Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008797.1 Hibiscus syriacus cultivar Beakdansim tig00111942_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: 1112200
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 5 of 5
Found at i:901481 original size:186 final size:186
Alignment explanation
Indices: 901167--901553 Score: 506
Period size: 186 Copynumber: 2.1 Consensus size: 186
901157 AACAATCCTT
* * *
901167 GGATTTCAACTTCACGACAAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCATCC
1 GGATTTCAACTTCACAACAAAGGATATCCAATTCAAGGCTCAACTTCAAAACGAAGGGGCCATCC
* * **
901232 ACGATTTCAACTTCACGATAAAGGATATTGTGCCCACCAGCAACATACAATACTTGGATTTCAAC
66 ACAATTTCAACTTCACGACAAAGGATATCATGCCCACCAGCAACATACAATACTTGGATTTCAAC
* * *
901297 TTCACGA-CAAAGAATATCCAATTCAAGGCTCAACTTTAGAACGAAGGGGTCATCCA
131 TTCACGATCAAAG-ATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCA
* * * * *
901353 GGATTTCAACTTCATAACGAATGATATCCGATTCGAGGCTCAACTTCAAAACGAAGGGGCCATCC
1 GGATTTCAACTTCACAACAAAGGATATCCAATTCAAGGCTCAACTTCAAAACGAAGGGGCCATCC
* * * * * * * *
901418 ATAATTTTAACTTCACGACGAATGATATCATGTCCACCAGTAATATACAATGCTTGGATTTCAAC
66 ACAATTTCAACTTCACGACAAAGGATATCATGCCCACCAGCAACATACAATACTTGGATTTCAAC
* * *
901483 TTCACGATGAATGATATCCAATTCAAGGCTTAACTTCACAACGAAGGGGCCATCCA
131 TTCACGATCAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCA
* *
901539 CGATTTTAACTTCAC
1 GGATTTCAACTTCAC
901554 GACGAAAAAT
Statistics
Matches: 171, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
186 168 0.98
187 3 0.02
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (186 bp):
GGATTTCAACTTCACAACAAAGGATATCCAATTCAAGGCTCAACTTCAAAACGAAGGGGCCATCC
ACAATTTCAACTTCACGACAAAGGATATCATGCCCACCAGCAACATACAATACTTGGATTTCAAC
TTCACGATCAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCA
Found at i:901572 original size:120 final size:120
Alignment explanation
Indices: 901353--901675 Score: 475
Period size: 120 Copynumber: 2.7 Consensus size: 120
901343 GGGTCATCCA
** * * * *
901353 GGATTTCAACTTCATAACGAATGATATCCGATTCGAGGCTCAACTTCAAAACGAAGGGGCCATCC
1 GGATTTCAACTTCACGATGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCC
** * * *
901418 ATAATTTTAACTTCACGACGAATGATATCATGTCCACCAGTAATATACAATGCTT
66 ATAATTTTAACTTCACGACGAAAAATATCATGTCCACCAGTAACATACAATACAT
*
901473 GGATTTCAACTTCACGATGAATGATATCCAATTCAAGGCTTAACTTCACAACGAAGGGGCCATCC
1 GGATTTCAACTTCACGATGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCC
** **
901538 ACGATTTTAACTTCACGACGAAAAATATTGTGTCCACCAGTAACATACAATACAT
66 ATAATTTTAACTTCACGACGAAAAATATCATGTCCACCAGTAACATACAATACAT
* *
901593 GGATTTCAACTTCACGATGAAGGATATCTAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCC
1 GGATTTCAACTTCACGATGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCC
*
901658 ATAATTTCAACTTCACGA
66 ATAATTTTAACTTCACGA
901676 TGAAGGATAT
Statistics
Matches: 181, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
120 181 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (120 bp):
GGATTTCAACTTCACGATGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCC
ATAATTTTAACTTCACGACGAAAAATATCATGTCCACCAGTAACATACAATACAT
Found at i:901600 original size:306 final size:306
Alignment explanation
Indices: 901060--901752 Score: 897
Period size: 306 Copynumber: 2.3 Consensus size: 306
901050 TCTAGATTGG
* * * * ** * * *
901060 ATTTCAACTTCACGACGAATGACATCCACTTCAAATCTCAACTTCACAACGAAGGAGCCATCCAC
1 ATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAACTTCAAAACGAAGGGGCCATCCAT
* *
901125 GATTTCAACTTCACGACGAAGGATATCATG----CC------A-ACAATCCTTGGATTTCAACTT
66 AATTTCAACTCCACGACGAAGGATATCATGTCCACCAGTAATATACAATCCTTGGATTTCAACTT
*
901179 CACGACAAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCATCCACGATTTCAACT
131 CACGACAAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTCAACT
* * *
901244 TCACGATAAAGGATATTGTGCCCACCAGCAACATACAATACTTGGATTTCAACTTCACGACAAAG
196 TCACGAGAAAGAATATTGTGCCCACCAGCAACATACAATACATGGATTTCAACTTCACGACAAAG
* * * *
901309 AATATCCAATTCAAGGCTCAACTTTAGAACGAAGGGGTCATCCAGG
261 AATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCAGA
* * * *
901355 ATTTCAACTTCATAACGAATGATATCCGATTCGAGGCTCAACTTCAAAACGAAGGGGCCATCCAT
1 ATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAACTTCAAAACGAAGGGGCCATCCAT
* * * *
901420 AATTTTAACTTCACGACGAATGATATCATGTCCACCAGTAATATACAATGCTTGGATTTCAACTT
66 AATTTCAACTCCACGACGAAGGATATCATGTCCACCAGTAATATACAATCCTTGGATTTCAACTT
** * * *
901485 CACGATGAATGATATCCAATTCAAGGCTTAACTTCACAACGAAGGGGCCATCCACGATTTTAACT
131 CACGACAAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTCAACT
* * **
901550 TCACGACGAAA-AATATTGTGTCCACCAGTAACATACAATACATGGATTTCAACTTCACGATGAA
196 TCACGA-GAAAGAATATTGTGCCCACCAGCAACATACAATACATGGATTTCAACTTCACGACAAA
* * *
901614 GGATATCTAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCATA
260 GAATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCAGA
* * *
901661 ATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCAT
1 ATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAACTTCAAAACGAAGGGGCCATCCAT
* *
901726 GATTTCAACTCCACGACGGAGGATATC
66 AATTTCAACTCCACGACGAAGGATATC
901753 GTGCCCACAA
Statistics
Matches: 339, Mismatches: 47, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
295 81 0.24
299 2 0.01
305 1 0.00
306 252 0.74
307 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (306 bp):
ATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAACTTCAAAACGAAGGGGCCATCCAT
AATTTCAACTCCACGACGAAGGATATCATGTCCACCAGTAATATACAATCCTTGGATTTCAACTT
CACGACAAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTCAACT
TCACGAGAAAGAATATTGTGCCCACCAGCAACATACAATACATGGATTTCAACTTCACGACAAAG
AATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCAGA
Found at i:901673 original size:32 final size:32
Alignment explanation
Indices: 901632--901735 Score: 95
Period size: 32 Copynumber: 3.2 Consensus size: 32
901622 AATTCAAGGC
901632 TCAACTTCACAACGAAGGGGCCATCCATAATT
1 TCAACTTCACAACGAAGGGGCCATCCATAATT
* * ** **
901664 TCAACTTCACGATGAA--GGATATCCAATTCAAGGC
1 TCAACTTCACAACGAAGGGGCCATCC-A-T-AA-TT
*
901698 TCAACTTCACAACGAAGGGGCCATCCATGATT
1 TCAACTTCACAACGAAGGGGCCATCCATAATT
901730 TCAACT
1 TCAACT
901736 CCACGACGGA
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
30 6 0.11
31 1 0.02
32 21 0.40
33 3 0.06
34 15 0.28
35 1 0.02
36 6 0.11
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (32 bp):
TCAACTTCACAACGAAGGGGCCATCCATAATT
Found at i:901715 original size:34 final size:34
Alignment explanation
Indices: 901598--901715 Score: 109
Period size: 34 Copynumber: 3.5 Consensus size: 34
901588 TACATGGATT
* * *
901598 TCAACTTCACGATGAAGGATATCTAATTCAAGGC
1 TCAACTTCACAACGAAGGATATCCAATTCAAGGC
** **
901632 TCAACTTCACAACGAAGGGGCCATCC-A-T-AA-TT
1 TCAACTTCACAACGAA--GGATATCCAATTCAAGGC
* *
901664 TCAACTTCACGATGAAGGATATCCAATTCAAGGC
1 TCAACTTCACAACGAAGGATATCCAATTCAAGGC
901698 TCAACTTCACAACGAAGG
1 TCAACTTCACAACGAAGG
901716 GGCCATCCAT
Statistics
Matches: 63, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
30 6 0.10
31 1 0.02
32 15 0.24
33 4 0.06
34 31 0.49
35 1 0.02
36 5 0.08
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.23
Consensus pattern (34 bp):
TCAACTTCACAACGAAGGATATCCAATTCAAGGC
Found at i:903816 original size:18 final size:19
Alignment explanation
Indices: 903787--903822 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
903777 TTGTTTATGT
903787 AAATATTATATTTAATTAC
1 AAATATTATATTTAATTAC
*
903806 AAATA-TATATTTTATTA
1 AAATATTATATTTAATTA
903823 TTTTTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATATTATATTTAATTAC
Found at i:903939 original size:14 final size:14
Alignment explanation
Indices: 903920--903946 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
903910 CCTTTTGTTT
903920 TTTTACTTATTTTA
1 TTTTACTTATTTTA
903934 TTTTACTTATTTT
1 TTTTACTTATTTT
903947 TTTATTTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTACTTATTTTA
Found at i:903946 original size:23 final size:23
Alignment explanation
Indices: 903920--903966 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
903910 CCTTTTGTTT
*
903920 TTTTACTTATTT-TATTTTACTTA
1 TTTT-CTTATTTATATTGTACTTA
*
903943 TTTTTTTATTTATATTGTACTTA
1 TTTTCTTATTTATATTGTACTTA
903966 T
1 T
903967 CTTGTTTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTTCTTATTTATATTGTACTTA
Found at i:903955 original size:26 final size:26
Alignment explanation
Indices: 903917--904049 Score: 80
Period size: 26 Copynumber: 5.0 Consensus size: 26
903907 ATACCTTTTG
*
903917 TTTTTTTACTTATTTTA-TTTTACTTA
1 TTTTTTTATTTATTTTATTTTTA-TTA
*
903943 TTTTTTTATTTA---TA-TTGTACTTA
1 TTTTTTTATTTATTTTATTTTTA-TTA
* *
903966 TCTTGTTTACCTTTCTTTTATTTTTATTA
1 T-TTTTTTA--TTTATTTTATTTTTATTA
903995 CCTTTATTTTATTTTATTTTATTTTTATT-
1 --TTT-TTTTA-TTTATTTTATTTTTATTA
* *
904024 TTATTTTTATTTATTTTCTATTTATT
1 TT-TTTTTATTTATTTTATTTTTATT
904050 TTTATCTTAT
Statistics
Matches: 86, Mismatches: 10, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
23 11 0.13
24 6 0.07
26 29 0.34
27 7 0.08
28 1 0.01
29 5 0.06
30 22 0.26
31 5 0.06
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.73
Consensus pattern (26 bp):
TTTTTTTATTTATTTTATTTTTATTA
Found at i:903986 original size:20 final size:20
Alignment explanation
Indices: 903963--904012 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
903953 TATATTGTAC
*
903963 TTATCTTGT-TTACCTTTCTT
1 TTAT-TTGTATTACCTTTATT
*
903983 TTATTTTTATTACCTTTATT
1 TTATTTGTATTACCTTTATT
904003 TTATTT-TATT
1 TTATTTGTATT
904013 TTATTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.70
Consensus pattern (20 bp):
TTATTTGTATTACCTTTATT
Found at i:904005 original size:5 final size:5
Alignment explanation
Indices: 903997--904062 Score: 71
Period size: 5 Copynumber: 12.6 Consensus size: 5
903987 TTTTATTACC
*
903997 TTTAT TTTAT TTTAT TTTATT TTTAT TTTAT TTT-T ATTTAT TTTCT ATTTATT
1 TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT -TTTAT TTTAT -TTTA-T
*
904050 TTTAT CTTAT TTT
1 TTTAT TTTAT TTT
904063 CTATTTATGT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
4 1 0.02
5 37 0.71
6 13 0.25
7 1 0.02
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:904022 original size:11 final size:11
Alignment explanation
Indices: 903997--904078 Score: 98
Period size: 11 Copynumber: 7.5 Consensus size: 11
903987 TTTTATTACC
903997 TTTATTTTA-T
1 TTTATTTTATT
904007 TTTATTTTATT
1 TTTATTTTATT
904018 TTTATTTTATT
1 TTTATTTTATT
904029 TTTA-TTTATT
1 TTTATTTTATT
904039 TTCTA-TTTATT
1 TT-TATTTTATT
*
904050 TTTATCTTATT
1 TTTATTTTATT
*
904061 TTCTATTTATGTT
1 TT-TATTT-TATT
904074 TTTAT
1 TTTAT
904079 CTCTTTTTTA
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
10 19 0.30
11 33 0.52
12 7 0.11
13 5 0.08
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:904086 original size:24 final size:22
Alignment explanation
Indices: 904002--904080 Score: 101
Period size: 21 Copynumber: 3.6 Consensus size: 22
903992 TTACCTTTAT
*
904002 TTTA-TTTTATTTTATTTT-TA
1 TTTATTTTTATCTTATTTTCTA
904022 TTTTATTTTTAT-TTATTTTCTA
1 -TTTATTTTTATCTTATTTTCTA
904044 TTTATTTTTATCTTATTTTCTA
1 TTTATTTTTATCTTATTTTCTA
904066 TTTATGTTTTTATCT
1 TTTA--TTTTTATCT
904081 CTTTTTTATC
Statistics
Matches: 53, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
21 22 0.42
22 22 0.42
24 9 0.17
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (22 bp):
TTTATTTTTATCTTATTTTCTA
Found at i:904123 original size:10 final size:9
Alignment explanation
Indices: 903981--904124 Score: 83
Period size: 11 Copynumber: 14.2 Consensus size: 9
903971 TTTACCTTTC
903981 TTTTATTTT
1 TTTTATTTT
* *
903990 TATTACCTTTA
1 TTTTA--TTTT
904001 TTTTATTTT
1 TTTTATTTT
904010 ATTTTATTTTT
1 -TTTTA-TTTT
904021 ATTTTATTTT
1 -TTTTATTTT
904031 TATTTATTTT
1 T-TTTATTTT
904041 CTATTTATTTT
1 -T-TTTATTTT
904052 TATCTTATTTT
1 T-T-TTATTTT
*
904063 CTATTTA-TGT
1 -T-TTTATTTT
904073 TTTTATCTCTT
1 TTTTAT-T-TT
904084 TTTTATCTTT
1 TTTTAT-TTT
*
904094 GTTTCATTTGT
1 -TTTTATTT-T
904105 TTTTATTTT
1 TTTTATTTT
*
904114 CTTTATTTT
1 TTTTATTTT
904123 TT
1 TT
904125 GTATATATAT
Statistics
Matches: 112, Mismatches: 10, Indels: 26
0.76 0.07 0.18
Matches are distributed among these distances:
8 4 0.04
9 19 0.17
10 34 0.30
11 52 0.46
12 3 0.03
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTTATTTT
Found at i:904131 original size:2 final size:2
Alignment explanation
Indices: 904126--904150 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
904116 TTATTTTTTG
904126 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
904151 TATCTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:915219 original size:12 final size:12
Alignment explanation
Indices: 915204--915229 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
915194 AACTAGTTAC
915204 AAGAATAGTATT
1 AAGAATAGTATT
915216 AAGAATAGTATT
1 AAGAATAGTATT
915228 AA
1 AA
915230 TGGATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (12 bp):
AAGAATAGTATT
Found at i:919648 original size:17 final size:17
Alignment explanation
Indices: 919621--919659 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
919611 AATTTACAAT
919621 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
919637 TAATTATAAATAATATC
1 TAATTATAAATAATATC
919654 TAATTA
1 TAATTA
919660 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:919735 original size:11 final size:11
Alignment explanation
Indices: 919719--919743 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
919709 AATATTGATT
919719 TGGGTTTTAAA
1 TGGGTTTTAAA
919730 TGGGTTTTAAA
1 TGGGTTTTAAA
919741 TGG
1 TGG
919744 ATTGGGTCTC
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:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (11 bp):
TGGGTTTTAAA
Found at i:921396 original size:2 final size:2
Alignment explanation
Indices: 921389--921418 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
921379 ATGACATCAT
921389 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
921419 AAAAGCATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:923016 original size:3 final size:3
Alignment explanation
Indices: 923010--923065 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
923000 TTTTTATATA
** * *
923010 TAT TAT TAT TAT CGT TAT T-T TAAT TAT TAT TAT TAG CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
923055 TAT TAT T-T TAT
1 TAT TAT TAT TAT
923066 ATACATATTA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 4 0.10
3 36 0.86
4 2 0.05
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:924600 original size:28 final size:28
Alignment explanation
Indices: 924533--924606 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
924523 TCTATTTGGC
924533 CCTTTAAGTTTCTGTTTTCCATTTTAGT
1 CCTTTAAGTTTCTGTTTTCCATTTTAGT
* * *
924561 CCTCTAACTTTCTGTTTTAGC-TTTTAGT
1 CCTTTAAGTTTCTGTTTT-CCATTTTAGT
* *
924589 TCTTTATGTTTCTGTTTT
1 CCTTTAAGTTTCTGTTTT
924607 TATTATTTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 37 0.97
29 1 0.03
ACGTcount: A:0.12, C:0.18, G:0.11, T:0.59
Consensus pattern (28 bp):
CCTTTAAGTTTCTGTTTTCCATTTTAGT
Found at i:930809 original size:36 final size:34
Alignment explanation
Indices: 930764--930882 Score: 114
Period size: 36 Copynumber: 3.4 Consensus size: 34
930754 ACAAAGTTGA
*
930764 TCTCACTTGAGATCGTTTTCTCAAAAACAAACTTTG
1 TCTCACTTGAGA-C-TTTTCTCAAAAACAAATTTTG
* *
930800 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGAC-TTTTCTC-AAAAACAAATTTTG
* * * *
930836 TCTCATTTGAGACTATATCT-TAAAGCAAATTTTG
1 TCTCACTTGAGACT-TTTCTCAAAAACAAATTTTG
*
930870 TCTCGCTTGAGAC
1 TCTCACTTGAGAC
930883 ATCATTTTCT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 23 0.33
35 7 0.10
36 39 0.57
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (34 bp):
TCTCACTTGAGACTTTTCTCAAAAACAAATTTTG
Found at i:930870 original size:34 final size:36
Alignment explanation
Indices: 930782--930883 Score: 129
Period size: 36 Copynumber: 2.9 Consensus size: 36
930772 GAGATCGTTT
* *
930782 TCTC-AAAAACAAACTTTGTCTCGCTTGAGACAATT
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
** *
930817 TCTCTAAAAACAAATTTTGTCTCATTTGAGACTATA
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
*
930853 TCT-T-AAAGCAAATTTTGTCTCGCTTGAGACA
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
930884 TCATTTTCTC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 23 0.40
35 5 0.09
36 29 0.51
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (36 bp):
TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
Found at i:931983 original size:28 final size:28
Alignment explanation
Indices: 931952--932013 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
931942 GAAACACATT
931952 ATCTTTGAG-CTTGTTT-TTCTTAAAACAA
1 ATCTTTGAGTC-TGTTTCTT-TTAAAACAA
*
931980 ATCTTTGAGTCTGTTTCTTTTGAAACAA
1 ATCTTTGAGTCTGTTTCTTTTAAAACAA
932008 ATCTTT
1 ATCTTT
932014 AATTTGGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 28 0.90
29 3 0.10
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (28 bp):
ATCTTTGAGTCTGTTTCTTTTAAAACAA
Found at i:932023 original size:28 final size:28
Alignment explanation
Indices: 931963--932033 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
931953 TCTTTGAGCT
* * *
931963 TGTTTTTCTTAAAACAAATCTTTGAGTC
1 TGTTTCTCTTGAAACAAATCTTTGAATC
* *
931991 TGTTTCTTTTGAAACAAATCTTT-AATT
1 TGTTTCTCTTGAAACAAATCTTTGAATC
932018 TGGTTTCTCTTGAAAC
1 T-GTTTCTCTTGAAAC
932034 CATAACTCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
27 3 0.08
28 33 0.92
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (28 bp):
TGTTTCTCTTGAAACAAATCTTTGAATC
Found at i:932114 original size:40 final size:40
Alignment explanation
Indices: 932059--932376 Score: 194
Period size: 40 Copynumber: 7.5 Consensus size: 40
932049 TGGCCAGCCG
* *
932059 TCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCATCCCTAGACCAGATC
* * * *
932099 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCCCTAG---ACCAGATC
* *
932141 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCATC-CC--TAGA---CCAGATC
* * *
932188 TCTTCATCACGTATGAGCCGTGTCATTCCC-AGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCA-TCCCTAGACCAGATC
* * * *
932228 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCCCTAG---ACCAGATC
* * *
932270 ATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAAAAC
1 -TCCTCATCACGTAGGAACCGTGTCATC-CC--TAGA---CCAGATC
* * ** * *
932317 TCTTCATCACGTATGAGTCGTGTCATTCCC-CGACCAGATT
1 TCCTCATCACGTAGGAACCGTGTCA-TCCCTAGACCAGATC
932357 TCCTCATCACGTAGGAACCG
1 TCCTCATCACGTAGGAACCG
932377 CGTTAACCTT
Statistics
Matches: 213, Mismatches: 40, Indels: 50
0.70 0.13 0.17
Matches are distributed among these distances:
39 2 0.01
40 78 0.37
42 2 0.01
43 65 0.31
44 2 0.01
46 58 0.27
47 6 0.03
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCTAGACCAGATC
Found at i:932276 original size:129 final size:129
Alignment explanation
Indices: 932062--932372 Score: 541
Period size: 129 Copynumber: 2.4 Consensus size: 129
932052 CCAGCCGTCC
* * * *
932062 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
* *
932127 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAAAACTCT
932191 TCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
932256 ATAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAAAACTCT
66 ATAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAAAACTCT
* * *
932320 TCATCACGTATGAGTCGTGTCATTCCCCGACCAGATTTCCTCATCACGTAGGA
1 TCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTCATCACGTAGGA
932373 ACCGCGTTAA
Statistics
Matches: 173, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 173 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (129 bp):
TCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
ATAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAAAACTCT
Found at i:932591 original size:3 final size:3
Alignment explanation
Indices: 932585--932641 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
932575 TTTTTATATA
** * *
932585 TAT TAT TAT TAT CGT TAT T-T TAAT TAT TAT TAT TAG CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
932630 TAT TAT T-T TAT T
1 TAT TAT TAT TAT T
932642 TACATATTAC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:934164 original size:29 final size:29
Alignment explanation
Indices: 934118--934208 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 29
934108 GCCCTTTAAG
*
934118 TTTCTGTTTTTCCATTTTAGTCCTCTAAC
1 TTTCTGTTTTACCATTTTAGTCCTCTAAC
* * * * **
934147 TTTCTGTTTTAGCTTTTTAGTTCTTTATG
1 TTTCTGTTTTACCATTTTAGTCCTCTAAC
** * *
934176 TTTCTGTTTTTATTATTTTGGTCCTGTAAC
1 TTTCTG-TTTTACCATTTTAGTCCTCTAAC
934206 TTT
1 TTT
934209 TTTATTTATT
Statistics
Matches: 46, Mismatches: 15, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
29 28 0.61
30 18 0.39
ACGTcount: A:0.12, C:0.15, G:0.11, T:0.62
Consensus pattern (29 bp):
TTTCTGTTTTACCATTTTAGTCCTCTAAC
Found at i:938066 original size:21 final size:21
Alignment explanation
Indices: 938017--938080 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
938007 ATATGAAATT
*
938017 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
938038 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
938060 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
938081 ACCCTCGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:939234 original size:16 final size:16
Alignment explanation
Indices: 939198--939235 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
939188 TTCACGTTTA
939198 AGAGAAAAAGAAGATG
1 AGAGAAAAAGAAGATG
939214 A-AGAAAGAAGAA-ATG
1 AGAGAAA-AAGAAGATG
939229 AGAGAAA
1 AGAGAAA
939236 TTTGGAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (16 bp):
AGAGAAAAAGAAGATG
Found at i:946734 original size:16 final size:16
Alignment explanation
Indices: 946713--946761 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
946703 TACTGCCTTA
946713 TCTTAAAACAGTACAG
1 TCTTAAAACAGTACAG
946729 TCTTAAAACAGTACAG
1 TCTTAAAACAGTACAG
946745 TCTTAAAACAGTACAG
1 TCTTAAAACAGTACAG
946761 T
1 T
946762 TGGTTTTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (16 bp):
TCTTAAAACAGTACAG
Found at i:948547 original size:2 final size:2
Alignment explanation
Indices: 948540--948575 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
948530 GCTTATGGAG
948540 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
948576 ATTTTTGTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:949762 original size:23 final size:24
Alignment explanation
Indices: 949719--949765 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
949709 TTGTTAAAAA
*
949719 TAAACAAAATTGCTAATATGATAT
1 TAAAAAAAATTGCTAATATGATAT
949743 TAAAAAAAATT-C-AATGATGATAT
1 TAAAAAAAATTGCTAAT-ATGATAT
949766 GATATTATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 8 0.38
24 10 0.48
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (24 bp):
TAAAAAAAATTGCTAATATGATAT
Found at i:952751 original size:12 final size:12
Alignment explanation
Indices: 952730--952754 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
952720 GAAAATGATC
952730 CAAAAAATGCTT
1 CAAAAAATGCTT
952742 CAAAAAATGCTT
1 CAAAAAATGCTT
952754 C
1 C
952755 TTACACTTCG
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:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (12 bp):
CAAAAAATGCTT
Found at i:954444 original size:19 final size:20
Alignment explanation
Indices: 954412--954449 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
954402 AAAATCATAT
* *
954412 TTTTTTATTATTTACTTTAA
1 TTTTTAATTATTTAATTTAA
954432 TTTTTAATT-TTTAATTTA
1 TTTTTAATTATTTAATTTA
954450 TTATTTCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTAATTATTTAATTTAA
Found at i:955272 original size:21 final size:21
Alignment explanation
Indices: 955248--955301 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
955238 TATCGCAAAT
955248 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
955269 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
955290 TCGCGTTGCGAT
1 TCGCGTTGCGAT
955302 GGTCTACAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:955356 original size:20 final size:21
Alignment explanation
Indices: 955331--955382 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
955321 TTTTCCCAAT
*
955331 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
955351 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
955372 TCGCAATGCGA
1 TCGCAATGCGA
955383 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:955396 original size:20 final size:20
Alignment explanation
Indices: 955371--955505 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
955361 AATTGGGAAA
955371 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
955391 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
955411 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
955432 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
955452 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
955472 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
955492 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
955506 TTTCAAAGCG
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 66 0.69
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:955415 original size:61 final size:61
Alignment explanation
Indices: 955368--955499 Score: 183
Period size: 61 Copynumber: 2.2 Consensus size: 61
955358 GCGAATTGGG
* * * * *
955368 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
955429 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
955490 ATAATCGCAA
1 AAAATCGCAA
955500 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:955717 original size:20 final size:21
Alignment explanation
Indices: 955672--955719 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
955662 TCTCTCACCC
955672 ATCTCCGACGAAATCCGTCCCT
1 ATCTCCGACGAAATCCGT-CCT
*
955694 ATCTCCGGCGAAATCCGT-CT
1 ATCTCCGACGAAATCCGTCCT
955714 ATCTCC
1 ATCTCC
955720 ATCTCTCAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 8 0.32
22 17 0.68
ACGTcount: A:0.21, C:0.40, G:0.15, T:0.25
Consensus pattern (21 bp):
ATCTCCGACGAAATCCGTCCT
Found at i:956224 original size:25 final size:24
Alignment explanation
Indices: 956170--956224 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
956160 TGTTTATTAT
* *
956170 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
956194 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
956220 TGTTT
1 TGTTT
956225 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:957363 original size:18 final size:18
Alignment explanation
Indices: 957342--957386 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
957332 TCCACTTCGG
*
957342 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
957360 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
957378 GAGCCATCA
1 GAGCCATCA
957387 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:957922 original size:19 final size:20
Alignment explanation
Indices: 957868--957934 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
957858 TAGTTTACTT
* *
957868 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
957888 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
957908 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
957927 TCGCAACG
1 TCGCAACG
957935 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:957942 original size:14 final size:14
Alignment explanation
Indices: 957923--958013 Score: 65
Period size: 14 Copynumber: 5.9 Consensus size: 14
957913 ATGCGAAATG
957923 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
957937 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
*
957956 AAAACCGCAACGAC
1 AAAATCGCAACGAC
* *
957970 AAAATCGCAATGCAAA
1 AAAATCGCAA--CGAC
957986 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
958002 AAAATCGCAACG
1 AAAATCGCAACG
958014 CGAAACACAA
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
14 30 0.50
15 1 0.02
16 8 0.13
17 2 0.03
18 10 0.17
19 9 0.15
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:957949 original size:33 final size:33
Alignment explanation
Indices: 957907--958018 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
957897 GGAAATGGCT
957907 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
957940 ATCGCAATGCGAAATGAAAACCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
957973 ATCGCAATGCAAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
958005 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
958019 CACAAATCGC
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 27 0.36
33 47 0.64
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:957964 original size:19 final size:19
Alignment explanation
Indices: 957907--957997 Score: 69
Period size: 14 Copynumber: 5.4 Consensus size: 19
957897 GGAAATGGCT
957907 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
957926 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
957940 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
957959 ACCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
957973 ATCGCAATGCAAAATG-AA
1 ATCGCAATGCGAAATGAAA
957991 ATCGCAA
1 ATCGCAA
957998 CGACAAAATC
Statistics
Matches: 55, Mismatches: 7, Indels: 21
0.66 0.08 0.25
Matches are distributed among these distances:
14 19 0.35
15 2 0.04
16 3 0.05
17 4 0.07
18 11 0.20
19 16 0.29
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:958066 original size:14 final size:14
Alignment explanation
Indices: 958047--958104 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
958037 TTTCATTTCG
958047 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
958061 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
958077 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
958093 CGTTGCGATTTT
1 CGTTGCGATTTT
958105 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:958111 original size:33 final size:33
Alignment explanation
Indices: 958030--958120 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
958020 ACAAATCGCA
*
958030 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
958063 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
958095 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
958121 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:958135 original size:20 final size:19
Alignment explanation
Indices: 958105--958160 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
958095 TTGCGATTTT
958105 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
*
958124 CATTTCCGCATTGCGATAGT
1 CATTT-CGCATTGCGATAGC
*
958144 CATTTTCGCGTTGCGAT
1 CA-TTTCGCATTGCGAT
958161 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:960047 original size:14 final size:14
Alignment explanation
Indices: 960028--960063 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
960018 ATTGTTTAAT
960028 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
960042 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
960056 TGATTTGT
1 TGATTTGT
960064 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:960255 original size:19 final size:19
Alignment explanation
Indices: 960200--960248 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
960190 ATCGCAACGA
960200 GAAAATCGCAACGCGAAAT
1 GAAAATCGCAACGCGAAAT
* *
960219 AAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGCGAAAT
960238 GAAAATCGCAA
1 GAAAATCGCAA
960249 GGAGAAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.12
Consensus pattern (19 bp):
GAAAATCGCAACGCGAAAT
Found at i:960311 original size:20 final size:20
Alignment explanation
Indices: 960294--960381 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
960284 CGATTTTCTA
960294 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
960314 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
* *
960334 ATTGCGATAACCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
960354 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
960374 GTTGCGAT
1 GTTGCGAT
960382 TTCCCCGTTG
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
19 3 0.05
20 49 0.89
21 3 0.05
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:960620 original size:20 final size:20
Alignment explanation
Indices: 960595--960644 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
960585 TTGAAGATGA
960595 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
960615 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
960635 TTGCGATTTT
1 TTGCGATTTT
960645 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:960715 original size:20 final size:21
Alignment explanation
Indices: 960671--960722 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
960661 ATAGTCAGTA
*
960671 TCGCATTGCGATTGTCCAAAT
1 TCGCATTGCGATTGTACAAAT
**
960692 TCGCATTGCGATT-TACTTAT
1 TCGCATTGCGATTGTACAAAT
960712 TCGCATTGCGA
1 TCGCATTGCGA
960723 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTGTACAAAT
Found at i:960938 original size:12 final size:12
Alignment explanation
Indices: 960919--960952 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
960909 CTCTCTGGCG
960919 ACATCCGTTCCT
1 ACATCCGTTCCT
*
960931 ATATCCGTTCCT
1 ACATCCGTTCCT
960943 ACATCC-TTCC
1 ACATCCGTTCC
960953 CCATCCGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:961541 original size:24 final size:24
Alignment explanation
Indices: 961507--961560 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
961497 GTATTCGAAA
* *
961507 TTTGATCTTGGTTAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
961531 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
961555 TTTGAT
1 TTTGAT
961561 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:961752 original size:12 final size:12
Alignment explanation
Indices: 961735--961759 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
961725 ATATAATCCT
961735 GAAGAAGAAAAA
1 GAAGAAGAAAAA
961747 GAAGAAGAAAAA
1 GAAGAAGAAAAA
961759 G
1 G
961760 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:964073 original size:19 final size:19
Alignment explanation
Indices: 964051--964181 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
964041 GGAAATTACT
964051 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
964070 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
964084 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
964103 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
964117 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* **
964136 ATCGCAA--C--TA-GGGA
1 ATCGCAATGCGAAATGAAA
964150 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
964169 ATCGCAACGCGAA
1 ATCGCAATGCGAA
964182 TTTAATTTTG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 27 0.33
15 3 0.04
16 5 0.06
17 5 0.06
18 3 0.04
19 39 0.48
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:964093 original size:33 final size:33
Alignment explanation
Indices: 964051--964177 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
964041 GGAAATTACT
964051 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
964084 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
964116 TTTCGCAATGCGAAATGAAAATCGCAACTAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
964150 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
964178 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:964158 original size:66 final size:66
Alignment explanation
Indices: 964052--964184 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
964042 GAAATTACTA
*
964052 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
964117 T
66 T
* *
964118 TCGCAATGCGAAATGAAAATCGCAACTAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
964183 T
66 T
964184 T
1 T
964185 AATTTTGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:964199 original size:19 final size:19
Alignment explanation
Indices: 964177--964218 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
964167 AAATCGCAAC
*
964177 GCGAATTTAATTTTGCGTT
1 GCGAATTTAATTTCGCGTT
* *
964196 GCGATTTTCATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
964215 GCGA
1 GCGA
964219 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.43
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:964219 original size:19 final size:19
Alignment explanation
Indices: 964186--964252 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
964176 CGCGAATTTA
*
964186 ATTTTGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
964205 ATTTCGCGTTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
*
964222 ---TCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
964238 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
964253 AGTACTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 23 0.59
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:964378 original size:14 final size:14
Alignment explanation
Indices: 964359--964395 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
964349 CATCAATTAA
964359 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
964373 ACAAATCACCTTTT
1 ACAAATCAACTTTT
964387 ACAAATCAA
1 ACAAATCAA
964396 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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:965839 original size:42 final size:41
Alignment explanation
Indices: 965793--965954 Score: 180
Period size: 42 Copynumber: 3.9 Consensus size: 41
965783 ATGACAGTTA
* * *
965793 CCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATATGGG
1 CCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATA-GGG
* * * *
965835 CCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGG
1 CCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAG-GG
* * *
965877 CCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGG
1 CCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATA-GGG
* * *
965919 CCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 CCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
965955 CAGGCGAGTC
Statistics
Matches: 98, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
41 1 0.01
42 96 0.98
43 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (41 bp):
CCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGGG
Found at i:965893 original size:84 final size:84
Alignment explanation
Indices: 965782--965957 Score: 325
Period size: 84 Copynumber: 2.1 Consensus size: 84
965772 CCTCTACAAA
* *
965782 GATGACAGTTACCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATATGGGCCTCTTCAACGA
1 GATGACAGTGACCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
965847 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
*
965866 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGACCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
965931 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
965950 GATGACAG
1 GATGACAG
965958 GCGAGTCGGG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (84 bp):
GATGACAGTGACCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:966352 original size:91 final size:90
Alignment explanation
Indices: 966176--966360 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
966166 ATTTCAAACT
*
966176 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
*
966241 AGAATTGGCAGCAACTGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
966269 TTCAACCAAAAGACAAAACAAAAAGATAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
966333 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
966360 T
1 T
966361 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 41 0.48
93 19 0.22
95 26 0.30
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:968050 original size:20 final size:19
Alignment explanation
Indices: 968005--968145 Score: 86
Period size: 19 Copynumber: 7.8 Consensus size: 19
967995 TCTTTTGGTT
968005 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
968024 GATAATGAGAATCGCAACGTG
1 GA-AATGAAAATCGCAACG-A
** *
968045 GAAATGACTATCGTAACGA
1 GAAATGAAAATCGCAACGA
*
968064 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
968078 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
968097 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
968111 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
968130 GAAATGAAAATTGCAA
1 GAAATGAAAATCGCAA
968146 TGCGATTTTG
Statistics
Matches: 94, Mismatches: 16, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
14 18 0.19
16 4 0.04
17 4 0.04
19 38 0.40
20 28 0.30
21 2 0.02
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:968087 original size:33 final size:33
Alignment explanation
Indices: 968030--968128 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
968020 ACGAGATAAT
* *
968030 GAGAATCGCAACGTGGAAATGACTATCGTAACGA
1 GAGAATCGCAACG-CGAAATGACTATCGCAACGA
*
968064 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
968097 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
968129 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 46 0.78
34 13 0.22
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:968169 original size:18 final size:19
Alignment explanation
Indices: 968146--968189 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
968136 AAAATTGCAA
**
968146 TGCGATTTTGGTTTCGCG-
1 TGCGATTTTCATTTCGCGT
968164 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
968183 TGCGATT
1 TGCGATT
968190 CTCTCGTAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:968827 original size:20 final size:20
Alignment explanation
Indices: 968742--968855 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
968732 CGCTATGTAA
* * *
968742 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
*
968762 ATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
968782 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
968803 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
968823 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
968843 ATCGCATTGCGAT
1 ATCGCATTGCGAT
968856 TTTCCCAATT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 62 0.78
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:968840 original size:61 final size:61
Alignment explanation
Indices: 968742--968858 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
968732 CGCTATGTAA
* * * *
968742 ATCGCGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
968803 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
968859 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:968874 original size:61 final size:61
Alignment explanation
Indices: 968742--968876 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
968732 CGCTATGTAA
* * * * ** *
968742 ATCGCGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
968803 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
968865 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
968877 TTACTTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:968966 original size:21 final size:21
Alignment explanation
Indices: 968926--968966 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
968916 ACTGTAGACC
**
968926 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
968947 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
968967 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:975949 original size:10 final size:10
Alignment explanation
Indices: 975926--975958 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
975916 CCCTTTTTAC
975926 TTTTTA-TTT
1 TTTTTATTTT
*
975935 CTTTTATTTT
1 TTTTTATTTT
975945 TTTTTATTTT
1 TTTTTATTTT
975955 TTTT
1 TTTT
975959 CTTTCTTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 5 0.24
10 16 0.76
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:975993 original size:15 final size:16
Alignment explanation
Indices: 975970--976002 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
975960 TTTCTTCCTC
*
975970 TTTATTTTATAT-TAT
1 TTTACTTTATATATAT
975985 TTTACTTTATATATAT
1 TTTACTTTATATATAT
976001 TT
1 TT
976003 ACCTCTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTACTTTATATATAT
Found at i:977084 original size:13 final size:13
Alignment explanation
Indices: 977066--977095 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
977056 TTCCTTTACC
977066 ATTTATTTTATTT
1 ATTTATTTTATTT
*
977079 ATTTATTTTTTTT
1 ATTTATTTTATTT
977092 ATTT
1 ATTT
977096 CTATTTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
ATTTATTTTATTT
Found at i:987551 original size:105 final size:105
Alignment explanation
Indices: 987369--988126 Score: 1300
Period size: 105 Copynumber: 7.2 Consensus size: 105
987359 AGGTTTTACC
*
987369 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
987434 ACGAAGGGACCGCTGGTTGTCAACAAACATTTATCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTATCAATTT
* * * *
987474 CAGAGCCAATCTCAACTTCACAAAGAAGGATATTGGACCCCAGACAACGCAAGTTCAACTTCAAG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
987539 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTATCAATTT
*
987579 CAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
987644 ACGAAGGGACCGCTGGTTGTCAACAAACATTTATCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTATCAATTT
* *
987684 CAGAGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
987749 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTATCAATTT
987789 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
987854 ACGAAGGGACCGCTGGTTGTCAACAAACATTTATCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTATCAATTT
* *
987894 CAGAGCCAATCTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
987959 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTATCAATTT
*
987999 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * ** * *
988064 GCGAAGGGACCGCTGGTTGTCAATAAACGATTTCCCAGTTC
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTATCAATTT
* *
988105 CAGAACCAGTTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACA
988127 GTGGAGGGTA
Statistics
Matches: 618, Mismatches: 34, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
105 589 0.95
106 29 0.05
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTATCAATTT
Found at i:990593 original size:29 final size:30
Alignment explanation
Indices: 990534--990593 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
990524 TATAATTTCT
**
990534 ATAATATATTGTGGTATTTATTTATTTTTA
1 ATAATATATTGTGGTATTTATTTATAGTTA
*
990564 ATAA-ATATTGTGGTATTTATTTGTAGTTA
1 ATAATATATTGTGGTATTTATTTATAGTTA
990593 A
1 A
990594 AGTATATCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (30 bp):
ATAATATATTGTGGTATTTATTTATAGTTA
Found at i:991189 original size:16 final size:16
Alignment explanation
Indices: 991153--991191 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
991143 TTAAAAACTT
*
991153 AAAAAGATAATAAAGA
1 AAAAATATAATAAAGA
* *
991169 TAAAATATAATAAATA
1 AAAAATATAATAAAGA
991185 AAAAATA
1 AAAAATA
991192 ATGAATACTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (16 bp):
AAAAATATAATAAAGA
Found at i:995904 original size:2 final size:2
Alignment explanation
Indices: 995897--995923 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
995887 TAGGTAAATG
995897 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
995924 ACTATGAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:999610 original size:3 final size:3
Alignment explanation
Indices: 999598--999633 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
999588 TCCATATAAC
999598 TCT TCTT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
999634 ACCGTGAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:1001658 original size:20 final size:20
Alignment explanation
Indices: 1001633--1001675 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1001623 TCTAAAAGCC
1001633 CATTTAGGACCATATAGATG
1 CATTTAGGACCATATAGATG
* * *
1001653 CATTTAGTAGCATATAGTTG
1 CATTTAGGACCATATAGATG
1001673 CAT
1 CAT
1001676 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:1006885 original size:20 final size:20
Alignment explanation
Indices: 1006860--1006901 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1006850 CTAAAAGCCT
*
1006860 ATTTAGGATCATATAGATGC
1 ATTTAGGAGCATATAGATGC
* *
1006880 ATTTAGTAGCATATAGTTGC
1 ATTTAGGAGCATATAGATGC
1006900 AT
1 AT
1006902 GTGGTGGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (20 bp):
ATTTAGGAGCATATAGATGC
Found at i:1008382 original size:23 final size:23
Alignment explanation
Indices: 1008349--1008408 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1008339 GATAAACTTT
*
1008349 ACTTCGTTGCATTTCTATACGAC
1 ACTTCGGTGCATTTCTATACGAC
* * *
1008372 ACTTCGGTGCAATTCTATGCGGC
1 ACTTCGGTGCATTTCTATACGAC
1008395 ACTTCGGTGCATTT
1 ACTTCGGTGCATTT
1008409 ATACAGGCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (23 bp):
ACTTCGGTGCATTTCTATACGAC
Found at i:1010386 original size:12 final size:12
Alignment explanation
Indices: 1010371--1010395 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1010361 TGAGGCATTG
1010371 TATGGGAGGAAA
1 TATGGGAGGAAA
1010383 TATGGGAGGAAA
1 TATGGGAGGAAA
1010395 T
1 T
1010396 GCAAAACACC
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:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (12 bp):
TATGGGAGGAAA
Found at i:1023094 original size:13 final size:13
Alignment explanation
Indices: 1023068--1023104 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1023058 GCCTTTTTAC
1023068 GCAGGGATTTATTT
1 GCAGGGA-TTATTT
1023082 GCAGGGATTATTT
1 GCAGGGATTATTT
*
1023095 GCAAGGATTA
1 GCAGGGATTA
1023105 CTTCCCATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.27, C:0.08, G:0.30, T:0.35
Consensus pattern (13 bp):
GCAGGGATTATTT
Found at i:1028690 original size:33 final size:33
Alignment explanation
Indices: 1028653--1028888 Score: 174
Period size: 33 Copynumber: 7.5 Consensus size: 33
1028643 AAAAAATTTG
* *
1028653 GGGTCGGGTCGGGTTTTTTTAAGTTTGCTATTC
1 GGGTCGGGTCGGGTTTTTTTAAGTGTGATATTC
* * *
1028686 GGGTCTGGTCGGGTTTTTTTAAATGTGATATTA
1 GGGTCGGGTCGGGTTTTTTTAAGTGTGATATTC
* * *
1028719 GGGTCAGGTCGGGTTTCTTTAA-----AAATTC
1 GGGTCGGGTCGGGTTTTTTTAAGTGTGATATTC
* * * * *
1028747 GGGATCGGGTCGGATTTTTTT---TTTAAAAATC
1 GGG-TCGGGTCGGGTTTTTTTAAGTGTGATATTC
* * *
1028778 GAGGTTGGGTCGGGTTTTTTGAGGTGTG--A-T-
1 G-GGTCGGGTCGGGTTTTTTTAAGTGTGATATTC
* * *
1028808 -GTTCGGGTAGGGTTTTTTTAAGTATGATATTC
1 GGGTCGGGTCGGGTTTTTTTAAGTGTGATATTC
*
1028840 GGGTCGGGTCAGGTTTTTTTAAGTGTGATATTC
1 GGGTCGGGTCGGGTTTTTTTAAGTGTGATATTC
*
1028873 GGGTCGGTTCGGGTTT
1 GGGTCGGGTCGGGTTT
1028889 GGGGTGAAAA
Statistics
Matches: 159, Mismatches: 30, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
28 27 0.17
29 14 0.09
30 1 0.01
31 22 0.14
32 3 0.02
33 90 0.57
34 2 0.01
ACGTcount: A:0.15, C:0.09, G:0.33, T:0.42
Consensus pattern (33 bp):
GGGTCGGGTCGGGTTTTTTTAAGTGTGATATTC
Found at i:1028796 original size:31 final size:32
Alignment explanation
Indices: 1028736--1028797 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
1028726 GTCGGGTTTC
1028736 TTTAAAAATTCGGGATCGGGTCGGATTTTTTT
1 TTTAAAAATTCGGGATCGGGTCGGATTTTTTT
* *
1028768 TTTAAAAA-TCGAGG-TTGGGTCGGGTTTTTT
1 TTTAAAAATTCG-GGATCGGGTCGGATTTTTT
1028798 GAGGTGTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.21, C:0.08, G:0.27, T:0.44
Consensus pattern (32 bp):
TTTAAAAATTCGGGATCGGGTCGGATTTTTTT
Found at i:1028815 original size:28 final size:28
Alignment explanation
Indices: 1028784--1028848 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
1028774 AATCGAGGTT
* * *
1028784 GGGTCGGGTTTTTTGAGGTGTGATGTTC
1 GGGTCGGGTTTTTTGAAGTATGATATTC
* *
1028812 GGGTAGGGTTTTTTTAAGTATGATATTC
1 GGGTCGGGTTTTTTGAAGTATGATATTC
1028840 GGGTCGGGT
1 GGGTCGGGT
1028849 CAGGTTTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.12, C:0.06, G:0.40, T:0.42
Consensus pattern (28 bp):
GGGTCGGGTTTTTTGAAGTATGATATTC
Found at i:1028874 original size:28 final size:28
Alignment explanation
Indices: 1028784--1028881 Score: 83
Period size: 28 Copynumber: 3.4 Consensus size: 28
1028774 AATCGAGGTT
* * * *
1028784 GGGTCGGGTTTTTTGAGGTGTGATGTTC
1 GGGTCAGGTTTTTTTAAGTGTGATATTC
*
1028812 GGGT-AGGGTTTTTTTAAGTATGATATTCGGGTC
1 GGGTCA-GGTTTTTTTAAGTGTGATA-T----TC
1028845 GGGTCAGGTTTTTTTAAGTGTGATATTC
1 GGGTCAGGTTTTTTTAAGTGTGATATTC
1028873 GGGTC-GGTT
1 GGGTCAGGTT
1028882 CGGGTTTGGG
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
27 4 0.07
28 26 0.46
29 1 0.02
32 1 0.02
33 24 0.42
34 1 0.02
ACGTcount: A:0.13, C:0.07, G:0.37, T:0.43
Consensus pattern (28 bp):
GGGTCAGGTTTTTTTAAGTGTGATATTC
Found at i:1030904 original size:2 final size:2
Alignment explanation
Indices: 1030897--1030990 Score: 65
Period size: 2 Copynumber: 50.0 Consensus size: 2
1030887 TCGGGCCGGG
* * * *
1030897 TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA 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
* * * * *
1030938 TA TA TA TA TT TA -A TT TA -A TT TA AA TT TA T- TA -A TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1030975 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
1030991 ATAATTTTTT
Statistics
Matches: 68, Mismatches: 18, Indels: 12
0.69 0.18 0.12
Matches are distributed among these distances:
1 6 0.09
2 62 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1031110 original size:36 final size:36
Alignment explanation
Indices: 1031063--1031145 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
1031053 GATTATTAAA
*
1031063 CCCGTCCCCGTCCCCGTTTAACATAAACGATTTTTC
1 CCCGTCCCCGTCCCCATTTAACATAAACGATTTTTC
* *
1031099 CCCGTCCCCGTCCCCATTTAGCATAAACGGTTTTTC
1 CCCGTCCCCGTCCCCATTTAACATAAACGATTTTTC
1031135 CCCGTCCCCGT
1 CCCGTCCCCGT
1031146 TTAATTCGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.16, C:0.42, G:0.13, T:0.29
Consensus pattern (36 bp):
CCCGTCCCCGTCCCCATTTAACATAAACGATTTTTC
Found at i:1032272 original size:80 final size:80
Alignment explanation
Indices: 1032136--1032292 Score: 296
Period size: 80 Copynumber: 2.0 Consensus size: 80
1032126 TGTACTTCAT
1032136 TTATGGTCAGCTTATCTTCAGCTCAAACACATGTAAAGTAGCTCAAATAATAAAAGGTTACCTTC
1 TTATGGTCAGCTTATCTTCAGCTCAAACACATGTAAAGTAGCTCAAATAATAAAAGGTTACCTTC
1032201 CACAAATGTGACATG
66 CACAAATGTGACATG
* *
1032216 TTATGGTCAGCTTATCTTCAGCTCAAACACATGTAAAGTAGCTCAAATAATGAAAGGTTATCTTC
1 TTATGGTCAGCTTATCTTCAGCTCAAACACATGTAAAGTAGCTCAAATAATAAAAGGTTACCTTC
1032281 CACAAATGTGAC
66 CACAAATGTGAC
1032293 CTGTCATAAC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (80 bp):
TTATGGTCAGCTTATCTTCAGCTCAAACACATGTAAAGTAGCTCAAATAATAAAAGGTTACCTTC
CACAAATGTGACATG
Found at i:1033087 original size:16 final size:15
Alignment explanation
Indices: 1033037--1033076 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
1033027 CATTTGATAA
*
1033037 CATTTCTATCACTAT
1 CATTTCTTTCACTAT
1033052 CATTTCTTTCACTAT
1 CATTTCTTTCACTAT
1033067 CATTTCTTTC
1 CATTTCTTTC
1033077 CATTTTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.20, C:0.28, G:0.00, T:0.53
Consensus pattern (15 bp):
CATTTCTTTCACTAT
Found at i:1035877 original size:43 final size:43
Alignment explanation
Indices: 1035787--1035877 Score: 96
Period size: 43 Copynumber: 2.1 Consensus size: 43
1035777 CAAAAAATTC
* ** *
1035787 TAATTTACTAATAGATAAAAAAAATGATAAATTGTTAATCTAT
1 TAATTTACTAATAAATAAAAAAAATGATAAATTACTAATCTAA
* *
1035830 TAATTTTCTAATAAATAATACAAAAT-ACTAAATTACTAAT-TAA
1 TAATTTACTAATAAATAA-AAAAAATGA-TAAATTACTAATCTAA
1035873 TAATT
1 TAATT
1035878 ATTATTTTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
43 24 0.60
44 16 0.40
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (43 bp):
TAATTTACTAATAAATAAAAAAAATGATAAATTACTAATCTAA
Found at i:1041675 original size:39 final size:39
Alignment explanation
Indices: 1041621--1041697 Score: 95
Period size: 38 Copynumber: 2.0 Consensus size: 39
1041611 AATTATCATA
1041621 TTTTTAAATATTTAAAATAAAAAAATACA-TTTAAAAATAT
1 TTTTTAAATATTT-AAATAAAAAAATA-ATTTTAAAAATAT
* **
1041661 TTTTTAATTA-TTAAATTTAAAAATAATTTTAAAAATA
1 TTTTTAAATATTTAAATAAAAAAATAATTTTAAAAATA
1041698 GGACCCACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 1 0.03
38 21 0.64
39 2 0.06
40 9 0.27
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (39 bp):
TTTTTAAATATTTAAATAAAAAAATAATTTTAAAAATAT
Found at i:1044553 original size:29 final size:29
Alignment explanation
Indices: 1044508--1044565 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1044498 GTGTTGGCCG
*
1044508 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
1044537 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
1044566 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:1044627 original size:14 final size:14
Alignment explanation
Indices: 1044608--1044701 Score: 125
Period size: 14 Copynumber: 6.4 Consensus size: 14
1044598 CGCTGGGCAT
1044608 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
1044622 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
1044636 CCGAGGCCATCGAGAGAA
1 CCGAGGCCATC---CG-A
1044654 TCCGAGGCCATCCGA
1 -CCGAGGCCATCCGA
1044669 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
1044683 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
1044697 ACGAG
1 CCGAG
1044702 CTATGCGAGG
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
14 57 0.79
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 11 0.15
ACGTcount: A:0.24, C:0.38, G:0.30, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:1044765 original size:33 final size:33
Alignment explanation
Indices: 1044693--1044767 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
1044683 CCGAGGCCAT
* *
1044693 CCGAACGAGCTATGCGAGGGCATCCAAGGGCAA
1 CCGAGCGAGCTATGCGAGGGAATCCAAGGGCAA
* *
1044726 CTGAGCGAGCTATGCGAGGGAATCCGAGGG-AA
1 CCGAGCGAGCTATGCGAGGGAATCCAAGGGCAA
1044758 GCCGAGCGAG
1 -CCGAGCGAG
1044768 GGTAGGTCGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
32 2 0.06
33 34 0.94
ACGTcount: A:0.28, C:0.24, G:0.39, T:0.09
Consensus pattern (33 bp):
CCGAGCGAGCTATGCGAGGGAATCCAAGGGCAA
Found at i:1044804 original size:29 final size:28
Alignment explanation
Indices: 1044771--1044855 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 28
1044761 GAGCGAGGGT
1044771 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAG-GCATGGCGACCTACA
1044800 AGGTCGCCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGA-GGCATGGCGACCTACA
1044829 AGGTCGCCCGGAGGTCATGGCGACCTA
1 AGGTCGCCCGGAGG-CATGGCGACCTA
1044856 TGTGTTGGGA
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
28 2 0.04
29 51 0.94
30 1 0.02
ACGTcount: A:0.20, C:0.31, G:0.36, T:0.13
Consensus pattern (28 bp):
AGGTCGCCCGGAGGCATGGCGACCTACA
Found at i:1044968 original size:29 final size:29
Alignment explanation
Indices: 1044926--1044982 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
1044916 GAGCAAGGGT
1044926 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
1044955 AGGTCGCCCGGAGTGCATGGCGACCTAC
1 AGGTCGCCCGGAGTGCATGGCGACCTAC
1044983 GGCCAACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.32, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:1053558 original size:2 final size:2
Alignment explanation
Indices: 1053553--1053577 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1053543 AAAAAAGTAA
1053553 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1053578 ACTTAATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1062731 original size:3 final size:3
Alignment explanation
Indices: 1062723--1062802 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
1062713 ATCATGCTTC
1062723 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1062771 ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1062803 CCCAAACACA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1065439 original size:37 final size:37
Alignment explanation
Indices: 1065366--1065440 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
1065356 GTTAAAAAAT
* *
1065366 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
1065403 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
1065440 A
1 A
1065441 AAGTTAATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:1065599 original size:13 final size:13
Alignment explanation
Indices: 1065581--1065605 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1065571 TTCAATGACA
1065581 GAAAAAAAAATTT
1 GAAAAAAAAATTT
1065594 GAAAAAAAAATT
1 GAAAAAAAAATT
1065606 AAGGGCATTT
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:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (13 bp):
GAAAAAAAAATTT
Found at i:1079061 original size:518 final size:518
Alignment explanation
Indices: 1078065--1079102 Score: 1778
Period size: 518 Copynumber: 2.0 Consensus size: 518
1078055 TGCGGGTTAT
1078065 ATCCCAATAGACTAGAAGGGTGCGTGAGCTTTAAGATGCAGTAATCCATCAAACACACCATGATA
1 ATCCCAATAGACTAGAAGGGTGCGTGAGCTTTAAGATGCAGTAATCCATCAAACACACCATGATA
* * *
1078130 TCTGCAGTAGTGTAGAGAGCAAATATCACAAGTATATTCACTAAGTAGATCAGATCAGTAGACTT
66 TCTACAGTAGCGTAGAGAGCAAATATCACAAGTATATTCACTAAGCAGATCAGATCAGTAGACTT
*
1078195 GATAGGTAGACGTTCAGTGATATGCAGTTAATATGTTTTAGCTATTTGTGTGTCGTTGAGCTAGT
131 GATAGGTAGACGTTCAGTGATATACAGTTAATATGTTTTAGCTATTTGTGTGTCGTTGAGCTAGT
1078260 TAGCTCAGCCTTCGGATTGTTTCCGTGGGCAAGTTAGTAGATCCAACAGGTGAGGAGCAATAGAT
196 TAGCTCAGCCTTCGGATTGTTTCCGTGGGCAAGTTAGTAGATCCAACAGGTGAGGAGCAATAGAT
*
1078325 AGAGCAAAACCCAATTCAGACCAATACAAATTCATAGTACATCTCAACATTTTTTAAAAGGTATG
261 AGAGCAAAACCCAATTCAGACCAATACAAATTCAGAGTACATCTCAACATTTTTTAAAAGGTATG
* *
1078390 TATATTTGTAAACTTTATTGTTCAATTGAGTCGTATTTTTAGTATAGCAGTTTGTATTATTTTTG
326 TATATTTGTAAACTTTATTGTTCAATTGAGTCGTAGTTTTAGTAGAGCAGTTTGTATTATTTTTG
* *
1078455 TAAAATGTAAATATTTTAATTTGGAACTCTTCAGTATAAATTTTATAGTTTATTTTACAGTTGTT
391 TAAAATATAAATATTTTAATTTGGAACTCCTCAGTATAAATTTTATAGTTTATTTTACAGTTGTT
* *
1078520 TTATATTTAAATAAAGTAAAAAAAGTTGGTCAGTCACT-TCAATGGTTCCGTGTAGCACCTTAA
456 TTATATTTAAATAAAGTAAAAAAAGTTGGTAAGCCACTCT-AATGGTTCCGTGTAGCACCTTAA
* * *
1078583 ATCCCAATAGACTAGAAGGGTGCGTGAGCTTTGAGATGCAGTAATCCCTCAAACATACCATGATA
1 ATCCCAATAGACTAGAAGGGTGCGTGAGCTTTAAGATGCAGTAATCCATCAAACACACCATGATA
* *
1078648 TCTACAGTAGCGTAGAGAGCGAATATCACAAGTATATTCACTAAGCATATCAGATCAGTAGACTT
66 TCTACAGTAGCGTAGAGAGCAAATATCACAAGTATATTCACTAAGCAGATCAGATCAGTAGACTT
**
1078713 GATAGGTAGATTTTCAGTGATATACAGTTAATATGTTTTAGCTATTTGTGTGTCGTTGAGCTAGT
131 GATAGGTAGACGTTCAGTGATATACAGTTAATATGTTTTAGCTATTTGTGTGTCGTTGAGCTAGT
* *
1078778 TAGTTTAGCCTTCGGATTGTTTCCGTGGGCAAGTTAGTAGATCCAACAGGTGAGGAGCAATAGAT
196 TAGCTCAGCCTTCGGATTGTTTCCGTGGGCAAGTTAGTAGATCCAACAGGTGAGGAGCAATAGAT
* **
1078843 AGAGCAAAACCCAATTCAGACCAATACAAATTCAGAGTATATCTCGGCATTTTTTAAAAGGTATG
261 AGAGCAAAACCCAATTCAGACCAATACAAATTCAGAGTACATCTCAACATTTTTTAAAAGGTATG
*
1078908 TATATTTGTAAACTTTATTGTTCAGTTGAGTCGTAGTTTTAGTAGAGCAGTTTGTATTATTTTTG
326 TATATTTGTAAACTTTATTGTTCAATTGAGTCGTAGTTTTAGTAGAGCAGTTTGTATTATTTTTG
1078973 TAAAATATAAATATTTTAATTTGGAACTCCTCAGTATAAATATTT-TA-TTTATTCTT-CAGTTG
391 TAAAATATAAATATTTTAATTTGGAACTCCTCAGTATAAAT-TTTATAGTTTATT-TTACAGTTG
**
1079035 TTTTATATTTAAATAAAGTAAAAAAAAGTTGGTAAGCCACTCTGGTGGTTCCGTGTAGCACCTTA
454 TTTTATATTTAAATAAAGT-AAAAAAAGTTGGTAAGCCACTCTAATGGTTCCGTGTAGCACCTTA
1079100 A
518 A
1079101 AT
1 AT
1079103 TGGTTAATTG
Statistics
Matches: 490, Mismatches: 26, Indels: 8
0.94 0.05 0.02
Matches are distributed among these distances:
517 31 0.06
518 455 0.93
519 4 0.01
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (518 bp):
ATCCCAATAGACTAGAAGGGTGCGTGAGCTTTAAGATGCAGTAATCCATCAAACACACCATGATA
TCTACAGTAGCGTAGAGAGCAAATATCACAAGTATATTCACTAAGCAGATCAGATCAGTAGACTT
GATAGGTAGACGTTCAGTGATATACAGTTAATATGTTTTAGCTATTTGTGTGTCGTTGAGCTAGT
TAGCTCAGCCTTCGGATTGTTTCCGTGGGCAAGTTAGTAGATCCAACAGGTGAGGAGCAATAGAT
AGAGCAAAACCCAATTCAGACCAATACAAATTCAGAGTACATCTCAACATTTTTTAAAAGGTATG
TATATTTGTAAACTTTATTGTTCAATTGAGTCGTAGTTTTAGTAGAGCAGTTTGTATTATTTTTG
TAAAATATAAATATTTTAATTTGGAACTCCTCAGTATAAATTTTATAGTTTATTTTACAGTTGTT
TTATATTTAAATAAAGTAAAAAAAGTTGGTAAGCCACTCTAATGGTTCCGTGTAGCACCTTAA
Found at i:1096821 original size:21 final size:21
Alignment explanation
Indices: 1096795--1096836 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1096785 GGACTTTGCA
*
1096795 TAGCCTCTTGAGCAATAAGGT
1 TAGCCTCTTGAACAATAAGGT
*
1096816 TAGCCTCTTGAACATTAAGGT
1 TAGCCTCTTGAACAATAAGGT
1096837 CACAGTGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (21 bp):
TAGCCTCTTGAACAATAAGGT
Found at i:1107124 original size:35 final size:34
Alignment explanation
Indices: 1107085--1107152 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
1107075 GTCCGATAAT
*
1107085 TTTTGTTAT-TATATTATAATTTTATTTTATTTTGG
1 TTTTGTTATGT-TATT-TAATTTTATGTTATTTTGG
*
1107120 TTTTGTTATGTTATTTTATTTTATGTTATTTTG
1 TTTTGTTATGTTATTTAATTTTATGTTATTTTG
1107153 TTGATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 16 0.53
35 13 0.43
36 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (34 bp):
TTTTGTTATGTTATTTAATTTTATGTTATTTTGG
Done.