Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008111.1 Hibiscus syriacus cultivar Beakdansim tig00110647_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: 1666726
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 64 characters in sequence are not A, C, G, or T
File 8 of 9
Found at i:1475501 original size:21 final size:21
Alignment explanation
Indices: 1475475--1475515 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1475465 CCGCGTAGAA
1475475 ATGTCCCGAAAGACCACATAG
1 ATGTCCCGAAAGACCACATAG
*
1475496 ATGTCCCGAAGGACCACATA
1 ATGTCCCGAAAGACCACATA
1475516 TAACACATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.29, G:0.20, T:0.15
Consensus pattern (21 bp):
ATGTCCCGAAAGACCACATAG
Found at i:1486607 original size:25 final size:25
Alignment explanation
Indices: 1486574--1486621 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1486564 AAAATGGTAA
*
1486574 ATTTTAATT-TTAATTTATTTATTCG
1 ATTTCAATTATTAATTT-TTTATTCG
*
1486599 ATTTCAATTATTTATTTTTTATT
1 ATTTCAATTATTAATTTTTTATT
1486622 ATTTTTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (25 bp):
ATTTCAATTATTAATTTTTTATTCG
Found at i:1490163 original size:32 final size:31
Alignment explanation
Indices: 1490115--1490200 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 31
1490105 AAGCAATAGA
*
1490115 GGGCATCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTG-AGATTCAACATCAAATATTG
*
1490147 GGGCATCATTTGAGATTCAACATCGAATATTG
1 GGGCATC-TTTGAGATTCAACATCAAATATTG
* *
1490179 GGGTATCTTTGGGGATTCAACA
1 GGGCATCTTT-GAGATTCAACA
1490201 ACCTGATGCG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
31 3 0.06
32 41 0.85
33 4 0.08
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (31 bp):
GGGCATCTTTGAGATTCAACATCAAATATTG
Found at i:1491002 original size:110 final size:106
Alignment explanation
Indices: 1490791--1491042 Score: 258
Period size: 110 Copynumber: 2.3 Consensus size: 106
1490781 AACATCTACG
* * * * * *
1490791 ATTTCAACTCCACGAC-AGAGGATATCGTGCCTACGAGACAACACGAGCTCAAGTTCACAGTGAA
1 ATTTCAACTTCACGACGA-AGGATATTG-GACT-CGAGACAACACAAGCTCAACTTCACAGCGAA
* * *
1490855 GGGGCAACTGATTGTCAACAAATAACTTTTCAGTTTCATTCAGAGTCA
63 GGGGCAACTGACTGTCAACAAACAACTTTTCA--AT--TTCAGAGTCA
*
1490903 ATTTCAACTTCAC-AGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGGAGG
1 ATTTCAACTTCACGA-CGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGG
** * *
1490967 GGCGGCTGGCTGTCAAGAAACAA-TTTTCCAATTTCAGAGTCA
65 GGCAACTGACTGTCAACAAACAACTTTT-CAATTTCAGAGTCA
* *
1491009 ATTTCAACTTCACGACGAATGATATTGGCCTCGA
1 ATTTCAACTTCACGACGAAGGATATTGGACTCGA
1491043 AACATCATAA
Statistics
Matches: 120, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
106 40 0.33
107 1 0.01
108 1 0.01
109 4 0.03
110 48 0.40
111 4 0.03
112 21 0.17
113 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (106 bp):
ATTTCAACTTCACGACGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGG
GCAACTGACTGTCAACAAACAACTTTTCAATTTCAGAGTCA
Found at i:1491284 original size:84 final size:84
Alignment explanation
Indices: 1491158--1492246 Score: 1357
Period size: 84 Copynumber: 13.0 Consensus size: 84
1491148 AAATCGTGCG
* * * * * * ** *
1491158 AACCAAAGACCTTCGAGTTCGACTGCACTTAGCTCAAAGGCACATCATTTGCAGCTTAGTTTAAG
1 AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAG
* *
1491223 TCGAGAAGGGTTATCTGCT
66 GCAAGAAGGGTTATCTGCT
* * * *
1491242 AACCAAATACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATAATTTGCAACATAATTCAAG
1 AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAG
* *
1491307 GCTAGAAGGGTTATCTGCC
66 GCAAGAAGGGTTATCTGCT
* *
1491326 AACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAACTCAAG
1 AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAG
1491391 GCAAGAAGGGTTATCTGCT
66 GCAAGAAGGGTTATCTGCT
*
1491410 AACCAAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAG
1 AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAG
* * *
1491475 GCTAGAAGGGTTATCTTCC
66 GCAAGAAGGGTTATCTGCT
* * * *
1491494 AACAAAAGACCTTCGAGTTCGACAACGCTCAGCTCCAAGGAACATCATTTACAACATAACTCAAG
1 AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAG
1491559 GCAAGAAGGGTTATCTGCT
66 GCAAGAAGGGTTATCTGCT
* * * * *
1491578 AACCAAAGACCTTCAAGTTCGACTACACTCAGCTCCAAGGCAAATCATTTACAATATAACTCAAG
1 AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAG
*
1491643 GCAAGAAGGGTTATCTTCT
66 GCAAGAAGGGTTATCTGCT
* *
1491662 AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAACATAACTCAAG
1 AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAG
*
1491727 GCAAGAAAGGTTATCTGCT
66 GCAAGAAGGGTTATCTGCT
* *
1491746 AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTACAAGGCACATCATTTGCAACATAGCTCAAG
1 AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAG
**** *
1491811 GCAAGAACAACTATTTG-T
66 GCAAGAAGGGTTATCTGCT
* * * * *
1491829 CAACC-AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
1 -AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAA
*
1491893 GGCAAGAAGGGTTATCTGCC
65 GGCAAGAAGGGTTATCTGCT
* * *
1491913 AACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTTCAGA-ATAGCTCAA
1 AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCA-ACATAACTCAA
*
1491977 GGCAATAAGGGTTATCTG-T
65 GGCAAGAAGGGTTATCTGCT
* * * * * *
1491996 CAACCAAAGACCTTCGAGTTCGATTACGCTCAGCTTCAAGCCATATCATTTGTAGCATAACTCAA
1 -AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAA
*
1492061 GGCGAGAAGGGTTATCTG-T
65 GGCAAGAAGGGTTATCTGCT
* * * * *
1492080 CACCAAAGACCTTTGAGTTCGACTACGCTTAGCTCCAAGGCATATCATTTGCAGCATAACTCAAG
1 AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAG
* * *
1492145 GCTAGAAGGGATATCT-AT
66 GCAAGAAGGGTTATCTGCT
* * * ** * * * *
1492163 CAA-CAAAGACCTTTGAGTTCTATTACATTCAGCTCAAAAGCATACCGGATTTG-AATCATAACT
1 -AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC--ATTTGCAA-CATAACT
*
1492226 CAAGGCGAGAAGGGTTATCTG
62 CAAGGCAAGAAGGGTTATCTG
1492247 TCAATAAACC
Statistics
Matches: 885, Mismatches: 108, Indels: 22
0.87 0.11 0.02
Matches are distributed among these distances:
83 180 0.20
84 675 0.76
85 30 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (84 bp):
AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAG
GCAAGAAGGGTTATCTGCT
Found at i:1495676 original size:3 final size:3
Alignment explanation
Indices: 1495662--1495700 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1495652 GTAAAAAGGG
*
1495662 AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1495701 GGCGCTGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1505107 original size:24 final size:24
Alignment explanation
Indices: 1505070--1505128 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
1505060 CAGGCAGAAG
*
1505070 AGAAGAAAATTTACTAATATCAAC
1 AGAAGAAAAATTACTAATATCAAC
* *
1505094 AGGAGAAAAATTACTAATATCAAG
1 AGAAGAAAAATTACTAATATCAAC
1505118 AGAAGAAAAAT
1 AGAAGAAAAAT
1505129 ACAATAGTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.20
Consensus pattern (24 bp):
AGAAGAAAAATTACTAATATCAAC
Found at i:1506306 original size:37 final size:37
Alignment explanation
Indices: 1506251--1506325 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
1506241 AACATAACGT
1506251 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
*
1506288 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1506325 T
1 T
1506326 CCATAAGCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:1506366 original size:13 final size:13
Alignment explanation
Indices: 1506350--1506380 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1506340 AATAGCCATT
1506350 GTAACTCATTATC
1 GTAACTCATTATC
*
1506363 GTAACTCATTATT
1 GTAACTCATTATC
1506376 GTAAC
1 GTAAC
1506381 ACTCAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (13 bp):
GTAACTCATTATC
Found at i:1506700 original size:3 final size:3
Alignment explanation
Indices: 1506694--1506780 Score: 51
Period size: 3 Copynumber: 29.7 Consensus size: 3
1506684 TTTTTTCTTC
1506694 TTA TTA TTA TTA -TA TATA CTTCA TTA TTA TTA TTA TTA -TA TT- TTA
1 TTA TTA TTA TTA TTA T-TA -TT-A TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
1506739 TATA TT- TTA TTT TTT TTA TCA TT- TTT TTA AT- TTA TTA TTA TT
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1506781 TTTTAAAACA
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
2 11 0.16
3 46 0.69
4 8 0.12
5 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1506793 original size:31 final size:31
Alignment explanation
Indices: 1506732--1506799 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
1506722 ATTATTATTA
* * ** *
1506732 TATTTTATATATTTTATTTTTTTTATCATTT
1 TATTTAATTTATTTTATTTTTTAAAACATTT
1506763 T-TTTAATTTATTATTATTTTTTAAAACATTT
1 TATTTAATTTATT-TTATTTTTTAAAACATTT
1506794 TATTTA
1 TATTTA
1506800 TATGCTTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 9 0.30
31 17 0.57
32 4 0.13
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (31 bp):
TATTTAATTTATTTTATTTTTTAAAACATTT
Found at i:1507040 original size:3 final size:3
Alignment explanation
Indices: 1507032--1507072 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1507022 TACTTACTGT
*
1507032 TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1507073 CTATTTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1507087 original size:9 final size:10
Alignment explanation
Indices: 1507031--1507086 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 10
1507021 TTACTTACTG
1507031 TTTATTATTA
1 TTTATTATTA
1507041 -TTATTATTA
1 TTTATTATTA
1507050 GTATTATTATTA
1 -T-TTATTATTA
1507062 -TTATTATTA
1 TTTATTATTA
1507071 TTCTATT-TTA
1 TT-TATTATTA
1507081 TTTATT
1 TTTATT
1507087 TCTATTTACC
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
9 22 0.54
10 6 0.15
11 4 0.10
12 9 0.22
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTATTATTA
Found at i:1507125 original size:19 final size:18
Alignment explanation
Indices: 1507098--1507141 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1507088 CTATTTACCC
1507098 TTTTTTTCCTCTAT-TTCA
1 TTTTTTTCCT-TATCTTCA
*
1507116 TTTTTATTCCTTATCTTTA
1 TTTTT-TTCCTTATCTTCA
1507135 TTTTTTT
1 TTTTTTT
1507142 TATCTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTTTCCTTATCTTCA
Found at i:1507245 original size:15 final size:16
Alignment explanation
Indices: 1507207--1507252 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
1507197 ATTATGTATA
* *
1507207 TATTATTA-TTATCAT
1 TATTATTATTTTTCTT
1507222 TATTATTATTTTTCTT
1 TATTATTATTTTTCTT
1507238 TATT-TTATTTTTCTT
1 TATTATTATTTTTCTT
1507253 ATCGTATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 19 0.68
16 9 0.32
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTATTATTTTTCTT
Found at i:1508499 original size:11 final size:12
Alignment explanation
Indices: 1508471--1508504 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1508461 TATTTAAACG
1508471 GGTATTGGGCTA
1 GGTATTGGGCTA
*
1508483 GGTATTGGG-TC
1 GGTATTGGGCTA
1508494 GGTATTGGGCT
1 GGTATTGGGCT
1508505 GGGAATCGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.12, C:0.09, G:0.44, T:0.35
Consensus pattern (12 bp):
GGTATTGGGCTA
Found at i:1508580 original size:24 final size:25
Alignment explanation
Indices: 1508520--1508580 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
1508510 TCGGGCCGGG
1508520 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
1508543 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
1508567 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
1508581 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:1508660 original size:13 final size:13
Alignment explanation
Indices: 1508616--1508647 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1508606 TTTAATATTT
1508616 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
*
1508629 ATCGGGGTGGGTA
1 ATCGGGGCGGGTA
1508642 ATCGGG
1 ATCGGG
1508648 TAATCGGGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.12, G:0.53, T:0.19
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:1510219 original size:18 final size:18
Alignment explanation
Indices: 1510190--1510239 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
1510180 TTTAAGAGAG
1510190 AGAAAC-AGTGCATGTGA
1 AGAAACGAGTGCATGTGA
1510207 AGAAACGAGTGCATGTGA
1 AGAAACGAGTGCATGTGA
1510225 AGAAACGAGTGCATG
1 AGAAACGAGTGCATG
1510240 CACGCACGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 6 0.19
18 26 0.81
ACGTcount: A:0.40, C:0.12, G:0.32, T:0.16
Consensus pattern (18 bp):
AGAAACGAGTGCATGTGA
Found at i:1511574 original size:13 final size:13
Alignment explanation
Indices: 1511556--1511586 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1511546 GTATATACTT
1511556 ATATAAGTATACA
1 ATATAAGTATACA
1511569 ATATAAGTATACA
1 ATATAAGTATACA
*
1511582 TTATA
1 ATATA
1511587 CTTATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (13 bp):
ATATAAGTATACA
Found at i:1511587 original size:34 final size:34
Alignment explanation
Indices: 1511549--1511613 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
1511539 CATATAAGTA
1511549 TATACTTAT-ATA-AGTATACAATATAAGTATACAT
1 TATACTTATAATATA-TATA-AATATAAGTATACAT
*
1511583 TATACTTATAATATATATATATATAAGTATA
1 TATACTTATAATATATATAAATATAAGTATA
1511614 TATATTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 20 0.71
35 7 0.25
36 1 0.04
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.42
Consensus pattern (34 bp):
TATACTTATAATATATATAAATATAAGTATACAT
Found at i:1511600 original size:2 final size:2
Alignment explanation
Indices: 1511589--1511773 Score: 65
Period size: 2 Copynumber: 92.5 Consensus size: 2
1511579 ACATTATACT
*
1511589 TA TA -A TA TA TA TA TA TA TA -A GTA TA TA TA T- TA TA TA CA -A
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
1511628 GTA TA TA TA TA -A GA -A TA TA TA T- TCG TA TA TA TA -A TA TA -A
1 -TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
* *
1511667 GTA TA TA -A GTA TA -A GTA TA TA TA TA -A GTG TA TA TA TA TA AA
1 -TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
1511708 GTA TA AA GTA TA TA AA CTA TA AA GTA TA -A GTA TA TA -A AA TA TA
1 -TA TA TA -TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA
1511751 TA TA GTA TA TA TA GTA TA TA TA T
1 TA TA -TA TA TA TA -TA TA TA TA T
1511774 GCATGAATGT
Statistics
Matches: 142, Mismatches: 13, Indels: 56
0.67 0.06 0.27
Matches are distributed among these distances:
1 14 0.10
2 113 0.80
3 15 0.11
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (2 bp):
TA
Found at i:1511648 original size:49 final size:48
Alignment explanation
Indices: 1511592--1511773 Score: 142
Period size: 53 Copynumber: 3.6 Consensus size: 48
1511582 TTATACTTAT
1511592 AATATATATATATATAAGTATATATATTATATACAAGTATATATATAAG
1 AATATATATATATATAAGTATATATATTATATA-AAGTATATATATAAG
*
1511641 AATATATATTCGTATATATAA-TATAAGTATATAAGTAT-AAGTATATATATAAG
1 AATATATA----TATATATAAGTAT-A-TATATTA-TATAAAGTATATATATAAG
* *
1511694 --TGTATATATATA-AAGTATAAAGTATATAAACTATAAAGTATAAGTATATAA-
1 AATATATATATATATAAGTAT--A-TATAT-TA-TATAAAGTAT-A-TATATAAG
1511745 AATATATATAGTATATATAGTATATATAT
1 AATATATATA-TATATA-AGTATATATAT
1511774 GCATGAATGT
Statistics
Matches: 111, Mismatches: 4, Indels: 32
0.76 0.03 0.22
Matches are distributed among these distances:
46 2 0.02
47 9 0.08
48 8 0.07
49 13 0.12
50 6 0.05
51 6 0.05
52 10 0.09
53 37 0.33
54 11 0.10
55 4 0.04
56 5 0.05
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (48 bp):
AATATATATATATATAAGTATATATATTATATAAAGTATATATATAAG
Found at i:1511719 original size:16 final size:16
Alignment explanation
Indices: 1511652--1511770 Score: 72
Period size: 16 Copynumber: 7.4 Consensus size: 16
1511642 ATATATATTC
1511652 GTATATATAA-TAT-AA
1 GTATATA-AAGTATAAA
1511667 GTATAT-AAGTAT-AA
1 GTATATAAAGTATAAA
* *
1511681 GTATATATATAAGTGTATA
1 G--TATATA-AAGTATAAA
1511700 -TATATAAAGTATAAA
1 GTATATAAAGTATAAA
*
1511715 GTATATAAACTATAAA
1 GTATATAAAGTATAAA
*
1511731 GTATA-AGTA-TATAAA
1 GTATATA-AAGTATAAA
* *
1511746 ATATATATAGTATATATA
1 GTATATAAAGTATA-A-A
1511764 GTATATA
1 GTATATA
1511771 TATGCATGAA
Statistics
Matches: 84, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
13 2 0.02
14 6 0.07
15 26 0.31
16 36 0.43
17 1 0.01
18 12 0.14
19 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (16 bp):
GTATATAAAGTATAAA
Found at i:1511721 original size:9 final size:9
Alignment explanation
Indices: 1511700--1511770 Score: 57
Period size: 9 Copynumber: 8.7 Consensus size: 9
1511690 TAAGTGTATA
1511700 TATATAAAG
1 TATATAAAG
1511709 --TATAAAG
1 TATATAAAG
1511716 TATATAAA-
1 TATATAAAG
*
1511724 -CTATAAAG
1 TATATAAAG
1511732 --TAT-AAG
1 TATATAAAG
*
1511738 TATATAAAA
1 TATATAAAG
*
1511747 TATATATAG
1 TATATAAAG
*
1511756 TATATATAG
1 TATATAAAG
1511765 TATATA
1 TATATA
1511771 TATGCATGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
6 3 0.06
7 16 0.31
8 3 0.06
9 30 0.58
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (9 bp):
TATATAAAG
Found at i:1511813 original size:23 final size:23
Alignment explanation
Indices: 1511772--1511816 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1511762 TAGTATATAT
*
1511772 ATGCATGAATGTACATATGTATG
1 ATGCATGAATATACATATGTATG
* *
1511795 ATGCATGTATATACTTATGTAT
1 ATGCATGAATATACATATGTAT
1511817 ATATATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (23 bp):
ATGCATGAATATACATATGTATG
Found at i:1511930 original size:2 final size:2
Alignment explanation
Indices: 1511925--1511974 Score: 91
Period size: 2 Copynumber: 24.5 Consensus size: 2
1511915 ATTTATGCAC
1511925 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1511967 AGT AT AT A
1 A-T AT AT A
1511975 ATTAAACATG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 45 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1512171 original size:22 final size:21
Alignment explanation
Indices: 1512137--1512179 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
1512127 TTAGACCATG
*
1512137 ACTAAAATGAAAGAAATAAAAA
1 ACTAAAATAAAAG-AATAAAAA
* *
1512159 ACTAAATTAAAAGTATAAAAA
1 ACTAAAATAAAAGAATAAAAA
1512180 TAATGATTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.19
Consensus pattern (21 bp):
ACTAAAATAAAAGAATAAAAA
Found at i:1512291 original size:11 final size:11
Alignment explanation
Indices: 1512277--1512301 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1512267 TCAAAATTTC
1512277 CTATTTTCCCT
1 CTATTTTCCCT
1512288 CTATTTTCCCT
1 CTATTTTCCCT
1512299 CTA
1 CTA
1512302 AATTCTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.36, G:0.00, T:0.52
Consensus pattern (11 bp):
CTATTTTCCCT
Found at i:1512394 original size:48 final size:47
Alignment explanation
Indices: 1512292--1512400 Score: 127
Period size: 48 Copynumber: 2.3 Consensus size: 47
1512282 TTCCCTCTAT
* *
1512292 TTTCCCTCTAAATT-CTCAATTTCCCTCTATACCCAAAATTTTCCAA
1 TTTCCCTCTAAATTCCTCAATTTCCCACTATACCCAAAATTCTCCAA
*
1512338 TTTTCCTCTAAATTCGCTCTAATTTCCCAACT-T-CCCAAAAATTCT-CAA
1 TTTCCCTCTAAATTC-CTC-AATTTCCC-ACTATACCC-AAAATTCTCCAA
1512386 TTTCCCTCTAAATTC
1 TTTCCCTCTAAATTC
1512401 ATAAATAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
46 13 0.24
48 23 0.43
49 16 0.30
50 2 0.04
ACGTcount: A:0.28, C:0.32, G:0.01, T:0.39
Consensus pattern (47 bp):
TTTCCCTCTAAATTCCTCAATTTCCCACTATACCCAAAATTCTCCAA
Found at i:1512486 original size:2 final size:2
Alignment explanation
Indices: 1512479--1512515 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1512469 ACTCACATGA
1512479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1512516 TCAATCTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1512707 original size:13 final size:12
Alignment explanation
Indices: 1512691--1512734 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 12
1512681 TGAAATTAAT
1512691 TTAATGATTATAA
1 TTAA-GATTATAA
1512704 TTAAGATTTATAA
1 TTAAGA-TTATAA
1512717 TATAAGAATTATAA
1 T-TAAG-ATTATAA
1512731 TTAA
1 TTAA
1512735 TATAGAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.07
13 14 0.50
14 11 0.39
15 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (12 bp):
TTAAGATTATAA
Found at i:1514005 original size:19 final size:16
Alignment explanation
Indices: 1513972--1514012 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 16
1513962 ATGATGATGC
1513972 AATGAAAAAAAAGAAA
1 AATGAAAAAAAAGAAA
1513988 AATGACAAAAAATGAGAAA
1 AATGA-AAAAAA--AGAAA
1514007 AATGAA
1 AATGAA
1514013 TTAGTACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.23
17 6 0.27
18 1 0.05
19 10 0.45
ACGTcount: A:0.73, C:0.02, G:0.15, T:0.10
Consensus pattern (16 bp):
AATGAAAAAAAAGAAA
Found at i:1515643 original size:2 final size:2
Alignment explanation
Indices: 1515636--1515676 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1515626 ATGAAACATG
1515636 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1515677 GTAGAATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1516400 original size:25 final size:26
Alignment explanation
Indices: 1516334--1516388 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
1516324 AAGTTTGAGC
1516334 TAAACGACACCGTTTTGGAAAACATA
1 TAAACGACACCGTTTTGGAAAACATA
1516360 TAAACGACACCGTTTTGGAAAA-ATA
1 TAAACGACACCGTTTTGGAAAACATA
1516385 TAAA
1 TAAA
1516389 TACCCCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 7 0.24
26 22 0.76
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (26 bp):
TAAACGACACCGTTTTGGAAAACATA
Found at i:1521706 original size:22 final size:22
Alignment explanation
Indices: 1521658--1521713 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
1521648 ATATAAAATT
*
1521658 TGTCCCGAAGGA-CTTTATATA
1 TGTCCCGAAGGACCTATATATA
*
1521679 TGTCCCGAAGGACCTATGTATA
1 TGTCCCGAAGGACCTATATATA
*
1521701 TTTCCCGAAGGAC
1 TGTCCCGAAGGAC
1521714 ATGTGTAACC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 12 0.39
22 19 0.61
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATATATA
Found at i:1521799 original size:31 final size:31
Alignment explanation
Indices: 1521761--1521826 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
1521751 CCTAGCTCTC
1521761 ATATCACATAACATGCGCATATATGATAGTT
1 ATATCACATAACATGCGCATATATGATAGTT
1521792 ATATCACATAACATGCGCATATATGATAGTT
1 ATATCACATAACATGCGCATATATGATAGTT
1521823 -TATC
1 ATATC
1521827 TCACTTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (31 bp):
ATATCACATAACATGCGCATATATGATAGTT
Found at i:1526228 original size:20 final size:21
Alignment explanation
Indices: 1526203--1526246 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1526193 GAATGACTTC
*
1526203 ATGTATA-TCCTGAAGGACCT
1 ATGTATAGTCCTGAAAGACCT
1526223 ATGTATATGTCCTGAAAGACCT
1 ATGTATA-GTCCTGAAAGACCT
1526245 AT
1 AT
1526247 ATAACCCTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
22 14 0.67
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (21 bp):
ATGTATAGTCCTGAAAGACCT
Found at i:1528600 original size:2 final size:2
Alignment explanation
Indices: 1528593--1528643 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
1528583 GCTTTCTAAA
1528593 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1528635 AT AT -T AT AT
1 AT AT AT AT AT
1528644 GTTTCAAAGC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1528744 original size:37 final size:37
Alignment explanation
Indices: 1528694--1528967 Score: 279
Period size: 37 Copynumber: 7.7 Consensus size: 37
1528684 AAAAAATATT
* *
1528694 TTTTTCAAACTATATAATATATATATTTTCAAAAATG
1 TTTTTAAAACTATATATTATATATATTTTCAAAAATG
* *
1528731 TTTTTAAAACTATATACTATATATAATTTCAAAAATG
1 TTTTTAAAACTATATATTATATATATTTTCAAAAATG
* *
1528768 TTTTT-AAATTATATATTATATATGTTTTCAAAAATG
1 TTTTTAAAACTATATATTATATATATTTTCAAAAATG
* * *
1528804 TTTTCAAAACTATATATTATATATAATTTCAAAAATA
1 TTTTTAAAACTATATATTATATATATTTTCAAAAATG
1528841 TTTTTAAAACTATATATTATATATATTTTC-AAAA--
1 TTTTTAAAACTATATATTATATATATTTTCAAAAATG
*
1528875 ---CT-AAA-TAT-TA-TATATA-A-TTTCAAAAAAAATG
1 TTTTTAAAACTATATATTATATATATTTTC---AAAAATG
* * *
1528906 -TTTCAAAACTATATATTATATATAATTTCAAAAATA
1 TTTTTAAAACTATATATTATATATATTTTCAAAAATG
* * *
1528942 TTTTCAAAACTACATAATATATATAT
1 TTTTTAAAACTATATATTATATATAT
1528968 ATATAATTTC
Statistics
Matches: 200, Mismatches: 21, Indels: 32
0.79 0.08 0.13
Matches are distributed among these distances:
25 4 0.02
26 1 0.00
27 6 0.03
28 2 0.01
29 7 0.04
30 3 0.01
31 1 0.00
34 3 0.01
35 3 0.01
36 43 0.22
37 122 0.61
38 1 0.00
39 4 0.02
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (37 bp):
TTTTTAAAACTATATATTATATATATTTTCAAAAATG
Found at i:1528801 original size:73 final size:74
Alignment explanation
Indices: 1528685--1528966 Score: 311
Period size: 73 Copynumber: 3.9 Consensus size: 74
1528675 TGTTTTCAAA
* * *
1528685 AAAAATATTTTTTTCAAACTATATAATATATATATTTTCAAAAATGTTTTTAAAACTATATACTA
1 AAAAATA--TTTTTAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAACTATATACTA
1528750 TATATAATTTC
64 TATATAATTTC
* * * *
1528761 AAAAATGTTTTT-AAATTATATATTATATATGTTTTCAAAAATGTTTTCAAAACTATATATTATA
1 AAAAATATTTTTAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAACTATATACTATA
1528825 TATAATTTC
66 TATAATTTC
*
1528834 AAAAATATTTTTAAAACTATATATTATATATATTTTC-AAAA------C-TAA--ATAT--TATA
1 AAAAATATTTTTAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAACTATATACTATA
1528887 TATAATTTC
66 TATAATTTC
* * * * * *
1528896 AAAAAAAATGTTTCAAAACTATATATTATATATAATTTCAAAAATATTTTCAAAACTACATAATA
1 -AAAAATAT-TTTTAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAACTATATACTA
1528961 TATATA
64 TATATA
1528967 TATATAATTT
Statistics
Matches: 176, Mismatches: 15, Indels: 30
0.80 0.07 0.14
Matches are distributed among these distances:
62 13 0.07
63 7 0.04
64 31 0.18
65 4 0.02
66 2 0.01
67 1 0.01
71 1 0.01
72 2 0.01
73 71 0.40
74 30 0.17
76 14 0.08
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (74 bp):
AAAAATATTTTTAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAACTATATACTATA
TATAATTTC
Found at i:1528868 original size:25 final size:25
Alignment explanation
Indices: 1528838--1528899 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
1528828 AATTTCAAAA
* *
1528838 ATATTTTTAAAACTATATATTATAT
1 ATATTTTCAAAACTAAATATTATAT
1528863 ATATTTTCAAAACTAAATATTATAT
1 ATATTTTCAAAACTAAATATTATAT
*
1528888 ATAATTTCAAAA
1 ATATTTTCAAAA
1528900 AAAATGTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATTTTCAAAACTAAATATTATAT
Found at i:1528874 original size:62 final size:64
Alignment explanation
Indices: 1528804--1528938 Score: 220
Period size: 64 Copynumber: 2.1 Consensus size: 64
1528794 TTCAAAAATG
* * *
1528804 TTTTCAAAACTATATATTATATATAATTTC-AAAAATAT-TTTTAAAACTATATATTATATATA
1 TTTTCAAAACTAAATATTATATATAATTTCAAAAAAAATGTTTCAAAACTATATATTATATATA
1528866 TTTTCAAAACTAAATATTATATATAATTTCAAAAAAAATGTTTCAAAACTATATATTATATATA
1 TTTTCAAAACTAAATATTATATATAATTTCAAAAAAAATGTTTCAAAACTATATATTATATATA
*
1528930 ATTTCAAAA
1 TTTTCAAAA
1528939 ATATTTTCAA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 29 0.43
63 7 0.10
64 31 0.46
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (64 bp):
TTTTCAAAACTAAATATTATATATAATTTCAAAAAAAATGTTTCAAAACTATATATTATATATA
Found at i:1528889 original size:101 final size:105
Alignment explanation
Indices: 1528695--1528967 Score: 328
Period size: 101 Copynumber: 2.6 Consensus size: 105
1528685 AAAAATATTT
* * * * *
1528695 TTTTC-AAACTATATAATATATATATTTTCAAAAATGTTTTTAAAACTATATACTATATATAATT
1 TTTTCAAAACTATATATTATATATAATTTCAAAAATATTTTTAAAACTATATAATATATATATTT
* *
1528759 TCAAAAATGTTTTTAAATTATATATTATATATGTTTTC-AAAAATG
66 TCAAAAA----TCTAAATTATATATTATATA--ATTTCAAAAAATG
*
1528804 TTTTCAAAACTATATATTATATATAATTTCAAAAATATTTTTAAAACTATATATTATATATATTT
1 TTTTCAAAACTATATATTATATATAATTTCAAAAATATTTTTAAAACTATATAATATATATATTT
1528869 TC-AAAA-CTAAA-TAT-TA-TATATAATTTCAAAAAAAATG
66 TCAAAAATCTAAATTATATATTATATAATTTC--AAAAAATG
* *
1528906 -TTTCAAAACTATATATTATATATAATTTCAAAAATATTTTCAAAACTACATAATATATATAT
1 TTTTCAAAACTATATATTATATATAATTTCAAAAATATTTTTAAAACTATATAATATATATAT
1528968 ATATAATTTC
Statistics
Matches: 150, Mismatches: 10, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
99 4 0.03
101 65 0.43
102 9 0.06
103 3 0.02
104 4 0.03
109 9 0.06
110 56 0.37
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (105 bp):
TTTTCAAAACTATATATTATATATAATTTCAAAAATATTTTTAAAACTATATAATATATATATTT
TCAAAAATCTAAATTATATATTATATAATTTCAAAAAATG
Found at i:1528967 original size:39 final size:38
Alignment explanation
Indices: 1528863--1528987 Score: 162
Period size: 39 Copynumber: 3.1 Consensus size: 38
1528853 TATATTATAT
1528863 ATATTTTCAAAACTAAATATTATATATAATTTCAAAAA
1 ATATTTTCAAAACTAAATATTATATATAATTTCAAAAA
* *
1528901 AAATGTTTCAAAACTATATATTATATATAATTTC-AAAA
1 ATAT-TTTCAAAACTAAATATTATATATAATTTCAAAAA
1528939 ATATTTTCAAAACTACATAATATATATATATATAATTTCAAAAA
1 ATATTTTC-AAA--AC-TAA-ATAT-TATATATAATTTCAAAAA
1528983 ATATT
1 ATATT
1528988 ATGTATATAT
Statistics
Matches: 75, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
37 4 0.05
38 13 0.17
39 28 0.37
40 2 0.03
41 2 0.03
42 4 0.05
43 13 0.17
44 9 0.12
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.40
Consensus pattern (38 bp):
ATATTTTCAAAACTAAATATTATATATAATTTCAAAAA
Found at i:1532091 original size:16 final size:16
Alignment explanation
Indices: 1532064--1532099 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
1532054 AAGAAATTAT
1532064 ATAAAAAAA-TTTAAA
1 ATAAAAAAATTTTAAA
1532079 ATAAAAAACATTTTAAA
1 ATAAAAAA-ATTTTAAA
1532096 ATAA
1 ATAA
1532100 GATAGGTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
16 1 0.05
17 10 0.53
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAAAAAAATTTTAAA
Found at i:1540136 original size:60 final size:58
Alignment explanation
Indices: 1539964--1540138 Score: 174
Period size: 60 Copynumber: 2.9 Consensus size: 58
1539954 TCTATGGCCC
* * * * *
1539964 TCATTTTAAATTGGTCCCTAAACTTTTAAATATTTTGATTTCATCCTTAAACTATGACTA
1 TCATTCTAAATTGGTCCCTAAACTTTTGAATA-TTTCATTTTATCC-TAAATTATGACTA
* * *
1540024 TCATTCTAAATTAGTCCTTAAACTTTTGAACT-TTTCATTTTCATTCCCAAATTATGATCT-
1 TCATTCTAAATTGGTCCCTAAACTTTTGAA-TATTTCATTTT-A-TCCTAAATTATGA-CTA
* *
1540084 TCATTCTAAACTGGTCCCCAAACTTTTTGAATATTTCAATTTTATCCTAAATTAT
1 TCATTCTAAATTGGTCCCTAAAC-TTTTGAATATTTC-ATTTTATCCTAAATTAT
1540139 ATGTGTATAC
Statistics
Matches: 95, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
59 7 0.07
60 65 0.68
61 18 0.19
62 5 0.05
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.45
Consensus pattern (58 bp):
TCATTCTAAATTGGTCCCTAAACTTTTGAATATTTCATTTTATCCTAAATTATGACTA
Found at i:1540365 original size:60 final size:59
Alignment explanation
Indices: 1540267--1540445 Score: 216
Period size: 60 Copynumber: 3.0 Consensus size: 59
1540257 ATGAAATTGT
* * *
1540267 GGATGAAATTGGAAGATCTAAAAGTTTAAGGACCAATTTAGAATGAGATTCATAGTTTTG-
1 GGATGAAATTGGAAGTTC-AAAAGTTTAAGGACTAATTTAGAATGAGACTCATAG-TTTGA
* * *
1540327 GGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAGAATAAGAGTCATTGTTTGA
1 GGATGAAATTGGAA-GTTCAAAAGTTTAAGGACTAATTTAGAATGAGACTCATAGTTTGA
* * * * *
1540387 GAAAGAAATTGGAAAGTTTAAAAGTTTAAGGACTAATTTAAAATGAGACTCATAATTTG
1 GGATGAAATTGG-AAGTTCAAAAGTTTAAGGACTAATTTAGAATGAGACTCATAGTTTG
1540446 GAGACATATA
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
59 4 0.04
60 94 0.91
61 5 0.05
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.32
Consensus pattern (59 bp):
GGATGAAATTGGAAGTTCAAAAGTTTAAGGACTAATTTAGAATGAGACTCATAGTTTGA
Found at i:1540688 original size:179 final size:183
Alignment explanation
Indices: 1540452--1540813 Score: 687
Period size: 179 Copynumber: 2.0 Consensus size: 183
1540442 TTTGGAGACA
1540452 TATAATGCAATTAACTCTAAAATTTAAATATATATAATCTTTTAAATATACTTAAAATAAATATA
1 TATAATGCAATTAACTCTAAAATTTAAATATATATAATCTTTTAAATATACTTAAAATAAATATA
1540517 TAGCACAATTACAACTCTTTACAGGGGATGGAGGAAGAAGATACATA-GAAAAAGAAAT-AAGTG
66 TAGCACAATTACAACTCTTTACAGGGGATGGAGGAAGAAGATACATAGGAAAAAGAAATAAAGTG
1540580 CTCTCAATGGG-TTTGAACCCATATCTTAAAATAGATAAGAAAAC-AAGATAT
131 CTCTCAATGGGTTTTGAACCCATATCTTAAAATAGATAAGAAAACAAAGATAT
1540631 TATAATGCAATTAACTCTAAAATTTAAATATATATAATCTTTTAAATATACTTAAAATAAATATA
1 TATAATGCAATTAACTCTAAAATTTAAATATATATAATCTTTTAAATATACTTAAAATAAATATA
1540696 TAGCACAATTACAACTCTTTACAGGGGATGGAGGAAGAAGATACATAGGAAAAAGAAATAAAGTG
66 TAGCACAATTACAACTCTTTACAGGGGATGGAGGAAGAAGATACATAGGAAAAAGAAATAAAGTG
*
1540761 CTCTCAATGGGTTTTGAACCCATATCTTAAAATATATAAGAAAACAAAGATAT
131 CTCTCAATGGGTTTTGAACCCATATCTTAAAATAGATAAGAAAACAAAGATAT
1540814 ACAGTTTAAT
Statistics
Matches: 178, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
179 112 0.63
180 11 0.06
181 16 0.09
182 32 0.18
183 7 0.04
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (183 bp):
TATAATGCAATTAACTCTAAAATTTAAATATATATAATCTTTTAAATATACTTAAAATAAATATA
TAGCACAATTACAACTCTTTACAGGGGATGGAGGAAGAAGATACATAGGAAAAAGAAATAAAGTG
CTCTCAATGGGTTTTGAACCCATATCTTAAAATAGATAAGAAAACAAAGATAT
Found at i:1551488 original size:41 final size:41
Alignment explanation
Indices: 1551419--1552072 Score: 596
Period size: 41 Copynumber: 16.1 Consensus size: 41
1551409 TAGCGGCATT
* * * *
1551419 TTTAGCGGCGTTTTTAGAACAAACGCCGCTAAATACTCGTAA
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAAGACTCGTAC
**
1551461 TTTAGTGGTATTTTTATACAAACGCCGCTAAAGACT-GTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
*** * * * *
1551501 TTTAACAGCATTTTTAGACAAAACGCCGCTAAATACTTGTAC
1 TTTAGTGGCGTTTTTATAC-AAACGCCGCTAAAGACTCGTAC
* * * * * *
1551543 TGTAATGGTGGTTTTAATACAAACGCCGCTAAAGAAT-ATAC
1 TTTAGTGG-CGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * *
1551584 TTTAGCGGCGTTTTTATACAAATGCCGCTATATACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
*
1551625 TTTAGTGGCGTTTTTATACAAACGCTGCTAAAGACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * * *
1551666 TTTA----CGTTTTATCTAAAAACACCGCTAAATACTTGTAC
1 TTTAGTGGCGTTTT-TATACAAACGCCGCTAAAGACTCGTAC
* * *
1551704 TTTAGTGGCGTTTTTAATACAAACGTCGCTAAAGAAT-ATAC
1 TTTAGTGGCGTTTTT-ATACAAACGCCGCTAAAGACTCGTAC
* * *
1551745 TTTAGCGGCG--TTTA-A-AAACGCCGCTATATACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
** *
1551782 TTTAGTGGCGTTTTTATACAAACATCGCTAAAAACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * * * * *
1551823 TTTAATGGCATTTTTAATACAGATGTCGCTATAGACTCGTAT
1 TTTAGTGGCGTTTTT-ATACAAACGCCGCTAAAGACTCGTAC
* *
1551865 TTTAGTGGCGTTTTTATACAAACGCCGCTAAGGACTCATAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * *
1551906 TTTAGTAGCGCTTTTATATAAACGCCGCTAAAGACTTGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* *
1551947 TTTAGTGGCGTTTTTATACAAACGCCGTTATAGACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
** * * *
1551988 TTTAGTGGCACTTTTATACAAACGCCGTTATATAC-C-TATGC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTA--C
* * *
1552029 TTTAGTAGCGTTTTTATACAAACGCCGCTATAGACTCGTGC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
1552070 TTT
1 TTT
1552073 GGAGTCGTTG
Statistics
Matches: 493, Mismatches: 99, Indels: 41
0.78 0.16 0.06
Matches are distributed among these distances:
36 13 0.03
37 19 0.04
38 26 0.05
39 9 0.02
40 41 0.08
41 285 0.58
42 92 0.19
43 8 0.02
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
Found at i:1551558 original size:42 final size:43
Alignment explanation
Indices: 1551429--1551575 Score: 144
Period size: 42 Copynumber: 3.6 Consensus size: 43
1551419 TTTAGCGGCG
* * *
1551429 TTTTTAGA-ACAAACGCCGCTAAATACTCGTAATTTAGTGGTA
1 TTTTTAGACACAAACGCCGCTAAATACTTGTACTTTAATGGTA
* * ** *
1551471 TTTTT--ATACAAACGCCGCTAAAGAC-TGTACTTTAACAGCA
1 TTTTTAGACACAAACGCCGCTAAATACTTGTACTTTAATGGTA
* *
1551511 TTTTTAGACA-AAACGCCGCTAAATACTTGTACTGTAATGGTG
1 TTTTTAGACACAAACGCCGCTAAATACTTGTACTTTAATGGTA
* *
1551553 GTTTTA-ATACAAACGCCGCTAAA
1 TTTTTAGACACAAACGCCGCTAAA
1551576 GAATATACTT
Statistics
Matches: 84, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
40 15 0.18
41 34 0.40
42 35 0.42
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (43 bp):
TTTTTAGACACAAACGCCGCTAAATACTTGTACTTTAATGGTA
Found at i:1552594 original size:21 final size:21
Alignment explanation
Indices: 1552565--1552617 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1552555 ATTTTGACTA
1552565 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1552586 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1552607 TCGCAATGCGA
1 TCGCATTGCGA
1552618 ATACGTAAAT
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:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1552632 original size:20 final size:20
Alignment explanation
Indices: 1552607--1552741 Score: 153
Period size: 20 Copynumber: 6.7 Consensus size: 20
1552597 TTTTCCTAAT
1552607 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
1552627 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* * *
1552648 TCGCAATGTGATTACGTAAT
1 TCGCAATGCGAATACGTAAA
*
1552668 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
1552688 TCGCAACGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
1552709 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1552729 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1552742 CTGACTATCG
Statistics
Matches: 93, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
20 62 0.67
21 31 0.33
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1552653 original size:41 final size:41
Alignment explanation
Indices: 1552607--1552741 Score: 157
Period size: 41 Copynumber: 3.3 Consensus size: 41
1552597 TTTTCCTAAT
* ** *
1552607 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTACGTAAA
* * *
1552648 TCGCAATGTGATTACGTAATTCGCAATGCG-ATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTACGTAAA
* * *
1552688 TCGCAACGCGAATTAGGAAAATCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAA-TACGTAAATCGCAATGCGAATTACGTAAA
1552729 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1552742 CTGACTATCG
Statistics
Matches: 78, Mismatches: 14, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
40 17 0.22
41 60 0.77
42 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.22
Consensus pattern (41 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATTACGTAAA
Found at i:1552677 original size:61 final size:61
Alignment explanation
Indices: 1552603--1552741 Score: 233
Period size: 61 Copynumber: 2.3 Consensus size: 61
1552593 GCGATTTTCC
* * *
1552603 TAATTCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATCGCAATGTGATTACG
1 TAATTCGCAATGCGAATACGTAAATCGCAACGCGAATTAGGAAAATCGCAATGCGAATACG
*
1552664 TAATTCGCAATGCGATTACGTAAATCGCAACGCGAATTAGGAAAATCGCAATGCGAATACG
1 TAATTCGCAATGCGAATACGTAAATCGCAACGCGAATTAGGAAAATCGCAATGCGAATACG
*
1552725 TAAATCGCAATGCGAAT
1 TAATTCGCAATGCGAAT
1552742 CTGACTATCG
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 72 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (61 bp):
TAATTCGCAATGCGAATACGTAAATCGCAACGCGAATTAGGAAAATCGCAATGCGAATACG
Found at i:1553355 original size:21 final size:21
Alignment explanation
Indices: 1553295--1553386 Score: 104
Period size: 20 Copynumber: 4.6 Consensus size: 21
1553285 TCTAAACTTT
*
1553295 AAATCGCAAC-ATGAAAATGA
1 AAATCGCAACGACGAAAATGA
1553315 AAATCGCAAC-ACGAAAATGA
1 AAATCGCAACGACGAAAATGA
**
1553335 CTATCGCAACGA-GAGAAATGA
1 AAATCGCAACGACGA-AAATGA
*
1553356 AAATCGCAACG-CG-AAATAA
1 AAATCGCAACGACGAAAATGA
1553375 AAATCGCAACGA
1 AAATCGCAACGA
1553387 GATAATCGCA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
19 16 0.26
20 29 0.47
21 17 0.27
ACGTcount: A:0.51, C:0.20, G:0.17, T:0.12
Consensus pattern (21 bp):
AAATCGCAACGACGAAAATGA
Found at i:1553377 original size:19 final size:19
Alignment explanation
Indices: 1553349--1553385 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1553339 CGCAACGAGA
*
1553349 GAAATGAAAATCGCAACGC
1 GAAATAAAAATCGCAACGC
1553368 GAAATAAAAATCGCAACG
1 GAAATAAAAATCGCAACG
1553386 AGATAATCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.19, G:0.19, T:0.11
Consensus pattern (19 bp):
GAAATAAAAATCGCAACGC
Found at i:1553381 original size:40 final size:40
Alignment explanation
Indices: 1553295--1553388 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 40
1553285 TCTAAACTTT
*
1553295 AAATCGCAAC-ATGAAAATGAAAATCGCAACACGAAAATGA
1 AAATCGCAACGA-GAAAATGAAAATCGCAACACGAAAATAA
** *
1553335 CTATCGCAACGAGAGAAATGAAAATCGCAACGCG-AAATAA
1 AAATCGCAACGAGA-AAATGAAAATCGCAACACGAAAATAA
1553375 AAATCGCAACGAGA
1 AAATCGCAACGAGA
1553389 TAATCGCAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 27 0.59
41 19 0.41
ACGTcount: A:0.51, C:0.19, G:0.18, T:0.12
Consensus pattern (40 bp):
AAATCGCAACGAGAAAATGAAAATCGCAACACGAAAATAA
Found at i:1553433 original size:19 final size:19
Alignment explanation
Indices: 1553411--1553555 Score: 94
Period size: 19 Copynumber: 8.1 Consensus size: 19
1553401 AAAACCAAAA
*
1553411 TCGCATTGTGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1553430 TCGCGTTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
* *
1553444 TCTCATTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
1553463 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1553482 TCGCGTTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
**
1553498 TCG--TTGCGATAGTCATTT
1 TCGCATTGCGATTTTCA-TT
*
1553516 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1553535 CTCTCGTTGCGATTTTCATT
1 -TCGCATTGCGATTTTCATT
1553555 T
1 T
1553556 AAAAAAAAAA
Statistics
Matches: 100, Mismatches: 14, Indels: 24
0.72 0.10 0.17
Matches are distributed among these distances:
14 15 0.15
16 8 0.08
17 6 0.06
18 4 0.04
19 39 0.39
20 28 0.28
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1553498 original size:52 final size:53
Alignment explanation
Indices: 1553411--1553548 Score: 197
Period size: 52 Copynumber: 2.6 Consensus size: 53
1553401 AAAACCAAAA
* * * *
1553411 TCGCATTGTGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGAT-TTTAATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATAGTCAATT
* *
1553463 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATAGTCAATT
*
1553516 TCGCGTTGCGATTTTCATTCTCTCGTTGCGATT
1 TCGCGTTGCGATTTTCATT-TCGCGTTGCGATT
1553549 TTCATTTAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
52 42 0.55
53 23 0.30
54 12 0.16
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (53 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATAGTCAATT
Found at i:1553548 original size:20 final size:20
Alignment explanation
Indices: 1553449--1553554 Score: 111
Period size: 20 Copynumber: 5.7 Consensus size: 20
1553439 GATTCTCTCA
*
1553449 TTGCGATTTTAATT-TCGCG
1 TTGCGATTTTCATTCTCGCG
1553468 TTGCGATTTTCATT-TCGCG
1 TTGCGATTTTCATTCTCGCG
1553487 TTGCGA--TTC--TCT--CG
1 TTGCGATTTTCATTCTCGCG
** *
1553501 TTGCGATAGTCATTTTCGCG
1 TTGCGATTTTCATTCTCGCG
*
1553521 TTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATTCTCGCG
1553541 TTGCGATTTTCATT
1 TTGCGATTTTCATT
1553555 TAAAAAAAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
14 8 0.11
15 1 0.01
16 3 0.04
17 3 0.04
18 2 0.03
19 24 0.33
20 32 0.44
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (20 bp):
TTGCGATTTTCATTCTCGCG
Found at i:1555413 original size:94 final size:94
Alignment explanation
Indices: 1555252--1555630 Score: 604
Period size: 94 Copynumber: 4.1 Consensus size: 94
1555242 TAGATTGCTT
* * *
1555252 AGTAAATTTATTCGGTTGCAGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1555317 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
* * *
1555346 AGTAAATTTATTCGGGTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACATTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1555411 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
1555440 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1555505 ATTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
1555533 AGTAAATTTGTTCGGTTACTTCCAATTCTGCTAAACTGTGTATTCTTT-ACTACTCTGAAGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAAC-ACTGTGAAGTTAG
1555597 TATTTGTCTTTGTTTTGTCTTTTGGTTG-A
65 TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1555626 AGTAA
1 AGTAA
1555631 TGCAATCCAT
Statistics
Matches: 267, Mismatches: 15, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
92 2 0.01
93 112 0.42
94 153 0.57
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1555607 original size:187 final size:187
Alignment explanation
Indices: 1555252--1555630 Score: 602
Period size: 187 Copynumber: 2.0 Consensus size: 187
1555242 TAGATTGCTT
* *
1555252 AGTAAATTTATTCGGTTGCAGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCAGCCAATACTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAAT
* *
1555317 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGGTGCTGCCAATTCTGCTAAAT
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGGTACTGCCAATTCTGCTAAAC
* *
1555382 TGTGTATTCTTTAACATTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * *
1555440 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAAT
1 AGTAAATTTATTCGGTTGCAGCCAATACTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAAT
* * *
1555505 ATTTGTC-TTTG-TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTACTTCCAATTCTGCTAAA
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-AAGTAAATTTATTCGGGTACTGCCAATTCTGCTAAA
1555568 CTGTGTATTCTTT-ACTACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
130 CTGTGTATTCTTTAAC-ACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
1555626 AGTAA
1 AGTAA
1555631 TGCAATCCAT
Statistics
Matches: 177, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
186 23 0.13
187 87 0.49
188 67 0.38
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (187 bp):
AGTAAATTTATTCGGTTGCAGCCAATACTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAAT
ATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGGTACTGCCAATTCTGCTAAAC
TGTGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:1555781 original size:20 final size:20
Alignment explanation
Indices: 1555737--1555793 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
1555727 ATGCGAAATG
**
1555737 AAAATCGCAACGCGAAA-TG
1 AAAATCGCAACGCGAAACCA
1555756 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
1555776 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
1555794 TATAATCGCG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.49, C:0.26, G:0.18, T:0.07
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:1555802 original size:19 final size:19
Alignment explanation
Indices: 1555697--1555792 Score: 111
Period size: 19 Copynumber: 4.9 Consensus size: 19
1555687 CATGAAACTT
*
1555697 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
** *
1555718 ACTATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
1555737 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
**
1555756 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAA-TG
1555776 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
1555793 CTATAATCGC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
19 38 0.58
20 17 0.26
21 10 0.15
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1555821 original size:19 final size:19
Alignment explanation
Indices: 1555799--1555936 Score: 93
Period size: 19 Copynumber: 7.8 Consensus size: 19
1555789 GAAACTATAA
1555799 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1555818 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1555832 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1555851 TCGTGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1555865 TCTCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1555884 TCGCGTTGCGA--TTCATT
1 TCGCGTTGCGATTTTCATT
**
1555901 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
1555922 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
1555937 AAGTTCCAGA
Statistics
Matches: 89, Mismatches: 16, Indels: 26
0.68 0.12 0.20
Matches are distributed among these distances:
14 17 0.19
16 5 0.06
17 22 0.25
19 31 0.35
21 14 0.16
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1555844 original size:33 final size:33
Alignment explanation
Indices: 1555802--1555897 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 33
1555792 ACTATAATCG
*
1555802 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
1555835 CGTTGCGATTTTCATTTCGTGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
1555868 CATTGCGATTTTTATTTCGCGTTGCGATTC
1 CGTTGCGATTTTCATTTCGCGTTGCGATTC
1555898 ATTTCGCGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:1556413 original size:21 final size:21
Alignment explanation
Indices: 1556389--1556455 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1556379 TCATTCCTCG
1556389 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1556410 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1556431 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1556452 AGAG
1 AGAG
1556456 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1556413 original size:42 final size:42
Alignment explanation
Indices: 1556337--1556455 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1556327 GACTCGCCTG
* * * * * * *
1556337 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1556379 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1556421 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1556456 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1557825 original size:14 final size:14
Alignment explanation
Indices: 1557806--1557841 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1557796 ATTGTTTAAT
1557806 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1557820 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1557834 TGATTTGT
1 TGATTTGT
1557842 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1558006 original size:33 final size:32
Alignment explanation
Indices: 1557964--1558032 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
1557954 ATGCGAAATG
1557964 AAAATCGCAACACGAAA-TGAAAATCACAACGAC
1 AAAATCGCAACACGAAACT-AAAATCACAACG-C
* *
1557997 AAAATCGCAACGCGAAACTAAAATCGCAACGC
1 AAAATCGCAACACGAAACTAAAATCACAACGC
1558029 AAAA
1 AAAA
1558033 CTAAATTCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 5 0.15
33 27 0.82
34 1 0.03
ACGTcount: A:0.54, C:0.25, G:0.13, T:0.09
Consensus pattern (32 bp):
AAAATCGCAACACGAAACTAAAATCACAACGC
Found at i:1558021 original size:19 final size:19
Alignment explanation
Indices: 1557948--1558042 Score: 78
Period size: 19 Copynumber: 5.3 Consensus size: 19
1557938 AAAAATGACT
*
1557948 ATCGCAATGCGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
*
1557967 ATCGCAACACGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
*
1557986 ATCACAA--CG--AC-AAA
1 ATCGCAACGCGAAACTAAA
1558000 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
*
1558019 ATCGCAACGCAAAACTAAA
1 ATCGCAACGCGAAACTAAA
*
1558038 TTCGC
1 ATCGC
1558043 GTTGCGATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
14 9 0.14
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 48 0.75
ACGTcount: A:0.48, C:0.24, G:0.15, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAACTAAA
Found at i:1558060 original size:19 final size:19
Alignment explanation
Indices: 1558038--1558155 Score: 85
Period size: 19 Copynumber: 6.7 Consensus size: 19
1558028 CAAAACTAAA
1558038 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1558057 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1558072 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1558090 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1558105 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
1558123 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
1558142 TTCTGCGTTGCGAT
1 TTC-GCGTTGCGAT
1558156 AAACATTAAG
Statistics
Matches: 74, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 36 0.49
20 9 0.12
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1558084 original size:33 final size:33
Alignment explanation
Indices: 1558042--1558135 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
1558032 ACTAAATTCG
*
1558042 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
1558075 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1558108 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1558136 AGTCATTTCT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:1558162 original size:20 final size:19
Alignment explanation
Indices: 1558120--1558162 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
1558110 TTGCGATTTT
**
1558120 CATTTCGCATTGCGATAGT
1 CATTTCGCATTGCGATAAA
*
1558139 CATTTCTGCGTTGCGATAAA
1 CATTTC-GCATTGCGATAAA
1558159 CATT
1 CATT
1558163 AAGATGATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (19 bp):
CATTTCGCATTGCGATAAA
Found at i:1560707 original size:24 final size:24
Alignment explanation
Indices: 1560673--1560726 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1560663 CTGAAAAATC
1560673 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1560697 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1560721 ATCAAA
1 ATCAAA
1560727 TTTCAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1561693 original size:20 final size:21
Alignment explanation
Indices: 1561586--1561733 Score: 139
Period size: 20 Copynumber: 7.4 Consensus size: 21
1561576 GTCAGAATCT
*
1561586 CGTTGCGATTTAC-TAAATCG
1 CGTTGCGATTTACGTAATTCG
*** *
1561606 CAACGCGA-TTACGTAAATCG
1 CGTTGCGATTTACGTAATTCG
**
1561626 CAATGCGA-TTACGT-ATTCG
1 CGTTGCGATTTACGTAATTCG
* * **
1561645 CGTTACGATTTTCCCAATTCG
1 CGTTGCGATTTACGTAATTCG
*
1561666 CATTGCGATTTACGTAATT-G
1 CGTTGCGATTTACGTAATTCG
1561686 CGTTGCGATTTACGTAA-TCG
1 CGTTGCGATTTACGTAATTCG
1561706 CGTTGCGATTTACGT-ATTCG
1 CGTTGCGATTTACGTAATTCG
1561726 CGTTGCGA
1 CGTTGCGA
1561734 ATTAGGAAAA
Statistics
Matches: 106, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
19 15 0.14
20 72 0.68
21 19 0.18
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (21 bp):
CGTTGCGATTTACGTAATTCG
Found at i:1561775 original size:21 final size:21
Alignment explanation
Indices: 1561729--1561775 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1561719 GTATTCGCGT
1561729 TGCGAATTAGGAAAATCGCAA
1 TGCGAATTAGGAAAATCGCAA
* * * *
1561750 CGCGAATTTGGGAAATCGTAA
1 TGCGAATTAGGAAAATCGCAA
1561771 TGCGA
1 TGCGA
1561776 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (21 bp):
TGCGAATTAGGAAAATCGCAA
Found at i:1565178 original size:43 final size:43
Alignment explanation
Indices: 1565117--1565490 Score: 464
Period size: 43 Copynumber: 8.7 Consensus size: 43
1565107 ATGGTAATTA
*
1565117 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACTTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
** *
1565160 GCGGCGTTTGTATCCAAAAACGCTTCTATAGATCTGAACTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
* ** * *
1565203 GCGACGTTTGTATCCAAAAATACTGCTATAGATATGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
* *
1565246 ACGGCATTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
*
1565289 GCGGCGTTTGT-TCCAAAAACGCCTCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
* *
1565331 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGATCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
*** * *
1565374 GCGGCGTTTGTGAAATAAAAACGCCACTATAGATCTCAACCTTTT
1 GCGGCGTTTGT-ATCCAAAAACGCCGCTATAGATCT-GACCTTTT
* * * *
1565419 GCGGCTTTTGT-TTCAAAAACGCCGCTATAGAACTTGACTTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATC-TGACCTTTT
* * *
1565462 GCGGCGTTTTTATTTCACAAACGCCGCTA
1 GCGGCGTTTGTA-TCCAAAAACGCCGCTA
1565491 ACATTAGCGA
Statistics
Matches: 284, Mismatches: 41, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
42 41 0.14
43 192 0.68
44 20 0.07
45 31 0.11
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:1568436 original size:50 final size:50
Alignment explanation
Indices: 1568376--1568475 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
1568366 AGCTCTAGAA
* *
1568376 TTGTTAAGTCAATTTAGACCAATTGGTTTATGCTTTGTCCTCTACAAACT
1 TTGTTAAGTCAATTTAGACCAATTAGTTTATGCTTTCTCCTCTACAAACT
1568426 TTGTTAAGTCAATTTAGACCAATTAGTTTATGCTTTCTCCTCTACAAACT
1 TTGTTAAGTCAATTTAGACCAATTAGTTTATGCTTTCTCCTCTACAAACT
1568476 AATCACAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (50 bp):
TTGTTAAGTCAATTTAGACCAATTAGTTTATGCTTTCTCCTCTACAAACT
Found at i:1571589 original size:5 final size:5
Alignment explanation
Indices: 1571574--1571613 Score: 64
Period size: 5 Copynumber: 8.0 Consensus size: 5
1571564 AAACGATTAC
1571574 TAAAA TAAAAA TAAAA T-AAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1571614 AGATAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
5 24 0.73
6 5 0.15
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:1571596 original size:9 final size:9
Alignment explanation
Indices: 1571582--1571658 Score: 61
Period size: 9 Copynumber: 8.4 Consensus size: 9
1571572 ACTAAAATAA
1571582 AAATAAAAT
1 AAATAAAAT
1571591 AAATAAAAT
1 AAATAAAAT
1571600 AAAATAAAAT
1 -AAATAAAAT
*
1571610 AAA-AAGAT
1 AAATAAAAT
*
1571618 AAAAAAAACT
1 AAATAAAA-T
*
1571628 CAAA-AAACT
1 -AAATAAAAT
1571637 AAATTAAAA-
1 AAA-TAAAAT
*
1571646 AAAGAAAAT
1 AAATAAAAT
1571655 AAAT
1 AAAT
1571659 GAAAGTAGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
8 14 0.25
9 22 0.40
10 16 0.29
11 3 0.05
ACGTcount: A:0.77, C:0.04, G:0.03, T:0.17
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1571596 original size:15 final size:16
Alignment explanation
Indices: 1571574--1571614 Score: 68
Period size: 14 Copynumber: 2.7 Consensus size: 16
1571564 AAACGATTAC
1571574 TAAAATAAAAATAAAA
1 TAAAATAAAAATAAAA
1571590 T-AAAT-AAAATAAAA
1 TAAAATAAAAATAAAA
1571604 TAAAATAAAAA
1 TAAAATAAAAA
1571615 GATAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 10 0.43
15 8 0.35
16 5 0.22
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
TAAAATAAAAATAAAA
Found at i:1571605 original size:19 final size:18
Alignment explanation
Indices: 1571575--1571657 Score: 80
Period size: 19 Copynumber: 4.4 Consensus size: 18
1571565 AACGATTACT
1571575 AAAATAAAAATAAAATAAA
1 AAAAT-AAAATAAAATAAA
1571594 TAAAATAAAATAAAATAAA
1 -AAAATAAAATAAAATAAA
*
1571613 AAGATAAAA-AAAACTCAAA
1 AAAATAAAATAAAA-T-AAA
* *
1571632 AAACTAAATTAAAA-AAA
1 AAAATAAAATAAAATAAA
1571649 GAAAATAAA
1 -AAAATAAA
1571658 TGAAAGTAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
17 7 0.13
18 16 0.30
19 22 0.41
20 9 0.17
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (18 bp):
AAAATAAAATAAAATAAA
Found at i:1571622 original size:14 final size:12
Alignment explanation
Indices: 1571574--1571623 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 12
1571564 AAACGATTAC
1571574 TAAAAT-AAAAA
1 TAAAATAAAAAA
1571585 TAAAATAAATAAAA
1 TAAAAT-AA-AAAA
1571599 TAAAATAAAATAA
1 TAAAATAAAA-AA
1571612 -AAAGATAAAAAA
1 TAAA-ATAAAAAA
1571624 AACTCAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 6 0.18
12 7 0.21
13 11 0.32
14 10 0.29
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (12 bp):
TAAAATAAAAAA
Found at i:1571741 original size:11 final size:10
Alignment explanation
Indices: 1571725--1571778 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
1571715 AAAATTAGTT
1571725 AAATAAAAAGA
1 AAATAAAAA-A
1571736 AAATAAATAAA
1 AAATAAA-AAA
*
1571747 ATATAAAATAA
1 AAATAAAA-AA
*
1571758 AAAT-AAAAG
1 AAATAAAAAA
1571767 AAATAAAAAA
1 AAATAAAAAA
1571777 AA
1 AA
1571779 CAAAAACAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
9 5 0.14
10 10 0.28
11 19 0.53
12 2 0.06
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (10 bp):
AAATAAAAAA
Found at i:1571752 original size:22 final size:21
Alignment explanation
Indices: 1571727--1571778 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
1571717 AATTAGTTAA
1571727 ATAAAAAGAAAATAAATA-AAAT
1 ATAAAAA-AAAATAAA-AGAAAT
1571749 ATAAAATAAAAATAAAAGAAAT
1 ATAAAA-AAAAATAAAAGAAAT
1571771 A-AAAAAAA
1 ATAAAAAAA
1571779 CAAAAACAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 3 0.11
21 5 0.18
22 19 0.68
23 1 0.04
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (21 bp):
ATAAAAAAAAATAAAAGAAAT
Found at i:1571777 original size:18 final size:17
Alignment explanation
Indices: 1571729--1571802 Score: 60
Period size: 18 Copynumber: 4.2 Consensus size: 17
1571719 TTAGTTAAAT
*
1571729 AAAAAGAAAATAAATAA
1 AAAAAGAAAAAAAATAA
*
1571746 AATATAA-AATAAAAATAA
1 AA-A-AAGAAAAAAAATAA
* *
1571764 AAGAAATAAAAAAAACAA
1 AA-AAAGAAAAAAAATAA
*
1571782 AAACAGAAAAAATAATAA
1 AAAAAGAAAAAA-AATAA
1571800 AAA
1 AAA
1571803 TGTCGTATTA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
17 12 0.27
18 31 0.69
19 2 0.04
ACGTcount: A:0.81, C:0.03, G:0.04, T:0.12
Consensus pattern (17 bp):
AAAAAGAAAAAAAATAA
Found at i:1571783 original size:9 final size:9
Alignment explanation
Indices: 1571725--1571802 Score: 50
Period size: 9 Copynumber: 8.0 Consensus size: 9
1571715 AAAATTAGTT
1571725 AAATAAAAAGA
1 AAAT-AAAA-A
1571736 AAATAAATAA
1 AAATAAA-AA
1571746 AATATAAAATAA
1 AA-AT-AAA-AA
*
1571758 AAATAAAAG
1 AAATAAAAA
1571767 AAATAAAAA
1 AAATAAAAA
*
1571776 AAACAAAAA
1 AAATAAAAA
*
1571785 CAGA-AAAAA
1 -AAATAAAAA
*
1571794 TAATAAAAA
1 AAATAAAAA
1571803 TGTCGTATTA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.02
9 27 0.48
10 11 0.20
11 9 0.16
12 8 0.14
ACGTcount: A:0.81, C:0.03, G:0.04, T:0.13
Consensus pattern (9 bp):
AAATAAAAA
Found at i:1571817 original size:45 final size:43
Alignment explanation
Indices: 1571767--1571866 Score: 105
Period size: 45 Copynumber: 2.2 Consensus size: 43
1571757 AAAATAAAAG
1571767 AAATAAAAAAAACAAAAACAGAAAAAAT-AATAAAAATGTCGTA-TT
1 AAATAAAAAAAA-AAAAA-AGAAAAAATAAATAAAAATGT-G-ACTT
* * *
1571812 AAATAATAAACAAAAAATAATAAAAAATAAATTAAAATGTGACTT
1 AAATAA-AAA-AAAAAAAAAGAAAAAATAAATAAAAATGTGACTT
1571857 AAATAAAAAA
1 AAATAAAAAA
1571867 GGACTAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
43 1 0.02
44 4 0.08
45 23 0.48
46 17 0.35
47 3 0.06
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (43 bp):
AAATAAAAAAAAAAAAAAGAAAAAATAAATAAAAATGTGACTT
Found at i:1571843 original size:14 final size:15
Alignment explanation
Indices: 1571811--1571843 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1571801 AATGTCGTAT
1571811 TAAATAATAAACAAA
1 TAAATAATAAACAAA
1571826 -AAATAATAAA-AAA
1 TAAATAATAAACAAA
1571839 TAAAT
1 TAAAT
1571844 TAAAATGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAATAATAAACAAA
Found at i:1572961 original size:19 final size:18
Alignment explanation
Indices: 1572938--1572981 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
1572928 ATATATTAAT
1572938 TAATAAAATAAAAAATAA
1 TAATAAAATAAAAAATAA
* * *
1572956 TCAATATAATATATAATAA
1 T-AATAAAATAAAAAATAA
1572975 TAATAAA
1 TAATAAA
1572982 TCATTTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TAATAAAATAAAAAATAA
Found at i:1573037 original size:38 final size:38
Alignment explanation
Indices: 1572979--1573179 Score: 203
Period size: 38 Copynumber: 5.1 Consensus size: 38
1572969 TAATAATAAT
* * *
1572979 AAATCATTTTTAAAACTATAT-ATGATATATGCTTTCAA
1 AAATTATTTTCAAAACTATATAAT-ATATATGTTTTCAA
1573017 AAATTATTTTCGAAAA-TATATAATATATATGTTTTCAA
1 AAATTATTTTC-AAAACTATATAATATATATGTTTTCAA
1573055 AAATTATTTTTCAAGAACTATATATTATATATAT-TTTTCAA
1 AAATTA-TTTTCAA-AACTATATA--ATATATATGTTTTCAA
* * *
1573096 AAATTGTTTTCAAAACTATATAATATATATATATATATTTTAA
1 AAATTATTTTCAAAAC--TAT-ATA-ATATATATGT-TTTCAA
*
1573139 AAATTGATTTTCAAAACTATATAATATATGT-TTTTCAA
1 AAATT-ATTTTCAAAACTATATAATATATATGTTTTCAA
1573177 AAA
1 AAA
1573180 CCATTTTCTA
Statistics
Matches: 142, Mismatches: 8, Indels: 26
0.81 0.05 0.15
Matches are distributed among these distances:
38 43 0.30
39 17 0.12
40 20 0.14
41 27 0.19
42 15 0.11
43 10 0.07
44 10 0.07
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (38 bp):
AAATTATTTTCAAAACTATATAATATATATGTTTTCAA
Found at i:1573123 original size:44 final size:45
Alignment explanation
Indices: 1573031--1573167 Score: 164
Period size: 44 Copynumber: 3.2 Consensus size: 45
1573021 TATTTTCGAA
* * *
1573031 AATATATAATATATATGTTTTCAAAAATTATTTTTCAAGAAC----T
1 AATATATTATATATATATTTTCAAAAATT-GTTTTCAA-AACTATAT
1573074 -ATATATTATATATAT-TTTTCAAAAATTGTTTTCAAAACTATAT
1 AATATATTATATATATATTTTCAAAAATTGTTTTCAAAACTATAT
1573117 AATATA-TATATATATATTTT-AAAAATTGATTTTCAAAACTATAT
1 AATATATTATATATATATTTTCAAAAATTG-TTTTCAAAACTATAT
1573161 AATATAT
1 AATATAT
1573168 GTTTTTCAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 14
0.84 0.02 0.14
Matches are distributed among these distances:
39 3 0.04
40 7 0.08
41 12 0.14
42 14 0.17
43 18 0.21
44 30 0.36
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (45 bp):
AATATATTATATATATATTTTCAAAAATTGTTTTCAAAACTATAT
Found at i:1573166 original size:79 final size:74
Alignment explanation
Indices: 1572979--1573244 Score: 214
Period size: 81 Copynumber: 3.4 Consensus size: 74
1572969 TAATAATAAT
* * * *
1572979 AAATCATTTTTAAAACTATATATGATATATGCTTTCAAAAATTATTTTCGAAAATATATAATATA
1 AAATTATTTTCAAAACTATATAT-ATATAT-TTTTCAAAAATTATTTTCAAAAATATATAATATA
*
1573044 TATGTTTTCAA
64 TATATTTTCAA
*
1573055 AAATTATTTTTCAAGAACTATATATTATATATATTTTTCAAAAATTGTTTTCAAAACTATATAAT
1 AAATTA-TTTTCAA-AAC--TATA-TATATATATTTTTCAAAAATTATTTTCAAAA--ATAT-AT
*
1573120 ATATATATATATATTTTAA
58 A-ATATATATAT-TTTCAA
* ** **
1573139 AAATTGATTTTCAAAACTATATAATATATGTTTTTCAAAAACCATTTTCTAAAAATTATATGTTA
1 AAATT-ATTTTCAAAACTATAT-ATATATATTTTTCAAAAATTATTTTC-AAAAA-TATATAATA
** *
1573204 TACGT-TTTTCGA
62 TATATATTTTCAA
*
1573216 AAA-TATTTTCAAAAATATACTATAT-TATT
1 AAATTATTTTCAAAACTATA-TATATATATT
1573245 ATATATTAAA
Statistics
Matches: 156, Mismatches: 19, Indels: 32
0.75 0.09 0.15
Matches are distributed among these distances:
74 3 0.02
75 18 0.12
76 7 0.04
77 13 0.08
78 4 0.03
79 24 0.15
80 14 0.09
81 36 0.23
82 7 0.04
83 12 0.08
84 17 0.11
85 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (74 bp):
AAATTATTTTCAAAACTATATATATATATTTTTCAAAAATTATTTTCAAAAATATATAATATATA
TATTTTCAA
Found at i:1573187 original size:81 final size:86
Alignment explanation
Indices: 1573031--1573192 Score: 219
Period size: 81 Copynumber: 1.9 Consensus size: 86
1573021 TATTTTCGAA
*
1573031 AATATATAATATATATGTTTTCAAAAATTATTTTTCAAGAACTATATATTATATATATTTTTCAA
1 AATATATAATATATATATTTTCAAAAATTATTTTTCAAGAACTATATA-TATATATATTTTTCAA
***
1573096 AAATTGTTTTC-AAAACTATAT
65 AAACCATTTTCTAAAACTATAT
*
1573117 AATATAT-ATATATATATTTT-AAAAATTGA-TTTTCAA-AACTATATA-ATATATGTTTTTCAA
1 AATATATAATATATATATTTTCAAAAATT-ATTTTTCAAGAACTATATATATATATATTTTTCAA
1573177 AAACCATTTTCTAAAA
65 AAACCATTTTCTAAAA
1573193 ATTATATGTT
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
81 22 0.32
82 4 0.06
83 9 0.13
84 14 0.20
85 13 0.19
86 7 0.10
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (86 bp):
AATATATAATATATATATTTTCAAAAATTATTTTTCAAGAACTATATATATATATATTTTTCAAA
AACCATTTTCTAAAACTATAT
Found at i:1573199 original size:39 final size:39
Alignment explanation
Indices: 1572979--1573248 Score: 196
Period size: 39 Copynumber: 6.8 Consensus size: 39
1572969 TAATAATAAT
* * * * **
1572979 AAATCATTTTTAAAACTATATATGATATAT-GCTTTCAA
1 AAATTATTTTCAAAAATATATATAATATATATTTTTCAA
*
1573017 AAATTATTTTC-GAAA-ATATATAATATATATGTTTTCAA
1 AAATTATTTTCAAAAATATATATAATATATAT-TTTTCAA
* *
1573055 AAATTATTTTTCAAGAACTATATATTATATATATTTTTCAA
1 AAATTA-TTTTCAA-AAATATATATAATATATATTTTTCAA
*
1573096 AAATTGTTTTCAAAACTATATAATATATATATATATATTTT-AA
1 AAATTATTTTCAAAA--ATAT-ATATA-ATATATAT-TTTTCAA
* *
1573139 AAATTGATTTTC-AAAA-CTATATAATATATGTTTTTCAA
1 AAATT-ATTTTCAAAAATATATATAATATATATTTTTCAA
** ** ** *
1573177 AAACCATTTTCTAAAAAT-TATATGTTATACGTTTTTCGA
1 AAATTATTTTC-AAAAATATATATAATATATATTTTTCAA
*
1573216 AAA-TATTTTCAAAAATATACTATATTATTATAT
1 AAATTATTTTCAAAAATATA-TATAATA-TATAT
1573249 ATTAAAAAAA
Statistics
Matches: 187, Mismatches: 26, Indels: 36
0.75 0.10 0.14
Matches are distributed among these distances:
36 12 0.06
37 18 0.10
38 41 0.22
39 42 0.22
40 11 0.06
41 18 0.10
42 18 0.10
43 18 0.10
44 9 0.05
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (39 bp):
AAATTATTTTCAAAAATATATATAATATATATTTTTCAA
Found at i:1574022 original size:29 final size:30
Alignment explanation
Indices: 1573962--1574022 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
1573952 ATGTTGCCGT
1573962 AGGTCGCCATGCCATCCGGGGCGACCTTGG
1 AGGTCGCCATGCCATCCGGGGCGACCTTGG
* *
1573992 AGGTCGCCATGGCATCC-GGGCGAGCTTGG
1 AGGTCGCCATGCCATCCGGGGCGACCTTGG
1574021 AG
1 AG
1574023 TCTCTGCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (30 bp):
AGGTCGCCATGCCATCCGGGGCGACCTTGG
Found at i:1574050 original size:8 final size:8
Alignment explanation
Indices: 1574039--1574077 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
1574029 CATGTCTGTG
1574039 CATGGCAA
1 CATGGCAA
1574047 CATGGCAA
1 CATGGCAA
* *
1574055 CGTGGCAC
1 CATGGCAA
1574063 CATGGCAA
1 CATGGCAA
*
1574071 CGTGGCA
1 CATGGCA
1574078 TGGGTCTAGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.28, C:0.28, G:0.31, T:0.13
Consensus pattern (8 bp):
CATGGCAA
Found at i:1574066 original size:16 final size:16
Alignment explanation
Indices: 1574041--1574077 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1574031 TGTCTGTGCA
1574041 TGGCAACATGGCAACG
1 TGGCAACATGGCAACG
*
1574057 TGGCACCATGGCAACG
1 TGGCAACATGGCAACG
1574073 TGGCA
1 TGGCA
1574078 TGGGTCTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.32, T:0.14
Consensus pattern (16 bp):
TGGCAACATGGCAACG
Found at i:1574504 original size:8 final size:9
Alignment explanation
Indices: 1574474--1574511 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1574464 GAGGTAAGTT
1574474 TTTTAATTA
1 TTTTAATTA
1574483 TTTTAATTA
1 TTTTAATTA
*
1574492 GTTT-ATTA
1 TTTTAATTA
1574500 TTTTAAATTA
1 TTTT-AATTA
1574510 TT
1 TT
1574512 AGTTTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:1574633 original size:28 final size:27
Alignment explanation
Indices: 1574594--1574646 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
1574584 ATATTAAAAA
1574594 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
1574622 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
1574647 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:1574652 original size:27 final size:29
Alignment explanation
Indices: 1574593--1574657 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
1574583 TATATTAAAA
1574593 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
1574622 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
1574648 AAATAGTTAA
1 AAATAATTAA
1574658 GTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:1574875 original size:21 final size:21
Alignment explanation
Indices: 1574850--1574889 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1574840 GTTAATTAGT
*
1574850 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGGTTAAGTTATATTA
1574871 TTGTTAGGTTAAGTTATAT
1 TTGTTAGGTTAAGTTATAT
1574890 CATATAGAAA
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:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (21 bp):
TTGTTAGGTTAAGTTATATTA
Found at i:1575102 original size:22 final size:22
Alignment explanation
Indices: 1575076--1575157 Score: 83
Period size: 22 Copynumber: 3.4 Consensus size: 22
1575066 TTAGTTTTTT
1575076 TAGTTTAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
1575098 TAGTTTATTAGTTAAAGTTATATTAAAGAA
1 TAG-----T--TTA-AGTTATATTAAAGAA
*
1575128 TAGTTAAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
1575150 TAGTTTAA
1 TAGTTTAA
1575158 TAGTTGTTCA
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
22 25 0.50
23 2 0.04
25 1 0.02
27 1 0.02
29 3 0.06
30 18 0.36
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.41
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAGAA
Found at i:1575110 original size:30 final size:30
Alignment explanation
Indices: 1575075--1575132 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
1575065 ATTAGTTTTT
*
1575075 TTAGTTTAAGTTATATTAAAGAATAGTTTA
1 TTAGTTAAAGTTATATTAAAGAATAGTTTA
1575105 TTAGTTAAAGTTATATTAAAGAATAGTT
1 TTAGTTAAAGTTATATTAAAGAATAGTT
1575133 AAAGTTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (30 bp):
TTAGTTAAAGTTATATTAAAGAATAGTTTA
Found at i:1575125 original size:11 final size:11
Alignment explanation
Indices: 1575109--1575147 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1575099 AGTTTATTAG
1575109 TTAAAGTTATA
1 TTAAAGTTATA
*
1575120 TTAAAG-AATA
1 TTAAAGTTATA
1575130 GTTAAAGTTATA
1 -TTAAAGTTATA
1575142 TTAAAG
1 TTAAAG
1575148 AATAGTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (11 bp):
TTAAAGTTATA
Found at i:1575752 original size:29 final size:29
Alignment explanation
Indices: 1575710--1575777 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
1575700 TCATTTTCCG
1575710 TGTGGCGAATGTACGATAACTCTGGAGGA
1 TGTGGCGAATGTACGATAACTCTGGAGGA
1575739 TGTGGCGAATGTACGATAACTCTGGAGGA
1 TGTGGCGAATGTACGATAACTCTGGAGGA
1575768 TGTGGC-AATG
1 TGTGGCGAATG
1575778 CAACTCGGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
28 4 0.10
29 35 0.90
ACGTcount: A:0.26, C:0.13, G:0.35, T:0.25
Consensus pattern (29 bp):
TGTGGCGAATGTACGATAACTCTGGAGGA
Found at i:1577531 original size:17 final size:17
Alignment explanation
Indices: 1577511--1577552 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1577501 ATTAGTATCA
1577511 AATAATTAAATATTAAT
1 AATAATTAAATATTAAT
* * *
1577528 AATAAATCATTATTAAT
1 AATAATTAAATATTAAT
1577545 AATAATTA
1 AATAATTA
1577553 CTAAATCATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAATTAAATATTAAT
Found at i:1577545 original size:14 final size:14
Alignment explanation
Indices: 1577517--1577577 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 14
1577507 ATCAAATAAT
*
1577517 TAAAT-ATTAATAA
1 TAAATCATTATTAA
1577530 TAAATCATTATTAA
1 TAAATCATTATTAA
*
1577544 T-AAT-A--ATTAC
1 TAAATCATTATTAA
* *
1577554 TAAATCATTAGTAT
1 TAAATCATTATTAA
1577568 TAAATCATTA
1 TAAATCATTA
1577578 AATATTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
10 5 0.13
11 3 0.08
12 2 0.05
13 8 0.21
14 21 0.54
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.41
Consensus pattern (14 bp):
TAAATCATTATTAA
Found at i:1577564 original size:59 final size:57
Alignment explanation
Indices: 1577469--1577595 Score: 159
Period size: 59 Copynumber: 2.2 Consensus size: 57
1577459 TTTTAGTATC
*
1577469 AAATCATTATTATAATTTCATTACTAGTAATCATTAGTATCAAATAATTAAATATTAATAA
1 AAATCATTATTATAA-TTAATTACTAG-AATCATTAGTATCAAATAATTAAATATT--TAA
* *
1577530 TAAATCATTATTAATAA-TAATTACTA-AATCATTAGTATTAAATCATTAAATATTTAA
1 -AAATCATTATT-ATAATTAATTACTAGAATCATTAGTATCAAATAATTAAATATTTAA
1577587 AAATCATTA
1 AAATCATTA
1577596 ATAAATTCGA
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
56 9 0.15
57 3 0.05
59 26 0.43
61 8 0.13
62 11 0.18
63 4 0.07
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (57 bp):
AAATCATTATTATAATTAATTACTAGAATCATTAGTATCAAATAATTAAATATTTAA
Found at i:1577759 original size:26 final size:26
Alignment explanation
Indices: 1577680--1577936 Score: 214
Period size: 26 Copynumber: 10.0 Consensus size: 26
1577670 ATTAGTAATA
*
1577680 ATTATTAAATCATTACTATTAAATCATT
1 ATTATTAAATCATTATTA-T-AATCATT
* *
1577708 ATTATAAAATCATTACTA-AATCATT
1 ATTATTAAATCATTATTATAATCATT
* *
1577733 AGTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATCATT
1577759 ATTATTAAATCATTA-T-T-ATCATT
1 ATTATTAAATCATTATTATAATCATT
*
1577782 ATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATCATT
* *
1577808 ATTACTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATCATT
* * *
1577834 ATTATCAAATCATTACTA-AATCATCAA
1 ATTATTAAATCATTATTATAATCAT--T
* *
1577861 ATCATT--A-CA-TATTAAAATCATT
1 ATTATTAAATCATTATTATAATCATT
*
1577883 ATTA-T-AATGATTATTACTAAATCATT
1 ATTATTAAATCATTATTA-T-AATCATT
* *
1577909 ATTA-TAACTTCATTACTAGTAATCATT
1 ATTATTAA-ATCATTATTA-TAATCATT
1577936 A
1 A
1577937 GTAAATCATT
Statistics
Matches: 190, Mismatches: 25, Indels: 29
0.78 0.10 0.12
Matches are distributed among these distances:
21 1 0.01
22 4 0.02
23 25 0.13
24 15 0.08
25 30 0.16
26 77 0.41
27 13 0.07
28 25 0.13
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.44
Consensus pattern (26 bp):
ATTATTAAATCATTATTATAATCATT
Found at i:1577793 original size:49 final size:51
Alignment explanation
Indices: 1577687--1577915 Score: 69
Period size: 49 Copynumber: 4.5 Consensus size: 51
1577677 ATAATTATTA
* * * *
1577687 AATCATTACTATTAAATCATTATTATAA-AATCATTACTAAATCATTAGTATT
1 AATCATTATTATTAAATCATTATTATAATGATTATTATTAAATCATTA-TA-T
* *
1577739 AAATCATTATTA-T-AATGATTATTATTAA--ATCATTATT--ATCATTATTATT
1 -AATCATTATTATTAAATCATTATTA-TAATGATTATTATTAAATCATTA-TA-T
* * *
1577788 AAATCATTATTA-T-AATGATTATTACTAA--ATCATTATTATAATGATTAT-T
1 -AATCATTATTATTAAATCATTATTA-TAATGATTATTATTA-AATCATTATAT
* * * * *
1577837 -ATCAAATCATTACTAAATC---ATCA-AATCATTACATATTAAAATCATTATTAT
1 AATC--ATTATTATTAAATCATTATTATAATGATTA-TTATT-AAATCATTA-TAT
* *
1577888 AATGATTATTACTAAATCATTATTATAA
1 AATCATTATTATTAAATCATTATTATAA
1577916 CTTCATTACT
Statistics
Matches: 142, Mismatches: 15, Indels: 37
0.73 0.08 0.19
Matches are distributed among these distances:
46 2 0.01
47 3 0.02
48 6 0.04
49 65 0.46
50 16 0.11
51 23 0.16
52 12 0.08
53 13 0.09
54 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (51 bp):
AATCATTATTATTAAATCATTATTATAATGATTATTATTAAATCATTATAT
Found at i:1577874 original size:75 final size:74
Alignment explanation
Indices: 1577667--1577926 Score: 196
Period size: 75 Copynumber: 3.4 Consensus size: 74
1577657 TTATTTCATA
* * * * *
1577667 ATTATTAGTAATAATTA-T-TAAATCATTACTATTAAATCATTATTATAAAATCATTACT-AAAT
1 ATTATTA-TAATGATTATTATAAATCATTAC---TAAATCATAATCAT-TAATCATTATTAAAAT
*
1577729 CATTAGTATTAAATC
61 CATTATTA-TAAATC
* * * * *
1577744 ATTATTATAATGATTATTATTAAATCATTA-T-TATCATTATTATTAAATCATTATTATAATGAT
1 ATTATTATAATGATTATTA-TAAATCATTACTAAATCATAATCATT-AATCATTATTAAAATCAT
1577807 TATTACTAAATC
64 TATTA-TAAATC
1577819 ATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATT-A-CA-TATTAAAATCA
1 ATTATTATAATGATTATTAT-AAATCATTACTAAATCAT--AATCATTAATCATTATTAAAATCA
*
1577881 TTATTAT-AATG
63 TTATTATAAATC
* *
1577892 ATTATTACTAAATCATTATTATAACTTCATTACTA
1 ATTATTA-T-AATGATTATTATAA-ATCATTACTA
1577927 GTAATCATTA
Statistics
Matches: 154, Mismatches: 16, Indels: 28
0.78 0.08 0.14
Matches are distributed among these distances:
73 10 0.06
74 25 0.16
75 79 0.51
76 11 0.07
77 14 0.09
79 15 0.10
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (74 bp):
ATTATTATAATGATTATTATAAATCATTACTAAATCATAATCATTAATCATTATTAAAATCATTA
TTATAAATC
Found at i:1577921 original size:14 final size:12
Alignment explanation
Indices: 1577667--1577947 Score: 180
Period size: 14 Copynumber: 22.3 Consensus size: 12
1577657 TTATTTCATA
*
1577667 ATTATTAGTAATA
1 ATTATTA-TAATC
1577680 ATTATTA-AATC
1 ATTATTATAATC
*
1577691 ATTACTATTAAATC
1 ATTATTA-T-AATC
1577705 ATTATTATAAAATC
1 ATTATTAT--AATC
*
1577719 ATTACTA-AATC
1 ATTATTATAATC
*
1577730 ATTAGTATTAAATC
1 ATTATTA-T-AATC
*
1577744 ATTATTATAATG
1 ATTATTATAATC
1577756 ATTATTATTAAATC
1 ATTATTA-T-AATC
* *
1577770 ATTATTATCATT
1 ATTATTATAATC
1577782 ATTATTA-AATC
1 ATTATTATAATC
*
1577793 ATTATTATAATG
1 ATTATTATAATC
1577805 ATTATTACTAAATC
1 ATTATTA-T-AATC
*
1577819 ATTATTATAATG
1 ATTATTATAATC
1577831 ATTATTATCAAATC
1 ATTATTAT--AATC
*
1577845 ATTACTA-AATC
1 ATTATTATAATC
* * *
1577856 ATCA-AATCATTAC
1 ATTATTAT-AAT-C
*
1577869 A-TATTAAAATC
1 ATTATTATAATC
*
1577880 ATTATTATAATG
1 ATTATTATAATC
1577892 ATTATTACTAAATC
1 ATTATTA-T-AATC
1577906 ATTATTATAACTTC
1 ATTATTATAA--TC
*
1577920 ATTACTAGTAATC
1 ATTATTA-TAATC
*
1577933 ATTAGTA-AATC
1 ATTATTATAATC
1577944 ATTA
1 ATTA
1577948 GTATCAAATA
Statistics
Matches: 215, Mismatches: 29, Indels: 50
0.73 0.10 0.17
Matches are distributed among these distances:
10 1 0.00
11 45 0.21
12 62 0.29
13 26 0.12
14 78 0.36
15 3 0.01
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (12 bp):
ATTATTATAATC
Found at i:1578102 original size:14 final size:14
Alignment explanation
Indices: 1578081--1578220 Score: 133
Period size: 14 Copynumber: 10.9 Consensus size: 14
1578071 ATTAGTAATA
1578081 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1578095 ACTATTAAATCATT
1 ATTATTAAATCATT
*
1578109 ATTA-TAAA--ATC
1 ATTATTAAATCATT
*
1578120 ATTACTAAATCATT
1 ATTATTAAATCATT
*
1578134 AGTATTAAATCATT
1 ATTATTAAATCATT
*
1578148 ATTA-T-AATGATT
1 ATTATTAAATCATT
1578160 ATTATTAAATC---
1 ATTATTAAATCATT
1578171 ATTATT--ATCATT
1 ATTATTAAATCATT
1578183 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1578197 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1578209 ATTACTAAATCA
1 ATTATTAAATCA
1578221 GACAAGTCAT
Statistics
Matches: 103, Mismatches: 11, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
9 3 0.03
11 12 0.12
12 30 0.29
13 8 0.08
14 50 0.49
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.46
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:1578160 original size:26 final size:26
Alignment explanation
Indices: 1578081--1578220 Score: 171
Period size: 26 Copynumber: 5.5 Consensus size: 26
1578071 ATTAGTAATA
1578081 ATTATTAAATCATTACTATTAAATCATT
1 ATTATTAAATCATTACTA-T-AATCATT
*
1578109 ATTATAAAATCATTACTA-AATCATT
1 ATTATTAAATCATTACTATAATCATT
* * *
1578134 AGTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTACTATAATCATT
1578160 ATTATTAAATCATTA-T-T-ATCATT
1 ATTATTAAATCATTACTATAATCATT
* *
1578183 ATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTACTATAATCATT
*
1578209 ATTACTAAATCA
1 ATTATTAAATCA
1578221 GACAAGTCAT
Statistics
Matches: 99, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.20
24 2 0.02
25 24 0.24
26 36 0.36
28 17 0.17
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTATTAAATCATTACTATAATCATT
Found at i:1578231 original size:49 final size:48
Alignment explanation
Indices: 1578081--1578235 Score: 177
Period size: 49 Copynumber: 3.1 Consensus size: 48
1578071 ATTAGTAATA
* *
1578081 ATTATTAAATCATTACTATTAAATCATTATTATAAAATCATTACTAAATCATT
1 ATTATTAAATCATTATTA-T-AATGATTATTAT-AAATCATTAC--AATCATT
* **
1578134 AGTATTAAATCATTATTATAATGATTATTATTAAATCATTATTATCATT
1 ATTATTAAATCATTATTATAATGATTATTA-TAAATCATTACAATCATT
*
1578183 ATTATTAAATCATTATTATAATGATTATTACTAAATCA-GACAAGTCATT
1 ATTATTAAATCATTATTATAATGATTATTA-TAAATCATTACAA-TCATT
1578232 ATTA
1 ATTA
1578236 CAAATCAAAC
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
48 2 0.02
49 51 0.57
51 19 0.21
52 2 0.02
53 16 0.18
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (48 bp):
ATTATTAAATCATTATTATAATGATTATTATAAATCATTACAATCATT
Found at i:1578247 original size:22 final size:23
Alignment explanation
Indices: 1578206--1578249 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1578196 TATTATAATG
*
1578206 ATTATTACTAAATCAGACAAGTC
1 ATTATTACTAAATCAAACAAGTC
1578229 ATTATTAC-AAATCAAACAAGT
1 ATTATTACTAAATCAAACAAGT
1578250 GTTCCGTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.30
Consensus pattern (23 bp):
ATTATTACTAAATCAAACAAGTC
Found at i:1581120 original size:16 final size:16
Alignment explanation
Indices: 1581099--1581139 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
1581089 AATCATTTAG
1581099 TAATGATTACTAATAA
1 TAATGATTACTAATAA
1581115 TAATGATTACTAATAA
1 TAATGATTACTAATAA
1581131 TAATGATTA
1 TAATGATTA
1581140 GTTTGATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (16 bp):
TAATGATTACTAATAA
Done.