Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007726.1 Hibiscus syriacus cultivar Beakdansim tig00109973_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: 404270
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:230980 original size:123 final size:122
Alignment explanation
Indices: 230675--230981 Score: 289
Period size: 123 Copynumber: 2.5 Consensus size: 122
230665 GTATCCTATG
* * * * ** * * *
230675 ATGTAAACTCCACCATGAATACAAATACATAATATCTTATGTATCCT-AAAATCCATTATCTATA
1 ATGTAAACTCCACAAAGAATACAAAGACATAAAAAATTA-GAATCCTAAAAAT-AATTATTTATA
*
230739 TCAAAACTCGGTGTATCCCAAAACACTCTCCCAACATTCCTATATTATCCATCTCTACA
64 TCAAAACTCGGTGTATCCCAAAACACTCTCCCAACATTCCTATAATATCCATCTCTACA
* * * * ** * * **
230798 ATGTAAACTCCACCACGAATACAAATACATAATATCTTATGTATCCTAAAATTCGTTATTTATAT
1 ATGTAAACTCCACAAAGAATACAAAGACATAAAAAATTA-GAATCCTAAAAATAATTATTTATAT
* * * *
230863 CAAAACTTGGTGTATCCCAAAATATTCTCCCAACATTCCTATAATATCCATCTTTACA
65 CAAAACTCGGTGTATCCCAAAACACTCTCCCAACATTCCTATAATATCCATCTCTACA
* *
230921 ATGTAAACTCCA-AAAG-TTACAGAGACTATAAAAGAATTA-AATCTCTCAAAAATAATTATTT
1 ATGTAAACTCCACAAAGAATACAAAGAC-ATAAAA-AATTAGAATC-CT-AAAAATAATTATTT
230982 CTCATAGTCA
Statistics
Matches: 158, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
121 10 0.06
122 9 0.06
123 135 0.85
124 4 0.03
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.32
Consensus pattern (122 bp):
ATGTAAACTCCACAAAGAATACAAAGACATAAAAAATTAGAATCCTAAAAATAATTATTTATATC
AAAACTCGGTGTATCCCAAAACACTCTCCCAACATTCCTATAATATCCATCTCTACA
Found at i:233604 original size:20 final size:20
Alignment explanation
Indices: 233568--233605 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
233558 ACAATCAATT
*
233568 ATAATTAATCTTGAAAAGTA
1 ATAATTAATCTTAAAAAGTA
233588 ATAATTAAT-TATAAAAAG
1 ATAATTAATCT-TAAAAAG
233606 GAATCTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (20 bp):
ATAATTAATCTTAAAAAGTA
Found at i:234737 original size:3 final size:3
Alignment explanation
Indices: 234714--234776 Score: 78
Period size: 3 Copynumber: 21.3 Consensus size: 3
234704 TTTTTTGTCC
*
234714 ATT ATT -TT -TT ATT ATT TTT ATT ATT ATT ATT AATT ATT A-T ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT AT-T
234758 ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
234777 AATAAAAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
2 6 0.11
3 42 0.78
4 6 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:234742 original size:25 final size:25
Alignment explanation
Indices: 234722--234776 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
234712 CCATTATTTT
* *
234722 TTATTATTTTTATTATTATTATTAA
1 TTATTATATATATTATTATTATTAA
234747 TTATTATATATATTATTATTATT-A
1 TTATTATATATATTATTATTATTAA
234771 TTATTA
1 TTATTA
234777 AATAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 7 0.25
25 21 0.75
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATTATATATATTATTATTATTAA
Found at i:234789 original size:31 final size:31
Alignment explanation
Indices: 234726--234792 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
234716 TATTTTTTAT
* * ** *
234726 TATTTTTATTATTATTATTAATTATTATATA
1 TATTATTATTATTATTATTAAATAAAAAATA
234757 TATTATTATTATTATTATTAAATAAAAAATA
1 TATTATTATTATTATTATTAAATAAAAAATA
234788 TATTA
1 TATTA
234793 CAGTCCCATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
TATTATTATTATTATTATTAAATAAAAAATA
Found at i:236137 original size:2 final size:2
Alignment explanation
Indices: 236130--236167 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
236120 TATTTTTATC
236130 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
236168 GTACAATTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:237657 original size:16 final size:16
Alignment explanation
Indices: 237636--237667 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
237626 ATTTTTTCAC
237636 TTTTTCTTTTCTTTCT
1 TTTTTCTTTTCTTTCT
237652 TTTTTCTTTTCTTTCT
1 TTTTTCTTTTCTTTCT
237668 GTCCCTCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTCTTTCT
Found at i:238449 original size:2 final size:2
Alignment explanation
Indices: 238442--238481 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
238432 TGGTTGTGTA
238442 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
238482 CCCAAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:239613 original size:2 final size:2
Alignment explanation
Indices: 239606--239670 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
239596 GTTATTATTT
239606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
239648 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
239671 TCTTTTTTCA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:239796 original size:2 final size:2
Alignment explanation
Indices: 239789--239830 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
239779 TTTCAACTTT
239789 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
239831 GTTTATATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:239928 original size:24 final size:25
Alignment explanation
Indices: 239896--239942 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
239886 CGTTTTTTTA
* *
239896 TATTTGTATATATTTTAT-TATTAC
1 TATTAGTATATATCTTATATATTAC
239920 TATTAGTATATATCTTATATATT
1 TATTAGTATATATCTTATATATT
239943 TTACTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (25 bp):
TATTAGTATATATCTTATATATTAC
Found at i:242734 original size:64 final size:65
Alignment explanation
Indices: 242666--242844 Score: 229
Period size: 64 Copynumber: 2.8 Consensus size: 65
242656 GATTTAATTG
*
242666 AACATCGAATGCATTTCATGCACCGATGCACTCTCCATGCATCGATGCACTCAGAATA-TTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACTCTCCATGCATCGATGCACTCAGAATATTTTTCA
* *** **
242730 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGTCTATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACTCTCCATGCATCGATGCACTCAGAATATTTTTCA
* * * *
242794 ATCATCGAATGCACTTCATGCATCGATGCACTCT-TAGTGCACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACTCTCCA-TGCATCGATGCACT
242845 AGGAGTCCAA
Statistics
Matches: 97, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
63 6 0.06
64 91 0.94
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTCCATGCATCGATGCACTCAGAATATTTTTCA
Found at i:242824 original size:17 final size:19
Alignment explanation
Indices: 242796--242844 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
242786 ATTTTTCAAT
242796 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
242814 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
242833 CACCGATGCACT
1 CATCGATGCACT
242845 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:248681 original size:44 final size:43
Alignment explanation
Indices: 248625--248746 Score: 113
Period size: 44 Copynumber: 2.8 Consensus size: 43
248615 TTTGTGCTTC
* *
248625 ATGCACCGATGCATTTAACA-ATGCATCGATGCATACCTTTGAAT
1 ATGCATCGATGCA-TTAACAGATGCACCGATGCATACC-TTGAAT
* ** *
248669 GTGCATCGATGCATTCGCATGATGCACCGATGCATGCCTTGAAT
1 ATGCATCGATGCATTAACA-GATGCACCGATGCATACCTTGAAT
* * *
248713 ATGCATCGATGTA-TAAGACCATGCACCGATGCAT
1 ATGCATCGATGCATTAACA-GATGCACCGATGCAT
248747 CCGTCGGGTT
Statistics
Matches: 63, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
43 20 0.32
44 28 0.44
45 15 0.24
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (43 bp):
ATGCATCGATGCATTAACAGATGCACCGATGCATACCTTGAAT
Found at i:251413 original size:64 final size:64
Alignment explanation
Indices: 251315--251506 Score: 230
Period size: 64 Copynumber: 3.0 Consensus size: 64
251305 ATGCATCAAA
* * * *
251315 CCATGCATCGATGCACCTATGAT-TTAATT-GAACATCGAATGCATTTCATGCACCGATGCACTC
1 CCATGCATCGATGCACC-AGGATATT-TTTCAAACATCGAATGCATTTCATGCATCGATGCACTC
251378 T
64 T
* **
251379 CCATGCATCGATGCACTC-GGA-ATATTTTCAAACATCGAATGCATTTGATGCATCGATGCACAA
1 CCATGCATCGATGCAC-CAGGATAT-TTTTCAAACATCGAATGCATTTCATGCATCGATGCACTC
*
251442 G
64 T
* *
251443 CCATGCATCGATGCACCAGGCTATTTTTCAAACATCGAATGCACTTCATGCATCGATGCACTCT
1 CCATGCATCGATGCACCAGGATATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACTCT
251507 TAGTGCACCG
Statistics
Matches: 108, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
63 6 0.06
64 99 0.92
65 3 0.03
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (64 bp):
CCATGCATCGATGCACCAGGATATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACTCT
Found at i:260387 original size:22 final size:21
Alignment explanation
Indices: 260357--260397 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
260347 CCCTAAATTG
*
260357 AAAAAAGAAAAGGAAAAGAGT
1 AAAAAAGAAAAAGAAAAGAGT
260378 AAAAAGAGAAAAAGAAAAGA
1 AAAAA-AGAAAAAGAAAAGA
260398 AAAGAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (21 bp):
AAAAAAGAAAAAGAAAAGAGT
Found at i:261575 original size:99 final size:99
Alignment explanation
Indices: 261402--261682 Score: 420
Period size: 99 Copynumber: 2.8 Consensus size: 99
261392 CAACCCGCGG
* * * *
261402 TTTCAACTTCACGACGAAGGGA-ATCGCGCACACAAGACAACACAAGCTCAACTTCACAGCGAAG
1 TTTCAACTTCACAACGAA-GGATATTG-G-ACTCAAGACAGCACAAGCTCAACTTCACAGCGAAG
* *
261466 GGGCGGCTGACTGTCAACTTTCCGATTTCAGAGCCAA
63 GGGCGGCTGACTGTCAACTTTCCAATTTCAAAGCCAA
261503 TTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGG
1 TTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGG
* *
261568 TGGCTGACTGTCAACTTTCCAATTTCAAAGCTAA
66 CGGCTGACTGTCAACTTTCCAATTTCAAAGCCAA
* * * *
261602 TTTCAACTTCACAACGAATGATATTGGACTCAAGATAGCACAAGCTCAACTTCACGGCAAAGGGG
1 TTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGG
261667 CGGCTGACTGTCAACT
66 CGGCTGACTGTCAACT
261683 AACAATTTCT
Statistics
Matches: 166, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
99 142 0.86
100 4 0.02
101 20 0.12
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (99 bp):
TTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGG
CGGCTGACTGTCAACTTTCCAATTTCAAAGCCAA
Found at i:263027 original size:24 final size:25
Alignment explanation
Indices: 262995--263041 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
262985 TTGTTTTTTT
* *
262995 TATTTGTATATATTTTAT-TATTAC
1 TATTAGTATATATCTTATATATTAC
263019 TATTAGTATATATCTTATATATT
1 TATTAGTATATATCTTATATATT
263042 TTACTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (25 bp):
TATTAGTATATATCTTATATATTAC
Found at i:269082 original size:21 final size:21
Alignment explanation
Indices: 269031--269083 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
269021 ATTATGACTG
269031 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
** *
269052 TCGCGTTGCGATTTTCCCATT
1 TCGCAATGCGATTTTCCAATT
269073 TCGCAATGCGA
1 TCGCAATGCGA
269084 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:269098 original size:20 final size:21
Alignment explanation
Indices: 269073--269124 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
269063 TTTTCCCATT
*
269073 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
269093 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
269114 TCGCAATGCGA
1 TCGCAATGCGA
269125 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:269137 original size:41 final size:41
Alignment explanation
Indices: 269110--269247 Score: 127
Period size: 41 Copynumber: 3.4 Consensus size: 41
269100 GCGAATTTGG
*
269110 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATTC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATTC
* * *
269151 AAAATTGCAACGCGATACTGACTTTCGCAACGCGAT--TCTG
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAAT-TC
*** * * * * *
269191 ACTTTTGCAACGCGATTCTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATTC
* *
269232 AGAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
269248 TTTCAAAGTT
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 1 0.01
40 32 0.41
41 44 0.56
42 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATTC
Found at i:269138 original size:20 final size:20
Alignment explanation
Indices: 269113--269227 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
269103 AATTTGGAAA
*
269113 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * **
269133 ATCGCAACGCGATAATTCAAA
1 ATCGCAACGCGAT-ACTGACT
*
269154 ATTGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
269174 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
269194 TTTGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
269214 TTCGCAACGAGATA
1 ATCGCAACGCGATA
269228 ATACAGAATC
Statistics
Matches: 77, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
20 62 0.81
21 15 0.19
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:269996 original size:24 final size:24
Alignment explanation
Indices: 269969--270022 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
269959 GTATTCGAAA
*
269969 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
269993 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
270017 TTTGAT
1 TTTGAT
270023 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:270214 original size:12 final size:12
Alignment explanation
Indices: 270197--270221 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
270187 ATATAATCCT
270197 GAAGAAGAAAAA
1 GAAGAAGAAAAA
270209 GAAGAAGAAAAA
1 GAAGAAGAAAAA
270221 G
1 G
270222 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:272551 original size:20 final size:19
Alignment explanation
Indices: 272523--272577 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
272513 CAATCATCTT
*
272523 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
272543 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
272562 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
272578 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:272565 original size:19 final size:19
Alignment explanation
Indices: 272530--272610 Score: 82
Period size: 19 Copynumber: 4.5 Consensus size: 19
272520 CTTAATGTCT
* **
272530 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
272550 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
272569 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
272583 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
272602 ATCGCAATG
1 ATCGCAATG
272611 AGGGAATCGC
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 26 0.51
20 9 0.18
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:272592 original size:33 final size:33
Alignment explanation
Indices: 272550--272643 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
272540 GGAAATGACT
272550 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
272583 ATCGCAATGCGAAATGAAAATCGCAATGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
272616 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
272644 CAAATTTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:272639 original size:19 final size:19
Alignment explanation
Indices: 272530--272641 Score: 64
Period size: 19 Copynumber: 6.4 Consensus size: 19
272520 CTTAATGTCT
* **
272530 ATCGCAACGCGGAAATGACT
1 ATCGCAAAGC-GAAATGAAA
*
272550 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
272569 ATCGC-AA-CG--A-GAGA
1 ATCGCAAAGCGAAATGAAA
*
272583 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
* **
272602 ATCGC-AA-TG--A-GGGA
1 ATCGCAAAGCGAAATGAAA
272616 ATCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
272635 ATCGCAA
1 ATCGCAA
272642 CGCAAATTTA
Statistics
Matches: 68, Mismatches: 14, Indels: 21
0.66 0.14 0.20
Matches are distributed among these distances:
14 15 0.22
15 5 0.07
16 3 0.04
17 3 0.04
18 4 0.06
19 29 0.43
20 9 0.13
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAAAGCGAAATGAAA
Found at i:272700 original size:19 final size:19
Alignment explanation
Indices: 272672--272743 Score: 91
Period size: 19 Copynumber: 4.1 Consensus size: 19
272662 GCGATTTTGT
*
272672 CGTTGTGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
272691 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
272710 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
272724 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
272743 C
1 C
272744 ATTACGATAG
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 10 0.22
16 3 0.07
17 3 0.07
19 29 0.64
ACGTcount: A:0.10, C:0.22, G:0.21, T:0.47
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:272758 original size:52 final size:52
Alignment explanation
Indices: 272653--272759 Score: 151
Period size: 52 Copynumber: 2.1 Consensus size: 52
272643 GCAAATTTAG
* * * * * **
272653 TTTCGCGTTGCGATTTTGTCGTTGTGATTTTCATTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTACGATAGTCA
272705 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTACGATAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTACGATAGTCA
272757 TTT
1 TTT
272760 TTGCCTTCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.48
Consensus pattern (52 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTACGATAGTCA
Found at i:272877 original size:14 final size:14
Alignment explanation
Indices: 272858--272894 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
272848 CATCAATTAA
272858 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
272872 ACAAATCATCTTTT
1 ACAAATCAACTTTT
272886 ACAAATCAA
1 ACAAATCAA
272895 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:274843 original size:19 final size:19
Alignment explanation
Indices: 274787--274852 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
274777 AAAAAAGACT
*
274787 ATCGCAACACGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
274806 ATCGTAA--CG--AT-AGA
1 ATCGCAACGCGAAATGAAA
274820 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
274839 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
274853 CCAAAAGACA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 8 0.21
15 2 0.05
16 2 0.05
17 2 0.05
18 2 0.05
19 22 0.58
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:274858 original size:19 final size:19
Alignment explanation
Indices: 274819--274858 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
274809 GTAACGATAG
**
274819 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
274838 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
274857 AA
1 AA
274859 GACAAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.50, C:0.25, G:0.17, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:274871 original size:12 final size:12
Alignment explanation
Indices: 274854--274880 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
274844 AACGCGAAAC
274854 CAAAAGACAAAA
1 CAAAAGACAAAA
274866 CAAAAGACAAAA
1 CAAAAGACAAAA
274878 CAA
1 CAA
274881 TGTTACTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.19, G:0.07, T:0.00
Consensus pattern (12 bp):
CAAAAGACAAAA
Found at i:275058 original size:94 final size:92
Alignment explanation
Indices: 274951--275231 Score: 442
Period size: 93 Copynumber: 3.1 Consensus size: 92
274941 ATGGATTGCA
* *
274951 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAA-AATACACAGTT
* *
275016 TAGCAGAATTGGCAGCAAACGAACAAAT
65 TAGCAGAATTGGCAGCAACCGAATAAAT
275044 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAAATACACAGTT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAAATACACAGTT
*
275109 TAGCATAATTGGCAGCAACCGAATAAAT
65 TAGCAGAATTGGCAGCAACCGAATAAAT
*
275137 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT---AATAAACAGTT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAAATACACAGTT
* *
275199 TAGCAGTATTGGCAGCAACCGCATAAAT
65 TAGCAGAATTGGCAGCAACCGAATAAAT
275227 TTACT
1 TTACT
275232 AAGCAATCTA
Statistics
Matches: 177, Mismatches: 9, Indels: 7
0.92 0.05 0.04
Matches are distributed among these distances:
90 40 0.23
92 19 0.11
93 71 0.40
94 47 0.27
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (92 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAAATACACAGTTT
AGCAGAATTGGCAGCAACCGAATAAAT
Found at i:276951 original size:20 final size:19
Alignment explanation
Indices: 276906--276962 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
276896 TCTTTTGGTT
276906 GAAATGAAAATCGCAACAA
1 GAAATGAAAATCGCAACAA
*
276925 GATAATGAAAATCGCAACACG
1 GA-AATGAAAATCGCAACA-A
**
276946 GAAATGACTATCGCAAC
1 GAAATGAAAATCGCAAC
276963 GAGAGAATCG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.49, C:0.19, G:0.18, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACAA
Found at i:276987 original size:33 final size:33
Alignment explanation
Indices: 276934--277051 Score: 209
Period size: 33 Copynumber: 3.5 Consensus size: 33
276924 AGATAATGAA
*
276934 AATCGCAACACGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGACTATCGCAACGAGAG
276968 AATCGCAACGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
*
277001 AATCGCAACGCGAAATGACAATCGCAACGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
277034 AATCGCAACGCGAAATGA
1 AATCGCAACGCGAAATGA
277052 AAATCACAAT
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
33 72 0.88
34 10 0.12
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACGAGAG
Found at i:276993 original size:19 final size:18
Alignment explanation
Indices: 276935--277051 Score: 78
Period size: 14 Copynumber: 6.9 Consensus size: 18
276925 GATAATGAAA
*
276935 ATCGCAACACGGAAATGAC
1 ATCGCAACGC-GAAATGAC
*
276954 TATCGCAA--CGAGA-GA-
1 -ATCGCAACGCGAAATGAC
276969 ATCGCAACGCGAAATGAC
1 ATCGCAACGCGAAATGAC
*
276987 TATCGCAA--CGAGA-GA-
1 -ATCGCAACGCGAAATGAC
277002 ATCGCAACGCGAAATGAC
1 ATCGCAACGCGAAATGAC
*
277020 AATCGCAA--CGAGA-GA-
1 -ATCGCAACGCGAAATGAC
277035 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
277052 AAATCACAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 29
0.69 0.05 0.26
Matches are distributed among these distances:
14 21 0.27
16 18 0.23
17 17 0.22
18 1 0.01
19 14 0.18
20 7 0.09
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (18 bp):
ATCGCAACGCGAAATGAC
Found at i:277109 original size:33 final size:33
Alignment explanation
Indices: 277061--277153 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
277051 AAAATCACAA
** *
277061 TGCGATTTTGGTTTCGCGTTGCGATTATCTTGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
* *
277094 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
**
277127 TGCGATAGTCATTTCCGCGTTGCGATT
1 TGCGATTTTCATTT-CGCGTTGCGATT
277154 TTCATTCTCG
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 40 0.78
34 11 0.22
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:277728 original size:20 final size:20
Alignment explanation
Indices: 277705--277798 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
277695 CGATAGTCAG
277705 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
277725 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
277745 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
277766 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
277786 ATTCGCATTGCGA
1 ATTCGCATTGCGA
277799 ATTATGAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 46 0.72
21 18 0.28
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:277757 original size:41 final size:40
Alignment explanation
Indices: 277705--277798 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 40
277695 CGATAGTCAG
* *
277705 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
277745 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
277786 ATTCGCATTGCGA
1 ATTCGCATTGCGA
277799 ATTATGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 13 0.27
41 35 0.73
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:277811 original size:41 final size:41
Alignment explanation
Indices: 277679--277854 Score: 130
Period size: 41 Copynumber: 4.3 Consensus size: 41
277669 CAAATGGCAC
*
277679 TATGTAAATCGCATTGCGA--TA-GTCAGATTCGCATTGCGATT
1 TATG-AAATCGCATTGCGATTTACGT-A-ATTCGCATTGCGAAT
* * * * * *
277720 TACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATT
1 TATGAAATCGCATTGCGATTTACGTAATTCGCATTGCGAAT
* *
277761 TACT-TAATCGCGTTGCGATTTACGT-ATTCGCATTGCGAAT
1 TA-TGAAATCGCATTGCGATTTACGTAATTCGCATTGCGAAT
* * * *
277801 TATGAAAATCGCAATGCGA-ATACGTAAATCGCAATGCGAAT
1 TATG-AAATCGCATTGCGATTTACGTAATTCGCATTGCGAAT
*
277842 TAGGAAAATCGCA
1 TATG-AAATCGCA
277855 ACGCGAATTT
Statistics
Matches: 110, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
39 1 0.01
40 33 0.30
41 73 0.66
42 2 0.02
43 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (41 bp):
TATGAAATCGCATTGCGATTTACGTAATTCGCATTGCGAAT
Found at i:277831 original size:20 final size:21
Alignment explanation
Indices: 277788--277881 Score: 118
Period size: 21 Copynumber: 4.5 Consensus size: 21
277778 ATTTACGTAT
* *
277788 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTAGGAAAA
* *
277809 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTAGGAAAA
277829 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * *
277850 TCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAAA
277871 TCGCAATGCGA
1 TCGCAATGCGA
277882 TAGTCAGAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 18 0.29
21 45 0.71
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:277831 original size:61 final size:61
Alignment explanation
Indices: 277707--277839 Score: 153
Period size: 61 Copynumber: 2.2 Consensus size: 61
277697 ATAGTCAGAT
* * * * * *
277707 TCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAATGCGATATACTAAA
* *
277768 TCGCGTTGCGATTTACGTATTCGCATTGCGAATTAT-GAAAATCGCAATGCGA-ATACGTAAA
1 TCGCATTGCGATTTACGTATTCGCATTGCG-ATTATCCAAAATCGCAATGCGATATAC-TAAA
*
277829 TCGCAATGCGA
1 TCGCATTGCGA
277840 ATTAGGAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
60 3 0.05
61 53 0.88
62 4 0.07
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (61 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAATGCGATATACTAAA
Found at i:277855 original size:41 final size:42
Alignment explanation
Indices: 277788--277881 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 42
277778 ATTTACGTAT
* * * *
277788 TCGCATTGCGAATTATGAAAATCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTAGGAAAATCGCAACGCGAATTACGGAAA
**
277829 TCGCAATGCGAATTAGGAAAATCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAAATCGCAACGCGAATTACGGAAA
277871 TCGCAATGCGA
1 TCGCAATGCGA
277882 TAGTCAGAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 30 0.65
42 16 0.35
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.21
Consensus pattern (42 bp):
TCGCAATGCGAATTAGGAAAATCGCAACGCGAATTACGGAAA
Found at i:279151 original size:44 final size:41
Alignment explanation
Indices: 279078--279162 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 41
279068 TTTTGGTATT
279078 AAAATAATATTATTAATTAATAATATTTTATTATTTATTAA
1 AAAATAATATTATTAATTAATAATATTTTATTATTTATTAA
*
279119 AAAATAATAGATTAGTTAACTT-ATAATTTTTTATTATTTATTAA
1 AAAATAAT--ATTA-TTAA-TTAATAATATTTTATTATTTATTAA
279163 TAATTATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
41 8 0.21
43 4 0.10
44 25 0.64
45 2 0.05
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (41 bp):
AAAATAATATTATTAATTAATAATATTTTATTATTTATTAA
Found at i:279488 original size:2 final size:2
Alignment explanation
Indices: 279481--279507 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
279471 TGTTCGTGTT
279481 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 T
279508 TATTAATTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:284287 original size:88 final size:88
Alignment explanation
Indices: 284138--284313 Score: 325
Period size: 88 Copynumber: 2.0 Consensus size: 88
284128 TATCGGAAGA
*
284138 CGTGCACATATCTTGCAGACACAATTCTCCTTAATCACTAAAGTCACTTGCTAACTGGTTGTGCA
1 CGTGCACATATCTTGCAGACACAATTCTCCTTAATCACTAAAGTCACTTGCTAACCGGTTGTGCA
284203 TATTGCCTTTTAGACTCAAATGC
66 TATTGCCTTTTAGACTCAAATGC
* *
284226 CGTGCACATATCTTGCAGACACAATTTTCCTTAATCATTAAAGTCACTTGCTAACCGGTTGTGCA
1 CGTGCACATATCTTGCAGACACAATTCTCCTTAATCACTAAAGTCACTTGCTAACCGGTTGTGCA
284291 TATTGCCTTTTAGACTCAAATGC
66 TATTGCCTTTTAGACTCAAATGC
284314 TAGATTGGGT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (88 bp):
CGTGCACATATCTTGCAGACACAATTCTCCTTAATCACTAAAGTCACTTGCTAACCGGTTGTGCA
TATTGCCTTTTAGACTCAAATGC
Found at i:284567 original size:21 final size:21
Alignment explanation
Indices: 284543--284586 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
284533 AAAGTTGGGA
*
284543 TTTAATTTAATTTCTTTGAGT
1 TTTAATTTAATTTCGTTGAGT
284564 TTTAATTTAATTTCGTTGAGT
1 TTTAATTTAATTTCGTTGAGT
284585 TT
1 TT
284587 GTATCCCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.11, T:0.61
Consensus pattern (21 bp):
TTTAATTTAATTTCGTTGAGT
Found at i:291105 original size:2 final size:2
Alignment explanation
Indices: 291098--291125 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
291088 CAATTTAGAA
291098 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
291126 CATACAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:293643 original size:17 final size:17
Alignment explanation
Indices: 293621--293675 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
293611 AATAATTTAA
293621 TTTAAATAAATTAAAAT
1 TTTAAATAAATTAAAAT
* *
293638 TTTAAA-AAGATAAAAAA
1 TTTAAATAA-ATTAAAAT
*
293655 TTTAAATCAAA-TCAAAT
1 TTTAAAT-AAATTAAAAT
293672 TTTA
1 TTTA
293676 TTCAATCATA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 2 0.07
17 25 0.83
18 1 0.03
19 2 0.07
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (17 bp):
TTTAAATAAATTAAAAT
Found at i:302511 original size:18 final size:19
Alignment explanation
Indices: 302480--302523 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
302470 TATTCTCTTA
* *
302480 TTTTTTTTACTTTAATTGC
1 TTTTATTTACTTTAATCGC
*
302499 TTTTATTTA-TTTAATCGT
1 TTTTATTTACTTTAATCGC
302517 TTTTATT
1 TTTTATT
302524 ACTACTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTATTTACTTTAATCGC
Found at i:305428 original size:19 final size:19
Alignment explanation
Indices: 305400--305438 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
305390 CAACCCATTG
*
305400 TTTTTTCTTTAAATTTTTA
1 TTTTTACTTTAAATTTTTA
**
305419 TTTTTACTTTTTATTTTTA
1 TTTTTACTTTAAATTTTTA
305438 T
1 T
305439 CGAGCATGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTACTTTAAATTTTTA
Found at i:305429 original size:13 final size:13
Alignment explanation
Indices: 305413--305437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
305403 TTTCTTTAAA
305413 TTTTTATTTTTAC
1 TTTTTATTTTTAC
305426 TTTTTATTTTTA
1 TTTTTATTTTTA
305438 TCGAGCATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTTAC
Found at i:306339 original size:22 final size:22
Alignment explanation
Indices: 306314--306361 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
306304 TGAATGAATG
*
306314 AAAAAAATAGCAGTTCGAAAGA
1 AAAAAAAGAGCAGTTCGAAAGA
* **
306336 AAAAAAAGGGTTGTTCGAAAGA
1 AAAAAAAGAGCAGTTCGAAAGA
306358 AAAA
1 AAAA
306362 GAGAGAGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.58, C:0.06, G:0.21, T:0.15
Consensus pattern (22 bp):
AAAAAAAGAGCAGTTCGAAAGA
Found at i:308726 original size:23 final size:23
Alignment explanation
Indices: 308696--308750 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
308686 GTTTTGAGAA
308696 CAAAGGAAGGAATACTTCTAAAT
1 CAAAGGAAGGAATACTTCTAAAT
308719 CAAAGGAAGGAATACTTCTAAAT
1 CAAAGGAAGGAATACTTCTAAAT
308742 CAAAGGAAG
1 CAAAGGAAG
308751 TATGCTCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.49, C:0.13, G:0.20, T:0.18
Consensus pattern (23 bp):
CAAAGGAAGGAATACTTCTAAAT
Found at i:318264 original size:24 final size:24
Alignment explanation
Indices: 318232--318282 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
318222 TCGTTATTCG
*
318232 CATAATATGGTTTAATCTTGTGTC
1 CATAATATGGTTTAATCCTGTGTC
318256 CATAATATGGTTTAATCCTGTGTC
1 CATAATATGGTTTAATCCTGTGTC
318280 CAT
1 CAT
318283 TTTGATCGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (24 bp):
CATAATATGGTTTAATCCTGTGTC
Found at i:325672 original size:66 final size:66
Alignment explanation
Indices: 325584--325713 Score: 199
Period size: 66 Copynumber: 2.0 Consensus size: 66
325574 ACAACTATTC
* * *
325584 GAAATCATAATATTTAAGTGTTATTTTTGTA-TTCTTAAAGTGTTGATATTTATTGTATTATACT
1 GAAATCAGAATATGTAAGTGTTATTTTTGTACGT-TTAAAGTGTTGATATTTATTGTATTATACT
325648 GA
65 GA
* *
325650 GAAATCAGAATGTGTAAGTGTTATTTTTGTACGTTTAAAGTGTTGATATTTATTGTGTTATACT
1 GAAATCAGAATATGTAAGTGTTATTTTTGTACGTTTAAAGTGTTGATATTTATTGTATTATACT
325714 AAATGTTTAC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 57 0.98
67 1 0.02
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.48
Consensus pattern (66 bp):
GAAATCAGAATATGTAAGTGTTATTTTTGTACGTTTAAAGTGTTGATATTTATTGTATTATACTG
A
Found at i:336716 original size:18 final size:19
Alignment explanation
Indices: 336695--336731 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
336685 TTTTTGATCC
336695 CTTGTTTGT-TTTAAATTT
1 CTTGTTTGTATTTAAATTT
*
336713 CTTGTTTGTATTTTAATTT
1 CTTGTTTGTATTTAAATTT
336732 GTGATTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.16, C:0.05, G:0.11, T:0.68
Consensus pattern (19 bp):
CTTGTTTGTATTTAAATTT
Found at i:337773 original size:21 final size:21
Alignment explanation
Indices: 337749--337866 Score: 175
Period size: 21 Copynumber: 5.6 Consensus size: 21
337739 TCATACCAAG
*
337749 GACGAGAAGACCATCCATAAA
1 GACGAGAAGACCATTCATAAA
337770 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCATAAA
* *
337791 GATGAGAAGACCATTCACAAA
1 GACGAGAAGACCATTCATAAA
*
337812 GACGAGAAGATCATTCATAAA
1 GACGAGAAGACCATTCATAAA
*
337833 GACGAGAAGAACATTCATAAA
1 GACGAGAAGACCATTCATAAA
337854 GAC-ATGAAGACCA
1 GACGA-GAAGACCA
337867 CTTCGCTTTG
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
20 1 0.01
21 87 0.99
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.14
Consensus pattern (21 bp):
GACGAGAAGACCATTCATAAA
Found at i:344306 original size:34 final size:34
Alignment explanation
Indices: 344158--344363 Score: 243
Period size: 34 Copynumber: 5.9 Consensus size: 34
344148 AGCAAAGTCA
* *
344158 ATCTTAAGCCTTCACCA-AAGAGGAGTGAAACAAACC
1 ATCTTAAGCCTTCA-CAGAAGAGTAGTGAAGC--ACC
* * * *
344194 ATCTTAAGCCTTCACCGGAGAGTAGTGAAGTAATC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAG-CACC
* * * *
344229 ACCTTAAGCCTTCATAGAAGAATAGTGAAGCAGTC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCA-CC
344264 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCACC
* *
344298 ATCTTAAGCCTTCATAGAGGAGTAGTGAAGCACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCACC
*
344332 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCA
344364 AATCCATCCA
Statistics
Matches: 146, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
34 63 0.43
35 59 0.40
36 24 0.16
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (34 bp):
ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCACC
Found at i:344580 original size:41 final size:42
Alignment explanation
Indices: 344484--344585 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
344474 TTCACGATTT
* * *
344484 ATAAGTCCTTCGGGCCATCAGTAAATCTTTCAAGCATGATGC
1 ATAAGTCCTTCGGGCCATCAGTAAAGCCTTCAAGCAAGATGC
* * * *
344526 TTAAATCCTTCGGGTCATCTGT-AAGCCTTCAGAGCAAGATG-
1 ATAAGTCCTTCGGGCCATCAGTAAAGCCTTCA-AGCAAGATGC
344567 ATAAGTCCTTCGGGCCATC
1 ATAAGTCCTTCGGGCCATC
344586 CATAAGACCT
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 23 0.47
42 26 0.53
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (42 bp):
ATAAGTCCTTCGGGCCATCAGTAAAGCCTTCAAGCAAGATGC
Found at i:344960 original size:215 final size:214
Alignment explanation
Indices: 344367--345604 Score: 2077
Period size: 214 Copynumber: 5.8 Consensus size: 214
344357 TGAAGCAAAT
344367 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAA
* * * *
344432 GAAGATGAAATTTTTAAAAACGAAGAATACGATTTTCAAAATTTCACGATTTATAAGTCCTTCGG
66 GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
* * *
344497 GCCATCAGTAAATCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTCAGAGCA
131 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
344562 AGATGATAAGTCCTTCGGG
196 AGATGATAAGTCCTTCGGG
* * *
344581 CCATCCATAAGACCTTCGGGTAAGATGTTTTCACATGAATTTGGAAATGAAAAATGATGTTTTAA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAA
344646 GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
66 GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
* *
344711 GCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTTATCTGTAAGCCTTTAGAGCA
131 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
344776 AGATGATAAGTCCTTCGGG
196 AGATGATAAGTCCTTCGGG
* * * *
344795 CCATCCATAAGACCTTCGGGTATGACGTTTTCACATGAATTTGGAAATGAAAAAATGATGTTTTA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATG-AAAAATGATGTTTTA
* *
344860 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAATTTTCACAATTTATAAGTCCTTCA
65 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
344925 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
130 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
*
344990 AAGATGATAAGTCATTCGGG
195 AAGATGATAAGTCCTTCGGG
* * * * *
345010 CCATCCATAAAACCTTCGGGTAGAATATTTTCAAATGAATTTGAAAATGGAAAATGATGTCTTAA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAA
345075 GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
66 GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
* * *
345140 GCTATCAGTAAGTCTTTCGAGCATGATGCTTAAATTCTTCGGGTCATCTATAAG---TTAGAGCA
131 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
345202 AGATGATAAGTCCTTCGGG
196 AGATGATAAGTCCTTCGGG
*
345221 CCATCCATAAAACCTTCGAGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATG-AAAAATGATGTTTTA
* * *
345286 AGAAGATGAAATTTTTGAAAATGAAGAATGCGATTTTCAAAATTTCACAATTTATATGTCCTTCG
65 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
* *
345351 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTTATCTGTGAGCCTTTAGAGC
130 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
345416 AAGATGATAAGTCCTTCGGG
195 AAGATGATAAGTCCTTCGGG
* *
345436 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACAAGAATTTTAAAATGAAAAATGATGTTTTAA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAA
**
345501 GAAGATGGAATTTTTGAAAACGAAGAATATGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
66 GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
* * *
345566 GACATCAGTAAGTCTTTCGAGCATGGTGTTTAAATCCTT
131 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTT
345605 TGGTTAATTT
Statistics
Matches: 960, Mismatches: 59, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
211 71 0.07
212 125 0.13
214 489 0.51
215 275 0.29
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (214 bp):
CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAA
GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
AGATGATAAGTCCTTCGGG
Found at i:345412 original size:426 final size:426
Alignment explanation
Indices: 344367--345604 Score: 2070
Period size: 426 Copynumber: 2.9 Consensus size: 426
344357 TGAAGCAAAT
344367 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATG-AAAAATGATGTTTTA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTA
* * *
344431 AGAAGATGAAATTTTTAAAAACGAAGAATACGATTTTCAAAATTTCACGATTTATAAGTCCTTCG
66 AGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
* * *
344496 GGCCATCAGTAAATCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTCAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
* * *
344561 AAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTA-AGATGTTTTCACATGAATTTGG
196 AAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGA-ATGTTTTCAAATGAATTTGA
344625 AAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTT
260 AAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTT
*
344690 CACAATTTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGT
325 CACAATTTATAAGTCCTTCGGG-CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGT
* *
344755 TATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGG
389 CATCTATAAG-C-TTAGAGCAAGATGATAAGTCCTTCGGG
* * * *
344795 CCATCCATAAGACCTTCGGGTATGACGTTTTCACATGAATTTGGAAATGAAAAAATGATGTTTTA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTA
* * *
344860 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAATTTTCACAATTTATAAGTCCTTCA
66 AGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
344925 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
* *
344990 AAGATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGAATATTTTCAAATGAATTTGAA
196 AAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGAATGTTTTCAAATGAATTTGAA
* *
345055 AATGGAAAATGATGTCTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTC
261 AATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTC
*
345120 ACAATTTATAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGCTTAAATTCTTCGGGTC
326 ACAATTTATAAGTCCTTCGGGC-ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTC
345185 ATCTATAAG-TTAGAGCAAGATGATAAGTCCTTCGGG
390 ATCTATAAGCTTAGAGCAAGATGATAAGTCCTTCGGG
*
345221 CCATCCATAAAACCTTCGAGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTA
* *
345286 AGAAGATGAAATTTTTGAAAATGAAGAATGCGATTTTCAAAATTTCACAATTTATATGTCCTTCG
66 AGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
* *
345351 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTTATCTGTGAGCCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
* *
345416 AAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACAA-GAATTTTA
196 AAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGAATGTTTTCA-AATGAATTTGA
**
345480 AAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATATGATTTTCAAAATTT
260 AAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTT
* *
345545 CACAATTTATAAGTCCTTCGGGACATCAGTAAGTCTTTCGAGCATGGTGTTTAAATCCTT
325 CACAATTTATAAGTCCTTCGGG-CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTT
345605 TGGTTAATTT
Statistics
Matches: 758, Mismatches: 47, Indels: 12
0.93 0.06 0.01
Matches are distributed among these distances:
426 383 0.51
427 3 0.00
428 46 0.06
429 325 0.43
430 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (426 bp):
CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTA
AGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
AAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGAATGTTTTCAAATGAATTTGAA
AATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTC
ACAATTTATAAGTCCTTCGGGCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCA
TCTATAAGCTTAGAGCAAGATGATAAGTCCTTCGGG
Found at i:354876 original size:3 final size:3
Alignment explanation
Indices: 354868--354931 Score: 75
Period size: 3 Copynumber: 23.0 Consensus size: 3
354858 TTTGTTTTAT
* *
354868 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
354912 TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
354932 CAAACAGGCC
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 10 0.19
3 44 0.81
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:354912 original size:19 final size:19
Alignment explanation
Indices: 354872--354929 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
354862 TTTTATTTAT
* *
354872 TATTATTATT-TTGTTTTAA
1 TATTATTATTATTATATT-A
354891 TATTATTATTATTATATTA
1 TATTATTATTATTATATTA
354910 TATTA-TATTATTATTATTA
1 TATTATTATTATTA-TATTA
354929 T
1 T
354930 TACAAACAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.23
19 22 0.63
20 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TATTATTATTATTATATTA
Found at i:357117 original size:28 final size:28
Alignment explanation
Indices: 357085--357140 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
357075 TAATTCTTTC
357085 TTTTCAAAA-ATTTTATATAATTTCATTA
1 TTTTCAAAATA-TTTATATAATTTCATTA
* * *
357113 TTTTCATAATATTTATATTATTTTATTA
1 TTTTCAAAATATTTATATAATTTCATTA
357141 ATGTTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTTCAAAATATTTATATAATTTCATTA
Found at i:357142 original size:20 final size:21
Alignment explanation
Indices: 357109--357157 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
357099 ATATAATTTC
357109 ATTATTTTCATAAT-ATTTAT
1 ATTATTTTCATAATGATTTAT
*
357129 ATTATTTT-ATTAATGTTTTAT
1 ATTATTTTCA-TAATGATTTAT
*
357150 TTTATTTT
1 ATTATTTT
357158 TCAAGTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 12 0.48
21 12 0.48
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTATTTTCATAATGATTTAT
Found at i:358655 original size:14 final size:14
Alignment explanation
Indices: 358617--358670 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
358607 TTACGTTTGA
*
358617 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
358631 TTTTACATTTGCAT
1 ATTTACATTTGCAT
358645 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
358660 CTTTGCATTTG
1 ATTTACATTTG
358671 TATTTTTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:362398 original size:4 final size:4
Alignment explanation
Indices: 362389--362488 Score: 81
Period size: 4 Copynumber: 26.8 Consensus size: 4
362379 CTCATCCAGC
* * *
362389 AAAG AAAG -AAG AAGG AAAAA AAAG AAAG AAAG AAA- AAA- AAA- AAAA
1 AAAG AAAG AAAG AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
* * *
362434 AAAA AAAA AAAG AAAG AAAG AAAG AAAG -AA- AAAG AAAA AAAG AAA-
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
362479 AAA- AAAG AAA
1 AAAG AAAG AAA
362489 ATGAAAAAAG
Statistics
Matches: 83, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
3 22 0.27
4 59 0.71
5 2 0.02
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:362464 original size:41 final size:40
Alignment explanation
Indices: 362409--362488 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
362399 GAAGGAAAAA
362409 AAAGAAAGAAAGAAAAAAAAAAAAAAAAAAAAAAAAGAAAG
1 AAAGAAAGAAAG-AAAAAAAAAAAAAAAAAAAAAAAGAAAG
* *
362450 AAAGAAAGAAAGAAAAAGAAAAAAAGAAAAAAAAAGAAA
1 AAAGAAAGAAAGAAAAAAAAAAAAAAAAAAAAAAAGAAA
362489 ATGAAAAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
40 25 0.68
41 12 0.32
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (40 bp):
AAAGAAAGAAAGAAAAAAAAAAAAAAAAAAAAAAAGAAAG
Found at i:362489 original size:8 final size:8
Alignment explanation
Indices: 362405--362503 Score: 98
Period size: 8 Copynumber: 12.5 Consensus size: 8
362395 AGAAGAAGGA
362405 AAAAAAAG
1 AAAAAAAG
*
362413 AAAGAAAG
1 AAAAAAAG
362421 AAAAAAA-
1 AAAAAAAG
362428 AAAAAAA-
1 AAAAAAAG
362435 AAAAAAA-
1 AAAAAAAG
*
362442 AAAGAAAG
1 AAAAAAAG
*
362450 AAAGAAAG
1 AAAAAAAG
362458 AAAGAAAAAG
1 -AA-AAAAAG
362468 AAAAAAAG
1 AAAAAAAG
362476 AAAAAAA-
1 AAAAAAAG
*
362483 AAGAAAATG
1 AA-AAAAAG
*
362492 AAAAAAGG
1 AAAAAAAG
362500 AAAA
1 AAAA
362504 TTGAATCAAG
Statistics
Matches: 80, Mismatches: 6, Indels: 10
0.83 0.06 0.10
Matches are distributed among these distances:
7 22 0.28
8 47 0.59
9 6 0.08
10 5 0.06
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (8 bp):
AAAAAAAG
Found at i:362494 original size:6 final size:6
Alignment explanation
Indices: 362389--362496 Score: 64
Period size: 6 Copynumber: 17.5 Consensus size: 6
362379 CTCATCCAGC
*
362389 AAAGAA AGAAGAA GGAAA-AA AAAGAAA GAAAGAA AAA-AA AAA-AA AAAAAA
1 AAAGAA A-AAGAA --AAAGAA AAAG-AA -AAAGAA AAAGAA AAAGAA AAAGAA
* * *
362439 AAAAAA GAAAGAA AGAA-AG AAAGAA AAAGAA AAA-AA GAAAAAA AAAGAA
1 AAAGAA -AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA -AAAGAA AAAGAA
*
362488 AATGAA AAA
1 AAAGAA AAA
362497 AGGAAAATTG
Statistics
Matches: 84, Mismatches: 6, Indels: 24
0.74 0.05 0.21
Matches are distributed among these distances:
5 17 0.20
6 40 0.48
7 20 0.24
8 6 0.07
9 1 0.01
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (6 bp):
AAAGAA
Found at i:362497 original size:1 final size:1
Alignment explanation
Indices: 362404--362489 Score: 73
Period size: 1 Copynumber: 86.0 Consensus size: 1
362394 AAGAAGAAGG
* * * * * * * * *
362404 AAAAAAAAGAAAGAAAGAAAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAGAAAGAAAGAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
362469 AAAAAAGAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAA
362490 TGAAAAAAGG
Statistics
Matches: 63, Mismatches: 22, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:362508 original size:15 final size:14
Alignment explanation
Indices: 362404--362504 Score: 58
Period size: 14 Copynumber: 7.7 Consensus size: 14
362394 AAGAAGAAGG
362404 AAAA-AAAA-GAAA
1 AAAAGAAAATGAAA
*
362416 GAAAGAAAA--AAA
1 AAAAGAAAATGAAA
**
362428 AAAA-AAAAAAAAA
1 AAAAGAAAATGAAA
*
362441 AAAAGAAAGAAAGAAA
1 AAAAG-AA-AATGAAA
* *
362457 GAAAGAAAAAGAAA
1 AAAAGAAAATGAAA
362471 AAAAG--AA--AAA
1 AAAAGAAAATGAAA
362481 AAAAGAAAATGAAA
1 AAAAGAAAATGAAA
*
362495 AAAGGAAAAT
1 AAAAGAAAAT
362505 TGAATCAAGA
Statistics
Matches: 73, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
10 8 0.11
11 4 0.05
12 13 0.18
13 11 0.15
14 23 0.32
15 4 0.05
16 10 0.14
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (14 bp):
AAAAGAAAATGAAA
Found at i:367435 original size:22 final size:22
Alignment explanation
Indices: 367410--367486 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
367400 ATCTACAATC
367410 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
367432 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
367454 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
367476 TTCAAAGATGA
1 TTCAAAGATGA
367487 AAGCTTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:371536 original size:21 final size:21
Alignment explanation
Indices: 371510--371592 Score: 62
Period size: 21 Copynumber: 3.8 Consensus size: 21
371500 CAGATCCCCA
*
371510 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
371531 GGGGGGAATCGGTTCCCCT-T
1 GGGGGGAATCGATTCCCCTGT
* * *
371551 CAAAGGGGGAATCGGTTCCCTCAG-
1 ---GGGGGGAATCGATTCCC-CTGT
371575 GGGGAGGAATCGATTCCC
1 GGGG-GGAATCGATTCCC
371593 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
20 1 0.02
21 20 0.40
22 12 0.24
23 16 0.32
24 1 0.02
ACGTcount: A:0.17, C:0.24, G:0.37, T:0.22
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:371571 original size:22 final size:22
Alignment explanation
Indices: 371532--371593 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
371522 TTCCCCTGTG
371532 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCCTTCAAA
**
371555 GGGGGAATCGGTTCCC-TCAGG
1 GGGGGAATCGGTTCCCTTCAAA
*
371576 GGGAGGAATCGATTCCCT
1 GGG-GGAATCGGTTCCCT
371594 CTGCACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.18
22 15 0.44
23 13 0.38
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.21
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCTTCAAA
Found at i:377910 original size:113 final size:112
Alignment explanation
Indices: 377713--378531 Score: 998
Period size: 113 Copynumber: 7.2 Consensus size: 112
377703 TTCAACAAAT
* * ** * * ** *
377713 TTGTTCAACCTTTTGCTTAAATCCATCACCCGATGGATCAGCAGTGCCAGTTAGAGTTCATAATG
1 TTGTTCAA-CTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATG
**
377778 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGT
65 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
** * *
377826 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATG
1 TTGTTCAA-CTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATG
* *
377891 AGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAAT
65 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* **
377939 TTGTTCAACTTTTCGCTTGAATTCATCA-TTCGATGGATCAGCATTACCAG-GTCGAGTTCATAA
1 TTGTTCAACTTTT-GCTTGAATTCATCACTT-GATGGATCAGCATTTCCAGAG-AAAGTTCATAA
378002 TGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT--G-AGAAC
63 TGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* **
378049 TTGTTCAACTTTTCGCTTGAATTCATCA-TTCGATGGATCAGCATTGCCAG-GTCGAGTTCATAA
1 TTGTTCAACTTTT-GCTTGAATTCATCACTT-GATGGATCAGCATTTCCAGAG-AAAGTTCATAA
*
378112 TGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
63 TGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
***
378162 TTGTTCAACTTTTCGCTTGAATTCATCA-TTCGATGGATCAGCATCAACATTGCCAG-AAGTTCA
1 TTGTTCAACTTTT-GCTTGAATTCATCACTT-GATGGATCAGCATTTCCA--G--AGAAAGTTCA
* * *
378225 TAATGAGAATAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAAT
60 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
** * * *
378278 TTGTTCAACCTTTTGCTCAAATCCATTACTTGATGGATCAGCATTTTCAGAGGAAA-TTCATAAT
1 TTGTTCAA-CTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGA-GAAAGTTCATAAT
378342 GAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAAC
64 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* * * * *
378390 TTGTTCAAATTTTTGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAA-TTCATAAT
1 TTGTTC-AACTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGA-AAGTTCATAAT
378454 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
64 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
*
378503 TTGTTCAATCTTTTGCATG-ATTCTATCAC
1 TTGTTCAA-CTTTTGCTTGAATTC-ATCAC
378532 AGAAGGAGAT
Statistics
Matches: 637, Mismatches: 49, Indels: 40
0.88 0.07 0.06
Matches are distributed among these distances:
110 106 0.17
111 3 0.00
112 112 0.18
113 314 0.49
114 3 0.00
115 1 0.00
116 90 0.14
117 7 0.01
118 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (112 bp):
TTGTTCAACTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGA
GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
Found at i:378144 original size:226 final size:223
Alignment explanation
Indices: 377713--378518 Score: 1077
Period size: 223 Copynumber: 3.6 Consensus size: 223
377703 TTCAACAAAT
* * * * * *
377713 TTGTTCAACCTTTT-GCTTAAATCCATCACCCGATGGATCAGCAGTGCCAGTTAGAGTTCATAAT
1 TTGTTCAA-CTTTTCGCTTGAATTCATCACTCGATGGATCAGCATTACCAGGTAGAGTTCATAAT
**
377777 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTTGC
65 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT-AGAAGAACTTGTTCAACCTTTTGC
* *
377842 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
129 TCAAATCCATCACTTGATGGATCAGCATTTCCAGAG-GAGTTCATAATGAGAAGAACTCATCTGA
* *
377907 AGAATGAAGAAGAAGTTCATAATGAGAAGAAT
193 AG-AGGAAGAAGAAGTTCATAATGAGAAGAAC
* *
377939 TTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATG
1 TTGTTCAACTTTTCGCTTGAATTCATCACTCGATGGATCAGCATTACCAGGTAGAGTTCATAATG
378004 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT-G-AGAACTTGTTCAA-CTTTTCGCT
66 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAGAAGAACTTGTTCAACCTTTT-GCT
** * * *
378066 TGAATTCATCA-TTCGATGGATCAGCATTGCCAG-GTCGAGTTCATAATGAGAATAACTCATCTG
130 CAAATCCATCACTT-GATGGATCAGCATTTCCAGAG--GAGTTCATAATGAGAAGAACTCATCTG
378129 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
192 AAG-AGGAAGAAGAAGTTCATAATGAGAAGAAC
* * * **
378162 TTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATCAACATTGCCAGAAGTTCATA
1 TTGTTCAACTTTTCGCTTGAATTCATCACTCGATGGATCAGCATTACCA--GGTAG-AGTTCATA
* * *
378227 ATGAGAATAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
63 ATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT-AGAAGAACTTGTTCAACCTTTT
* * *
378292 GCTCAAATCCATTACTTGATGGATCAGCATTTTCAGAGGAAATTCATAATGAGAAGAACTCATCT
127 GCTCAAATCCATCACTTGATGGATCAGCATTTCCAGAGG-AGTTCATAATGAGAAGAACTCATCT
378357 GAAGAGGAAGAAGAAGTTCATAATGAGAAGAAC
191 GAAGAGGAAGAAGAAGTTCATAATGAGAAGAAC
* * * * * * *
378390 TTGTTCAAATTTTTGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAG-AGAATTCATAAT
1 TTGTTCAACTTTTCGCTTGAATTCATCACTCGATGGATCAGCATTACCAG-GTAGAGTTCATAAT
*
378454 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGC
65 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT-AGAAGAACTTGTTCAACCTTTTGC
378519 ATGATTCTAT
Statistics
Matches: 514, Mismatches: 51, Indels: 31
0.86 0.09 0.05
Matches are distributed among these distances:
222 8 0.02
223 142 0.28
224 1 0.00
225 77 0.15
226 141 0.27
228 71 0.14
229 66 0.13
230 8 0.02
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (223 bp):
TTGTTCAACTTTTCGCTTGAATTCATCACTCGATGGATCAGCATTACCAGGTAGAGTTCATAATG
AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAGAAGAACTTGTTCAACCTTTTGCTC
AAATCCATCACTTGATGGATCAGCATTTCCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGA
GGAAGAAGAAGTTCATAATGAGAAGAAC
Found at i:378873 original size:3 final size:3
Alignment explanation
Indices: 378865--378921 Score: 75
Period size: 3 Copynumber: 20.0 Consensus size: 3
378855 TTTGTTTTAT
* *
378865 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
378910 TTA TTA TTA TTA
1 TTA TTA TTA TTA
378922 CAAACAGGCC
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
2 6 0.12
3 43 0.88
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:378882 original size:23 final size:23
Alignment explanation
Indices: 378855--378921 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
378845 TTTTATTTCA
378855 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTATTTATTATTATTAT
*
378878 TTTGTTTTA-ATATTATTATTAT
1 TTTGTTTTATTTATTATTATTAT
* *
378900 TAT-TATTATATTATTATTATTA
1 TTTGTTTTAT-TTATTATTATTA
378922 CAAACAGGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.11
22 14 0.37
23 20 0.53
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (23 bp):
TTTGTTTTATTTATTATTATTAT
Found at i:380235 original size:3 final size:3
Alignment explanation
Indices: 380222--380276 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
380212 TTATTTGCAA
* *
380222 TAT TAT T-T TAT TAT TAT TAT TACT T-T AAT TAT TAT T-T CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
*
380265 TAT TAT TTT TAT
1 TAT TAT TAT TAT
380277 ATAAATAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
2 4 0.10
3 36 0.86
4 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:383596 original size:22 final size:21
Alignment explanation
Indices: 383571--383780 Score: 102
Period size: 22 Copynumber: 9.3 Consensus size: 21
383561 AGTTTTGTCA
*
383571 AAAAAATAATA-TATGGTTTTT
1 AAAAAAT-ATAGTATAGTTTTT
*
383592 GAAAATATATAGTATAGTTTTT
1 -AAAAAATATAGTATAGTTTTT
* *
383614 AAAAACATATGGTGTAGTTTTT
1 AAAAA-ATATAGTATAGTTTTT
* *
383636 GAAAACATGTTA-TATAGTTTTTTT
1 -AAAAAAT-ATAGTATAG--TTTTT
* *
383660 AAAAAAACACATAATATAGTTTTT
1 --AAAAA-ATATAGTATAGTTTTT
* *
383684 GAAAATATATAATATAG-TTTT
1 -AAAAAATATAGTATAGTTTTT
*
383705 AAAAACATATGGTATAGTTTTTT
1 AAAAA-ATATAGTATAG-TTTTT
*
383728 AAAACATATATAATATATAGTTTTT
1 AAAA-A-ATAT-A-GTATAGTTTTT
* * *
383753 GAAAATATCTAGCATAGTTTTT
1 -AAAAAATATAGTATAGTTTTT
383775 AAAAAA
1 AAAAAA
383781 AAACATATTA
Statistics
Matches: 145, Mismatches: 27, Indels: 33
0.71 0.13 0.16
Matches are distributed among these distances:
20 4 0.03
21 25 0.17
22 54 0.37
23 18 0.12
24 18 0.12
25 11 0.08
26 15 0.10
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.41
Consensus pattern (21 bp):
AAAAAATATAGTATAGTTTTT
Found at i:383684 original size:92 final size:89
Alignment explanation
Indices: 383557--383734 Score: 266
Period size: 91 Copynumber: 2.0 Consensus size: 89
383547 ATCATATAAC
* * *
383557 ATATAGTTTTGTCAAAAAAATAATATATGGTTTTTGAAAATATATAGTATAGTTTTTAAAAACAT
1 ATATAGTTTTGTCAAAAAAACAATATATAGTTTTTGAAAATATATAATATAG-TTTTAAAAACAT
*
383622 ATGGTGTAGTTTTTGAAAACATGTT
65 ATGGTATAGTTTTTGAAAACATGTT
* *
383647 ATATAGTTTTTTTAAAAAAACACATAATATAGTTTTTGAAAATATATAATATAGTTTTAAAAACA
1 ATATAGTTTTGTCAAAAAAACA-AT-ATATAGTTTTTGAAAATATATAATATAGTTTTAAAAACA
*
383712 TATGGTATAGTTTTTTAAAACAT
64 TATGGTATAGTTTTTGAAAACAT
383735 ATATAATATA
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
90 19 0.24
91 34 0.43
92 26 0.33
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42
Consensus pattern (89 bp):
ATATAGTTTTGTCAAAAAAACAATATATAGTTTTTGAAAATATATAATATAGTTTTAAAAACATA
TGGTATAGTTTTTGAAAACATGTT
Found at i:383726 original size:69 final size:70
Alignment explanation
Indices: 383628--383779 Score: 177
Period size: 69 Copynumber: 2.2 Consensus size: 70
383618 ACATATGGTG
* * **
383628 TAGTTTTTGAAAACATGTTATATAGTTTTTTTAAAA-A-A-ACACATAATATAGTTTTTGAAAAT
1 TAGTTTTTAAAAACATATGGTATAG-TTTTTTAAAACATATACA-AT-ATATAGTTTTTGAAAAT
*
383690 ATATAATA
63 ATATAACA
* *
383698 TAG-TTTTAAAAACATATGGTATAGTTTTTTAAAACATATATAATATATAGTTTTTGAAAATATC
1 TAGTTTTTAAAAACATATGGTATAGTTTTTTAAAACATATACAATATATAGTTTTTGAAAATATA
*
383762 TAGCA
66 TAACA
383767 TAGTTTTTAAAAA
1 TAGTTTTTAAAAA
383780 AAAACATATT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
68 10 0.14
69 43 0.61
70 15 0.21
71 2 0.03
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (70 bp):
TAGTTTTTAAAAACATATGGTATAGTTTTTTAAAACATATACAATATATAGTTTTTGAAAATATA
TAACA
Found at i:383860 original size:21 final size:21
Alignment explanation
Indices: 383834--383886 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
383824 TATGTAATAT
383834 ATATATATATATATATTGAAAA
1 ATATATATATATAT-TTGAAAA
*
383856 CATAT-TATATA-ATTTTAAAA
1 -ATATATATATATATTTGAAAA
383876 ATATA-ATATAT
1 ATATATATATAT
383887 TATATAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 9 0.33
20 6 0.22
21 2 0.07
22 6 0.22
23 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
ATATATATATATATTTGAAAA
Found at i:383886 original size:26 final size:25
Alignment explanation
Indices: 383857--383919 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 25
383847 TATTGAAAAC
383857 ATATTATATAATTTTAAAAATATAAT
1 ATATTATATAATTTTAAAAATAT-AT
* * *
383883 ATATTATATAGTTTTTAGAATATAT
1 ATATTATATAATTTTAAAAATATAT
383908 ATATATATATAA
1 ATAT-TATATAA
383920 GCTTGTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 6 0.19
26 26 0.81
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (25 bp):
ATATTATATAATTTTAAAAATATAT
Found at i:383892 original size:28 final size:25
Alignment explanation
Indices: 383829--383919 Score: 68
Period size: 26 Copynumber: 3.8 Consensus size: 25
383819 AAACATATGT
* *
383829 AATATATATATATATAT-ATATT-G
1 AATATATATATATATATAATTTTAA
*
383852 AA-A-ACATAT-TATATAATTTTAA
1 AATATATATATATATATAATTTTAA
* *
383874 AA-ATATAATATATTATATAGTTTTTAG
1 AATATAT-ATATA-TATATA-ATTTTAA
383901 AATATATATATATATATAA
1 AATATATATATATATATAA
383920 GCTTGTTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
20 5 0.09
21 9 0.17
22 4 0.08
23 3 0.06
24 4 0.08
26 12 0.23
27 12 0.23
28 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (25 bp):
AATATATATATATATATAATTTTAA
Found at i:386116 original size:12 final size:12
Alignment explanation
Indices: 386099--386131 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
386089 ACCTAGGATG
386099 CTTGATTTATTT
1 CTTGATTTATTT
386111 CTTGATTTATTT
1 CTTGATTTATTT
*
386123 CTTGCTTTA
1 CTTGATTTA
386132 GTTTTTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.09, T:0.64
Consensus pattern (12 bp):
CTTGATTTATTT
Found at i:388325 original size:13 final size:13
Alignment explanation
Indices: 388307--388375 Score: 70
Period size: 13 Copynumber: 5.5 Consensus size: 13
388297 CATTGAATTT
388307 GTTAAAGTAAAGA
1 GTTAAAGTAAAGA
***
388320 GTTAAA-TAATTT
1 GTTAAAGTAAAGA
388332 GTTAAAGTAAAGA
1 GTTAAAGTAAAGA
***
388345 GTTAAA-TAATTT
1 GTTAAAGTAAAGA
388357 GTTAAAGTAAAGA
1 GTTAAAGTAAAGA
388370 GTTAAA
1 GTTAAA
388376 TAATTTTGTT
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
12 18 0.43
13 24 0.57
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.33
Consensus pattern (13 bp):
GTTAAAGTAAAGA
Found at i:388336 original size:25 final size:25
Alignment explanation
Indices: 388302--388386 Score: 161
Period size: 25 Copynumber: 3.4 Consensus size: 25
388292 TTCCCCATTG
388302 AATTTGTTAAAGTAAAGAGTTAAAT
1 AATTTGTTAAAGTAAAGAGTTAAAT
388327 AATTTGTTAAAGTAAAGAGTTAAAT
1 AATTTGTTAAAGTAAAGAGTTAAAT
388352 AATTTGTTAAAGTAAAGAGTTAAAT
1 AATTTGTTAAAGTAAAGAGTTAAAT
388377 AATTTTGTTA
1 AA-TTTGTTA
388387 GTAAATCTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 52 0.88
26 7 0.12
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.39
Consensus pattern (25 bp):
AATTTGTTAAAGTAAAGAGTTAAAT
Found at i:397064 original size:18 final size:18
Alignment explanation
Indices: 397041--397076 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
397031 AAGCAAAAGG
*
397041 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
397059 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
397077 CAACCGGCTT
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:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:397503 original size:20 final size:20
Alignment explanation
Indices: 397478--397515 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
397468 ACGCTTATTT
*
397478 CGCGTTGTGAATTTACCTTC
1 CGCGTTGCGAATTTACCTTC
397498 CGCGTTGCGAATTTACCT
1 CGCGTTGCGAATTTACCT
397516 ACAACATGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGAATTTACCTTC
Found at i:397599 original size:25 final size:25
Alignment explanation
Indices: 397561--397608 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
397551 TTGAAAATTA
*
397561 AACATTGTCGTGGGTACATTATTTG
1 AACATTGTCATGGGTACATTATTTG
*
397586 AACATTGTTATGGGTACATTATT
1 AACATTGTCATGGGTACATTATT
397609 GGAAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (25 bp):
AACATTGTCATGGGTACATTATTTG
Found at i:398003 original size:24 final size:25
Alignment explanation
Indices: 397976--398030 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
397966 TTTCAAATTC
*
397976 ATTTCATATGT-AATTAGAGTTTGA
1 ATTTCAAATGTCAATTAGAGTTTGA
* *
398000 ATTT-AAATTTCAATTTGAGTTTGA
1 ATTTCAAATGTCAATTAGAGTTTGA
398024 ATTTCAA
1 ATTTCAA
398031 TATAAATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 20 0.77
25 2 0.08
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (25 bp):
ATTTCAAATGTCAATTAGAGTTTGA
Found at i:398016 original size:18 final size:18
Alignment explanation
Indices: 397995--398031 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
397985 GTAATTAGAG
397995 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
398013 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
398031 T
1 T
398032 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:398038 original size:24 final size:24
Alignment explanation
Indices: 397987--398039 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
397977 TTTCATATGT
* * *
397987 AATTAGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
398011 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
398035 AATTT
1 AATTT
398040 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:398386 original size:39 final size:39
Alignment explanation
Indices: 398343--398425 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
398333 GATGCTCATC
398343 AAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAAATCA
1 AAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAAATCA
* *
398382 AAATCCAAATCTCATATGGTGCCAAGCGAAAGGAAATCA
1 AAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAAATCA
398421 AAATC
1 AAATC
398426 TACAACTTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (39 bp):
AAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAAATCA
Found at i:398648 original size:20 final size:20
Alignment explanation
Indices: 398604--398641 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
398594 GCAATCAATG
*
398604 CGAAATTCAAATTCGCAACA
1 CGAAAGTCAAATTCGCAACA
398624 CGAAAGTCAAATTCGCAA
1 CGAAAGTCAAATTCGCAA
398642 ACCGAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.13, T:0.18
Consensus pattern (20 bp):
CGAAAGTCAAATTCGCAACA
Found at i:398675 original size:20 final size:20
Alignment explanation
Indices: 398650--398777 Score: 92
Period size: 20 Copynumber: 6.8 Consensus size: 20
398640 AAACCGAAAA
398650 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTT
* *
398670 TCGCGTTGCAAATTTGACTA
1 TCGCGTTGCGAATTTGACTT
** *
398690 TCGC--AAC--ACTT-A-TT
1 TCGCGTTGCGAATTTGACTT
398704 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTT
* *
398724 T--CGTTGTGAATTTAACTT
1 TCGCGTTGCGAATTTGACTT
* * *
398742 TTGCATTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTT
* *
398762 TCGCGCTACGAATTTG
1 TCGCGTTGCGAATTTG
398778 TACCTTCAAC
Statistics
Matches: 81, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
14 5 0.06
15 1 0.01
16 4 0.05
18 20 0.25
19 1 0.01
20 50 0.62
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTT
Found at i:398734 original size:18 final size:18
Alignment explanation
Indices: 398707--398756 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
398697 ACTTATTTCG
*
398707 CGTTGCGAATTTGACTTT
1 CGTTGCGAATTTAACTTT
*
398725 CGTTGTGAATTTAACTTTT
1 CGTTGCGAATTTAAC-TTT
*
398744 GCATTGCGAATTT
1 -CGTTGCGAATTT
398757 GACTATCGCG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 13 0.50
19 3 0.12
20 10 0.38
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (18 bp):
CGTTGCGAATTTAACTTT
Found at i:398968 original size:59 final size:62
Alignment explanation
Indices: 398836--398973 Score: 158
Period size: 59 Copynumber: 2.2 Consensus size: 62
398826 TTTTAGAAAC
*
398836 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATAAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGC-AAAAAATAAATCTTATTTACAAATAAAATT
398901 A
62 A
* * ** *
398902 AAC-AATCAACTTTTACAAATCAATT-AATC-AAAAATAAATCTTATTTCCTCAT-CAATTA
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAATAAATCTTATTTACAAATAAAATTA
398960 AACAAATCAACTTT
1 AACAAATCAACTTT
398974 CAATGTAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
58 8 0.12
59 29 0.45
61 3 0.05
65 22 0.34
66 3 0.05
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (62 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAATAAATCTTATTTACAAATAAAATTA
Found at i:400090 original size:21 final size:21
Alignment explanation
Indices: 400029--400124 Score: 72
Period size: 21 Copynumber: 4.6 Consensus size: 21
400019 ATGAATCAGG
* *
400029 CTCTTGAACGGT-GGACGGGAC
1 CTCTTGAACGATGGGA-GGGGC
* *
400050 CTCTTAAACGATGACG-GGGGC
1 CTCTTGAACGATG-GGAGGGGC
*
400071 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* * *
400092 TTCTTCG-ATGATGAGAGGGGC
1 CTCTT-GAACGATGGGAGGGGC
400113 CTCTTGAACGAT
1 CTCTTGAACGAT
400125 AAGAGGAACC
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
20 2 0.04
21 53 0.93
22 1 0.02
23 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.36, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:400129 original size:21 final size:21
Alignment explanation
Indices: 400049--400141 Score: 64
Period size: 21 Copynumber: 4.4 Consensus size: 21
400039 GTGGACGGGA
* *
400049 CCTCTTAAACGATGACG-GGGG
1 CCTCTTGAACGAT-AAGAGGGG
* **
400070 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATAAGAGGGG
* * *
400091 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATAAGAGGGG
**
400112 CCTCTTGAACGATAAGAGGAA
1 CCTCTTGAACGATAAGAGGGG
400133 CCTCTTGAA
1 CCTCTTGAA
400142 TGATGATAGG
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.04
21 53 0.95
22 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATAAGAGGGG
Found at i:400657 original size:21 final size:21
Alignment explanation
Indices: 400640--400679 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
400630 TTTTCAAAGG
400640 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
400661 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
400680 GACTAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:400729 original size:19 final size:19
Alignment explanation
Indices: 400705--400743 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
400695 TCGAATGCAT
400705 TCCATGCACCGATACACTC
1 TCCATGCACCGATACACTC
* *
400724 TCCATGCATCGATGCACTC
1 TCCATGCACCGATACACTC
400743 T
1 T
400744 GATTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.13, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATACACTC
Found at i:400768 original size:64 final size:65
Alignment explanation
Indices: 400640--400804 Score: 199
Period size: 64 Copynumber: 2.5 Consensus size: 65
400630 TTTTCAAAGG
* *
400640 CATGCACCGATGCATCAATACCATGCATCGATGCA-TCAATGACTAAATTGAAACATCGAATGCA
1 CATGCACCGATACA-CAAT-CCATGCATCGATGCACTC-ATGACTAAATTAAAACATCGAATGCA
400704 TTC
63 TTC
** * * *
400707 CATGCACCGATACACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTT
1 CATGCACCGATACACAATCCATGCATCGATGCACTCATGACTAAATTAAAACATCGAATGCATTC
* * *
400771 GATGCATCGATGCACAATCCATGCATCGATGCAC
1 CATGCACCGATACACAATCCATGCATCGATGCAC
400805 CAGGCTATTT
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 53 0.62
65 15 0.18
66 4 0.05
67 13 0.15
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (65 bp):
CATGCACCGATACACAATCCATGCATCGATGCACTCATGACTAAATTAAAACATCGAATGCATTC
Found at i:400841 original size:18 final size:17
Alignment explanation
Indices: 400815--400850 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
400805 CAGGCTATTT
400815 TTCAAGCATCGAATGCAC
1 TTCAAGCATCG-ATGCAC
*
400833 TTCATGCATCGATGCAC
1 TTCAAGCATCGATGCAC
400850 T
1 T
400851 CTTAGTGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (17 bp):
TTCAAGCATCGATGCAC
Found at i:404186 original size:24 final size:24
Alignment explanation
Indices: 404159--404207 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
404149 TTTGAAAATA
404159 ATTTGCCAAAATATTTTTGGGCGG
1 ATTTGCCAAAATATTTTTGGGCGG
404183 ATTTGCCAAAATATTTTTGGGCGG
1 ATTTGCCAAAATATTTTTGGGCGG
404207 A
1 A
404208 AGCCACAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (24 bp):
ATTTGCCAAAATATTTTTGGGCGG
Found at i:404217 original size:22 final size:23
Alignment explanation
Indices: 404163--404217 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 23
404153 AAAATAATTT
*
404163 GCCAAAATATTTTTGGGCGGATTT
1 GCCAAAATATTTTTGGGCGGA-TA
404187 GCCAAAATATTTTTGGGCGGA-A
1 GCCAAAATATTTTTGGGCGGATA
*
404209 GCCACAATA
1 GCCAAAATA
404218 CCGCTTGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 8 0.28
24 21 0.72
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (23 bp):
GCCAAAATATTTTTGGGCGGATA
Done.