Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 64
Found at i:5293635 original size:11 final size:11
Alignment explanation
Indices: 5293619--5293679 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
5293609 AAAATTACAT
5293619 TATTAAAAATA
1 TATTAAAAATA
*
5293630 TATTAAAAACA
1 TATTAAAAATA
* *
5293641 CTATTGATAAT-
1 -TATTAAAAATA
5293652 TA-T-AAAAT-
1 TATTAAAAATA
5293660 T-TTAAAAATA
1 TATTAAAAATA
5293670 TATTAAAAAT
1 TATTAAAAAT
5293680 TCTATAATAC
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
8 6 0.15
9 6 0.15
10 3 0.08
11 18 0.45
12 7 0.17
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:5294189 original size:8 final size:7
Alignment explanation
Indices: 5294172--5294201 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
5294162 GTCTTTGTAA
5294172 TAAACCC
1 TAAACCC
5294179 TAAACCCC
1 TAAA-CCC
5294187 TAAACCC
1 TAAACCC
5294194 TAAACCC
1 TAAACCC
5294201 T
1 T
5294202 TAATTCGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:5294190 original size:15 final size:15
Alignment explanation
Indices: 5294172--5294200 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5294162 GTCTTTGTAA
5294172 TAAACCCTAAACCCC
1 TAAACCCTAAACCCC
5294187 TAAACCCTAAACCC
1 TAAACCCTAAACCC
5294201 TTAATTCGAT
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:0.41, C:0.45, G:0.00, T:0.14
Consensus pattern (15 bp):
TAAACCCTAAACCCC
Found at i:5294592 original size:18 final size:19
Alignment explanation
Indices: 5294560--5294595 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
5294550 AATGACACCT
5294560 GAAAATTTAAAACAAATAA
1 GAAAATTTAAAACAAATAA
5294579 GAAAATTT-AAACAAATA
1 GAAAATTTAAAACAAATA
5294596 TCATTGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.22
Consensus pattern (19 bp):
GAAAATTTAAAACAAATAA
Found at i:5302287 original size:39 final size:39
Alignment explanation
Indices: 5302221--5302374 Score: 170
Period size: 39 Copynumber: 3.9 Consensus size: 39
5302211 TCAGTATGGG
* * *
5302221 CTTACCCT-ATGCACAAAGTAGATGAGCCTGCGGTAAGGT
1 CTTACCCTGA-GCACAAAGCAGAGGAGCCTGCGGTAAGGA
* * *
5302260 CTTATCCT-ATGTACAAAGCAGAGGAGCCTGCAGTAAGGA
1 CTTACCCTGA-GCACAAAGCAGAGGAGCCTGCGGTAAGGA
* *
5302299 CTTACCCTGAGCACAAAGTC-GAGGAGCTTGCGATAAGGA
1 CTTACCCTGAGCACAAAG-CAGAGGAGCCTGCGGTAAGGA
* *
5302338 CTTACCCTGAGCACAAAGCCGAGGAGCCTACGGTAAG
1 CTTACCCTGAGCACAAAGCAGAGGAGCCTGCGGTAAG
5302375 TGGTAAGGTC
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
38 1 0.01
39 95 0.97
40 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (39 bp):
CTTACCCTGAGCACAAAGCAGAGGAGCCTGCGGTAAGGA
Found at i:5302336 original size:78 final size:78
Alignment explanation
Indices: 5302212--5302366 Score: 188
Period size: 78 Copynumber: 2.0 Consensus size: 78
5302202 CATGTACACT
* * * * * * *
5302212 CAGTATGGGCTTACCCTATGCACAAAGTAGATGAGCCTGCGGTAAGGTCTTATCCT-ATGTACAA
1 CAGTAAGGACTTACCCTATGCACAAAGTAGAGGAGCCTGCGATAAGGACTTACCCTGA-GCACAA
5302276 AGCAGAGGAGCCTG
65 AGCAGAGGAGCCTG
* *
5302290 CAGTAAGGACTTACCCTGA-GCACAAAGTCGAGGAGCTTGCGATAAGGACTTACCCTGAGCACAA
1 CAGTAAGGACTTACCCT-ATGCACAAAGTAGAGGAGCCTGCGATAAGGACTTACCCTGAGCACAA
*
5302354 AGCCGAGGAGCCT
65 AGCAGAGGAGCCT
5302367 ACGGTAAGTG
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
78 63 0.97
79 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (78 bp):
CAGTAAGGACTTACCCTATGCACAAAGTAGAGGAGCCTGCGATAAGGACTTACCCTGAGCACAAA
GCAGAGGAGCCTG
Found at i:5310411 original size:53 final size:56
Alignment explanation
Indices: 5310349--5310475 Score: 152
Period size: 61 Copynumber: 2.2 Consensus size: 56
5310339 ACCCAGCTCT
5310349 ACCCAAAATC-C-ACACCAC-TCGAAGCTCCTTAATCCCCTGATCCCGATTTTAAG
1 ACCCAAAATCACAACACCACATCGAAGCTCCTTAATCCCCTGATCCCGATTTTAAG
* * **
5310402 ACCCAAAATCACAAATAATACCCCGATTTAAGCTCCTTAATCCCCTGATCCCGATTTTAAG
1 ACCCAAAATCAC----AACACCAC-ATCGAAGCTCCTTAATCCCCTGATCCCGATTTTAAG
5310463 ACCCAAAATCACA
1 ACCCAAAATCACA
5310476 TATAATACCC
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
53 10 0.16
54 1 0.02
57 1 0.02
59 5 0.08
61 45 0.73
ACGTcount: A:0.35, C:0.35, G:0.08, T:0.23
Consensus pattern (56 bp):
ACCCAAAATCACAACACCACATCGAAGCTCCTTAATCCCCTGATCCCGATTTTAAG
Found at i:5310427 original size:33 final size:33
Alignment explanation
Indices: 5310390--5310491 Score: 99
Period size: 33 Copynumber: 3.2 Consensus size: 33
5310380 ATCCCCTGAT
5310390 CCCGATTTTAAGACCCAAAATCACAAATAATAC
1 CCCGATTTTAAGACCCAAAATCACAAATAATAC
** ** *
5310423 CCCGA-TTTAAG-CTCCTTAATC-C-CCTGAT--
1 CCCGATTTTAAGAC-CCAAAATCACAAATAATAC
*
5310451 CCCGATTTTAAGACCCAAAATCACATATAATAC
1 CCCGATTTTAAGACCCAAAATCACAAATAATAC
5310484 CCCGATTT
1 CCCGATTT
5310492 GTGTAGATCT
Statistics
Matches: 52, Mismatches: 10, Indels: 14
0.68 0.13 0.18
Matches are distributed among these distances:
28 5 0.10
29 12 0.23
30 5 0.10
31 5 0.10
32 12 0.23
33 13 0.25
ACGTcount: A:0.35, C:0.30, G:0.08, T:0.26
Consensus pattern (33 bp):
CCCGATTTTAAGACCCAAAATCACAAATAATAC
Found at i:5310445 original size:61 final size:61
Alignment explanation
Indices: 5310370--5310491 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
5310360 ACACCACTCG
5310370 AAGCTCCTTAATCCCCTGATCCCGATTTTAAGACCCAAAATCACAAATAATACCCCGATTT
1 AAGCTCCTTAATCCCCTGATCCCGATTTTAAGACCCAAAATCACAAATAATACCCCGATTT
*
5310431 AAGCTCCTTAATCCCCTGATCCCGATTTTAAGACCCAAAATCACATATAATACCCCGATTT
1 AAGCTCCTTAATCCCCTGATCCCGATTTTAAGACCCAAAATCACAAATAATACCCCGATTT
5310492 GTGTAGATCT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.34, C:0.31, G:0.08, T:0.27
Consensus pattern (61 bp):
AAGCTCCTTAATCCCCTGATCCCGATTTTAAGACCCAAAATCACAAATAATACCCCGATTT
Found at i:5311488 original size:45 final size:45
Alignment explanation
Indices: 5311360--5312289 Score: 310
Period size: 42 Copynumber: 21.6 Consensus size: 45
5311350 CTACAAAATC
* * * *
5311360 GACTTC-TCTTCATGAGAAAGTTAAGAATGACAACACCAATAGATT
1 GACTTCTTCTTCACGAGAAAGTCAAGAA-GACAACACTAAAAGATT
* * *
5311405 GAC-TCCTCTT--CGTACG-AAGTCAAGAATATAATCACTAAAAGATT
1 GACTTCTTCTTCACG-A-GAAAGTCAAGAAGACAA-CACTAAAAGATT
* *
5311449 GA-TTCTTCTTCACGAGAAAGTTAAGAAGGACAACACTAAAAGGTT
1 GACTTCTTCTTCACGAGAAAGTCAAGAA-GACAACACTAAAAGATT
* * * *
5311494 AACTTC-TCTTCACGAGAAAGTCAATGACA-ACATCACTAGAAGGTT
1 GACTTCTTCTTCACGAGAAAGTCAA-GA-AGACAACACTAAAAGATT
* * * *
5311539 GACTTATT-TTCACGAGAAAGTCAAGAATGGCAATACTGAAAGATT
1 GACTTCTTCTTCACGAGAAAGTCAAGAA-GACAACACTAAAAGATT
* * * * * * *
5311584 AACTTC-TCTTAATGAGAAAGTCAA-TA-ATAACATTGAAAGATT
1 GACTTCTTCTTCACGAGAAAGTCAAGAAGACAACACTAAAAGATT
* ** * * * *
5311626 GAC-TCCTCTTCACGAGGGAGTCGAG-A-ATAACATTGAAAGATT
1 GACTTCTTCTTCACGAGAAAGTCAAGAAGACAACACTAAAAGATT
* * * ** * * *
5311668 GAC-TCCTATTCATGAGGGAGTCAA-AA-ATAACATTGAAAGATT
1 GACTTCTTCTTCACGAGAAAGTCAAGAAGACAACACTAAAAGATT
* ** * * * *
5311710 GAC-TCCTCTTCACGAGGGAGTCAAGAATGACAATATTGAAATATT
1 GACTTCTTCTTCACGAGAAAGTCAAGAA-GACAACACTAAAAGATT
* * * ** * * *
5311755 TACTTC-TCTTCACAAGAAAGTCAAGAATAACATTAATGAAAGATG
1 GACTTCTTCTTCACGAGAAAGTCAAGAA-GACAACACTAAAAGATT
* * * * * *
5311800 GACTT-ATCTTCAAGAGAAAGTCAA-TA-ATAACATTGAAAGATT
1 GACTTCTTCTTCACGAGAAAGTCAAGAAGACAACACTAAAAGATT
* ** * *
5311842 TAC-TCTTCTTCACGAGGGAGTCAAGAATGACAATACTGAAAGATT
1 GACTTCTTCTTCACGAGAAAGTCAAGAA-GACAACACTAAAAGATT
* * * *
5311887 GA-TT-TTCCTTCACGAGAAAGTCAA-TA-ATAACATTGAAAGATT
1 GACTTCTT-CTTCACGAGAAAGTCAAGAAGACAACACTAAAAGATT
* ** * * * *
5311929 GAC-TCCTCTTCACGAGGGAGTTAAG-A-ATAACATTGAAAGATT
1 GACTTCTTCTTCACGAGAAAGTCAAGAAGACAACACTAAAAGATT
** * * *
5311971 GAC-TCTTCTTCACGAGGGAGTCAAG-A-ATAACATTGAAAGATT
1 GACTTCTTCTTCACGAGAAAGTCAAGAAGACAACACTAAAAGATT
* * * * * *
5312013 GACTCCTT-TTCACGAGGAAGTCAAG-A-ACGACATTGAAATATT
1 GACTTCTTCTTCACGAGAAAGTCAAGAAGACAACACTAAAAGATT
** * * * *
5312055 GACTTC-TCTTCATAAGAAAGTTAAG-A-ATAACATTGAAAGATT
1 GACTTCTTCTTCACGAGAAAGTCAAGAAGACAACACTAAAAGATT
* * * * *
5312097 GAC-TCCTCTTCATGAGAAAGTCAAG-A-ATAACATTGAAAGATT
1 GACTTCTTCTTCACGAGAAAGTCAAGAAGACAACACTAAAAGATT
* * * * * * * *
5312139 GAC-TCATCTACATGAGAGAGTCAAG-A-ACGACATTGAAAGAGT
1 GACTTCTTCTTCACGAGAAAGTCAAGAAGACAACACTAAAAGATT
* * * * * *
5312181 AACTT-ATCTTTACGAGAAAGTCAAGAATA-AA-ATTGAAAGATT
1 GACTTCTTCTTCACGAGAAAGTCAAGAAGACAACACTAAAAGATT
* * * *
5312223 GACTTC-TCTTCACGAGAAAGCCAAG-A-ATAACATTGAAAGATT
1 GACTTCTTCTTCACGAGAAAGTCAAGAAGACAACACTAAAAGATT
* * *
5312265 GAC-TCCTCTTCATGAGAGAGTCAAG
1 GACTTCTTCTTCACGAGAAAGTCAAG
5312290 TTGAAGCTTC
Statistics
Matches: 722, Mismatches: 120, Indels: 89
0.78 0.13 0.10
Matches are distributed among these distances:
40 1 0.00
41 11 0.02
42 436 0.60
43 15 0.02
44 40 0.06
45 205 0.28
46 13 0.02
47 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (45 bp):
GACTTCTTCTTCACGAGAAAGTCAAGAAGACAACACTAAAAGATT
Found at i:5311616 original size:90 final size:90
Alignment explanation
Indices: 5311366--5311616 Score: 244
Period size: 90 Copynumber: 2.8 Consensus size: 90
5311356 AATCGACTTC
* * * * * * *
5311366 TCTTCATGAGAAAGTTAAGAATGACAACACCAATAGATTGACTCCTCTT--CGTACG-AAGTCAA
1 TCTTCACGAGAAAGTCAAGAAGGACAACACTAAAAGATTAACTTCTCTTAACG-A-GAAAGTCAA
* *
5311428 GAATATA-ATCACTAAAAGATTGATTCT
64 TAATA-ACATCACTAAAAGATTGATTAT
* * * *
5311455 TCTTCACGAGAAAGTTAAGAAGGACAACACTAAAAGGTTAACTTCTCTTCACGAGAAAGTCAATG
1 TCTTCACGAGAAAGTCAAGAAGGACAACACTAAAAGATTAACTTCTCTTAACGAGAAAGTCAATA
* * *
5311520 ACAACATCACTAGAAGGTTGACTTAT
66 ATAACATCACTAAAAGATTGA-TTAT
* * *
5311546 T-TTCACGAGAAAGTCAAGAATGG-CAATACTGAAAGATTAACTTCTCTTAATGAGAAAGTCAAT
1 TCTTCACGAGAAAGTCAAGAA-GGACAACACTAAAAGATTAACTTCTCTTAACGAGAAAGTCAAT
5311609 AATAACAT
65 AATAACAT
5311617 TGAAAGATTG
Statistics
Matches: 135, Mismatches: 21, Indels: 11
0.81 0.13 0.07
Matches are distributed among these distances:
89 44 0.33
90 83 0.61
91 8 0.06
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (90 bp):
TCTTCACGAGAAAGTCAAGAAGGACAACACTAAAAGATTAACTTCTCTTAACGAGAAAGTCAATA
ATAACATCACTAAAAGATTGATTAT
Found at i:5311635 original size:42 final size:42
Alignment explanation
Indices: 5311547--5312289 Score: 759
Period size: 42 Copynumber: 17.4 Consensus size: 42
5311537 TTGACTTATT
* * * *
5311547 TTCACGAGAAAGTCAAGAATGGCAATACTGAAAGATTAACTTCTC
1 TTCACGAGAAAGTCAAGAAT---AACATTGAAAGATTGACTCCTC
* * *
5311592 TTAATGAGAAAGTCAATAATAACATTGAAAGATTGACTCCTC
1 TTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTCCTC
** * *
5311634 TTCACGAGGGAGTCGAGAATAACATTGAAAGATTGACTCCTA
1 TTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTCCTC
* ** *
5311676 TTCATGAGGGAGTCAAAAATAACATTGAAAGATTGACTCCTC
1 TTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTCCTC
** * * * *
5311718 TTCACGAGGGAGTCAAGAATGACAATATTGAAATATTTACTTCTC
1 TTCACGAGAAAGTCAAGAAT---AACATTGAAAGATTGACTCCTC
* * **
5311763 TTCACAAGAAAGTCAAGAATAACATTAATGAAAGATGGACTTATC
1 TTCACGAGAAAGTCAAGAATAACA-T--TGAAAGATTGACTCCTC
* * * *
5311808 TTCAAGAGAAAGTCAATAATAACATTGAAAGATTTACTCTTC
1 TTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTCCTC
** * **
5311850 TTCACGAGGGAGTCAAGAATGACAATACTGAAAGATTGA-TTTTCC
1 TTCACGAGAAAGTCAAGAATAAC-AT--TGAAAGATTGACTCCT-C
*
5311895 TTCACGAGAAAGTCAATAATAACATTGAAAGATTGACTCCTC
1 TTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTCCTC
** * *
5311937 TTCACGAGGGAGTTAAGAATAACATTGAAAGATTGACTCTTC
1 TTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTCCTC
** *
5311979 TTCACGAGGGAGTCAAGAATAACATTGAAAGATTGACTCCTT
1 TTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTCCTC
* ** * *
5312021 TTCACGAGGAAGTCAAGAACGACATTGAAATATTGACTTCTC
1 TTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTCCTC
** *
5312063 TTCATAAGAAAGTTAAGAATAACATTGAAAGATTGACTCCTC
1 TTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTCCTC
* *
5312105 TTCATGAGAAAGTCAAGAATAACATTGAAAGATTGACTCATC
1 TTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTCCTC
* * * ** * * **
5312147 TACATGAGAGAGTCAAGAACGACATTGAAAGAGTAACTTATC
1 TTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTCCTC
* * *
5312189 TTTACGAGAAAGTCAAGAATAAAATTGAAAGATTGACTTCTC
1 TTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTCCTC
*
5312231 TTCACGAGAAAGCCAAGAATAACATTGAAAGATTGACTCCTC
1 TTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTCCTC
* *
5312273 TTCATGAGAGAGTCAAG
1 TTCACGAGAAAGTCAAG
5312290 TTGAAGCTTC
Statistics
Matches: 586, Mismatches: 101, Indels: 25
0.82 0.14 0.04
Matches are distributed among these distances:
42 459 0.78
43 5 0.01
44 6 0.01
45 116 0.20
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (42 bp):
TTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTCCTC
Found at i:5317803 original size:22 final size:23
Alignment explanation
Indices: 5317775--5317817 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
5317765 AGAACCCGTG
5317775 GGGGGTATCGATTCCC-CTGCAA
1 GGGGGTATCGATTCCCTCTGCAA
5317797 GGGGGTATCGATTCCCTCTGC
1 GGGGGTATCGATTCCCTCTGC
5317818 CCTATAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.14, C:0.28, G:0.33, T:0.26
Consensus pattern (23 bp):
GGGGGTATCGATTCCCTCTGCAA
Found at i:5327447 original size:17 final size:18
Alignment explanation
Indices: 5327415--5327449 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5327405 AATATCAACA
*
5327415 CCATGTTTTTTTTGAAAC
1 CCATGTTTTTTCTGAAAC
5327433 CCATG-TTTTTCTGAAAC
1 CCATGTTTTTTCTGAAAC
5327450 AATATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (18 bp):
CCATGTTTTTTCTGAAAC
Found at i:5327793 original size:7 final size:7
Alignment explanation
Indices: 5327781--5327828 Score: 96
Period size: 7 Copynumber: 6.9 Consensus size: 7
5327771 ATATATTATA
5327781 ATAACGC
1 ATAACGC
5327788 ATAACGC
1 ATAACGC
5327795 ATAACGC
1 ATAACGC
5327802 ATAACGC
1 ATAACGC
5327809 ATAACGC
1 ATAACGC
5327816 ATAACGC
1 ATAACGC
5327823 ATAACG
1 ATAACG
5327829 TAAAGTGGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.44, C:0.27, G:0.15, T:0.15
Consensus pattern (7 bp):
ATAACGC
Found at i:5330307 original size:33 final size:33
Alignment explanation
Indices: 5330254--5330349 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 33
5330244 GTTGTTTCTC
* *
5330254 TTGTCTCATTTTTTTATTGTC-AGAGTGCATGAA
1 TTGTCTCCTTTGTTTATTGTCGA-AGTGCATGAA
*
5330287 TTGTCTCCTTTGTTTCTTGTCGAAGTGCATGAA
1 TTGTCTCCTTTGTTTATTGTCGAAGTGCATGAA
*
5330320 TTGTTTCCTTTGTTTATTGTCGTAA-TGCAT
1 TTGTCTCCTTTGTTTATTGTCG-AAGTGCAT
5330350 CAATGCTAGC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
33 53 0.95
34 3 0.05
ACGTcount: A:0.17, C:0.15, G:0.19, T:0.50
Consensus pattern (33 bp):
TTGTCTCCTTTGTTTATTGTCGAAGTGCATGAA
Found at i:5336255 original size:17 final size:18
Alignment explanation
Indices: 5336233--5336266 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5336223 TTGAAAGGTC
*
5336233 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
5336250 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
5336267 ACATAATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:5337413 original size:24 final size:25
Alignment explanation
Indices: 5337386--5337493 Score: 91
Period size: 24 Copynumber: 4.5 Consensus size: 25
5337376 AATTATTTTA
*
5337386 TCTGATTTCTGACT-TGAATTCTAT
1 TCTGATTTCTGACTATGAATTCTGT
* *
5337410 TCTGA-TACATGAC-CTGAATTCTGT
1 TCTGATTTC-TGACTATGAATTCTGT
* * *
5337434 TCTGATTTCT-AATCTGGATTCTGT
1 TCTGATTTCTGACTATGAATTCTGT
* *
5337458 TCTGATATCTG-TTATGAATTCTGT
1 TCTGATTTCTGACTATGAATTCTGT
*
5337482 TTTGATTTCTGA
1 TCTGATTTCTGA
5337494 TATCTCCGTT
Statistics
Matches: 67, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
23 3 0.04
24 62 0.93
25 2 0.03
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (25 bp):
TCTGATTTCTGACTATGAATTCTGT
Found at i:5337438 original size:12 final size:12
Alignment explanation
Indices: 5337423--5337492 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
5337413 GATACATGAC
5337423 CTGAATTCTGTT
1 CTGAATTCTGTT
* **
5337435 CTGATTTCTAAT
1 CTGAATTCTGTT
*
5337447 CTGGATTCTGTT
1 CTGAATTCTGTT
5337459 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
*
5337471 ATGAATTCTGTT
1 CTGAATTCTGTT
* *
5337483 TTGATTTCTG
1 CTGAATTCTG
5337493 ATATCTCCGT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:5337461 original size:48 final size:48
Alignment explanation
Indices: 5337386--5337491 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 48
5337376 AATTATTTTA
* *
5337386 TCTGATTTCTGACTTGAATTCTATTCTGATA-CATGACCTGAATTCTGT
1 TCTGATTTCTAACTTGAATTCTATTCTGATATC-TGACATGAATTCTGT
* * **
5337434 TCTGATTTCTAA-TCTGGATTCTGTTCTGATATCTGTTATGAATTCTGT
1 TCTGATTTCTAACT-TGAATTCTATTCTGATATCTGACATGAATTCTGT
*
5337482 TTTGATTTCT
1 TCTGATTTCT
5337492 GATATCTCCG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
47 1 0.02
48 47 0.96
49 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.15, T:0.49
Consensus pattern (48 bp):
TCTGATTTCTAACTTGAATTCTATTCTGATATCTGACATGAATTCTGT
Found at i:5338490 original size:17 final size:17
Alignment explanation
Indices: 5338468--5338501 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5338458 ATACTTGTCT
*
5338468 TTATTAGTATCTATACC
1 TTATTAGTATCAATACC
5338485 TTATTAGTATCAATACC
1 TTATTAGTATCAATACC
5338502 CCTTGCTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (17 bp):
TTATTAGTATCAATACC
Found at i:5340105 original size:30 final size:31
Alignment explanation
Indices: 5340035--5340106 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
5340025 TTTTATTTAA
* * * *
5340035 AATTCAAATTCCATTCTTATCTTTAGCAACT
1 AATTCAAATTCCACTATTATCTTCAACAACT
*
5340066 AATTCAAATTCCACTATTATCTTCAACAGCT
1 AATTCAAATTCCACTATTATCTTCAACAACT
5340097 AA-TCAAATTC
1 AATTCAAATTC
5340107 AAATTCCAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 8 0.22
31 28 0.78
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.38
Consensus pattern (31 bp):
AATTCAAATTCCACTATTATCTTCAACAACT
Found at i:5348922 original size:2 final size:2
Alignment explanation
Indices: 5348910--5348949 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
5348900 GTTACAATTT
5348910 TA TA CTA 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
5348950 TATCGTCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5355723 original size:29 final size:29
Alignment explanation
Indices: 5355682--5355740 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
5355672 TTATTTTATC
** *
5355682 TTATTCGAATTTATTCACTGATTTTTATTT
1 TTATTCGAATTTAGCCACTG-TTTGTATTT
*
5355712 TTATTC-ATTTTAGCCACTGTTTGTATTT
1 TTATTCGAATTTAGCCACTGTTTGTATTT
5355740 T
1 T
5355741 ATTTATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 9 0.36
29 10 0.40
30 6 0.24
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.59
Consensus pattern (29 bp):
TTATTCGAATTTAGCCACTGTTTGTATTT
Found at i:5359597 original size:21 final size:21
Alignment explanation
Indices: 5359571--5359619 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
5359561 CAACAAAGTG
* *
5359571 CCACATATTTATCTCGAAGGA
1 CCACATAATTATCACGAAGGA
5359592 CCACATAATTATCACGAAGGA
1 CCACATAATTATCACGAAGGA
5359613 CCACATA
1 CCACATA
5359620 GACCCTCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (21 bp):
CCACATAATTATCACGAAGGA
Found at i:5362109 original size:117 final size:117
Alignment explanation
Indices: 5361889--5362109 Score: 300
Period size: 117 Copynumber: 1.9 Consensus size: 117
5361879 TCTCATTCTA
* * * * * * *
5361889 TGATGGAATTGAACTAAGGTTAAACCAGTTTTTCTTATTATGAACTTCTTCTCCCTCGCTGGATG
1 TGATGGAATTGAACCAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCACCGGACG
* *
5361954 AGTTCTTCTCATTATGAACTCTCATTTGGAAATATTGATCCACCTCCTTATG
66 AGTTCTTCTCATTATGAACTCTCATCTGAAAATATTGATCCACCTCCTTATG
* *
5362006 TGATGGAGTTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCACCGGACG
1 TGATGGAATTGAACCAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCACCGGACG
* * *
5362071 AGTTCTTCTCCTTATGAACTC-CCTGCTGAAAATGTTGAT
66 AGTTCTTCTCATTATGAACTCTCAT-CTGAAAATATTGAT
5362110 GCAAGGTTGA
Statistics
Matches: 89, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
116 2 0.02
117 87 0.98
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (117 bp):
TGATGGAATTGAACCAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCACCGGACG
AGTTCTTCTCATTATGAACTCTCATCTGAAAATATTGATCCACCTCCTTATG
Found at i:5362121 original size:91 final size:89
Alignment explanation
Indices: 5362020--5362331 Score: 437
Period size: 91 Copynumber: 3.4 Consensus size: 89
5362010 GGAGTTGAAC
* *
5362020 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCACCGGACGAGTTCTTCTCCTTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTCC-GA-GAGTTCTTCTCATTA
* *
5362085 TGAACTCC-CTGCTGAAAATGTTGATG
64 TGAATTCCTC-GCTGGAAATGTTGATG
*
5362111 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTCAGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC-TCCGA-GAGTTCTTCTCATTA
*
5362176 TGAATTCCTCGCTGGAAATGTTAATG
64 TGAATTCCTCGCTGGAAATGTTGATG
* ** *
5362202 CAAGGTTGAACAAGTTCTTCTCATTATGGACTTCTTCTCTTTCTTCCGATATGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC-TCCGAGA-GTTCTTCTCATTA
* *
5362267 TGAATTACTCGCTGGAAATATTGATG
64 TGAATTCCTCGCTGGAAATGTTGATG
*
5362293 CAAGGTTGAGCAAGTTCTTCTCATTATGAACTTCTTCTC
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
5362332 ATTATGAACT
Statistics
Matches: 201, Mismatches: 17, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
90 1 0.00
91 198 0.99
92 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (89 bp):
CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTCCGAGAGTTCTTCTCATTATG
AATTCCTCGCTGGAAATGTTGATG
Found at i:5362329 original size:17 final size:17
Alignment explanation
Indices: 5362307--5362341 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5362297 GTTGAGCAAG
5362307 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
5362324 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
5362341 T
1 T
5362342 CCTCGCTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.49
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:5362354 original size:69 final size:69
Alignment explanation
Indices: 5362255--5362400 Score: 238
Period size: 69 Copynumber: 2.1 Consensus size: 69
5362245 TTCCGATATG
* * *
5362255 TTCTTCTCATTATGAATTACTCGCTGGAAATATTGATGCAAGGTTGAGCAAGTTCTTCTCATTAT
1 TTCTTCTCATTATGAACTACTCGCTAGAAATATTGATGCAAGGTTGAACAAGTTCTTCTCATTAT
5362320 GAAC
66 GAAC
* * *
5362324 TTCTTCTCATTATGAACTCCTCGCTAGAAATGTTGATGCAAGGTTGAATAAGTTCTTCTCATTAT
1 TTCTTCTCATTATGAACTACTCGCTAGAAATATTGATGCAAGGTTGAACAAGTTCTTCTCATTAT
5362389 GAAC
66 GAAC
5362393 TTCTTCTC
1 TTCTTCTC
5362401 CCTCGTCAGA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (69 bp):
TTCTTCTCATTATGAACTACTCGCTAGAAATATTGATGCAAGGTTGAACAAGTTCTTCTCATTAT
GAAC
Found at i:5364525 original size:23 final size:21
Alignment explanation
Indices: 5364492--5364546 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 21
5364482 AAAAAATTTC
* *
5364492 TTTTTTCTTTTCTTTTTCTCTA
1 TTTTTTATTTTCTTCTTCT-TA
5364514 TTCTTTTATTTTTCTTCTTCTTA
1 TT-TTTTA-TTTTCTTCTTCTTA
5364537 TTTTCTTATT
1 TTTT-TTATT
5364547 CCTTATTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 6 0.21
23 11 0.39
24 11 0.39
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTTATTTTCTTCTTCTTA
Found at i:5372035 original size:19 final size:20
Alignment explanation
Indices: 5372001--5372051 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
5371991 TTTGTCTTGA
5372001 AGTATCGATACTCCTCGAAG
1 AGTATCGATACTCCTCGAAG
*
5372021 AGTATCGAT-CTCCTCGAGG
1 AGTATCGATACTCCTCGAAG
*
5372040 AGTACCGATACT
1 AGTATCGATACT
5372052 ACTAGATGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (20 bp):
AGTATCGATACTCCTCGAAG
Found at i:5373766 original size:21 final size:21
Alignment explanation
Indices: 5373742--5373786 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
5373732 ATACTCGAGC
5373742 TAGATTCAATGCAATGGATGA
1 TAGATTCAATGCAATGGATGA
*
5373763 TAGATTCAATGCAGTGGATGA
1 TAGATTCAATGCAATGGATGA
5373784 TAG
1 TAG
5373787 GCTCGATGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.29
Consensus pattern (21 bp):
TAGATTCAATGCAATGGATGA
Found at i:5373795 original size:21 final size:21
Alignment explanation
Indices: 5373742--5373795 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
5373732 ATACTCGAGC
*
5373742 TAGATTCAATGCAATGGATGA
1 TAGACTCAATGCAATGGATGA
* *
5373763 TAGATTCAATGCAGTGGATGA
1 TAGACTCAATGCAATGGATGA
* *
5373784 TAGGCTCGATGC
1 TAGACTCAATGC
5373796 GCTTACTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (21 bp):
TAGACTCAATGCAATGGATGA
Found at i:5378371 original size:22 final size:22
Alignment explanation
Indices: 5378343--5378389 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
5378333 TTCAATCCAG
5378343 AAAAATTATTTAAAATATATTA
1 AAAAATTATTTAAAATATATTA
* *
5378365 AAAAATTATTTAATATATGTTA
1 AAAAATTATTTAAAATATATTA
5378387 AAA
1 AAA
5378390 GACATTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAAAATTATTTAAAATATATTA
Found at i:5378450 original size:22 final size:21
Alignment explanation
Indices: 5378418--5378468 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
5378408 TACATATAAA
5378418 TAAATATATTTATCTAAT-TTATT
1 TAAAT-TATTT-T-TAATATTATT
5378441 TAAATTATTTTTAATAATTATT
1 TAAATTATTTTTAAT-ATTATT
5378463 TAAATT
1 TAAATT
5378469 GAATATTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.15
21 1 0.04
22 16 0.62
23 5 0.19
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TAAATTATTTTTAATATTATT
Found at i:5380597 original size:194 final size:193
Alignment explanation
Indices: 5380243--5380598 Score: 482
Period size: 194 Copynumber: 1.8 Consensus size: 193
5380233 GTTTTGCTAT
* *
5380243 AATATCTCTTTCGTCACATATAAGTTGATTTTAATGTATTTTTGTGACAATATAAATTATCAATA
1 AATATCTCTTTCGTCACATATAAGTTGATTTTAATGTATTTATGTGACAATATAAATCATCAATA
** * *
5380308 ACGAAATCTTATTTACTTTAGTGACTTAACCAACTGTCATAGAATATAAATTATAAAGTGACGTT
66 ACGAAATCTTACATAATTTAGTGACATAACCAACTGTCATAGAATATAAATTATAAAGTGACGTT
* * *
5380373 ATGCATAAACGTCATTCATAATAGTATTAGGTAACATTTATATTATGTCACTAAAAATGTGAC
131 ATACATAAACGTCATCCATAATACTATTAGGTAACATTTATATTATGTCACTAAAAATGTGAC
*
5380436 AATATCTCTTTCGTCACATATATA-TTGATTTTAATGTATTATATGTGACGATATAAATCATCAA
1 AATATCTCTTTCGTCACATATA-AGTTGATTTTAATGTATT-TATGTGACAATATAAATCATCAA
** ** * * *
5380500 TAACGAAAT-TTCACATAATTTAGTGACATAATTAGTTGTCATTGAATATTAATTATATAGTGAC
64 TAACGAAATCTT-ACATAATTTAGTGACATAACCAACTGTCATAGAATATAAATTATAAAGTGAC
* * **
5380564 GTTATATATAAATGTCATCCATGCTACTATTAGGT
128 GTTATACATAAACGTCATCCATAATACTATTAGGT
5380599 GACGATATGC
Statistics
Matches: 139, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
193 40 0.29
194 99 0.71
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (193 bp):
AATATCTCTTTCGTCACATATAAGTTGATTTTAATGTATTTATGTGACAATATAAATCATCAATA
ACGAAATCTTACATAATTTAGTGACATAACCAACTGTCATAGAATATAAATTATAAAGTGACGTT
ATACATAAACGTCATCCATAATACTATTAGGTAACATTTATATTATGTCACTAAAAATGTGAC
Found at i:5380643 original size:193 final size:192
Alignment explanation
Indices: 5380243--5380650 Score: 473
Period size: 194 Copynumber: 2.1 Consensus size: 192
5380233 GTTTTGCTAT
* *
5380243 AATATCTCTTTCGTCACATATAAGTTGATTTTAATGTATTTTTGTGACAATATAAATTATCAATA
1 AATATCTCTTTCGTCACATATAAGTTGATTTTAATGTATTTATGTGACAATATAAATCATCAATA
** * *
5380308 ACGAAATCTTATTTACTTTAGTGACTTAACCAACTGTCATAGAATATAAATTATAAAGTGACGTT
66 ACGAAATCTTACATAATTTAGTGACATAACCAACTGTCATAGAATATAAATTATAAAGTGACGTT
* * * * *
5380373 ATGCATAAACGTCATTCATAATAGTATTAGGTAACATTTATATTATGTCACTAAAAATGTGAC
131 ATACATAAACGTCATCCATAATACTATTAGGTAACA-TTATACTACGTCACTAAAAATGTGAC
*
5380436 AATATCTCTTTCGTCACATATATA-TTGATTTTAATGTATTATATGTGACGATATAAATCATCAA
1 AATATCTCTTTCGTCACATATA-AGTTGATTTTAATGTATT-TATGTGACAATATAAATCATCAA
** ** * * *
5380500 TAACGAAAT-TTCACATAATTTAGTGACATAATTAGTTGTCATTGAATATTAATTATATAGTGAC
64 TAACGAAATCTT-ACATAATTTAGTGACATAACCAACTGTCATAGAATATAAATTATAAAGTGAC
* * ** * * * *
5380564 GTTATATATAAATGTCATCCATGCTACTATTAGGTGACGA-TATGCTACGTTACTAACAATGTGA
128 GTTATACATAAACGTCATCCATAATACTATTAGGTAAC-ATTATACTACGTCACTAAAAATGTGA
5380628 C
192 C
* *
5380629 AAT-TTTCTTTTCGTCACGTATA
1 AATATCTC-TTTCGTCACATATA
5380651 CAATTAAATT
Statistics
Matches: 181, Mismatches: 29, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
192 3 0.02
193 76 0.42
194 101 0.56
195 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (192 bp):
AATATCTCTTTCGTCACATATAAGTTGATTTTAATGTATTTATGTGACAATATAAATCATCAATA
ACGAAATCTTACATAATTTAGTGACATAACCAACTGTCATAGAATATAAATTATAAAGTGACGTT
ATACATAAACGTCATCCATAATACTATTAGGTAACATTATACTACGTCACTAAAAATGTGAC
Found at i:5385218 original size:22 final size:23
Alignment explanation
Indices: 5385186--5385235 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
5385176 GTTATGTAGA
*
5385186 GGGCCCGAGTTTGGATTTT-CTT
1 GGGCCCCAGTTTGGATTTTGCTT
* *
5385208 GGGCCCCAGTTTGGGTTTTGTTT
1 GGGCCCCAGTTTGGATTTTGCTT
5385231 GGGCC
1 GGGCC
5385236 TGGTTTGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.06, C:0.20, G:0.36, T:0.38
Consensus pattern (23 bp):
GGGCCCCAGTTTGGATTTTGCTT
Found at i:5385486 original size:17 final size:17
Alignment explanation
Indices: 5385464--5385505 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
5385454 AAGTCTACAT
*
5385464 TTAAATTAGATTAAAAA
1 TTAAATTAAATTAAAAA
*
5385481 TTAAATTAAATTCAAAA
1 TTAAATTAAATTAAAAA
*
5385498 GTAAATTA
1 TTAAATTA
5385506 TGCGTGAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (17 bp):
TTAAATTAAATTAAAAA
Found at i:5392013 original size:146 final size:145
Alignment explanation
Indices: 5391581--5391991 Score: 554
Period size: 146 Copynumber: 2.8 Consensus size: 145
5391571 AAATTCCATG
* * * * * * *
5391581 TATCGATACTTAATATATGTGCATCGATACATTTTGTGTGAAAATTGTTTGAGAATCATAATGGA
1 TATCGATACTTAATA-ATGTGTATCGATACATTTGGCGTGCAAATTGTTTGACAATCATACTAGA
*
5391646 ATAAAAGTATCCATACCT-GCATAAGAAGTATCGTTACTTGGACATTTTCATACTTTGCATACAT
65 ATAAAAGTATCCATA-CTGGCATAAGAAGTATCGATACTTGGACATTTTCATACTTTGCATACAT
*
5391710 TGTTTCGAAATTATAAA
129 TGTTTCAAAATTATAAA
* * *
5391727 TATTGATACTTTAATAATGTGTATCGATACATTTGGCGTACAAATTGTTTGACAATTATACTAGA
1 TATCGATAC-TTAATAATGTGTATCGATACATTTGGCGTGCAAATTGTTTGACAATCATACTAGA
* * * * *
5391792 ATAACAGTATCCATATTGGCATAAGATGTATTGATACTTGGATATTTTCATACTTTGCATACATT
65 ATAAAAGTATCCATACTGGCATAAGAAGTATCGATACTTGGACATTTTCATACTTTGCATACATT
5391857 GTTTCAAAATTATAAA
130 GTTTCAAAATTATAAA
* * * *
5391873 TATCGACACTCTAATAATGTGTATTGATACATCTGGCGTGCAAATTGTTTGACAAGCATACTAGA
1 TATCGATACT-TAATAATGTGTATCGATACATTTGGCGTGCAAATTGTTTGACAATCATACTAGA
* * * *
5391938 ATAAAAGTATCCGTACTGGCATAAGAAGTATCAATATTTGGACAGTTTCATACT
65 ATAAAAGTATCCATACTGGCATAAGAAGTATCGATACTTGGACATTTTCATACT
5391992 CTACAATTTT
Statistics
Matches: 229, Mismatches: 33, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
145 2 0.01
146 221 0.97
147 6 0.03
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (145 bp):
TATCGATACTTAATAATGTGTATCGATACATTTGGCGTGCAAATTGTTTGACAATCATACTAGAA
TAAAAGTATCCATACTGGCATAAGAAGTATCGATACTTGGACATTTTCATACTTTGCATACATTG
TTTCAAAATTATAAA
Found at i:5403398 original size:2 final size:2
Alignment explanation
Indices: 5403391--5403424 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
5403381 TTTATCTCCT
5403391 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
5403425 GTATGCATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5403944 original size:3 final size:3
Alignment explanation
Indices: 5403936--5403984 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
5403926 TCTGTTTCAT
*
5403936 TTA TTA TTA TTA TTA TTA TTA TT- TTA TT- TTA ATA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5403981 TTA T
1 TTA T
5403985 ATTTATTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 6 0.15
3 35 0.85
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5403971 original size:22 final size:22
Alignment explanation
Indices: 5403935--5403989 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 22
5403925 ATCTGTTTCA
*
5403935 TTTATTATTATTATTATTATTAT
1 TTTATT-TTAATATTATTATTAT
5403958 TTTATTTTAATATTATTATTAT
1 TTTATTTTAATATTATTATTAT
*
5403980 ATTATATTTA
1 TTTAT-TTTA
5403990 TTAAATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 19 0.66
23 10 0.34
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTATTTTAATATTATTATTAT
Found at i:5403972 original size:28 final size:28
Alignment explanation
Indices: 5403935--5403991 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
5403925 ATCTGTTTCA
*
5403935 TTTATTATTATTATTATTATTAT-TTTAT
1 TTTAATATTATTATTA-TATTATATTTAT
5403963 TTTAATATTATTATTATATTATATTTAT
1 TTTAATATTATTATTATATTATATTTAT
5403991 T
1 T
5403992 AAATAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (28 bp):
TTTAATATTATTATTATATTATATTTAT
Found at i:5403973 original size:19 final size:20
Alignment explanation
Indices: 5403939--5403984 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
5403929 GTTTCATTTA
*
5403939 TTATTATTATTATTATTATT
1 TTATTATTAATATTATTATT
5403959 TTATT-TTAATATTATTATT
1 TTATTATTAATATTATTATT
*
5403978 ATATTAT
1 TTATTAT
5403985 ATTTATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTATTAATATTATTATT
Found at i:5405439 original size:12 final size:12
Alignment explanation
Indices: 5405409--5405458 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
5405399 TGTTATTTTA
5405409 TATTTTAATTAT
1 TATTTTAATTAT
**
5405421 TGCTTTAATTAT
1 TATTTTAATTAT
5405433 TATTTT-ATTAT
1 TATTTTAATTAT
5405444 TATTTTTAATT-T
1 TA-TTTTAATTAT
5405456 TAT
1 TAT
5405459 AAATAACTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
11 8 0.25
12 21 0.66
13 3 0.09
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:5405700 original size:33 final size:32
Alignment explanation
Indices: 5405650--5405713 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
5405640 TAGAAGTCCT
* *
5405650 TTTATAATATTTCTAAATAAATAAATATTTTA
1 TTTATAATATATATAAATAAATAAATATTTTA
* *
5405682 TTTATAAATATATATAAATTAATATATATTTT
1 TTTAT-AATATATATAAATAAATAAATATTTT
5405714 TCATAATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 5 0.19
33 22 0.81
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (32 bp):
TTTATAATATATATAAATAAATAAATATTTTA
Found at i:5414715 original size:46 final size:46
Alignment explanation
Indices: 5414641--5414728 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
5414631 TGACCAGAAA
* * * * *
5414641 TCTGTGCATAAGTCACATGAAATAATGAATGTGTTGTCAAATAGCG
1 TCTGTGCAGAAGCCACAAGAAAGAATGAATGTGTTATCAAATAGCG
*
5414687 TCTGTGCAGAAGCCACAAGAAAGGATGAATGTGTTATCAAAT
1 TCTGTGCAGAAGCCACAAGAAAGAATGAATGTGTTATCAAAT
5414729 GTTTTACTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (46 bp):
TCTGTGCAGAAGCCACAAGAAAGAATGAATGTGTTATCAAATAGCG
Found at i:5415194 original size:22 final size:22
Alignment explanation
Indices: 5415164--5415283 Score: 204
Period size: 22 Copynumber: 5.5 Consensus size: 22
5415154 TCTACATTCC
*
5415164 TCAAAGATGATAGATTCTCTCT
1 TCAAAGATGATAGATTCTCTTT
*
5415186 TCAATGATGATAGATTCTCTTT
1 TCAAAGATGATAGATTCTCTTT
*
5415208 TCAAAGATGATAGATTCTCTCT
1 TCAAAGATGATAGATTCTCTTT
5415230 TCAAAGATGATAGATTCTCTTT
1 TCAAAGATGATAGATTCTCTTT
*
5415252 TTAAAGATGATAGATTCTCTTT
1 TCAAAGATGATAGATTCTCTTT
5415274 TCAAAGATGA
1 TCAAAGATGA
5415284 AAGCTTTGTT
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 91 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (22 bp):
TCAAAGATGATAGATTCTCTTT
Found at i:5416109 original size:74 final size:76
Alignment explanation
Indices: 5415958--5416134 Score: 241
Period size: 74 Copynumber: 2.3 Consensus size: 76
5415948 CTATTTCTCA
* * *
5415958 CATCTGTAAGTCCTACAATGAATAATGTTTCCAAAAAGCCTTCGAGAGTTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTG-ATAATATTTCCAAAAAGCCTTCGAGAGTCTTTTTGATGTTTTCA
*
5416023 AAGCCTTAGGGT
65 AAACCTTAGGGT
* *
5416035 CATCTGTAAGTCCTACAGTG-TGATATTTCCAAAAAGCCTTCGGGAG-CTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGATAATATTTCCAAAAAGCCTTCGAGAGTCTTTTTGATGTTTTCAA
*
5416098 AACCTTCGGGT
66 AACCTTAGGGT
* *
5416109 CAGCTGTAAGCCCTACAGTGCATAAT
1 CATCTGTAAGTCCTACAGTG-ATAAT
5416135 TTTTTTTTCT
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
74 43 0.49
75 23 0.26
76 3 0.03
77 19 0.22
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGATAATATTTCCAAAAAGCCTTCGAGAGTCTTTTTGATGTTTTCAA
AACCTTAGGGT
Found at i:5416360 original size:112 final size:112
Alignment explanation
Indices: 5416163--5417598 Score: 2049
Period size: 112 Copynumber: 12.6 Consensus size: 112
5416153 TTCCAGGTAT
5416163 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
5416228 AACTTTTTGCTAGAATTCATCATTCGATGGATCAGCATTTCCAGAAG
66 AACTTTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAG
*
5416275 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
5416340 AACTTTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAG
66 AACTTTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAG
*
5416387 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
5416452 AA-TCTTTTGCTTGAATTCATCATTGGATGGATCAGCATTTCCAGAAG
66 AACT-TTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAG
5416499 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
**
5416564 AACTTTTTGCTTGAATTCATCATTCGATGGATCAATATTTCCAGAAG
66 AACTTTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAG
* *
5416611 AGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGGAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
5416676 AA-TCTTTTGCTTGAATTCATCATTCGATGGATCAACATTTCCAGAAG
66 AACT-TTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAG
*
5416723 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
5416788 AA-TCTTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAG
66 AACT-TTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAG
5416835 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
5416900 AACTTTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAG
66 AACTTTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAG
*
5416947 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
5417012 AATCTTTTT-CTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAG
66 AA-CTTTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAG
* * *
5417059 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * *** *
5417124 AACCTTTTGTTTGAATTCATCACTCGATGGATCAATTTTTCCAGAGAA
66 AACTTTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGA-AG
* * *
5417172 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAGCTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * *** * * *
5417237 AACCTTTTGCATG-ATTCTATCACAGAAGGAGATAGATCATCATCAATTTTTCCAGAGAA
66 AACTTTTTGCTTGAATTC-AT--C---ATTCGAT-G--GATCAGC-A--TTTCCAGA-AG
* *
5417296 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * *** *
5417361 AACCTTTT-CTTTGAATTCATCACTCGATGGATCAATTTTTCCAGAGAA
66 AACTTTTTGC-TTGAATTCATCATTCGATGGATCAGCATTTCCAGA-AG
* *
5417409 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * * * ** * *
5417474 AACCTTTTGTTTGACTTTATCACAGAAGGAGATAGATCAACATCAACATTTCTAGAAG
66 AACTTTTTGCTTGAATTCAT--C------A-TTCGAT--GGATCAGCATTTCCAGAAG
* * *
5417532 TGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
5417596 AAC
66 AAC
5417599 CTTGCCTTAA
Statistics
Matches: 1214, Mismatches: 77, Indels: 56
0.90 0.06 0.04
Matches are distributed among these distances:
111 7 0.01
112 849 0.70
113 169 0.14
115 2 0.00
116 4 0.00
118 5 0.00
119 5 0.00
121 5 0.00
122 36 0.03
123 33 0.03
124 95 0.08
125 4 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (112 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAG
Found at i:5417305 original size:124 final size:124
Alignment explanation
Indices: 5417154--5417601 Score: 579
Period size: 124 Copynumber: 3.7 Consensus size: 124
5417144 CACTCGATGG
5417154 ATCAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA-AAAGTTCA
1 ATCAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA-TTCA
* * * *
5417218 TAATGAGAAGAGCTTATTCAACCTTTTGCATGATTCTATCACAGAAGGAGATAGATCATC
65 TAATGAGAAGAACTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGAGATAGATCAAC
5417278 ATCAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
1 ATCAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
* * **
5417343 AATGAGAAGAATTTGTTCAACCTTTT-CTTTGAATTC-ATCAC---------TCGAT--GG
66 AATGAGAAGAACTTGTTCAACCTTTTGC-TTG-ATTCTATCACAGAAGGAGATAGATCAAC
* *
5417391 ATCAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCAT
1 ATCAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
* *
5417456 AATGAGAAGAGCTTGTTCAACCTTTTGTTTGACTT-TATCACAGAAGGAGATAGATCAAC
66 AATGAGAAGAACTTGTTCAACCTTTTGCTTGA-TTCTATCACAGAAGGAGATAGATCAAC
** * **
5417515 ATCAACATTTCTAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAATTCAT
1 ATCAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
*
5417578 AATGAGAAGAATTTGTTCAACCTT
66 AATGAGAAGAACTTGTTCAACCTT
5417602 GCCTTAATTT
Statistics
Matches: 283, Mismatches: 24, Indels: 36
0.83 0.07 0.10
Matches are distributed among these distances:
112 1 0.00
113 97 0.34
115 4 0.01
122 38 0.13
123 33 0.12
124 103 0.36
125 7 0.02
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (124 bp):
ATCAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
AATGAGAAGAACTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGAGATAGATCAAC
Found at i:5417941 original size:3 final size:3
Alignment explanation
Indices: 5417933--5417975 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
5417923 TTTGTTTCAT
*
5417933 TTA TTA TTA TTA TTA TT- TTA TT- TTA ATA TTA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5417976 ATTTATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 6 0.17
3 29 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5417962 original size:22 final size:23
Alignment explanation
Indices: 5417931--5417980 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
5417921 CATTTGTTTC
* *
5417931 ATTTATTATTATTATTATTTTAT
1 ATTTAATATTATTATTATATTAT
5417954 -TTTAATATTATTATTATATTAT
1 ATTTAATATTATTATTATATTAT
5417976 ATTTA
1 ATTTA
5417981 TTAAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
ATTTAATATTATTATTATATTAT
Found at i:5418655 original size:21 final size:21
Alignment explanation
Indices: 5418626--5418673 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
5418616 AAGGGAAAAA
**
5418626 GAGG-TCGGATTTGGCCAGGG
1 GAGGTTCGGATTCAGCCAGGG
5418646 GAGGTTCGGATTCAGCCAGGG
1 GAGGTTCGGATTCAGCCAGGG
5418667 GAGGTTC
1 GAGGTTC
5418674 AGAACTTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.17, C:0.17, G:0.46, T:0.21
Consensus pattern (21 bp):
GAGGTTCGGATTCAGCCAGGG
Found at i:5419437 original size:12 final size:12
Alignment explanation
Indices: 5419407--5419449 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
5419397 TGTTATTTTA
5419407 TATTTTAATTAT
1 TATTTTAATTAT
**
5419419 TGCTTTAATTAT
1 TATTTTAATTAT
5419431 TATTTT-ATTAT
1 TATTTTAATTAT
5419442 TATTTTAA
1 TATTTTAA
5419450 ATTTATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:5426707 original size:18 final size:18
Alignment explanation
Indices: 5426684--5426719 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5426674 TAAATCAAAC
*
5426684 AAGATGATGAATATTAGA
1 AAGATGATGAATAATAGA
5426702 AAGATGATGAATAATAGA
1 AAGATGATGAATAATAGA
5426720 TAATAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (18 bp):
AAGATGATGAATAATAGA
Found at i:5443077 original size:20 final size:20
Alignment explanation
Indices: 5443052--5443104 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
5443042 TCTGCCCAAT
*
5443052 ACTCCATTGAGCCCGAAGGG
1 ACTCCACTGAGCCCGAAGGG
5443072 ACTCCACTGAGCCCGAAGGG
1 ACTCCACTGAGCCCGAAGGG
5443092 ACTCCACTGAGCC
1 ACTCCACTGAGCC
5443105 AAGTTCTTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.36, G:0.26, T:0.13
Consensus pattern (20 bp):
ACTCCACTGAGCCCGAAGGG
Found at i:5446699 original size:268 final size:265
Alignment explanation
Indices: 5446202--5446837 Score: 664
Period size: 268 Copynumber: 2.4 Consensus size: 265
5446192 CTATTTCTGC
* * * * *
5446202 AGGGTAGATCAGA-TCGAG-AAACATTGATTCA-TTCCACTGTTCTTTAGTGAAGATTGAATCGG
1 AGGGGAGATAAGACTCGAGAAAACATTGATCCACTT-CACTGTTCTTCAGGGAAGATTGAATC-G
* * * * * * *
5446264 AATCGATTTGTTTTACTACTTTTCAGGAAAACCAAATCTGAAAGAAGAAGAATCTGCTCAACTGC
64 AATTGATTTGCTTCATTACTATTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCAACTAC
* * * ** * ** *
5446329 TCTTTAGGGGAGATCGGACTCTTGAAAACTTTGTTCCATTTCACAATTCTTCATTAAAGTTTGAA
129 TATTTAGGGGAGAACAGACTCGAGAAAACTTTATTCCATTT--CAATTCTTCAGGAAAGATTGAA
* *
5446394 TCATAATCAATTTGCTTCACTGCTCTTCAAAAAGACCAAATATGAAAGAATAAT-AAT-TTGCTC
192 TCAGAATCAATTTGCTTCACTGCTCTTCAAAAAGACCAAATATGAAAGAAT-ATGAATCTT-ATC
*
5446457 CACTACTCTTT
255 AACTACTCTTT
*
5446468 AGGGGAGATCAA-ACTCTAGAAAACATTGATCCACTTCACTGTTCTTCAGGGAAGATTGAATCAG
1 AGGGGAGAT-AAGACTCGAGAAAACATTGATCCACTTCACTGTTCTTCAGGGAAGATTGAATC-G
* *
5446532 AATTGATTTGCTTCATTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTTG-TCCACTA
64 AATTGATTTGCTTCATTACTATTCAGGAAGACCAAATCTGAAAGAAGAAGAATC-TGCTCAACTA
* * *
5446596 CTATTTAGGGGATAACAGACTCGAGAAAACTTTAATT-CACTTT-ATTTCACTTCAGGGAAGATT
128 CTATTTAGGGGAGAACAGACTCGAGAAAACTTT-ATTCCA-TTTCAATT--CTTCAGGAAAGATT
* * **
5446659 GAATCAGAATCGATTTGCTTCAGTGCTCTTCAGGAAGACCAAATATGAAAGAATATGAATCTTAT
189 GAATCAGAATCAATTTGCTTCACTGCTCTTCAAAAAGACCAAATATGAAAGAATATGAATCTTAT
5446724 CAACTACTCTTT
254 CAACTACTCTTT
* * * * * *
5446736 AGGGGAGATAAGACTCGAGAAATC-TCTTATCTACTTCAATGCTCTTCA-GGAAGATTAAATCGA
1 AGGGGAGATAAGACTCGAGAAAACAT-TGATCCACTTCACTGTTCTTCAGGGAAGATTGAATCGA
* * * *
5446799 ACGTGGTTTGCTTCGTTGCTATTCAGGAAGACCAAATCT
65 A-TTGATTTGCTTCATTACTATTCAGGAAGACCAAATCT
5446838 AAAAAGCAAA
Statistics
Matches: 310, Mismatches: 46, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
266 15 0.05
267 54 0.17
268 230 0.74
269 11 0.04
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (265 bp):
AGGGGAGATAAGACTCGAGAAAACATTGATCCACTTCACTGTTCTTCAGGGAAGATTGAATCGAA
TTGATTTGCTTCATTACTATTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCAACTACTA
TTTAGGGGAGAACAGACTCGAGAAAACTTTATTCCATTTCAATTCTTCAGGAAAGATTGAATCAG
AATCAATTTGCTTCACTGCTCTTCAAAAAGACCAAATATGAAAGAATATGAATCTTATCAACTAC
TCTTT
Found at i:5446783 original size:134 final size:134
Alignment explanation
Indices: 5446250--5446835 Score: 533
Period size: 134 Copynumber: 4.4 Consensus size: 134
5446240 GTTCTTTAGT
* * * * * * *
5446250 GAAGATTGAATCGGAATCGATTTGTTTTACTACTTTTCAGGAAAACCAAATCTGAAAGAAGAAGA
1 GAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGA
* * ** ** ** *
5446315 ATCTGCTCAACTGCTCTTTAGGGGAGATCGGACTCTTGAAAACTTTGTTCCATTTCACAAT--TC
66 ATCTTCTCAACTACTCTTTAGGGGAGATAAGACTCGAGAAAACTTTAATCCACTT--CAATGCTC
**
5446378 TTCATT
129 TTCAGG
* * * * ** * *
5446384 AAAGTTTGAATCATAATCAATTTGCTTCACTGCTCTTCAAAAAGACCAAATATGAAAGAATAATA
1 GAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGA
* * * * * *
5446449 AT-TTGCTCCACTACTCTTTAGGGGAGATCAA-ACTCTAGAAAACATTGATCCACTTCACTGTTC
66 ATCTT-CTCAACTACTCTTTAGGGGAGAT-AAGACTCGAGAAAACTTTAATCCACTTCAATGCTC
5446512 TTCAGG
129 TTCAGG
* * * *
5446518 GAAGATTGAATCAGAATTGATTTGCTTCATTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAGA
1 GAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGA
* * * * * * * * *
5446583 ATCTTGTCCACTACTATTTAGGGGATA-ACAGACTCGAGAAAACTTTAATTCACTTTATTTCACT
66 ATCTTCTCAACTACTCTTTAGGGGAGATA-AGACTCGAGAAAACTTTAATCCACTTCAATGCTCT
5446647 TCAGG
130 TCAGG
* * *
5446652 GAAGATTGAATCAGAATCGATTTGCTTCAGTGCTCTTCAGGAAGACCAAATATGAAAGAATATGA
1 GAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGA
* * *
5446717 ATCTTATCAACTACTCTTTAGGGGAGATAAGACTCGAGAAATCTCTT-ATCTACTTCAATGCTCT
66 ATCTTCTCAACTACTCTTTAGGGGAGATAAGACTCGAGAAAACT-TTAATCCACTTCAATGCTCT
5446781 TCA-G
130 TCAGG
* * ** *
5446785 GAAGATTAAATC-GAA-CGTGGTTTGCTTCGTTGCTATTCAGGAAGACCAAAT
1 GAAGATTGAATCAGAATC--GATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
5446836 CTAAAAAGCA
Statistics
Matches: 368, Mismatches: 73, Indels: 23
0.79 0.16 0.05
Matches are distributed among these distances:
131 1 0.00
132 7 0.02
133 43 0.12
134 312 0.85
135 5 0.01
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (134 bp):
GAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGA
ATCTTCTCAACTACTCTTTAGGGGAGATAAGACTCGAGAAAACTTTAATCCACTTCAATGCTCTT
CAGG
Found at i:5447733 original size:135 final size:135
Alignment explanation
Indices: 5447543--5447851 Score: 380
Period size: 135 Copynumber: 2.3 Consensus size: 135
5447533 GAAAACACTA
* * *
5447543 AAAGATTG-ACTTCTATTCATAAGAAAGTCAAGAAGGAA-AACACTAAAAGATTGACTCCTCTTC
1 AAAGATTGAAC-TCTCTTCATGAGAAAGTCAAGAA-TAACAACACTAAAAGATTGACTCCTCTTC
* * *
5447606 GCGAGAAAGTCAAGAA-GTACAACACTA-AAATATTAACTT-TTCTTTATGAGAAAGTCAAGGAA
64 ACGAGAAAGTCAAGAATG-ACAACAC-AGAAATATTAACTTCTT-TTCACGAGAAAGTCAA-GAA
*
5447668 -GACAAAACTG
125 TAACAAAACTG
* *
5447678 AAAGATTG-ACTCATCTTCGTGAGAAAGTCAAGAATAACAACACTAAAAGATTGACTTCTCTTCA
1 AAAGATTGAACTC-TCTTCATGAGAAAGTCAAGAATAACAACACTAAAAGATTGACTCCTCTTCA
* *
5447742 CGAGAAAGTCAAGAATGACAATACAGAAATATTAACTTCTTTTCACGATAAAGTCAAGAATAACA
65 CGAGAAAGTCAAGAATGACAACACAGAAATATTAACTTCTTTTCACGAGAAAGTCAAGAATAACA
*
5447807 ATACTG
130 AAACTG
* *
5447813 AAAGATTGAATTCTCTTCATGAGAAAGTCAATAATAACA
1 AAAGATTGAACTCTCTTCATGAGAAAGTCAAGAATAACA
5447852 TTGAAAGATC
Statistics
Matches: 152, Mismatches: 15, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
134 8 0.05
135 138 0.91
136 6 0.04
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (135 bp):
AAAGATTGAACTCTCTTCATGAGAAAGTCAAGAATAACAACACTAAAAGATTGACTCCTCTTCAC
GAGAAAGTCAAGAATGACAACACAGAAATATTAACTTCTTTTCACGAGAAAGTCAAGAATAACAA
AACTG
Found at i:5447757 original size:45 final size:45
Alignment explanation
Indices: 5447474--5447851 Score: 340
Period size: 45 Copynumber: 8.4 Consensus size: 45
5447464 TCATTTCTGC
* * * **
5447474 GAGAAAATCAAGAATAACACCACTAAAAGGTTGAC-TCATCTTTGT
1 GAGAAAGTCAAGAATAACAACACTAAAAGATTGACTTC-TCTTCAT
* * *
5447519 GAGAAAGCCAA-AACGAA-AACACTAAAAGATTGACTTCTATTCAT
1 GAGAAAGTCAAGAA-TAACAACACTAAAAGATTGACTTCTCTTCAT
* * * **
5447563 AAGAAAGTCAAGAAGGAA-AACACTAAAAGATTGACTCCTCTTCGC
1 GAGAAAGTCAAGAA-TAACAACACTAAAAGATTGACTTCTCTTCAT
* * * *
5447608 GAGAAAGTCAAGAAGT-ACAACACTAAAATATTAACTTTTCTTTAT
1 GAGAAAGTCAAGAA-TAACAACACTAAAAGATTGACTTCTCTTCAT
* * * *
5447653 GAGAAAGTCAAGGAA-GACAAAACTGAAAGATTGAC-TCATCTTCGT
1 GAGAAAGTCAA-GAATAACAACACTAAAAGATTGACTTC-TCTTCAT
*
5447698 GAGAAAGTCAAGAATAACAACACTAAAAGATTGACTTCTCTTCAC
1 GAGAAAGTCAAGAATAACAACACTAAAAGATTGACTTCTCTTCAT
* * * * * *
5447743 GAGAAAGTCAAGAATGACAATAC-AGAAATATTAACTTCTTTTCAC
1 GAGAAAGTCAAGAATAACAACACTA-AAAGATTGACTTCTCTTCAT
* * * *
5447788 GATAAAGTCAAGAATAACAATACTGAAAGATTGAATTCTCTTCAT
1 GAGAAAGTCAAGAATAACAACACTAAAAGATTGACTTCTCTTCAT
*
5447833 GAGAAAGTCAATAATAACA
1 GAGAAAGTCAAGAATAACA
5447852 TTGAAAGATC
Statistics
Matches: 271, Mismatches: 51, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
44 36 0.13
45 230 0.85
46 5 0.02
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (45 bp):
GAGAAAGTCAAGAATAACAACACTAAAAGATTGACTTCTCTTCAT
Found at i:5447859 original size:42 final size:42
Alignment explanation
Indices: 5447543--5447956 Score: 265
Period size: 45 Copynumber: 9.4 Consensus size: 42
5447533 GAAAACACTA
* * * * *
5447543 AAAGATTGACTTCTATTCATAAGAAAGTCAAGAAGGAAAACACTA
1 AAAGATTGACTTCTCTTCATGAGAAAGTCAAG-A--ATAACATTG
* ** * *
5447588 AAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGTACAACACTA
1 AAAGATTGACTTCTCTTCATGAGAAAGTCAAGAA-T--AACATTG
* * * * * * *
5447633 AAATATTAACTTTTCTTTATGAGAAAGTCAAGGAAGACAAAACTG
1 AAAGATTGACTTCTCTTCATGAGAAAGTCAA-G-A-ATAACATTG
* * *
5447678 AAAGATTGAC-TCATCTTCGTGAGAAAGTCAAGAATAACAACACTA
1 AAAGATTGACTTC-TCTTCATGAGAAAGTCAAGAAT---AACATTG
* * *
5447723 AAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATGACAATACAG
1 AAAGATTGACTTCTCTTCATGAGAAAGTCAAGAATAAC-AT--TG
* * * * *
5447768 AAATATTAACTTCTTTTCACGATAAAGTCAAGAATAACAATACTG
1 AAAGATTGACTTCTCTTCATGAGAAAGTCAAGAATAAC-AT--TG
* *
5447813 AAAGATTGAATTCTCTTCATGAGAAAGTCAATAATAACATTG
1 AAAGATTGACTTCTCTTCATGAGAAAGTCAAGAATAACATTG
* * * ** * *
5447855 AAAGATCGACTCCACTTCATGAGGGAGTCAGGAATGACATTG
1 AAAGATTGACTTCTCTTCATGAGAAAGTCAAGAATAACATTG
* * *
5447897 AAAGATCGACTTTTCTTCAGGATG-AAGTCAAGAATAACATTG
1 AAAGATTGACTTCTCTTCATGA-GAAAGTCAAGAATAACATTG
*
5447939 AAAGATTGACTCCTCTTC
1 AAAGATTGACTTCTCTTC
5447957 GCAAAGGAGT
Statistics
Matches: 292, Mismatches: 62, Indels: 33
0.75 0.16 0.09
Matches are distributed among these distances:
42 87 0.30
43 3 0.01
44 5 0.02
45 192 0.66
46 3 0.01
47 1 0.00
48 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (42 bp):
AAAGATTGACTTCTCTTCATGAGAAAGTCAAGAATAACATTG
Found at i:5447966 original size:84 final size:84
Alignment explanation
Indices: 5447811--5447972 Score: 209
Period size: 84 Copynumber: 1.9 Consensus size: 84
5447801 ATAACAATAC
* * * **
5447811 TGAAAGATTGAATTCTCTTCATGAGAAAGTCAATAATAACATTGAAAGATCGACTCCACTTCATG
1 TGAAAGATCGAATTCTCTTCAGGAGAAAGTCAAGAATAACATTGAAAGATCGACTCCACTTCACA
*
5447876 AGGGAGTCAGGAATGACAT
66 AAGGAGTCAGGAATGACAT
* * * * *
5447895 TGAAAGATCGACTTTTCTTCAGGATG-AAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCGC
1 TGAAAGATCGAATTCTCTTCAGGA-GAAAGTCAAGAATAACATTGAAAGATCGACTCCACTTCAC
5447959 AAAGGAGTCAGGAA
65 AAAGGAGTCAGGAA
5447973 ATAACACAGA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
84 65 0.98
85 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (84 bp):
TGAAAGATCGAATTCTCTTCAGGAGAAAGTCAAGAATAACATTGAAAGATCGACTCCACTTCACA
AAGGAGTCAGGAATGACAT
Found at i:5448009 original size:43 final size:42
Alignment explanation
Indices: 5447793--5448015 Score: 187
Period size: 42 Copynumber: 5.2 Consensus size: 42
5447783 TTCACGATAA
* * * * **
5447793 AGTCAAGAATAACAATACTGAAAGATTGAATTCTCTTCATGAGAA
1 AGTCAAGAATAAC-AT--TGAAAGATCGACTCCTCTTCGTGAGGG
* * *
5447838 AGTCAATAATAACATTGAAAGATCGACTCCACTTCATGAGGG
1 AGTCAAGAATAACATTGAAAGATCGACTCCTCTTCGTGAGGG
* * ** * *
5447880 AGTCAGGAATGACATTGAAAGATCGACTTTTCTTCAG-GATGA
1 AGTCAAGAATAACATTGAAAGATCGACTCCTCTTC-GTGAGGG
* ** *
5447922 AGTCAAGAATAACATTGAAAGATTGACTCCTCTTCGCAAAGG
1 AGTCAAGAATAACATTGAAAGATCGACTCCTCTTCGTGAGGG
* ** *
5447964 AGTCAGGAAATAACACAGAAAGATTGACTCCTCTTCGTGAGGG
1 AGTCAAG-AATAACATTGAAAGATCGACTCCTCTTCGTGAGGG
5448007 AGTCAAGAA
1 AGTCAAGAA
5448016 AGGCAAAGAT
Statistics
Matches: 144, Mismatches: 31, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
41 1 0.01
42 93 0.65
43 36 0.25
44 2 0.01
45 12 0.08
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.24
Consensus pattern (42 bp):
AGTCAAGAATAACATTGAAAGATCGACTCCTCTTCGTGAGGG
Found at i:5448853 original size:260 final size:259
Alignment explanation
Indices: 5448377--5449182 Score: 1001
Period size: 260 Copynumber: 3.1 Consensus size: 259
5448367 GATTTTGGAA
* * * * *
5448377 TTTACT-GGTAAGAAACTTTGGAAATCAATTTCTTATTTTTCAAAAAATTCATTTTATGAAAACA
1 TTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTCTTCAAAAATTTTATTTTATGAAAACA
* * * * *
5448441 TTAAATGAGAAAA-TTTGAAAATTGCTTTCTCATCTTTTTGCAAATCATGTGAAAACATCATATC
66 CTAAATGA-AAAACTTTGAAAATTGCTTTCTCATTTTTTTGAAAATCATATGAAAACATCCTATC
* * * * * *
5448505 CAAAGGTCTTATAGATGACCTGAAAAACTTATCATCTTACTCGAAAGACTGACAAATGACCCGAA
130 CGAAGGTCTTATAGATGACCCGAAAGACTTATCATCTTGCTCGAAAGACTAACAGATGACCCGAA
* * *
5448570 GGATTTAATCATCATGCTCGAAAGACTTACTGGTGACCTAAAGGACTT-CTCAAATTTTGGAAAT
195 GGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTAC-C-AATTTTGGAAAT
5448634 AG
258 AG
* * * * *
5448636 TTTACTGGGTAAGGATCTTTGGAAATCGCTTTCTTACTCCTCAAAAATTTTATTTTATGAAAATA
1 TTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTCTTCAAAAATTTTATTTTATGAAAACA
* *
5448701 CTAAATGAAAAACTTTAAAAATCGCTTTCTCATTTTTTTGAAAATCATATGAAAACATCCTATCC
66 CTAAATGAAAAACTTTGAAAATTGCTTTCTCATTTTTTTGAAAATCATATGAAAACATCCTATCC
* * * * *
5448766 GAAGGTCTTATAGATGACCCGAAGGACTTATCATCTTGCTCAAAACACTAATAGATGACCTGAAG
131 GAAGGTCTTATAGATGACCCGAAAGACTTATCATCTTGCTCGAAAGACTAACAGATGACCCGAAG
* ** *
5448831 GATTTAATTATCATGCTCGAAAGACTTACTGATGGCCCAAATAACTTACCAATTTTGAAAATAG
196 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAG
* * * * *
5448895 TTTATTGGGTAAGAAGCTTTAGAAATCACTTTCTTACTCTTCAAAAATTTCT-TTTTCTGGAAAC
1 TTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTCTTCAAAAATTT-TATTTTATGAAAAC
* * *
5448959 ACTAAATGAGAAACTTTGAAAATTGCTTTCTCGTTACTTTTTGAAAATCATACGAAAACATCCTA
65 ACTAAATGAAAAACTTTGAAAATTGCTTTCTCATT--TTTTTGAAAATCATATGAAAACATCCTA
* ** * * * * * *
5449024 CCCGAAGGTCTTACGGATGGCCC-AGATGACTTATCATCTCGCTCGAAAGACTTAGAGATAACCC
128 TCCGAAGGTCTTATAGATGACCCGA-AAGACTTATCATCTTGCTCGAAAGACTAACAGATGACCC
* * *
5449088 GAAGGATTTAATCACCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTGGGAAA
192 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAA
5449153 TAG
257 TAG
* *
5449156 TTTACTAGGTATGAAACTTTGGAAATC
1 TTTACTGGGTAAGAAACTTTGGAAATC
5449183 GTTTTAAATC
Statistics
Matches: 467, Mismatches: 73, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
259 107 0.23
260 199 0.43
261 161 0.34
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (259 bp):
TTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTCTTCAAAAATTTTATTTTATGAAAACA
CTAAATGAAAAACTTTGAAAATTGCTTTCTCATTTTTTTGAAAATCATATGAAAACATCCTATCC
GAAGGTCTTATAGATGACCCGAAAGACTTATCATCTTGCTCGAAAGACTAACAGATGACCCGAAG
GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAG
Found at i:5449348 original size:174 final size:182
Alignment explanation
Indices: 5449003--5449356 Score: 546
Period size: 174 Copynumber: 2.0 Consensus size: 182
5448993 TACTTTTTGA
*
5449003 AAATCATACGAAAACATCCTACCCGAAGGTCTTACGGATGGCCCAGATGACTTATCATCTCGCTC
1 AAATCATACGAAAACATCCTACCCGAAGGTCTTACGGATGACCCAGATGACTTATCATCTCGC-C
* *
5449068 GAAAGACTTAGAGATAACCCGAAGGATTTAATCACCATGCTCGAAAGACTTACTGATGGCCCGAA
65 GAAAGACTGAGAGATAA--CGAAGGATTTAATCACCATGCTCGAAAGACTTACTGATGGCCCAAA
5449133 GGACTTACCAATTTGGGAAATAGTTTACTAGGTATGAAACTTTGGAAATCGTTTT
128 GGACTTACCAATTTGGGAAATAGTTTACTAGGTATGAAACTTTGGAAATCGTTTT
5449188 AAATCATACGAAAACATCCTACCCGAA-GTCTTACGGATGACCC-GATGACTTATCATCTCG-CG
1 AAATCATACGAAAACATCCTACCCGAAGGTCTTACGGATGACCCAGATGACTTATCATCTCGCCG
* *
5449250 AAAG-CTGAGAGAT-A-GAAGGATTT-ATCA-CATGCTCGAAAGATTTACTGATGGCCCAAATGA
66 AAAGACTGAGAGATAACGAAGGATTTAATCACCATGCTCGAAAGACTTACTGATGGCCCAAAGGA
* *
5449310 CTTACTAATTTGGGAAATAGTTTACTGGGT-TCGAAACTTTGGAAATC
131 CTTACCAATTTGGGAAATAGTTTACTAGGTAT-GAAACTTTGGAAATC
5449357 ACTTTCTTAC
Statistics
Matches: 161, Mismatches: 7, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
173 1 0.01
174 73 0.45
175 4 0.02
176 9 0.06
179 1 0.01
180 8 0.05
181 6 0.04
183 17 0.11
184 15 0.09
185 27 0.17
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (182 bp):
AAATCATACGAAAACATCCTACCCGAAGGTCTTACGGATGACCCAGATGACTTATCATCTCGCCG
AAAGACTGAGAGATAACGAAGGATTTAATCACCATGCTCGAAAGACTTACTGATGGCCCAAAGGA
CTTACCAATTTGGGAAATAGTTTACTAGGTATGAAACTTTGGAAATCGTTTT
Found at i:5450009 original size:235 final size:254
Alignment explanation
Indices: 5449677--5450256 Score: 921
Period size: 235 Copynumber: 2.3 Consensus size: 254
5449667 TTACCCGAAG
* * ** *
5449677 GACTTATCATCTCGCACGCAAGACTTACAGATGACCCAAAGGATTTAATCATTATGCTCGAAAGA
1 GACTTATCATCTTGCTCAAAAGACTTACAGATGA-CC-GAGGATTTAATCATTATGCTCGAAAGA
5449742 CTT-ATGATGGCCCGAAGGACTTACCAATTTGGGTAATATTTTACTGGGTAA-GAAC-TT-GAAA
64 CTTAATGATGGCCCGAAGGACTTACCAATTTGGGTAATATTTTACTGGGTAAGGAACTTTGGAAA
5449803 -TGC-TTCTTACTT-TC-AAAA-TCA-TTTGTGAAAATG-T-AATG-GAAACTTTGGAAATCACT
129 TTGCTTTCTTACTTCTCAAAAATTCATTTTGTGAAAATGCTAAATGAGAAACTTTGGAAATCACT
5449859 TTCTCGTTT-TCAAATTCATGTGAAAACATCCTA-CCGAAGGTCTTA-CGTT-GCCC-AA-
194 TTCTCGTTTATCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTACCGTTGGCCCAAAT
5449914 GACTTATCATCTTGCTC-AAAGACTTACAGATGACCGAGGATTTAATCATTATGCTCGAAAGACT
1 GACTTATCATCTTGCTCAAAAGACTTACAGATGACCGAGGATTTAATCATTATGCTCGAAAGACT
5449978 TAATGATGGCCCGAAGGACTTACCAATTTGGGTAATATTTTACTGGGTAAGGAACTTTGGAAATT
66 TAATGATGGCCCGAAGGACTTACCAATTTGGGTAATATTTTACTGGGTAAGGAACTTTGGAAATT
5450043 GCTTTCTTACTTCTCAAAAATTCATTTTGTGAAAATGCTAAATGAGAAACTTTGGAAATCACTTT
131 GCTTTCTTACTTCTCAAAAATTCATTTTGTGAAAATGCTAAATGAGAAACTTTGGAAATCACTTT
5450108 CTCGTTTATCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTACCGTTGGCCCAAAT
196 CTCGTTTATCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTACCGTTGGCCCAAAT
5450167 GACTTATCATCTTGCTCAAAAGACTTACAGATGACCGTAAGGATTTAATCATTATGCTCGAAAGA
1 GACTTATCATCTTGCTCAAAAGACTTACAGATGACCG--AGGATTTAATCATTATGCTCGAAAGA
* *
5450232 CTTACTTATGGCCCGAAGGACTTAC
64 CTTAATGATGGCCCGAAGGACTTAC
5450257 TAAGTAAGAA
Statistics
Matches: 315, Mismatches: 6, Indels: 25
0.91 0.02 0.07
Matches are distributed among these distances:
234 29 0.09
235 50 0.16
236 19 0.06
237 17 0.05
238 4 0.01
239 3 0.01
240 9 0.03
241 2 0.01
242 4 0.01
243 3 0.01
244 12 0.04
245 1 0.00
246 4 0.01
247 27 0.09
248 24 0.08
249 12 0.04
250 4 0.01
251 4 0.01
252 2 0.01
253 17 0.05
254 19 0.06
256 49 0.16
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (254 bp):
GACTTATCATCTTGCTCAAAAGACTTACAGATGACCGAGGATTTAATCATTATGCTCGAAAGACT
TAATGATGGCCCGAAGGACTTACCAATTTGGGTAATATTTTACTGGGTAAGGAACTTTGGAAATT
GCTTTCTTACTTCTCAAAAATTCATTTTGTGAAAATGCTAAATGAGAAACTTTGGAAATCACTTT
CTCGTTTATCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTACCGTTGGCCCAAAT
Found at i:5458308 original size:3 final size:3
Alignment explanation
Indices: 5458300--5458358 Score: 93
Period size: 3 Copynumber: 19.7 Consensus size: 3
5458290 TACAAATGAA
*
5458300 AAT AAT AAT AAT AAAT AAT AAT GAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5458345 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
5458359 CGGGTCTCCA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5464423 original size:45 final size:45
Alignment explanation
Indices: 5464374--5464777 Score: 511
Period size: 45 Copynumber: 9.0 Consensus size: 45
5464364 TGTTACGGAA
* * *
5464374 ATAAATGAAAATGTATAACGGTGCATTATTGGCATAAAAGGAGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
* ** *
5464419 ATAAATGAAAATACATAAATGTGCATTATCGACATAAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
* * * * * *
5464464 ATAAATAAAAATTCATAATGATGTATTATCGGCATAAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
* * * *
5464509 ATAAATGAAAACGCATAATGTTGCATTATCGGCATAAAAGGTTCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
* * * *
5464554 ATAAATAAAAATGCATAACGATGCATTATAGGCATAAAAGGTGAC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
* * *
5464599 ATAAATGAAAATGCATAACGGTGCATTATCGACAGAAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
* *
5464644 ATAAATGAAAATTCATAACGGTGCTTTATCGGCATAAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
* ** * *
5464689 ATAAATGAAAATGCATAACGGTACATTATCGATATAAAAGTTTCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
* *
5464734 ATAAATAAAAATGCATAACGGTGCATTATTGGCATAAAAGGTGC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGC
5464778 AACTTATGGT
Statistics
Matches: 304, Mismatches: 55, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 304 1.00
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (45 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
Found at i:5471753 original size:45 final size:45
Alignment explanation
Indices: 5471354--5471758 Score: 542
Period size: 45 Copynumber: 9.0 Consensus size: 45
5471344 TGTTACTGAA
* * * * * *
5471354 ATAAATGAAAATACATAACGGTGCATTATTGGAAGAAAAAGTGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
* * *
5471399 ATAAATGAAAATGCATAA-GGTCCATTATCGGCATAAAAGATGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
* * *
5471443 ATAAATGAAAATGCATAACGGTGCATTATCGGTATTAAAGTTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
* *
5471488 ATAAATGAAAATGCATAAGGGTGCATTATCGGCATAAAAGGTTCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
* *
5471533 ATAAATGAAAATGCATAATGGTGCATTATCGGTATAAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
* ** * *
5471578 ATAAATGAAAATGCATAATGGTGCATTATTAGCAAAAAAGGTGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
* * *
5471623 ATAAATGAAAATACATAACGGTGTATTATCGGCATAAAAGGTGGC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
* *
5471668 ATAAATGAAAATGCAAAACGGTGCATTATCGACATAAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
** *
5471713 ATAAATGAAAATGCATAACGGTGCATTATTAGCATTAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
5471758 A
1 A
5471759 CTTATAGTAT
Statistics
Matches: 317, Mismatches: 42, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
44 38 0.12
45 279 0.88
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (45 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
Found at i:5479252 original size:18 final size:19
Alignment explanation
Indices: 5479229--5479264 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
5479219 GTTCATTTAC
5479229 TTATTTTTAT-TTTTTATT
1 TTATTTTTATATTTTTATT
5479247 TTATTTTTATATTTTTAT
1 TTATTTTTATATTTTTAT
5479265 ATTTTATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (19 bp):
TTATTTTTATATTTTTATT
Found at i:5482517 original size:38 final size:38
Alignment explanation
Indices: 5482442--5482518 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 38
5482432 GTTAGAAAAT
* *
5482442 ATTTATATATTTTCTTTAAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTGAAAATCATAAA
* * *
5482480 ATTTATATAATTTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATTGAAAATCATAAA
5482518 A
1 A
5482519 AAGTTTAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 14 0.42
39 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (38 bp):
ATTTATATATTTTCTTTAAAAAAATTGAAAATCATAAA
Found at i:5483009 original size:9 final size:9
Alignment explanation
Indices: 5482995--5483044 Score: 84
Period size: 9 Copynumber: 5.6 Consensus size: 9
5482985 ATTCAGAACT
5482995 GAAATTTTA
1 GAAATTTTA
5483004 GAAATTTT-
1 GAAATTTTA
5483012 GAAATTTTA
1 GAAATTTTA
5483021 GAAATTTTA
1 GAAATTTTA
5483030 GAAATTTTA
1 GAAATTTTA
5483039 GGAAAT
1 -GAAAT
5483045 ATAATAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.21
9 26 0.67
10 5 0.13
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (9 bp):
GAAATTTTA
Found at i:5483016 original size:17 final size:17
Alignment explanation
Indices: 5482994--5483044 Score: 84
Period size: 17 Copynumber: 2.9 Consensus size: 17
5482984 TATTCAGAAC
5482994 TGAAATTTTAGAAATTT
1 TGAAATTTTAGAAATTT
5483011 TGAAATTTTAGAAATTT
1 TGAAATTTTAGAAATTT
5483028 TAGAAATTTTAGGAAAT
1 T-GAAATTTTA-GAAAT
5483045 ATAATAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 18 0.56
18 9 0.28
19 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (17 bp):
TGAAATTTTAGAAATTT
Found at i:5493809 original size:32 final size:32
Alignment explanation
Indices: 5493771--5493837 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
5493761 ATCCCTCTTG
*
5493771 CTTATGGCTTAGTTGTGAATTTCATCCCTCAA
1 CTTATGGCTAAGTTGTGAATTTCATCCCTCAA
*
5493803 CTTATGGCTAAGTTGTGAATTTCATCCCTCGA
1 CTTATGGCTAAGTTGTGAATTTCATCCCTCAA
5493835 CTT
1 CTT
5493838 CCCAAACACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.40
Consensus pattern (32 bp):
CTTATGGCTAAGTTGTGAATTTCATCCCTCAA
Found at i:5500254 original size:29 final size:29
Alignment explanation
Indices: 5500194--5500283 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
5500184 TTAAACTATG
* * * *
5500194 AAATATTGAAACATTTAATAAACTTAAC-T
1 AAATATTAAAACAATAAATAAA-ATAACAT
5500223 AAATATTAAAACAATAAATAAAATAACAT
1 AAATATTAAAACAATAAATAAAATAACAT
*
5500252 AAA-A-TAACAAC-ATAAAATAAAAATAAAAT
1 AAATATTAA-AACAAT-AAAT-AAAATAACAT
5500281 AAA
1 AAA
5500284 CCTAAATATA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
27 5 0.10
28 12 0.23
29 35 0.67
ACGTcount: A:0.67, C:0.08, G:0.01, T:0.24
Consensus pattern (29 bp):
AAATATTAAAACAATAAATAAAATAACAT
Found at i:5500265 original size:13 final size:12
Alignment explanation
Indices: 5500247--5500283 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
5500237 TAAATAAAAT
5500247 AACATAAAATAA
1 AACATAAAATAA
5500259 CAACATAAAATAA
1 -AACATAAAATAA
5500272 AA-ATAAAATAA
1 AACATAAAATAA
5500283 A
1 A
5500284 CCTAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 10 0.42
12 2 0.08
13 12 0.50
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AACATAAAATAA
Found at i:5502718 original size:408 final size:407
Alignment explanation
Indices: 5501960--5502751 Score: 1140
Period size: 408 Copynumber: 1.9 Consensus size: 407
5501950 GTAGGTGTCG
* * * * **
5501960 CTGATTCAAAGTGTTGAGAATTAAGTAATAGGTCGAACAAGTTCTTCTCATTATGAACTTTTTAT
1 CTGATTCAAAGTGTGGAGAATCAAGCAATAGGTCGAACAAGTTCTTCTCAATATGAACTTCCTAT
* * * *
5502025 CCCTCTATCGGATGAGTTCTTCTCATTGTGAACTCTCCATCGGAAATGACAATCCCTTAAGTGAG
66 CCCTCTATCAGATGAGTTCTTCTCATTATGAACTCTCCATCAGAAATGACAATCCCTCAAGTGAG
* * * *
5502090 GCATTGTTGATTCGAATTGTTACGAATTGAGCAATAGGTTGAAAAAGCTCTTCTCATTAAGAACT
131 GCATTGCTGATTCGAATTGGTAC-AATCGAGCAATAGGTTCAAAAAGCTCTTCTCATTAAGAACT
* * * * *
5502155 TCTTCTCCCTCTGTAGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCAATCCCTCA
195 TCTACTCCCTCTATAGAATGAGTTCTTCTCATTATGAACTCTCCATCGGAAATATCAATCCCTCA
* * * *
5502220 AGCGAGGCGTTACTGATTTGAAGTGTGATGAATCGAGCAATAGGTCGAACAAGTTATTCTCATTC
260 AGCGAGGCATTACTAATTCGAAGTGTGATGAATCGAGCAATAGGTCGAACAAGTTATTCTCATTA
*
5502285 TGAACGTTTTCTCCCTGTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATCGGAAATGACAAT
325 TGAACGTTTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATCGGAAATGACAAT
5502350 CCCTCAAGCGTGGCATTC
390 CCCTCAAGCGTGGCATTC
* * *
5502368 CTGATTCGAAGTGTGGTGAATCAAGCAATAGGTCGAACAAGTTCTTCTCAATATGAACTTCCTCT
1 CTGATTCAAAGTGTGGAGAATCAAGCAATAGGTCGAACAAGTTCTTCTCAATATGAACTTCCTAT
* * **
5502433 CCCTCTATCAGATGAGTTCTTCTCATTATTAACTCTCCATTAGAAATGTTAATCCCTCAAGTGAG
66 CCCTCTATCAGATGAGTTCTTCTCATTATGAACTCTCCATCAGAAATGACAATCCCTCAAGTGAG
*** * *
5502498 TTGTTGCTGATTCGAAGTATGGTA-AATCGAGCAATAGG-TCAAATAAGTTCTTCTCATTATGAA
131 GCATTGCTGATTCGAA-T-TGGTACAATCGAGCAATAGGTTCAAA-AAGCTCTTCTCATTAAGAA
*
5502561 CTTCTACTCCCTCTATCGAATGAGTTCTTCTCATTATGAACTCTCCATCGGAAATATCAATCCCT
193 CTTCTACTCCCTCTATAGAATGAGTTCTTCTCATTATGAACTCTCCATCGGAAATATCAATCCCT
* * *
5502626 CAAGCGAGGTATTACTAATTCGATGTGTGGTGAATCGAGCAATAGGTCGAACAAGTTATTCTCAT
258 CAAGCGAGGCATTACTAATTCGAAGTGTGATGAATCGAGCAATAGGTCGAACAAGTTATTCTCAT
* *
5502691 TATGAAC-TTATTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
323 TATGAACGTT-TTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATCGGAAAT
5502752 ATCAATCGGT
Statistics
Matches: 338, Mismatches: 42, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
407 6 0.02
408 327 0.97
409 1 0.00
410 4 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (407 bp):
CTGATTCAAAGTGTGGAGAATCAAGCAATAGGTCGAACAAGTTCTTCTCAATATGAACTTCCTAT
CCCTCTATCAGATGAGTTCTTCTCATTATGAACTCTCCATCAGAAATGACAATCCCTCAAGTGAG
GCATTGCTGATTCGAATTGGTACAATCGAGCAATAGGTTCAAAAAGCTCTTCTCATTAAGAACTT
CTACTCCCTCTATAGAATGAGTTCTTCTCATTATGAACTCTCCATCGGAAATATCAATCCCTCAA
GCGAGGCATTACTAATTCGAAGTGTGATGAATCGAGCAATAGGTCGAACAAGTTATTCTCATTAT
GAACGTTTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATCGGAAATGACAATC
CCTCAAGCGTGGCATTC
Found at i:5502752 original size:136 final size:136
Alignment explanation
Indices: 5501986--5502758 Score: 994
Period size: 136 Copynumber: 5.7 Consensus size: 136
5501976 AGAATTAAGT
* *
5501986 AATAGGTCGAACAAGTTCTTCTCATTATGAACTTTTTATCCCTCTATCGGATGAGTTCTTCTCAT
1 AATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCAT
* * * ** * ***
5502051 TGTGAACTCTCCATCGGAAATGA-CAATCCCTTAAGTGAGGCATTGTTGATTCGAATTGTTACGA
66 TATGAACTCTCCATCGGAAAT-ATCAATCCCTCAAGCGAGGCATTACTGATTCGAAGTGTGGTGA
*
5502115 ATTGAGC
130 ATCGAGC
* * * * * *
5502122 AATAGGTTGAAAAAGCTCTTCTCATTAAGAACTTCTTCTCCCTCTGTAGGATGAGTTCTTCTCAT
1 AATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCAT
* * * * *
5502187 TATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGGCGTTACTGATTTGAAGTGTGATGAA
66 TATGAACTCTCCATCGGAAATATCAATCCCTCAAGCGAGGCATTACTGATTCGAAGTGTGGTGAA
5502252 TCGAGC
131 TCGAGC
* * * *
5502258 AATAGGTCGAACAAGTTATTCTCATTCTGAACGTT-TTCTCCCTGTGTCGGATGAGTTCTTCTCA
1 AATAGGTCGAACAAGTTCTTCTCATTATGAAC-TTCTTCTCCCTCTATCGGATGAGTTCTTCTCA
* *
5502322 TTATGAACTCTCCATCGGAAATGA-CAATCCCTCAAGCGTGGCATTCCTGATTCGAAGTGTGGTG
65 TTATGAACTCTCCATCGGAAAT-ATCAATCCCTCAAGCGAGGCATTACTGATTCGAAGTGTGGTG
*
5502386 AATCAAGC
129 AATCGAGC
* * *
5502394 AATAGGTCGAACAAGTTCTTCTCAATATGAACTTCCTCTCCCTCTATCAGATGAGTTCTTCTCAT
1 AATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCAT
* ** * * * *** * * *
5502459 TATTAACTCTCCATTAGAAATGTTAATCCCTCAAGTGAGTTGTTGCTGATTCGAAGTATGGTAAA
66 TATGAACTCTCCATCGGAAATATCAATCCCTCAAGCGAGGCATTACTGATTCGAAGTGTGGTGAA
5502524 TCGAGC
131 TCGAGC
* * * *
5502530 AATAGGTCAAATAAGTTCTTCTCATTATGAACTTCTACTCCCTCTATCGAATGAGTTCTTCTCAT
1 AATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCAT
* * *
5502595 TATGAACTCTCCATCGGAAATATCAATCCCTCAAGCGAGGTATTACTAATTCGATGTGTGGTGAA
66 TATGAACTCTCCATCGGAAATATCAATCCCTCAAGCGAGGCATTACTGATTCGAAGTGTGGTGAA
5502660 TCGAGC
131 TCGAGC
* * *
5502666 AATAGGTCGAACAAGTTATTCTCATTATGAACTTATTCTCCCTCTTTCGGATGAGTTCTTCTCAT
1 AATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCAT
*
5502731 TATGAACTCTCCATTGGAAATATCAATC
66 TATGAACTCTCCATCGGAAATATCAATC
5502759 GGTTTATCTT
Statistics
Matches: 546, Mismatches: 86, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
135 2 0.00
136 542 0.99
137 2 0.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (136 bp):
AATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCAT
TATGAACTCTCCATCGGAAATATCAATCCCTCAAGCGAGGCATTACTGATTCGAAGTGTGGTGAA
TCGAGC
Found at i:5503703 original size:5 final size:5
Alignment explanation
Indices: 5503689--5503771 Score: 66
Period size: 5 Copynumber: 16.2 Consensus size: 5
5503679 GAACCTCTCA
*
5503689 TTTT- TTTTC TTTTC -TTT- TTTTC TTTTC TTTTTC TTTTTC CTTTC TTTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC -TTTTC TTTTC -TTTTC
*
5503739 CTTTC TTTTCC TTTAT- TTTTC ATTTTC TTTTC T
1 TTTTC TTTT-C TTT-TC TTTTC -TTTTC TTTTC T
5503772 CTTAGGCGTA
Statistics
Matches: 66, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
4 11 0.17
5 30 0.45
6 24 0.36
7 1 0.02
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:5503707 original size:6 final size:6
Alignment explanation
Indices: 5503692--5503774 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
5503682 CCTCTCATTT
* *
5503692 TTTTTC -TTTTC TTTTTT TCTTTTC TTTTTC TTTTTC -CTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* * * *
5503739 -CTTTC -TTTTC -CTTTA TTTTTC ATTTTC TTTTCTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT-TC TT
5503775 AGGCGTAATA
Statistics
Matches: 60, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
5 20 0.33
6 31 0.52
7 9 0.15
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:5503708 original size:13 final size:13
Alignment explanation
Indices: 5503690--5503747 Score: 64
Period size: 13 Copynumber: 4.3 Consensus size: 13
5503680 AACCTCTCAT
5503690 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
5503703 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
*
5503716 TTTTTCTT-TTTCC
1 TTTTT-TTCTTTTC
*
5503729 TTTCTTTTTCCTTTC
1 -TT-TTTTTCTTTTC
5503744 TTTT
1 TTTT
5503748 CCTTTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 24 0.63
14 8 0.21
15 6 0.16
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:5503716 original size:18 final size:17
Alignment explanation
Indices: 5503689--5503774 Score: 79
Period size: 17 Copynumber: 5.1 Consensus size: 17
5503679 GAACCTCTCA
*
5503689 TTTT-TTTTCTTTTCTTT
1 TTTTCTTTTCTTTT-TCT
5503706 TTTTCTTTTCTTTTTCT
1 TTTTCTTTTCTTTTTCT
*
5503723 TTTTCCTTTCTTTTTC-
1 TTTTCTTTTCTTTTTCT
* * *
5503739 CTTTCTTTTC-CTTTAT
1 TTTTCTTTTCTTTTTCT
5503755 TTTTCATTTTCTTTTCTCT
1 TTTTC-TTTTCTTTT-TCT
5503774 T
1 T
5503775 AGGCGTAATA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
15 3 0.05
16 12 0.22
17 26 0.47
18 11 0.20
19 3 0.05
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTCTTTTCTTTTTCT
Found at i:5503719 original size:11 final size:11
Alignment explanation
Indices: 5503692--5503774 Score: 68
Period size: 11 Copynumber: 7.7 Consensus size: 11
5503682 CCTCTCATTT
5503692 TTTTTCTTTTC
1 TTTTTCTTTTC
5503703 --TTT-TTTTC
1 TTTTTCTTTTC
5503711 -TTTTCTTTTTC
1 TTTTTC-TTTTC
*
5503722 TTTTTCCTTTC
1 TTTTTCTTTTC
*
5503733 TTTTTCCTTTC
1 TTTTTCTTTTC
* *
5503744 -TTTTCCTTTA
1 TTTTTCTTTTC
5503754 TTTTTCATTTTC
1 TTTTTC-TTTTC
5503766 TTTTCTCTT
1 TTTT-TCTT
5503775 AGGCGTAATA
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
8 5 0.08
9 6 0.10
10 9 0.15
11 25 0.41
12 14 0.23
13 2 0.03
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:5506762 original size:64 final size:63
Alignment explanation
Indices: 5506657--5506775 Score: 157
Period size: 64 Copynumber: 1.9 Consensus size: 63
5506647 ATTGTTCAAG
* * * **
5506657 GTGTATCGATGCACATGAAGTGCATCGATGCACTATTTTAAAATAAAAACATCGAACGCCATCA
1 GTGTATCGATGCACAAGAACTGCATCGATGCACCACCTT-AAATAAAAACATCGAACGCCATCA
* * *
5506721 GTGTATCGATGCACAAGTACTGCATCGATGCACCCCCTTAAATACAAACATCGAA
1 GTGTATCGATGCACAAGAACTGCATCGATGCACCACCTTAAATAAAAACATCGAA
5506776 TAGGATTTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
63 15 0.32
64 32 0.68
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAACTGCATCGATGCACCACCTTAAATAAAAACATCGAACGCCATCA
Found at i:5507825 original size:22 final size:22
Alignment explanation
Indices: 5507796--5507866 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
5507786 GTTAGGTACA
5507796 AGAGGATATAATTACAAGATAC
1 AGAGGATATAATTACAAGATAC
*
5507818 AGATGATAGT--TT--AAGTATA-
1 AGAGGATA-TAATTACAAG-ATAC
5507837 AGAGGATATAATTACAAGATAC
1 AGAGGATATAATTACAAGATAC
5507859 AGAGGATA
1 AGAGGATA
5507867 GTAAGAATTG
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
18 1 0.03
19 10 0.25
20 5 0.12
21 5 0.12
22 18 0.45
23 1 0.03
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.25
Consensus pattern (22 bp):
AGAGGATATAATTACAAGATAC
Found at i:5511588 original size:64 final size:64
Alignment explanation
Indices: 5511480--5511599 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 64
5511470 ATTGTTCAAG
* * **
5511480 GTGTATCGATGCACATGAAGTGCATCGATGCACTATTTTAAAATAAAAACATCGAACGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCACCTTAAAATAAAAACATCGAACGCCATCA
* * *
5511544 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCCTT-AAATACAAACATCGAA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCA-CCACCTTAAAATAAAAACATCGAA
5511600 TAGGATTTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
64 45 0.94
65 3 0.06
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (64 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCACCTTAAAATAAAAACATCGAACGCCATCA
Found at i:5525987 original size:13 final size:12
Alignment explanation
Indices: 5525967--5526025 Score: 52
Period size: 11 Copynumber: 5.1 Consensus size: 12
5525957 AAACTTAATT
5525967 AACA-AAATTAA
1 AACATAAATTAA
*
5525978 AACAATAAATAAA
1 AAC-ATAAATTAA
*
5525991 AACATAAAATAA
1 AACATAAATTAA
*
5526003 AA-ATAAAATAA
1 AACATAAATTAA
*
5526014 AA-ATAAAATAA
1 AACATAAATTAA
5526025 A
1 A
5526026 CCTAAATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
11 24 0.56
12 10 0.23
13 9 0.21
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (12 bp):
AACATAAATTAA
Found at i:5526007 original size:6 final size:6
Alignment explanation
Indices: 5525970--5526025 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
5525960 CTTAATTAAC
* * *
5525970 AAAATT AAAACA ATAAATA AAAACA TAAAATA AAAAT- AAAATA AAAAT-
1 AAAATA AAAATA A-AAATA AAAATA -AAAATA AAAATA AAAATA AAAATA
5526018 AAAATA AA
1 AAAATA AA
5526026 CCTAAATATA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
5 10 0.24
6 21 0.51
7 10 0.24
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:5526031 original size:11 final size:11
Alignment explanation
Indices: 5525984--5526025 Score: 66
Period size: 11 Copynumber: 3.6 Consensus size: 11
5525974 TTAAAACAAT
5525984 AAATAAAAACATA
1 AAAT-AAAA-ATA
5525997 AAATAAAAATA
1 AAATAAAAATA
5526008 AAATAAAAATA
1 AAATAAAAATA
5526019 AAATAAA
1 AAATAAA
5526026 CCTAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 21 0.72
12 4 0.14
13 4 0.14
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:5530606 original size:18 final size:18
Alignment explanation
Indices: 5530580--5530640 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
5530570 TCTTAACCAA
*
5530580 CCAGTCGAACCAGCCTTG
1 CCAGCCGAACCAGCCTTG
*
5530598 CCAGCCGAACCAG-TTCTG
1 CCAGCCGAACCAGCCT-TG
* *
5530616 CCAGTCGAACAAGCCTTG
1 CCAGCCGAACCAGCCTTG
*
5530634 CCTGCCG
1 CCAGCCG
5530641 CACTATCCTG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
17 1 0.03
18 32 0.94
19 1 0.03
ACGTcount: A:0.21, C:0.39, G:0.23, T:0.16
Consensus pattern (18 bp):
CCAGCCGAACCAGCCTTG
Found at i:5537411 original size:3 final size:3
Alignment explanation
Indices: 5537403--5537470 Score: 91
Period size: 3 Copynumber: 22.0 Consensus size: 3
5537393 TACTAAATTT
* * *
5537403 TTA TTA TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5537451 TTA TATA TATA TTA TTA TTA
1 TTA T-TA T-TA TTA TTA TTA
5537471 AAAAAAATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 51 0.88
4 7 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:5539080 original size:23 final size:22
Alignment explanation
Indices: 5539034--5539078 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5539024 ATATTATAAA
5539034 AAATTATAATTTAATTTTATTT
1 AAATTATAATTTAATTTTATTT
*
5539056 AAATTATTATATTAATATTTATT
1 AAATTATAAT-TTAAT-TTTATT
5539079 AATATCGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATTATAATTTAATTTTATTT
Found at i:5539154 original size:23 final size:26
Alignment explanation
Indices: 5539128--5539182 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 26
5539118 CCTTTTCTGA
*
5539128 TATTTCTAACTA-A-ATAAA-TATTT
1 TATTTCTAAATATATATAAATTATTT
*
5539151 TATTTATAAATATATATAAATTATTT
1 TATTTCTAAATATATATAAATTATTT
5539177 T-TTTCT
1 TATTTCT
5539183 TTTTTTCTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 10 0.38
24 1 0.04
25 9 0.35
26 6 0.23
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (26 bp):
TATTTCTAAATATATATAAATTATTT
Found at i:5550383 original size:8 final size:8
Alignment explanation
Indices: 5550370--5550426 Score: 80
Period size: 8 Copynumber: 6.9 Consensus size: 8
5550360 ATGCTTGAAG
5550370 GAAAAAAA
1 GAAAAAAA
5550378 GAAAAAAA
1 GAAAAAAA
5550386 GAAAAAAA
1 GAAAAAAA
5550394 GAAAGAAAA
1 GAAA-AAAA
5550403 GAAAAAAA
1 GAAAAAAA
5550411 -AAGAGAAAA
1 GAA-A-AAAA
5550420 GAAAAAA
1 GAAAAAA
5550427 GGGGGTCAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
7 2 0.04
8 28 0.62
9 13 0.29
10 2 0.04
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:5550393 original size:17 final size:17
Alignment explanation
Indices: 5550370--5550426 Score: 91
Period size: 17 Copynumber: 3.4 Consensus size: 17
5550360 ATGCTTGAAG
5550370 GAAAAAAAGAAA-AAAA
1 GAAAAAAAGAAAGAAAA
5550386 GAAAAAAAGAAAGAAAA
1 GAAAAAAAGAAAGAAAA
5550403 GAAAAAAA-AAGAGAAAA
1 GAAAAAAAGAA-AGAAAA
5550420 GAAAAAA
1 GAAAAAA
5550427 GGGGGTCAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
16 14 0.36
17 25 0.64
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
GAAAAAAAGAAAGAAAA
Found at i:5551626 original size:114 final size:114
Alignment explanation
Indices: 5551426--5551987 Score: 830
Period size: 114 Copynumber: 5.0 Consensus size: 114
5551416 TGCCATGCGC
5551426 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* * *
5551491 TTCGGTA-GAAACCACAGAACCAATCATTGAATTTGAAAGATGAATGTGA
66 TTTGGTATG-AACCATAAAACCAATCATTGAATTTGAAAGATGAATGTGA
5551540 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
*
5551605 TTTGGTATGAACCATAGAACCAATCATTGAATTTGAAAGATGAATGTGA
66 TTTGGTATGAACCATAAAACCAATCATTGAATTTGAAAGATGAATGTGA
* *
5551654 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* * * * *
5551719 TTTGGTATGAACCCTAAAATCAATCATTGAATTTGAAAAATGAATTTGC
66 TTTGGTATGAACCATAAAACCAATCATTGAATTTGAAAGATGAATGTGA
* *
5551768 TCATAGTAGAAATAAGAATACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* * * * * *
5551833 TTTGGTATGAACCCTAAAATCAATCATTGGATTTGAAAAATGAATTTGC
66 TTTGGTATGAACCATAAAACCAATCATTGAATTTGAAAGATGAATGTGA
* * * *
5551882 TCATAGCAAAAAGAAGAAGACCCAATAGCA---TCTGGAAGTGTTCTTTGAGTCATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* *
5551944 TTCGGTAAGAACCACT-AAACCAATCATTGTAA-TTGAAAGATGAA
66 TTTGGTATGAACCA-TAAAACCAATCATTG-AATTTGAAAGATGAA
5551988 CTGCATGATC
Statistics
Matches: 420, Mismatches: 25, Indels: 9
0.93 0.06 0.02
Matches are distributed among these distances:
111 64 0.15
112 2 0.00
114 353 0.84
115 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (114 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
TTTGGTATGAACCATAAAACCAATCATTGAATTTGAAAGATGAATGTGA
Found at i:5553029 original size:116 final size:111
Alignment explanation
Indices: 5552728--5553260 Score: 626
Period size: 113 Copynumber: 4.7 Consensus size: 111
5552718 AACAGCAGTA
* * *
5552728 CCAGTTAGAGTTCATAATGAGAAGAACTCACCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGGTAGAGTTCATAATGAGAAGAACTCATCT-GA-AAGGAAGAAGAAGTTCATAATGAGAAGA
* * * * ** * *
5552793 ACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTA
64 ATTTGTTCAACCTTTTGCTTAAATTCATTATTTGATGGATCAACATTG
* * *
5552841 CCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGGTAGAGTTCATAATGAGAAGAACTCATCTG--AAAGGAAGAAGAAGTTCATAATGAGAAGA
* *
5552906 ATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATGGATTAACATTG
64 ATTTGTTCAACCTTTTGCTTAAATTCATTATTTGATGGATCAACATTG
5552954 CCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAGGGAAGAAGAAGTTCATAATGAGA
1 CCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAA-A-GGAAGAAGAAGTTCATAATGAGA
* *
5553019 AGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATGGATTAACATTG
61 AGAATTTGTTCAACCTTTTGCTTAAATTCATTATTTGATGGATCAACATTG
* *
5553070 CCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTG-AA-TAAGAAGAAATTCATAATGAGAAG
1 CCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAAGGAAGAAGAAGTTCATAATGAGAAG
* * * * *** *
5553133 AATTTGTTCAACCTTTTGCTCAAATCCATAACTTGATGGATCAGTTTTT
63 AATTTGTTCAACCTTTTGCTTAAATTCATTATTTGATGGATCAACATTG
* * *
5553182 CCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG-AA-GAAGAAGAAGTTCACAATGAGAAGAG
1 CCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAAGGAAGAAGAAGTTCATAATGAGAAGAA
*
5553244 CTTGTTCAACCTTTTGC
65 TTTGTTCAACCTTTTGC
5553261 ATAATTCTAT
Statistics
Matches: 377, Mismatches: 35, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
109 47 0.12
110 1 0.00
112 84 0.22
113 120 0.32
114 4 0.01
115 3 0.01
116 118 0.31
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (111 bp):
CCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAAGGAAGAAGAAGTTCATAATGAGAAGAAT
TTGTTCAACCTTTTGCTTAAATTCATTATTTGATGGATCAACATTG
Found at i:5553098 original size:229 final size:223
Alignment explanation
Indices: 5552728--5553260 Score: 655
Period size: 229 Copynumber: 2.4 Consensus size: 223
5552718 AACAGCAGTA
* * *
5552728 CCAGTTAGAGTTCATAATGAGAAGAACTCACCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGA
* * * * *
5552793 ACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCGAGTTCATAA
65 ACTTGTTCAACCTTTTGCTTAAATTCATCATTCAATGGATCAACATTACCAGGTAGAGTTCATAA
5552858 TAAGAAGAA-C-TCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
130 TAAGAAGAACCGTCATCTGAAAAA-GAAG-A-AA-TTCATAATGAGAAGAATTTGTTCAACCTTT
* * * * * *
5552921 TGTTTAAATTCATTATTTGATGGATTAACATTG
191 TGCTCAAATCCATAACTTGATGGATCAACATTG
5552954 CCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAGGGAAGAAGAAGTTCATAATGAGA
1 CCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGA-GGAAGAAGAAGTTCATAATGAGA
* * * ** * *
5553019 AGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATGGATTAACATTGCCAGGTAGAGTTCA
62 AGAACTTGTTCAACCTTTTGCTTAAATTCATCATTCAATGGATCAACATTACCAGGTAGAGTTCA
* *
5553084 TAATGAGAAGAACTCGTCATCTGAATAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTT
127 TAATAAGAAGAAC-CGTCATCTGAAAAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTT
*** *
5553149 TGCTCAAATCCATAACTTGATGGATCAGTTTTT
191 TGCTCAAATCCATAACTTGATGGATCAACATTG
* *
5553182 CCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG-A-A-GAAGAAGAAGTTCACAATGAGAAGA
1 CCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA
*
5553243 GCTTGTTCAACCTTTTGC
65 ACTTGTTCAACCTTTTGC
5553261 ATAATTCTAT
Statistics
Matches: 267, Mismatches: 32, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
221 39 0.15
223 1 0.00
224 1 0.00
225 7 0.03
226 26 0.10
228 78 0.29
229 98 0.37
230 1 0.00
231 5 0.02
232 11 0.04
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (223 bp):
CCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA
CTTGTTCAACCTTTTGCTTAAATTCATCATTCAATGGATCAACATTACCAGGTAGAGTTCATAAT
AAGAAGAACCGTCATCTGAAAAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
AAATCCATAACTTGATGGATCAACATTG
Found at i:5553400 original size:124 final size:122
Alignment explanation
Indices: 5553179--5553471 Score: 389
Period size: 124 Copynumber: 2.4 Consensus size: 122
5553169 TGGATCAGTT
5553179 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG-A-AGAAGAAGAAGTTCACAATGAGAAG
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAGAAGTTCACAATGAGAAG
* * * * * * *
5553242 AGCTTGTTCAACCTTTTGCATAATTCTATTACAGAAAGAGATAGATTAGCATCAACC
66 AGCTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATAGATCAACATCAACC
*
5553299 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA-GAG-AAGAAGAAGTTCACAATGAGA
* * * *
5553364 AGAGCTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACATCATCC
64 AGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATAGATCAACATCAACC
* *
5553423 ---CCAGCGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAGAAGAA
1 TTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAGA-AGAAGAA
5553472 TTTATTCAAC
Statistics
Matches: 153, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
120 38 0.25
121 15 0.10
122 30 0.20
123 2 0.01
124 68 0.44
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (122 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAGAAGTTCACAATGAGAAG
AGCTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATAGATCAACATCAACC
Found at i:5553578 original size:3 final size:3
Alignment explanation
Indices: 5553572--5553633 Score: 79
Period size: 3 Copynumber: 20.0 Consensus size: 3
5553562 ACTAATTTTT
* * *
5553572 TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
5553621 TATA TTA TTA TTA
1 T-TA TTA TTA TTA
5553634 AAAAAATAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 45 0.87
4 7 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:5556799 original size:46 final size:45
Alignment explanation
Indices: 5556686--5556822 Score: 148
Period size: 46 Copynumber: 3.0 Consensus size: 45
5556676 AAGAACTATT
* * * *
5556686 GAATTACAGGTTAGTGTATCTTCATTGGATTGTAATTCCAATTACT
1 GAATTACAGGTT-GTGTATCCTCATTGGATGGTAATTCTAATTACC
* * *
5556732 GAATTACTCGCTTGTGCATCCTCATTGGATGGTAATTCTAATTACC
1 GAATTAC-AGGTTGTGTATCCTCATTGGATGGTAATTCTAATTACC
* * * *
5556778 GAATTGCAGGTTGGTATATCCTCATCGGATGGTTATTCTAATTAC
1 GAATTACAGGTT-GTGTATCCTCATTGGATGGTAATTCTAATTAC
5556823 TAAGTAATCG
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
45 3 0.04
46 69 0.92
47 3 0.04
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (45 bp):
GAATTACAGGTTGTGTATCCTCATTGGATGGTAATTCTAATTACC
Found at i:5557099 original size:86 final size:86
Alignment explanation
Indices: 5556997--5557170 Score: 348
Period size: 86 Copynumber: 2.0 Consensus size: 86
5556987 TAGCTCACCC
5556997 TTTAGTTTTCTTCTTTATACAAGTATGGTTATTTTCATTATACTTTATACTTTTATCAAATTTGG
1 TTTAGTTTTCTTCTTTATACAAGTATGGTTATTTTCATTATACTTTATACTTTTATCAAATTTGG
5557062 GTTTTATTGAATTTTTTGACA
66 GTTTTATTGAATTTTTTGACA
5557083 TTTAGTTTTCTTCTTTATACAAGTATGGTTATTTTCATTATACTTTATACTTTTATCAAATTTGG
1 TTTAGTTTTCTTCTTTATACAAGTATGGTTATTTTCATTATACTTTATACTTTTATCAAATTTGG
5557148 GTTTTATTGAATTTTTTGACA
66 GTTTTATTGAATTTTTTGACA
5557169 TT
1 TT
5557171 ATCTATATGA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 88 1.00
ACGTcount: A:0.24, C:0.09, G:0.10, T:0.56
Consensus pattern (86 bp):
TTTAGTTTTCTTCTTTATACAAGTATGGTTATTTTCATTATACTTTATACTTTTATCAAATTTGG
GTTTTATTGAATTTTTTGACA
Found at i:5558619 original size:2 final size:2
Alignment explanation
Indices: 5558612--5558646 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5558602 ATTTTAAAAC
5558612 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5558647 CCCCCATCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5558845 original size:24 final size:24
Alignment explanation
Indices: 5558813--5558882 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
5558803 ACGGAGATAT
*
5558813 CAGAAATCAAAAGAGAATTCAGAA
1 CAGAAATCAAAACAGAATTCAGAA
* * * *
5558837 CAGATATCAGAACAGAATCCAGAT
1 CAGAAATCAAAACAGAATTCAGAA
*
5558861 CAGAAATCATAACAGAATTCAG
1 CAGAAATCAAAACAGAATTCAG
5558883 GTCATGTATC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.51, C:0.17, G:0.16, T:0.16
Consensus pattern (24 bp):
CAGAAATCAAAACAGAATTCAGAA
Found at i:5558846 original size:12 final size:11
Alignment explanation
Indices: 5558826--5558878 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
5558816 AAATCAAAAG
5558826 AGAATTCAGAAC
1 AGAA-TCAGAAC
5558838 AGATATCAGAAC
1 AGA-ATCAGAAC
*
5558850 AGAATCCAGATC
1 AGAAT-CAGAAC
*
5558862 AGAAATCATAAC
1 AG-AATCAGAAC
5558874 AGAAT
1 AGAAT
5558879 TCAGGTCATG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 5 0.14
12 26 0.74
13 4 0.11
ACGTcount: A:0.51, C:0.17, G:0.15, T:0.17
Consensus pattern (11 bp):
AGAATCAGAAC
Found at i:5558917 original size:24 final size:24
Alignment explanation
Indices: 5558842--5558917 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
5558832 CAGAACAGAT
* * *
5558842 ATCAGAACAGAA-TCCAGATCAGAA
1 ATCATAACAGAATTCAAG-TCATAA
* **
5558866 ATCATAACAGAATTCAGGTCATGT
1 ATCATAACAGAATTCAAGTCATAA
5558890 ATCATAACAGAATTCAAGTCGA-AA
1 ATCATAACAGAATTCAAGTC-ATAA
5558914 ATCA
1 ATCA
5558918 GATAAAATAT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
24 37 0.90
25 4 0.10
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCATAACAGAATTCAAGTCATAA
Found at i:5565543 original size:41 final size:42
Alignment explanation
Indices: 5565475--5565558 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 42
5565465 TTTGTGATAA
*
5565475 ACCTTTTAGATTTATGATTTGTAGTTTGATTATTGAATTATT
1 ACCTTTTAGATTTATAATTTGTAGTTTGATTATTGAATTATT
* * * **
5565517 ACCTTTT-TATTTATAATTTTTTGTTTGATTATTTTATTATT
1 ACCTTTTAGATTTATAATTTGTAGTTTGATTATTGAATTATT
5565558 A
1 A
5565559 TATTATCTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 29 0.81
42 7 0.19
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.61
Consensus pattern (42 bp):
ACCTTTTAGATTTATAATTTGTAGTTTGATTATTGAATTATT
Found at i:5566260 original size:17 final size:17
Alignment explanation
Indices: 5566235--5566273 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
5566225 AAAACAAATT
5566235 GAGGCGAAGCGAAACTA
1 GAGGCGAAGCGAAACTA
*
5566252 GAGGTGAAGCGAAACTA
1 GAGGCGAAGCGAAACTA
5566269 GAGGC
1 GAGGC
5566274 TATCTCTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.38, T:0.08
Consensus pattern (17 bp):
GAGGCGAAGCGAAACTA
Found at i:5570243 original size:11 final size:11
Alignment explanation
Indices: 5570227--5570260 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
5570217 TGAATGAATG
5570227 AAAAAAGAAAA
1 AAAAAAGAAAA
5570238 AAAAAAGAAAA
1 AAAAAAGAAAA
5570249 AAAAAAGAAAA
1 AAAAAAGAAAA
5570260 A
1 A
5570261 GAGAATAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:5571702 original size:134 final size:134
Alignment explanation
Indices: 5571486--5572155 Score: 833
Period size: 134 Copynumber: 5.0 Consensus size: 134
5571476 AACTCAATTA
* * *
5571486 AATCTTCCTTGAGTAACAATGGAATGAATCAACAT-CCCAGATCTGATTTTCCCTCAAGAAGAAG
1 AATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAG
* * * *
5571550 CGGAACATATATCTCTCTTTCAAGATTTGATACTCTCTGAGTAACAGTGGAACAAGTCTGCCTCG
66 CGGAACATATCTCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAAAAAGTCTGCCTCG
5571615 ATTC
131 ATTC
* * * * *
5571619 AATCTTCCATGAGTGACAGTGGAATGAATCAACATCCCTAGATCTGATTTTCACTTAAGATGAAG
1 AATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAG
* * * * * *
5571684 CGGAACAGATCTCTCTCTTTCAAGATTTGATATTCCCTTAGTAATAGTGGAAAAACTTTACCTCG
66 CGGAACATATCTCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAAAAAGTCTGCCTCG
5571749 ATTC
131 ATTC
* * * * *
5571753 AATCATCCCTGAGTGACAGTGAAATGAATCAACATCCCCAGATCTGATTTTCCCTTAATAATAAG
1 AATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAG
* * * * * ** *
5571818 CAGAATATATCCCTCTCTTTCAAGATTTGATATTGCCTGAGTAACAATGGAATGAGTCTGCCTTG
66 CGGAACATATCTCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAAAAAGTCTGCCTCG
5571883 ATTC
131 ATTC
* * * * * *
5571887 AATCTTCCCTAAGTAACAGTGGAAGGAATCAACATCCCC-TATCTAATTTTCCCTCAAGAAAAAG
1 AATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAG
* * * * * * *
5571951 TGAAACATATCCCTCTCTTTCAAGATTAGATATTCTCTGAGTAACAGTGGAACAAGTCTACCTCG
66 CGGAACATATCTCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAAAAAGTCTGCCTCG
*
5572016 TTTC
131 ATTC
* * *
5572020 AATCTTCCCTGAGTGAAAGTGGAATGAATCAACATCCCCAGATATGATTTTTCCTCAAGAAGAAG
1 AATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAG
* * * **
5572085 CAGAACATATCTCTCTCTTCCAGGATTTGATATTCCCTGAGTAACAGTTAAAAAAGTCTGGCCT-
66 CGGAACATATCTCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAAAAAGTCT-GCCTC
5572149 GATTC
130 GATTC
5572154 AA
1 AA
5572156 CGTTTCTCGA
Statistics
Matches: 450, Mismatches: 84, Indels: 5
0.83 0.16 0.01
Matches are distributed among these distances:
133 143 0.32
134 304 0.68
135 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (134 bp):
AATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAG
CGGAACATATCTCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAAAAAGTCTGCCTCG
ATTC
Found at i:5572154 original size:267 final size:266
Alignment explanation
Indices: 5571486--5572155 Score: 851
Period size: 267 Copynumber: 2.5 Consensus size: 266
5571476 AACTCAATTA
* *
5571486 AATCTTCCTTGAGT-AACAATGGAATGAATCAACAT-CCCAGATCTGATTTTCCCTCAAGAAGAA
1 AATCTTCCCTGAGTGAA-AGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAA
* * * * *
5571549 GCGGAACATATATCTCTCTTTCAAGATTTGATACTCTCTGAGTAACAGTGGAACAAGTCTGCCTC
65 GCAGAACATATCTCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAAAAAGTCTGCCT-
* * * * *
5571614 GATTCAATCTTCCATGAGTGACAGTGGAATGAATCAACATCCCTAGATCTGATTTTCACTTAAGA
129 GATTCAATCTTCCATAAGTAACAGTGGAAGGAATCAACATCCCTA-ATCTAATTTTCACTCAAGA
** * * * * * *
5571679 TGAAGCGGAACAGATCTCTCTCTTTCAAGATTTGATATTCCCTTAGTAATAGTGGAAAAACTTTA
193 AAAAGCGAAACAGATCCCTCTCTTTCAAGATTAGATATTCCCTGAGTAACAGTGGAAAAACTCTA
5571744 CCTCGATTC
258 CCTCGATTC
* * * * * *
5571753 AATCATCCCTGAGTGACAGTGAAATGAATCAACATCCCCAGATCTGATTTTCCCTTAATAATAAG
1 AATCTTCCCTGAGTGAAAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAG
* * * * **
5571818 CAGAATATATCCCTCTCTTTCAAGATTTGATATTGCCTGAGTAACAATGGAATGAGTCTGCCTTG
66 CAGAACATATCTCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAAAAAGTCTGCC-TG
* *
5571883 ATTCAATCTTCCCTAAGTAACAGTGGAAGGAATCAACATCCCCT-ATCTAATTTTCCCTCAAGAA
130 ATTCAATCTTCCATAAGTAACAGTGGAAGGAATCAACAT-CCCTAATCTAATTTTCACTCAAGAA
* * * * *
5571947 AAAGTGAAACATATCCCTCTCTTTCAAGATTAGATATTCTCTGAGTAACAGTGGAACAAGTCTAC
194 AAAGCGAAACAGATCCCTCTCTTTCAAGATTAGATATTCCCTGAGTAACAGTGGAAAAACTCTAC
*
5572012 CTCGTTTC
259 CTCGATTC
* *
5572020 AATCTTCCCTGAGTGAAAGTGGAATGAATCAACATCCCCAGATATGATTTTTCCTCAAGAAGAAG
1 AATCTTCCCTGAGTGAAAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAG
* * **
5572085 CAGAACATATCTCTCTCTTCCAGGATTTGATATTCCCTGAGTAACAGTTAAAAAAGTCTGGCCTG
66 CAGAACATATCTCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAAAAAGTCT-GCCTG
5572150 ATTCAA
130 ATTCAA
5572156 CGTTTCTCGA
Statistics
Matches: 341, Mismatches: 57, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
267 218 0.64
268 118 0.35
269 5 0.01
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (266 bp):
AATCTTCCCTGAGTGAAAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAG
CAGAACATATCTCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAAAAAGTCTGCCTGA
TTCAATCTTCCATAAGTAACAGTGGAAGGAATCAACATCCCTAATCTAATTTTCACTCAAGAAAA
AGCGAAACAGATCCCTCTCTTTCAAGATTAGATATTCCCTGAGTAACAGTGGAAAAACTCTACCT
CGATTC
Found at i:5572370 original size:3 final size:3
Alignment explanation
Indices: 5572364--5572411 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
5572354 ATAATAATAT
* * * * *
5572364 TTA TTA TTA TTA TTA TCA TTA TCA TTA CTA ATA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5572412 ATACTTTTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:5574624 original size:126 final size:127
Alignment explanation
Indices: 5574490--5574824 Score: 370
Period size: 131 Copynumber: 2.6 Consensus size: 127
5574480 TTTCAGCCGA
* *
5574490 AGTAATAAATGACTGCTTTAATATATGAGAGGTCATTTATTCTCGATTGGAAATAATTTGATATT
1 AGTAATAAATGATTGCTTTAA-ATATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATT
* * * *** *
5574555 GTCGTTTTCTCTCGAAT-TAAT-ATTTTAAGATGGAATAGTGGTATATCTTCATTTTAATTAG
65 ATCGTTTTCACTCGAATATAATAATTTTAAGATGAAATAGTAACATATCTTCATTTCAATTAG
* * **
5574616 AGTAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTGGATTGGAAATCGTTAGATATT
1 AGTAATAAATGATTGCTTTAA-ATATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATT
* ** * * *
5574681 ATCGTTTTCACTTGAATCGATGTTGAATTTTAAGATGAAATAGTAACATCTCTTTATTTCAATTG
65 ATCGTTTTCACTCGAAT--ATAAT-AATTTTAAGATGAAATAGTAACATATCTTCATTTCAATTA
5574746 G
127 G
* * * * *
5574747 GGTAATAAATGATTGTTTTAAAGTA-AAAAGGGTCATTTATTCTCAATTGGAAATAATTAGATAT
1 AGTAATAAATGATTGCTTTAAA-TATGAGA-GGTCATTTATTCTCGATTGGAAATAATTAGATAT
5574811 TATCGTTTTCACTC
64 TATCGTTTTCACTC
5574825 TTAAAATTAT
Statistics
Matches: 172, Mismatches: 30, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
126 72 0.42
129 2 0.01
130 2 0.01
131 96 0.56
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (127 bp):
AGTAATAAATGATTGCTTTAAATATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTA
TCGTTTTCACTCGAATATAATAATTTTAAGATGAAATAGTAACATATCTTCATTTCAATTAG
Found at i:5575352 original size:20 final size:20
Alignment explanation
Indices: 5575327--5575385 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
5575317 ATCAGATTGT
*
5575327 CCAGGGGGTATAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
* *
5575347 CCAGGGAGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
5575367 CCAGGGGGTACCGATTCCC
1 CCAGGGGGTACAGATTCCC
5575386 TCTGTCTAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.34, G:0.29, T:0.15
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:5576658 original size:19 final size:20
Alignment explanation
Indices: 5576634--5576681 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
5576624 AACGATTTTC
*
5576634 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
5576653 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
5576673 TTTTGAAAA
1 TTTTGAAAA
5576682 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:5578858 original size:12 final size:12
Alignment explanation
Indices: 5578841--5578900 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
5578831 CGGAAATCAA
5578841 AACAGAATTCAG
1 AACAGAATTCAG
*
5578853 AACAG-ATATCAA
1 AACAGAAT-TCAG
*
5578865 AACAGAATCCAG
1 AACAGAATTCAG
* *
5578877 ATCAGAAATCAG
1 AACAGAATTCAG
5578889 AACAGAATTCAG
1 AACAGAATTCAG
5578901 GTCATGTATC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 2 0.05
12 34 0.89
13 2 0.05
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.15
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:5578863 original size:24 final size:24
Alignment explanation
Indices: 5578836--5578923 Score: 106
Period size: 24 Copynumber: 3.7 Consensus size: 24
5578826 GATATCGGAA
*
5578836 ATCAAAACAGAATTCAGAACAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* *
5578860 ATCAAAACAGAATCCAGATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
* *
5578884 ATCAGAACAGAATTCAGGTCATG-T
1 ATCAAAACAGAATTCAGATCA-GAT
*
5578908 ATCATAACAGAATTCA
1 ATCAAAACAGAATTCA
5578924 AGTCGGAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
24 54 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:5578911 original size:48 final size:48
Alignment explanation
Indices: 5578833--5578937 Score: 124
Period size: 48 Copynumber: 2.2 Consensus size: 48
5578823 GGAGATATCG
*
5578833 GAAATCAAAACAGAATTCAGAACAGATATCAAAACAGAATCC-AGATCA
1 GAAATCAGAACAGAATTCAGAACAGATATCAAAACAGAATCCAAG-TCA
** * * *
5578881 GAAATCAGAACAGAATTCAGGTCATG-TATCATAACAGAATTCAAGTCG
1 GAAATCAGAACAGAATTCAGAACA-GATATCAAAACAGAATCCAAGTCA
5578929 GAAATCAGA
1 GAAATCAGA
5578938 TAAAATATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
48 46 0.94
49 3 0.06
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.18
Consensus pattern (48 bp):
GAAATCAGAACAGAATTCAGAACAGATATCAAAACAGAATCCAAGTCA
Done.