Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009185.1 Hibiscus syriacus cultivar Beakdansim tig00112758_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 682201
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:4990 original size:20 final size:20
Alignment explanation
Indices: 4965--5008 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4955 ATCATCAGAC
4965 AATGCAACTAAATGCTTCTA
1 AATGCAACTAAATGCTTCTA
* * *
4985 AATGCATCTATATGGTTCTA
1 AATGCAACTAAATGCTTCTA
5005 AATG
1 AATG
5009 GGTCTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (20 bp):
AATGCAACTAAATGCTTCTA
Found at i:6665 original size:14 final size:14
Alignment explanation
Indices: 6646--6688 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
6636 ATAGAGTATA
*
6646 AATTTTAATTTAAT
1 AATTTTAATTAAAT
*
6660 AATTTTCATTAAAT
1 AATTTTAATTAAAT
6674 -A-TTTAATTAAAT
1 AATTTTAATTAAAT
6686 AAT
1 AAT
6689 AAAATAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 10 0.42
13 2 0.08
14 12 0.50
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTTTAATTAAAT
Found at i:7670 original size:29 final size:29
Alignment explanation
Indices: 7637--7712 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
7627 TCCCCAAGCA
* *
7637 TAGGTCGTCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
7666 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
*
7695 TAGGTCGCGATGCACTCC
1 TAGGTCGCCATGCACTCC
7713 CTCATGCTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.13, C:0.34, G:0.30, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:9704 original size:27 final size:27
Alignment explanation
Indices: 9674--9734 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
9664 TCCTAAATGT
*
9674 TATTGTTTCTAGCTGTATTGTGCTTGC
1 TATTGTTTCTAGCTGTATTGTGCTTAC
* *
9701 TATTGTTTCTAGTTGTATTGTGCTTAT
1 TATTGTTTCTAGCTGTATTGTGCTTAC
9728 TATTGTT
1 TATTGTT
9735 CTTACTTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.13, C:0.10, G:0.20, T:0.57
Consensus pattern (27 bp):
TATTGTTTCTAGCTGTATTGTGCTTAC
Found at i:9743 original size:27 final size:27
Alignment explanation
Indices: 9674--9744 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 27
9664 TCCTAAATGT
*
9674 TATTGTTTCTAGC-TGTATTGTGCTTGC
1 TATTGTTTCTA-CTTGTATTGTGCTTAC
* *
9701 TATTGTTTCTAGTTGTATTGTGCTTAT
1 TATTGTTTCTACTTGTATTGTGCTTAC
9728 TATTG-TTCTTACTTGTA
1 TATTGTTTC-TACTTGTA
9745 GTTTTATTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 3 0.08
27 35 0.92
ACGTcount: A:0.14, C:0.11, G:0.18, T:0.56
Consensus pattern (27 bp):
TATTGTTTCTACTTGTATTGTGCTTAC
Found at i:11783 original size:17 final size:15
Alignment explanation
Indices: 11745--11786 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
11735 TTTCAACATA
11745 AATTAAAAATAAGAT
1 AATTAAAAATAAGAT
11760 -ATCTAAAACATATAGAT
1 AAT-TAAAA-ATA-AGAT
11777 AATTAAAAAT
1 AATTAAAAAT
11787 TTTAAGAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.09
15 5 0.22
16 5 0.22
17 9 0.39
18 2 0.09
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (15 bp):
AATTAAAAATAAGAT
Found at i:13469 original size:4 final size:4
Alignment explanation
Indices: 13460--13528 Score: 129
Period size: 4 Copynumber: 17.2 Consensus size: 4
13450 TAACACATAC
*
13460 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
13508 ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT A
13529 AAGATGCACT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 63 1.00
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:14036 original size:529 final size:528
Alignment explanation
Indices: 13000--14057 Score: 2039
Period size: 526 Copynumber: 2.0 Consensus size: 528
12990 TCGTTTGCAG
13000 AAGATGCACTCGTAGGAGCGTTTGGGGGTCACGGCGTCGCACTTGACTCGATCGACCGGATCGTT
1 AAGATGCACTCGTAGGAGCGTTTGGGGGTCACGGCGTCGCACTTGACTCGATCGACCGGATCGTT
13065 TTCTTCGCTCAAAGAATCGGAGCTCGGTTGCTTCATGGCTGATTCCATCCTCAAAGAAAAAAAGA
66 TTCTTCGCTCAAAGAATCGGAGCTCGGTTGCTTCATGGCTGATTCCATCCTCAAAGAAAAAAAGA
13130 AAGTGGTCAAGGGTTAGAGAGAGAAGAAGAAGGAAACGAGGAGACAATTGGAAGACATAGGCTTT
131 AAGTGGTCAAGGGTTA-AGAGAGAAGAAGAAGGAAACGAGGAGACAATTGGAAGACATAGGCTTT
13195 GTCATTGCATTTGCTTTGTATTTGTTGACAAGTGAAGACTAGGTTTTGGCGTTTGTGTTAGGATT
195 GTCATTGCATTTGCTTTGTATTTGTTGACAAGTGAAGACTAGGTTTTGGCGTTTGTGTTAGGATT
13260 TTTCCCTTGAGTCGGCTTTATGATGGATCCATTTTCTCTTATTTTACTTCGTAATATAAAATAGG
260 TTTCCCTTGAGTCGGCTTTATGATGGATCCATTTTCTCTTATTTTACTTCGTAATATAAAATAGG
13325 ATAAACTGCACATTTAGTATTCTTACTATCACTTTTATTCCATTTTGATACCCAATTTATTTTCT
325 ATAAACTGCACATTTAGTATTCTTACTATCACTTTTATTCCATTTTGATACCCAATTTATTTTCT
13390 TTTCAAAATCATACCTAACGTTAAGTTAATGGAGGAAGGTAATGGGCAAGTGTAAAAAAATAACA
390 TTTCAAAATCATACCTAACGTTAAGTTAATGGAGGAAGGTAATGGGCAAGTGTAAAAAAATAACA
*
13455 CATACACATACATACATACATACATACATACATACATGCATACATACATACATACATACATACAT
455 CATACACATACATACATACATACATACATACATACATACATACATACATACATACATACATACAT
13520 ACATACATA
520 ACATACATA
13529 AAGATGCACTCGTAGGAGCGTTTGGGGGTCACGGCGTCGCACTTGACTCGATCGACCGGATCGTT
1 AAGATGCACTCGTAGGAGCGTTTGGGGGTCACGGCGTCGCACTTGACTCGATCGACCGGATCGTT
13594 TTCTTCGCTCAAAGAATCGGAGCTCGGTTGCTTCATGGCTGATTCCATCCTCAAAGAAAAAAAGA
66 TTCTTCGCTCAAAGAATCGGAGCTCGGTTGCTTCATGGCTGATTCCATCCTCAAAGAAAAAAAGA
13659 AAGTGGTCAA-GGTT-AGAGAGAAGAAGAAGGAAACGAGGAGACAATTGGAAGACATAGGCTTTG
131 AAGTGGTCAAGGGTTAAGAGAGAAGAAGAAGGAAACGAGGAGACAATTGGAAGACATAGGCTTTG
13722 TCATTGCATTTGCTTTGTATTTGTTGACAAGTGAAGACTAGGTTTTGGCGTTTGTGTTAGGATTT
196 TCATTGCATTTGCTTTGTATTTGTTGACAAGTGAAGACTAGGTTTTGGCGTTTGTGTTAGGATTT
13787 TTCCCTTGAGTCGGCTTTATGATGGATCCATTTTCTCTTATTTTACTTCGTAATATAAAATAGGA
261 TTCCCTTGAGTCGGCTTTATGATGGATCCATTTTCTCTTATTTTACTTCGTAATATAAAATAGGA
13852 TAAACTGCACATTTAGTATTCTTACTATCACTTTTATTCCATTTTGATACCCAATTTATTTTCTT
326 TAAACTGCACATTTAGTATTCTTACTATCACTTTTATTCCATTTTGATACCCAATTTATTTTCTT
13917 TTCAAAATCATACCTAACGTTAAGTTAATGGAGGAAGGTAATGGGCAAGTGTAAAAAAAATAACA
391 TTCAAAATCATACCTAACGTTAAGTTAATGGAGGAAGGTAATGGGCAAGTGT-AAAAAAATAACA
* *
13982 CATACATACATACATACATACATACATACATACATGCATACATGCATACATACATACATACATAC
455 CATAC--ACATACATACATACATACATACATACATACATACATACATACATACATACATACATAC
14047 ATACATACATA
518 ATACATACATA
14058 CATACATACA
Statistics
Matches: 523, Mismatches: 3, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
526 296 0.57
527 17 0.03
528 4 0.01
529 206 0.39
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (528 bp):
AAGATGCACTCGTAGGAGCGTTTGGGGGTCACGGCGTCGCACTTGACTCGATCGACCGGATCGTT
TTCTTCGCTCAAAGAATCGGAGCTCGGTTGCTTCATGGCTGATTCCATCCTCAAAGAAAAAAAGA
AAGTGGTCAAGGGTTAAGAGAGAAGAAGAAGGAAACGAGGAGACAATTGGAAGACATAGGCTTTG
TCATTGCATTTGCTTTGTATTTGTTGACAAGTGAAGACTAGGTTTTGGCGTTTGTGTTAGGATTT
TTCCCTTGAGTCGGCTTTATGATGGATCCATTTTCTCTTATTTTACTTCGTAATATAAAATAGGA
TAAACTGCACATTTAGTATTCTTACTATCACTTTTATTCCATTTTGATACCCAATTTATTTTCTT
TTCAAAATCATACCTAACGTTAAGTTAATGGAGGAAGGTAATGGGCAAGTGTAAAAAAATAACAC
ATACACATACATACATACATACATACATACATACATACATACATACATACATACATACATACATA
CATACATA
Found at i:14948 original size:8 final size:8
Alignment explanation
Indices: 13981--14947 Score: 1649
Period size: 8 Copynumber: 121.5 Consensus size: 8
13971 AAAAAATAAC
*
13981 ACATACAT
1 ACATGCAT
*
13989 ACATACAT
1 ACATGCAT
*
13997 ACATACAT
1 ACATGCAT
*
14005 ACATACAT
1 ACATGCAT
14013 ACATGCAT
1 ACATGCAT
14021 ACATGCAT
1 ACATGCAT
14029 --A--CAT
1 ACATGCAT
*
14033 ACATACAT
1 ACATGCAT
*
14041 ACATACAT
1 ACATGCAT
*
14049 ACATACAT
1 ACATGCAT
*
14057 ACATACAT
1 ACATGCAT
*
14065 ACATACAT
1 ACATGCAT
*
14073 ACATACAT
1 ACATGCAT
*
14081 ACATACAT
1 ACATGCAT
*
14089 ACATACAT
1 ACATGCAT
*
14097 ACATACAT
1 ACATGCAT
*
14105 ACATACAT
1 ACATGCAT
*
14113 ACATACAT
1 ACATGCAT
*
14121 ACATACAT
1 ACATGCAT
14129 ACATGCAT
1 ACATGCAT
14137 ACATGCAT
1 ACATGCAT
14145 ACATGCAT
1 ACATGCAT
14153 ACATGCAT
1 ACATGCAT
*
14161 ACATACAT
1 ACATGCAT
*
14169 ACATACAT
1 ACATGCAT
14177 ACATGCAT
1 ACATGCAT
14185 ACATGCAT
1 ACATGCAT
14193 ACATGCAT
1 ACATGCAT
14201 ACATGCAT
1 ACATGCAT
*
14209 ACATACAT
1 ACATGCAT
14217 ACATGCAT
1 ACATGCAT
14225 ACAT--AT
1 ACATGCAT
*
14231 GCATGCAT
1 ACATGCAT
**
14239 GTATGCAT
1 ACATGCAT
**
14247 GTATGCATT
1 ACATGCA-T
14256 ACATGCAT
1 ACATGCAT
14264 ACATGCAT
1 ACATGCAT
14272 ACATGCAT
1 ACATGCAT
14280 ACATGCAT
1 ACATGCAT
14288 ACATGCAT
1 ACATGCAT
14296 ACATGCAT
1 ACATGCAT
14304 ACATGCAT
1 ACATGCAT
14312 ACATGCAT
1 ACATGCAT
14320 ACATGCAT
1 ACATGCAT
14328 ACATGCAT
1 ACATGCAT
14336 ACATGCAT
1 ACATGCAT
14344 ACATGCAT
1 ACATGCAT
14352 ACATGCAT
1 ACATGCAT
14360 ACATGCAT
1 ACATGCAT
14368 ACATGCAT
1 ACATGCAT
14376 ACATGCAT
1 ACATGCAT
14384 ACATGCAT
1 ACATGCAT
14392 ACATGCAT
1 ACATGCAT
14400 ACATGCAT
1 ACATGCAT
14408 ACATGCAT
1 ACATGCAT
14416 ACATGCAT
1 ACATGCAT
14424 ACATGCAT
1 ACATGCAT
14432 ACATGCAT
1 ACATGCAT
14440 ACATGCAT
1 ACATGCAT
14448 ACATGCAT
1 ACATGCAT
14456 ACATGCAT
1 ACATGCAT
14464 ACATGCAT
1 ACATGCAT
14472 ACATGCAT
1 ACATGCAT
14480 ACATGCAT
1 ACATGCAT
14488 ACATGCAT
1 ACATGCAT
14496 ACATGCAT
1 ACATGCAT
14504 ACATGCAT
1 ACATGCAT
14512 ACATGCAT
1 ACATGCAT
14520 ACATGCAT
1 ACATGCAT
14528 ACATGCAT
1 ACATGCAT
14536 ACATGCAT
1 ACATGCAT
14544 ACATGCAT
1 ACATGCAT
14552 ACATGCAT
1 ACATGCAT
14560 ACATGCAT
1 ACATGCAT
14568 ACATGCAT
1 ACATGCAT
14576 ACATGCAT
1 ACATGCAT
14584 ACATGCAT
1 ACATGCAT
14592 ACATGCAT
1 ACATGCAT
14600 ACATGCAT
1 ACATGCAT
14608 ACATGCAT
1 ACATGCAT
14616 ACATGCAT
1 ACATGCAT
14624 ACATGCAT
1 ACATGCAT
14632 ACATGCAT
1 ACATGCAT
14640 ACATGCAT
1 ACATGCAT
14648 ACATGCAT
1 ACATGCAT
14656 ACATGCAT
1 ACATGCAT
14664 ACATGCAT
1 ACATGCAT
14672 ACATGCAT
1 ACATGCAT
14680 ACATGCAT
1 ACATGCAT
14688 ACATGCAT
1 ACATGCAT
14696 ACATGCAT
1 ACATGCAT
14704 ACATGCAT
1 ACATGCAT
14712 ACATGCAT
1 ACATGCAT
14720 ACATGCAT
1 ACATGCAT
14728 ACATGCAT
1 ACATGCAT
14736 ACATGCAT
1 ACATGCAT
14744 ACATGCAT
1 ACATGCAT
14752 ACATGCAT
1 ACATGCAT
14760 ACATGCAT
1 ACATGCAT
14768 ACATGCAT
1 ACATGCAT
14776 ACATGCAT
1 ACATGCAT
14784 ACATGCAT
1 ACATGCAT
14792 ACATGCAT
1 ACATGCAT
14800 ACATGCAT
1 ACATGCAT
14808 ACATGCAT
1 ACATGCAT
14816 ACATGCAT
1 ACATGCAT
14824 ACATGCAT
1 ACATGCAT
14832 ACATGCAT
1 ACATGCAT
14840 ACATGCAT
1 ACATGCAT
14848 ACATGCAT
1 ACATGCAT
14856 ACATGCAT
1 ACATGCAT
14864 ACATGCAT
1 ACATGCAT
14872 ACATGCAT
1 ACATGCAT
14880 ACATGCAT
1 ACATGCAT
14888 ACATGCAT
1 ACATGCAT
14896 ACATGCAT
1 ACATGCAT
14904 ACATGCAT
1 ACATGCAT
14912 ACATGCAT
1 ACATGCAT
14920 ACATGCAT
1 ACATGCAT
*
14928 ACATACAT
1 ACATGCAT
*
14936 ACATACAT
1 ACATGCAT
14944 ACAT
1 ACAT
14948 AGATACCAAA
Statistics
Matches: 941, Mismatches: 11, Indels: 14
0.97 0.01 0.01
Matches are distributed among these distances:
4 3 0.00
6 7 0.01
8 925 0.98
9 6 0.01
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (8 bp):
ACATGCAT
Found at i:15590 original size:4 final size:4
Alignment explanation
Indices: 15583--16431 Score: 1647
Period size: 4 Copynumber: 213.8 Consensus size: 4
15573 TGTAAAAAAA
15583 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
15631 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
15679 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
15727 ATAC ATAC ATAC ATAC ATAC ATAC ATAC -TAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
15774 -TAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
15821 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
15869 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT-C ATAC ATAT ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
15916 ATAC ATAC ATAC ATAC AT-- ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
15962 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16010 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16058 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16106 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16154 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16202 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16250 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16298 ATAC -TAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16345 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16393 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
16432 TAAGTTTAGA
Statistics
Matches: 837, Mismatches: 2, Indels: 12
0.98 0.00 0.01
Matches are distributed among these distances:
2 2 0.00
3 12 0.01
4 823 0.98
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:18548 original size:13 final size:13
Alignment explanation
Indices: 18530--18554 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18520 AAATAAAAAT
18530 AAATAACAATTTA
1 AAATAACAATTTA
18543 AAATAACAATTT
1 AAATAACAATTT
18555 TTATTATTTA
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATAACAATTTA
Found at i:20916 original size:21 final size:21
Alignment explanation
Indices: 20878--20928 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
20868 ACATAGTATT
20878 AAATAA-AAATAATAATAGAA
1 AAATAAGAAATAATAATAGAA
20898 AAATAAGAAAT-ATATATAGAA
1 AAATAAGAAATAATA-ATAGAA
*
20919 ACATATAGAA
1 AAATA-AGAA
20929 CAAAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 9 0.33
21 14 0.52
22 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.22
Consensus pattern (21 bp):
AAATAAGAAATAATAATAGAA
Found at i:21078 original size:2 final size:2
Alignment explanation
Indices: 21071--21115 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
21061 GTATACTTAA
21071 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21113 AT A
1 AT A
21116 CTAATATTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35059 original size:28 final size:28
Alignment explanation
Indices: 34988--35064 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
34978 TTGTATTGCG
** * *
34988 TCGTCGAGCCGGTGCTTGAAATATTATG
1 TCGTCGAGCCAATGCTTGAAACATTATA
* * *
35016 TCTTTGAGCCAGTGCTTGAAACATTATA
1 TCGTCGAGCCAATGCTTGAAACATTATA
*
35044 TCGTCGAGTCAATGCTTGAAA
1 TCGTCGAGCCAATGCTTGAAA
35065 ACAACAGTGG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (28 bp):
TCGTCGAGCCAATGCTTGAAACATTATA
Found at i:36677 original size:31 final size:32
Alignment explanation
Indices: 36635--36705 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
36625 ATTCAAAGAG
*
36635 CATTTTATTATAATTTGAT-AAGTTTAATGAC
1 CATTTTATTATAATTTGATAAAATTTAATGAC
* *
36666 CATTTTGTTATATTTTGATAAAATTTAATGAC
1 CATTTTATTATAATTTGATAAAATTTAATGAC
*
36698 AATTTTAT
1 CATTTTAT
36706 AATTTTTGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 17 0.50
32 17 0.50
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (32 bp):
CATTTTATTATAATTTGATAAAATTTAATGAC
Found at i:36703 original size:32 final size:31
Alignment explanation
Indices: 36636--36705 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 31
36626 TTCAAAGAGC
* *
36636 ATTTTATTATAATTTGATAAGTTTAATGACC
1 ATTTTATTATAATTTGATAAATTTAATGACA
* *
36667 ATTTTGTTATATTTTGATAAAATTTAATGACA
1 ATTTTATTATAATTTGAT-AAATTTAATGACA
36699 ATTTTAT
1 ATTTTAT
36706 AATTTTTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 16 0.48
32 17 0.52
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (31 bp):
ATTTTATTATAATTTGATAAATTTAATGACA
Found at i:36713 original size:31 final size:31
Alignment explanation
Indices: 36636--36714 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
36626 TTCAAAGAGC
* * * *
36636 ATTTTATTATAATTTGATAAGTTTAATGACC
1 ATTTTATAATATTTTGATAAATTTAATGACA
* *
36667 ATTTTGTTATATTTTGATAAAATTTAATGACA
1 ATTTTATAATATTTTGAT-AAATTTAATGACA
36699 ATTTTATAAT-TTTTGA
1 ATTTTATAATATTTTGA
36715 AACTTTAGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 22 0.54
32 19 0.46
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (31 bp):
ATTTTATAATATTTTGATAAATTTAATGACA
Found at i:59616 original size:12 final size:12
Alignment explanation
Indices: 59599--59624 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
59589 ACACCGTCAA
59599 CCAAATCCACCT
1 CCAAATCCACCT
59611 CCAAATCCACCT
1 CCAAATCCACCT
59623 CC
1 CC
59625 TATTCCTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (12 bp):
CCAAATCCACCT
Found at i:60913 original size:17 final size:17
Alignment explanation
Indices: 60880--60913 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
60870 TTGAATATTT
* *
60880 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
60897 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
60914 GATTTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:65384 original size:15 final size:16
Alignment explanation
Indices: 65357--65386 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
65347 GTTATAAAAT
65357 AAAATTTTATTAATAC
1 AAAATTTTATTAATAC
65373 AAAATTTT-TTAATA
1 AAAATTTTATTAATA
65387 ATTAGTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAATTTTATTAATAC
Found at i:74594 original size:19 final size:19
Alignment explanation
Indices: 74570--74608 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
74560 TCGAATGCAT
74570 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
74589 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
74608 T
1 T
74609 GAATTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:74625 original size:65 final size:63
Alignment explanation
Indices: 74507--74715 Score: 215
Period size: 65 Copynumber: 3.2 Consensus size: 63
74497 TATTCAAAGG
** *
74507 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAATTAATT-GAACATCGAATGCAT
1 CATGCACCGATGCACTC--TCCATGCATCGATGCATC--TGAATTTTTTCAAACATCGAATGCAT
*
74570 TC
62 TT
74572 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATTTTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCA-TCTGAATTTTTTC-AAACATCGAATGCATTT
* * *** * ** *
74637 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTCTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAAT-TTTTTCAAACATCGAATGCATTT
*
74701 CATGCATCGATGCAC
1 CATGCACCGATGCAC
74716 ACTTGGTGCA
Statistics
Matches: 125, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
63 8 0.06
64 51 0.41
65 64 0.51
66 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATTTTTTCAAACATCGAATGCATTT
Found at i:74731 original size:64 final size:64
Alignment explanation
Indices: 74507--74736 Score: 216
Period size: 64 Copynumber: 3.6 Consensus size: 64
74497 TATTCAAAGG
* * * *
74507 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAATTAAT-T--GAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATT-TTCTCAAAACATCGAATGCA
*
74569 TTC
62 TTT
* * * *
74572 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATTTTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATTTTCTCAAAACATCGAATGCATTT
* ** **
74637 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTCTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAAT-TTTCTCAAAACATCGAATGCATTT
*** *
74701 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
74737 AGTGTTCCAA
Statistics
Matches: 138, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
62 1 0.01
63 6 0.04
64 67 0.49
65 64 0.46
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATTTTCTCAAAACATCGAATGCATTT
Found at i:75814 original size:14 final size:14
Alignment explanation
Indices: 75795--75822 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
75785 TGAATACGGA
75795 AGAGTTTCATCGTG
1 AGAGTTTCATCGTG
75809 AGAGTTTCATCGTG
1 AGAGTTTCATCGTG
75823 TACAACCGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (14 bp):
AGAGTTTCATCGTG
Found at i:80489 original size:20 final size:21
Alignment explanation
Indices: 80460--80515 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
80450 TTTGTGCTTC
*
80460 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
80480 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
80502 ATGCATCGATGCAT
1 ATGCATCGATGCAT
80516 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:83134 original size:19 final size:19
Alignment explanation
Indices: 83110--83148 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
83100 TCGAATGCAT
*
83110 TCCATGTACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
83129 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
83148 T
1 T
83149 GAATTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.36, G:0.15, T:0.28
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:83252 original size:64 final size:63
Alignment explanation
Indices: 83047--83256 Score: 190
Period size: 65 Copynumber: 3.3 Consensus size: 63
83037 TATTCAAAGG
* * **
83047 CATGCACCGATGCATC-AGTCCATGCATCGATGCATCGATGAATTAATTGAACATCGAATGCATT
1 CATGCACCGATGCA-CAAG-CCATGCATCGATGCATC-AGGTATTAATCAAACATCGAATGCATT
*
83111 C
63 T
* *** * * **
83112 CATGTACCGATGCACTCTCCATGCATCGATGCACTC-TGAATTTTTTCAAAACATCGAATGCATT
1 CATGCACCGATGCACAAGCCATGCATCGATGCA-TCAGGTA-TTAATC-AAACATCGAATGCATT
83176 T
63 T
* * *
83177 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTACTCAAACATCGAATGCATTT
1 CATGCACCGATGCACAAGCCATGCATCGATGCATCAGG-TATTAATCAAACATCGAATGCATTT
*
83241 CATGCATCGATGCACA
1 CATGCACCGATGCACA
83257 CTTGGTGCAC
Statistics
Matches: 120, Mismatches: 19, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
63 4 0.03
64 53 0.44
65 62 0.52
66 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (63 bp):
CATGCACCGATGCACAAGCCATGCATCGATGCATCAGGTATTAATCAAACATCGAATGCATTT
Found at i:84998 original size:30 final size:30
Alignment explanation
Indices: 84923--84998 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
84913 TAATGGCAGA
* * *
84923 AAACA-TCATGTATAAAATTGAGAATTTTT
1 AAACATTCATGTATGAAACTGAGAATTTAT
*
84952 AAACATT-ATATATGAAACTGAGAATTTGAT
1 AAACATTCATGTATGAAACTGAGAATTT-AT
*
84982 ATA-ATTCATGTATGAAA
1 AAACATTCATGTATGAAA
84999 GGGGTATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 25 0.66
30 13 0.34
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.36
Consensus pattern (30 bp):
AAACATTCATGTATGAAACTGAGAATTTAT
Found at i:93833 original size:2 final size:2
Alignment explanation
Indices: 93828--93854 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
93818 ACGAGACAAT
93828 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
93855 ACAGAAATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:96106 original size:19 final size:19
Alignment explanation
Indices: 96068--96108 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
96058 GAATAAATAT
*
96068 AAAGAAAATACAAAAGGAA
1 AAAGAAAATACAAAAAGAA
96087 AAAGAAAATA-AAGAAAGAA
1 AAAGAAAATACAA-AAAGAA
96106 AAA
1 AAA
96109 TAGAATAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.05
Consensus pattern (19 bp):
AAAGAAAATACAAAAAGAA
Found at i:104652 original size:19 final size:19
Alignment explanation
Indices: 104614--104654 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
104604 GAATAAATAT
*
104614 AAAGAAAATACAAAAGGAA
1 AAAGAAAATACAAAAAGAA
104633 AAAGAAAATA-AAGAAAGAA
1 AAAGAAAATACAA-AAAGAA
104652 AAA
1 AAA
104655 TAGAATAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.05
Consensus pattern (19 bp):
AAAGAAAATACAAAAAGAA
Found at i:104786 original size:2 final size:2
Alignment explanation
Indices: 104781--104827 Score: 62
Period size: 2 Copynumber: 23.5 Consensus size: 2
104771 TATATAAGTA
104781 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
104822 AGT AT A
1 A-T AT A
104828 AATAAATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.05
2 35 0.85
3 4 0.10
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:104834 original size:4 final size:4
Alignment explanation
Indices: 104825--104849 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
104815 ATACTATAGT
104825 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
104850 AAGAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:104955 original size:2 final size:2
Alignment explanation
Indices: 104950--105007 Score: 61
Period size: 2 Copynumber: 29.5 Consensus size: 2
104940 AACGAAAAAA
104950 AT AT AT AT AT AT AT A- AGT A- AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
104990 AT A- AT AT ACT AT AGT AT A
1 AT AT AT AT A-T AT A-T AT A
105008 AATAAATAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
1 4 0.08
2 40 0.82
3 5 0.10
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:104973 original size:19 final size:19
Alignment explanation
Indices: 104949--105008 Score: 79
Period size: 19 Copynumber: 3.1 Consensus size: 19
104939 GAACGAAAAA
104949 AATATATATATATATA-AGT
1 AATATATATATATATATA-T
104968 AATATATATATATATATAT
1 AATATATATATATATATAT
104987 AATATA-ATATACTATAGTAT
1 AATATATATATA-TATA-TAT
105007 AA
1 AA
105009 ATAAATAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.13
19 27 0.71
20 6 0.16
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (19 bp):
AATATATATATATATATAT
Found at i:104978 original size:180 final size:178
Alignment explanation
Indices: 104714--105072 Score: 634
Period size: 180 Copynumber: 2.0 Consensus size: 178
104704 ACATATATTA
104714 AAATTTACATAAGAAAAATATATGCAATAGAATAAAATATATAAAGAACGAAAAAAATATATAAG
1 AAATTTACATAAGAAAAATATATGCAATAGAATAAAATATATAAAGAACGAAAAAAATATATAAG
104779 TAATATATATATATATATATATATATATAATATAATATACTATAGTATAAATAAATAAATAAATA
66 TAATATATATATATATATATATATATATAATATAATATACTATAGTATAAATAAATAAATAAATA
*
104844 AATAAAAAGAAAAAAAATATAGTATATTATAACAATGTATATATACGTAT
131 AAGAAAAAG--AAAAAATATAGTATATTATAACAATGTATATATACGTAT
104894 AAATTTACATAAGAAAAATATATGCAATAGAATAAAATATATAAAGAACGAAAAAAATATAT-A-
1 AAATTTACATAAGAAAAATATATGCAATAGAATAAAATATATAAAGAACGAAAAAAATATATAAG
104957 T-ATATATAAGTAATATATATATATATATATAATATAATATACTATAGTATAAATAAATAAATAA
66 TAATATAT-A-T-ATATATATATATATATATAATATAATATACTATAGTATAAATAAATAAATAA
*
105021 ATAAAGAAAAAGAAAAAATATAGTATATTATAACAATGTATATGTACGTAT
128 ATAAAGAAAAAGAAAAAATATAGTATATTATAACAATGTATATATACGTAT
105072 A
1 A
105073 TATATAGAGA
Statistics
Matches: 174, Mismatches: 2, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
177 6 0.03
178 41 0.24
179 2 0.01
180 125 0.72
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (178 bp):
AAATTTACATAAGAAAAATATATGCAATAGAATAAAATATATAAAGAACGAAAAAAATATATAAG
TAATATATATATATATATATATATATATAATATAATATACTATAGTATAAATAAATAAATAAATA
AAGAAAAAGAAAAAATATAGTATATTATAACAATGTATATATACGTAT
Found at i:107055 original size:15 final size:15
Alignment explanation
Indices: 107035--107064 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
107025 ATATTTTATT
*
107035 TTTAAAAAAAGTAAA
1 TTTAAAAAAAATAAA
107050 TTTAAAAAAAATAAA
1 TTTAAAAAAAATAAA
107065 GTTTTATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
TTTAAAAAAAATAAA
Found at i:107672 original size:23 final size:23
Alignment explanation
Indices: 107646--107693 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
107636 GCGATTATTA
107646 ATTTGAATCTTGTTTTTCAAATC
1 ATTTGAATCTTGTTTTTCAAATC
*** *
107669 ATTTTCTTGTTGTTTTTCAAATC
1 ATTTGAATCTTGTTTTTCAAATC
107692 AT
1 AT
107694 GTCCTTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.56
Consensus pattern (23 bp):
ATTTGAATCTTGTTTTTCAAATC
Found at i:107707 original size:23 final size:23
Alignment explanation
Indices: 107655--107708 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
107645 AATTTGAATC
* *
107655 TTGTTTTTCAAATCATTTTCTTG
1 TTGTTTTTCAAATCATGTCCTTG
*
107678 TTGTTTTTCAAATCATGTCCTTT
1 TTGTTTTTCAAATCATGTCCTTG
*
107701 TTTTTTTT
1 TTGTTTTT
107709 TGAGTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.15, C:0.13, G:0.07, T:0.65
Consensus pattern (23 bp):
TTGTTTTTCAAATCATGTCCTTG
Found at i:109684 original size:33 final size:32
Alignment explanation
Indices: 109640--109714 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 32
109630 TATAAATTAT
** *
109640 TTATTAAATTAAAATATTAAATATGTAATAATA
1 TTATTAAATTAAAATAAGAAAAATGTAAT-ATA
* *
109673 TTATTATATTAAAATAAGAAAAATGTACTATA
1 TTATTAAATTAAAATAAGAAAAATGTAATATA
109705 TTATTAAATT
1 TTATTAAATT
109715 TATTAATACA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 12 0.33
33 24 0.67
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (32 bp):
TTATTAAATTAAAATAAGAAAAATGTAATATA
Found at i:110640 original size:15 final size:15
Alignment explanation
Indices: 110620--110662 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
110610 AAATACAAAC
110620 TACAATAACATAAAA
1 TACAATAACATAAAA
* *
110635 TACAATACCAGAAAA
1 TACAATAACATAAAA
*
110650 TAAAATAACATAA
1 TACAATAACATAA
110663 TTATTGTCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.65, C:0.14, G:0.02, T:0.19
Consensus pattern (15 bp):
TACAATAACATAAAA
Found at i:125977 original size:23 final size:22
Alignment explanation
Indices: 125929--125977 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
125919 ATGCGATCCT
* *
125929 TCGGGACAAATACATAGGTCAT
1 TCGGGACAAATACATAGGCCAC
* *
125951 TCGGGACAAATTTCATATGCCAC
1 TCGGGACAAA-TACATAGGCCAC
125974 TCGG
1 TCGG
125978 TGGGACTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (22 bp):
TCGGGACAAATACATAGGCCAC
Found at i:127858 original size:21 final size:21
Alignment explanation
Indices: 127832--127872 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
127822 AGATTACGCA
*
127832 GGGGGTA-CAGATTCCCCCCTG
1 GGGGGTATC-GATTACCCCCTG
127853 GGGGGTATCGATTACCCCCT
1 GGGGGTATCGATTACCCCCT
127873 AAATGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.15, C:0.32, G:0.32, T:0.22
Consensus pattern (21 bp):
GGGGGTATCGATTACCCCCTG
Found at i:128781 original size:22 final size:22
Alignment explanation
Indices: 128756--128815 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
128746 GGTCTACGCA
* *
128756 GTCCTTCGGGATATATACAGT-G
1 GTCCTTCGGGACAAATACA-TAG
128778 GTCCTTCGGGACAAATACATAG
1 GTCCTTCGGGACAAATACATAG
*
128800 GTCCTTCGAGACAAAT
1 GTCCTTCGGGACAAAT
128816 TTCATATGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (22 bp):
GTCCTTCGGGACAAATACATAG
Found at i:132262 original size:2 final size:2
Alignment explanation
Indices: 132257--132295 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
132247 AATTACTAAT
132257 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
132296 TGTTAATCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:132736 original size:2 final size:2
Alignment explanation
Indices: 132717--132763 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
132707 ATACTTCTAC
* *
132717 TA TA TT TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
132759 TA TA T
1 TA TA T
132764 TTAATTACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:138943 original size:51 final size:51
Alignment explanation
Indices: 138884--138985 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
138874 TATCCACATA
138884 CAAACAGAAAGTAGTTTGTTAGTATTACTATAATTGCAAAAGCAAATTCAG
1 CAAACAGAAAGTAGTTTGTTAGTATTACTATAATTGCAAAAGCAAATTCAG
138935 CAAACAGAAAGTAGTTTGTTAGTATTACTATAATTGCAAAAGCAAATTCAG
1 CAAACAGAAAGTAGTTTGTTAGTATTACTATAATTGCAAAAGCAAATTCAG
138986 ATGCATAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (51 bp):
CAAACAGAAAGTAGTTTGTTAGTATTACTATAATTGCAAAAGCAAATTCAG
Found at i:140937 original size:22 final size:22
Alignment explanation
Indices: 140893--140935 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
140883 TAATTTTTTT
* *
140893 TAATTTTTTTTTTCATTAAAAA
1 TAATATTTTTATTCATTAAAAA
140915 TAATATTTTTATT-ATTAAAAA
1 TAATATTTTTATTCATTAAAAA
140936 ATTAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TAATATTTTTATTCATTAAAAA
Found at i:141164 original size:17 final size:14
Alignment explanation
Indices: 141129--141156 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
141119 TAAGTAGTAA
141129 TTTTAATTTATTAT
1 TTTTAATTTATTAT
141143 TTTTAATTTATTAT
1 TTTTAATTTATTAT
141157 GATGTTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTAATTTATTAT
Found at i:141355 original size:2 final size:2
Alignment explanation
Indices: 141330--141379 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
141320 AAAAATGATT
* * *
141330 TA TA TT TA T- TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
141371 TA TA TA TA T
1 TA TA TA TA T
141380 TTACTAATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:143712 original size:65 final size:63
Alignment explanation
Indices: 143636--143799 Score: 217
Period size: 65 Copynumber: 2.6 Consensus size: 63
143626 CATTGAATAA
* *
143636 ATTG-AACATCGAATGCATTATATGCATCGATGCACATA-CCATGCATCGATGCACTCAGG-TTT
1 ATTGAAACATCGAATGCATT-TATGCATCGATGCACA-AGCCATGCATCGATGCACTCGGGCTTG
* *
143698 TTATGAAAACATCGAATGCATTTGATGCATCGATGCTCAAGCCATGCATCGATGCACTCGGGCTT
1 AT-TG-AAACATCGAATGCATTT-ATGCATCGATGCACAAGCCATGCATCGATGCACTCGGGCTT
143763 G
63 G
143764 ATTGAAACATCGAATGCACTTTATGCATCGATGCAC
1 ATTGAAACATCGAATGCA-TTTATGCATCGATGCAC
143800 TAAGGGTCCA
Statistics
Matches: 89, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 29 0.33
65 54 0.61
66 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (63 bp):
ATTGAAACATCGAATGCATTTATGCATCGATGCACAAGCCATGCATCGATGCACTCGGGCTTG
Found at i:152365 original size:38 final size:38
Alignment explanation
Indices: 152322--152402 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 38
152312 ACCATGCATC
*
152322 GATGCACTCAGG-TTTTTATGAAAACATCAAATGCA-TTT
1 GATGCACTCAGGCTTGTT-TG-AAACATCAAATGCACTTT
* *
152360 GATGCACTCGGGCTTGTTTGAAACATCGAATGCACTTT
1 GATGCACTCAGGCTTGTTTGAAACATCAAATGCACTTT
152398 -ATGCA
1 GATGCA
152403 TCGATGCACT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
37 18 0.47
38 16 0.42
39 4 0.11
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (38 bp):
GATGCACTCAGGCTTGTTTGAAACATCAAATGCACTTT
Found at i:152406 original size:18 final size:19
Alignment explanation
Indices: 152383--152431 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
152373 TTGTTTGAAA
152383 CATCGAATGCACT-TTA-TG
1 CATCG-ATGCACTCTTAGTG
152401 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTTAGTG
*
152420 CACCGATGCACT
1 CATCGATGCACT
152432 AAGGGTCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.25
18 8 0.29
19 13 0.46
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (19 bp):
CATCGATGCACTCTTAGTG
Found at i:155107 original size:16 final size:16
Alignment explanation
Indices: 155086--155116 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
155076 AAGATATGAC
155086 ATAGAAATAGAAAGAA
1 ATAGAAATAGAAAGAA
155102 ATAGAAATAGAAAGA
1 ATAGAAATAGAAAGA
155117 TTCTGCCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.13
Consensus pattern (16 bp):
ATAGAAATAGAAAGAA
Found at i:157989 original size:28 final size:28
Alignment explanation
Indices: 157958--158015 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
157948 TTTCGGGTTT
*
157958 GGGTCGGGTTTTTTTAAGTTTAATATTC
1 GGGTCGGGTTTTTTTAAGTGTAATATTC
*
157986 GGGTCGGGTTTTTTTAAGTGTGATATTC
1 GGGTCGGGTTTTTTTAAGTGTAATATTC
158014 GG
1 GG
158016 TTATGGTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.16, C:0.07, G:0.31, T:0.47
Consensus pattern (28 bp):
GGGTCGGGTTTTTTTAAGTGTAATATTC
Found at i:158023 original size:28 final size:28
Alignment explanation
Indices: 157958--158024 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
157948 TTTCGGGTTT
* *
157958 GGGTCGGGTTTTTTTAAGTTTAATATTC
1 GGGTAGGGTTTTTTTAAGTGTAATATTC
* *
157986 GGGTCGGGTTTTTTTAAGTGTGATATTC
1 GGGTAGGGTTTTTTTAAGTGTAATATTC
* *
158014 GGTTATGGTTT
1 GGGTAGGGTTT
158025 GGGTTTAGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.15, C:0.06, G:0.30, T:0.49
Consensus pattern (28 bp):
GGGTAGGGTTTTTTTAAGTGTAATATTC
Found at i:168330 original size:23 final size:23
Alignment explanation
Indices: 168280--168337 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
168270 TTGTAACATG
168280 TTCTCTGCCTTTATGACATATTT
1 TTCTCTGCCTTTATGACATATTT
* * * * *
168303 ATCTCTGTCTTTGTGGCATGTTT
1 TTCTCTGCCTTTATGACATATTT
*
168326 TTCTCTACCTTT
1 TTCTCTGCCTTT
168338 TGGTAGCTTA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.12, C:0.22, G:0.12, T:0.53
Consensus pattern (23 bp):
TTCTCTGCCTTTATGACATATTT
Found at i:168649 original size:775 final size:759
Alignment explanation
Indices: 167321--168827 Score: 1840
Period size: 775 Copynumber: 1.9 Consensus size: 759
167311 AAACTCTAGC
*
167321 CACTTTCTTCCTCCTCCTCTCTCTTTTTTTCTTCTTTACAAATTGTGACAATTTTATTGATCAAT
1 CACTTTCTTCCTCCTCCTCTCTCTTTTTTTCTTCTTTACAAATTGTGACAATTTTATTGATCAAA
* * *
167386 CCAACTTTTTCTTCTTTAATTTTGTTTAACCGACAGCGGCATCGGTTTTGATGTTGGTTGTCGCT
66 CCAACTTTTTCTTCTTTAATTTTGTTTAACCGACAGCGGCACCGATTTTGATGTTAGTTGTCGCT
* * *
167451 TGCCAGTTATCTTTTTTCTTTTTCTTTTTTAGTTTTTTAATAAAAATAATTATGTCTTTGTGACA
131 CGCCAG-TA------TTCTTTTTCTTTTATAGTTTTTTAATAAAAATAATTATGTCTTTGTAACA
* * * * * *
167516 TGTTTTTTGTATTATATACGTTTATCTTTGCCTTTGTGACAATTTTTTTCTGCCTTTTTGGTAGC
189 TGTTCTCTGTATTATACACATTTATCTCTGCCTTTGTGACAATTTTTTTCTACCTTTTTGGTAGC
* *
167581 TTACGATTTTTTTCTTCGTTTATATTTTTTTCACAGGTTGGATTTGACATCGCCACGACTGATTA
254 TTACGATTTTTTTCTTCGTTTATATTTTTTTCACAGATTGGATTTGACATCGCCACGACTGATCA
** * * * * *
167646 AGATGACGTTTATTAGTTGTCGTGTTGATCTTCCCTGCTTTAGACCCTCAGATTGGTTTGGATAT
319 AGATGACACTTATTAGTTATCATGTTGATCTTCCCTGCTTTAGACCCTCAAATTGATTTGGATAC
* *
167711 GCGTTTTGCGCTAGTAGATGTTTTATCACGTCGCTTGACTCTGATTTGTGATTTGTCGGTGGTCT
384 ACGTTTTGCGCTAGTAGATGTTTTATCACGTCGCTTGACTCTGATTTGTGATTTGTCAGTGGTCT
* * * *
167776 TTTAATAGTTTTATTCCCTTTTGTGGTTCGTTTACCGATACAATCATATTTTTTTCGTATCTTTA
449 TTTAATAGTTTCATCCCCTTTTGTGGTTCGTTTACCGATACAATCATATTTATATCGTATCTTTA
*
167841 TTTTATTCGAGCATTGGTTAGGTTTTTAACATTTTCCTTTTA-TGATCTA-GTGACTAGTTTTTG
514 TTTTATTCAAGCATTGGTTAGGTTTTTAACATTTTCCTTTTATTGATCTAGGTGACTAGTTTTTG
* *
167904 TGTTAATGGTTATAGAAAAATGTCCTAATTATAATTTCGTTTACATTTACGGTTATGCTCGTAAA
579 TGTTAATGGTTATAGAAAAATGTCCTAATTATAATTTAGTTTACATTTACGGTTATACTCGTAAA
* * * * *
167969 TCTTCATTGTCATTCTGAATATTTTCTATTTTTAATAAAACTAGTGGCTTTCTATAAAAAAATGA
644 TCTTCATTATAATTCTGAATAATTTCTATTTTTAATAAAACTAAT--CTATC-A-AAAAAAATGA
168034 ATCAAATTTACAAATTTCAAAAATAATAAAATTAAAGGATTGTAACAAACCTAAT
705 ATCAAATTTACAAATTTCAAAAATAATAAAATTAAAGGATTGTAACAAACCTAAT
* *
168089 CACTTTCTTCCTCCTCATCTCTCTCCCTTTTCTTCTTCTTCTTTACAACTTGTGTCAATTTTATT
1 CACTTTCTTCCTCCTC--CTCTCT--C-TTT-TT-TTCTTCTTTACAAATTGTGACAATTTTATT
* * * *
168154 GATCAAACCATCTTTTTCTTCTTTAATTTTGTTTAACCGACGGCGGTACCTATTTTGATGTTAGT
59 GATCAAACCAACTTTTTCTTCTTTAATTTTGTTTAACCGACAGCGGCACCGATTTTGATGTTAGT
*
168219 TGTCGC-CGCC-G-A-T-TTTTT-TTTTATAGTTTTTTAATAAGAATAATTATGTCTTTGTAACA
124 TGTCGCTCGCCAGTATTCTTTTTCTTTTATAGTTTTTTAATAAAAATAATTATGTCTTTGTAACA
* * *
168278 TGTTCTCTGCCT-TTATGACATATTTATCTCTGTCTTTGTGGC-ATGTTTTTCTCTACC-TTTTG
189 TGTTCTCTG--TATTAT-ACACATTTATCTCTGCCTTTGTGACAAT-TTTTT-TCTACCTTTTTG
* * *
168340 GTAGCTTACGGTTTTTTGCCCTTATTTTTTCCGTTTCT-TATTTTTTCACAAGATTGGATTTGAC
249 GTAGCTTAC-G---ATT----TT-TTTCTT-CGTTTATAT-TTTTTTCAC-AGATTGGATTTGAC
* * * * *
168404 ATCGTCATGACTGATCAAGAT-ATCACTTATTTGTTATCATGTTGATCTTCCTTGCTTTGGA-CC
302 ATCGCCACGACTGATCAAGATGA-CACTTATTAGTTATCATGTTGATCTTCCCTGCTTTAGACCC
* * * * *
168467 TCAAATTGATTTGGATACACGTTTTGCGCTCGTTGATAGTTTTCTCACGTTGTTTGACTCTGATT
366 TCAAATTGATTTGGATACACGTTTTGCGCTAGTAGAT-GTTTTATCACGTCGCTTGACTCTGATT
*
168532 TGTGATTTGTCAGTGGTCTTTTAGTAGTTTCATCCCCTTTTGTGGTTCGTTTACCGATACAGA-C
430 TGTGATTTGTCAGTGGTCTTTTAATAGTTTCATCCCCTTTTGTGGTTCGTTTACCGATACA-ATC
* *
168596 ATATTTATAT-GTATCTTTATTTTATTCAAGCATTGGTTAGATTTTTTAACATTTTCTTTTTATG
494 ATATTTATATCGTATCTTTATTTTATTCAAGCATTGGTTAG-GTTTTTAACATTTTCCTTTTA--
** * * *
168660 GTCCTTGTGTGATCTAGGTGGTTAGTTTTTGTGTTAATGGTTATAGAAAATTTTCCTAATTATAT
556 -------T-TGATCTAGGTGACTAGTTTTTGTGTTAATGGTTATAGAAAAATGTCCTAATTATAA
*
168725 TTTAGTTTACGTTTACGGTTATACTCGTAAATCTTCATTATAATTCTGAATAATTTCTATTTTTA
613 TTTAGTTTACATTTACGGTTATACTCGTAAATCTTCATTATAATTCTGAATAATTTCTATTTTTA
*
168790 ATAAAACTAATCTATCAAAAAAATTGAATCAAATTTAC
678 ATAAAACTAATCTATCAAAAAAAATGAATCAAATTTAC
168828 TTATTTACAT
Statistics
Matches: 630, Mismatches: 69, Indels: 65
0.82 0.09 0.09
Matches are distributed among these distances:
762 45 0.07
763 11 0.02
764 40 0.06
765 6 0.01
768 18 0.03
770 6 0.01
771 1 0.00
772 3 0.00
773 10 0.02
774 83 0.13
775 262 0.42
776 1 0.00
783 20 0.03
784 1 0.00
785 4 0.01
786 7 0.01
787 112 0.18
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.47
Consensus pattern (759 bp):
CACTTTCTTCCTCCTCCTCTCTCTTTTTTTCTTCTTTACAAATTGTGACAATTTTATTGATCAAA
CCAACTTTTTCTTCTTTAATTTTGTTTAACCGACAGCGGCACCGATTTTGATGTTAGTTGTCGCT
CGCCAGTATTCTTTTTCTTTTATAGTTTTTTAATAAAAATAATTATGTCTTTGTAACATGTTCTC
TGTATTATACACATTTATCTCTGCCTTTGTGACAATTTTTTTCTACCTTTTTGGTAGCTTACGAT
TTTTTTCTTCGTTTATATTTTTTTCACAGATTGGATTTGACATCGCCACGACTGATCAAGATGAC
ACTTATTAGTTATCATGTTGATCTTCCCTGCTTTAGACCCTCAAATTGATTTGGATACACGTTTT
GCGCTAGTAGATGTTTTATCACGTCGCTTGACTCTGATTTGTGATTTGTCAGTGGTCTTTTAATA
GTTTCATCCCCTTTTGTGGTTCGTTTACCGATACAATCATATTTATATCGTATCTTTATTTTATT
CAAGCATTGGTTAGGTTTTTAACATTTTCCTTTTATTGATCTAGGTGACTAGTTTTTGTGTTAAT
GGTTATAGAAAAATGTCCTAATTATAATTTAGTTTACATTTACGGTTATACTCGTAAATCTTCAT
TATAATTCTGAATAATTTCTATTTTTAATAAAACTAATCTATCAAAAAAAATGAATCAAATTTAC
AAATTTCAAAAATAATAAAATTAAAGGATTGTAACAAACCTAAT
Found at i:174559 original size:24 final size:24
Alignment explanation
Indices: 174522--174586 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 24
174512 TCATAATATT
174522 TTTTATATATTAACTTTA-AAAATTA
1 TTTT-TATATTAACTTTATAAAA-TA
*
174547 TTTTTATATTAAC-TTATTAAATA
1 TTTTTATATTAACTTTATAAAATA
174570 TATTTTATTATTAACTT
1 T-TTTTA-TATTAACTT
174587 GATTTAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
23 6 0.17
24 17 0.49
25 11 0.31
26 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTTATATTAACTTTATAAAATA
Found at i:174593 original size:27 final size:25
Alignment explanation
Indices: 174522--174605 Score: 93
Period size: 25 Copynumber: 3.3 Consensus size: 25
174512 TCATAATATT
174522 TTTTATATATTAAC-T-TTAAAAATTA
1 TTTTAT-TATTAACTTATTAAAAA-TA
*
174547 TTTT-TATATTAACTTATTAAATATA
1 TTTTAT-TATTAACTTATTAAAAATA
174572 TTTTATTATTAACTTGATTTAAAAATA
1 TTTTATTATTAACTT-A-TTAAAAATA
174599 TTTTATT
1 TTTTATT
174606 TTTATTTTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
24 9 0.17
25 20 0.38
26 8 0.15
27 15 0.29
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (25 bp):
TTTTATTATTAACTTATTAAAAATA
Found at i:174618 original size:27 final size:27
Alignment explanation
Indices: 174544--174622 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 27
174534 ACTTTAAAAA
*
174544 TTATTTTTATATTAACTTATTAAATATATT
1 TTATTTTTATATTAA--T-TTAAAAATATT
* *
174574 TTATTATTA-ACTTGATTTAAAAATATT
1 TTATTTTTATA-TTAATTTAAAAATATT
*
174601 TTATTTTTATTTTAATTTAAAA
1 TTATTTTTATATTAATTTAAAA
174623 GTGTATATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
27 28 0.68
28 1 0.02
29 1 0.02
30 11 0.27
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (27 bp):
TTATTTTTATATTAATTTAAAAATATT
Found at i:175563 original size:4 final size:4
Alignment explanation
Indices: 175554--175606 Score: 61
Period size: 4 Copynumber: 13.2 Consensus size: 4
175544 CATACAAATA
* * * * *
175554 TATG TATG TATG TGTG TATG TGTG TGTG TATG TGTG TGTG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
175602 TATG T
1 TATG T
175607 GTATTGCTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.15, C:0.00, G:0.34, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:175573 original size:12 final size:12
Alignment explanation
Indices: 175556--175602 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
175546 TACAAATATA
175556 TGTATGTATGTG
1 TGTATGTATGTG
*
175568 TGTATGTGTGTG
1 TGTATGTATGTG
*
175580 TGTATGTGTGTG
1 TGTATGTATGTG
175592 TGTATGTATGT
1 TGTATGTATGT
175603 ATGTGTATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.13, C:0.00, G:0.36, T:0.51
Consensus pattern (12 bp):
TGTATGTATGTG
Found at i:175591 original size:16 final size:16
Alignment explanation
Indices: 175554--175608 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
175544 CATACAAATA
* *
175554 TATGTATGTATGTGTG
1 TATGTGTGTATGTATG
*
175570 TATGTGTGTGTGTATG
1 TATGTGTGTATGTATG
*
175586 TGTGTGTGTATGTATG
1 TATGTGTGTATGTATG
175602 TATGTGT
1 TATGTGT
175609 ATTGCTCACC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.51
Consensus pattern (16 bp):
TATGTGTGTATGTATG
Found at i:181928 original size:2 final size:2
Alignment explanation
Indices: 181921--182031 Score: 222
Period size: 2 Copynumber: 55.5 Consensus size: 2
181911 GAGGCAACAT
181921 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
181963 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
182005 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
182032 AGAACGAAAG
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 109 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:185866 original size:514 final size:515
Alignment explanation
Indices: 184896--185927 Score: 2030
Period size: 514 Copynumber: 2.0 Consensus size: 515
184886 TTGGAATAGG
184896 GTTCTTAATAAGAATTAGAAGTGAAATTTGACTTGTCACTAAGCTAACTAAGAAGTATGAGGTGT
1 GTTCTTAATAAGAATTAGAAGTGAAATTTGACTTGTCACTAAGCTAACTAAGAAGTATGAGGTGT
184961 TAGAATTCAAATTAGAACATGTTGGAATTTGGGTTAGATTCTTAAATTCTACATGGAGAATTAGA
66 TAGAATTCAAATTAGAACATGTTGGAATTTGGGTTAGATTCTTAAATTCTACATGGAGAATTAGA
185026 TTTATAAGTTTTAGAAGTATTTAATGGATAATAATTAGTTTAAGTAAGAGTATGCAAGTTAGGGA
131 TTTATAAGTTTTAGAAGTATTTAATGG--AATAATTAGTTTAAGTAAGAGTATGCAAGTTAGGGA
*
185091 TATTAAAAGAGGGGAAATATAAAGTGTCAAGTAGGGTAAGAAGAGATTTTCGTGCTTAAATGACA
194 TATTAAAAGAGGGGAAATATAAAGTGTCAAGTAGGGTAAGAAGAGATTTTCATGCTTAAATGACA
185156 TTTTTGGGTAATGTGCATCGATGCACATTCATTATGCACCGATGCATCAATGATAAATCCCATAA
259 TTTTTGGGTAATGTGCATCGATGCACATTCATTATGCACCGATGCATCAATGATAAATCCCATAA
185221 ATTTGTTGAAGGTGCATCGATGCATTAATTTTAATACAAACATCGAATGTCGTCAGTGCATCGAT
324 ATTTGTTGAAGGTGCATCGATGCATTAATTTTAATACAAACATCGAATGTCGTCAGTGCATCGAT
185286 GCATAAGGAGTGCATTGATGCATTTCTAATAAAATGAACATCGAATGCCCTCAGTGCATCGATGC
389 GCATAAGGAGTGCATTGATGCATTTCTAATAAAATGAACATCGAATGCCCTCAGTGCATCGATGC
185351 ATCAGGAGTGCATCGATGCATGCCTCCATTAAAAGATGAAAATGGCTTTTCTTTTAGCCTAA
454 ATCAGGAGTGCATCGATGCATGCCTCCATTAAAAGATGAAAATGGCTTTTCTTTTAGCCTAA
185413 GTTCTTAATAAGAATTAGAAGTGAAATTTGACTTGTCACTAAGCTAACTAAGAAGTATGAGGTGT
1 GTTCTTAATAAGAATTAGAAGTGAAATTTGACTTGTCACTAAGCTAACTAAGAAGTATGAGGTGT
185478 TAGAATTCAAATTAGAACATGTTGGAATTTGGGTTAGATTCTTAAATTCTACATGGAGAATTAGA
66 TAGAATTCAAATTAGAACATGTTGGAATTTGGGTTAGATTCTTAAATTCTACATGGAGAATTAGA
185543 TTTATAAGTTTTAGAAGTATTTAATGG-ATAATTAGTTTAAGTAAGAGTATGCAAGTTAGGGATA
131 TTTATAAGTTTTAGAAGTATTTAATGGAATAATTAGTTTAAGTAAGAGTATGCAAGTTAGGGATA
185607 TTAAAAGAGGGGAAATATAAAGTGTCAAGTAGGGTAAGAAGAGATTTTCATGCTTAAATGACATT
196 TTAAAAGAGGGGAAATATAAAGTGTCAAGTAGGGTAAGAAGAGATTTTCATGCTTAAATGACATT
185672 TTTGGGTAATGTGCATCGATGCACATTCATTATGCACCGATGCATCAATGATAAATCCCATAAAT
261 TTTGGGTAATGTGCATCGATGCACATTCATTATGCACCGATGCATCAATGATAAATCCCATAAAT
185737 TTGTTGAAGGTGCATCGATGCATTAATTTTAATACAAACATCGAATGTCGTCAGTGCATCGATGC
326 TTGTTGAAGGTGCATCGATGCATTAATTTTAATACAAACATCGAATGTCGTCAGTGCATCGATGC
185802 ATAAGGAGTGCATTGATGCATTTCTAATAAAATGAACATCGAATGCCCTCAGTGCATCGATGCAT
391 ATAAGGAGTGCATTGATGCATTTCTAATAAAATGAACATCGAATGCCCTCAGTGCATCGATGCAT
185867 CAGGAGTGCATCGATGCATGCCTCCATTAAAAGATGAAAATGGCTTTTCTTTTAGCCTAA
456 CAGGAGTGCATCGATGCATGCCTCCATTAAAAGATGAAAATGGCTTTTCTTTTAGCCTAA
185927 G
1 G
185928 AAATGATAGT
Statistics
Matches: 514, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
514 357 0.69
517 157 0.31
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (515 bp):
GTTCTTAATAAGAATTAGAAGTGAAATTTGACTTGTCACTAAGCTAACTAAGAAGTATGAGGTGT
TAGAATTCAAATTAGAACATGTTGGAATTTGGGTTAGATTCTTAAATTCTACATGGAGAATTAGA
TTTATAAGTTTTAGAAGTATTTAATGGAATAATTAGTTTAAGTAAGAGTATGCAAGTTAGGGATA
TTAAAAGAGGGGAAATATAAAGTGTCAAGTAGGGTAAGAAGAGATTTTCATGCTTAAATGACATT
TTTGGGTAATGTGCATCGATGCACATTCATTATGCACCGATGCATCAATGATAAATCCCATAAAT
TTGTTGAAGGTGCATCGATGCATTAATTTTAATACAAACATCGAATGTCGTCAGTGCATCGATGC
ATAAGGAGTGCATTGATGCATTTCTAATAAAATGAACATCGAATGCCCTCAGTGCATCGATGCAT
CAGGAGTGCATCGATGCATGCCTCCATTAAAAGATGAAAATGGCTTTTCTTTTAGCCTAA
Found at i:187455 original size:149 final size:149
Alignment explanation
Indices: 187275--187735 Score: 849
Period size: 149 Copynumber: 3.1 Consensus size: 149
187265 GAGTCGAGGG
* * *
187275 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
187340 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
187405 TATGGCATTACGGTGCAAT
131 TATGGCATTACGGTGCAAT
187424 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
187489 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
187554 TATGGCATTACGGTGCAAT
131 TATGGCATTACGGTGCAAT
187573 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
187638 ACTTGATCCCTAGTATATGTATATGATTCTTAAGG---AATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
*
187700 TATGGCACTACGGTGCAAT
131 TATGGCATTACGGTGCAAT
187719 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
187736 TGCAATTATA
Statistics
Matches: 307, Mismatches: 4, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
145 1 0.00
146 60 0.20
149 246 0.80
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCATTACGGTGCAAT
Found at i:187736 original size:23 final size:23
Alignment explanation
Indices: 187703--187747 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
187693 ATTATTATAT
*
187703 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
187726 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
187748 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:188726 original size:11 final size:12
Alignment explanation
Indices: 188699--188726 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
188689 CTGATCTTCC
188699 TTTTTGTTTCGA
1 TTTTTGTTTCGA
188711 TTTTTGTTTCGA
1 TTTTTGTTTCGA
188723 TTTT
1 TTTT
188727 AAATCAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.14, T:0.71
Consensus pattern (12 bp):
TTTTTGTTTCGA
Found at i:205553 original size:17 final size:18
Alignment explanation
Indices: 205517--205554 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
205507 TCAAGTGGCT
*
205517 TAATTGAATGCATTTAAA
1 TAATTGAATGCATCTAAA
*
205535 TAATTGAGTG-ATCTAAA
1 TAATTGAATGCATCTAAA
205552 TAA
1 TAA
205555 CAAAATTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (18 bp):
TAATTGAATGCATCTAAA
Found at i:206684 original size:24 final size:24
Alignment explanation
Indices: 206648--206705 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
206638 TGAAATTTCA
**
206648 GACATAAGCCCCACCAGGCCAGTG
1 GACATAATACCCACCAGGCCAGTG
206672 GACATAATACCCACCAGGCCAGTG
1 GACATAATACCCACCAGGCCAGTG
206696 GACATAATAC
1 GACATAATAC
206706 GAGTGTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.34, C:0.33, G:0.21, T:0.12
Consensus pattern (24 bp):
GACATAATACCCACCAGGCCAGTG
Found at i:210831 original size:4 final size:4
Alignment explanation
Indices: 210822--210864 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
210812 CAATGCATGT
210822 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
210865 CATAGTTGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:212767 original size:64 final size:64
Alignment explanation
Indices: 212698--212917 Score: 257
Period size: 64 Copynumber: 3.5 Consensus size: 64
212688 TTGAAGGTGT
** **
212698 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCAAATGCAATTCGTG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCAAATGCAATTCGTG
212761 C
64 C
** *
212762 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGTAACATCGAATGCAATTCGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCGTGC
* * * * * **
212826 ATCGATGCATAAGTAGTGCATCGATGCAT-CCAGTAATAATACAACATCGAATACATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCGTGC
* *
212889 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
212918 ACCTTCATTA
Statistics
Matches: 138, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
63 54 0.39
64 79 0.57
65 5 0.04
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCGTGC
Found at i:213612 original size:31 final size:31
Alignment explanation
Indices: 213574--213636 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
213564 AGGGTCGAGG
*
213574 GTTTACCTATGTTCTTC-GGAACATATGGACT
1 GTTTACCTAGGTTCTTCTGGAAC-TATGGACT
*
213605 GTTTACCTAGGTTCTTCTGGATCTATGGACT
1 GTTTACCTAGGTTCTTCTGGAACTATGGACT
213636 G
1 G
213637 GTCCTTCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCTGGAACTATGGACT
Found at i:214667 original size:15 final size:15
Alignment explanation
Indices: 214647--214675 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
214637 GTGTTAACTA
214647 AATAAAAAAATGTTC
1 AATAAAAAAATGTTC
214662 AATAAAAAAATGTT
1 AATAAAAAAATGTT
214676 TTAGCGAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (15 bp):
AATAAAAAAATGTTC
Found at i:216463 original size:24 final size:26
Alignment explanation
Indices: 216430--216479 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
216420 TTAAATTTTA
* *
216430 ATGACTAAATTAAA-AAATTAAAAAT
1 ATGACTAAATAAAATAAATAAAAAAT
216455 ATGA-TAAATAAAATAAATAAAAAAT
1 ATGACTAAATAAAATAAATAAAAAAT
216480 TCAATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (26 bp):
ATGACTAAATAAAATAAATAAAAAAT
Found at i:222690 original size:2 final size:2
Alignment explanation
Indices: 222685--222738 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
222675 ATCTTGTAAT
222685 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
222727 TA TA TA TA TA TA
1 TA TA TA TA TA TA
222739 GAGAGAGAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:222743 original size:2 final size:2
Alignment explanation
Indices: 222738--222776 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
222728 ATATATATAT
222738 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
222777 TATTATGGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:229904 original size:2 final size:2
Alignment explanation
Indices: 229897--229922 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
229887 AATATGTAAA
229897 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
229923 TTAACCTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:230018 original size:108 final size:109
Alignment explanation
Indices: 229903--230103 Score: 289
Period size: 108 Copynumber: 1.8 Consensus size: 109
229893 TAAAATATAT
* *
229903 ATATATATATATATATATATTTAACCTCCTTCACAGACAGCTAGAGAAAAGCCATCTCAGGAAAC
1 ATATATATAT-TATAT-TATTTAACCTCCTCCACAGACAGCTAGAGAAAAGCCAACTCAGGAAAC
229968 ATGAAAC-AAAAACAAGTAAAA-TCAAAGTTTGAACTATACATACAA
64 ATGAAACAAAAAACAAG-AAAAGTCAAAGTTTGAACTATACATACAA
* ** *
230013 ATATATATATTATATTATTTAGCCTCCTCCTTAGACAGCTAGAGAAAAGCCAACTCTGGAAACAT
1 ATATATATATTATATTATTTAACCTCCTCCACAGACAGCTAGAGAAAAGCCAACTCAGGAAACAT
* *
230078 GCACCAAAAAACAAGAAAAGTCAAAG
66 GAAACAAAAAACAAGAAAAGTCAAAG
230104 ATTAATGCAC
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
108 51 0.63
109 20 0.25
110 10 0.12
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.24
Consensus pattern (109 bp):
ATATATATATTATATTATTTAACCTCCTCCACAGACAGCTAGAGAAAAGCCAACTCAGGAAACAT
GAAACAAAAAACAAGAAAAGTCAAAGTTTGAACTATACATACAA
Found at i:230180 original size:5 final size:5
Alignment explanation
Indices: 230170--230286 Score: 227
Period size: 5 Copynumber: 23.6 Consensus size: 5
230160 GACCAAACAC
230170 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
230220 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATA-T ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
230269 ATATT ATATT ATATT ATA
1 ATATT ATATT ATATT ATA
230287 GAGTATCATC
Statistics
Matches: 111, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.04
5 107 0.96
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:231623 original size:14 final size:14
Alignment explanation
Indices: 231604--231638 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
231594 TTGTTTCACC
231604 AAAAATATTTTTCG
1 AAAAATATTTTTCG
231618 AAAAATATTTTTCG
1 AAAAATATTTTTCG
*
231632 TAAAATA
1 AAAAATA
231639 AATTACTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (14 bp):
AAAAATATTTTTCG
Found at i:231815 original size:23 final size:24
Alignment explanation
Indices: 231758--231834 Score: 60
Period size: 26 Copynumber: 3.4 Consensus size: 24
231748 AAATAACAAA
231758 TACAATA--AATAATATTATTTAT
1 TACAATATTAATAATATTATTTAT
* *
231780 TATAATAACTTAATATTATTATTT-T
1 TACAAT-A-TTAATAATATTATTTAT
231805 TACAATATTAA-AATA--ATTTAT
1 TACAATATTAATAATATTATTTAT
*
231826 T-TAATATTA
1 TACAATATTA
231835 TTTATGTCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
20 11 0.24
21 2 0.04
22 8 0.18
23 5 0.11
24 1 0.02
25 6 0.13
26 12 0.27
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (24 bp):
TACAATATTAATAATATTATTTAT
Found at i:231927 original size:21 final size:20
Alignment explanation
Indices: 231903--231959 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 20
231893 AGTATATTCT
231903 ATTAAAATAAAAATATTATAA
1 ATTAAAATAAAAATATTAT-A
* * *
231924 ATT-ATAT-TAATTATT-T-
1 ATTAAAATAAAAATATTATA
231940 ATTAAAATAAAAATATTATA
1 ATTAAAATAAAAATATTATA
231960 TTATATTACC
Statistics
Matches: 26, Mismatches: 6, Indels: 9
0.63 0.15 0.22
Matches are distributed among these distances:
16 3 0.12
17 3 0.12
18 7 0.27
19 7 0.27
20 3 0.12
21 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTAAAATAAAAATATTATA
Found at i:231931 original size:26 final size:28
Alignment explanation
Indices: 231879--231933 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
231869 ATAACTTTAT
* *
231879 AAATAAAAAAGATTAGTATATTCTATTA
1 AAATAAAAAAGATTAGTAAATTATATTA
*
231907 AAAT-AAAAATATTA-TAAATTATATTA
1 AAATAAAAAAGATTAGTAAATTATATTA
231933 A
1 A
231934 TTATTTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.46
27 9 0.38
28 4 0.17
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (28 bp):
AAATAAAAAAGATTAGTAAATTATATTA
Found at i:231943 original size:37 final size:36
Alignment explanation
Indices: 231897--231967 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 36
231887 AAGATTAGTA
231897 TATTCTATTAAAATAAAAATATTATAAATTATATTAAT
1 TATTCTATTAAAATAAAAATATTAT--ATTATATTAAT
231935 TATT-TATTAAAATAAAAATATTATATTATATTA
1 TATTCTATTAAAATAAAAATATTATATTATATTA
231968 CCAATTTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 9 0.27
37 20 0.61
38 4 0.12
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (36 bp):
TATTCTATTAAAATAAAAATATTATATTATATTAAT
Found at i:231975 original size:35 final size:36
Alignment explanation
Indices: 231902--231975 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
231892 TAGTATATTC
**
231902 TATTAAAATAAAAATATTATAAATTATATTAATTATT
1 TATTAAAATAAAAATATTAT-AATTATATTAACAATT
*
231939 TATTAAAATAAAAATATTAT-ATTATATTACCAATT
1 TATTAAAATAAAAATATTATAATTATATTAACAATT
231974 TA
1 TA
231976 ACTACTCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 14 0.41
37 20 0.59
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (36 bp):
TATTAAAATAAAAATATTATAATTATATTAACAATT
Found at i:233374 original size:13 final size:13
Alignment explanation
Indices: 233356--233383 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
233346 TAACCAATGA
233356 AAACATAGACAAT
1 AAACATAGACAAT
233369 AAACATAGACAAT
1 AAACATAGACAAT
233382 AA
1 AA
233384 TCTCTCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (13 bp):
AAACATAGACAAT
Found at i:234664 original size:19 final size:19
Alignment explanation
Indices: 234626--234671 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
234616 CTTCAACTAC
* *
234626 AAGTTCCTACCTTCATTTT
1 AAGTTCATACCTTCACTTT
*
234645 AAGTTCATACCTTCCCTTT
1 AAGTTCATACCTTCACTTT
*
234664 AAATTCAT
1 AAGTTCAT
234672 TGAGCAGATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.43
Consensus pattern (19 bp):
AAGTTCATACCTTCACTTT
Found at i:238176 original size:31 final size:31
Alignment explanation
Indices: 238138--238262 Score: 223
Period size: 31 Copynumber: 4.0 Consensus size: 31
238128 TGACCTATGT
238138 AACTGTCCATATGTTCCGAAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
238169 AACTGTCCATATGTTCCGAAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
238200 AACTGTCCATATGTTCTGAAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
* *
238231 AACTGTCCATATGTTTCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
238262 A
1 A
238263 CCCTCGACTC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 90 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:238735 original size:19 final size:19
Alignment explanation
Indices: 238711--238758 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
238701 ACCTTAGCCT
238711 TGCTTTGATTCAATCCTAA
1 TGCTTTGATTCAATCCTAA
**
238730 TGCTTTGATTTGATCCTAA
1 TGCTTTGATTCAATCCTAA
*
238749 TTCTTTGATT
1 TGCTTTGATT
238759 GTTCCGGAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50
Consensus pattern (19 bp):
TGCTTTGATTCAATCCTAA
Found at i:239394 original size:3 final size:3
Alignment explanation
Indices: 239386--239415 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
239376 AGCACACGGG
239386 GAA GAA GAA GCAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA G-AA GAA GAA GAA GAA GAA GA
239416 TAACTCTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:240230 original size:20 final size:20
Alignment explanation
Indices: 240202--240255 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
240192 ATTTCTTCTT
240202 CTCTCTTTTCCTTTAAGAAC
1 CTCTCTTTTCCTTTAAGAAC
*
240222 CTTTCTTTTCCTTTAAGAAC
1 CTCTCTTTTCCTTTAAGAAC
240242 CTCTCTTTTCCTTT
1 CTCTCTTTTCCTTT
240256 CCTTTCCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.15, C:0.30, G:0.04, T:0.52
Consensus pattern (20 bp):
CTCTCTTTTCCTTTAAGAAC
Found at i:245812 original size:2 final size:2
Alignment explanation
Indices: 245805--245829 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
245795 AACAGTTTTC
245805 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
245830 TCATATGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:259846 original size:7 final size:7
Alignment explanation
Indices: 259834--259861 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
259824 AAGGGGTCTG
259834 GGAATAT
1 GGAATAT
259841 GGAATAT
1 GGAATAT
259848 GGAATAT
1 GGAATAT
259855 GGAATAT
1 GGAATAT
259862 TTTAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (7 bp):
GGAATAT
Found at i:275351 original size:33 final size:32
Alignment explanation
Indices: 275304--275375 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 32
275294 TTTTTTATTT
* * *
275304 ATTTGTTTCTTAATGTTTTTATTTAATTATGG
1 ATTTTTTTCTTAATGATTTCATTTAATTATGG
*
275336 ACTTTTTTTCTTAATGATTTCATTTAATTATGT
1 A-TTTTTTTCTTAATGATTTCATTTAATTATGG
275369 ATTTTTT
1 ATTTTTT
275376 ATTTATTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 7 0.20
33 28 0.80
ACGTcount: A:0.22, C:0.06, G:0.08, T:0.64
Consensus pattern (32 bp):
ATTTTTTTCTTAATGATTTCATTTAATTATGG
Found at i:275393 original size:47 final size:44
Alignment explanation
Indices: 275338--275441 Score: 122
Period size: 47 Copynumber: 2.3 Consensus size: 44
275328 AATTATGGAC
* *
275338 TTTT-TTTCTTAATGATTT-CATTTAATTATGTATTTTTTATTTA
1 TTTTGTTTCTTAATG-TTTGCATTTAATTATGGACTTTTTATTTA
* *
275381 TTTATTTGTTTCTTGATGTTTGTATTTAATTATGGACTTTTTATTTA
1 --T-TTTGTTTCTTAATGTTTGCATTTAATTATGGACTTTTTATTTA
275428 TTTTGTTTCTTAAT
1 TTTTGTTTCTTAAT
275442 TTTTTATTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
44 12 0.24
45 2 0.04
46 6 0.12
47 31 0.61
ACGTcount: A:0.20, C:0.05, G:0.09, T:0.66
Consensus pattern (44 bp):
TTTTGTTTCTTAATGTTTGCATTTAATTATGGACTTTTTATTTA
Found at i:275491 original size:13 final size:14
Alignment explanation
Indices: 275473--275507 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
275463 AATTGTAGCA
275473 TTTGTATTTAA-TG
1 TTTGTATTTAATTG
275486 TTTGTATTTAATTG
1 TTTGTATTTAATTG
*
275500 TTTTTATT
1 TTTGTATT
275508 ATTTAGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (14 bp):
TTTGTATTTAATTG
Found at i:277660 original size:63 final size:63
Alignment explanation
Indices: 277585--277744 Score: 225
Period size: 63 Copynumber: 2.5 Consensus size: 63
277575 TCGAAATGGA
* * * * **
277585 GTGCATGGATGCACTGCA-TAGTGCATCGATGCACTGCA-TGGTGCATCGATGCACTAGTGGCAG
1 GTGCATGGATGCACTGCAGGAGTGCATGGATGCACTGCAGGGGTGCATAGATGCACTACAGG--G
*
277648 GTGCATGAATGCACTGCAGGAGTGCATGGATGCACTGCAGGGGTGCATAGATGCACTACAGGG
1 GTGCATGGATGCACTGCAGGAGTGCATGGATGCACTGCAGGGGTGCATAGATGCACTACAGGG
277711 GTGCATGGATGCACTGCAGGAGTGCATGGATGCA
1 GTGCATGGATGCACTGCAGGAGTGCATGGATGCA
277745 ATTTGACACC
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
63 51 0.59
64 18 0.21
65 18 0.21
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.21
Consensus pattern (63 bp):
GTGCATGGATGCACTGCAGGAGTGCATGGATGCACTGCAGGGGTGCATAGATGCACTACAGGG
Found at i:277674 original size:21 final size:21
Alignment explanation
Indices: 277582--277744 Score: 188
Period size: 21 Copynumber: 7.8 Consensus size: 21
277572 CATTCGAAAT
277582 GGAGTGCATGGATGCACTGCA
1 GGAGTGCATGGATGCACTGCA
* *
277603 -TAGTGCATCGATGCACTGCA
1 GGAGTGCATGGATGCACTGCA
* * *
277623 TG-GTGCATCGATGCACTAG-T
1 GGAGTGCATGGATGCACT-GCA
*
277643 GGCAGGTGCATGAATGCACTGCA
1 GG-A-GTGCATGGATGCACTGCA
277666 GGAGTGCATGGATGCACTGCA
1 GGAGTGCATGGATGCACTGCA
* * *
277687 GGGGTGCATAGATGCACTACA
1 GGAGTGCATGGATGCACTGCA
*
277708 GGGGTGCATGGATGCACTGCA
1 GGAGTGCATGGATGCACTGCA
277729 GGAGTGCATGGATGCA
1 GGAGTGCATGGATGCA
277745 ATTTGACACC
Statistics
Matches: 121, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
20 34 0.28
21 70 0.58
22 2 0.02
23 15 0.12
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.21
Consensus pattern (21 bp):
GGAGTGCATGGATGCACTGCA
Found at i:277999 original size:21 final size:20
Alignment explanation
Indices: 277971--278009 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
277961 GTTTACTGAG
277971 AAAAGATATCAATTGTTAAT
1 AAAAGATATCAATTGTTAAT
277991 AAAATGATATCAATTGTTA
1 AAAA-GATATCAATTGTTA
278010 CCAATTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (20 bp):
AAAAGATATCAATTGTTAAT
Found at i:279167 original size:19 final size:20
Alignment explanation
Indices: 279122--279169 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
279112 CTCTAAATCT
*
279122 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* * *
279142 CTCTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
279161 TTTTCAAAA
1 TTTTCAAAA
279170 GAAAATCATT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:280339 original size:20 final size:22
Alignment explanation
Indices: 280314--280353 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
280304 TGTTGTATAT
280314 AGCCG-TTGGGGAT-ATTTTGA
1 AGCCGTTTGGGGATGATTTTGA
280334 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
280354 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.17, C:0.10, G:0.35, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGA
Found at i:280587 original size:21 final size:21
Alignment explanation
Indices: 280519--280703 Score: 198
Period size: 21 Copynumber: 8.7 Consensus size: 21
280509 TCGAAATGGA
*
280519 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
* * *
280539 GTGCATCGATACACTAG-TGGCAG
1 GTGCATGGATGCACT-GCAGG--G
280562 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
*
280583 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
* * *
280603 GTACATCGATGCACTAG-TGGCAG
1 GTGCATGGATGCACT-GCAGG--G
280626 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
*
280647 GTGCATGGATGCACTGCAAGG
1 GTGCATGGATGCACTGCAGGG
*
280668 GTGCATGGATGCACTGCAAGG
1 GTGCATGGATGCACTGCAGGG
280689 GTGCATGGATGCACT
1 GTGCATGGATGCACT
280704 TTTACACCCT
Statistics
Matches: 139, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
20 27 0.19
21 78 0.56
22 2 0.01
23 32 0.23
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.22
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:280596 original size:64 final size:64
Alignment explanation
Indices: 280519--280682 Score: 283
Period size: 64 Copynumber: 2.5 Consensus size: 64
280509 TCGAAATGGA
*
280519 GTGCATGGATGCACTGCATGGTGCATCGATACACTAGTGGCAGGTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGGCAGGTGCATGGATGCACTGCAGGG
*
280583 GTGCATGGATGCACTGCATGGTACATCGATGCACTAGTGGCAGGTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGGCAGGTGCATGGATGCACTGCAGGG
* *
280647 GTGCATGGATGCACTGCAAGGGTGCATGGATGCACT
1 GTGCATGGATGCACTGC-ATGGTGCATCGATGCACT
280683 GCAAGGGTGC
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
64 79 0.84
65 15 0.16
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.22
Consensus pattern (64 bp):
GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGGCAGGTGCATGGATGCACTGCAGGG
Found at i:282722 original size:27 final size:27
Alignment explanation
Indices: 282690--282755 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
282680 GAGAAGGCGG
* * *
282690 AGAGAAGAG-GAGGAAAGGGAGAGGGAA
1 AGAGAAGAGAG-GGAAAGAGAAAGAGAA
282717 AGAGAAGAGAGGGAAAGAGAAAGAGAA
1 AGAGAAGAGAGGGAAAGAGAAAGAGAA
282744 AGAGAAAGAGAG
1 AGAG-AAGAGAG
282756 AGAGATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 26 0.76
28 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (27 bp):
AGAGAAGAGAGGGAAAGAGAAAGAGAA
Found at i:282728 original size:15 final size:15
Alignment explanation
Indices: 282708--282755 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
282698 GGAGGAAAGG
282708 GAGAGGGAAAGAGAA
1 GAGAGGGAAAGAGAA
282723 GAGAGGGAAAGAGAA
1 GAGAGGGAAAGAGAA
282738 -AGA--GAAAGAGAAA
1 GAGAGGGAAAGAG-AA
282751 GAGAG
1 GAGAG
282756 AGAGATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 7 0.23
13 2 0.07
14 6 0.20
15 15 0.50
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (15 bp):
GAGAGGGAAAGAGAA
Found at i:282740 original size:6 final size:6
Alignment explanation
Indices: 282714--282760 Score: 58
Period size: 6 Copynumber: 7.3 Consensus size: 6
282704 AAGGGAGAGG
*
282714 GAAAGA GAAGAGA GGGAAAGA GAAAGA GAAAGA GAAAGA GAGAGA GA
1 GAAAGA GAA-AGA --GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GA
282761 TTTAAATGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
6 28 0.76
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:288849 original size:26 final size:27
Alignment explanation
Indices: 288820--288881 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 27
288810 CTAAAGAGAT
*
288820 GGGAAAAAGTTT-AAAGGCTAGAGGTA
1 GGGAGAAAGTTTCAAAGGCTAGAGGTA
*
288846 GGGAGAAA-TTTCAAGGGCTAGAGGTA
1 GGGAGAAAGTTTCAAAGGCTAGAGGTA
*
288872 AGGAGAAAGT
1 GGGAGAAAGT
288882 GAATCCTACT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.10
26 27 0.87
27 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.37, T:0.18
Consensus pattern (27 bp):
GGGAGAAAGTTTCAAAGGCTAGAGGTA
Found at i:292842 original size:21 final size:21
Alignment explanation
Indices: 292818--292859 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
292808 GCACCAAAGT
292818 AAGAGCCTCAGGAGAACCAGG
1 AAGAGCCTCAGGAGAACCAGG
*
292839 AAGAGCCTCAGGATAACCAGG
1 AAGAGCCTCAGGAGAACCAGG
292860 TAGGGGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.24, G:0.31, T:0.07
Consensus pattern (21 bp):
AAGAGCCTCAGGAGAACCAGG
Found at i:298180 original size:20 final size:20
Alignment explanation
Indices: 298157--298201 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
298147 CGAATTTGTT
298157 ATTCGAAACACATAAGTCAA
1 ATTCGAAACACATAAGTCAA
*
298177 ATTCGTAACACATAAGTCAA
1 ATTCGAAACACATAAGTCAA
298197 ATTCG
1 ATTCG
298202 CAAAGCGCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.24
Consensus pattern (20 bp):
ATTCGAAACACATAAGTCAA
Found at i:298385 original size:23 final size:23
Alignment explanation
Indices: 298359--298404 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
298349 CTACGGCAAC
*
298359 ATCCGTACTCATCTCCGACGAAA
1 ATCCGTACCCATCTCCGACGAAA
* *
298382 ATCCGTCCCCATTTCCGACGAAA
1 ATCCGTACCCATCTCCGACGAAA
298405 TTTGTCCCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.37, G:0.13, T:0.22
Consensus pattern (23 bp):
ATCCGTACCCATCTCCGACGAAA
Found at i:298425 original size:22 final size:22
Alignment explanation
Indices: 298368--298427 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
298358 CATCCGTACT
* **
298368 CATCTCCGACGAAAATCCGTCCC
1 CATCTCAGACG-AAATTTGTCCC
* *
298391 CATTTCCGACGAAATTTGTCCC
1 CATCTCAGACGAAATTTGTCCC
*
298413 CATCTCAGGCGAAAT
1 CATCTCAGACGAAAT
298428 CTATCTATCT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
22 21 0.68
23 10 0.32
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.23
Consensus pattern (22 bp):
CATCTCAGACGAAATTTGTCCC
Found at i:302490 original size:42 final size:42
Alignment explanation
Indices: 302426--302522 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
302416 CCCCACTTTG
* * *
302426 AGAGCCATCACCTGATAGAGCCGATTCTACAGCTCGAC-ACTC
1 AGAGCCATCACCTGATAGAGCCGATTATACACCTCCACAAC-C
* *
302468 AGAGCCATCACTTGATCA-AGCCGATTATACACCTCCACAACG
1 AGAGCCATCACCTGAT-AGAGCCGATTATACACCTCCACAACC
302510 AGAGCCATCACCT
1 AGAGCCATCACCT
302523 ATTCCATCAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 44 0.94
43 3 0.06
ACGTcount: A:0.31, C:0.34, G:0.16, T:0.19
Consensus pattern (42 bp):
AGAGCCATCACCTGATAGAGCCGATTATACACCTCCACAACC
Found at i:303129 original size:21 final size:19
Alignment explanation
Indices: 303082--303131 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
303072 CACCTGTCAT
* *
303082 CGTTCAAGAGGCCCCCTAT
1 CGTTCAAGAGGCCCCCCAC
*
303101 CTTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGG-CCC-CCCAC
303122 CGTTCAAGAG
1 CGTTCAAGAG
303132 CCCGATTCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 10 0.40
20 3 0.12
21 12 0.48
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (19 bp):
CGTTCAAGAGGCCCCCCAC
Found at i:304282 original size:35 final size:35
Alignment explanation
Indices: 304235--304326 Score: 175
Period size: 35 Copynumber: 2.6 Consensus size: 35
304225 ACCTAGATAA
304235 TTTGTTGTAACAATCAACTACTTGATACGAATAACT
1 TTTG-TGTAACAATCAACTACTTGATACGAATAACT
304271 TTTGTGTAACAATCAACTACTTGATACGAATAACT
1 TTTGTGTAACAATCAACTACTTGATACGAATAACT
304306 TTTGTGTAACAATCAACTACT
1 TTTGTGTAACAATCAACTACT
304327 ATCTTTACCA
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 52 0.93
36 4 0.07
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (35 bp):
TTTGTGTAACAATCAACTACTTGATACGAATAACT
Found at i:305447 original size:14 final size:15
Alignment explanation
Indices: 305411--305448 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
305401 TAAATCATTG
305411 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
305426 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
305441 AAAAATTA
1 AAAAATTA
305449 GAGATGAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:305648 original size:20 final size:19
Alignment explanation
Indices: 305612--305715 Score: 93
Period size: 20 Copynumber: 5.2 Consensus size: 19
305602 CATGTTGCAA
*
305612 AATT-AAAATTCGTGTTGCG
1 AATTCAAAA-TCGAGTTGCG
305631 AATTCGAAAATCGAGTTGCG
1 AATTC-AAAATCGAGTTGCG
*
305651 ATTTCAAAAATCGAGTTGCG
1 AATTC-AAAATCGAGTTGCG
* * *
305671 ATTTTCCAAATTCGCGTTGCG
1 A-ATT-CAAAATCGAGTTGCG
*
305692 AATTCAGAAATCGAGTTGTG
1 AATTCA-AAATCGAGTTGCG
305712 AATT
1 AATT
305716 TGAATTTTAG
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
19 6 0.08
20 44 0.62
21 20 0.28
22 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (19 bp):
AATTCAAAATCGAGTTGCG
Found at i:305689 original size:21 final size:20
Alignment explanation
Indices: 305625--305709 Score: 98
Period size: 20 Copynumber: 4.2 Consensus size: 20
305615 TAAAATTCGT
* *
305625 GTTGCGAATTCGAAAATCGA
1 GTTGCGATTTCAAAAATCGA
305645 GTTGCGATTTCAAAAATCGA
1 GTTGCGATTTCAAAAATCGA
* * *
305665 GTTGCGATTTTCCAAATTCGC
1 GTTGCGA-TTTCAAAAATCGA
* *
305686 GTTGCGAATTCAGAAATCGA
1 GTTGCGATTTCAAAAATCGA
305706 GTTG
1 GTTG
305710 TGAATTTGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 37 0.69
21 17 0.31
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (20 bp):
GTTGCGATTTCAAAAATCGA
Found at i:305790 original size:20 final size:20
Alignment explanation
Indices: 305767--305833 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
305757 TGACTTATGT
305767 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
**
305787 GTTGCGATTTACAGATTCAT
1 GTTGCGATTTACAGATTCGC
*
305807 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAGATTCGC
305827 GTTGCGA
1 GTTGCGA
305834 ATTTGGAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Done.