Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009592.1 Hibiscus syriacus cultivar Beakdansim tig00116971_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: 7920512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 39
Found at i:2183989 original size:21 final size:21
Alignment explanation
Indices: 2183958--2184012 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
2183948 CTGTTTTCTT
2183958 TATAT-ATATATATATATATA
1 TATATAATATATATATATATA
2183978 TATATAATATATATATATATA
1 TATATAATATATATATATATA
2183999 TATATAATATATAT
1 TATATAATATATAT
2184013 TCTTTCGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 5 0.15
21 29 0.85
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATATAATATATATATATATA
Found at i:2185995 original size:29 final size:30
Alignment explanation
Indices: 2185945--2186001 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
2185935 TTAGTATGTA
* *
2185945 TACTATGCGTAAATTGTAGAA-TAGTCTTG
1 TACTATGCATAAATTATAGAATTAGTCTTG
*
2185974 TACTATGCATAAATTATGGAATTAGTCT
1 TACTATGCATAAATTATAGAATTAGTCT
2186002 GTGTTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.39
Consensus pattern (30 bp):
TACTATGCATAAATTATAGAATTAGTCTTG
Found at i:2187157 original size:3 final size:3
Alignment explanation
Indices: 2187149--2187225 Score: 82
Period size: 3 Copynumber: 25.7 Consensus size: 3
2187139 ATAAATCAAT
* * * * * * * *
2187149 ATA ATA ATA ATA ATA ATA ATA ATT ATT ATT ATT ATT ATT ATT ATA ATT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2187197 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2187226 TGATTCGAGA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
ATA
Found at i:2187520 original size:161 final size:165
Alignment explanation
Indices: 2187349--2187674 Score: 592
Period size: 159 Copynumber: 2.0 Consensus size: 165
2187339 AGGGCCAAAT
2187349 ATAGAGGAAAAGATGAAAATAAATATGAAACATATAAATAATTATTCAATTATGTTAAAATATTA
1 ATAGAGGAAAAGATGAAAAT-AA-ATGAAACATATAAATAATTATTCAATTATGTTAAAATATTA
2187414 A-TTTTATTATTGAAAATTTT-AAATTAT-AAATGACAATTAAATTTTTT-AA-ATATATAGATT
64 ATTTTTATTATTGAAAATTTTAAAATTATAAAATGACAATTAAATTTTTTAAATATATATAGATT
2187474 GATCA-TAAAATTTATCAAACTATTATAAATTAGTTA
129 GATCATTAAAATTTATCAAACTATTATAAATTAGTTA
2187510 ATAGAGGAAAAGATGAAAATAAATGAAACATATAAATAATTATTCAATTATGTTAAAATATTAAT
1 ATAGAGGAAAAGATGAAAATAAATGAAACATATAAATAATTATTCAATTATGTTAAAATATTAAT
2187575 TTTTATTATTGAAAATTTTAAAATTATAAAATGACAATTAAATTTTTTAAATATATATAGATTGA
66 TTTTATTATTGAAAATTTTAAAATTATAAAATGACAATTAAATTTTTTAAATATATATAGATTGA
2187640 TCATTAAAATTTATCAAACTATTATAAATTAGTTA
131 TCATTAAAATTTATCAAACTATTATAAATTAGTTA
2187675 TTAAACTTAT
Statistics
Matches: 159, Mismatches: 0, Indels: 8
0.95 0.00 0.05
Matches are distributed among these distances:
159 42 0.26
160 21 0.13
161 27 0.17
162 20 0.13
163 2 0.01
164 16 0.10
165 31 0.19
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (165 bp):
ATAGAGGAAAAGATGAAAATAAATGAAACATATAAATAATTATTCAATTATGTTAAAATATTAAT
TTTTATTATTGAAAATTTTAAAATTATAAAATGACAATTAAATTTTTTAAATATATATAGATTGA
TCATTAAAATTTATCAAACTATTATAAATTAGTTA
Found at i:2187686 original size:31 final size:31
Alignment explanation
Indices: 2187642--2187726 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
2187632 TAGATTGATC
* * *
2187642 ATTAAAATTTATCAAACTATTATAAATTAGTT
1 ATTAAAACTTATCAAA-TATTATAAAATAATT
2187674 ATT-AAACTTATCAAATTATTATAAAATAATT
1 ATTAAAACTTATCAAA-TATTATAAAATAATT
*
2187705 CTTAAAACTTATCAAATATTAT
1 ATTAAAACTTATCAAATATTAT
2187727 TAGTATTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
31 32 0.68
32 15 0.32
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.42
Consensus pattern (31 bp):
ATTAAAACTTATCAAATATTATAAAATAATT
Found at i:2190140 original size:21 final size:21
Alignment explanation
Indices: 2190116--2190156 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2190106 CAACTCATTT
*
2190116 TCCAAATTCGCGTTGCGATAG
1 TCCAAATTCGCATTGCGATAG
2190137 TCCAAATTCGCATTGCGATA
1 TCCAAATTCGCATTGCGATA
2190157 TCGCAACGCG
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:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (21 bp):
TCCAAATTCGCATTGCGATAG
Found at i:2190184 original size:73 final size:74
Alignment explanation
Indices: 2190082--2190228 Score: 226
Period size: 73 Copynumber: 2.0 Consensus size: 74
2190072 GACCAACAAA
* *
2190082 ATCGCAACGCAATCTCAAACTTCGCAACTC-ATTTTCCAAATTCGCGTTGCGATAGTCCAAATTC
1 ATCGCAACGCAATCTCAAACTTCGCAACTCAATTTT-CAAATCCGCGTTGCGATAGTCCAAAATC
2190146 GCATTGCGAT
65 GCATTGCGAT
* * *
2190156 ATCGCAACGCGATCTTAAA-TTCGTAACTCAATTTTCAAATCCGCGTTGCGATAGTCCAAAATCG
1 ATCGCAACGCAATCTCAAACTTCGCAACTCAATTTTCAAATCCGCGTTGCGATAGTCCAAAATCG
2190220 CATTGCGAT
66 CATTGCGAT
2190229 TTTCCATTTC
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
73 45 0.67
74 22 0.33
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (74 bp):
ATCGCAACGCAATCTCAAACTTCGCAACTCAATTTTCAAATCCGCGTTGCGATAGTCCAAAATCG
CATTGCGAT
Found at i:2190582 original size:40 final size:40
Alignment explanation
Indices: 2190506--2190756 Score: 353
Period size: 40 Copynumber: 6.5 Consensus size: 40
2190496 AAACAAATAC
2190506 AATGGAAAATCGCAATGCGATTTTGGACTATCGCAACGCGA
1 AATGGAAAATCGCAATGCGA-TTTGGACTATCGCAACGCGA
*
2190547 AATGGAAAATCACAATGCGATTTGGACTATCGCAACGCG-
1 AATGGAAAATCGCAATGCGATTTGGACTATCGCAACGCGA
2190586 AAT-G--AATCGCAATGCGATTTGGACTATCGCAACGC--
1 AATGGAAAATCGCAATGCGATTTGGACTATCGCAACGCGA
2190621 AAT-G--AATCGCAA-GCGATTTGGACTATCGCAACGC-A
1 AATGGAAAATCGCAATGCGATTTGGACTATCGCAACGCGA
* * *
2190656 AATGGAAAATCACAACGCGAATTTGGACTATCGCAACACGA
1 AATGGAAAATCGCAATGCG-ATTTGGACTATCGCAACGCGA
*
2190697 AATGGAAAATTGCAATGCGATTTGGACTATCGCAACGCGA
1 AATGGAAAATCGCAATGCGATTTGGACTATCGCAACGCGA
*
2190737 AATGGAAAATCGCAACGCGA
1 AATGGAAAATCGCAATGCGA
2190757 AACTGGAAAT
Statistics
Matches: 193, Mismatches: 10, Indels: 15
0.89 0.05 0.07
Matches are distributed among these distances:
34 22 0.11
35 15 0.08
36 31 0.16
38 8 0.04
39 6 0.03
40 75 0.39
41 36 0.19
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (40 bp):
AATGGAAAATCGCAATGCGATTTGGACTATCGCAACGCGA
Found at i:2190596 original size:16 final size:16
Alignment explanation
Indices: 2190575--2190636 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 16
2190565 GATTTGGACT
2190575 ATCGCAACGCGAATGA
1 ATCGCAACGCGAATGA
* *
2190591 ATCGCAATGCGATTTGGA
1 ATCGCAACGCGA-AT-GA
2190609 CTATCGCAACGC-AATGA
1 --ATCGCAACGCGAATGA
2190626 ATCGCAA-GCGA
1 ATCGCAACGCGA
2190637 TTTGGACTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
14 2 0.05
15 8 0.22
16 11 0.30
17 3 0.08
18 3 0.08
19 1 0.03
20 9 0.24
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (16 bp):
ATCGCAACGCGAATGA
Found at i:2190757 original size:20 final size:20
Alignment explanation
Indices: 2190506--2190774 Score: 146
Period size: 20 Copynumber: 13.8 Consensus size: 20
2190496 AAACAAATAC
*
2190506 AATGGAAAATCGCAATGCGA
1 AATGGAAAATCGCAACGCGA
** **
2190526 TTTTGGACTATCGCAACGCGA
1 -AATGGAAAATCGCAACGCGA
* *
2190547 AATGGAAAATCACAATGCGA
1 AATGGAAAATCGCAACGCGA
** **
2190567 TTTGGACTATCGCAACGCG-
1 AATGGAAAATCGCAACGCGA
*
2190586 AAT-G--AATCGCAATGCGA
1 AATGGAAAATCGCAACGCGA
** **
2190603 TTTGGACTATCGCAACGC--
1 AATGGAAAATCGCAACGCGA
2190621 AAT-G--AATCGCAA-GCGA
1 AATGGAAAATCGCAACGCGA
** **
2190637 TTTGGACTATCGCAACGC-A
1 AATGGAAAATCGCAACGCGA
*
2190656 AATGGAAAATCACAACGCGA
1 AATGGAAAATCGCAACGCGA
* ** *
2190676 ATTTGGACTATCGCAACACGA
1 A-ATGGAAAATCGCAACGCGA
* *
2190697 AATGGAAAATTGCAATGCGA
1 AATGGAAAATCGCAACGCGA
** **
2190717 TTTGGACTATCGCAACGCGA
1 AATGGAAAATCGCAACGCGA
2190737 AATGGAAAATCGCAACGCGA
1 AATGGAAAATCGCAACGCGA
*
2190757 AACTGGAAATTCGCAACG
1 AA-TGGAAAATCGCAACG
2190775 AATTTGGAAA
Statistics
Matches: 177, Mismatches: 58, Indels: 26
0.68 0.22 0.10
Matches are distributed among these distances:
14 2 0.01
15 7 0.04
16 11 0.06
17 3 0.02
18 3 0.02
19 22 0.12
20 85 0.48
21 44 0.25
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (20 bp):
AATGGAAAATCGCAACGCGA
Found at i:2196877 original size:30 final size:30
Alignment explanation
Indices: 2196843--2196953 Score: 116
Period size: 30 Copynumber: 3.7 Consensus size: 30
2196833 CATATGTGAA
*
2196843 TTAAAGATTAAGGGCTTATTTGGAAACAAG
1 TTAAAGATTAAGGGCTTATTTGGATACAAG
* * * *
2196873 TTAAAGTTTAAGGTCTTATTTGGCTGCAAG
1 TTAAAGATTAAGGGCTTATTTGGATACAAG
* *
2196903 TTAAAGATTAGGGGCTTATGTGGATACTAA-
1 TTAAAGATTAAGGGCTTATTTGGATAC-AAG
* * *
2196933 CTAAAGTTTAAGGGTTTATTT
1 TTAAAGATTAAGGGCTTATTT
2196954 AGGTGTAATA
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
30 62 0.97
31 2 0.03
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.37
Consensus pattern (30 bp):
TTAAAGATTAAGGGCTTATTTGGATACAAG
Found at i:2200311 original size:2 final size:2
Alignment explanation
Indices: 2200304--2200331 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2200294 TAAAAGCATA
2200304 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
2200332 GGTTAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2200833 original size:11 final size:11
Alignment explanation
Indices: 2200817--2200863 Score: 76
Period size: 11 Copynumber: 4.3 Consensus size: 11
2200807 TAGTACTTAA
2200817 GTTTCAAAATT
1 GTTTCAAAATT
2200828 GTTTCAAAATT
1 GTTTCAAAATT
2200839 GTTTCAAAATT
1 GTTTCAAAATT
* *
2200850 GTTTTAAATTT
1 GTTTCAAAATT
2200861 GTT
1 GTT
2200864 ATTTTAATCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.32, C:0.06, G:0.11, T:0.51
Consensus pattern (11 bp):
GTTTCAAAATT
Found at i:2202815 original size:18 final size:18
Alignment explanation
Indices: 2202777--2202814 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2202767 TTCCACTACC
* *
2202777 TTTGGTATTGGTACCCCT
1 TTTGGTATCGGTACCACT
2202795 TTTGGTATCGGTACCA-T
1 TTTGGTATCGGTACCACT
2202812 TTT
1 TTT
2202815 TCATTATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.47
Consensus pattern (18 bp):
TTTGGTATCGGTACCACT
Found at i:2202896 original size:106 final size:105
Alignment explanation
Indices: 2202707--2202896 Score: 301
Period size: 106 Copynumber: 1.8 Consensus size: 105
2202697 AAAAATAATA
*** *
2202707 TTTTATTATGAAATTTGAGCAATGTTGGTAGTATTGATACTACATTGTGAGTATCGATACTTCCA
1 TTTTATTATGAAATTTGAGCAAAACTGGTAGTATTGATAATACATTGTGAGTATCGATACTTCCA
*
2202772 CTACCTTTGGTATTGGTACCCCTTTTGGTATCGGTACCAT
66 CTACCTTTGGTATCGGTACCCCTTTTGGTATCGGTACCAT
*
2202812 TTTTCATTATGAAATTTGAGCAAAACTGGTAGTATTGATAATATATTGTGAGTATCGATACTTCC
1 TTTT-ATTATGAAATTTGAGCAAAACTGGTAGTATTGATAATACATTGTGAGTATCGATACTTCC
2202877 GA-TACCTTTGGTATCGGTAC
65 -ACTACCTTTGGTATCGGTAC
2202897 TATATGAACA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
105 4 0.05
106 72 0.94
107 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (105 bp):
TTTTATTATGAAATTTGAGCAAAACTGGTAGTATTGATAATACATTGTGAGTATCGATACTTCCA
CTACCTTTGGTATCGGTACCCCTTTTGGTATCGGTACCAT
Found at i:2211470 original size:16 final size:16
Alignment explanation
Indices: 2211449--2211508 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 16
2211439 ACATCATTGT
2211449 ATTCTTTTTTAGCATA
1 ATTCTTTTTTAGCATA
* *
2211465 ATTCTTTTTAAATCATTA
1 ATTCTTTTT-TAGCA-TA
2211483 TATTCTTTTTTAGCATA
1 -ATTCTTTTTTAGCATA
2211500 ATTCTTTTT
1 ATTCTTTTT
2211509 ACATCATTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
16 18 0.49
17 5 0.14
18 5 0.14
19 9 0.24
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.60
Consensus pattern (16 bp):
ATTCTTTTTTAGCATA
Found at i:2211487 original size:35 final size:35
Alignment explanation
Indices: 2211436--2211516 Score: 144
Period size: 35 Copynumber: 2.3 Consensus size: 35
2211426 ATACATTGGA
*
2211436 TTTACATCATTGTATTCTTTTTTAGCATAATTCTT
1 TTTACATCATTATATTCTTTTTTAGCATAATTCTT
*
2211471 TTTAAATCATTATATTCTTTTTTAGCATAATTCTT
1 TTTACATCATTATATTCTTTTTTAGCATAATTCTT
2211506 TTTACATCATT
1 TTTACATCATT
2211517 GTACAGATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.26, C:0.14, G:0.04, T:0.57
Consensus pattern (35 bp):
TTTACATCATTATATTCTTTTTTAGCATAATTCTT
Found at i:2211494 original size:20 final size:19
Alignment explanation
Indices: 2211436--2211494 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
2211426 ATACATTGGA
*
2211436 TTTACATCATTGTATTCTTT
1 TTTA-ATCATTATATTCTTT
*
2211456 TTT-AGCA-TA-ATTCTTT
1 TTTAATCATTATATTCTTT
*
2211472 TTAAATCATTATATTCTTT
1 TTTAATCATTATATTCTTT
2211491 TTTA
1 TTTA
2211495 GCATAATTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
16 9 0.29
17 4 0.13
18 5 0.16
19 10 0.32
20 3 0.10
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTAATCATTATATTCTTT
Found at i:2220896 original size:19 final size:18
Alignment explanation
Indices: 2220868--2220918 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 18
2220858 TTAATTTTAC
*
2220868 AAATATAAAAAAATCAGAA
1 AAATACAAAAAAATC-GAA
2220887 AAATACAAAAAAATCGAA
1 AAATACAAAAAAATCGAA
2220905 AAATTACAAAAAAA
1 AAA-TACAAAAAAA
2220919 AAAAATAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 6 0.20
19 24 0.80
ACGTcount: A:0.75, C:0.08, G:0.04, T:0.14
Consensus pattern (18 bp):
AAATACAAAAAAATCGAA
Found at i:2226462 original size:29 final size:29
Alignment explanation
Indices: 2226418--2226501 Score: 73
Period size: 30 Copynumber: 2.8 Consensus size: 29
2226408 GCTGCAAGAG
2226418 AAAAACAAAAACTTAAGGTATTAAATAGCA-
1 AAAAA-AAAAA-TTAAGGTATTAAATAGCAC
* * *
2226448 AAAGAAAAAAATTAAAGTACTAAAATAGTAC
1 AAA-AAAAAAATTAAGGTA-TTAAATAGCAC
*
2226479 AAACAAAAAATTAAAGG-ATTAAA
1 AAAAAAAAAATT-AAGGTATTAAA
2226502 ATAGAAGGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
29 11 0.25
30 25 0.57
31 8 0.18
ACGTcount: A:0.64, C:0.07, G:0.10, T:0.19
Consensus pattern (29 bp):
AAAAAAAAAATTAAGGTATTAAATAGCAC
Found at i:2226474 original size:30 final size:30
Alignment explanation
Indices: 2226440--2226505 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
2226430 TTAAGGTATT
*
2226440 AAATAGCA-AAAGAAAAAAATTAAAGTACTA
1 AAATAGCACAAA-AAAAAAATTAAAGGACTA
* * *
2226470 AAATAGTACAAACAAAAAATTAAAGGATTA
1 AAATAGCACAAAAAAAAAATTAAAGGACTA
2226500 AAATAG
1 AAATAG
2226506 AAGGATCTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.65, C:0.06, G:0.11, T:0.18
Consensus pattern (30 bp):
AAATAGCACAAAAAAAAAATTAAAGGACTA
Found at i:2238936 original size:23 final size:22
Alignment explanation
Indices: 2238906--2238959 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
2238896 CGATTCAACC
2238906 TAAATTTTTTT-G-ATTTTTCAT
1 TAAATTTTTTTGGTATTTTT-AT
2238927 TAAATGTTTTTTGGTATTTTTAT
1 TAAAT-TTTTTTGGTATTTTTAT
*
2238950 TTAATTTTTT
1 TAAATTTTTT
2238960 AAATAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.17
22 11 0.38
23 7 0.24
24 6 0.21
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (22 bp):
TAAATTTTTTTGGTATTTTTAT
Found at i:2243079 original size:25 final size:24
Alignment explanation
Indices: 2243051--2243126 Score: 84
Period size: 23 Copynumber: 3.2 Consensus size: 24
2243041 CCACTAGGGG
2243051 CTATGAAATTTATCCCGAAGGACCA
1 CTATGAAA-TTATCCCGAAGGACCA
* *
2243076 CTATGAAA-TGTCCCGTAGGACCA
1 CTATGAAATTATCCCGAAGGACCA
* * *
2243099 CTATGAAA-TGTCTCGTAGGACCA
1 CTATGAAATTATCCCGAAGGACCA
2243122 CTATG
1 CTATG
2243127 TCCCAAAGGA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
23 40 0.83
25 8 0.17
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (24 bp):
CTATGAAATTATCCCGAAGGACCA
Found at i:2243095 original size:23 final size:23
Alignment explanation
Indices: 2243063--2243126 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
2243053 ATGAAATTTA
*
2243063 TCCCGAAGGACCACTATGAAATG
1 TCCCGTAGGACCACTATGAAATG
2243086 TCCCGTAGGACCACTATGAAATG
1 TCCCGTAGGACCACTATGAAATG
*
2243109 TCTCGTAGGACCACTATG
1 TCCCGTAGGACCACTATG
2243127 TCCCAAAGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (23 bp):
TCCCGTAGGACCACTATGAAATG
Found at i:2243400 original size:2 final size:2
Alignment explanation
Indices: 2243389--2243419 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2243379 AACATGTATC
2243389 AT AT -T 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
2243420 CCGCAATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2243855 original size:2 final size:2
Alignment explanation
Indices: 2243848--2243879 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2243838 GATTACGTAA
2243848 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
2243880 CTTATATCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2247893 original size:5 final size:5
Alignment explanation
Indices: 2247878--2247917 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
2247868 TGATTTATGA
2247878 GATAT -ATAT GATAT GATAGAT GATAT GATAT GATAT GATA
1 GATAT GATAT GATAT GAT--AT GATAT GATAT GATAT GATA
2247918 GATGTGAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 4 0.12
5 23 0.72
7 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (5 bp):
GATAT
Found at i:2247902 original size:12 final size:12
Alignment explanation
Indices: 2247885--2247921 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2247875 TGAGATATAT
2247885 ATGATATGATAG
1 ATGATATGATAG
2247897 ATGATATGAT--
1 ATGATATGATAG
2247907 ATGATATGATAG
1 ATGATATGATAG
2247919 ATG
1 ATG
2247922 TGAACATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.43
12 13 0.57
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (12 bp):
ATGATATGATAG
Found at i:2247911 original size:22 final size:21
Alignment explanation
Indices: 2247878--2247921 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 21
2247868 TGATTTATGA
2247878 GATATATATGATATGATAGAT
1 GATATATATGATATGATAGAT
2247899 GATATGATATGATATGATAGAT
1 GATAT-ATATGATATGATAGAT
2247921 G
1 G
2247922 TGAACATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.36
Consensus pattern (21 bp):
GATATATATGATATGATAGAT
Found at i:2247930 original size:22 final size:22
Alignment explanation
Indices: 2247883--2247931 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2247873 TATGAGATAT
**
2247883 ATATGATATGATAGATGATATG
1 ATATGATATGATAGATGATAAC
2247905 ATATGATATGATAGATG-TGAAC
1 ATATGATATGATAGATGAT-AAC
2247927 ATATG
1 ATATG
2247932 CAAATGACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.35
Consensus pattern (22 bp):
ATATGATATGATAGATGATAAC
Found at i:2254434 original size:19 final size:19
Alignment explanation
Indices: 2254410--2254506 Score: 95
Period size: 19 Copynumber: 4.7 Consensus size: 19
2254400 AATAGCCAGA
*
2254410 GTGCATCGATGCATGGTTT
1 GTGCATCGATGCATGGTAT
* *
2254429 GTGCATCGATGCATCAAATGCACT
1 GTGCATCGATGCAT----GGTA-T
*
2254453 GAGTGCATCAATGCATGGTAT
1 G--TGCATCGATGCATGGTAT
2254474 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
2254493 GTGCATCGATGCAT
1 GTGCATCGATGCAT
2254507 AAAATGCATT
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
19 45 0.70
21 2 0.03
22 2 0.03
23 1 0.02
24 2 0.03
26 12 0.19
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.30
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:2254441 original size:64 final size:66
Alignment explanation
Indices: 2254373--2254523 Score: 163
Period size: 64 Copynumber: 2.3 Consensus size: 66
2254363 GAGTGTATCA
* * *
2254373 ATGCATAAAATACATTTGATGTTTCA-AAATAGCCA-G-A-GTGCATCGATGCATGGTTTGTGCA
1 ATGCATAAAATGCATTTGATGTTGCATAAAT-G-CAGGTATGTGCATCGATGCATGGTATGTGCA
2254434 TCG
64 TCG
* * *
2254437 ATGCATCAAATGCA-CTGA-G-TGCATCAATGCATGGTATGTGCATCGATGCATGGTATGTGCAT
1 ATGCATAAAATGCATTTGATGTTGCATAAATGCA-GGTATGTGCATCGATGCATGGTATGTGCAT
2254499 CG
65 CG
*
2254501 ATGCATAAAATGCATTCGATGTT
1 ATGCATAAAATGCATTTGATGTT
2254524 CAATTTATTC
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
60 2 0.03
61 4 0.06
62 5 0.07
63 4 0.06
64 51 0.73
65 2 0.03
66 1 0.01
67 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (66 bp):
ATGCATAAAATGCATTTGATGTTGCATAAATGCAGGTATGTGCATCGATGCATGGTATGTGCATC
G
Found at i:2256828 original size:44 final size:42
Alignment explanation
Indices: 2256779--2256873 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 42
2256769 GGCTTTATGC
*
2256779 ATCGATGCACATTAAAGGCGTGCATC-AGTGCACCT-TCATGGTGT
1 ATCGATGCACATTAAAGG-ATGCATCGA-TGCA-CTGTCA-GGTGT
* *
2256823 ATCGATGCACATTCAAGGATGCATCGATGCACTGTTAGGTGT
1 ATCGATGCACATTAAAGGATGCATCGATGCACTGTCAGGTGT
2256865 ATCGATGCA
1 ATCGATGCA
2256874 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
42 16 0.35
43 12 0.26
44 18 0.39
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.27
Consensus pattern (42 bp):
ATCGATGCACATTAAAGGATGCATCGATGCACTGTCAGGTGT
Found at i:2256870 original size:20 final size:21
Alignment explanation
Indices: 2256779--2256873 Score: 70
Period size: 21 Copynumber: 4.4 Consensus size: 21
2256769 GGCTTTATGC
* *
2256779 ATCGATGCACATTAAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* *
2256802 ATC-AGTGCACCTTCATGGTGT
1 ATCGA-TGCACATTCAAGGTGT
*
2256823 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
2256845 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
2256865 ATCGATGCA
1 ATCGATGCA
2256874 TTAAGCACAA
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
20 11 0.19
21 21 0.36
22 16 0.27
23 11 0.19
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.27
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:2256872 original size:42 final size:44
Alignment explanation
Indices: 2256779--2256873 Score: 117
Period size: 42 Copynumber: 2.2 Consensus size: 44
2256769 GGCTTTATGC
*
2256779 ATCGATGCACATTAAAGGCGTGCATCAGTGCACCTTCATGGTGT
1 ATCGATGCACATTAAAGGCATGCATCAGTGCACCTTCATGGTGT
* *
2256823 ATCGATGCACATTCAAGG-ATGCATC-GATGCA-CTGTTA-GGTGT
1 ATCGATGCACATTAAAGGCATGCATCAG-TGCACCT-TCATGGTGT
2256865 ATCGATGCA
1 ATCGATGCA
2256874 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
42 17 0.37
43 12 0.26
44 17 0.37
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATTAAAGGCATGCATCAGTGCACCTTCATGGTGT
Found at i:2262728 original size:45 final size:45
Alignment explanation
Indices: 2262679--2262853 Score: 314
Period size: 45 Copynumber: 3.9 Consensus size: 45
2262669 AAAATAGCCA
2262679 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACT
1 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACT
2262724 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACT
1 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACT
2262769 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACT
1 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACT
* * * *
2262814 GAGTGCATCGATGCATGGTATGTACATTGATGCATAAAAT
1 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAAT
2262854 ACATTCGATG
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 126 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (45 bp):
GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACT
Found at i:2262731 original size:26 final size:26
Alignment explanation
Indices: 2262700--2262829 Score: 108
Period size: 26 Copynumber: 5.5 Consensus size: 26
2262690 TGCATGGTTT
2262700 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
* **
2262726 GTGCATCGATG---C--ATG--GTTT
1 GTGCATCGATGCATCAAATGCACTGA
2262745 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
* **
2262771 GTGCATCGATG---C--ATG--GTTT
1 GTGCATCGATGCATCAAATGCACTGA
2262790 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
2262816 GTGCATCGATGCAT
1 GTGCATCGATGCAT
2262830 GGTATGTACA
Statistics
Matches: 78, Mismatches: 12, Indels: 28
0.66 0.10 0.24
Matches are distributed among these distances:
19 24 0.31
21 6 0.08
22 2 0.03
23 2 0.03
24 6 0.08
26 38 0.49
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (26 bp):
GTGCATCGATGCATCAAATGCACTGA
Found at i:2262735 original size:90 final size:89
Alignment explanation
Indices: 2262634--2262830 Score: 281
Period size: 90 Copynumber: 2.2 Consensus size: 89
2262624 GGTGCAATAA
**
2262634 GAGTGCATCGATGCAT-AAAATGCATTCGATGTTTCAAAATAGC-CAGAGTGCATCGATGCATGG
1 GAGTGCATCGATGCATGAAAATGCA-TCGATGCATC-AAAT-GCACAGAGTGCATCGATGCATGG
2262697 TTTGTGCATCGATGCATCAAATGCACT
63 TTTGTGCATCGATGCATCAAATGCACT
**** *
2262724 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACTGAGTGCATCGATGCATGGTT
1 GAGTGCATCGATGCAT-GAAAATGCATCGATGCATCAAATGCACAGAGTGCATCGATGCATGGTT
2262789 TGTGCATCGATGCATCAAATGCACT
65 TGTGCATCGATGCATCAAATGCACT
2262814 GAGTGCATCGATGCATG
1 GAGTGCATCGATGCATG
2262831 GTATGTACAT
Statistics
Matches: 97, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
89 3 0.03
90 82 0.85
91 8 0.08
92 4 0.04
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (89 bp):
GAGTGCATCGATGCATGAAAATGCATCGATGCATCAAATGCACAGAGTGCATCGATGCATGGTTT
GTGCATCGATGCATCAAATGCACT
Found at i:2265363 original size:2 final size:2
Alignment explanation
Indices: 2265351--2265400 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
2265341 TATTTTATTC
*
2265351 AT AT GT 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
2265393 AT AT AT AT
1 AT AT AT AT
2265401 CCGTAATTAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2267061 original size:17 final size:17
Alignment explanation
Indices: 2267016--2267061 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
2267006 TTATCATGAA
*
2267016 CATA-TTTATCAGTAAT
1 CATATTTTATCACTAAT
2267032 CATATTATTATCACTAATT
1 CATATT-TTATCACTAA-T
2267051 CAT-TTTTATCA
1 CATATTTTATCA
2267062 TATAAGCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 4 0.15
17 7 0.27
18 11 0.42
19 4 0.15
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (17 bp):
CATATTTTATCACTAAT
Found at i:2267371 original size:23 final size:23
Alignment explanation
Indices: 2267303--2267388 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 23
2267293 TCGTATAAAT
*
2267303 TTGCACCGAAGTGCCATGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
2267326 TTTGTC-CCGAAG-GACCGCATAGAA
1 -TTG-CACCGAAGTG-CCACGTAGAA
2267350 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
2267373 ATGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
2267389 TATAAGATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
22 1 0.02
23 32 0.63
24 17 0.33
25 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:2270918 original size:14 final size:15
Alignment explanation
Indices: 2270899--2270927 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2270889 TTCTTGCTTA
2270899 TACACA-CTACTATT
1 TACACATCTACTATT
2270913 TACACATCTACTATT
1 TACACATCTACTATT
2270928 CCTTTTCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (15 bp):
TACACATCTACTATT
Found at i:2272902 original size:14 final size:14
Alignment explanation
Indices: 2272879--2272910 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2272869 TGAACAATAA
*
2272879 AATACGGTATGAAC
1 AATACCGTATGAAC
2272893 AATACCGTATGAAC
1 AATACCGTATGAAC
2272907 AATA
1 AATA
2272911 ATGAACAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.22
Consensus pattern (14 bp):
AATACCGTATGAAC
Found at i:2273706 original size:23 final size:23
Alignment explanation
Indices: 2273640--2273725 Score: 104
Period size: 23 Copynumber: 3.7 Consensus size: 23
2273630 TCGTATAAAT
2273640 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
2273663 TTTGTC-CCGAAG-GACCGCGTAGAA
1 -TTG-CACCGAAGTG-CCACGTAGAA
2273687 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
2273710 ATGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
2273726 TATAAGATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
22 1 0.02
23 33 0.61
24 19 0.35
25 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:2275297 original size:54 final size:54
Alignment explanation
Indices: 2275220--2275395 Score: 244
Period size: 54 Copynumber: 3.3 Consensus size: 54
2275210 ACTAGTAACT
** * *
2275220 CGTGCCCACGCCTTAACTAAAGACCCCTTCTGCGATAGCTTAGAATGAATAAGC
1 CGTGCCCACGCCTTAACTAAAGACCTTTTCTGCGATAGCTCAAAATGAATAAGC
* * * *
2275274 CGTGTCCACACCTTAACTGAAGACCTTTTCTGCGATAACTCAAAATGAATAAGC
1 CGTGCCCACGCCTTAACTAAAGACCTTTTCTGCGATAGCTCAAAATGAATAAGC
* * *
2275328 CGTGCCCACGCGTTAATTAAAGACCTTTTCTGCGATAGCTCAAAATGAATAAGT
1 CGTGCCCACGCCTTAACTAAAGACCTTTTCTGCGATAGCTCAAAATGAATAAGC
*
2275382 CATGCCCACGCCTT
1 CGTGCCCACGCCTT
2275396 TGAGGAAACC
Statistics
Matches: 105, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 105 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (54 bp):
CGTGCCCACGCCTTAACTAAAGACCTTTTCTGCGATAGCTCAAAATGAATAAGC
Found at i:2275897 original size:24 final size:24
Alignment explanation
Indices: 2275833--2275907 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
2275823 ACTACGGTGT
*
2275833 AATTCTACGTGGCACTTCGGTGC-
1 AATTCTACGTGGCACTTTGGTGCA
*
2275856 -ATCTCTACGCGGTC-CTTTGG-GACA
1 AAT-TCTACGTGG-CACTTTGGTG-CA
2275880 AATTCTACGTGGCACTTTGGTGCA
1 AATTCTACGTGGCACTTTGGTGCA
2275904 AATT
1 AATT
2275908 TATATGAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
22 3 0.07
23 15 0.36
24 21 0.50
25 3 0.07
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (24 bp):
AATTCTACGTGGCACTTTGGTGCA
Found at i:2282725 original size:54 final size:54
Alignment explanation
Indices: 2282649--2282824 Score: 280
Period size: 54 Copynumber: 3.3 Consensus size: 54
2282639 CTAGTAACTT
* ** * * * *
2282649 GTGCCCACGCCTTAACTAAAGACCCCTTCTACGACAGCTTAGAATGAATAAGCC
1 GTGCCCACGCCTTAACTGAAGACCTTTTCTGCGATAGCTCAAAATGAATAAGCC
*
2282703 GTGCCCACGCCTTAACTGAAGACCTTTTCTGCGATAACTCAAAATGAATAAGCC
1 GTGCCCACGCCTTAACTGAAGACCTTTTCTGCGATAGCTCAAAATGAATAAGCC
2282757 GTGCCCACGCCTTAACTGAAGACCTTTTCTGCGATAGCTCAAAATGAATAAGCC
1 GTGCCCACGCCTTAACTGAAGACCTTTTCTGCGATAGCTCAAAATGAATAAGCC
2282811 GTGCCCACGCCTTA
1 GTGCCCACGCCTTA
2282825 TGCGGAAACC
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 113 1.00
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.23
Consensus pattern (54 bp):
GTGCCCACGCCTTAACTGAAGACCTTTTCTGCGATAGCTCAAAATGAATAAGCC
Found at i:2283350 original size:24 final size:24
Alignment explanation
Indices: 2283272--2283360 Score: 98
Period size: 23 Copynumber: 3.8 Consensus size: 24
2283262 ACATATTATA
*
2283272 TGGCACTACGGTGC-AATTCTACG
1 TGGCACTTCGGTGCAAATTCTACG
2283295 TGGCACTTCGGTGC--ATCTCTACG
1 TGGCACTTCGGTGCAAAT-TCTACG
*
2283318 CTGTC-CTTCGG-GACAAATTCTACG
1 -TGGCACTTCGGTG-CAAATTCTACG
2283342 TGGCACTTCGGTGCAAATT
1 TGGCACTTCGGTGCAAATT
2283361 TATATGAGTT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
22 3 0.05
23 29 0.52
24 21 0.38
25 3 0.05
ACGTcount: A:0.19, C:0.27, G:0.25, T:0.29
Consensus pattern (24 bp):
TGGCACTTCGGTGCAAATTCTACG
Found at i:2284906 original size:21 final size:21
Alignment explanation
Indices: 2284880--2284920 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2284870 TTTTTCAGTT
2284880 AGGGGGGAATC-GATACCCCCC
1 AGGGGGGAATCTG-TACCCCCC
2284901 AGGGGGGAATCTGTACCCCC
1 AGGGGGGAATCTGTACCCCC
2284921 TGCACATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.22, C:0.32, G:0.34, T:0.12
Consensus pattern (21 bp):
AGGGGGGAATCTGTACCCCCC
Found at i:2287023 original size:21 final size:21
Alignment explanation
Indices: 2286975--2287148 Score: 63
Period size: 21 Copynumber: 8.4 Consensus size: 21
2286965 ATGACTATCA
*
2286975 CAATGCGATTTTCCATTTTCG
1 CAATGCGATTTTCCATATTCG
**
2286996 CGTTGCGATTTTCCCA-ATTCG
1 CAATGCGATTTT-CCATATTCG
* ** * *
2287017 CAATGCGAATTTGGAAAATCG
1 CAATGCGATTTTCCATATTCG
* * ** * *
2287038 TAATGCGAATTTGGAAAATCG
1 CAATGCGATTTTCCATATTCG
** *
2287059 CAATGCGATACT-GACTA-TCG
1 CAATGCGATTTTCCA-TATTCG
* *
2287079 CAATGCAATTTGCC-TAATTCG
1 CAATGCGATTTTCCAT-ATTCG
* *
2287100 CATTGCGA-TTTACATATTCG
1 CAATGCGATTTTCCATATTCG
**
2287120 CGTTGCGATTTT-CATAATTCG
1 CAATGCGATTTTCCAT-ATTCG
2287141 CAATGCGA
1 CAATGCGA
2287149 ATACGTAAAT
Statistics
Matches: 117, Mismatches: 27, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
19 1 0.01
20 33 0.28
21 80 0.68
22 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
CAATGCGATTTTCCATATTCG
Found at i:2287120 original size:20 final size:21
Alignment explanation
Indices: 2287093--2287148 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
2287083 GCAATTTGCC
2287093 TAATTCGCATTGCGATTTACA
1 TAATTCGCATTGCGATTTACA
* *
2287114 T-ATTCGCGTTGCGATTTTCA
1 TAATTCGCATTGCGATTTACA
*
2287134 TAATTCGCAATGCGA
1 TAATTCGCATTGCGA
2287149 ATACGTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.38
Consensus pattern (21 bp):
TAATTCGCATTGCGATTTACA
Found at i:2287163 original size:20 final size:20
Alignment explanation
Indices: 2287138--2287249 Score: 127
Period size: 20 Copynumber: 5.5 Consensus size: 20
2287128 TTTTCATAAT
2287138 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
2287158 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2287178 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
2287199 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2287219 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
2287239 TCGCAATGCGA
1 TCGCAATGCGA
2287250 TTTACATAGC
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.04
20 57 0.74
21 17 0.22
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2287169 original size:41 final size:40
Alignment explanation
Indices: 2287132--2287257 Score: 130
Period size: 41 Copynumber: 3.1 Consensus size: 40
2287122 TTGCGATTTT
*
2287132 CATAATTCGCAATGCGAATACGTAAATCGCAACGCGATTA
1 CATAAATCGCAATGCGAATACGTAAATCGCAACGCGATTA
* * *
2287172 -AGTAAATCGCAATGCGAATTAGGAAAATCGCAACGCGAATA
1 CA-TAAATCGCAATGCGAA-TACGTAAATCGCAACGCGATTA
* * * *
2287213 CGTAAATCGCAATGCGAAT-CTTACTATCGCAATGCGATTTA
1 CATAAATCGCAATGCGAATACGTA-AATCGCAACGCGA-TTA
2287254 CATA
1 CATA
2287258 GCGCCATTCG
Statistics
Matches: 69, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
39 2 0.03
40 27 0.39
41 40 0.58
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (40 bp):
CATAAATCGCAATGCGAATACGTAAATCGCAACGCGATTA
Found at i:2287861 original size:33 final size:33
Alignment explanation
Indices: 2287773--2287863 Score: 101
Period size: 33 Copynumber: 2.7 Consensus size: 33
2287763 CGAGAATGAA
** *
2287773 AATCGCAACGCGAAAATAACTATCGCAACGAGAG
1 AATCGCAACGCGAAACCAA-AATCGCAACGAGAG
* ** *
2287807 AATCGCAACGTGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAACCAAAATCGCAACGAGAG
*
2287840 AATCGCAACGCGACACCAAAATCG
1 AATCGCAACGCGAAACCAAAATCG
2287864 TATTGCGATT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
33 32 0.67
34 16 0.33
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAACCAAAATCGCAACGAGAG
Found at i:2287902 original size:14 final size:14
Alignment explanation
Indices: 2287883--2287938 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
2287873 TTTCATTTCG
2287883 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2287897 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
2287916 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2287930 CGTTGCGAT
1 CGTTGCGAT
2287939 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2287912 original size:33 final size:33
Alignment explanation
Indices: 2287866--2287959 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
2287856 CAAAATCGTA
**
2287866 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
2287899 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
2287932 TTGCGATAGTCATTTCCGCGTTGCGATT
1 TTGCGATAGTCATTT-CGCGTTGCGATT
2287960 TTCATTATCT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 46 0.79
34 12 0.21
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.41
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:2287964 original size:20 final size:20
Alignment explanation
Indices: 2287930--2287987 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
2287920 GCGATTCTCT
**
2287930 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCCG
*
2287950 CGTTGCGATTTTCATTAT-CT
1 CGTTGCGATTTTCATT-TCCG
2287970 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
2287988 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCG
Found at i:2290156 original size:21 final size:21
Alignment explanation
Indices: 2290132--2290198 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2290122 TCATTCCTCG
2290132 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2290153 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2290174 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2290195 AGAG
1 AGAG
2290199 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:2290156 original size:42 final size:42
Alignment explanation
Indices: 2290080--2290198 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
2290070 GACTCGCCTG
* * * * * * *
2290080 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
2290122 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
2290164 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
2290199 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:2291574 original size:14 final size:14
Alignment explanation
Indices: 2291555--2291604 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
2291545 ATTGTTTAAT
2291555 TGATTTGTAAAATG
1 TGATTTGTAAAATG
2291569 TGATTTGTAAAATG
1 TGATTTGTAAAATG
2291583 TGATTTGTAAAA-G
1 TGATTTGTAAAATG
2291596 TTGATTTGT
1 -TGATTTGT
2291605 TTAATTGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 1 0.03
14 34 0.97
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAATG
Found at i:2291733 original size:19 final size:19
Alignment explanation
Indices: 2291711--2291802 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 19
2291701 AAAAATTACT
2291711 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2291730 ATCGCAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
*
2291744 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2291763 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2291777 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2291796 ATCGCAA
1 ATCGCAA
2291803 CGAGGGAATC
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.35
15 2 0.04
16 3 0.05
17 3 0.05
18 2 0.04
19 27 0.47
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2291753 original size:33 final size:33
Alignment explanation
Indices: 2291711--2291837 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
2291701 AAAAATTACT
*
2291711 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2291744 ATCGCAATGCAAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2291777 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2291810 ATCGCAAAGCGGAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2291838 TGAATTTAGT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2291864 original size:19 final size:19
Alignment explanation
Indices: 2291842--2291882 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
2291832 GCAACGTGAA
2291842 TTTAGTTTCGCGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
*
2291861 TTTAGTTTCGTGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
2291880 TTT
1 TTT
2291883 GTCATTGCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.12, G:0.24, T:0.54
Consensus pattern (19 bp):
TTTAGTTTCGCGTTGCGAT
Found at i:2291896 original size:33 final size:32
Alignment explanation
Indices: 2291854--2291978 Score: 144
Period size: 33 Copynumber: 3.8 Consensus size: 32
2291844 TAGTTTCGCG
** * *
2291854 TTGCGATTTTAGTTTCGTGTTGCGATTTTGTCA
1 TTGCGATTTTA-TTTCGCATTGCGATTATCTCA
*
2291887 TTGCGATTTTTATTTCGCATTGCGATTCTCT-A
1 TTGCGA-TTTTATTTCGCATTGCGATTATCTCA
*
2291919 GTTGCGATTTTCATTTCGCATTGCGATTATCTCG
1 -TTGCGATTTT-ATTTCGCATTGCGATTATCTCA
2291953 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTT-ATTTCGCATTGCGAT
2291979 AGTAATTTCC
Statistics
Matches: 82, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
32 5 0.06
33 72 0.88
34 5 0.06
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (32 bp):
TTGCGATTTTATTTCGCATTGCGATTATCTCA
Found at i:2291909 original size:19 final size:19
Alignment explanation
Indices: 2291885--2291978 Score: 66
Period size: 19 Copynumber: 5.5 Consensus size: 19
2291875 GCGATTTTGT
2291885 CATTGCGATTTTTATTTCG
1 CATTGCGATTTTTATTTCG
*
2291904 CATTGCGATTCTCTA----G
1 CATTGCGATT-TTTATTTCG
*
2291920 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTTATTTCG
*
2291937 CATTGCGA---TTATCTCG
1 CATTGCGATTTTTATTTCG
*
2291953 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTTATTTCG
2291970 CATTGCGAT
1 CATTGCGAT
2291979 AGTAATTTCC
Statistics
Matches: 56, Mismatches: 7, Indels: 24
0.64 0.08 0.28
Matches are distributed among these distances:
13 2 0.04
14 14 0.25
16 7 0.12
17 7 0.12
19 23 0.41
20 3 0.05
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (19 bp):
CATTGCGATTTTTATTTCG
Found at i:2291959 original size:66 final size:66
Alignment explanation
Indices: 2291853--2291978 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 66
2291843 TTAGTTTCGC
** * * *
2291853 GTTGCGATTTTAGTTTCGTGTTGCGATTTTGTCATTGCGATTTTTATTTCGCATTGCGATTCTCT
1 GTTGCGATTTTAGTTTCGCATTGCGATTATCTCATTGCGATTTTCATTTCGCATTGCGATTCTCT
2291918 A
66 A
*
2291919 GTTGCGATTTTCA-TTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 GTTGCGATTTT-AGTTTCGCATTGCGATTATCTCATTGCGATTTTCATTTCGCATTGCGAT
2291979 AGTAATTTCC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 52 0.98
67 1 0.02
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (66 bp):
GTTGCGATTTTAGTTTCGCATTGCGATTATCTCATTGCGATTTTCATTTCGCATTGCGATTCTCT
A
Found at i:2292044 original size:20 final size:20
Alignment explanation
Indices: 2291972--2292044 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
2291962 TCATTTCGCA
* **
2291972 TTGCGATAGTAATTTCCGCG
1 TTGCGATAGTCATTTCCATG
* ***
2291992 TTGCGATAGACATTAAGATG
1 TTGCGATAGTCATTTCCATG
2292012 ATTGCGA-ACGTCATTTCCATG
1 -TTGCGATA-GTCATTTCCATG
2292033 TTGCGATAGTCA
1 TTGCGATAGTCA
2292045 AATGATTGCC
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
20 24 0.62
21 15 0.38
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCATG
Found at i:2292796 original size:33 final size:33
Alignment explanation
Indices: 2292749--2292880 Score: 149
Period size: 33 Copynumber: 4.0 Consensus size: 33
2292739 GGAAATTACT
* *
2292749 ATCATAATGCGAAATGAAAATCGCAACGAGATA
1 ATCACAATGCGAAATGAAAATCGCAACGAGAAA
* *
2292782 ATCACAATGCGAAATGAAAATCGCAACTAGAGA
1 ATCACAATGCGAAATGAAAATCGCAACGAGAAA
* * *
2292815 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCACAATGCGAAATGAAAATCGCAACGAGAAA
* * * *
2292848 ATCGCAACGCGAAACT-AAAATCGTAACGCGAAA
1 ATCACAATGCGAAA-TGAAAATCGCAACGAGAAA
2292881 CTAAAATAAC
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
33 85 0.99
34 1 0.01
ACGTcount: A:0.48, C:0.20, G:0.17, T:0.14
Consensus pattern (33 bp):
ATCACAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:2292869 original size:19 final size:19
Alignment explanation
Indices: 2292814--2292919 Score: 107
Period size: 19 Copynumber: 5.8 Consensus size: 19
2292804 GCAACTAGAG
*
2292814 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACT-AA
2292833 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
2292847 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
2292866 AATCGTAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
**
2292885 AATAACAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
* *
2292904 AATTGTAACGCGAAAC
1 AATCGCAACGCGAAAC
2292920 AAAGTGTTTG
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 57 0.77
ACGTcount: A:0.50, C:0.22, G:0.15, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:2294513 original size:12 final size:12
Alignment explanation
Indices: 2294496--2294520 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2294486 TCTTCGAGGA
2294496 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2294508 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2294520 C
1 C
2294521 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2295569 original size:20 final size:20
Alignment explanation
Indices: 2295544--2295693 Score: 131
Period size: 20 Copynumber: 7.5 Consensus size: 20
2295534 AATTTGGAAA
*
2295544 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
2295564 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
2295585 ATCGTAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2295605 TTCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2295625 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
2295645 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * * *
2295665 TTCACAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
2295685 TTCGCAACG
1 ATCGCAACG
2295694 AGATTCTGAA
Statistics
Matches: 111, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.02
20 94 0.85
21 13 0.12
22 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2295694 original size:20 final size:20
Alignment explanation
Indices: 2295590--2295702 Score: 172
Period size: 20 Copynumber: 5.7 Consensus size: 20
2295580 ACAAAATCGT
*
2295590 AACGCGATACTGACTTTCGC
1 AACGCGATTCTGACTTTCGC
* *
2295610 AATGCGATACTGACTTTCGC
1 AACGCGATTCTGACTTTCGC
2295630 AACGCGATTCTGACTTTCGC
1 AACGCGATTCTGACTTTCGC
*
2295650 AACGCGATTCTGACTTTCAC
1 AACGCGATTCTGACTTTCGC
*
2295670 AACGAGATTCTGACTTTCGC
1 AACGCGATTCTGACTTTCGC
*
2295690 AACGAGATTCTGA
1 AACGCGATTCTGA
2295703 AAATCGCAAT
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 87 1.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (20 bp):
AACGCGATTCTGACTTTCGC
Found at i:2295710 original size:60 final size:60
Alignment explanation
Indices: 2295554--2295711 Score: 181
Period size: 60 Copynumber: 2.6 Consensus size: 60
2295544 ATCGCAATGC
* ** * * * * *
2295554 GATACTGACTATCGCAACGAGATAATACAAAATCGTAACGCGATACTGACTTTCGCAATGC
1 GATACTGACTTTCGCAACGAGATTCT-GAAAATCGCAACGCGATACTGACTTTCACAACGA
* *** *
2295615 GATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATTCTGACTTTCACAACGA
1 GATACTGACTTTCGCAACGAGATTCTGAAAATCGCAACGCGATACTGACTTTCACAACGA
*
2295675 GATTCTGACTTTCGCAACGAGATTCTGAAAATCGCAA
1 GATACTGACTTTCGCAACGAGATTCTGAAAATCGCAA
2295712 TCATCTTCAA
Statistics
Matches: 79, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 57 0.72
61 22 0.28
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (60 bp):
GATACTGACTTTCGCAACGAGATTCTGAAAATCGCAACGCGATACTGACTTTCACAACGA
Found at i:2295950 original size:20 final size:20
Alignment explanation
Indices: 2295925--2295972 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
2295915 CAACGGGGAA
2295925 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
2295945 ATCGCAACGCGAAGATGGCT
1 ATCGCAACGCGAAAATGGCT
2295965 ATCGCAAC
1 ATCGCAAC
2295973 TAGAAAATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:2297672 original size:41 final size:42
Alignment explanation
Indices: 2297618--2297709 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
2297608 CCTCTTCAAC
* * * *
2297618 GATGACAGTGGCCTCTTGAAC-GGTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACAAGTAGAGGGGACTCTTGAGG
* *
2297659 GATGATAGGGGCCTCTTGAACAATTAGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACAAGTAGAGGGGACTCTTGAGG
2297701 GATGACAGG
1 GATGACAGG
2297710 TGAGTCGGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 19 0.44
42 24 0.56
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACAAGTAGAGGGGACTCTTGAGG
Found at i:2297674 original size:21 final size:21
Alignment explanation
Indices: 2297645--2297705 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
2297635 GAACGGTGGG
*
2297645 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* *** *
2297666 GGGGCCTCTTGAACAATTAGA
1 GGGGACTCTTGAGGGATGAGA
2297687 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
2297706 CAGGTGAGTC
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.13, G:0.39, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:2298068 original size:20 final size:20
Alignment explanation
Indices: 2298043--2298135 Score: 78
Period size: 20 Copynumber: 4.7 Consensus size: 20
2298033 GAAGAATAGT
*
2298043 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
2298063 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* * * *
2298083 TGACTATCGCAACGCGGAAA
1 TTACTTTCGCAACACGAAAA
* * * *
2298103 TGACTATCGCAACGCGGAAA
1 TTACTTTCGCAACACGAAAA
* *
2298123 TGACTATCGCAAC
1 TTACTTTCGCAAC
2298136 GCGGAAATGG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.20
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:2298093 original size:40 final size:40
Alignment explanation
Indices: 2298049--2298174 Score: 148
Period size: 40 Copynumber: 3.2 Consensus size: 40
2298039 TAGTTTACTT
* *
2298049 TCGCAACAC-GAAACTTACTTTCGCAACGCGAAAATGACTA
1 TCGCAACACGGAAA-TGACTATCGCAACGCGAAAATGACTA
* *
2298089 TCGCAACGCGGAAATGACTATCGCAACGCGGAAATGACTA
1 TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
* * * **
2298129 TCGCAACGCGGAAATGGCTATCGCAATGCG-AAATGAAAA
1 TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
2298168 TCGCAAC
1 TCGCAAC
2298175 GACAAAATCG
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 14 0.18
40 59 0.77
41 4 0.05
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (40 bp):
TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
Found at i:2298136 original size:20 final size:20
Alignment explanation
Indices: 2298069--2298175 Score: 162
Period size: 20 Copynumber: 5.4 Consensus size: 20
2298059 AAACTTACTT
*
2298069 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
2298089 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
2298109 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2298129 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
2298149 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
2298168 TCGCAACG
1 TCGCAACG
2298176 ACAAAATCGC
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
19 14 0.17
20 66 0.82
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2298241 original size:14 final size:14
Alignment explanation
Indices: 2298222--2298280 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
2298212 TTTCATTTCG
2298222 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2298236 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
2298253 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
2298269 CGTTGCAATTTT
1 CGTTGCGATTTT
2298281 TATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 17 0.46
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2298253 original size:33 final size:33
Alignment explanation
Indices: 2298206--2298296 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
2298196 ACAAATCGCA
*
2298206 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
2298238 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
* *
2298271 TTGCAATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
2298297 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 6 0.11
33 49 0.89
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:2298304 original size:19 final size:20
Alignment explanation
Indices: 2298282--2298324 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2298272 TGCAATTTTT
2298282 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
2298301 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
2298321 ATTT
1 ATTT
2298325 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:2298315 original size:20 final size:20
Alignment explanation
Indices: 2298290--2298335 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2298280 TTATTTCGCA
2298290 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
2298310 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
2298330 TTGCGA
1 TTGCGA
2298336 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:2298893 original size:18 final size:18
Alignment explanation
Indices: 2298870--2298917 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
2298860 CGGGTCGATC
2298870 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
2298888 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
2298906 AGGTGATGGCTC
1 AGGTGATGGCTC
2298918 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:2300284 original size:20 final size:20
Alignment explanation
Indices: 2300236--2300294 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2300226 AATAGTTTCT
* *
2300236 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
2300256 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
2300276 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
2300295 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:2300582 original size:22 final size:22
Alignment explanation
Indices: 2300557--2300600 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2300547 GATGAAGATA
2300557 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2300579 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2300601 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2300886 original size:41 final size:41
Alignment explanation
Indices: 2300767--2300904 Score: 170
Period size: 41 Copynumber: 3.4 Consensus size: 41
2300757 CGCTTTGAAA
* * * *
2300767 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTTAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** * * *
2300808 ATTGCGTTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
2300848 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
2300889 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
2300905 CTAAATTCGC
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 32 0.41
41 47 0.59
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.37
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:2300901 original size:20 final size:20
Alignment explanation
Indices: 2300787--2300900 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
2300777 GATTATGTAT
* *
2300787 TATCTCGTTGCGAAAGTTAG
1 TATCGCGTTGCGAAAGTCAG
* * *
2300807 TATTGCGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
2300827 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
2300847 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
2300868 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
2300888 TATCGCGTTGCGA
1 TATCGCGTTGCGA
2300901 TTTTCTAAAT
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
19 3 0.04
20 58 0.75
21 14 0.18
22 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:2300919 original size:21 final size:21
Alignment explanation
Indices: 2300890--2300962 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
2300880 ATAGTCAGTA
*
2300890 TCGCGTTGCGATTTTCTAAAT
1 TCGCATTGCGATTTTCTAAAT
*
2300911 TCGCATTGCGATTTTCAAAAT
1 TCGCATTGCGATTTTCTAAAT
* *
2300932 TCGCATTGCGATTTACT-TAT
1 TCGCATTGCGATTTTCTAAAT
2300952 TCGCATTGCGA
1 TCGCATTGCGA
2300963 ATTGAGAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 13 0.28
21 34 0.72
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCTAAAT
Found at i:2300920 original size:41 final size:40
Alignment explanation
Indices: 2300834--2300962 Score: 132
Period size: 41 Copynumber: 3.1 Consensus size: 40
2300824 AAGTATCGAG
* * * *
2300834 TTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCG
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCTAAT-TCGCA
2300875 TTGCGATAGTCAGTATCGCGTTGCGATTTTCTAAATTCGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCT-AATTCGCA
** ** * * *
2300916 TTGCGATTTTCAAAATTCGCATTGCGATTTACTTATTCGCA
1 TTGCGATAGTCAGTA-TCGCGTTGCGATTTTCTAATTCGCA
2300957 TTGCGA
1 TTGCGA
2300963 ATTGAGAAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
41 58 0.77
42 17 0.23
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (40 bp):
TTGCGATAGTCAGTATCGCGTTGCGATTTTCTAATTCGCA
Found at i:2300973 original size:42 final size:42
Alignment explanation
Indices: 2300890--2300973 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
2300880 ATAGTCAGTA
* * **
2300890 TCGCGTTGCGATTTTCTAAATTCGCATTGCGATTTTCAAAAT
1 TCGCATTGCGATTTACTAAATTCGCATTGCGATTGACAAAAT
* *
2300932 TCGCATTGCGATTTACT-TATTCGCATTGCGAATTGAGAAAAT
1 TCGCATTGCGATTTACTAAATTCGCATTGCG-ATTGACAAAAT
2300974 CGTAACGCGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 12 0.34
42 23 0.66
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (42 bp):
TCGCATTGCGATTTACTAAATTCGCATTGCGATTGACAAAAT
Found at i:2301004 original size:21 final size:22
Alignment explanation
Indices: 2300952--2301004 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2300942 ATTTACTTAT
2300952 TCGCATTGCG-AATTGAGAAAA
1 TCGCATTGCGAAATTGAGAAAA
* **
2300973 TCGTAACGCGAAATTG-GAAAA
1 TCGCATTGCGAAATTGAGAAAA
2300994 TCGCATTGCGA
1 TCGCATTGCGA
2301005 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGAGAAAA
Found at i:2311633 original size:16 final size:16
Alignment explanation
Indices: 2311612--2311647 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
2311602 AAGTTTACTC
2311612 AATTC-AAATAAATTTA
1 AATTCAAAAT-AATTTA
2311628 AATTCAAAATAATTTA
1 AATTCAAAATAATTTA
2311644 AATT
1 AATT
2311648 GAATCAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTCAAAATAATTTA
Found at i:2311667 original size:2 final size:2
Alignment explanation
Indices: 2311656--2311698 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2311646 TTGAATCAAA
2311656 AT AT -T 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
2311697 AT
1 AT
2311699 CAATTTAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2313749 original size:59 final size:57
Alignment explanation
Indices: 2313573--2313752 Score: 177
Period size: 59 Copynumber: 3.1 Consensus size: 57
2313563 GTCCTCAAGG
* * ** *
2313573 TATGACCTTCATTTTAAATCGGTCCCTAAACTTTTAAATTTTCC-ATCTTTATCCTAAAC
1 TATGA-CTTCATTCTAAATTGGTCCCTAAACTTTTAAACATTCCAAT-TTCATCC-AAAC
* * * *
2313632 TATGACTATCATTCTAAATTAGT-TCTCAAACTTTTGAACATTTCAATTTCATCCCAAAC
1 TATGACT-TCATTCTAAATTGGTCCCT-AAACTTTTAAACATTCCAATTTCAT-CCAAAC
2313691 -ATGATCTTCATTCTAAATTGGTCCCTAAACTTTTTAAACATTCCAATTTCATCTCAAAC
1 TATGA-CTTCATTCTAAATTGGTCCCTAAAC-TTTTAAACATTCCAATTTCATC-CAAAC
2313750 TAT
1 TAT
2313753 TAATTAAACT
Statistics
Matches: 99, Mismatches: 13, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
58 27 0.27
59 66 0.67
60 6 0.06
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.41
Consensus pattern (57 bp):
TATGACTTCATTCTAAATTGGTCCCTAAACTTTTAAACATTCCAATTTCATCCAAAC
Found at i:2317387 original size:20 final size:19
Alignment explanation
Indices: 2317343--2317396 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
2317333 TGGATCACGG
** *
2317343 AATGTAAAATTATTAGTAG
1 AATGTAAAATTACCAGTAA
2317362 AATGTAAAATTACCAGTGAA
1 AATGTAAAATTACCAGT-AA
*
2317382 AATGTAAGATTACCA
1 AATGTAAAATTACCA
2317397 TGGAATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (19 bp):
AATGTAAAATTACCAGTAA
Found at i:2317625 original size:37 final size:37
Alignment explanation
Indices: 2317552--2317626 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
2317542 ATTGAAAAAT
* *
2317552 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
2317589 ATTTATATAATTTTTTTTATAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
2317626 A
1 A
2317627 AGGTTTATTG
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:0.03, G:0.01, T:0.48
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:2318125 original size:10 final size:10
Alignment explanation
Indices: 2318112--2318149 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
2318102 ATTTTTTTGC
2318112 TTTATTTTAG
1 TTTATTTTAG
2318122 TTTA-TTT-G
1 TTTATTTTAG
2318130 CTTTATTTTAG
1 -TTTATTTTAG
2318141 TTTATTTTA
1 TTTATTTTA
2318150 CAACTTACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 1 0.04
9 7 0.28
10 16 0.64
11 1 0.04
ACGTcount: A:0.18, C:0.03, G:0.08, T:0.71
Consensus pattern (10 bp):
TTTATTTTAG
Found at i:2318131 original size:19 final size:19
Alignment explanation
Indices: 2318107--2318147 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2318097 TTCTTATTTT
2318107 TTTGCTTTATTTTAGTTTA
1 TTTGCTTTATTTTAGTTTA
2318126 TTTGCTTTATTTTAGTTTA
1 TTTGCTTTATTTTAGTTTA
2318145 TTT
1 TTT
2318148 TACAACTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.15, C:0.05, G:0.10, T:0.71
Consensus pattern (19 bp):
TTTGCTTTATTTTAGTTTA
Found at i:2318631 original size:43 final size:42
Alignment explanation
Indices: 2318561--2318662 Score: 152
Period size: 43 Copynumber: 2.4 Consensus size: 42
2318551 CCTAAACCTG
2318561 AACCCGACCCGACCCGACCTGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGACCCGACCTGACCCGAATATCACACTT-AAAA
* * *
2318604 AACTCGACTCGACCCGA-CTCGACCCGAATATCACTCTTAAAA
1 AACCCGACCCGACCCGACCT-GACCCGAATATCACACTTAAAA
2318646 AACCCGACCCGACCCGA
1 AACCCGACCCGACCCGA
2318663 ACAAAATAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
42 21 0.40
43 32 0.60
ACGTcount: A:0.34, C:0.40, G:0.13, T:0.13
Consensus pattern (42 bp):
AACCCGACCCGACCCGACCTGACCCGAATATCACACTTAAAA
Found at i:2318954 original size:256 final size:257
Alignment explanation
Indices: 2318564--2319142 Score: 795
Period size: 262 Copynumber: 2.2 Consensus size: 257
2318554 AAACCTGAAC
2318564 CCGACCCGACCCGACCTGACCCGAATATCACACTTAAAAAAACTCGACTCGACCCGACTCGACCC
1 CCGA-CCGA-CCGACC-GACCCGAATATCACACTTAAAAAAA----ACTCGACCCGACTCGACCC
*
2318629 GAATATCACTCTTAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGA
59 GAATATCACACTT-AAAAA--C-ACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGA
2318694 ATATATGAATTAGAAAT-CCGACCCGACTC-GACCCGAAATAAT-AAAAAATTATTTTTATTTAA
120 ATATATGAATTAGAAATCCCGACCCGAC-CGGACCCGAAATAATAAAAAAATTATTTTTATTTAA
*
2318756 TAAAAACAGTGACTTAATCCGACCGGACCCGAATTATATATATTTTC-AGGTCGGTCCAGTTTTT
184 TAAAAACAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTCGA-GTCGGTCCAGTTTTT
2318820 TTCACCCTAAA
248 TT-ACCCTAAA
*
2318831 CCGACTCGACCTGACCGACCCGAATATCACACTTAAAAAAAACCCGACCCGACTCGACCCGAATA
1 CCGAC-CGACC-GACCGACCCGAATATCACACTTAAAAAAAACTCGACCCGACTCGACCCGAATA
* *
2318896 TCACACTT-AAAA-ACTCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCTGAATATATGAA
64 TCACACTTAAAAACACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAA
2318959 TTAGAAATCCAACCCGACCCGACCGGACCCGAAATAATAAAAAAATTATTTTTATTTAATAAAAA
129 TTAGAAAT----CCCGACCCGACCGGACCCGAAATAATAAAAAAATTATTTTTATTTAATAAAAA
* * *
2319024 CAGTGACTTAATCTGACCCGACCTGAATTATATATATTTTCGAGTCGGTCCCGTTTTTTTACCCT
190 CAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTCGAGTCGGTCCAGTTTTTTTACCCT
2319089 AAA
255 AAA
* * *
2319092 -C--CCGAAC--CCGACCCGAATATCACACTT-AAAAAAACTCGATCCGACCCGACC
1 CCGACCGACCGACCGACCCGAATATCACACTTAAAAAAAACTCGACCCGACTCGACC
2319143 AAAATAAAGT
Statistics
Matches: 290, Mismatches: 12, Indels: 34
0.86 0.04 0.10
Matches are distributed among these distances:
253 21 0.07
254 20 0.07
256 57 0.20
257 4 0.01
258 1 0.00
260 6 0.02
261 31 0.11
262 110 0.38
263 1 0.00
266 28 0.10
267 11 0.04
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.22
Consensus pattern (257 bp):
CCGACCGACCGACCGACCCGAATATCACACTTAAAAAAAACTCGACCCGACTCGACCCGAATATC
ACACTTAAAAACACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATT
AGAAATCCCGACCCGACCGGACCCGAAATAATAAAAAAATTATTTTTATTTAATAAAAACAGTGA
CTTAATCCGACCCGACCCGAATTATATATATTTTCGAGTCGGTCCAGTTTTTTTACCCTAAA
Found at i:2319545 original size:27 final size:29
Alignment explanation
Indices: 2319502--2319555 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
2319492 TCGCTTCTTC
2319502 TTAAAAAATTGATTTTTTTATT-TTTTCA
1 TTAAAAAATTGATTTTTTTATTCTTTTCA
2319530 TTAAAAAATTGA-TTTTTTATTCTTTT
1 TTAAAAAATTGATTTTTTTATTCTTTT
2319556 AAAATTATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (29 bp):
TTAAAAAATTGATTTTTTTATTCTTTTCA
Found at i:2325107 original size:18 final size:19
Alignment explanation
Indices: 2325086--2325131 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2325076 AAATGTTAAG
2325086 ATTATTATAAAA-ATAAAA
1 ATTATTATAAAATATAAAA
2325104 ATTAATT-TAAAATATAAAA
1 ATT-ATTATAAAATATAAAA
*
2325123 AATATTATA
1 ATTATTATA
2325132 TTAACTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTATTATAAAATATAAAA
Found at i:2342779 original size:14 final size:14
Alignment explanation
Indices: 2342760--2342798 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
2342750 TTCTTTTTGT
2342760 TTCTCTTCTTCTTC
1 TTCTCTTCTTCTTC
2342774 TTCTCTTCTTCTTC
1 TTCTCTTCTTCTTC
*
2342788 ATCTCTTCTTC
1 TTCTCTTCTTC
2342799 CATATTCCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.03, C:0.36, G:0.00, T:0.62
Consensus pattern (14 bp):
TTCTCTTCTTCTTC
Found at i:2342780 original size:11 final size:12
Alignment explanation
Indices: 2342766--2342798 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
2342756 TTGTTTCTCT
2342766 TCTTCTTCTTC-
1 TCTTCTTCTTCA
2342777 TCTTCTTCTTCA
1 TCTTCTTCTTCA
2342789 TC-TCTTCTTC
1 TCTTCTTCTTC
2342799 CATATTCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 19 0.90
12 2 0.10
ACGTcount: A:0.03, C:0.36, G:0.00, T:0.61
Consensus pattern (12 bp):
TCTTCTTCTTCA
Found at i:2344662 original size:21 final size:20
Alignment explanation
Indices: 2344630--2344668 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2344620 TTCCAAAACA
2344630 AGGGATAAGTAAGATAGATTG
1 AGGGATAAGTAAGA-AGATTG
2344651 AGGGA-AAGGTAAGAAGAT
1 AGGGATAA-GTAAGAAGAT
2344669 ATAGGTGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.46, C:0.00, G:0.36, T:0.18
Consensus pattern (20 bp):
AGGGATAAGTAAGAAGATTG
Found at i:2345057 original size:22 final size:22
Alignment explanation
Indices: 2345029--2345089 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
2345019 GGTTCTACGT
*
2345029 GGTCATTCGGGACATATACAGA
1 GGTCATTCGGGACAAATACAGA
* *
2345051 GGTCATTCGGGATAAATACATA
1 GGTCATTCGGGACAAATACAGA
* *
2345073 GGTCCTTTGGGACAAAT
1 GGTCATTCGGGACAAAT
2345090 TTCATATGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (22 bp):
GGTCATTCGGGACAAATACAGA
Found at i:2350583 original size:22 final size:23
Alignment explanation
Indices: 2350555--2350607 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
2350545 GACCGAAATT
*
2350555 ACTGTAGCAAGGGTATCGGTA-C
1 ACTGTAGCAAGGGTATCGATACC
2350577 ACTGTAGC-AGGGTATCGATACC
1 ACTGTAGCAAGGGTATCGATACC
*
2350599 CCTGTAGCA
1 ACTGTAGCA
2350608 TTCTGGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (23 bp):
ACTGTAGCAAGGGTATCGATACC
Found at i:2351046 original size:14 final size:14
Alignment explanation
Indices: 2351027--2351056 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2351017 ATCAACTAAG
2351027 AAGTTTTACCCAAT
1 AAGTTTTACCCAAT
2351041 AAGTTTTACCCAAT
1 AAGTTTTACCCAAT
2351055 AA
1 AA
2351057 TCTAGAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (14 bp):
AAGTTTTACCCAAT
Found at i:2354154 original size:16 final size:16
Alignment explanation
Indices: 2354122--2354162 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2354112 GTTTACTTCA
*
2354122 GAATGATT-AAGTGTT
1 GAATGATTCAAATGTT
2354137 GAATGATTCAAATGTT
1 GAATGATTCAAATGTT
*
2354153 GAATAATTCA
1 GAATGATTCA
2354163 GAGGTTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.37
Consensus pattern (16 bp):
GAATGATTCAAATGTT
Found at i:2354241 original size:23 final size:23
Alignment explanation
Indices: 2354215--2354278 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
2354205 TTTACTGACT
2354215 CTGAATCATTCAGCACTGTTTTG
1 CTGAATCATTCAGCACTGTTTTG
2354238 CTGAATCATTCAGCACTGTTTTG
1 CTGAATCATTCAGCACTGTTTTG
*
2354261 CTGAATCAGTCAGCACTG
1 CTGAATCATTCAGCACTG
2354279 AATCATTCAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (23 bp):
CTGAATCATTCAGCACTGTTTTG
Found at i:2362231 original size:71 final size:71
Alignment explanation
Indices: 2362115--2362328 Score: 392
Period size: 71 Copynumber: 3.0 Consensus size: 71
2362105 ATGCACGTCT
*
2362115 CGAACCTATGGCCTTTGTGTTATTAGCACGACACTCTAGTAAAGTGAGCTAATTGGTCATTTGAT
1 CGAACCTATGACCTTTGTGTTATTAGCACGACACTCTAGTAAAGTGAGCTAATTGGTCATTTGAT
2362180 TTTTAA
66 TTTTAA
2362186 CGAACCTATGACCTTTGTGTTATTAGCACGACACTCTAGTAAAGTGAGCTAATTGGTCATTTGAT
1 CGAACCTATGACCTTTGTGTTATTAGCACGACACTCTAGTAAAGTGAGCTAATTGGTCATTTGAT
2362251 TTTTAA
66 TTTTAA
* * *
2362257 CGAACCTATGACATTTGTGTTATTAGCACGACACTCTAATAAACTGAGCTAATTGGTCATTTGAT
1 CGAACCTATGACCTTTGTGTTATTAGCACGACACTCTAGTAAAGTGAGCTAATTGGTCATTTGAT
2362322 TTTTAA
66 TTTTAA
2362328 C
1 C
2362329 ATTGTAATTT
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 139 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (71 bp):
CGAACCTATGACCTTTGTGTTATTAGCACGACACTCTAGTAAAGTGAGCTAATTGGTCATTTGAT
TTTTAA
Found at i:2369526 original size:38 final size:38
Alignment explanation
Indices: 2369476--2369555 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
2369466 AATCCAAGCA
2369476 ATTT-ACAGAGGTTCGGATGCTGCAACAATGCGAGAGT
1 ATTTAACAGAGGTTCGGATGCTGCAACAATGCGAGAGT
2369513 ATTTAACAGAGGTTCGGATGCTGCAACAATGCGAGAGT
1 ATTTAACAGAGGTTCGGATGCTGCAACAATGCGAGAGT
2369551 ATTTA
1 ATTTA
2369556 CTTCGTTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 4 0.10
38 38 0.90
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (38 bp):
ATTTAACAGAGGTTCGGATGCTGCAACAATGCGAGAGT
Found at i:2373415 original size:27 final size:28
Alignment explanation
Indices: 2373353--2373417 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
2373343 TGACTCATGT
* *
2373353 TTTAAATTAATTCTTCAAATTTAAATAT
1 TTTATATTAATTCTTCAAATTTAAATAA
**
2373381 TTTATATTAATTCTT-AAATTCTCTATAA
1 TTTATATTAATTCTTCAAATT-TAAATAA
2373409 TTT-TATTAA
1 TTTATATTAA
2373418 CATGATTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 11 0.34
28 21 0.66
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTATATTAATTCTTCAAATTTAAATAA
Found at i:2374440 original size:14 final size:12
Alignment explanation
Indices: 2374412--2374436 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2374402 TTTAATTTAT
2374412 ATAAATTTTAAA
1 ATAAATTTTAAA
2374424 ATAAATTTTAAA
1 ATAAATTTTAAA
2374436 A
1 A
2374437 AATATGATAA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAAATTTTAAA
Found at i:2375242 original size:2 final size:2
Alignment explanation
Indices: 2375235--2375263 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2375225 TGCTGTTCTT
2375235 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2375264 TTTTTGTACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2377454 original size:60 final size:60
Alignment explanation
Indices: 2377322--2377469 Score: 190
Period size: 60 Copynumber: 2.5 Consensus size: 60
2377312 GAGCTGGCAA
* * * * * * *
2377322 AAGGCGCATCCCCGGGGACGCGCTTTACCCGGGTTTTCGCTGAGTTGGATGCCATGTGTGG
1 AAGGCGCATCCCCGGGGACGCGCCTT-CACGGGTTCTCGATGACTCGGATGCCACGTGTGG
*
2377383 AAGGCGCATCCCCGGGGACGCGCCTTCACGGGATTCT-GATGACTCGGCTGCCACGTGTGG
1 AAGGCGCATCCCCGGGGACGCGCCTTCACGGG-TTCTCGATGACTCGGATGCCACGTGTGG
*
2377443 AAGGCGCATCCCCGGGGACGCACCTTC
1 AAGGCGCATCCCCGGGGACGCGCCTTC
2377470 CATTAAATAC
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
60 49 0.64
61 28 0.36
ACGTcount: A:0.15, C:0.31, G:0.34, T:0.20
Consensus pattern (60 bp):
AAGGCGCATCCCCGGGGACGCGCCTTCACGGGTTCTCGATGACTCGGATGCCACGTGTGG
Found at i:2377695 original size:15 final size:15
Alignment explanation
Indices: 2377677--2377714 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
2377667 AAATAGTTAT
*
2377677 TATATTTTATATTAA
1 TATATTTTATATAAA
2377692 TATA-TTTATATAAA
1 TATATTTTATATAAA
2377706 TATTATTTT
1 TA-TATTTT
2377715 TTTTATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 11 0.55
15 6 0.30
16 3 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATATTTTATATAAA
Found at i:2377712 original size:35 final size:35
Alignment explanation
Indices: 2377666--2377752 Score: 108
Period size: 35 Copynumber: 2.5 Consensus size: 35
2377656 TAGTATTTTT
2377666 TAAATAGTTATTATATTTTATATT-AAT-ATATTTATA
1 TAAATA-TTATT-TATTTT-TATTAAATAATATTTATA
2377702 TAAATATTATTT-TTTTTATTAAAATAATATTTATA
1 TAAATATTATTTATTTTTATT-AAATAATATTTATA
*
2377737 TAATTATTATTTATTT
1 TAAATATTATTTATTT
2377753 AGAATTATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
32 4 0.09
33 4 0.09
34 4 0.09
35 25 0.54
36 9 0.20
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (35 bp):
TAAATATTATTTATTTTTATTAAATAATATTTATA
Found at i:2377918 original size:17 final size:16
Alignment explanation
Indices: 2377896--2377949 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
2377886 TAATGTTAAT
2377896 ATTTAAATTTATTTTTA
1 ATTTAAA-TTATTTTTA
* *
2377913 ATTTAAAGTTATTATGA
1 ATTTAAA-TTATTTTTA
* *
2377930 ATTTATATTAATTTTA
1 ATTTAAATTATTTTTA
2377946 ATTT
1 ATTT
2377950 TTTATAATGT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 10 0.33
17 20 0.67
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
ATTTAAATTATTTTTA
Done.