Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 51
Found at i:551012 original size:18 final size:20
Alignment explanation
Indices: 550984--551034 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 20
550974 GGGATTAAAG
550984 AAAATATATTATTAAAATA-T
1 AAAA-ATATTATTAAAATATT
551004 -AAAATATTA--AAAATATT
1 AAAAATATTATTAAAATATT
551021 AAAAATATATATTA
1 AAAAATAT-TATTA
551035 TAAAATAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
16 6 0.23
17 1 0.04
18 13 0.50
19 5 0.19
21 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATATTATTAAAATATT
Found at i:551504 original size:27 final size:27
Alignment explanation
Indices: 551457--551530 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 27
551447 CCAAATTATC
551457 AAACCTCAAACCATAAAATCATAAACCAT
1 AAACC-CAAACC-TAAAATCATAAACCAT
*
551486 AAAACCCAAACCT-AAATCATAAACCCT
1 -AAACCCAAACCTAAAATCATAAACCAT
551513 AAACCCTAAACCTCAAAA
1 AAACCC-AAACCT-AAAA
551531 CTTATATCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 6 0.15
27 19 0.47
28 1 0.03
29 9 0.22
30 5 0.12
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (27 bp):
AAACCCAAACCTAAAATCATAAACCAT
Found at i:551506 original size:20 final size:21
Alignment explanation
Indices: 551478--551524 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
551468 CATAAAATCA
551478 TAAACCATAAAACCC-AAA-CC
1 TAAACCAT-AAACCCTAAACCC
*
551498 TAAATCATAAACCCTAAACCC
1 TAAACCATAAACCCTAAACCC
551519 TAAACC
1 TAAACC
551525 TCAAAACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 6 0.26
20 10 0.43
21 7 0.30
ACGTcount: A:0.51, C:0.34, G:0.00, T:0.15
Consensus pattern (21 bp):
TAAACCATAAACCCTAAACCC
Found at i:551565 original size:28 final size:27
Alignment explanation
Indices: 551512--551565 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 27
551502 TCATAAACCC
*
551512 TAAACCCTAAACCTCAAAACTTATATCT
1 TAAACCCTAAA-CTCAAAACTAATATCT
551540 TAAACCCTAAA-TCATAAACCTAATAT
1 TAAACCCTAAACTCA-AAA-CTAATAT
551566 TAAAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 3 0.13
27 3 0.13
28 17 0.74
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (27 bp):
TAAACCCTAAACTCAAAACTAATATCT
Found at i:553169 original size:2 final size:2
Alignment explanation
Indices: 553162--553201 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
553152 ATAATAAGGA
553162 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
553202 CTTCATCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:555786 original size:57 final size:57
Alignment explanation
Indices: 555697--555914 Score: 355
Period size: 57 Copynumber: 3.8 Consensus size: 57
555687 AGATGAAGCT
* *
555697 TGATCTTCCGGATCTTGCAAGCATAACCGTTTAGGCAATCTGCTAGACTCACCAGCC
1 TGATCTTCCGGATCTTGCAAGCGTAACTGTTTAGGCAATCTGCTAGACTCACCAGCC
* *
555754 TGATCTTCCAGATCTTGCAAGCGTAACTGTTTAGGCAATCTGCTATACTCACCAGCC
1 TGATCTTCCGGATCTTGCAAGCGTAACTGTTTAGGCAATCTGCTAGACTCACCAGCC
* *
555811 AGATCTTCCGGATCTTGCAAGGGTAACTGTTTAGGCAATCTGCTAGACTCACCAGCC
1 TGATCTTCCGGATCTTGCAAGCGTAACTGTTTAGGCAATCTGCTAGACTCACCAGCC
* * *
555868 CGATCTTCCGGACCTTGCAAGGGTAACTGTTTAGGCAATCTGCTAGA
1 TGATCTTCCGGATCTTGCAAGCGTAACTGTTTAGGCAATCTGCTAGA
555915 TTCATCATGC
Statistics
Matches: 151, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 151 1.00
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (57 bp):
TGATCTTCCGGATCTTGCAAGCGTAACTGTTTAGGCAATCTGCTAGACTCACCAGCC
Found at i:571066 original size:2 final size:2
Alignment explanation
Indices: 571061--571096 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
571051 CCGGGCTTAA
571061 AT AT AT A- AT AT A- AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
571097 ATAATTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:571111 original size:3 final size:3
Alignment explanation
Indices: 571090--571146 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
571080 TATATATATA
* *
571090 TAT TAT AAT AAT TATT TAT TAT TAT TAAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
571137 TA- TAT TAT TA
1 TAT TAT TAT TA
571147 ATACTATTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 41 0.84
4 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:571120 original size:17 final size:17
Alignment explanation
Indices: 571098--571146 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
571088 TATATTATAA
571098 TAATTATTTATTATTAT
1 TAATTATTTATTATTAT
571115 TAATTA-TTATTATTAT
1 TAATTATTTATTATTAT
571131 T-ATTATTATATTATTA
1 TAATTATT-TATTATTA
571147 ATACTATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.13
16 12 0.40
17 14 0.47
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TAATTATTTATTATTAT
Found at i:572586 original size:18 final size:18
Alignment explanation
Indices: 572563--572598 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
572553 ATATAACACA
572563 TATGTCCCGAAGGACCGC
1 TATGTCCCGAAGGACCGC
572581 TATGTCCCGAAGGACCGC
1 TATGTCCCGAAGGACCGC
572599 GTAGACCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAAGGACCGC
Found at i:574347 original size:6 final size:6
Alignment explanation
Indices: 574336--574363 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
574326 ATCGAGTTTT
574336 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
574364 CGCAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:576589 original size:19 final size:19
Alignment explanation
Indices: 576565--576603 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
576555 GTAAATGATT
*
576565 CAAAGTTACA-GATCTTTGA
1 CAAAGTAACATGAT-TTTGA
576584 CAAAGTAACATGATTTTGA
1 CAAAGTAACATGATTTTGA
576603 C
1 C
576604 CTTACCCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (19 bp):
CAAAGTAACATGATTTTGA
Found at i:578345 original size:147 final size:147
Alignment explanation
Indices: 578074--578828 Score: 1161
Period size: 147 Copynumber: 5.1 Consensus size: 147
578064 GATGGTGGTT
* * * * * *
578074 GCTCAACTTCACAGTGAAGGAGCGTCTGTCATCAAATAACTTTCTAGTTTCATTCAGAGCCAATT
1 GCTCAACTTCACAGCGAAGGGGCGTCTGTCAACAAACAACCTTCCAGTTTCATTCAGAGCCAATT
578139 TCAACTTCACGGCGAAGGATATTGGACTCGAAACAACACAAGATTGGATTTCAACTTCACAACAA
66 TCAACTTCACGGCGAAGGATATTGGACTCGAAACAACACAAGATTGGATTTCAACTTCACAACAA
*
578204 AGAATATCCAATTCAAA
131 AGGATATCCAATTCAAA
* * *
578221 GATAAACTTCACAGCAAAGGGGCGTCTGTCAACAAACAACCTTCCAGTTTCATTCAGAGCCAATT
1 GCTCAACTTCACAGCGAAGGGGCGTCTGTCAACAAACAACCTTCCAGTTTCATTCAGAGCCAATT
* * *
578286 TCAACTTCACGGCGAAGGATATTGGACTCGAAACAATAAAAGATTGGATTTCAACTTCACAACGA
66 TCAACTTCACGGCGAAGGATATTGGACTCGAAACAACACAAGATTGGATTTCAACTTCACAACAA
578351 AGGATATCCAATTCAAA
131 AGGATATCCAATTCAAA
* *
578368 GCTCAACTTCACAGCGAAGGGGCGTCTGTCAACAAACAACCTTCCAGATTCATTTAG-GTCCAAT
1 GCTCAACTTCACAGCGAAGGGGCGTCTGTCAACAAACAACCTTCCAGTTTCATTCAGAG-CCAAT
*
578432 TTCAACTTCACGGTGAAGGATATTGGACTCGAAACAACACAAGATTGGATTTCAACTTCACAACA
65 TTCAACTTCACGGCGAAGGATATTGGACTCGAAACAACACAAGATTGGATTTCAACTTCACAACA
*
578497 AATGATATCCAATTCAAA
130 AAGGATATCCAATTCAAA
* * * *
578515 GCTCAACTTCACAGCGAAGGGGCGTCTATCAATAAATAACTTTCCAGTTTCATTCAGAGCCAATT
1 GCTCAACTTCACAGCGAAGGGGCGTCTGTCAACAAACAACCTTCCAGTTTCATTCAGAGCCAATT
* ** ** *
578580 TCAACTTCACGGCGAATGATATTGGGTTCGAAACAACACAAGATTATATTTCAACTTCACAACGA
66 TCAACTTCACGGCGAAGGATATTGGACTCGAAACAACACAAGATTGGATTTCAACTTCACAACAA
578645 AGGATATCCAATTCAAA
131 AGGATATCCAATTCAAA
* * * * *
578662 GTTCAACTTCATAGCTAAGGGGCGTTTGTCAATAAACAACCTTCCAGTTTCATTCAGAGCCAATT
1 GCTCAACTTCACAGCGAAGGGGCGTCTGTCAACAAACAACCTTCCAGTTTCATTCAGAGCCAATT
* * *
578727 TCAACTTCACGGCGAAGGATATTGGACTCCAAACAACATAAGATTGGATTTCAACTTCACGACAA
66 TCAACTTCACGGCGAAGGATATTGGACTCGAAACAACACAAGATTGGATTTCAACTTCACAACAA
*
578792 AGGATATCCAATTCAAG
131 AGGATATCCAATTCAAA
*
578809 GCTCAACTTCACAACGAAGG
1 GCTCAACTTCACAGCGAAGG
578829 ATATAGTGCC
Statistics
Matches: 548, Mismatches: 58, Indels: 4
0.90 0.10 0.01
Matches are distributed among these distances:
146 1 0.00
147 546 1.00
148 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (147 bp):
GCTCAACTTCACAGCGAAGGGGCGTCTGTCAACAAACAACCTTCCAGTTTCATTCAGAGCCAATT
TCAACTTCACGGCGAAGGATATTGGACTCGAAACAACACAAGATTGGATTTCAACTTCACAACAA
AGGATATCCAATTCAAA
Found at i:578994 original size:55 final size:55
Alignment explanation
Indices: 578928--579064 Score: 229
Period size: 55 Copynumber: 2.5 Consensus size: 55
578918 GGCCATCCAC
* * *
578928 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATACAACTATTG
1 GATTTCAACTTCACGATGAAAGATATCGTGCCCACAAGCAGCAATACAACCATTG
*
578983 GATTTCAACTTCACGATGAAAGATATCGTGCCCACAAGCAGCAATGCAACCATTG
1 GATTTCAACTTCACGATGAAAGATATCGTGCCCACAAGCAGCAATACAACCATTG
*
579038 GATTTTAACTTCACGATGAAAGATATC
1 GATTTCAACTTCACGATGAAAGATATC
579065 CAATTCAAGG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 77 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (55 bp):
GATTTCAACTTCACGATGAAAGATATCGTGCCCACAAGCAGCAATACAACCATTG
Found at i:579105 original size:176 final size:176
Alignment explanation
Indices: 578811--579185 Score: 534
Period size: 176 Copynumber: 2.1 Consensus size: 176
578801 AATTCAAGGC
* * * * *
578811 TCAACTTCACAACGAAGGATATAGTGCCCACAAGCAGCAATGCAACCCTTGGATTTCAACTTTAC
1 TCAACTTCACGATGAAGGATATCGTGCCCACAAGCAGCAATGCAACCATTGGATTTCAACTTCAC
* *
578876 AACGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTCAACTTCA
66 AACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGACATCCACGATTTCAACTTCA
* *
578941 CGACGAAGGATATCGTGCCCACAAGCAGCAATACAACTATTGGATT
131 CGACGAAGGATATCGTGCCCACAAGAAGCAATACAACCATTGGATT
* *
578987 TCAACTTCACGATGAAAGATATCGTGCCCACAAGCAGCAATGCAACCATTGGATTTTAACTTCAC
1 TCAACTTCACGATGAAGGATATCGTGCCCACAAGCAGCAATGCAACCATTGGATTTCAACTTCAC
* * * * *
579052 GATGAAAGATATCCAATTCAAGGCTCAATTTCACAATGAATGGGACATCCACGATTTCAACTTCA
66 AACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGACATCCACGATTTCAACTTCA
* * * * * *
579117 TGACGAATGATATTGTGCCCACAAGAAGTAATGCAACCCTTGGATT
131 CGACGAAGGATATCGTGCCCACAAGAAGCAATACAACCATTGGATT
* *
579163 TCAAATTCATGATGAAGGATATC
1 TCAACTTCACGATGAAGGATATC
579186 CAATTCAAAG
Statistics
Matches: 174, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
176 174 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (176 bp):
TCAACTTCACGATGAAGGATATCGTGCCCACAAGCAGCAATGCAACCATTGGATTTCAACTTCAC
AACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGACATCCACGATTTCAACTTCA
CGACGAAGGATATCGTGCCCACAAGAAGCAATACAACCATTGGATT
Found at i:579263 original size:120 final size:121
Alignment explanation
Indices: 578983--579378 Score: 560
Period size: 121 Copynumber: 3.3 Consensus size: 121
578973 ACAACTATTG
* * * * * *
578983 GATTTCAACTTCACGATGAAAGATATCGTGCCCACAAGCAGCAATGCAACCATTGGATTTTAACT
1 GATTTCAACTTCATGACGAAAGATATCGTGCCCACAAGAAGCAATGCAACCCTTGGATTTCAAAT
* * * *
579048 TCACGATGAAAGATATCCAATTCAAGGCTCAATTTCACAATGAATGGGACATCCAC
66 TCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGGGACATCCAC
* * *
579104 GATTTCAACTTCATGACGAATGATATTGTGCCCACAAGAAGTAATGCAACCCTTGGATTTCAAAT
1 GATTTCAACTTCATGACGAAAGATATCGTGCCCACAAGAAGCAATGCAACCCTTGGATTTCAAAT
* * *
579169 TCATGATGAAGGATATCCAATTCAAAGCTCAACTTCAC-ACGAATGAGTCATCCAC
66 TCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGGGACATCCAC
* *
579224 GATTTCAACTTTATGACGAAGGATATCGTGCCCACAAGAAGCAATGCAACCCTTGGATTTCAAAT
1 GATTTCAACTTCATGACGAAAGATATCGTGCCCACAAGAAGCAATGCAACCCTTGGATTTCAAAT
* * * *
579289 TCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGGGCCATCCAC
66 TCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGGGACATCCAC
* * *
579345 GATTTCAACTTCATGACGAACGATGTCGTACCCA
1 GATTTCAACTTCATGACGAAAGATATCGTGCCCA
579379 ACGGATCGAC
Statistics
Matches: 244, Mismatches: 30, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
120 110 0.45
121 134 0.55
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (121 bp):
GATTTCAACTTCATGACGAAAGATATCGTGCCCACAAGAAGCAATGCAACCCTTGGATTTCAAAT
TCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGGGACATCCAC
Found at i:579688 original size:86 final size:86
Alignment explanation
Indices: 579433--579928 Score: 570
Period size: 86 Copynumber: 5.8 Consensus size: 86
579423 TAGCCCAGTG
* * * ** * * *
579433 CAGCATAACTCAAGGCGATAAGGGTTATCTGTC-ATTAAAAGACCTTCGAGTTCAATTACACTAA
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAA-ACCTTCGAGTTCGATTACATTCA
* *
579497 GCTCAAAGGCGCATCCAATTTA
65 GCTCAAAGGCACATCAAATTTA
* * ** * * * * * * *
579519 CAACATAACTCAAGATGATAAGGGTTATCTGTCAACC-AAGACTTTCAAGTTTGATTACACTCAG
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAAACCTTCGAGTTCGATTACATTCAG
579583 CTCAAAGGCACATCAAATTTA
66 CTCAAAGGCACATCAAATTTA
* * * *
579604 TAGCATAGCTCAAGGCGAGAAGGACTATCTGTCAACCAAAAACCTTCGAGTTCAATTATATTCAG
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAAACCTTCGAGTTCGATTACATTCAG
*
579669 CTCAAAGTCACATCAAATTTA
66 CTCAAAGGCACATCAAATTTA
* *
579690 TAGCATAGCTCAAGGCCAGAAGGGCTATCTGTCAACCAAAAACCTTCGAGTTCGATTACATTCAG
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAAACCTTCGAGTTCGATTACATTCAG
* *
579755 CTCAGAGGCATATCAAATTTA
66 CTCAAAGGCACATCAAATTTA
* *
579776 CAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAA-CAAAAGACCTTCGAGTTCGATTAAATTCA
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAA-ACCTTCGAGTTCGATTACATTCA
* * *
579840 ACTCATAGGCATATCAAATTTA
65 GCTCAAAGGCACATCAAATTTA
* * * * *
579862 CAGTATAGCTCAAGGCGAGAAGGGCTATCTGTTAA-CAAAAA-CTGACGTGTTCGATTTCATTCA
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAAACCT-TCGAGTTCGATTACATTCA
579925 GCTC
65 GCTC
579929 GATGACAGCG
Statistics
Matches: 356, Mismatches: 50, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
84 2 0.01
85 91 0.26
86 262 0.74
87 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (86 bp):
CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAAACCTTCGAGTTCGATTACATTCAG
CTCAAAGGCACATCAAATTTA
Found at i:579903 original size:257 final size:257
Alignment explanation
Indices: 579434--579903 Score: 629
Period size: 257 Copynumber: 1.8 Consensus size: 257
579424 AGCCCAGTGC
* * * **
579434 AGCATAACTCAAGGCGATAAGGGTTATCTGTCATTAAAAGACCTTCGAGTTCAATTACACTAAGC
1 AGCATAACTCAAGGCCAGAAGGGCTATCTGTCACCAAAAGACCTTCGAGTTCAATTACACTAAGC
* * * * * * *
579499 TCAAAGGCGCATCCAATTTACAACATAACTCAAGATGATAAGGGTTATCTGTCAACCAAGACTTT
66 TCAAAGGCACATCAAATTTACAACATAACTCAAGACGAGAAGGGCTATCTGTCAACAAAGACCTT
* * * *
579564 CAAGTTTGATTACACTCAGCTCAAAGGCACATCAAATTTATAGCATAGCTCAAGGCGAGAAGGAC
131 CAAGTTCGATTAAACTCAACTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGCGAGAAGGAC
579629 TATCTGTCAACCAAAAACCTTCGAGTTCAATTATATTCAGCTCAAAGTCACATCAAATTTAT
196 TATCTGTCAACCAAAAACCTTCGAGTTCAATTATATTCAGCTCAAAGTCACATCAAATTTAT
* * * *
579691 AGCATAGCTCAAGGCCAGAAGGGCTATCTGTCAACCAAAA-ACCTTCGAGTTCGATTACATTCAG
1 AGCATAACTCAAGGCCAGAAGGGCTATCTGTC-ACCAAAAGACCTTCGAGTTCAATTACACTAAG
* * * *
579755 CTCAGAGGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACC
65 CTCAAAGGCACATCAAATTTACAACATAACTCAAGACGAGAAGGGCTATCTGTCAAC-AAAGACC
* * * * *
579820 TTCGAGTTCGATTAAATTCAACTCATAGGCATATCAAATTTACAGTATAGCTCAAGGCGAGAAGG
129 TTCAAGTTCGATTAAACTCAACTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGCGAGAAGG
* *
579885 GCTATCTGTTAA-CAAAAAC
194 ACTATCTGTCAACCAAAAAC
579904 TGACGTGTTC
Statistics
Matches: 180, Mismatches: 31, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
257 104 0.58
258 76 0.42
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (257 bp):
AGCATAACTCAAGGCCAGAAGGGCTATCTGTCACCAAAAGACCTTCGAGTTCAATTACACTAAGC
TCAAAGGCACATCAAATTTACAACATAACTCAAGACGAGAAGGGCTATCTGTCAACAAAGACCTT
CAAGTTCGATTAAACTCAACTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGCGAGAAGGAC
TATCTGTCAACCAAAAACCTTCGAGTTCAATTATATTCAGCTCAAAGTCACATCAAATTTAT
Found at i:581438 original size:20 final size:19
Alignment explanation
Indices: 581409--581447 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
581399 TTGGGAATAC
581409 TTTTTAATAATATTTTTAT
1 TTTTTAATAATATTTTTAT
581428 TTTTTATATAATATTTTTAT
1 TTTTTA-ATAATATTTTTAT
581448 ATTCAATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTAATAATATTTTTAT
Found at i:588919 original size:18 final size:18
Alignment explanation
Indices: 588898--588942 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
588888 CTCCGCAACC
588898 ACCGCCGCCGCCGCTAAA
1 ACCGCCGCCGCCGCTAAA
588916 ACCGCCGCCGCCGCTAAA
1 ACCGCCGCCGCCGCTAAA
588934 ACCGCCGCC
1 ACCGCCGCC
588943 CTTCAAATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.53, G:0.22, T:0.04
Consensus pattern (18 bp):
ACCGCCGCCGCCGCTAAA
Found at i:595449 original size:19 final size:20
Alignment explanation
Indices: 595427--595463 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
595417 TAGCATTTTA
595427 AAAAAT-AAAACTT-AAAAT
1 AAAAATGAAAACTTGAAAAT
595445 AAAAATGAAAACTTGAAAA
1 AAAAATGAAAACTTGAAAA
595464 GATAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.19
Consensus pattern (20 bp):
AAAAATGAAAACTTGAAAAT
Found at i:595660 original size:21 final size:21
Alignment explanation
Indices: 595634--595676 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
595624 TTTTAAATTC
595634 AAACTTTAAAATTTAAAAACA
1 AAACTTTAAAATTTAAAAACA
595655 AAACTTTAAAATTTAAAAACA
1 AAACTTTAAAATTTAAAAACA
595676 A
1 A
595677 GTCTCCTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (21 bp):
AAACTTTAAAATTTAAAAACA
Found at i:596595 original size:17 final size:17
Alignment explanation
Indices: 596575--596607 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
596565 CTCATGTATA
596575 TTTCTATTTTCTTTTCT
1 TTTCTATTTTCTTTTCT
*
596592 TTTCTTTTTTCTTTTC
1 TTTCTATTTTCTTTTC
596608 AAACTGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTATTTTCTTTTCT
Found at i:600177 original size:23 final size:22
Alignment explanation
Indices: 600151--600219 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 22
600141 CACCACAGCT
600151 CGTATAAATGCACCGAAGTGCCA
1 CGTA-AAATGCACCGAAGTGCCA
* *
600174 CGTAAAATTGCACCGTAGTGCCG
1 CGTAAAA-TGCACCGAAGTGCCA
600197 CGTAGAAATGCACCGAAGTGCCA
1 CGTA-AAATGCACCGAAGTGCCA
600220 TATAAGGTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.08
23 34 0.85
24 3 0.08
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (22 bp):
CGTAAAATGCACCGAAGTGCCA
Found at i:601651 original size:30 final size:30
Alignment explanation
Indices: 601617--601673 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
601607 TGCACTTCCT
601617 GTGCATCGATACACACTGAACAATTTCCAA
1 GTGCATCGATACACACTGAACAATTTCCAA
601647 GTGCATCGATACACACTGAACAATTTC
1 GTGCATCGATACACACTGAACAATTTC
601674 TGGAAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (30 bp):
GTGCATCGATACACACTGAACAATTTCCAA
Found at i:605098 original size:23 final size:23
Alignment explanation
Indices: 605072--605140 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
605062 CACCACAGCT
* *
605072 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* * * *
605095 CGTAGAATTATACCGTAGTGCCG
1 CGTAGAAATACACCGAAGTGCCA
605118 CGTAGAAATACACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
605141 TATAAGGTTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:605418 original size:22 final size:23
Alignment explanation
Indices: 605356--605418 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
605346 ATTTCACATT
*
605356 TTTCACATAAATACGTAGTTCAC
1 TTTCACATAAACACGTAGTTCAC
605379 TTTCACATAAACACGTAGTTCAC
1 TTTCACATAAACACGTAGTTCAC
*
605402 TTTCACAT-AGCACGTAG
1 TTTCACATAAACACGTAG
605419 ATTATGTCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 8 0.21
23 30 0.79
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (23 bp):
TTTCACATAAACACGTAGTTCAC
Found at i:605613 original size:2 final size:2
Alignment explanation
Indices: 605555--605598 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
605545 ATGTCTTATC
605555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
605597 AT
1 AT
605599 TCACAAGTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:612252 original size:67 final size:67
Alignment explanation
Indices: 612174--612306 Score: 189
Period size: 67 Copynumber: 2.0 Consensus size: 67
612164 AAAGAAGAAA
* *
612174 TAAAATCACTTCTTTTTCATTTCTGTTTAT-GTAAGCTTGTTA-GCTATATAATCAATGCTCTGT
1 TAAAATCACTTCTTTTTCATTTCTATTTATGGGAA-CTTG-TAGGCTATATAATCAATGCTCTGT
612237 TAGC
64 TAGC
* **
612241 TAAAATCACTTCTTTTTCATTTCTATTTCTGGGAACTTGTAGGCTATATAATTGATGCTCTGTTA
1 TAAAATCACTTCTTTTTCATTTCTATTTATGGGAACTTGTAGGCTATATAATCAATGCTCTGTTA
612306 G
66 G
612307 TTTGTTAGTA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
66 2 0.03
67 54 0.92
68 3 0.05
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.46
Consensus pattern (67 bp):
TAAAATCACTTCTTTTTCATTTCTATTTATGGGAACTTGTAGGCTATATAATCAATGCTCTGTTA
GC
Found at i:614972 original size:94 final size:94
Alignment explanation
Indices: 614807--614994 Score: 322
Period size: 94 Copynumber: 2.0 Consensus size: 94
614797 GCATTGATTC
* *
614807 GGGTTTGATTAAATCCTGTTACCCTCTTTGTCTACTGAACTTCGATGTGAATTTATTAGTTGACT
1 GGGTTTGATTAAATCCTGTTACCCTATTTGTCTACTGAACTTCGATATGAATTTATTAGTTGACT
* *
614872 CGCTTCTATTATTTGATTTTTGTGTAATA
66 CACTTCTATTATTTGATTTTGGTGTAATA
* *
614901 GGGTTTGATTAAATTCTGTTACCCTATTTGTCTACTGATCTTCGATATGAATTTATTAGTTGACT
1 GGGTTTGATTAAATCCTGTTACCCTATTTGTCTACTGAACTTCGATATGAATTTATTAGTTGACT
614966 CACTTCTATTATTTGATTTTGGTGTAATA
66 CACTTCTATTATTTGATTTTGGTGTAATA
614995 CAGTTTTCTA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 88 1.00
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.47
Consensus pattern (94 bp):
GGGTTTGATTAAATCCTGTTACCCTATTTGTCTACTGAACTTCGATATGAATTTATTAGTTGACT
CACTTCTATTATTTGATTTTGGTGTAATA
Found at i:617658 original size:15 final size:15
Alignment explanation
Indices: 617640--617671 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
617630 CTTTGTTCTA
*
617640 TATTTTTTAGTATTT
1 TATTTTATAGTATTT
617655 TATTTTATAGTATTT
1 TATTTTATAGTATTT
617670 TA
1 TA
617672 ATTGTTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (15 bp):
TATTTTATAGTATTT
Found at i:623011 original size:19 final size:22
Alignment explanation
Indices: 622978--623021 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
622968 CTCCCTTCCC
622978 TTTCTCTCTCATGTTTTT-TCT
1 TTTCTCTCTCATGTTTTTCTCT
622999 TTTCTCT-TC-TGTTTTTCTCT
1 TTTCTCTCTCATGTTTTTCTCT
623019 TTT
1 TTT
623022 TTGTTTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.32
20 8 0.36
21 7 0.32
ACGTcount: A:0.02, C:0.23, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTCTCTCTCATGTTTTTCTCT
Found at i:624044 original size:134 final size:133
Alignment explanation
Indices: 623838--624192 Score: 439
Period size: 131 Copynumber: 2.7 Consensus size: 133
623828 GGTGATACGG
* * * * * * *
623838 CTCCTACATGATGAGGAGATATAGTCGGTGGATGACACGGTTCCTACGCGATGAGAACGGTTGGT
1 CTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGTTTCTACGCGATGAGGACGGCTGGC
* ** *
623903 CATCTTTAGGGATGATTATAATACGGTTCCTAAGCGATGAGGATGACTGGTTATCT-AGGTATGA
66 CATCTTTAGGGATGA-TATAACACGGTTCCTAAGCGATGAGGACAACTGGTTATCTAAGAT-TGA
623967 CACGA
129 CACGA
* * * * *
623972 CTCCTACGTGATGAGGAGATCTGGTCGGAGGATGACACGGTTTCTACGTGATGAGGATGACTGAC
1 CTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGTTTCTACGCGATGAGGACGGCTGGC
* * * *
624037 CATCTTTAGGGATG--ATAACACGGTTCCTACGTGATGAGGACAACTGGTTATCTAAGATTTACG
66 CATCTTTAGGGATGATATAACACGGTTCCTAAGCGATGAGGACAACTGGTTATCTAAGATTGACA
* *
624100 TGG
131 CGA
*
624103 CTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGG-TTCTTACACGATGAGGACGGCTGG
1 CTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGTTTC-TACGCGATGAGGACGGCTGG
624167 CCATCTTTAGGGATGATGATAACACG
65 CCATCTTTAGGGATGAT-ATAACACG
624193 ATGAGGACGA
Statistics
Matches: 188, Mismatches: 28, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
130 3 0.02
131 107 0.57
132 3 0.02
134 75 0.40
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (133 bp):
CTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGTTTCTACGCGATGAGGACGGCTGGC
CATCTTTAGGGATGATATAACACGGTTCCTAAGCGATGAGGACAACTGGTTATCTAAGATTGACA
CGA
Found at i:624571 original size:37 final size:36
Alignment explanation
Indices: 624512--624638 Score: 104
Period size: 37 Copynumber: 3.6 Consensus size: 36
624502 TCAAAGATGA
***
624512 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
1 TGTTTCAAGAGAAACAAACTCAAGAGAGAC-AAATTT
* *
624549 TATTTCAAGAGAAACAAACTCAA-AGA-TC----TT
1 TGTTTCAAGAGAAACAAACTCAAGAGAGACAAATTT
* ***
624579 TGTTTCAAGATAAACTGTCTCAAGAGAGACTAAATTT
1 TGTTTCAAGAGAAACAAACTCAAGAGAGAC-AAATTT
*
624616 TGTTTCAAGGGAAACAAACTCAA
1 TGTTTCAAGAGAAACAAACTCAA
624639 AGATTTTTTT
Statistics
Matches: 67, Mismatches: 16, Indels: 14
0.69 0.16 0.14
Matches are distributed among these distances:
30 20 0.30
31 3 0.04
32 1 0.01
35 1 0.01
36 3 0.04
37 39 0.58
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACAAACTCAAGAGAGACAAATTT
Found at i:624594 original size:67 final size:66
Alignment explanation
Indices: 624380--624691 Score: 360
Period size: 65 Copynumber: 4.7 Consensus size: 66
624370 TATTTAGGGA
* * * * *
624380 TTTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAA-TTCGTTTCAAGGGAAACGATCTCAAATA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACAAACTCAAAGA
624444 T
66 T
** * * * *
624445 GATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCT-TTTGAAGGGAAA-AGATCTCAAAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACA-AACTCAAAG
624508 AT
65 AT
** * *
624510 GATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTATTTCAAGAGAAACAAACTCAAAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACAAACTCAAAGA
624575 T
66 T
* *
624576 CTTTGTTTCAAGATAAACTGTCTCAAGAGAGACTAAATTTTGTTTCAAGGGAAACAAACTCAAAG
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACAAACTCAAAG
624641 ATTTTT
65 A----T
* * *
624647 TTATGTTTCAAGAGAAATTATCTCAAGAGAGACAAAACTTTGTTT
1 TT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTT
624692 TAAAAGAAAC
Statistics
Matches: 212, Mismatches: 25, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
65 91 0.43
66 21 0.10
67 60 0.28
70 2 0.01
71 38 0.18
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (66 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACAAACTCAAAGA
T
Found at i:624700 original size:37 final size:36
Alignment explanation
Indices: 624646--624791 Score: 141
Period size: 37 Copynumber: 3.9 Consensus size: 36
624636 CAAAGATTTT
*
624646 TTTATGTTTCAAGAGAAATTATCTCAAGAGAGACAAAA
1 TTTAT-TTT-AAGAGAAATTGTCTCAAGAGAGACAAAA
* * * *
624684 CTTTGTTTTAAAAGAAACTGTGTCAAGAGAGACAAAA
1 -TTTATTTTAAGAGAAATTGTCTCAAGAGAGACAAAA
* * *
624721 TTAATTTTTAGAGAAAATTGTCTCAAGCGAGACAAAA
1 TTTATTTTAAGAG-AAATTGTCTCAAGAGAGACAAAA
*
624758 TTTATTTTTAAGA-ACAACTTGTCTCAAGCGAGAC
1 TTTA-TTTTAAGAGA-AA-TTGTCTCAAGAGAGAC
624792 GACCCTGTAA
Statistics
Matches: 89, Mismatches: 14, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
36 10 0.11
37 49 0.55
38 26 0.29
39 4 0.04
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (36 bp):
TTTATTTTAAGAGAAATTGTCTCAAGAGAGACAAAA
Found at i:625421 original size:23 final size:23
Alignment explanation
Indices: 625395--625447 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
625385 ATTGCAACTA
*
625395 AGTGCCACGTAGAATTGCACAGG
1 AGTGCCACGTAGAATTACACAGG
* * *
625418 AGTGCCCCGTAGAATTACACCGT
1 AGTGCCACGTAGAATTACACAGG
625441 AGTGCCA
1 AGTGCCA
625448 TATATAATGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.19
Consensus pattern (23 bp):
AGTGCCACGTAGAATTACACAGG
Found at i:626090 original size:18 final size:19
Alignment explanation
Indices: 626053--626089 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
626043 TTTTTTATTA
*
626053 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
626072 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
626090 TCTAGCGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:626141 original size:21 final size:21
Alignment explanation
Indices: 626117--626159 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
626107 TCATATTCGT
*
626117 TTGAGGGGGTATCAATTCCCC
1 TTGAAGGGGTATCAATTCCCC
* * *
626138 TTGAATGGGTATCGATTTCCC
1 TTGAAGGGGTATCAATTCCCC
626159 T
1 T
626160 AACCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (21 bp):
TTGAAGGGGTATCAATTCCCC
Found at i:632167 original size:23 final size:24
Alignment explanation
Indices: 632141--632195 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
632131 CAGCTCATAT
632141 AATTGCACCT-AAGTGCCACGTAG
1 AATTGCACCTGAAGTGCCACGTAG
* *
632164 AATTGCA-CTGGAGTGCCGCGTAG
1 AATTGCACCTGAAGTGCCACGTAG
*
632187 AATTACACC
1 AATTGCACC
632196 GTAGTGTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.07
23 24 0.89
24 1 0.04
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (24 bp):
AATTGCACCTGAAGTGCCACGTAG
Found at i:632201 original size:23 final size:23
Alignment explanation
Indices: 632152--632201 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
632142 ATTGCACCTA
* *
632152 AGTGCCACGTAGAATTGCACTGG
1 AGTGCCACGTAGAATTACACCGG
* *
632175 AGTGCCGCGTAGAATTACACCGT
1 AGTGCCACGTAGAATTACACCGG
632198 AGTG
1 AGTG
632202 TCATATAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (23 bp):
AGTGCCACGTAGAATTACACCGG
Found at i:632855 original size:18 final size:19
Alignment explanation
Indices: 632818--632854 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
632808 TTTTTTATTA
*
632818 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
632837 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
632855 TCTAGCGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:632906 original size:21 final size:21
Alignment explanation
Indices: 632882--632924 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
632872 TCATATTCGT
*
632882 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
632903 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
632924 T
1 T
632925 AGCCCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:633908 original size:36 final size:36
Alignment explanation
Indices: 633861--633932 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
633851 TTCTAAGCAT
633861 GAGCTTTGTGTCTGAGAGCCACGTGTCAACTACCAA
1 GAGCTTTGTGTCTGAGAGCCACGTGTCAACTACCAA
633897 GAGCTTTGTGTCTGAGAGCCACGTGTCAACTACCAA
1 GAGCTTTGTGTCTGAGAGCCACGTGTCAACTACCAA
633933 AATCCACTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (36 bp):
GAGCTTTGTGTCTGAGAGCCACGTGTCAACTACCAA
Found at i:634938 original size:25 final size:23
Alignment explanation
Indices: 634899--634990 Score: 71
Period size: 23 Copynumber: 3.8 Consensus size: 23
634889 TCTTTGCATG
*
634899 TTTTTCTTGTCTTCTTTGCTTTTTC
1 TTTTTCTT-T-TTCTTTGATTTTTC
*
634924 TTTTGGTTTTTTTCTTT-ATTTTTTTC
1 TTTT--TCTTTTTCTTTGA--TTTTTC
634950 TTTTTCTTTTTCTTTGATTTTT-
1 TTTTTCTTTTTCTTTGATTTTTC
* *
634972 TTCTTTGTTTTTATTTGAT
1 TT-TTTCTTTTTCTTTGAT
634991 CTTTGTACTT
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
22 2 0.04
23 19 0.34
24 10 0.18
25 11 0.20
26 11 0.20
27 3 0.05
ACGTcount: A:0.04, C:0.11, G:0.08, T:0.77
Consensus pattern (23 bp):
TTTTTCTTTTTCTTTGATTTTTC
Found at i:634945 original size:24 final size:24
Alignment explanation
Indices: 634899--634990 Score: 73
Period size: 24 Copynumber: 3.8 Consensus size: 24
634889 TCTTTGCATG
*
634899 TTTTTCTTGTCTTCTTTG-CTTTTTC
1 TTTTTCTT-T-TTCTTTGATTTTTTC
*
634924 TTTTGGTTTTTTTCTTT-ATTTTTTTC
1 TTTT--TCTTTTTCTTTGA-TTTTTTC
634950 TTTTTCTTTTTCTTTGATTTTTT-
1 TTTTTCTTTTTCTTTGATTTTTTC
* * *
634973 TCTTTGTTTTTATTTGAT
1 TTTTTCTTTTTCTTTGAT
634991 CTTTGTACTT
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
23 15 0.27
24 16 0.29
25 11 0.20
26 11 0.20
27 3 0.05
ACGTcount: A:0.04, C:0.11, G:0.08, T:0.77
Consensus pattern (24 bp):
TTTTTCTTTTTCTTTGATTTTTTC
Found at i:634946 original size:13 final size:12
Alignment explanation
Indices: 634930--634983 Score: 74
Period size: 12 Copynumber: 4.4 Consensus size: 12
634920 TTTCTTTTGG
634930 TTTTTTTCTTTA
1 TTTTTTTCTTTA
634942 TTTTTTTCTTT-
1 TTTTTTTCTTTA
634953 TTCTTTTTCTTTGA
1 TT-TTTTTCTTT-A
*
634967 TTTTTTTCTTTG
1 TTTTTTTCTTTA
634979 TTTTT
1 TTTTT
634984 ATTTGATCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
11 2 0.05
12 25 0.66
13 9 0.24
14 2 0.05
ACGTcount: A:0.04, C:0.09, G:0.04, T:0.83
Consensus pattern (12 bp):
TTTTTTTCTTTA
Found at i:634971 original size:37 final size:40
Alignment explanation
Indices: 634908--634983 Score: 113
Period size: 37 Copynumber: 2.0 Consensus size: 40
634898 GTTTTTCTTG
*
634908 TCTTCTTTGCTTTTTCTTTTGGTTTTTTTCTTTATTTTTT
1 TCTTCTTTGCTTTTTCTTTTGATTTTTTTCTTTATTTTTT
*
634948 TCTT-TTT-CTTTTTC-TTTGATTTTTTTCTTTGTTTTT
1 TCTTCTTTGCTTTTTCTTTTGATTTTTTTCTTTATTTTT
634984 ATTTGATCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 20 0.59
38 7 0.21
39 3 0.09
40 4 0.12
ACGTcount: A:0.03, C:0.12, G:0.07, T:0.79
Consensus pattern (40 bp):
TCTTCTTTGCTTTTTCTTTTGATTTTTTTCTTTATTTTTT
Found at i:634982 original size:23 final size:24
Alignment explanation
Indices: 634932--634990 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
634922 TCTTTTGGTT
634932 TTTTTCTTT-ATTTTTTTCTTTTTC
1 TTTTTCTTTGATTTTTTTC-TTTTC
*
634956 TTTTTCTTTGATTTTTTTC-TTTG
1 TTTTTCTTTGATTTTTTTCTTTTC
*
634979 TTTTTATTTGAT
1 TTTTTCTTTGAT
634991 CTTTGTACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 14 0.44
24 9 0.28
25 9 0.28
ACGTcount: A:0.07, C:0.08, G:0.05, T:0.80
Consensus pattern (24 bp):
TTTTTCTTTGATTTTTTTCTTTTC
Found at i:635001 original size:24 final size:23
Alignment explanation
Indices: 634956--635003 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
634946 TTTCTTTTTC
* * *
634956 TTTTTCTTTGATTTTTTTCTTTG
1 TTTTTATTTGATTTTGTACTTTG
634979 TTTTTATTTGATCTTTGTACTTTG
1 TTTTTATTTGAT-TTTGTACTTTG
635003 T
1 T
635004 ATTTGGTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.08, C:0.08, G:0.10, T:0.73
Consensus pattern (23 bp):
TTTTTATTTGATTTTGTACTTTG
Found at i:635311 original size:19 final size:19
Alignment explanation
Indices: 635287--635325 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
635277 GAAAACAATG
*
635287 TAATTAATGTATGATAGAA
1 TAATTAATGCATGATAGAA
635306 TAATTAATGCATGATAGAA
1 TAATTAATGCATGATAGAA
635325 T
1 T
635326 TATTTTCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (19 bp):
TAATTAATGCATGATAGAA
Found at i:642381 original size:29 final size:29
Alignment explanation
Indices: 642339--642394 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
642329 TCCACACAAT
642339 AGGACTTTGAAGAGGAATCCCCATGTCGA
1 AGGACTTTGAAGAGGAATCCCCATGTCGA
642368 AGGACTTTGAAGAGGAATCCCCATGTC
1 AGGACTTTGAAGAGGAATCCCCATGTC
642395 AGTTAACAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.21
Consensus pattern (29 bp):
AGGACTTTGAAGAGGAATCCCCATGTCGA
Found at i:645087 original size:21 final size:21
Alignment explanation
Indices: 645061--645108 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
645051 CACTGAAGGA
*
645061 TTGATCTTTTTTCATGAGGGG
1 TTGATCTTTTTTCATGAGAGG
645082 TTGATCTTTTTTCATGAGAGG
1 TTGATCTTTTTTCATGAGAGG
*
645103 TCGATC
1 TTGATC
645109 ATTTGTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.12, G:0.25, T:0.46
Consensus pattern (21 bp):
TTGATCTTTTTTCATGAGAGG
Found at i:646556 original size:11 final size:11
Alignment explanation
Indices: 646534--646615 Score: 69
Period size: 11 Copynumber: 7.3 Consensus size: 11
646524 CTCAAAAAAA
646534 ATTAAGAGCTCG
1 ATTAA-AGCTCG
646546 ATTAAAGCTCG
1 ATTAAAGCTCG
*
646557 ATTGAAA-CTTG
1 ATT-AAAGCTCG
*
646568 ATTCTAAGCTCG
1 ATT-AAAGCTCG
646580 ATTGAAA-CTCG
1 ATT-AAAGCTCG
* *
646591 ATTAAAACTTG
1 ATTAAAGCTCG
*
646602 ATTCAAGCTCG
1 ATTAAAGCTCG
646613 ATT
1 ATT
646616 TTGAGCTCAA
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
10 3 0.05
11 38 0.67
12 16 0.28
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (11 bp):
ATTAAAGCTCG
Found at i:646576 original size:23 final size:23
Alignment explanation
Indices: 646542--646593 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
646532 AAATTAAGAG
*
646542 CTCGATT-AAAGCTCGATTGAAA
1 CTCGATTCTAAGCTCGATTGAAA
*
646564 CTTGATTCTAAGCTCGATTGAAA
1 CTCGATTCTAAGCTCGATTGAAA
646587 CTCGATT
1 CTCGATT
646594 AAAACTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (23 bp):
CTCGATTCTAAGCTCGATTGAAA
Found at i:646578 original size:34 final size:33
Alignment explanation
Indices: 646540--646615 Score: 118
Period size: 34 Copynumber: 2.3 Consensus size: 33
646530 AAAAATTAAG
*
646540 AGCTCGATT-AAAGCTCGATTGAAACTTGATTCTA
1 AGCTCGATTGAAA-CTCGATTAAAACTTGATTC-A
646574 AGCTCGATTGAAACTCGATTAAAACTTGATTCA
1 AGCTCGATTGAAACTCGATTAAAACTTGATTCA
646607 AGCTCGATT
1 AGCTCGATT
646616 TTGAGCTCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
33 10 0.25
34 27 0.68
35 3 0.08
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (33 bp):
AGCTCGATTGAAACTCGATTAAAACTTGATTCA
Found at i:648032 original size:21 final size:20
Alignment explanation
Indices: 648006--648058 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
647996 AATGTTGTTC
* *
648006 AAACTCTAAATTATAAACCCT
1 AAACTCTAAACT-TAAACCAT
*
648027 AAACTCTAACCCTTAAACCAT
1 AAACTCTAA-ACTTAAACCAT
648048 AAACTCTAAAC
1 AAACTCTAAAC
648059 CCTATCACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (20 bp):
AAACTCTAAACTTAAACCAT
Found at i:648916 original size:11 final size:11
Alignment explanation
Indices: 648900--648925 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
648890 TAATCATCAA
648900 TAATTTATTTT
1 TAATTTATTTT
648911 TAATTTATTTT
1 TAATTTATTTT
648922 TAAT
1 TAAT
648926 AATGAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TAATTTATTTT
Found at i:649514 original size:19 final size:19
Alignment explanation
Indices: 649490--649530 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
649480 TTTTACCCTT
*
649490 GAACATGCTCATCCTTTAA
1 GAACATGCTCATCATTTAA
*
649509 GAACATGTTCATCATTTAA
1 GAACATGCTCATCATTTAA
649528 GAA
1 GAA
649531 TGAAAGTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (19 bp):
GAACATGCTCATCATTTAA
Found at i:649664 original size:19 final size:19
Alignment explanation
Indices: 649640--649676 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
649630 TTGGATAATG
649640 TAAATAA-TTAAATAAATAA
1 TAAATAATTTAAA-AAATAA
649659 TAAATAATTTAAAAAATA
1 TAAATAATTTAAAAAATA
649677 TTTTTTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAATAATTTAAAAAATAA
Found at i:649905 original size:16 final size:16
Alignment explanation
Indices: 649849--649921 Score: 87
Period size: 16 Copynumber: 4.7 Consensus size: 16
649839 CGCTCATTTA
649849 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
*
649863 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
*
649879 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
* * *
649895 ATAAATAAACATGATC
1 ATAAATGAACACGAAC
649911 ATAAATGAACA
1 ATAAATGAACA
649922 TAAACGTTGG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 44 0.86
ACGTcount: A:0.59, C:0.18, G:0.10, T:0.14
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:651035 original size:14 final size:14
Alignment explanation
Indices: 651018--651066 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
651008 AATGAACATA
651018 AACGAACATAACCG
1 AACGAACATAACCG
651032 AACGAACAT-A---
1 AACGAACATAACCG
651042 AACGAACATAACCG
1 AACGAACATAACCG
*
651056 AATGAACATAA
1 AACGAACATAA
651067 ACAAACGTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
10 9 0.30
11 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.55, C:0.22, G:0.12, T:0.10
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:651038 original size:24 final size:24
Alignment explanation
Indices: 651011--651068 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
651001 ATAAATGAAT
651011 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
651035 GAACATAAACGAACATAACCGAAT
1 GAACATAAACGAACATAACCGAAC
651059 GAACATAAAC
1 GAACATAAAC
651069 AAACGTTCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.55, C:0.22, G:0.12, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:652098 original size:44 final size:43
Alignment explanation
Indices: 651956--652119 Score: 145
Period size: 43 Copynumber: 3.8 Consensus size: 43
651946 GTTTGTTAAC
* * ** * * *
651956 CAAAAATGCTGCAATAGGTACTGATATTTAGCGGCGTGTGTCTT
1 CAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCAT-TTTTTT
* * **
652000 -AAAAACGTCGCAATAGGTGTTAATATTTAGCGGTGTTTTTTT
1 CAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCATTTTTTT
* *
652042 CAAAAACGCCGCAATAAGTGTTGATATTTCGCGGCATTTTTTT
1 CAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCATTTTTTT
* *
652085 -ATGCAAACGCCGCAATAGGTG-TGGTATTTAGCGGC
1 CA--AAAACGCCGCAATAGGTGTTGATATTTAGCGGC
652120 GCTTTCAGGG
Statistics
Matches: 98, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
42 5 0.05
43 77 0.79
44 16 0.16
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (43 bp):
CAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCATTTTTTT
Found at i:652136 original size:44 final size:44
Alignment explanation
Indices: 652088--652276 Score: 197
Period size: 44 Copynumber: 4.3 Consensus size: 44
652078 TTTTTTTATG
* * * * * *
652088 CAAACGCCGCAATAGGTGTGGTATTTAGCGGCGCTTTCAGGGTA
1 CAAACGCCGCAATAGGTCTGGTATATAGCGACGTTTTTAGGATA
** * * *
652132 CAAACATCGCTATAGGACTGGTATATAGCGATGTTTTTAGGATA
1 CAAACGCCGCAATAGGTCTGGTATATAGCGACGTTTTTAGGATA
*
652176 CAAACGCCGCGATAGGTCTGGTATATAGCGACGTTTTTAGGATA
1 CAAACGCCGCAATAGGTCTGGTATATAGCGACGTTTTTAGGATA
* * *
652220 CAAACGCCGCTAA-AAGT-AGGTACATAGCGACGTTTCTT--GATA
1 CAAACGCCGC-AATAGGTCTGGTATATAGCGACGTTT-TTAGGATA
652262 CAAACGCCGCAATAG
1 CAAACGCCGCAATAG
652277 TGTTAATATT
Statistics
Matches: 121, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.02
42 15 0.12
43 16 0.13
44 87 0.72
45 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (44 bp):
CAAACGCCGCAATAGGTCTGGTATATAGCGACGTTTTTAGGATA
Found at i:662662 original size:42 final size:43
Alignment explanation
Indices: 662616--662718 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 43
662606 CTTTATAGTA
*
662616 GCGTTTATTACA-AAAAACGCCACTATGAATG-AACCTATTGCG
1 GCGTTT-TTACATAAAAACGCCACTATGAATGAAACCTACTGCG
* * * *
662658 GCGTTTTTAGATACAAACGCCACTATTAATGAAACCTACTGTG
1 GCGTTTTTACATAAAAACGCCACTATGAATGAAACCTACTGCG
*
662701 GCGTTTGT--ATAAAAACGC
1 GCGTTTTTACATAAAAACGC
662719 GTCTAAAGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
41 13 0.25
42 23 0.44
43 16 0.31
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (43 bp):
GCGTTTTTACATAAAAACGCCACTATGAATGAAACCTACTGCG
Found at i:664365 original size:41 final size:41
Alignment explanation
Indices: 664314--664434 Score: 127
Period size: 42 Copynumber: 2.9 Consensus size: 41
664304 GTTTGTCTAA
* *
664314 AAACGACGCTAAAGTACTATTTATTGTGGCGTTTGAGGTAT
1 AAACGCCGCTAAATTACTATTTATTGTGGCGTTTGAGGTAT
* * * *
664355 AAACGCCGCTAATTTA-TCATTCGATTGCGGCGTTTGCGGTAT
1 AAACGCCGCTAAATTACT-ATT-TATTGTGGCGTTTGAGGTAT
* * *
664397 AAACGCCGCTACATTACCACTATATTGTGGCGTTTGAG
1 AAACGCCGCTAAATTACTA-TTTATTGTGGCGTTTGAG
664435 CTGAAACGCC
Statistics
Matches: 63, Mismatches: 13, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
40 1 0.02
41 16 0.25
42 45 0.71
43 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (41 bp):
AAACGCCGCTAAATTACTATTTATTGTGGCGTTTGAGGTAT
Found at i:664429 original size:42 final size:42
Alignment explanation
Indices: 664335--664434 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
664325 AAGTACTATT
* * *
664335 TATTGTGGCGTTTGAGGTATAAACGCCGCTAATTTATCATTC
1 TATTGTGGCGTTTGAGGTATAAACGCCGCTAATTTACCACTA
* * *
664377 GATTGCGGCGTTTGCGGTATAAACGCCGCTACA-TTACCACTA
1 TATTGTGGCGTTTGAGGTATAAACGCCGCTA-ATTTACCACTA
664419 TATTGTGGCGTTTGAG
1 TATTGTGGCGTTTGAG
664435 CTGAAACGCC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
42 47 0.98
43 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (42 bp):
TATTGTGGCGTTTGAGGTATAAACGCCGCTAATTTACCACTA
Found at i:664484 original size:83 final size:82
Alignment explanation
Indices: 664301--664484 Score: 185
Period size: 83 Copynumber: 2.2 Consensus size: 82
664291 ACACTATTAT
* * * * *
664301 GGCGTTTGTCTAAAAACGACGCTAAAGTACTATTTATTGTGGCGTTTGAGGTATAAACGCCGCTA
1 GGCGTTTGTGTAAAAACGACGCTAAAGTACCATATATTGTGGCGTTTGAGCTAGAAACGCCGCTA
*
664366 ATTTATCATTCGATTGC
66 AATTATCATTCGATTGC
* * * * *
664383 GGCGTTTGCGGTATAAACGCCGCTACATTACCACTATATTGTGGCGTTTGAGCT-GAAACGCCG-
1 GGCGTTTG-TGTAAAAACGACGCTAAAGTACCA-TATATTGTGGCGTTTGAGCTAGAAACGCCGC
* *
664446 TAAAATT-TCTTCTCTATTGC
64 T-AAATTATCAT-TCGATTGC
664466 GGCGTTTGTTGTAAAAACG
1 GGCGTTTG-TGTAAAAACG
664485 TCACTATATG
Statistics
Matches: 82, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
82 12 0.15
83 52 0.63
84 18 0.22
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (82 bp):
GGCGTTTGTGTAAAAACGACGCTAAAGTACCATATATTGTGGCGTTTGAGCTAGAAACGCCGCTA
AATTATCATTCGATTGC
Found at i:666342 original size:2 final size:2
Alignment explanation
Indices: 666297--666333 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
666287 TAGTGAGAAT
666297 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
666334 GCATATATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:669415 original size:21 final size:21
Alignment explanation
Indices: 669389--669438 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
669379 AATGAACAAA
* *
669389 GGAAAAGAGAATTACCTTGTT
1 GGAAAAGAGAATTACCATGCT
669410 GGAAAAGAGAATTACCATGCT
1 GGAAAAGAGAATTACCATGCT
669431 GGAAAAGA
1 GGAAAAGA
669439 AGATGAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.44, C:0.10, G:0.26, T:0.20
Consensus pattern (21 bp):
GGAAAAGAGAATTACCATGCT
Found at i:672390 original size:140 final size:140
Alignment explanation
Indices: 672138--672418 Score: 553
Period size: 140 Copynumber: 2.0 Consensus size: 140
672128 CACATTAATC
672138 TTATTCAGATCAACCCGAATACCCTCAACTGAAACAACATGACCAAAGAATGCTACCTCACTCAA
1 TTATTCAGATCAACCCGAATACCCTCAACTGAAACAACATGACCAAAGAATGCTACCTCACTCAA
672203 CCAAAACTCACACTTCAAAAACTTCGCATACAATGTCTTCTCCTTAACACCTTTAAGACAACCCT
66 CCAAAACTCACACTTCAAAAACTTCGCATACAATGTCTTCTCCTTAACACCTTTAAGACAACCCT
672268 AAGGTGTGAA
131 AAGGTGTGAA
672278 TTATTCAGATCAACCCGAATACCCTCAACTGAAACAACATGACCAAAGAATGCTACCTCACTCAA
1 TTATTCAGATCAACCCGAATACCCTCAACTGAAACAACATGACCAAAGAATGCTACCTCACTCAA
*
672343 CCAAAACTCACACTTCAAAAACTTCGCATATAATGTCTTCTCCTTAACACCTTTAAGACAACCCT
66 CCAAAACTCACACTTCAAAAACTTCGCATACAATGTCTTCTCCTTAACACCTTTAAGACAACCCT
672408 AAGGTGTGAA
131 AAGGTGTGAA
672418 T
1 T
672419 CATGATCTTC
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.38, C:0.30, G:0.09, T:0.23
Consensus pattern (140 bp):
TTATTCAGATCAACCCGAATACCCTCAACTGAAACAACATGACCAAAGAATGCTACCTCACTCAA
CCAAAACTCACACTTCAAAAACTTCGCATACAATGTCTTCTCCTTAACACCTTTAAGACAACCCT
AAGGTGTGAA
Found at i:673226 original size:17 final size:17
Alignment explanation
Indices: 673204--673242 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
673194 ACCTCAGGTA
673204 CACTCAATCCACGAGTG
1 CACTCAATCCACGAGTG
673221 CACTCAATCCACGAGTG
1 CACTCAATCCACGAGTG
673238 CACTC
1 CACTC
673243 TCTCTTAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.38, G:0.15, T:0.18
Consensus pattern (17 bp):
CACTCAATCCACGAGTG
Found at i:674074 original size:44 final size:43
Alignment explanation
Indices: 673998--674104 Score: 110
Period size: 44 Copynumber: 2.4 Consensus size: 43
673988 CGAATGGATG
* *
673998 TAAATGAACAAAATAAACGAACGTAAACGAACACAAA-CTAACA
1 TAAATGAACAAAATAAACGAACGTAAAAGAACACAAATCGAA-A
* * *
674041 TAAATGAACACAAATGAA-TAATCGTAAAAGAACATAAATCGAAA
1 TAAATGAACA-AAATAAACGAA-CGTAAAAGAACACAAATCGAAA
*
674085 TAAATGAACATAAACAAACG
1 TAAATGAACA-AAATAAACG
674105 TAACCAAACA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
43 12 0.24
44 36 0.71
45 3 0.06
ACGTcount: A:0.60, C:0.15, G:0.10, T:0.15
Consensus pattern (43 bp):
TAAATGAACAAAATAAACGAACGTAAAAGAACACAAATCGAAA
Found at i:678631 original size:24 final size:24
Alignment explanation
Indices: 678586--678638 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
678576 AGATTGAGTT
* * *
678586 AAACATAAATGAACGAACATAAAC
1 AAACATAAACGAACAAAAATAAAC
*
678610 AAACATAAACGAATAAAAATAAAC
1 AAACATAAACGAACAAAAATAAAC
*
678634 GAACA
1 AAACA
678639 AATTAACATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.66, C:0.15, G:0.08, T:0.11
Consensus pattern (24 bp):
AAACATAAACGAACAAAAATAAAC
Found at i:680165 original size:7 final size:7
Alignment explanation
Indices: 680153--680203 Score: 59
Period size: 7 Copynumber: 7.0 Consensus size: 7
680143 CACCATCAGA
680153 ATTTTTT
1 ATTTTTT
680160 ATTTTTT
1 ATTTTTT
680167 ATTTTTT
1 ATTTTTT
*
680174 ATATTTT
1 ATTTTTT
680181 ATCTTTATT
1 AT-TTT-TT
680190 -TTTTCTT
1 ATTTT-TT
680197 ATTTTTT
1 ATTTTTT
680204 CAGTTTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
7 29 0.76
8 7 0.18
9 2 0.05
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (7 bp):
ATTTTTT
Found at i:680820 original size:19 final size:19
Alignment explanation
Indices: 680796--680835 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
680786 ATCAGATATC
680796 CAGTACCCACACTCATTCT
1 CAGTACCCACACTCATTCT
680815 CAGTACCCACACTCATTCT
1 CAGTACCCACACTCATTCT
680834 CA
1 CA
680836 TTTCCTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.42, G:0.05, T:0.25
Consensus pattern (19 bp):
CAGTACCCACACTCATTCT
Found at i:686621 original size:14 final size:14
Alignment explanation
Indices: 686602--686635 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
686592 GTGGGAGATT
686602 GTTGAAAATTCAAA
1 GTTGAAAATTCAAA
686616 GTTGAAAATTCAAA
1 GTTGAAAATTCAAA
686630 GTTGAA
1 GTTGAA
686636 TTTGTTGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (14 bp):
GTTGAAAATTCAAA
Found at i:688363 original size:5 final size:5
Alignment explanation
Indices: 688353--688378 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
688343 TGACTTAGAA
688353 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
688379 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:689430 original size:19 final size:19
Alignment explanation
Indices: 689395--689442 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
689385 TTAAATTCAA
*
689395 TTTTCAAAATTTCATTTTGT
1 TTTTCAAAATCTCATTTT-T
689415 TTTTCAAAATCT-ATTTTT
1 TTTTCAAAATCTCATTTTT
689433 TCTTTCAAAA
1 T-TTTCAAAA
689443 GAAAATCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 2 0.08
19 13 0.50
20 11 0.42
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTTCAAAATCTCATTTTT
Found at i:691712 original size:2 final size:2
Alignment explanation
Indices: 691705--691740 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
691695 TTACCTAGTT
691705 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
691741 GAGGAAGACT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:695617 original size:21 final size:21
Alignment explanation
Indices: 695593--695653 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
695583 CCAACTTTGA
695593 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
695614 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
695628 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
695649 AAATG
1 AAATG
695654 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:695674 original size:36 final size:35
Alignment explanation
Indices: 695587--695701 Score: 187
Period size: 35 Copynumber: 3.3 Consensus size: 35
695577 TGGCAACCAA
695587 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
695622 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
695657 CTTTGAAAAATGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
695693 -GTTGAAAAT
1 CTTTGAAAAT
695702 ATGAATGAGT
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
34 5 0.07
35 43 0.57
36 28 0.37
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:698081 original size:6 final size:6
Alignment explanation
Indices: 698070--698094 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
698060 CTCCATCTAC
698070 CCGATT CCGATT CCGATT CCGATT C
1 CCGATT CCGATT CCGATT CCGATT C
698095 ACCGAGGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.16, T:0.32
Consensus pattern (6 bp):
CCGATT
Found at i:741218 original size:23 final size:23
Alignment explanation
Indices: 741188--741231 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
741178 GAAGTCGGAG
741188 GTGGGGCTTCCGCTTAATTGGCC
1 GTGGGGCTTCCGCTTAATTGGCC
741211 GTGGGGCTTCCGCTTAATTGG
1 GTGGGGCTTCCGCTTAATTGG
741232 AAGAAGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.36, T:0.32
Consensus pattern (23 bp):
GTGGGGCTTCCGCTTAATTGGCC
Found at i:741299 original size:3 final size:3
Alignment explanation
Indices: 741291--741321 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
741281 GTTTTACTTT
741291 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
741322 ATTTACATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:754032 original size:57 final size:57
Alignment explanation
Indices: 753962--754076 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
753952 GAGATGTCAT
753962 TGTCTTGTTTTAATGGAAGGGATTTGAAGTGTTATCCAAAAATGGTTGAGCATTTAC
1 TGTCTTGTTTTAATGGAAGGGATTTGAAGTGTTATCCAAAAATGGTTGAGCATTTAC
754019 TGTCTTGTTTTAATGGAAGGGATTTGAAGTGTTATCCAAAAATGGTTGAGCATTTAC
1 TGTCTTGTTTTAATGGAAGGGATTTGAAGTGTTATCCAAAAATGGTTGAGCATTTAC
754076 T
1 T
754077 TTTCCTTCTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (57 bp):
TGTCTTGTTTTAATGGAAGGGATTTGAAGTGTTATCCAAAAATGGTTGAGCATTTAC
Found at i:760423 original size:26 final size:26
Alignment explanation
Indices: 760369--760422 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
760359 GGCTTAAAGG
760369 TTTGTTTTTTTGGGCTTGATCTTTTT
1 TTTGTTTTTTTGGGCTTGATCTTTTT
* *
760395 TTTG-TTTTTTGGGTTTGATATTTTT
1 TTTGTTTTTTTGGGCTTGATCTTTTT
760420 TTT
1 TTT
760423 TTTAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.06, C:0.04, G:0.19, T:0.72
Consensus pattern (26 bp):
TTTGTTTTTTTGGGCTTGATCTTTTT
Found at i:762096 original size:64 final size:64
Alignment explanation
Indices: 762011--762234 Score: 245
Period size: 64 Copynumber: 3.5 Consensus size: 64
762001 TGTTTGAATG
* ** **
762011 TGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATTC
1 TGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTC
762074 A
64 A
* **
762075 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
* ** ** * ** *
762139 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATACTACATCGAATACCTTTTA
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
* *
762203 TGCACCGATGCATCAGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAGTAGTGCATCGATGCAT
762235 ACCTTCATTA
Statistics
Matches: 136, Mismatches: 22, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
64 130 0.96
65 6 0.04
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
Found at i:762560 original size:12 final size:12
Alignment explanation
Indices: 762542--762577 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
762532 TATATATGTT
762542 CATGTGATATGA
1 CATGTGATATGA
*
762554 TATGTGATATGA
1 CATGTGATATGA
*
762566 CCTGTGATATGA
1 CATGTGATATGA
762578 AAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:762734 original size:15 final size:15
Alignment explanation
Indices: 762716--762748 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
762706 AAGGGTATAA
762716 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
762731 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
762746 TAG
1 TAG
762749 GAGTCCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.30
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:769010 original size:64 final size:64
Alignment explanation
Indices: 768924--769147 Score: 227
Period size: 64 Copynumber: 3.5 Consensus size: 64
768914 TATTTGAATG
* ** **
768924 TGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATACAATTC
1 TGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATACAATTC
768987 A
64 A
* * * **
768988 TGCATTGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATACAATTCA
* * ** ** ** *
769052 TGCATCGATGCATAAGGAGTGCATCAATGCATCCCAGCAATAATACTACATCGAATACCTTTTA
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATACAATTCA
* *
769116 TGCACCGATGCATCAGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAGTAGTGCATCGATGCAT
769148 ACCTTCATTA
Statistics
Matches: 131, Mismatches: 27, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
64 125 0.95
65 6 0.05
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATACAATTCA
Found at i:769662 original size:18 final size:15
Alignment explanation
Indices: 769623--769655 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
769613 GAGGGTATAA
769623 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
769638 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
769653 TAG
1 TAG
769656 GAGTCCTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:770678 original size:47 final size:47
Alignment explanation
Indices: 770637--770832 Score: 358
Period size: 47 Copynumber: 4.2 Consensus size: 47
770627 TATGGTCTCT
*
770637 TTTCATGTCTTAATGCA-CCATTTCATGCATTTTAAATTATGGCATCC
1 TTTCATGCCTTAATGCATCC-TTTCATGCATTTTAAATTATGGCATCC
770684 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAAATTATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAAATTATGGCATCC
770731 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAAATTATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAAATTATGGCATCC
*
770778 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAAATTATGACATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAAATTATGGCATCC
770825 TTTCATGC
1 TTTCATGC
770833 ATTTTAATTA
Statistics
Matches: 146, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
47 144 0.99
48 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.43
Consensus pattern (47 bp):
TTTCATGCCTTAATGCATCCTTTCATGCATTTTAAATTATGGCATCC
Found at i:770703 original size:20 final size:23
Alignment explanation
Indices: 770678--770925 Score: 166
Period size: 20 Copynumber: 10.7 Consensus size: 23
770668 TTAAATTATG
770678 GCATCCTTTCATGC-CTT-A-AT
1 GCATCCTTTCATGCACTTAATAT
*
770698 GCATCCTTTCATGCATTTTAAATTAT
1 GCATCCTTTCATGCA-CTT-AA-TAT
770724 GGCATCCTTTCATGC-CTT-A-AT
1 -GCATCCTTTCATGCACTTAATAT
*
770745 GCATCCTTTCATGCATTTTAAATTAT
1 GCATCCTTTCATGCA-CTT-AA-TAT
770771 GGCATCCTTTCATGC-CTT-A-AT
1 -GCATCCTTTCATGCACTTAATAT
*
770792 GCATCCTTTCATGCATTTTAAATTAT
1 GCATCCTTTCATGCA-CTT-AA-TAT
*
770818 GACATCCTTTCATGCATTTTAATTAT
1 G-CATCCTTTCATGCA-CTTAA-TAT
770844 GGCATCCTTTCATGC-CTT-A-AT
1 -GCATCCTTTCATGCACTTAATAT
* *
770865 GCATCATTTCATGCATTTTAATTAT
1 GCATCCTTTCATGCA-CTTAA-TAT
*
770890 GGCATCATTTCATGC-CTT-A-AT
1 -GCATCCTTTCATGCACTTAATAT
770911 GCATCCTTTCATGCA
1 GCATCCTTTCATGCA
770926 TTTTAATTAT
Statistics
Matches: 189, Mismatches: 10, Indels: 57
0.74 0.04 0.22
Matches are distributed among these distances:
20 68 0.36
21 8 0.04
22 8 0.04
23 5 0.03
24 7 0.04
25 6 0.03
26 40 0.21
27 47 0.25
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.42
Consensus pattern (23 bp):
GCATCCTTTCATGCACTTAATAT
Found at i:770859 original size:73 final size:73
Alignment explanation
Indices: 770746--770904 Score: 275
Period size: 73 Copynumber: 2.2 Consensus size: 73
770736 TGCCTTAATG
*
770746 CATCCTTTCATGCATTTTAAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
1 CATCCTTTCATGCATTTTAAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTT
770811 AAATTATGA
66 -AATTATGA
770820 CATCCTTTCATGCATTTT-AATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTT
1 CATCCTTTCATGCATTTTAAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTT
*
770884 AATTATGG
66 AATTATGA
*
770892 CATCATTTCATGC
1 CATCCTTTCATGC
770905 CTTAATGCAT
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
72 19 0.23
73 45 0.55
74 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.43
Consensus pattern (73 bp):
CATCCTTTCATGCATTTTAAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTT
AATTATGA
Found at i:770879 original size:46 final size:46
Alignment explanation
Indices: 770820--770936 Score: 216
Period size: 46 Copynumber: 2.5 Consensus size: 46
770810 TAAATTATGA
*
770820 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCATTTCATGCCTTAATG
*
770866 CATCATTTCATGCATTTTAATTATGGCATCATTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCATTTCATGCCTTAATG
770912 CATCCTTTCATGCATTTTAATTATG
1 CATCCTTTCATGCATTTTAATTATG
770937 AATTCGATTT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 68 1.00
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.44
Consensus pattern (46 bp):
CATCCTTTCATGCATTTTAATTATGGCATCATTTCATGCCTTAATG
Found at i:771555 original size:17 final size:17
Alignment explanation
Indices: 771533--771597 Score: 121
Period size: 17 Copynumber: 3.8 Consensus size: 17
771523 CTTCCCTTTG
771533 TTAGTATCGATACCTTA
1 TTAGTATCGATACCTTA
771550 TTAGTATCGATACCTTA
1 TTAGTATCGATACCTTA
*
771567 TTAATATCGATACCTTA
1 TTAGTATCGATACCTTA
771584 TTAGTATCGATACC
1 TTAGTATCGATACC
771598 CCTTGCATCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 46 1.00
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (17 bp):
TTAGTATCGATACCTTA
Found at i:772587 original size:2 final size:2
Alignment explanation
Indices: 772582--772612 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
772572 TAATAAAAAT
772582 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
772613 CAAGTCACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:775579 original size:29 final size:30
Alignment explanation
Indices: 775543--775614 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 30
775533 TTATATAAAA
* *
775543 TTTGAAATTTTAA-AAAAAATATGTTATTT
1 TTTGAAATTTTAATAAAAAATATATTAATT
* *
775572 TTTGAAATTTGGAATTAAAGAATATATTAATT
1 TTTGAAATTT-TAA-TAAAAAATATATTAATT
775604 TTTGAAATTTT
1 TTTGAAATTTT
775615 TATTTAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 10 0.29
30 2 0.06
32 23 0.66
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.49
Consensus pattern (30 bp):
TTTGAAATTTTAATAAAAAATATATTAATT
Found at i:776256 original size:11 final size:11
Alignment explanation
Indices: 776240--776272 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
776230 GTTAGATAAA
776240 ATCATTAGTTT
1 ATCATTAGTTT
776251 ATCATTAGTTT
1 ATCATTAGTTT
*
776262 ACCATTA-TTT
1 ATCATTAGTTT
776272 A
1 A
776273 CTAATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.30, C:0.12, G:0.06, T:0.52
Consensus pattern (11 bp):
ATCATTAGTTT
Found at i:779167 original size:30 final size:30
Alignment explanation
Indices: 779049--779156 Score: 101
Period size: 30 Copynumber: 3.6 Consensus size: 30
779039 AGAGTCGAGG
* *
779049 GTTACTTAGGTTCTTCGGAATCTATGGACA
1 GTTACCTAGGTTCTTCGGAATATATGGACA
* * * *
779079 ATTATCTATGTTCTTCAGG-ACATATGGACA
1 GTTACCTAGGTTCTTC-GGAATATATGGACA
* ** **
779109 GATACCTATATTCTTCATAATATATGGACA
1 GTTACCTAGGTTCTTCGGAATATATGGACA
779139 GTTACCTAGGTTCTTCGG
1 GTTACCTAGGTTCTTCGG
779157 GACTTATGGA
Statistics
Matches: 58, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
30 56 0.97
31 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (30 bp):
GTTACCTAGGTTCTTCGGAATATATGGACA
Found at i:783494 original size:30 final size:30
Alignment explanation
Indices: 783458--783576 Score: 132
Period size: 30 Copynumber: 4.0 Consensus size: 30
783448 AGAGTCGAGG
*
783458 GTTACCTAAGTTCTTCGGAATC-TATGGACA
1 GTTACCTATGTTCTTCGGAA-CATATGGACA
* * *
783488 GTTACCTATGTTCTTTGGGACATAGGGACA
1 GTTACCTATGTTCTTCGGAACATATGGACA
** *
783518 AATACCTATGTTCTTCAGAACATATGGACA
1 GTTACCTATGTTCTTCGGAACATATGGACA
* * *
783548 GTTACCTAGGTTCTTCGGGACCTATGGAC
1 GTTACCTATGTTCTTCGGAACATATGGAC
783577 CGGTCCTTTG
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
29 1 0.01
30 71 0.99
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (30 bp):
GTTACCTATGTTCTTCGGAACATATGGACA
Found at i:786748 original size:23 final size:23
Alignment explanation
Indices: 786633--786749 Score: 94
Period size: 23 Copynumber: 5.1 Consensus size: 23
786623 AGCTCGTATA
* *
786633 AATTGTACCGAAGTG-CCACATAA
1 AATTGTCCCGAAG-GACCACATAG
* *
786656 AAATGTCCCGAATGACCACATAG
1 AATTGTCCCGAAGGACCACATAG
* ** *
786679 -ATATGTCTCGAAGGATTACGTAG
1 AAT-TGTCCCGAAGGACCACATAG
* * **
786702 AAATGTCCCTAAGGACCATGTAG
1 AATTGTCCCGAAGGACCACATAG
786725 AATTGTCCCGAAGGACCACATAG
1 AATTGTCCCGAAGGACCACATAG
786748 AA
1 AA
786750 CCCTCGACTC
Statistics
Matches: 71, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
22 2 0.03
23 68 0.96
24 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (23 bp):
AATTGTCCCGAAGGACCACATAG
Found at i:786749 original size:46 final size:46
Alignment explanation
Indices: 786633--786749 Score: 112
Period size: 46 Copynumber: 2.5 Consensus size: 46
786623 AGCTCGTATA
* * *
786633 AATTGTACCGAAGTG-CCACATAAAAATGTCCCGAATGACCACATAG
1 AATTGTCCCGAAG-GACCACATAGAAATGTCCCGAAGGACCACATAG
* ** * * **
786679 -ATATGTCTCGAAGGATTACGTAGAAATGTCCCTAAGGACCATGTAG
1 AAT-TGTCCCGAAGGACCACATAGAAATGTCCCGAAGGACCACATAG
786725 AATTGTCCCGAAGGACCACATAGAA
1 AATTGTCCCGAAGGACCACATAGAA
786750 CCCTCGACTC
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
45 3 0.06
46 49 0.91
47 2 0.04
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (46 bp):
AATTGTCCCGAAGGACCACATAGAAATGTCCCGAAGGACCACATAG
Found at i:793751 original size:23 final size:23
Alignment explanation
Indices: 793667--793770 Score: 102
Period size: 23 Copynumber: 4.5 Consensus size: 23
793657 ATAAATTGCA
* *
793667 CCGAAGTG-CCACATAGAAATGAC
1 CCGAAG-GACCACGTAGAAATGTC
* * *
793690 CCGAATGACCACATAGATATGTC
1 CCGAAGGACCACGTAGAAATGTC
* **
793713 TCGAAGGATTACGTAGAAATGTC
1 CCGAAGGACCACGTAGAAATGTC
* *
793736 CCGAAGGACCATGTAGAATTGTC
1 CCGAAGGACCACGTAGAAATGTC
793759 CCGAAGGACCAC
1 CCGAAGGACCAC
793771 ATATAACCCT
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
22 1 0.02
23 64 0.98
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (23 bp):
CCGAAGGACCACGTAGAAATGTC
Found at i:793892 original size:16 final size:16
Alignment explanation
Indices: 793852--793907 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
793842 TTTATATCAT
*
793852 TTCACATAAACATGTA
1 TTCACATAGACATGTA
*
793868 TTCACATAGACGTGTA
1 TTCACATAGACATGTA
793884 TTCACATAGACAAT-T-
1 TTCACATAGAC-ATGTA
793899 TTCACATAG
1 TTCACATAG
793908 CTTGTGTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
15 9 0.25
16 26 0.72
17 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.32
Consensus pattern (16 bp):
TTCACATAGACATGTA
Found at i:795890 original size:20 final size:20
Alignment explanation
Indices: 795865--795911 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
795855 GTATAGCAAT
*
795865 GAACCGGCTGAAAACCGATA
1 GAACCGGCTAAAAACCGATA
* *
795885 GAACCGACTAAAAACTGATA
1 GAACCGGCTAAAAACCGATA
*
795905 AAACCGG
1 GAACCGG
795912 GGTTAACCGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (20 bp):
GAACCGGCTAAAAACCGATA
Found at i:807480 original size:7 final size:7
Alignment explanation
Indices: 807468--807542 Score: 55
Period size: 7 Copynumber: 10.4 Consensus size: 7
807458 CAAAAAGGGC
807468 AAAAAGA
1 AAAAAGA
807475 AAAAAGA
1 AAAAAGA
807482 AAAGAAGCA
1 AAA-AAG-A
*
807491 AAAAAGG
1 AAAAAGA
807498 AAAAA-A
1 AAAAAGA
*
807504 CAAAAGA
1 AAAAAGA
*
807511 ACAAA-A
1 AAAAAGA
*
807517 AGAAAGA
1 AAAAAGA
*
807524 ACAAAGA
1 AAAAAGA
807531 TCAAAAAGA
1 --AAAAAGA
807540 AAA
1 AAA
807543 GGGGACAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
6 9 0.17
7 29 0.54
8 6 0.11
9 10 0.19
ACGTcount: A:0.77, C:0.07, G:0.15, T:0.01
Consensus pattern (7 bp):
AAAAAGA
Found at i:807493 original size:31 final size:28
Alignment explanation
Indices: 807454--807511 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
807444 AGATTCAATC
*
807454 AGAACAAAAAGGGCAAAAAGAAAAAAGAAA
1 AGAACAAAAAAGG-AAAAA-AAAAAAGAAA
*
807484 AGAAGCAAAAAAGGAAAAAACAAAAGAA
1 AGAA-CAAAAAAGGAAAAAAAAAAAGAA
807512 CAAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.32
30 9 0.36
31 8 0.32
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (28 bp):
AGAACAAAAAAGGAAAAAAAAAAAGAAA
Found at i:807501 original size:23 final size:23
Alignment explanation
Indices: 807468--807542 Score: 70
Period size: 24 Copynumber: 3.4 Consensus size: 23
807458 CAAAAAGGGC
*
807468 AAAAAG-AAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAAACAAAAGAA-CA
*
807491 AAAAAGGAAAAAACAAAAGAAC-
1 AAAAAGAAAAAAACAAAAGAACA
* *
807513 AAAAAG-AAAGAAC-AAAGATC-
1 AAAAAGAAAAAAACAAAAGAACA
807533 AAAAAGAAAA
1 AAAAAGAAAA
807543 GGGGACAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.26
21 9 0.19
22 6 0.13
23 7 0.15
24 13 0.28
ACGTcount: A:0.77, C:0.07, G:0.15, T:0.01
Consensus pattern (23 bp):
AAAAAGAAAAAAACAAAAGAACA
Found at i:807516 original size:13 final size:12
Alignment explanation
Indices: 807468--807528 Score: 56
Period size: 12 Copynumber: 5.0 Consensus size: 12
807458 CAAAAAGGGC
807468 AAAAAGAA-AAA
1 AAAAAGAACAAA
807479 AGAAAAGAAGC-AA
1 A-AAAAGAA-CAAA
*
807492 AAAAGGAA-AAA
1 AAAAAGAACAAA
807503 ACAAAAGAACAAA
1 A-AAAAGAACAAA
807516 AAGAAAGAACAAA
1 AA-AAAGAACAAA
807529 GATCAAAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
11 4 0.10
12 20 0.49
13 17 0.41
ACGTcount: A:0.79, C:0.07, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAGAACAAA
Found at i:807535 original size:20 final size:21
Alignment explanation
Indices: 807467--807542 Score: 91
Period size: 20 Copynumber: 3.5 Consensus size: 21
807457 ACAAAAAGGG
*
807467 CAAAAAGAAAAAAGAAAAGAA
1 CAAAAAGAAAAAACAAAAGAA
807488 GCAAAAAAGGAAAAAACAAAAGAA
1 -C-AAAAA-GAAAAAACAAAAGAA
* *
807512 CAAAAAGAAAGAAC-AAAGAT
1 CAAAAAGAAAAAACAAAAGAA
807532 CAAAAAGAAAA
1 CAAAAAGAAAA
807543 GGGGACAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
20 15 0.31
21 7 0.15
22 6 0.12
23 6 0.12
24 14 0.29
ACGTcount: A:0.76, C:0.08, G:0.14, T:0.01
Consensus pattern (21 bp):
CAAAAAGAAAAAACAAAAGAA
Found at i:808172 original size:22 final size:22
Alignment explanation
Indices: 808144--808187 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
808134 AGCTATCCCA
*
808144 TCAAACCTTTGAACATCAAATG
1 TCAAACCATTGAACATCAAATG
*
808166 TCAAACCATTGAGCATCAAATG
1 TCAAACCATTGAACATCAAATG
808188 GACAAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (22 bp):
TCAAACCATTGAACATCAAATG
Found at i:809870 original size:43 final size:44
Alignment explanation
Indices: 809809--809958 Score: 116
Period size: 43 Copynumber: 3.5 Consensus size: 44
809799 CAGAGCCAAT
809809 TTCAACTTCAC-AGCGAAGGATATTGGACTCAAGACAACGCAAG
1 TTCAACTTCACGAGCGAAGGATATTGGACTCAAGACAACGCAAG
*** ** * *
809852 TTCAACTTCACGA-CGAAGGGACCGCTGGTTGTCAATA-AA--CAAC
1 TTCAACTTCACGAGCGAA-GGA-TATTGG-ACTCAAGACAACGCAAG
* * *
809895 TTCCCAATTTCA-TAGCGAAGGATATTGGACTCCAGACAACGCAAG
1 TT--CAACTTCACGAGCGAAGGATATTGGACTCAAGACAACGCAAG
809940 TTCAACTTCACGA-CGAAGG
1 TTCAACTTCACGAGCGAAGG
809959 GACCGCTGGT
Statistics
Matches: 77, Mismatches: 19, Indels: 22
0.65 0.16 0.19
Matches are distributed among these distances:
42 4 0.05
43 38 0.49
44 9 0.12
45 21 0.27
46 5 0.06
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (44 bp):
TTCAACTTCACGAGCGAAGGATATTGGACTCAAGACAACGCAAG
Found at i:809969 original size:88 final size:88
Alignment explanation
Indices: 809815--809994 Score: 342
Period size: 88 Copynumber: 2.0 Consensus size: 88
809805 CAATTTCAAC
809815 TTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
1 TTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
809880 TTGTCAATAAACAACTTCCCAAT
66 TTGTCAATAAACAACTTCCCAAT
* *
809903 TTCATAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
1 TTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
809968 TTGTCAATAAACAACTTCCCAAT
66 TTGTCAATAAACAACTTCCCAAT
809991 TTCA
1 TTCA
809995 GAACCAATTT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (88 bp):
TTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
TTGTCAATAAACAACTTCCCAAT
Found at i:810064 original size:194 final size:200
Alignment explanation
Indices: 809729--810257 Score: 773
Period size: 194 Copynumber: 2.6 Consensus size: 200
809719 ATATCATGTC
* * * *
809729 ACTCCTGACAACGAAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
809794 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGATTCAAGACAACGCAAGTTCAACT
* * *
809859 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC-T-TC-CCAATTTC-A-T-AGCGAAGGAT
131 TCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTCACCAATTTCAACTCAACGAAGGAT
809918 ATTGG
196 ATTGG
809923 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
809988 AATTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGATTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGATTCAAGACAACGCAAGTTCAACT
*
810053 TCATGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAATTTTAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC--------A-CCAATTTCAAC-T-
810118 ACAACGAAGGATATTGG
185 -CAACGAAGGATATTGG
* * *
810135 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTATCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
810200 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGATTCAAGACAACACAAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGATTCAAGACAACGCAAG
810258 GACGGCTGGT
Statistics
Matches: 300, Mismatches: 17, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
194 156 0.52
195 1 0.00
196 2 0.01
206 8 0.03
207 1 0.00
209 1 0.00
212 131 0.44
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (200 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGATTCAAGACAACGCAAGTTCAACT
TCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTCACCAATTTCAACTCAACGAAGGAT
ATTGG
Found at i:810097 original size:106 final size:106
Alignment explanation
Indices: 809903--810257 Score: 584
Period size: 106 Copynumber: 3.3 Consensus size: 106
809893 ACTTCCCAAT
*
809903 TTCATAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
1 TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* *
809968 TTGTCAATAAACAACTTCCCAATTTCAGAACCAATTTCAAC
66 TTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAAC
* * *
810009 TTCACAGCGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCACTGG
1 TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* *
810074 TTGTCAACAAACAACTTCTCAATTTTAGAGCCAATTTCAAC
66 TTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAAC
*
810115 TTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
1 TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* *
810180 TTATCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAAC
66 TTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAAC
* * *
810221 TTCACAGCGAAGGATATTGGATTCAAGACAACACAAG
1 TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
810258 GACGGCTGGT
Statistics
Matches: 229, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 229 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
TTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAAC
Found at i:815109 original size:35 final size:35
Alignment explanation
Indices: 815017--815127 Score: 161
Period size: 35 Copynumber: 3.1 Consensus size: 35
815007 CCATTATCAT
* * *
815017 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTA
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCA
815052 TTTTTCAAAGAAAACATTTACCAAACTTTGAAAACCA
1 -TTTTCAAAG-AAACATTTACCAAACTTTGAAAACCA
815089 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
815124 TTTT
1 TTTT
815128 TTCAAAGTTG
Statistics
Matches: 70, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
35 30 0.43
36 14 0.20
37 8 0.11
38 18 0.26
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32
Consensus pattern (35 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:815143 original size:35 final size:36
Alignment explanation
Indices: 815016--815161 Score: 135
Period size: 35 Copynumber: 4.1 Consensus size: 36
815006 CCCATTATCA
*
815016 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
815051 ATTTTTCAAAGAAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG--AACAGTTACCAAACTTTGAAAACCAT
*
815089 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
815125 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
815159 TTT
1 TTT
815162 AATACTTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 16
0.82 0.04 0.13
Matches are distributed among these distances:
34 14 0.14
35 36 0.37
36 17 0.17
37 9 0.09
38 21 0.21
39 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Done.