: 1499392
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.28
Warning! 217494 characters in sequence are not A, C, G, or T
File 2 of 8
Found at i:157338 original size:41 final size:41
Alignment explanation
Indices: 157281--157374 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
157271 CTGCCAAGAA
*
157281 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
157322 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
157363 ATGTATCGATAC
1 ATGTATCGATAC
157375 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:158035 original size:34 final size:34
Alignment explanation
Indices: 157995--158060 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
157985 CCCGTTTATT
157995 AAAAAATCTCCCCCTTAATCAAGTAATTCATAAA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCATAAA
158029 AAAAAATCTCCCCCTTAATCAAGTAATTCATA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCATA
158061 TCAAAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.45, C:0.24, G:0.03, T:0.27
Consensus pattern (34 bp):
AAAAAATCTCCCCCTTAATCAAGTAATTCATAAA
Found at i:159869 original size:13 final size:13
Alignment explanation
Indices: 159851--159889 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
159841 ATAATCACCC
*
159851 TGTATCGATACAG
1 TGTATCGATACAA
159864 TGTATCGATACAA
1 TGTATCGATACAA
159877 TGTATCGATACAA
1 TGTATCGATACAA
159890 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:159900 original size:20 final size:20
Alignment explanation
Indices: 159875--159953 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
159865 GTATCGATAC
159875 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
159895 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
159920 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
159940 CATGTATCGATACA
1 AATGTATCGATACA
159954 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:161988 original size:15 final size:15
Alignment explanation
Indices: 161968--161998 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
161958 ATTTCGTTTG
*
161968 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
161983 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
161998 G
1 G
161999 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:166117 original size:21 final size:21
Alignment explanation
Indices: 166091--166166 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
166081 CTGCCAAGAA
*
166091 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
166112 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
166132 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
166153 ATGTATCGATACAT
1 ATGTATCGATACAT
166167 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:166137 original size:20 final size:20
Alignment explanation
Indices: 166112--166184 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
166102 CATCTTTTTT
166112 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
166132 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
166153 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
166173 ATGTATCGATAC
1 ATGTATCGATAC
166185 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:166148 original size:41 final size:41
Alignment explanation
Indices: 166091--166184 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
166081 CTGCCAAGAA
*
166091 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
166132 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
166173 ATGTATCGATAC
1 ATGTATCGATAC
166185 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:174443 original size:21 final size:19
Alignment explanation
Indices: 174419--174472 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
174409 TTCAACAATT
174419 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAA-AGT-AA
* **
174440 TGTATCGATACATAAGTGT
1 TGTATCGATACAAAAGTAA
174459 TGTATCGATACAAA
1 TGTATCGATACAAA
174473 GCTATCCTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:179065 original size:679 final size:676
Alignment explanation
Indices: 177635--179626 Score: 3023
Period size: 679 Copynumber: 2.9 Consensus size: 676
177625 CGTTGCGACA
* *
177635 ATATGCTAGAAACTCAAAGAGCATTCTTTGATAAGAATGGTTTAGGATATAATGCTTTTGAGAAA
1 ATATGCTAGAAACTCAAAGAGCATTCTTTGATAAGAATGGTTTAGGATACAATGCCTTTGAGAAA
*
177700 GAAACAAAATTCAAGAATTTCTTTGTTAAGCATAATTATGATGCCTCATGCATGTCTAT-ATTAT
66 GAAACAAAATTCAAGAATTTCTTTGTTAAGCATAATTATGATGCCTCATGCATGTAT-TCATTAT
*
177764 GTCATAAACAAGGACATACCTTTCACACATGTAATTATAGAATAAATAAATTTAGAGGTAAAATA
130 GTCATAAACAAGGACATACCTTTCACACATGTAATTATAGAATAAATAAATTTACAGGTAAAATA
* * *
177829 ATTAAGAAAATATGGATACCTAAAGGAATCGAGACTTCTAATGATGAAGTAATAAAATAGTTTCA
195 ATTAAGAAAATATGGATACCTAAAGGAATCGGGACTTCTAATGATGAAGTAATAAAATGGATTCA
*
177894 AAAAGGATCAAAGGTATTAAACACTAATGAAAAAGGACCCAATAAAGTTTGGGTACCTAAATCAA
260 AAAAGGATCAAAGGTATTAAACACTAATGAAAAAGGACCCAAGAAAGTTTGGGTACCTAAATCAA
* *
177959 AGAATTGATCTTTGTA-TGCG-GGAATTAGATCATTGCTATAAGGCAAAGGAATTAAAGAAGAAC
325 AGAATTGATCTTTGTAGT-CGAGGGA--AG--CATTGCTATAAGGCAAAGGAATCAAAGAAGAAC
* * * *
178022 TTTTGGTACCTTGATAGTGGATGCTCAAAGCACATG-GTGGAAGATAAGAGCTTATTCTTGGAGA
385 TTTTGGTACCTTGATAGTGGATGCTTAAGGCACATGACTGG-AGACAAGAGCTTATTCTTGGAGA
* * * * *
178086 TCAAACCAAAAGAAAGTGGATGTGTTACGTTTGGCGACAATTTGAAAAGAAG-AATTAAAAGAAT
449 TCAAACCAAAAGAAGGTGGATGTGTTACCTTTGGCGACAA-TTCAAAAGGAGAAATTGAAAGAAT
* * * * *
178150 CGGCACCAAT-GTAACAATTCTTCATTTTGTATTGAAGATTTTTTATATATCAATGGTCTTAAGC
513 CGGCACCATTGGTAACAACTCTTCATTTTGTATTGAAAATGTTTTATATGTCAAT-GTCTTAAGC
*
178214 ACAACCTCCCAAGCATTAGTCAATTATGTGACAAGGGTATGAAAGTTGTATTTGCATGAATCATT
577 ACAACCTCCTAAGCATTAGTCAATTATGTGACAAGGGTATGAAAGTTGTATTTGCATGAATCATT
178279 CACCATGTTTTATATGTCATATCAAAAGTTGAATC
642 CACCATGTTTTATATGTCATATCAAAAGTTGAATC
* * *
178314 ATATACTAGAAACTCAAAGAGCATTTTTTGATAAGAATGATTTAGGATACAATGCCTTTGAGAAA
1 ATATGCTAGAAACTCAAAGAGCATTCTTTGATAAGAATGGTTTAGGATACAATGCCTTTGAGAAA
*
178379 GAAACAAAATTCAAGAATTTCTTTCTTAAGCATAATTATGATGCCTCATGCATGTATTCATTATG
66 GAAACAAAATTCAAGAATTTCTTTGTTAAGCATAATTATGATGCCTCATGCATGTATTCATTATG
* * *
178444 TCATAAACAAGGACATACCTTTCACACATGTAATTGTAGAATAAATAAATTTATAGGTAAAACAA
131 TCATAAACAAGGACATACCTTTCACACATGTAATTATAGAATAAATAAATTTACAGGTAAAATAA
*
178509 TTAAGAAAATATGGATACCTAAAGGAATCGGGACTTCTAATGATGAAGTAATAAAATGGATTCTA
196 TTAAGAAAATATGGATACCTAAAGGAATCGGGACTTCTAATGATGAAGTAATAAAATGGATTCAA
* * * *
178574 AAAGGATCAAAGATATTAAACACTAATGAAAAAGGACCCAAGAAAGTTTAGGTACCTATATTAAA
261 AAAGGATCAAAGGTATTAAACACTAATGAAAAAGGACCCAAGAAAGTTTGGGTACCTAAATCAAA
* *
178639 GAATTGATCTTTGTACGTACGAGGCGAAGCATTACTATAAGGCAAATGAATCAAAGAAGAACTTT
326 GAATTGATCTTTGTA-GT-CGAGG-GAAGCATTGCTATAAGGCAAAGGAATCAAAGAAGAACTTT
*
178704 TGGTACCTTGATAGTGGATGCTTAAGGCACATGACTAGAGACAAGAGCTTATTCTTGGAGATCAA
388 TGGTACCTTGATAGTGGATGCTTAAGGCACATGACTGGAGACAAGAGCTTATTCTTGGAGATCAA
* *
178769 ACCAAAAGAAGGTGGATATGTTACCTTTGGTGACAATTCAAAAGGAGAAATTGAAAGAATCGGCA
453 ACCAAAAGAAGGTGGATGTGTTACCTTTGGCGACAATTCAAAAGGAGAAATTGAAAGAATCGGCA
** * *
178834 CCATTGGTAACAACTCTTCATTTTACATTGAAAATGTTTTATATGTCAATAGTCTGAAGCAGAAC
518 CCATTGGTAACAACTCTTCATTTTGTATTGAAAATGTTTTATATGTCAAT-GTCTTAAGCACAAC
* *
178899 CTCCTAAGTATTAGTCAATTATATGACAAGGGTATGAAAGTTGTATTTGCATGAATCATTCACCA
582 CTCCTAAGCATTAGTCAATTATGTGACAAGGGTATGAAAGTTGTATTTGCATGAATCATTCACCA
*
178964 TGTTTTATATGTCATATCAAAAGTTGAATG
647 TGTTTTATATGTCATATCAAAAGTTGAATC
* *
178994 ATATGCTAGAAATTCAAAGAGCATTCTTTGATAAGGATGGTTTAGGATACAATGCCTTTGAGAAA
1 ATATGCTAGAAACTCAAAGAGCATTCTTTGATAAGAATGGTTTAGGATACAATGCCTTTGAGAAA
* * * *
179059 -AAACAAAATTCAGGAATTTCTTTGTTAAGCACAATTATGATACCTCATGCATGTGTTCATTATG
66 GAAACAAAATTCAAGAATTTCTTTGTTAAGCATAATTATGATGCCTCATGCATGTATTCATTATG
* * * *
179123 TCATAAACAAGGGCATAGCTTTCACACATGTAATTATAAAATAAATAAATTTACAAGTAAAATAA
131 TCATAAACAAGGACATACCTTTCACACATGTAATTATAGAATAAATAAATTTACAGGTAAAATAA
* * * * *
179188 TTAAGAAAATGTGGATACCTAAAGGAAGCGGGACTTTTAATAATGAAGTAATAAAATGGATTCCA
196 TTAAGAAAATATGGATACCTAAAGGAATCGGGACTTCTAATGATGAAGTAATAAAATGGATTCAA
**
179253 AAAGGATCAAAGGTATTAAACACTAATGAAAAAGGACCCAAGAAAGTTTGGGTACCTAAATCGGA
261 AAAGGATCAAAGGTATTAAACACTAATGAAAAAGGACCCAAGAAAGTTTGGGTACCTAAATCAAA
* * * *
179318 GAATTAATCTTTGCATGTCGGAGGTGGAGCATTGCTAGAAGGCAAAGGAATCAAA-AATGAACTT
326 GAATTGATCTTTGTA-GTC-GAGG-GAAGCATTGCTATAAGGCAAAGGAATCAAAGAA-GAACTT
* * *
179382 TTGGTACCATGATAGTGGATACTTAAGGCACATGACTGGAGACGAA-AGCCTATTCTTGGAGATC
387 TTGGTACCTTGATAGTGGATGCTTAAGGCACATGACTGGAGAC-AAGAGCTTATTCTTGGAGATC
* * *
179446 AAACCAAAAGAAGCTGGATGTGTTACCTTTGGCGACAATTCGAAAGGA-ACAATTGAAGGAATCG
451 AAACCAAAAGAAGGTGGATGTGTTACCTTTGGCGACAATTCAAAAGGAGA-AATTGAAAGAATCG
* *
179510 GCACCATTGGTAACAACTCTTTATTTTGTATTGAAAGTGTTTTATATGTCAATGATCTTAAGCAC
515 GCACCATTGGTAACAACTCTTCATTTTGTATTGAAAATGTTTTATATGTCAATG-TCTTAAGCAC
*
179575 AACCTCCTAAGCATTAGTTAATTATGTGACAAGGGTATGAAAGTTGTATTTG
579 AACCTCCTAAGCATTAGTCAATTATGTGACAAGGGTATGAAAGTTGTATTTG
179627 AATCACAAAA
Statistics
Matches: 1196, Mismatches: 104, Indels: 26
0.90 0.08 0.02
Matches are distributed among these distances:
678 15 0.01
679 968 0.81
680 205 0.17
681 5 0.00
682 2 0.00
683 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (676 bp):
ATATGCTAGAAACTCAAAGAGCATTCTTTGATAAGAATGGTTTAGGATACAATGCCTTTGAGAAA
GAAACAAAATTCAAGAATTTCTTTGTTAAGCATAATTATGATGCCTCATGCATGTATTCATTATG
TCATAAACAAGGACATACCTTTCACACATGTAATTATAGAATAAATAAATTTACAGGTAAAATAA
TTAAGAAAATATGGATACCTAAAGGAATCGGGACTTCTAATGATGAAGTAATAAAATGGATTCAA
AAAGGATCAAAGGTATTAAACACTAATGAAAAAGGACCCAAGAAAGTTTGGGTACCTAAATCAAA
GAATTGATCTTTGTAGTCGAGGGAAGCATTGCTATAAGGCAAAGGAATCAAAGAAGAACTTTTGG
TACCTTGATAGTGGATGCTTAAGGCACATGACTGGAGACAAGAGCTTATTCTTGGAGATCAAACC
AAAAGAAGGTGGATGTGTTACCTTTGGCGACAATTCAAAAGGAGAAATTGAAAGAATCGGCACCA
TTGGTAACAACTCTTCATTTTGTATTGAAAATGTTTTATATGTCAATGTCTTAAGCACAACCTCC
TAAGCATTAGTCAATTATGTGACAAGGGTATGAAAGTTGTATTTGCATGAATCATTCACCATGTT
TTATATGTCATATCAAAAGTTGAATC
Found at i:185617 original size:19 final size:20
Alignment explanation
Indices: 185577--185626 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
185567 CCTCACATTA
*
185577 TATCGATACATGCAGGATTG
1 TATCGATACATGCAAGATTG
*
185597 TATCGATACAT-CAATATTG
1 TATCGATACATGCAAGATTG
185616 TATCGATACAT
1 TATCGATACAT
185627 AGTGAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
TATCGATACATGCAAGATTG
Found at i:185696 original size:19 final size:20
Alignment explanation
Indices: 185672--185709 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
185662 TAAATTTCAA
185672 ATGCA-TGTATCGATACATT
1 ATGCATTGTATCGATACATT
185691 ATGCATTGTATCGATACAT
1 ATGCATTGTATCGATACAT
185710 GGAGCATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (20 bp):
ATGCATTGTATCGATACATT
Found at i:187783 original size:13 final size:13
Alignment explanation
Indices: 187765--187789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
187755 ATATTGCTTA
187765 GTATCGATACATT
1 GTATCGATACATT
187778 GTATCGATACAT
1 GTATCGATACAT
187790 GTTCGTAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:190569 original size:21 final size:19
Alignment explanation
Indices: 190544--190594 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 19
190534 TTTCAATAAT
190544 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAA-AGT-A
* *
190565 TTGTATCGATACATAAGTG
1 TTGTATCGATACAAAAGTA
190584 TTGTATCGATA
1 TTGTATCGATA
190595 TAATGTATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.39
20 3 0.11
21 14 0.50
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACAAAAGTA
Found at i:190589 original size:19 final size:19
Alignment explanation
Indices: 190544--190628 Score: 83
Period size: 19 Copynumber: 4.7 Consensus size: 19
190534 TTTCAATAAT
* *
190544 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACATA-AGT-G
190565 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
190584 TTGTATCGAT--ATAA---
1 TTGTATCGATACATAAGTG
190598 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
190616 GTGTATCGATACA
1 TTGTATCGATACA
190629 ATGCATCGAT
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
13 9 0.16
15 4 0.07
17 4 0.07
19 22 0.39
20 3 0.05
21 14 0.25
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:190607 original size:32 final size:32
Alignment explanation
Indices: 190566--190667 Score: 159
Period size: 32 Copynumber: 3.2 Consensus size: 32
190556 AAACAGTAAT
* *
190566 TGTATCGATACATAAGTGTTGTATCGATATAA
1 TGTATCGATACATAAGTGGTGTATCGATACAA
190598 TGTATCGATACATAAGTGGTGTATCGATACAA
1 TGTATCGATACATAAGTGGTGTATCGATACAA
* * *
190630 TGCATCGATACATAAGTGGTATATTGATACAA
1 TGTATCGATACATAAGTGGTGTATCGATACAA
190662 TGTATC
1 TGTATC
190668 ACTACGAAGC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATAAGTGGTGTATCGATACAA
Found at i:202135 original size:13 final size:13
Alignment explanation
Indices: 202117--202141 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
202107 CAAGACACAT
202117 TGTATCGATACAA
1 TGTATCGATACAA
202130 TGTATCGATACA
1 TGTATCGATACA
202142 TGATGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:202139 original size:33 final size:33
Alignment explanation
Indices: 202097--202161 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
202087 TACCACTGTT
202097 TGTATCGATACAAGA-CACATTGTATCGATACAA
1 TGTATCGATACAAGATCA-ATTGTATCGATACAA
* *
202130 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCGATACAAGATCAATTGTATCGATACA
202162 TTGCTTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (33 bp):
TGTATCGATACAAGATCAATTGTATCGATACAA
Found at i:209724 original size:13 final size:13
Alignment explanation
Indices: 209706--209732 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
209696 ACAATGTTCT
209706 TTGTATCAATACA
1 TTGTATCAATACA
209719 TTGTATCAATACA
1 TTGTATCAATACA
209732 T
1 T
209733 GAGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TTGTATCAATACA
Found at i:213306 original size:13 final size:13
Alignment explanation
Indices: 213268--213341 Score: 88
Period size: 13 Copynumber: 6.2 Consensus size: 13
213258 AAAAGATCAA
*
213268 TGTATCGATACAA
1 TGTATCGATACAT
213281 TGTATCGATACAT
1 TGTATCGATACAT
213294 TGTATCGATACAT
1 TGTATCGATACAT
213307 TG-A--G-TA-A-
1 TGTATCGATACAT
*
213314 TGTATCAATACAT
1 TGTATCGATACAT
213327 TGTATCGATACAT
1 TGTATCGATACAT
213340 TG
1 TG
213342 AGTAATGTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
7 2 0.04
8 2 0.04
9 2 0.04
10 1 0.02
11 2 0.04
12 2 0.04
13 41 0.79
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:213319 original size:20 final size:20
Alignment explanation
Indices: 213294--213360 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
213284 ATCGATACAT
213294 TGTATCGATACATTGAGTAA
1 TGTATCGATACATTGAGTAA
*
213314 TGTATCAATAC----A-T--
1 TGTATCGATACATTGAGTAA
213327 TGTATCGATACATTGAGTAA
1 TGTATCGATACATTGAGTAA
213347 TGTATCGATACATT
1 TGTATCGATACATT
213361 TCCTTGGCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 10 0.26
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
20 24 0.63
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATTGAGTAA
Found at i:213325 original size:33 final size:33
Alignment explanation
Indices: 213279--213360 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
213269 GTATCGATAC
213279 AATGTATCGATACATTGTATCGATACATTGAGT
1 AATGTATCGATACATTGTATCGATACATTGAGT
*
213312 AATGTATCAATACATTGTATCGATACATTGAGT
1 AATGTATCGATACATTGTATCGATACATTGAGT
213345 AATGTATCGATACATT
1 AATGTATCGATACATT
213361 TCCTTGGCAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (33 bp):
AATGTATCGATACATTGTATCGATACATTGAGT
Found at i:213414 original size:19 final size:18
Alignment explanation
Indices: 213390--213511 Score: 86
Period size: 19 Copynumber: 7.1 Consensus size: 18
213380 AGCGATGCAT
213390 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
213409 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
213422 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
213441 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
213454 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
* * *
213473 TGTATCAATACAGTTACTGTT
1 TGTATCGATACA--AACT-TA
213494 TGTATCGATACAAA-TTA
1 TGTATCGATACAAACTTA
213511 T
1 T
213512 TTGAAATTCA
Statistics
Matches: 82, Mismatches: 6, Indels: 32
0.68 0.05 0.27
Matches are distributed among these distances:
13 22 0.27
14 2 0.02
16 4 0.05
17 2 0.02
18 3 0.04
19 34 0.41
20 3 0.04
21 12 0.15
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.36
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:213423 original size:32 final size:32
Alignment explanation
Indices: 213382--213484 Score: 179
Period size: 32 Copynumber: 3.2 Consensus size: 32
213372 AGCTTCTTAG
* *
213382 CGATGCATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
213414 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
213446 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
213478 CAATACA
1 CGATACA
213485 GTTACTGTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 68 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:213427 original size:13 final size:13
Alignment explanation
Indices: 213409--213465 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
213399 ACAAAACTTA
213409 TGTATCGATACAT
1 TGTATCGATACAT
213422 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
213440 ATGTATCGATACAT
1 -TGTATCGATACAT
213454 TGTATCGATACA
1 TGTATCGATACA
213466 ACACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:214588 original size:33 final size:33
Alignment explanation
Indices: 214551--214617 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
214541 CAAGAGTTGA
214551 TCACTTCAC-CTTCGCAACACAT-GAGTGAGCACT
1 TCACTTCACTC-TCGCAACACATGGA-TGAGCACT
* *
214584 TCACTTCACTCTCGCAGCGCATGGATGAGCACT
1 TCACTTCACTCTCGCAACACATGGATGAGCACT
214617 T
1 T
214618 TAGTGCACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 27 0.90
34 3 0.10
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (33 bp):
TCACTTCACTCTCGCAACACATGGATGAGCACT
Found at i:215584 original size:20 final size:19
Alignment explanation
Indices: 215541--215596 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
215531 GTATCGATAC
* **
215541 ATTGTATCAATACATGTTA
1 ATTGTATCGATACATGACA
215560 ATTGTATCGATACATGCACA
1 ATTGTATCGATACATG-ACA
215580 ATTGTATCGATACATGA
1 ATTGTATCGATACATGA
215597 AACTGGGAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:218768 original size:20 final size:20
Alignment explanation
Indices: 218743--218784 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
218733 ACTAAGAAAA
218743 GTGTTACCTTTGAGGCTAAG
1 GTGTTACCTTTGAGGCTAAG
218763 GTGTTACCTTTGAGGCTAAG
1 GTGTTACCTTTGAGGCTAAG
218783 GT
1 GT
218785 ATAACCTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.31, T:0.36
Consensus pattern (20 bp):
GTGTTACCTTTGAGGCTAAG
Found at i:218791 original size:20 final size:20
Alignment explanation
Indices: 218748--218792 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
218738 GAAAAGTGTT
* *
218748 ACCTTTGAGGCTAAGGTGTT
1 ACCTTTGAGGCTAAGGTATA
218768 ACCTTTGAGGCTAAGGTATA
1 ACCTTTGAGGCTAAGGTATA
218788 ACCTT
1 ACCTT
218793 ACAACTTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ACCTTTGAGGCTAAGGTATA
Found at i:218826 original size:35 final size:34
Alignment explanation
Indices: 218799--218932 Score: 164
Period size: 35 Copynumber: 3.9 Consensus size: 34
218789 CCTTACAACT
*
218799 TATCTTTTCACAGGCTAAGATAGAACCT-TCTCCC
1 TATCTTTTCAAAGGCTAAGATAGAACCTCT-TCCC
*** *
218833 TATCAGCTCACAA-GCTAGGATAGAACCTCTTCCC
1 TATCTTTTCA-AAGGCTAAGATAGAACCTCTTCCC
218867 TATCTTTTTCAAAGGCTAAGATAGAACCTCTTCCC
1 TATC-TTTTCAAAGGCTAAGATAGAACCTCTTCCC
*
218902 TATTTTTTTCAAAGGCTAAGATAGAACCTCT
1 TA-TCTTTTCAAAGGCTAAGATAGAACCTCT
218933 CAATCACTTA
Statistics
Matches: 85, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
34 31 0.36
35 53 0.62
36 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (34 bp):
TATCTTTTCAAAGGCTAAGATAGAACCTCTTCCC
Found at i:218855 original size:34 final size:34
Alignment explanation
Indices: 218806--218904 Score: 112
Period size: 34 Copynumber: 2.9 Consensus size: 34
218796 ACTTATCTTT
*
218806 TCACAGGCTAAGATAGAACCT-TCTCCCTATCAGC
1 TCACAAGCTAAGATAGAACCTCT-TCCCTATCAGC
* ***
218840 TCACAAGCTAGGATAGAACCTCTTCCCTATCTTTT
1 TCACAAGCTAAGATAGAACCTCTTCCCTATC-AGC
218875 TCA-AAGGCTAAGATAGAACCTCTTCCCTAT
1 TCACAA-GCTAAGATAGAACCTCTTCCCTAT
218905 TTTTTTCAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
34 29 0.52
35 27 0.48
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.28
Consensus pattern (34 bp):
TCACAAGCTAAGATAGAACCTCTTCCCTATCAGC
Found at i:219396 original size:20 final size:20
Alignment explanation
Indices: 219371--219408 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
219361 CCGTTGGGCC
219371 AAATGTATCAATACAATTCA
1 AAATGTATCAATACAATTCA
**
219391 AAATGTATTGATACAATT
1 AAATGTATCAATACAATT
219409 TAAACATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (20 bp):
AAATGTATCAATACAATTCA
Found at i:220341 original size:321 final size:321
Alignment explanation
Indices: 219759--220404 Score: 1292
Period size: 321 Copynumber: 2.0 Consensus size: 321
219749 ATGAAAACTT
219759 ATTTTGTGATTTTCAAAGTATCTTTACAAAATCACTTATATTTTTAGTTAATTTGTTTTATCAAA
1 ATTTTGTGATTTTCAAAGTATCTTTACAAAATCACTTATATTTTTAGTTAATTTGTTTTATCAAA
219824 ACCAAAAGCTTAACAATCTCCCCCTTTTTGATGTAACAAAACTCAAAAATAAATTTGGTTGACTT
66 ACCAAAAGCTTAACAATCTCCCCCTTTTTGATGTAACAAAACTCAAAAATAAATTTGGTTGACTT
219889 TACTCCCCCTCAATTATTTAAAGAATTTCAATGAATGTATTTTCGGAAACGTTCATGATCTTACC
131 TACTCCCCCTCAATTATTTAAAGAATTTCAATGAATGTATTTTCGGAAACGTTCATGATCTTACC
219954 AAGCGTTATGTGTATTATCTCCATTTTTGTCATCCAAGCTTGTAACCTATACCTTGATACATCAA
196 AAGCGTTATGTGTATTATCTCCATTTTTGTCATCCAAGCTTGTAACCTATACCTTGATACATCAA
220019 CAACTCACAAAAAATATTAGAAATAATCACAATATGAGTTTTGAATACCAATCTAAATTGA
261 CAACTCACAAAAAATATTAGAAATAATCACAATATGAGTTTTGAATACCAATCTAAATTGA
220080 ATTTTGTGATTTTCAAAGTATCTTTACAAAATCACTTATATTTTTAGTTAATTTGTTTTATCAAA
1 ATTTTGTGATTTTCAAAGTATCTTTACAAAATCACTTATATTTTTAGTTAATTTGTTTTATCAAA
220145 ACCAAAAGCTTAACAATCTCCCCCTTTTTGATGTAACAAAACTCAAAAATAAATTTGGTTGACTT
66 ACCAAAAGCTTAACAATCTCCCCCTTTTTGATGTAACAAAACTCAAAAATAAATTTGGTTGACTT
220210 TACTCCCCCTCAATTATTTAAAGAATTTCAATGAATGTATTTTCGGAAACGTTCATGATCTTACC
131 TACTCCCCCTCAATTATTTAAAGAATTTCAATGAATGTATTTTCGGAAACGTTCATGATCTTACC
220275 AAGCGTTATGTGTATTATCTCCATTTTTGTCATCCAAGCTTGTAACCTATACCTTGATACATCAA
196 AAGCGTTATGTGTATTATCTCCATTTTTGTCATCCAAGCTTGTAACCTATACCTTGATACATCAA
220340 CAACTCACAAAAAATATTAGAAATAATCACAATATGAGTTTTGAATACCAATCTAAATTGA
261 CAACTCACAAAAAATATTAGAAATAATCACAATATGAGTTTTGAATACCAATCTAAATTGA
220401 ATTT
1 ATTT
220405 ATAATCTATT
Statistics
Matches: 325, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
321 325 1.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (321 bp):
ATTTTGTGATTTTCAAAGTATCTTTACAAAATCACTTATATTTTTAGTTAATTTGTTTTATCAAA
ACCAAAAGCTTAACAATCTCCCCCTTTTTGATGTAACAAAACTCAAAAATAAATTTGGTTGACTT
TACTCCCCCTCAATTATTTAAAGAATTTCAATGAATGTATTTTCGGAAACGTTCATGATCTTACC
AAGCGTTATGTGTATTATCTCCATTTTTGTCATCCAAGCTTGTAACCTATACCTTGATACATCAA
CAACTCACAAAAAATATTAGAAATAATCACAATATGAGTTTTGAATACCAATCTAAATTGA
Found at i:220557 original size:17 final size:16
Alignment explanation
Indices: 220535--220596 Score: 79
Period size: 17 Copynumber: 3.8 Consensus size: 16
220525 CTCAAGTTTA
*
220535 TAACACTTCTCCTTTTT
1 TAACACTTCTCC-TCTT
*
220552 TAACACTTCTCCCTCTA
1 TAACACTTCT-CCTCTT
*
220569 TAACACTTCTCCCCTT
1 TAACACTTCTCCTCTT
220585 TAACACTTCTCC
1 TAACACTTCTCC
220597 CTCATTTCGC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
16 16 0.40
17 22 0.55
18 2 0.05
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.40
Consensus pattern (16 bp):
TAACACTTCTCCTCTT
Found at i:220592 original size:33 final size:34
Alignment explanation
Indices: 220533--220599 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
220523 TCCTCAAGTT
**
220533 TATAACACTTCTCCTTTTTTAACACTTCTCCCTC
1 TATAACACTTCTCCTCCTTTAACACTTCTCCCTC
220567 TATAACACTTCTCC-CCTTTAACACTTCTCCCTC
1 TATAACACTTCTCCTCCTTTAACACTTCTCCCTC
220600 ATTTCGCCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.55
34 14 0.45
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.40
Consensus pattern (34 bp):
TATAACACTTCTCCTCCTTTAACACTTCTCCCTC
Found at i:228525 original size:42 final size:43
Alignment explanation
Indices: 228478--228778 Score: 210
Period size: 42 Copynumber: 7.2 Consensus size: 43
228468 TCAAACCATA
* * *
228478 GAGACTTTCTTACCCT-CAGTCTGCCTGTCAGCTTTGACCCTG
1 GAGACTTTCTTACTCTAAAGTCTGCCTGTCAGCTTTGACCTTG
* * * * *
228520 GAGACTGTCTCA-TCTAAAGTCTGCTTGTCGGCTTTGACCTTA
1 GAGACTTTCTTACTCTAAAGTCTGCCTGTCAGCTTTGACCTTG
* * * ** *
228562 GAGACTGTCTCA-TCTAAAGTTTGCCT-TTGGCTTCGACCTTG
1 GAGACTTTCTTACTCTAAAGTCTGCCTGTCAGCTTTGACCTTG
* * * * * *
228603 GAAACTTTCCTACCTCT-CAGTCTACCTGTCGGCTTTGACCTTA
1 GAGACTTTCTTA-CTCTAAAGTCTGCCTGTCAGCTTTGACCTTG
* * * * * *
228646 GAGA-TTGCCT-CATCTAAAGTCTACCTGTCACCTTTGACCCTA
1 GAGACTTTCTTAC-TCTAAAGTCTGCCTGTCAGCTTTGACCTTG
* *
228688 GAGACTTTCTTACTCT-TAGTCTGCTTGTCAGCTTTGAGCC-TG
1 GAGACTTTCTTACTCTAAAGTCTGCCTGTCAGCTTTGA-CCTTG
** *
228730 GAGACTGCCTTA-TCTAAATTCTGCCT-TCAGCTTTGACCTTG
1 GAGACTTTCTTACTCTAAAGTCTGCCTGTCAGCTTTGACCTTG
*
228771 GAAACTTT
1 GAGACTTT
228779 TCCACTTTTT
Statistics
Matches: 204, Mismatches: 44, Indels: 23
0.75 0.16 0.08
Matches are distributed among these distances:
40 3 0.01
41 45 0.22
42 128 0.63
43 27 0.13
44 1 0.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.36
Consensus pattern (43 bp):
GAGACTTTCTTACTCTAAAGTCTGCCTGTCAGCTTTGACCTTG
Found at i:228709 original size:84 final size:83
Alignment explanation
Indices: 228495--228778 Score: 293
Period size: 84 Copynumber: 3.4 Consensus size: 83
228485 TCTTACCCTC
* *
228495 AGTCTGCCTGTCAGCTTTGACCCTGGAGACTGTCTCA-TCTAAAGTCTGCTTGTCGGCTTTGACC
1 AGTCTGCCT-TCAGCTTTGACCCTGGAGACTTTCTTACTCT-AAGTCTGCTTGTCGGCTTTGACC
*
228559 TTAGAGACTGTCTCATCTAA
64 TTAGAGACTGCCTCATCTAA
* ** * * * * * * *
228579 AGTTTGCCTTTGGCTTCGACCTTGGAAACTTTCCTACCTCTCAGTCTACCTGTCGGCTTTGACCT
1 AGTCTGCCTTCAGCTTTGACCCTGGAGACTTTCTTA-CTCTAAGTCTGCTTGTCGGCTTTGACCT
*
228644 TAGAGATTGCCTCATCTAA
65 TAGAGACTGCCTCATCTAA
* * * * *
228663 AGTCTACCTGTCACCTTTGACCCTAGAGACTTTCTTACTCTTAGTCTGCTTGTCAGCTTTGAGCC
1 AGTCTGCCT-TCAGCTTTGACCCTGGAGACTTTCTTACTCTAAGTCTGCTTGTCGGCTTTGA-CC
* *
228728 -TGGAGACTGCCTTATCTAA
64 TTAGAGACTGCCTCATCTAA
* * *
228747 ATTCTGCCTTCAGCTTTGACCTTGGAAACTTT
1 AGTCTGCCTTCAGCTTTGACCCTGGAGACTTT
228779 TCCACTTTTT
Statistics
Matches: 159, Mismatches: 37, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
83 38 0.24
84 97 0.61
85 24 0.15
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.36
Consensus pattern (83 bp):
AGTCTGCCTTCAGCTTTGACCCTGGAGACTTTCTTACTCTAAGTCTGCTTGTCGGCTTTGACCTT
AGAGACTGCCTCATCTAA
Found at i:229840 original size:45 final size:45
Alignment explanation
Indices: 229776--229900 Score: 187
Period size: 45 Copynumber: 2.8 Consensus size: 45
229766 CAACAATGAT
* * * * *
229776 GAAGTCAAGGCAACATGGAACAGCAAAGCAACAATGAAGAAATTG
1 GAAGACAAAGCAACGTGGAACAGCAAAGCAACAAGGAAGAAAATG
*
229821 GAAGACAAAGCAACGTGGAATAGCAAAGCAACAAGGAAGAAAATG
1 GAAGACAAAGCAACGTGGAACAGCAAAGCAACAAGGAAGAAAATG
*
229866 GAAGACAAAGCAAAGTGGAACAGCAAAGCAACAAG
1 GAAGACAAAGCAACGTGGAACAGCAAAGCAACAAG
229901 CTGAAAATGG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 72 1.00
ACGTcount: A:0.52, C:0.15, G:0.26, T:0.07
Consensus pattern (45 bp):
GAAGACAAAGCAACGTGGAACAGCAAAGCAACAAGGAAGAAAATG
Found at i:230085 original size:31 final size:30
Alignment explanation
Indices: 230048--230116 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
230038 AAACAATACG
* **
230048 AGCAGCTCCTACAGCAACTTTCAGTAGCTCC
1 AGCAGCTCC-ACAGCAACTTCCAACAGCTCC
*
230079 AGCAGCTTCCACAGTAACTTCCAACAGCTCC
1 AGCAGC-TCCACAGCAACTTCCAACAGCTCC
*
230110 AGTAGCT
1 AGCAGCT
230117 TAGCAACCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
30 1 0.03
31 28 0.88
32 3 0.09
ACGTcount: A:0.28, C:0.35, G:0.16, T:0.22
Consensus pattern (30 bp):
AGCAGCTCCACAGCAACTTCCAACAGCTCC
Found at i:230151 original size:40 final size:39
Alignment explanation
Indices: 230103--230181 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 39
230093 TAACTTCCAA
*
230103 CAGCTCCAGTAGCTT-AGCAACCATGAGCAGCTCCCACAG
1 CAGCTCCAGCAG-TTCAGCAACCATGAGCAGCTCCCACAG
*
230142 CAGCTTCCAGCAGTTCAGCAACCATGAGCAGCTCCTACAG
1 CAGC-TCCAGCAGTTCAGCAACCATGAGCAGCTCCCACAG
230182 TAGCCATTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 6 0.17
40 30 0.83
ACGTcount: A:0.28, C:0.35, G:0.20, T:0.16
Consensus pattern (39 bp):
CAGCTCCAGCAGTTCAGCAACCATGAGCAGCTCCCACAG
Found at i:230201 original size:40 final size:39
Alignment explanation
Indices: 230118--230201 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 39
230108 CCAGTAGCTT
*
230118 AGCAACCATGAGCAGCTCCCACAGCAGCTTCCAGCAGTTC
1 AGCAACCATGAGCAGCTCCCACAGCAGCTTCCAGCAG-AC
* *
230158 AGCAACCATGAGCAGCTCCTACAGTAGCCATTCCAGCA-AC
1 AGCAACCATGAGCAGCTCCCACAGCAG-C-TTCCAGCAGAC
230198 AGCA
1 AGCA
230202 GCAGCCAACG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 30 0.77
41 1 0.03
42 8 0.21
ACGTcount: A:0.31, C:0.36, G:0.19, T:0.14
Consensus pattern (39 bp):
AGCAACCATGAGCAGCTCCCACAGCAGCTTCCAGCAGAC
Found at i:230314 original size:40 final size:41
Alignment explanation
Indices: 230270--230365 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 41
230260 CGCGATAGCC
* * *
230270 TTCAGCAGCTCAGCAACCACGAGTAGCTCCCACAGCAG-CT
1 TTCAGCAGCTCAGCAACAACGAGCAGCTCCCACAGCAGTCG
* * * *
230310 TTCAGCAACTCCGCAACAATGAGCAGCTCCTACAGCAGTCG
1 TTCAGCAGCTCAGCAACAACGAGCAGCTCCCACAGCAGTCG
230351 TTCTAGCAGCT-AGCA
1 TTC-AGCAGCTCAGCA
230366 GTAGCCAATG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
40 32 0.71
41 7 0.16
42 6 0.13
ACGTcount: A:0.28, C:0.34, G:0.20, T:0.18
Consensus pattern (41 bp):
TTCAGCAGCTCAGCAACAACGAGCAGCTCCCACAGCAGTCG
Found at i:230337 original size:163 final size:164
Alignment explanation
Indices: 230113--230420 Score: 429
Period size: 163 Copynumber: 1.9 Consensus size: 164
230103 CAGCTCCAGT
* * ** *
230113 AGCTTAGCAACCATGAGCAGCTCCCACAGCAGCTTCCAGCAGTTCAGCAACCATGAGCAGCTCCT
1 AGCTCAGCAACCACGAGCAGCTCCCACAGCAGCTTCCAGCAACTCAGCAACAATGAGCAGCTCCT
* * *
230178 ACAGTAGCCATTCCAGCAAC-AGCAGCAGCCAACGATAGCTTTAGTAGCTCCCACAGCAACCTCC
66 ACAGCAGCCATTCCAGCAACTAGCAGCAGCCAACGAAAGCTTCAGTAGCTCCCACAGCAACCTCC
230242 AATAGCTCCAACAGCTTTCGCGATAGCCTTCAGC
131 AATAGCTCCAACAGCTTTCGCGATAGCCTTCAGC
* * *
230276 AGCTCAGCAACCACGAGTAGCTCCCACAGCAGCTTTCAGCAACTCCGCAACAATGAGCAGCTCCT
1 AGCTCAGCAACCACGAGCAGCTCCCACAGCAGCTTCCAGCAACTCAGCAACAATGAGCAGCTCCT
* * * * * * **
230341 ACAGCAGTCGTTCTAGCAGCTAGCAGTAGCCAATGAAAGCTTCAGTAGCTCCCACAGCAACCTTT
66 ACAGCAGCCATTCCAGCAACTAGCAGCAGCCAACGAAAGCTTCAGTAGCTCCCACAGCAACCTCC
*
230406 AGTAGCTCCAACAGC
131 AATAGCTCCAACAGC
230421 CTCCTACAGC
Statistics
Matches: 124, Mismatches: 20, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
163 72 0.58
164 52 0.42
ACGTcount: A:0.29, C:0.34, G:0.19, T:0.18
Consensus pattern (164 bp):
AGCTCAGCAACCACGAGCAGCTCCCACAGCAGCTTCCAGCAACTCAGCAACAATGAGCAGCTCCT
ACAGCAGCCATTCCAGCAACTAGCAGCAGCCAACGAAAGCTTCAGTAGCTCCCACAGCAACCTCC
AATAGCTCCAACAGCTTTCGCGATAGCCTTCAGC
Found at i:234149 original size:36 final size:34
Alignment explanation
Indices: 234097--234184 Score: 113
Period size: 34 Copynumber: 2.5 Consensus size: 34
234087 GTTAAATTTG
* *
234097 AAGCTAAGGTATAACCTTACAACCCTATCTTTTCAC
1 AAGCTAAGATAAAACCTT-C-ACCCTATCTTTTCAC
*
234133 AAGCTAAGATAAAACCTTCTCCCTATCTTTTCAC
1 AAGCTAAGATAAAACCTTCACCCTATCTTTTCAC
* *
234167 AGGCTAAGATAGAACCTT
1 AAGCTAAGATAAAACCTT
234185 TTCCTTATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 30 0.64
35 1 0.02
36 16 0.34
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (34 bp):
AAGCTAAGATAAAACCTTCACCCTATCTTTTCAC
Found at i:234206 original size:35 final size:34
Alignment explanation
Indices: 234119--234218 Score: 130
Period size: 34 Copynumber: 2.9 Consensus size: 34
234109 AACCTTACAA
*
234119 CCCTATCTTTTCACAA-GCTAAGATAAAACCTTCT
1 CCCTATCTTTTCA-AAGGCTAAGATAGAACCTTCT
* *
234153 CCCTATCTTTTCACAGGCTAAGATAGAACCTTTT
1 CCCTATCTTTTCAAAGGCTAAGATAGAACCTTCT
* *
234187 CCTTATATTTTTCAAAGGCTAAGATAGAACCT
1 CCCTAT-CTTTTCAAAGGCTAAGATAGAACCT
234219 CTCAATCACT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
33 1 0.02
34 34 0.59
35 23 0.40
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (34 bp):
CCCTATCTTTTCAAAGGCTAAGATAGAACCTTCT
Found at i:234707 original size:21 final size:20
Alignment explanation
Indices: 234659--234715 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
234649 CTGTTAGGCT
234659 AAATGTATCAATACAATTCA
1 AAATGTATCAATACAATTCA
*
234679 AAATGTATCAATACAATTTA
1 AAATGTATCAATACAATTCA
*
234699 AACATGTATCGATACAA
1 AA-ATGTATCAATACAA
234716 AACACAGGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 21 0.62
21 13 0.38
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (20 bp):
AAATGTATCAATACAATTCA
Found at i:236499 original size:92 final size:92
Alignment explanation
Indices: 236393--236582 Score: 308
Period size: 92 Copynumber: 2.1 Consensus size: 92
236383 AATGCAAAGC
*
236393 TTTATTAAAAGGTTTTTAAAGAAAATTTTCATTTTAGTACTCCCACTTAATAACTACTCCCCCTT
1 TTTATTAAAAGGTTTTCAAAGAAAATTTTCATTTTAGTACTCCCACTTAATAACTACTCCCCCTT
*
236458 TTTGTTATCCCTCTCATTTTAAACCAA
66 TTTGTTATCCCTCTCATTTTAAACAAA
* * * * * *
236485 TTTATTAAGAGGTTTTCGAGGAAAATTTTCGTTTTAGTACTCCCCCTTAATAACTACTCCCTCTT
1 TTTATTAAAAGGTTTTCAAAGAAAATTTTCATTTTAGTACTCCCACTTAATAACTACTCCCCCTT
236550 TTTGTTATCCCTCTCATTTTAAACAAA
66 TTTGTTATCCCTCTCATTTTAAACAAA
236577 TTTATT
1 TTTATT
236583 TCGAATAAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.44
Consensus pattern (92 bp):
TTTATTAAAAGGTTTTCAAAGAAAATTTTCATTTTAGTACTCCCACTTAATAACTACTCCCCCTT
TTTGTTATCCCTCTCATTTTAAACAAA
Found at i:243245 original size:52 final size:52
Alignment explanation
Indices: 243164--243284 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
243154 TGAAGAGTTA
*
243164 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
243216 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
243268 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
243285 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:243297 original size:52 final size:51
Alignment explanation
Indices: 243164--243304 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
243154 TGAAGAGTTA
243164 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
243216 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
243268 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
243305 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:243311 original size:13 final size:13
Alignment explanation
Indices: 243293--243317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
243283 CAAAGATCAG
243293 TGTATCGATACAA
1 TGTATCGATACAA
243306 TGTATCGATACA
1 TGTATCGATACA
243318 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:243401 original size:13 final size:13
Alignment explanation
Indices: 243383--243407 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
243373 CAAAAAAATA
243383 TGTATCGATACAT
1 TGTATCGATACAT
243396 TGTATCGATACA
1 TGTATCGATACA
243408 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:243403 original size:33 final size:33
Alignment explanation
Indices: 243361--243427 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
243351 AGTAGCTTAA
243361 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
243394 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
243427 A
1 A
243428 GATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:244520 original size:170 final size:171
Alignment explanation
Indices: 244226--244619 Score: 682
Period size: 170 Copynumber: 2.3 Consensus size: 171
244216 TTTTAGAGAT
* *
244226 GATGAAGGTGCTAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
*
244291 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGGTGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
244356 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* *
244397 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA-ATGATGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
*
244461 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
244526 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* *
244567 GATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GAT-GAAGA--TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
244620 GTGCCAATGT
Statistics
Matches: 211, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
170 121 0.57
171 50 0.24
173 40 0.19
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.25
Consensus pattern (171 bp):
GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
Found at i:244638 original size:43 final size:44
Alignment explanation
Indices: 244572--244902 Score: 306
Period size: 43 Copynumber: 7.0 Consensus size: 44
244562 TTAAAGATGG
* *
244572 AAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
244616 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
244659 AAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 AAA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
244708 -AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
244751 CAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 --A-A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
244800 AAAGGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 --A--A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGAC-T-----T
* *
244856 GGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTT
1 --AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
244902 A
1 A
244903 GAGGGGTTGC
Statistics
Matches: 241, Mismatches: 27, Indels: 38
0.79 0.09 0.12
Matches are distributed among these distances:
43 74 0.31
44 4 0.02
45 1 0.00
46 3 0.01
47 2 0.01
48 3 0.01
49 74 0.31
50 39 0.16
51 2 0.01
52 36 0.15
54 1 0.00
56 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (44 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:244707 original size:92 final size:93
Alignment explanation
Indices: 244533--244902 Score: 546
Period size: 92 Copynumber: 3.9 Consensus size: 93
244523 GGATGTCAAC
* * *
244533 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAG
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAGA--TGCCAATATGCTGATTCAAG
*
244598 GCCAGCTATATTGGACTTAAAGGTGCCAAT
64 GCCAGCGATATTGGACTTAAAGGTGCCAAT
*
244628 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGATGCCAATATGCTGATTCAAGGC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAGATGCCAATATGCTGATTCAAGGC
244692 CAGCGATATTGGACTTAAAGGTGCCAAT
66 CAGCGATATTGGACTTAAAGGTGCCAAT
*
244720 GTGCTGAGTCAAGGCCAGCTACATTGGACTTCAAGAT-GAAGATGCCAATATGCTGATTCAAGGC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAGATGCCAATATGCTGATTCAAGGC
244784 CAGCGATATTGGACTTAAAGGATGAAGGTGCCAAT
66 CAGCGATATTGGACTT-----A--AAGGTGCCAAT
*
244819 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAG
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG--AAGATGCCAATATGCTGATTCAAG
* *
244884 GCCAGCTATATTGGGCTTA
64 GCCAGCGATATTGGACTTA
244903 GAGGGGTTGC
Statistics
Matches: 256, Mismatches: 9, Indels: 18
0.90 0.03 0.06
Matches are distributed among these distances:
92 127 0.50
94 4 0.02
95 36 0.14
97 2 0.01
99 47 0.18
100 1 0.00
102 39 0.15
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (93 bp):
GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAGATGCCAATATGCTGATTCAAGGC
CAGCGATATTGGACTTAAAGGTGCCAAT
Found at i:244825 original size:50 final size:49
Alignment explanation
Indices: 244534--244902 Score: 402
Period size: 49 Copynumber: 7.6 Consensus size: 49
244524 GATGTCAACG
* * *
244534 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
* * *
244586 TGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* *
244629 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
244678 TGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* *
244721 TGCTGAGTCAAGGCCAGCTACATTGGACTTCAAGATGAAGATGCCAATA
1 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
244770 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGATGAAGGTGCCAATG
1 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA-GATGAAGGTGCCAATA
244820 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
* * *
244872 TGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCTGAGTCAAGGCCAGCTACATTGGACTTA
244903 GAGGGGTTGC
Statistics
Matches: 272, Mismatches: 29, Indels: 32
0.82 0.09 0.10
Matches are distributed among these distances:
43 76 0.28
45 1 0.00
47 2 0.01
48 1 0.00
49 80 0.29
50 45 0.17
52 67 0.25
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
Found at i:245016 original size:34 final size:33
Alignment explanation
Indices: 244976--245515 Score: 439
Period size: 33 Copynumber: 16.3 Consensus size: 33
244966 GGGAAGGAAA
*
244976 AAAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGG
1 AAAAAG-TGCCACGGAGTTGTGGGCTTTAAAA-GG
*
245010 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGA
1 -AAAA-AGTGCCACGGAGTTGTGGGCTTTAAAAGG
245045 AAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
1 AAAAAGTGCCACGGAGTTGTGGGCTTT-AAAA-GG
*
245080 AAAAAGAGTGCCACGGAGTTATGGGCTTTAAAA-G
1 -AAAA-AGTGCCACGGAGTTGTGGGCTTTAAAAGG
*
245114 AAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-G
1 AA-AAAGTGCCACGGAGTTGTGGGCTTT-AAAAGG
* * * *
245148 AAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGG
1 AA-AAAG-TGCCACGGA-GT-TGTGGGCTTTA--AAAGG
* *
245187 AGAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGG
1 AAAAAG-TGCCACGGAGTTGTGGGCTTTAAAA-GG
*
245221 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGA
1 -AAAA-AGTGCCACGGAGTTGTGGGCTTTAAAAGG
*
245256 AAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAGTGCCACGGAGTTGTGGGCTTTAAAAGG
245289 AAAAAGGTGCCACGGAGTTGTGGGC-TTAAACA-G
1 AAAAA-GTGCCACGGAGTTGTGGGCTTTAAA-AGG
* *
245322 -----GTGCCACGGAGTTGTGGAC-TTAAAGATGA
1 AAAAAGTGCCACGGAGTTGTGGGCTTTAAA-A-GG
* * *
245351 AAAAAGTGCCACAGAATTGTGGGCTTCAAAAGG
1 AAAAAGTGCCACGGAGTTGTGGGCTTTAAAAGG
* *
245384 -----GTGCCACGGAGTTGTGGAC-TTAAAGATGA
1 AAAAAGTGCCACGGAGTTGTGGGCTTTAAA-A-GG
*
245413 AAAAAGTGCCACGGAATTGTGGGCTTTAAAAGG
1 AAAAAGTGCCACGGAGTTGTGGGCTTTAAAAGG
* *
245446 -----GTGCCACAGAGTTGTGGAC-TTAAAAGG
1 AAAAAGTGCCACGGAGTTGTGGGCTTTAAAAGG
*
245473 AACAAGGTGCCACGGAGTTGTGGGCTTT-AAA-G
1 AA-AAAGTGCCACGGAGTTGTGGGCTTTAAAAGG
*
245505 AAAAAATGCCA
1 AAAAAGTGCCA
245516 TTAAGTCGTG
Statistics
Matches: 418, Mismatches: 44, Indels: 90
0.76 0.08 0.16
Matches are distributed among these distances:
27 36 0.09
28 33 0.08
29 1 0.00
31 7 0.02
32 3 0.01
33 108 0.26
34 86 0.21
35 64 0.15
36 32 0.08
37 33 0.08
38 13 0.03
39 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.20
Consensus pattern (33 bp):
AAAAAGTGCCACGGAGTTGTGGGCTTTAAAAGG
Found at i:245058 original size:33 final size:33
Alignment explanation
Indices: 244975--245515 Score: 464
Period size: 34 Copynumber: 16.4 Consensus size: 33
244965 TGGGAAGGAA
*
244975 AAAAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGG
1 AAAAAAG-TGCCACGGAGTTGTGGGCTTTAAAA--G
245010 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
1 AAAAA-AGTGCCACGGAGTTGTGGGCTTTAAAAG
245044 AAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
1 AAAAAAGTGCCACGGAGTTGTGGGCTTT-AAAA--G
*
245080 AAAAAGAGTGCCACGGAGTTATGGGCTTTAAAAG
1 AAAAA-AGTGCCACGGAGTTGTGGGCTTTAAAAG
* *
245114 AAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG
1 AAAAAAGTGCCACGGAGTTGTGGGCTTT-AAAAG
* * * * *
245148 AAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGG
1 AAAAAAG-TGCCACGGA-GT-TGTGGGCTTTA--AAAG
* * *
245186 GAGAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGG
1 AAAAAAG-TGCCACGGAGTTGTGGGCTTTAAAA--G
245221 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
1 AAAAA-AGTGCCACGGAGTTGTGGGCTTTAAAAG
245255 AAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAAGTGCCACGGAGTTGTGGGCTTT-AAAAG
*
245289 AAAAAGGTGCCACGGAGTTGTGGGC-TTAAACAG
1 AAAAAAGTGCCACGGAGTTGTGGGCTTTAAA-AG
*
245322 ------GTGCCACGGAGTTGTGGAC-TTAAAGATG
1 AAAAAAGTGCCACGGAGTTGTGGGCTTTAAA-A-G
* * *
245350 AAAAAAGTGCCACAGAATTGTGGGCTTCAAAAG
1 AAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAG
* *
245383 -----GGTGCCACGGAGTTGTGGAC-TTAAAGATG
1 AAAAAAGTGCCACGGAGTTGTGGGCTTTAAA-A-G
*
245412 AAAAAAGTGCCACGGAATTGTGGGCTTTAAAAG
1 AAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAG
* * *
245445 -----GGTGCCACAGAGTTGTGGAC-TTAAAAGG
1 AAAAAAGTGCCACGGAGTTGTGGGCTTTAAAA-G
* *
245473 AACAAGGTGCCACGGAGTTGTGGGCTTT-AAAG
1 AAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAG
245505 AAAAAA-TGCCA
1 AAAAAAGTGCCA
245516 TTAAGTCGTG
Statistics
Matches: 424, Mismatches: 41, Indels: 86
0.77 0.07 0.16
Matches are distributed among these distances:
27 34 0.08
28 35 0.08
29 1 0.00
31 5 0.01
32 8 0.02
33 96 0.23
34 99 0.23
35 63 0.15
36 34 0.08
37 33 0.08
38 16 0.04
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.20
Consensus pattern (33 bp):
AAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAG
Found at i:245240 original size:141 final size:141
Alignment explanation
Indices: 244975--245515 Score: 446
Period size: 141 Copynumber: 4.1 Consensus size: 141
244965 TGGGAAGGAA
* * * *
244975 AAAAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGA-GT-TGTGGGCT
1 AAAAAAG-TGCCACGGAGTTGTGGGCTTTAAAA-AGAAAAAG-GTGCCACCGACTTGTGTGGGCT
* * * *
245037 TTA--AAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTT
63 TTAGGAAGGGAGAAAGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACGGAGTT
245100 ATGGGCTTTAAAAG
128 ATGGGCTTTAAAAG
* * * *
245114 AAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTTGCCACCGACTTGTGTGGGCTTT
1 AAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGG-TGCCACCGACTTGTGTGGGCTTT
*
245179 AGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTG
65 AGGAAGGGAGAAAG-TGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTA
245242 TGGGCTTTAAAAG
129 TGGGCTTTAAAAG
* *
245255 AAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGA-GT-TGTGGGC-TTA
1 AAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACCGACTTGTGTGGGCTTTA
* * * * *
245317 --AA--CAG---GTGCCACGGAGTTGTGGAC-TT--AAAGATGAAAAA-AGTGCCACAGAATTGT
66 GGAAGGGAGAAAGTGCCACGGAGTTGTGGACTTTGAAAAG-GGAAAAAGAGTGCCACGGAGTTAT
*
245371 GGGCTTCAAAAG
130 GGGCTTTAAAAG
* * * * * *
245383 -----GGTGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAGTGCCACGGA-AT-TGTGGGCTTT
1 AAAAAAGTGCCACGGAGTTGTGGGCTTTAAA-AAGAAAAAGGTGCCACCGACTTGTGTGGGCTTT
* * * *
245440 A--AA---AG--GGTGCCACAGAGTTGTGGAC-TT-AAAA-GGAACAAG-GTGCCACGGAGTTGT
65 AGGAAGGGAGAAAGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTAT
245494 GGGCTTT-AAAG
130 GGGCTTTAAAAG
245505 AAAAAA-TGCCA
1 AAAAAAGTGCCA
245516 TTAAGTCGTG
Statistics
Matches: 348, Mismatches: 36, Indels: 49
0.80 0.08 0.11
Matches are distributed among these distances:
122 9 0.03
123 69 0.20
124 25 0.07
125 3 0.01
126 5 0.01
128 29 0.08
129 26 0.07
130 1 0.00
133 2 0.01
135 2 0.01
137 4 0.01
138 38 0.11
139 12 0.03
140 19 0.05
141 77 0.22
142 10 0.03
143 17 0.05
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.20
Consensus pattern (141 bp):
AAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACCGACTTGTGTGGGCTTTA
GGAAGGGAGAAAGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTATG
GGCTTTAAAAG
Found at i:245390 original size:28 final size:27
Alignment explanation
Indices: 245356--245472 Score: 90
Period size: 28 Copynumber: 4.0 Consensus size: 27
245346 GATGAAAAAA
*
245356 GTGCCACAGAATTGTGGGCTTCAAAAGG
1 GTGCCACAGAATTGTGGACTT-AAAAGG
* * *
245384 GTGCCACGGAGTTGTGGACTTAAAGATGAAAAAA
1 GTGCCACAGAATTGTGGACTTAAA-A-G-----G
* *
245418 GTGCCACGGAATTGTGGGCTTTAAAAGG
1 GTGCCACAGAATTGTGGAC-TTAAAAGG
*
245446 GTGCCACAGAGTTGTGGACTTAAAAGG
1 GTGCCACAGAATTGTGGACTTAAAAGG
245473 AACAAGGTGC
Statistics
Matches: 71, Mismatches: 10, Indels: 17
0.72 0.10 0.17
Matches are distributed among these distances:
27 11 0.15
28 35 0.49
29 1 0.01
33 1 0.01
34 18 0.25
35 5 0.07
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.22
Consensus pattern (27 bp):
GTGCCACAGAATTGTGGACTTAAAAGG
Found at i:245396 original size:62 final size:61
Alignment explanation
Indices: 245194--245503 Score: 390
Period size: 62 Copynumber: 4.9 Consensus size: 61
245184 GGGAGAAAGA
245194 TGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
1 TGCCACGGAGTTGTGGACTTAAAA-GGAAAAA-AGTGCCACGGAGTTGTGGGCTTTAAAAG----
*
245259 AAG
60 -GG
* * *
245262 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGC-TTAAACA-GG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAA-AGGG
* * * *
245323 TGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTCAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAA-AGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* *
245385 TGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAA-AGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* * *
245447 TGCCACAGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAA
245504 GAAAAAATGC
Statistics
Matches: 220, Mismatches: 17, Indels: 17
0.87 0.07 0.07
Matches are distributed among these distances:
60 5 0.02
61 73 0.33
62 88 0.40
66 5 0.02
67 20 0.09
68 23 0.10
69 6 0.03
ACGTcount: A:0.33, C:0.14, G:0.32, T:0.21
Consensus pattern (61 bp):
TGCCACGGAGTTGTGGACTTAAAAGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAGGG
Found at i:253912 original size:52 final size:52
Alignment explanation
Indices: 253831--253951 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
253821 TGAAGAGTTA
*
253831 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
253883 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
253935 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
253952 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:253964 original size:52 final size:51
Alignment explanation
Indices: 253831--253971 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
253821 TGAAGAGTTA
253831 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
253883 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
253935 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
253972 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:253978 original size:13 final size:13
Alignment explanation
Indices: 253960--253984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
253950 CAAAGATCAG
253960 TGTATCGATACAA
1 TGTATCGATACAA
253973 TGTATCGATACA
1 TGTATCGATACA
253985 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:254068 original size:13 final size:13
Alignment explanation
Indices: 254050--254074 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
254040 CAAAAAAATA
254050 TGTATCGATACAT
1 TGTATCGATACAT
254063 TGTATCGATACA
1 TGTATCGATACA
254075 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:254070 original size:33 final size:33
Alignment explanation
Indices: 254028--254094 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
254018 AGTAGCTTAA
254028 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
254061 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
254094 A
1 A
254095 GATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:256895 original size:15 final size:15
Alignment explanation
Indices: 256875--256908 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
256865 CAACAAATTG
*
256875 TCTTTTTATTTATTT
1 TCTTTTGATTTATTT
256890 TCTTTTGATTTATTT
1 TCTTTTGATTTATTT
256905 TCTT
1 TCTT
256909 CTTTCAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (15 bp):
TCTTTTGATTTATTT
Found at i:258961 original size:13 final size:13
Alignment explanation
Indices: 258943--258969 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
258933 ACTTTTCACT
258943 ATGTATCGATACA
1 ATGTATCGATACA
258956 ATGTATCGATACA
1 ATGTATCGATACA
258969 A
1 A
258970 ACAGTGGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:261454 original size:13 final size:13
Alignment explanation
Indices: 261436--261460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
261426 ATGTTGCATA
261436 GTATCGATACATT
1 GTATCGATACATT
261449 GTATCGATACAT
1 GTATCGATACAT
261461 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:261569 original size:13 final size:13
Alignment explanation
Indices: 261551--261575 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
261541 ACACACAGTA
261551 TGTATCGATACAT
1 TGTATCGATACAT
261564 TGTATCGATACA
1 TGTATCGATACA
261576 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:263195 original size:9 final size:9
Alignment explanation
Indices: 263181--263214 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
263171 AACCATCAAG
263181 GATGATGAA
1 GATGATGAA
263190 GATGATGAA
1 GATGATGAA
*
263199 GATGATGAT
1 GATGATGAA
263208 GATGATG
1 GATGATG
263215 GTGACTCAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.26
Consensus pattern (9 bp):
GATGATGAA
Found at i:263196 original size:3 final size:3
Alignment explanation
Indices: 263181--263214 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
263171 AACCATCAAG
* *
263181 GAT GAT GAA GAT GAT GAA GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
263215 GTGACTCAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:267743 original size:13 final size:13
Alignment explanation
Indices: 267724--267762 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
267714 ACAGCATTCT
267724 CTGTATCGATACA
1 CTGTATCGATACA
*
267737 TTGTATCGATACA
1 CTGTATCGATACA
267750 CTGTATCGATACA
1 CTGTATCGATACA
267763 AGGAGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:267929 original size:20 final size:20
Alignment explanation
Indices: 267894--267934 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
267884 CAAATTTCTT
267894 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAA-ACATC
267916 GTTTTTCA-TCAAAAACATC
1 GTTTTTCACTCAAAAACATC
267935 ATCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 6 0.32
22 8 0.42
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.39
Consensus pattern (20 bp):
GTTTTTCACTCAAAAACATC
Found at i:270223 original size:13 final size:13
Alignment explanation
Indices: 270205--270229 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
270195 ATGTTGCATA
270205 GTATCGATACATT
1 GTATCGATACATT
270218 GTATCGATACAT
1 GTATCGATACAT
270230 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:270338 original size:13 final size:13
Alignment explanation
Indices: 270320--270344 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
270310 ACACACAGTA
270320 TGTATCGATACAT
1 TGTATCGATACAT
270333 TGTATCGATACA
1 TGTATCGATACA
270345 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:270341 original size:32 final size:33
Alignment explanation
Indices: 270300--270367 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
270290 GTAGCTAAAC
**
270300 TTGTATCGATACA-CACAGTATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
*
270332 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
270365 TTG
1 TTG
270368 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:272225 original size:22 final size:23
Alignment explanation
Indices: 272180--272225 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
272170 AACTATATAA
* *
272180 TAATTCAAAGAAAATATAATTAT
1 TAATTAAAAGAAAATATAAATAT
*
272203 TAATTAAAATAAAA-ATAAATAT
1 TAATTAAAAGAAAATATAAATAT
272225 T
1 T
272226 GATGTGCACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
TAATTAAAAGAAAATATAAATAT
Found at i:272469 original size:16 final size:15
Alignment explanation
Indices: 272446--272486 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
272436 GTTAATTAAT
272446 AATAAATTATTTTTA
1 AATAAATTATTTTTA
*
272461 AAGTAAATT-TTATTA
1 AA-TAAATTATTTTTA
272476 AAT-AATTATTT
1 AATAAATTATTT
272487 ATCAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
13 4 0.18
14 3 0.14
15 9 0.41
16 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
AATAAATTATTTTTA
Found at i:274573 original size:5 final size:5
Alignment explanation
Indices: 274563--274628 Score: 62
Period size: 5 Copynumber: 13.2 Consensus size: 5
274553 ATTGTTTTAA
* * * * *
274563 CTTTG CTTTG CGTTG CTTTTC CTTTG CTTTG CTTTG TTTTG -TTCG CTTTA
1 CTTTG CTTTG CTTTG C-TTTG CTTTG CTTTG CTTTG CTTTG CTTTG CTTTG
*
274613 CCTTG CTTTG CTTTG C
1 CTTTG CTTTG CTTTG C
274629 CCTGCTCTGC
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
4 3 0.06
5 42 0.88
6 3 0.06
ACGTcount: A:0.02, C:0.23, G:0.18, T:0.58
Consensus pattern (5 bp):
CTTTG
Found at i:274587 original size:21 final size:20
Alignment explanation
Indices: 274563--274602 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
274553 ATTGTTTTAA
274563 CTTTGCTTTGCGTTGCTTTTC
1 CTTTGCTTTGCGTTG-TTTTC
*
274584 CTTTGCTTTGCTTTGTTTT
1 CTTTGCTTTGCGTTGTTTT
274603 GTTCGCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.20, G:0.17, T:0.62
Consensus pattern (20 bp):
CTTTGCTTTGCGTTGTTTTC
Found at i:275720 original size:4 final size:4
Alignment explanation
Indices: 275711--275744 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
275701 ATCAGGTCAG
*
275711 CTTT CTTT CTTC CTTT CTTT CTTT CTATT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT CT-TT CTTT C
275745 CTTTTCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:275789 original size:2 final size:2
Alignment explanation
Indices: 275782--275810 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
275772 ATCATTGTTT
275782 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
275811 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:275815 original size:2 final size:2
Alignment explanation
Indices: 275810--275847 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
275800 ACACACACAC
275810 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
275848 TGTTGTTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:281197 original size:21 final size:19
Alignment explanation
Indices: 281156--281198 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
281146 AAGTAAGGTC
281156 AATGTCACATTAACAACTT
1 AATGTCACATTAACAACTT
*
281175 AATGTCTAGATTAACATACTT
1 AATGTC-ACATTAACA-ACTT
281196 AAT
1 AAT
281199 TGTGAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (19 bp):
AATGTCACATTAACAACTT
Found at i:286602 original size:27 final size:27
Alignment explanation
Indices: 286561--286612 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
286551 ATTGCTTATC
* *
286561 AAATCTTTTACCATCTCCTTCCCCTTT
1 AAATCTTTTAACATCGCCTTCCCCTTT
*
286588 AAATCTTTTAACATCGCCTTGCCCT
1 AAATCTTTTAACATCGCCTTCCCCT
286613 GATAGTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.35, G:0.04, T:0.40
Consensus pattern (27 bp):
AAATCTTTTAACATCGCCTTCCCCTTT
Found at i:287645 original size:12 final size:12
Alignment explanation
Indices: 287628--287691 Score: 69
Period size: 12 Copynumber: 5.4 Consensus size: 12
287618 ATTTTATATA
*
287628 TTTTCCTTCATT
1 TTTTCCTTTATT
287640 TTTTCCTTT-TT
1 TTTTCCTTTATT
287651 TTTT-CTTTATT
1 TTTTCCTTTATT
* *
287662 TTCTCTTTTATT
1 TTTTCCTTTATT
*
287674 TTTTACCTTTTTT
1 TTTT-CCTTTATT
287687 TTTTC
1 TTTTC
287692 TTTTCTTCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
10 4 0.09
11 11 0.26
12 18 0.42
13 10 0.23
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTCCTTTATT
Found at i:294622 original size:18 final size:18
Alignment explanation
Indices: 294601--294640 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
294591 ATTCAATTTA
294601 TTTTATG-AGTTTCTCATT
1 TTTTATGTA-TTTCTCATT
*
294619 TTTTATGTATTTTTCATT
1 TTTTATGTATTTCTCATT
294637 TTTT
1 TTTT
294641 TCATTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (18 bp):
TTTTATGTATTTCTCATT
Found at i:294751 original size:17 final size:17
Alignment explanation
Indices: 294717--294766 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
294707 TAATGACTAC
*
294717 TAATTTTAATTTTCTTT
1 TAATTTTAATTTTATTT
294734 TAATTTTGAA-TTTATTT
1 TAATTTT-AATTTTATTT
*
294751 T-ATTTT-CTTTTATTT
1 TAATTTTAATTTTATTT
294766 T
1 T
294767 TAAAATAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 8 0.28
16 5 0.17
17 14 0.48
18 2 0.07
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (17 bp):
TAATTTTAATTTTATTT
Found at i:295132 original size:20 final size:20
Alignment explanation
Indices: 295109--295181 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
295099 ACAATTCAAA
295109 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
295129 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
*
295150 GTATCGATGCATGTTGCAAT
1 GTATCGATACATGTTGCAAT
295170 GTATCGATACAT
1 GTATCGATACAT
295182 AAAAAAGATG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:295152 original size:21 final size:21
Alignment explanation
Indices: 295126--295202 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
295116 TACATGTTGC
295126 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
* ****
295147 AATGTATCGATGCATG-TTGC
1 AATGTATCGATACATGAAAAA
295167 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
295187 AGATGTATCGATACAT
1 A-ATGTATCGATACAT
295203 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:295163 original size:41 final size:41
Alignment explanation
Indices: 295109--295202 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
295099 ACAATTCAAA
295109 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAA-AT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAAGAT
*
295150 GTATCGATGCATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
295191 GTATCGATACAT
1 GTATCGATACAT
295203 TTCTTGGCAG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
40 6 0.12
41 44 0.88
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:295259 original size:13 final size:13
Alignment explanation
Indices: 295241--295266 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
295231 TACAGCAAGT
295241 ATGTATCGATACA
1 ATGTATCGATACA
295254 ATGTATCGATACA
1 ATGTATCGATACA
295267 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:299347 original size:15 final size:15
Alignment explanation
Indices: 299327--299357 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
299317 TAAAAATGTC
*
299327 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
299342 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
299357 C
1 C
299358 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:303268 original size:31 final size:31
Alignment explanation
Indices: 303233--303293 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
303223 AATTTTGATA
303233 TGAATTACTTGATTAAGGGGGAGATTTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTTT
303264 TGAATTACTTGATTAAGGGGGAGATTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTT
303294 AATAAACGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.44
Consensus pattern (31 bp):
TGAATTACTTGATTAAGGGGGAGATTTTTTT
Found at i:303937 original size:20 final size:20
Alignment explanation
Indices: 303914--303986 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
303904 ACAATTCAAA
303914 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
303934 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
303955 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
303975 GTATCGATACAT
1 GTATCGATACAT
303987 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:303957 original size:21 final size:21
Alignment explanation
Indices: 303931--304007 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
303921 TACATGTTGC
303931 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
303952 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
303972 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
303992 AGATGTATCGATACAT
1 A-ATGTATCGATACAT
304008 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:303965 original size:41 final size:41
Alignment explanation
Indices: 303914--304007 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
303904 ACAATTCAAA
303914 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAA-AT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAAGAT
303955 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
303996 GTATCGATACAT
1 GTATCGATACAT
304008 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 6 0.12
41 46 0.88
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:304064 original size:13 final size:13
Alignment explanation
Indices: 304046--304071 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
304036 TACAGCAAGT
304046 ATGTATCGATACA
1 ATGTATCGATACA
304059 ATGTATCGATACA
1 ATGTATCGATACA
304072 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:305726 original size:155 final size:153
Alignment explanation
Indices: 305423--305754 Score: 369
Period size: 155 Copynumber: 2.2 Consensus size: 153
305413 GCTATTTTGC
* ** *
305423 AATTTTAAAAAGTTTAAGGACTAAATTACAAAAAGTTTAAAATTTTTTCTGAGTATTCTTGCTTG
1 AATTTTAAAAAGTTCAAGGACTAAATTACAAAAAGTTTAAAATTTTTTCTGAGTAACCTTGCTTA
* * * ** * *
305488 GATAAAAGACCCAAGTGCCACAGGAGGATTGTTTCATGCGCTTCTAAGGATATTTTAGGCCTTTT
66 GACAAAAGACCCAACTACCACAGGAGGACCGTTTCATGCACTTCTAAAGATATTTTAGGCCTTTT
* * *
305553 AACAGGTTAGGGATCTTTTTGTA
131 AACAGATTAAGGACCTTTTTGTA
* * *
305576 AATTTTAAAAAGTTCAAGGATTAAATTGCAAAAAGTTTAAAATTTTTTCTTTGGGTAACCTTGCT
1 AATTTTAAAAAGTTCAAGGACTAAATTACAAAAAGTTTAAAATTTTTTC--TGAGTAACCTTGCT
* * * * * * * *
305641 TAGCCAAAAGTCCCTACTACCATAGGTGGACCGTTTCATGCATTTCTAAATATATTTTAGGTCTT
64 TAGACAAAAGACCCAACTACCACAGGAGGACCGTTTCATGCACTTCTAAAGATATTTTAGGCCTT
*
305706 TTAA-TGTATTAAGGACCTTTTTGTA
129 TTAACAG-ATTAAGGACCTTTTTGTA
* * *
305731 AATTTTAGAAAGTTTAAAGACTAA
1 AATTTTAAAAAGTTCAAGGACTAA
305755 TTTGTAAATT
Statistics
Matches: 146, Mismatches: 30, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
153 46 0.32
154 1 0.01
155 99 0.68
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.38
Consensus pattern (153 bp):
AATTTTAAAAAGTTCAAGGACTAAATTACAAAAAGTTTAAAATTTTTTCTGAGTAACCTTGCTTA
GACAAAAGACCCAACTACCACAGGAGGACCGTTTCATGCACTTCTAAAGATATTTTAGGCCTTTT
AACAGATTAAGGACCTTTTTGTA
Found at i:311163 original size:23 final size:24
Alignment explanation
Indices: 311127--311190 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
311117 ATTCCTTTTG
* *
311127 AAATATCCTTAAGAGAGGCTCTAA
1 AAATATCCTCAAGAGAGGCTCCAA
*
311151 AAA-ATCCTCAAGAGAGGTTCCAA
1 AAATATCCTCAAGAGAGGCTCCAA
*
311174 AAATATCCTCGAGAGAG
1 AAATATCCTCAAGAGAG
311191 ACTTTGAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 20 0.57
24 15 0.43
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (24 bp):
AAATATCCTCAAGAGAGGCTCCAA
Found at i:311658 original size:16 final size:16
Alignment explanation
Indices: 311589--311660 Score: 67
Period size: 16 Copynumber: 4.2 Consensus size: 16
311579 TAAAATTTTC
311589 TTCTTTTTTTTTC-TT
1 TTCTTTTTTTTTCTTT
311604 TTCTTTTTTTTTTCCTTT
1 TTC-TTTTTTTTT-CTTT
*
311622 GTT-TTATTAGTTTTCCTTT
1 -TTCTT-TT--TTTTTCTTT
311641 TTCTTTTTTTTTCTTT
1 TTCTTTTTTTTTCTTT
311657 TTCT
1 TTCT
311661 AAGAGGTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
15 3 0.06
16 21 0.45
17 3 0.06
18 8 0.17
19 8 0.17
20 4 0.09
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.81
Consensus pattern (16 bp):
TTCTTTTTTTTTCTTT
Found at i:311718 original size:24 final size:24
Alignment explanation
Indices: 311691--311752 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
311681 TTGTAAAAAT
*
311691 CTTTGAAAATGTCCTTGA-AAGAGG
1 CTTTGAAAATGTCCTCGAGAA-AGG
311715 CTTTTG-AAATGTCCTCGAGAAAGG
1 C-TTTGAAAATGTCCTCGAGAAAGG
* *
311739 CTTTTAGAATGTCC
1 CTTTGAAAATGTCC
311753 CAATTGAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 3 0.09
24 23 0.72
25 6 0.19
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (24 bp):
CTTTGAAAATGTCCTCGAGAAAGG
Found at i:311994 original size:37 final size:37
Alignment explanation
Indices: 311907--311994 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 37
311897 TCTTTAAAAA
311907 ATCCTTAAGAAAGGTTTGAAAATATCATCGTTGAAAT
1 ATCCTTAAGAAAGGTTTGAAAATATCATCGTTGAAAT
* * ** * *
311944 ATCCTCAACAAAGGTTTGTTAATATCCTTGTTGAAAT
1 ATCCTTAAGAAAGGTTTGAAAATATCATCGTTGAAAT
*
311981 ATCCTTGAGAAAGG
1 ATCCTTAAGAAAGG
311995 CTCTAAAAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (37 bp):
ATCCTTAAGAAAGGTTTGAAAATATCATCGTTGAAAT
Found at i:312030 original size:38 final size:39
Alignment explanation
Indices: 311968--312041 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 39
311958 TTTGTTAATA
* *
311968 TCCTTGTTGAAATATCCTTGAGAAAGGCTCTAAAAACAT
1 TCCTTGTTGAAATATCCTTAAGAAAGACTCTAAAAACAT
** *
312007 TCCTT-TTGAAATATTTTTAAGAAAGACTTTAAAAA
1 TCCTTGTTGAAATATCCTTAAGAAAGACTCTAAAAA
312042 TATCTATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 25 0.83
39 5 0.17
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (39 bp):
TCCTTGTTGAAATATCCTTAAGAAAGACTCTAAAAACAT
Found at i:313854 original size:2 final size:2
Alignment explanation
Indices: 313847--313880 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
313837 TATGTTAGCA
313847 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
313881 GGTGAAGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:316232 original size:16 final size:16
Alignment explanation
Indices: 316211--316245 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
316201 TAGTGATCAT
316211 TTTGATAGAGATCGAC
1 TTTGATAGAGATCGAC
316227 TTTGATAGAGATCGAC
1 TTTGATAGAGATCGAC
316243 TTT
1 TTT
316246 CATTAGGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (16 bp):
TTTGATAGAGATCGAC
Found at i:317080 original size:165 final size:163
Alignment explanation
Indices: 316867--317422 Score: 472
Period size: 166 Copynumber: 3.4 Consensus size: 163
316857 TAAAAATTAT
* * * * *
316867 TATTATTAGTTAATTACAATTAAATCAGTTTTTCAAAATACTTTTA-TTTCATGAATTTTTCAAT
1 TATTATTATTTAATT-CAATTAAATCA-ATTTTAAAAATTCATTTATTTTCATGAATTTTTCAAT
* * * *
316931 TTTTTCTTGAAATCTTT-T-TATTTCTGAAATACGAAATTTTATT-TTTCGTAAAT-TTTTTCAG
64 TTTTTCTTAAAAT-TTTATGT-TTTC-GAAATACGAAATTTT-TTACTCCGTAAATGTTTTTCAA
* *
316992 GAGGA-TTTTCATTGGTTCAAAATTTTTAATATTCATCAAA
125 G-GGATTTTTC-TTGATTCAAAATTTTTAAAATTCATCAAA
* * *
317032 TATTATTATTTAACTCATATTAAATCAATTTTGAAAAATTCATTTATTTTCATGAGTTTTTCATT
1 TATTATTATTTAATTCA-ATTAAATCAATTTT-AAAAATTCATTTATTTTCATGAATTTTTCAAT
* * * *
317097 TTTTTGTTAAAATTTTCATGTTTTCGAAATACGGAGTTTTTTACTCCGTAAATGTTTTTGAAGGG
64 TTTTTCTTAAAATTTT-ATGTTTTCGAAATACGAAATTTTTTACTCCGTAAATGTTTTTCAAGGG
* *
317162 ATTTTTCTTGATTTATAATTTTTAAAATTCATCAAA
128 ATTTTTCTTGATTCAAAATTTTTAAAATTCATCAAA
*
317198 TATTATTATTTAATTCAGAGTAAATCAATTTTAAAAATTCATTTATTTTCAT-AAGTTTTTC-A-
1 TATTATTATTTAATTCA-ATTAAATCAATTTTAAAAATTCATTTATTTTCATGAA-TTTTTCAAT
* * * * * * * * **
317260 TTTTTCTTCTAAATTTCCT-TATTTTCAAAAAACTAAGTTTTCTACTCCATAAATGTTTTT-GGG
64 TTTTTCTT-AAAATTT--TATGTTTTCGAAATACGAAATTTTTTACTCCGTAAATGTTTTTCAAG
* *
317323 AGGATTTTT-TCGATTTAAAATTTTTAAAATTCATCAAA
126 -GGATTTTTCTTGATTCAAAATTTTTAAAATTCATCAAA
* * * * * * * *
317361 TATTGTTATTAAATTCCTATGAAATCAGTTTGGGAAAATTTAATTTATTTT-ATGAATTTTTC
1 TATTATTATTTAATT-CAATTAAATCAATTT--TAAAAATTCATTTATTTTCATGAATTTTTC
317423 TTTTTTTTTC
Statistics
Matches: 326, Mismatches: 47, Indels: 37
0.80 0.11 0.09
Matches are distributed among these distances:
163 58 0.18
164 64 0.20
165 80 0.25
166 106 0.33
167 17 0.05
168 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (163 bp):
TATTATTATTTAATTCAATTAAATCAATTTTAAAAATTCATTTATTTTCATGAATTTTTCAATTT
TTTCTTAAAATTTTATGTTTTCGAAATACGAAATTTTTTACTCCGTAAATGTTTTTCAAGGGATT
TTTCTTGATTCAAAATTTTTAAAATTCATCAAA
Found at i:317166 original size:166 final size:164
Alignment explanation
Indices: 316977--317430 Score: 533
Period size: 166 Copynumber: 2.8 Consensus size: 164
316967 TTTTATTTTT
* * * *
316977 CGTAAAT-TTTTTCAGGAGGATTTTCATTGGTTCAAAATTTTTAATATTCATCAAATATTATTAT
1 CGTAAATGTTTTTGAGGAGGATTTTC-TTGATTTAAAATTTTTAAAATTCATCAAATATTATTAT
* *
317041 TTAACTCATATTAAATCAATTTTGAAAAATTCATTTATTTTCATGAGTTTTTCATTTTTTTGTTA
65 TTAATTCATATTAAATCAATTTTGAAAAATTCATTTATTTTCATGAGTTTTTCATTTTTTT-CT-
* * * * * *
317106 AAATTTTCATGTTTTCGAAATACGGAGTTTTTTACTC
128 AAATTTCCATATTTTCAAAAAACGAAGTTTTCTACTC
* *
317143 CGTAAATGTTTTTGAAG-GGATTTTTCTTGATTTATAATTTTTAAAATTCATCAAATATTATTAT
1 CGTAAATGTTTTTGAGGAGGA-TTTTCTTGATTTAAAATTTTTAAAATTCATCAAATATTATTAT
* * *
317207 TTAATTCAGAGTAAATCAATTTT-AAAAATTCATTTATTTTCATAAGTTTTTCATTTTTCTTCTA
65 TTAATTCATATTAAATCAATTTTGAAAAATTCATTTATTTTCATGAGTTTTTCATTTTT-TTCTA
* *
317271 AATTTCCTTATTTTCAAAAAACTAAGTTTTCTACTC
129 AATTTCCATATTTTCAAAAAACGAAGTTTTCTACTC
* *
317307 CATAAATGTTTTTG-GGAGGATTTT-TTCGATTTAAAATTTTTAAAATTCATCAAATATTGTTAT
1 CGTAAATGTTTTTGAGGAGGATTTTCTT-GATTTAAAATTTTTAAAATTCATCAAATATTATTAT
* * * * * * * * *
317370 TAAATTCCTATGAAATCAGTTTGGGAAAATTTAATTTATTTT-ATGAATTTTTCTTTTTTTT
65 TTAATTCATATTAAATCAATTT-TGAAAAATTCATTTATTTTCATGAGTTTTTCATTTTTTT
317431 TCATATAACA
Statistics
Matches: 246, Mismatches: 35, Indels: 17
0.83 0.12 0.06
Matches are distributed among these distances:
162 2 0.01
163 57 0.23
164 59 0.24
165 50 0.20
166 66 0.27
167 12 0.05
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (164 bp):
CGTAAATGTTTTTGAGGAGGATTTTCTTGATTTAAAATTTTTAAAATTCATCAAATATTATTATT
TAATTCATATTAAATCAATTTTGAAAAATTCATTTATTTTCATGAGTTTTTCATTTTTTTCTAAA
TTTCCATATTTTCAAAAAACGAAGTTTTCTACTC
Found at i:321192 original size:20 final size:20
Alignment explanation
Indices: 321142--321193 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
321132 ATCGATACAA
321142 TTTGCATCGATACATTATTC
1 TTTGCATCGATACATTATTC
* ** *
321162 ATTATAGCGATACATTATTC
1 TTTGCATCGATACATTATTC
321182 TTTGCATCGATA
1 TTTGCATCGATA
321194 TAATCGGGAA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (20 bp):
TTTGCATCGATACATTATTC
Found at i:325160 original size:28 final size:28
Alignment explanation
Indices: 325092--325975 Score: 917
Period size: 28 Copynumber: 30.8 Consensus size: 28
325082 AAAAGAGTCA
* *
325092 CCACTGGCTTGTGGGCTTTGAAAAGAGTG
1 CCACTGACTTGTGGGCTTTG-AAAGGGTG
* **
325121 CTACTGTTTTGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* *
325149 CCACTAACTTGTGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* **
325177 CCACTAACTTGTGGGCTTTGAAAAAAGTG
1 CCACTGACTTGTGGGCTTTG-AAAGGGTG
* *
325206 CCACTAACTTGTGGGCTTTGAAAAGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
325234 CCACTGACTTGCGTGGGCTTTGAAAGGGTG
1 CCACTGACTT--GTGGGCTTTGAAAGGGTG
* *
325264 CCATTGACTGGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* ** *
325292 CCATTGACTCATGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * *
325320 CCACTAACTTGTGGGCTTTGAAAAAAGTTG
1 CCACTGACTTGTGGGCTTTG--AAAGGGTG
* * *
325350 CCACCGACTTGTGGGCTTTGAAAAGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * * * *
325378 CCACTGACTTATGAGCTTTGAAAAAAGTTA
1 CCACTGACTTGTGGGCTTTG--AAAGGGTG
* * *
325408 CCACCGACTCGTGTGGGCTTTGAAAAGATG
1 CCACTGACT--TGTGGGCTTTGAAAGGGTG
*
325438 CCACTGACTTGTGGGCTTTGAAAAGAGTG
1 CCACTGACTTGTGGGCTTTG-AAAGGGTG
*
325467 CCACTGACTTGTGGGCTTTGAAAAGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
**
325495 CCACTGACTTGTGGGCTTTGAAAGAATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
**
325523 CCACTGACTTGTGGGCTTTGAAAAAAGTG
1 CCACTGACTTGTGGGCTTTG-AAAGGGTG
*
325552 -CAGCTGACTTGTGGGCTTTGGAAGGGTG
1 CCA-CTGACTTGTGGGCTTTGAAAGGGTG
* *
325580 CCATTGACTTATGTGGGCTTTGAAAGAGTG
1 CCACTGAC-T-TGTGGGCTTTGAAAGGGTG
*
325610 CCACTGACTTGTGTGGGCTTTAAAAGGGTG
1 CCACTGAC-T-TGTGGGCTTTGAAAGGGTG
* * * * *
325640 CCAGTAACTTGTGGTCTTTAAAAGAGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
*
325668 CCACTGACTTGTGGGGTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
*
325696 CCATTGA-TTGGTGGGCTTTGAAAGGGTG
1 CCACTGACTT-GTGGGCTTTGAAAGGGTG
* * *
325724 CCACTAACTCGTGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
*
325752 CCACTGACTTGTGGGCTTTGAAAAGAGTTG
1 CCACTGACTTGTGGGCTTTG-AAAG-GGTG
* ** *
325782 CCACCGACTCATGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * *
325810 CCATTGACTTATGGGCTTTGAAAAGAGTTG
1 CCACTGACTTGTGGGCTTTG-AAAG-GGTG
* * *
325840 CCACCGACTCGTGTGGGCTTTGAAAAGATG
1 CCACTGACT--TGTGGGCTTTGAAAGGGTG
*
325870 CCACTGACTTGTGGGCTTTGAAATGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
*
325898 CAACTGACTTGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * *
325926 CCACTAACTTGTGGGCTTTGAACGAGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
*
325954 CCACTGACTTGTAGGCTTTGAA
1 CCACTGACTTGTGGGCTTTGAA
325976 GAGATGAACA
Statistics
Matches: 729, Mismatches: 103, Indels: 47
0.83 0.12 0.05
Matches are distributed among these distances:
27 2 0.00
28 431 0.59
29 107 0.15
30 167 0.23
31 3 0.00
32 19 0.03
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (28 bp):
CCACTGACTTGTGGGCTTTGAAAGGGTG
Found at i:325712 original size:346 final size:346
Alignment explanation
Indices: 325044--325965 Score: 1134
Period size: 346 Copynumber: 2.7 Consensus size: 346
325034 ACTTATGTGG
* * * * *
325044 GCTTTGAAAAGAGTTGCCACCGACTCGTCTAGGCTTTGAAAAGAGTCACCACTGGCTTGTGGGCT
1 GCTTTGAAAAAAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGT-GCCACTGACTTGTGGGCT
* ** * * *
325109 TTGAAAAGAGTGCTACTGTTTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGG
65 TTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGA
* * *
325174 ATGCCACTAACTTGTGGGCTTTGAAAAAAGTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACT
130 ATGCCACTGACTTGTGGGCTTTGAAAAAAGTG-CACTGACTTGTGGGCTTTGAAAGGGTGCCACT
* * * * * *
325239 GACTTGCGTGGGCTTTGAAAGGGTGCCATTGAC-TG-GTGGGCTTTGAAAGGGTGCCATTGACTC
194 GACTT-TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCAGTAACTC
* *
325302 ATGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAAGTTGCCACCGACTTGTGGGCT
258 ATGGGCTTTAAAAGGATGCCACTAACTTGTGGGCTTTG-AAAAAGGTGCCACCGACTTGTGGGCT
* *
325367 TTGAAAAGATGCCACTGACTTATGA
322 TTGAAAAGATGCCACTAACTCATGA
*
325392 GCTTTGAAAAAAGTTACCACCGACTCGTGTGGGCTTTGAAAAGA-TGCCACTGACTTGTGGGCTT
1 GCTTTGAAAAAAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT
325456 TGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAA
66 TGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAA
* *
325521 TGCCACTGACTTGTGGGCTTTGAAAAAAGTGCAGCTGACTTGTGGGCTTTGGAAGGGTGCCATTG
131 TGCCACTGACTTGTGGGCTTTGAAAAAAGTGCA-CTGACTTGTGGGCTTTGAAAGGGTGCCACTG
**
325586 ACTTATGTGGGCTTTGAAAGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCAGTAACTTG
195 ACTT-TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCAGTAACTCA
* * * * **
325651 TGGTCTTTAAAA-GAGTGCCACTGACTTGTGGGGTTTG-AAAGGGTGCCATTGA-TTGGTGGGCT
259 TGGGCTTTAAAAGGA-TGCCACTAACTTGTGGGCTTTGAAAAAGGTGCCACCGACTT-GTGGGCT
* * * *
325713 TTGAAAGGGTGCCACTAACTCGTGG
322 TTGAAAAGATGCCACTAACTCATGA
* * * * **
325738 GCTTTG--AAAGGATGCCACTGACT--TGTGGGCTTTGAAAAGAGTTGCCACCGACTCATGGGCT
1 GCTTTGAAAAAAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCT
* * * *
325799 TTGAAAGGA-TGCCATTGACTTATGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGA
65 TTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-G-TGCCACTGACT--TGTGGGCTTTGA
**
325863 AA-AGATGCCACTGACTTGTGGGCTTTG-AAATGGTGCAACTGACTTGTGGGCTTTGAAAGGGTG
126 AAGA-ATGCCACTGACTTGTGGGCTTTGAAAAAAGTGC-ACTGACTTGTGGGCTTTGAAAGGGTG
* *
325926 CCACTAAC-TTGTGGGCTTTGAACGAGTGCCACTGACTTGT
189 CCACTGACTTTGTGGGCTTTGAAAGAGTGCCACTGACTTGT
325966 AGGCTTTGAA
Statistics
Matches: 504, Mismatches: 57, Indels: 30
0.85 0.10 0.05
Matches are distributed among these distances:
342 17 0.03
343 25 0.05
344 68 0.13
345 15 0.03
346 242 0.48
347 43 0.09
348 94 0.19
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (346 bp):
GCTTTGAAAAAAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT
TGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAA
TGCCACTGACTTGTGGGCTTTGAAAAAAGTGCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA
CTTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCAGTAACTCATG
GGCTTTAAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAGGTGCCACCGACTTGTGGGCTTTGA
AAAGATGCCACTAACTCATGA
Found at i:325765 original size:432 final size:429
Alignment explanation
Indices: 325039--325975 Score: 1371
Period size: 432 Copynumber: 2.2 Consensus size: 429
325029 CATTAACTTA
* * * * *
325039 TGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTCTAGGCTTTGAAAAGAGTCACCACTGGCTTGT
1 TGTGGGCTTTGAAAAG-G-TGCCACTGACT--TGTGGGCTTTG-AAAGAGT-GCCACTGACTTGT
* **
325104 GGGCTTTGAAAAGAGTGCTACTGTTTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTG
60 GGGCTTTGAAAAAAGTGCTACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTG
325169 AAAGGATGCCACTAACTTGTGGGCTTTGAAAAAAGTGCCACTAACTTGTGGGCTTTGAAAAGGTG
125 AAAGGATGCCACTAACTTGTGGGCTTTGAAAAAAGTGCCACTAACTTGTGGGCTTTGAAAAGGTG
* *
325234 CCACTGACTTGCGTGGGCTTTGAAAGGGTGCCATTGACTGGTGGGCTTTGAAAGGGTGCCATTGA
190 CCACTGACTT-CGTGGGCTTTGAAAGGGTGCCATTGACTGGTGGGCTTTGAAAGGGTGCCACTAA
**
325299 CTCATGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAAGTTGCCACCGACTTGTGG
254 CTCATGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAAGTTGCCACCGACTCATGG
325364 GCTTTGAAAAGATGCCACTGACTTATGAGCTTTGAAAAAAGTTACCACCGACTCGTGTGGGCTTT
319 GCTTTGAAAAGATGCCACTGACTTATGAGCTTTGAAAAAAGTTACCACCGACTCGTGTGGGCTTT
*
325429 GAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
384 GAAAAGATGCCACTGACTTGTGGGCTTTGAAAAG-GTGCAACTGACT
*
325476 TGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAATGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTT
* * *
325541 TGAAAAAAGTGC-AGCTGACTTGTGGGCTTTGGAAGGGTGCCATTGACTTATGTGGGCTTTGAAA
66 TGAAAAAAGTGCTA-CTGACTTGTGGGCTTTGAAAGGGTGCCACTAAC-T-TGTGGGCTTTGAAA
* ** * *
325605 -GAGTGCCACTGACTTGTGTGGGCTTT-AAAAGGGTGCCAGTAACTTGTGGTCTTT-AAAAGAGT
128 GGA-TGCCACTAAC-T-TGTGGGCTTTGAAAAAAGTGCCACTAACTTGTGGGCTTTGAAAAG-GT
* *
325667 GCCACTGACTT-GTGGGGTTTGAAAGGGTGCCATTGATTGGTGGGCTTTGAAAGGGTGCCACTAA
189 GCCACTGACTTCGTGGGCTTTGAAAGGGTGCCATTGACTGGTGGGCTTTGAAAGGGTGCCACTAA
* * *
325731 CTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCATGG
254 CTCATGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAAGTTGCCACCGACTCATGG
* * * * *
325796 GCTTTGAAAGGATGCCATTGACTTATGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTT
319 GCTTTGAAAAGATGCCACTGACTTATGAGCTTTGAAAAAAGTTACCACCGACTCGTGTGGGCTTT
*
325861 GAAAAGATGCCACTGACTTGTGGGCTTTGAAATGGTGCAACTGACT
384 GAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCAACTGACT
* * * *
325907 TGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAACGAGTGCCACTGACTTGTAGGCTT
1 TGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTT
325972 TGAA
66 TGAA
325976 GAGATGAACA
Statistics
Matches: 455, Mismatches: 38, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
430 1 0.00
431 131 0.29
432 211 0.46
433 37 0.08
434 38 0.08
435 20 0.04
436 1 0.00
437 16 0.04
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (429 bp):
TGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTT
TGAAAAAAGTGCTACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGA
TGCCACTAACTTGTGGGCTTTGAAAAAAGTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTG
ACTTCGTGGGCTTTGAAAGGGTGCCATTGACTGGTGGGCTTTGAAAGGGTGCCACTAACTCATGG
GCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAAGTTGCCACCGACTCATGGGCTTTGA
AAAGATGCCACTGACTTATGAGCTTTGAAAAAAGTTACCACCGACTCGTGTGGGCTTTGAAAAGA
TGCCACTGACTTGTGGGCTTTGAAAAGGTGCAACTGACT
Found at i:327218 original size:22 final size:23
Alignment explanation
Indices: 327193--327244 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
327183 GCCTATTTTT
327193 GTTTTTTGTTATT-TTTTTCTTG
1 GTTTTTTGTTATTATTTTTCTTG
* *
327215 GTTTTTTGTTTTTATTTTTTTTG
1 GTTTTTTGTTATTATTTTTCTTG
327238 GTTTTTT
1 GTTTTTT
327245 CTGTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.04, C:0.02, G:0.13, T:0.81
Consensus pattern (23 bp):
GTTTTTTGTTATTATTTTTCTTG
Found at i:327220 original size:23 final size:21
Alignment explanation
Indices: 327193--327254 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 21
327183 GCCTATTTTT
327193 GTTTTTTGTTATTTTTTTCTTG
1 GTTTTTTGTT-TTTTTTTCTTG
*
327215 GTTTTTTGTTTTTATTTTTTTTG
1 GTTTTTTG-TTTT-TTTTTCTTG
* *
327238 GTTTTTTCTGTTTTTTT
1 GTTTTTTGTTTTTTTTT
327255 GTTTTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 5 0.14
22 13 0.37
23 17 0.49
ACGTcount: A:0.03, C:0.03, G:0.13, T:0.81
Consensus pattern (21 bp):
GTTTTTTGTTTTTTTTTCTTG
Found at i:327242 original size:8 final size:7
Alignment explanation
Indices: 327188--327261 Score: 60
Period size: 7 Copynumber: 9.7 Consensus size: 7
327178 TTTGGGCCTA
327188 TTTTTGT
1 TTTTTGT
327195 TTTTTGT
1 TTTTTGT
327202 TATTTT-T
1 T-TTTTGT
*
327209 TTCTTGGT
1 TT-TTTGT
327217 TTTTTGT
1 TTTTTGT
*
327224 TTTTATTT
1 TTTT-TGT
327232 TTTTTGGTT
1 TTTTT-G-T
327241 TTTTCTGTT
1 TTTT-TG-T
327250 TTTTTGT
1 TTTTTGT
327257 TTTTT
1 TTTTT
327262 TTAGGTATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
6 1 0.02
7 27 0.48
8 15 0.27
9 12 0.21
10 1 0.02
ACGTcount: A:0.03, C:0.03, G:0.12, T:0.82
Consensus pattern (7 bp):
TTTTTGT
Found at i:327261 original size:17 final size:17
Alignment explanation
Indices: 327205--327261 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
327195 TTTTTGTTAT
*
327205 TTTTTTCTTGGTTTTTTG
1 TTTTTTC-TGTTTTTTTG
*
327223 TTTTTAT-T-TTTTTTGG
1 TTTTT-TCTGTTTTTTTG
327239 TTTTTTCTGTTTTTTTG
1 TTTTTTCTGTTTTTTTG
327256 TTTTTT
1 TTTTTT
327262 TTAGGTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 1 0.03
16 12 0.36
17 14 0.42
18 5 0.15
19 1 0.03
ACGTcount: A:0.02, C:0.04, G:0.12, T:0.82
Consensus pattern (17 bp):
TTTTTTCTGTTTTTTTG
Found at i:327262 original size:8 final size:8
Alignment explanation
Indices: 327188--327262 Score: 68
Period size: 8 Copynumber: 9.6 Consensus size: 8
327178 TTTGGGCCTA
327188 TTTTTG-T
1 TTTTTGTT
327195 TTTTTG-T
1 TTTTTGTT
*
327202 TATTT-TT
1 TTTTTGTT
* *
327209 TTCTTGGT
1 TTTTTGTT
327217 TTTTTGTT
1 TTTTTGTT
327225 TTTATT-TT
1 TTT-TTGTT
*
327233 TTTTGGTT
1 TTTTTGTT
327241 TTTTCTGTT
1 TTTT-TGTT
327250 TTTTTGTT
1 TTTTTGTT
327258 TTTTT
1 TTTTT
327263 TAGGTATAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
7 16 0.29
8 30 0.55
9 9 0.16
ACGTcount: A:0.03, C:0.03, G:0.12, T:0.83
Consensus pattern (8 bp):
TTTTTGTT
Found at i:329723 original size:13 final size:13
Alignment explanation
Indices: 329682--329735 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
329672 TCGTTACAAG
329682 CAATGTATCGATA
1 CAATGTATCGATA
*
329695 CAAT-T-TC-CT-
1 CAATGTATCGATA
329704 C-ATGTATCGATA
1 CAATGTATCGATA
329716 CAATGTATCGATA
1 CAATGTATCGATA
*
329729 CATTGTA
1 CAATGTA
329736 CCATGTATCG
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 3 0.09
11 3 0.09
12 2 0.06
13 21 0.64
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:329723 original size:34 final size:33
Alignment explanation
Indices: 329682--329749 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
329672 TCGTTACAAG
*
329682 CAATGTATCGATACAATT-TCCTCATGTATCGATA
1 CAATGTATCGATAC-ATTGTAC-CATGTATCGATA
329716 CAATGTATCGATACATTGTACCATGTATCGATA
1 CAATGTATCGATACATTGTACCATGTATCGATA
329749 C
1 C
329750 TAATAGTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 16 0.50
34 16 0.50
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (33 bp):
CAATGTATCGATACATTGTACCATGTATCGATA
Done.