Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 33 of 55
Found at i:6535614 original size:21 final size:21
Alignment explanation
Indices: 6535568--6535650 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 21
6535558 TTAAACTAAC
* *
6535568 AAACTAATATAAT-ATAACTT
1 AAACTAACAAAATAATAACTT
* *
6535588 AAACTAAGAAAATAATAATTT
1 AAACTAACAAAATAATAACTT
* * *
6535609 ATACTAACAAACTAATTAAACCCT
1 AAACTAACAAAATAA-T-AA-CTT
*
6535633 AAACTAACAAACTAATAA
1 AAACTAACAAAATAATAA
6535651 TTTCATTTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 11 0.22
21 18 0.36
22 3 0.06
23 3 0.06
24 15 0.30
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.27
Consensus pattern (21 bp):
AAACTAACAAAATAATAACTT
Found at i:6537158 original size:36 final size:36
Alignment explanation
Indices: 6537111--6537213 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
6537101 CAAGCTAAGG
* *
6537111 TTGTTTCAAGGGAAACTGTCTCAAGTGAGAGAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
* *
6537147 TTGTTTCAAGGGAAATTATCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
*
6537183 TTGTTTAAAGGGAAACTGTCTCAAGGGAGAC
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGAC
6537214 TGTCTCAAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (36 bp):
TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
Found at i:6537209 original size:51 final size:51
Alignment explanation
Indices: 6537152--6537261 Score: 166
Period size: 51 Copynumber: 2.2 Consensus size: 51
6537142 AAAATTTGTT
* *
6537152 TCAAGGGAAATTATCTCAAGGGAGACAAAATTTGTTTAAAGGGAAACTGTC
1 TCAAGGGAAACTATCTCAAGGGAGACAAAATTTGTTTAAAGAGAAACTGTC
* * * *
6537203 TCAAGGGAGACTGTCTCAAGGGAGACGAAATTTGTTTCAAGAGAAACTGTC
1 TCAAGGGAAACTATCTCAAGGGAGACAAAATTTGTTTAAAGAGAAACTGTC
6537254 TCAAGGGA
1 TCAAGGGA
6537262 GATAAAAGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (51 bp):
TCAAGGGAAACTATCTCAAGGGAGACAAAATTTGTTTAAAGAGAAACTGTC
Found at i:6537226 original size:15 final size:15
Alignment explanation
Indices: 6537190--6537228 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
6537180 AATTTGTTTA
*
6537190 AAGGGAAACTGTCTC
1 AAGGGAGACTGTCTC
6537205 AAGGGAGACTGTCTC
1 AAGGGAGACTGTCTC
6537220 AAGGGAGAC
1 AAGGGAGAC
6537229 GAAATTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.33, T:0.15
Consensus pattern (15 bp):
AAGGGAGACTGTCTC
Found at i:6537243 original size:36 final size:36
Alignment explanation
Indices: 6537203--6537320 Score: 182
Period size: 36 Copynumber: 3.3 Consensus size: 36
6537193 GGAAACTGTC
* **
6537203 TCAAGGGAGACTGTCTCAAGGGAGACGAAATTTGTT
1 TCAAGGGAAACTGTCTCAAGGGAGAAAAAATTTGTT
* * *
6537239 TCAAGAGAAACTGTCTCAAGGGAGATAAAAGTTGTT
1 TCAAGGGAAACTGTCTCAAGGGAGAAAAAATTTGTT
6537275 TCAAGGGAAACTGTCTCAAGGGAGAAAAAATTTGTT
1 TCAAGGGAAACTGTCTCAAGGGAGAAAAAATTTGTT
6537311 TCAAGGGAAA
1 TCAAGGGAAA
6537321 AAGATTCAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 74 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (36 bp):
TCAAGGGAAACTGTCTCAAGGGAGAAAAAATTTGTT
Found at i:6537262 original size:51 final size:51
Alignment explanation
Indices: 6537165--6537263 Score: 171
Period size: 51 Copynumber: 1.9 Consensus size: 51
6537155 AGGGAAATTA
*
6537165 TCTCAAGGGAGACAAAATTTGTTTAAAGGGAAACTGTCTCAAGGGAGACTG
1 TCTCAAGGGAGACAAAATTTGTTTAAAGAGAAACTGTCTCAAGGGAGACTG
* *
6537216 TCTCAAGGGAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGA
1 TCTCAAGGGAGACAAAATTTGTTTAAAGAGAAACTGTCTCAAGGGAGA
6537264 TAAAAGTTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.23
Consensus pattern (51 bp):
TCTCAAGGGAGACAAAATTTGTTTAAAGAGAAACTGTCTCAAGGGAGACTG
Found at i:6537262 original size:87 final size:87
Alignment explanation
Indices: 6537116--6537299 Score: 280
Period size: 87 Copynumber: 2.1 Consensus size: 87
6537106 TAAGGTTGTT
* * * *
6537116 TCAAGGGAAACTGTCTCAAGTGAGAGAAAATTTGTTTCAAGGGAAATTATCTCAAGGGAGACAAA
1 TCAAGGGAGACTGTCTCAAGGGAGAGAAAATTTGTTTCAAGAGAAACTATCTCAAGGGAGACAAA
*
6537181 ATTTGTTTAAAGGGAAACTGTC
66 AGTTGTTTAAAGGGAAACTGTC
* *
6537203 TCAAGGGAGACTGTCTCAAGGGAGACG-AAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGATAA
1 TCAAGGGAGACTGTCTCAAGGGAGA-GAAAATTTGTTTCAAGAGAAACTATCTCAAGGGAGACAA
*
6537267 AAGTTGTTTCAAGGGAAACTGTC
65 AAGTTGTTTAAAGGGAAACTGTC
6537290 TCAAGGGAGA
1 TCAAGGGAGA
6537300 AAAAATTTGT
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
87 87 0.99
88 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.24
Consensus pattern (87 bp):
TCAAGGGAGACTGTCTCAAGGGAGAGAAAATTTGTTTCAAGAGAAACTATCTCAAGGGAGACAAA
AGTTGTTTAAAGGGAAACTGTC
Found at i:6537373 original size:67 final size:66
Alignment explanation
Indices: 6537272--6537510 Score: 361
Period size: 67 Copynumber: 3.6 Consensus size: 66
6537262 GATAAAAGTT
* * * * *
6537272 GTTTCAAGGGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAAAAGATTCAAATATTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
6537337 G
66 G
* * *
6537338 CGTTTAAAGAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGGAAACAGATTCAAAGATTT
1 -GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTT
*
6537403 TA
65 TG
*
6537405 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACATATTCAAAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACAGATTCAAAGATTT
6537470 TG
65 TG
*
6537472 GTTTCAAGAGAAACTGTCTCAAAAGAGACAAAATTTGTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTT
6537511 CTGAAAGGAA
Statistics
Matches: 156, Mismatches: 15, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
66 37 0.24
67 119 0.76
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (66 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
G
Found at i:6537418 original size:30 final size:29
Alignment explanation
Indices: 6537372--6537485 Score: 77
Period size: 30 Copynumber: 3.6 Consensus size: 29
6537362 AGAGACGAAA
* *
6537372 TTTGTTTAAAGGGAAACAGATTCAAAGAT
1 TTTGTTTCAAGAGAAACAGATTCAAAGAT
*
6537401 TTTAGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAAT
1 TTT-GTTTCAAGAGAAACAGAT-TC-A-A-AG-----AT
* *
6537439 TTTGTTTCAAGGGAAACATATTCAAAGAT
1 TTTGTTTCAAGAGAAACAGATTCAAAGAT
6537468 TTTGGTTTCAAGAGAAAC
1 TTT-GTTTCAAGAGAAAC
6537486 TGTCTCAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 23
0.69 0.07 0.24
Matches are distributed among these distances:
29 9 0.14
30 28 0.42
31 1 0.02
32 1 0.02
33 2 0.03
34 2 0.03
35 1 0.02
36 1 0.02
37 15 0.23
38 6 0.09
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (29 bp):
TTTGTTTCAAGAGAAACAGATTCAAAGAT
Found at i:6537455 original size:37 final size:38
Alignment explanation
Indices: 6537394--6537544 Score: 112
Period size: 37 Copynumber: 4.2 Consensus size: 38
6537384 GAAACAGATT
6537394 CAAAGATTTTAGTTTCAAGAGAAACTGTCTCAAGAGAGA
1 CAAA-ATTTTAGTTTCAAGAGAAACTGTCTCAAGAGAGA
* *
6537433 CAAAATTTT-GTTTCAAGGGAAACATAT-TC-A-A-AG-
1 CAAAATTTTAGTTTCAAGAGAAAC-TGTCTCAAGAGAGA
* *
6537466 ----ATTTTGGTTTCAAGAGAAACTGTCTCAAAAGAGA
1 CAAAATTTTAGTTTCAAGAGAAACTGTCTCAAGAGAGA
* * *
6537500 CAAAA-TTT-GTTCTGAA-AGGAAAATGTCTCAAGTGAGA
1 CAAAATTTTAGTT-TCAAGA-GAAACTGTCTCAAGAGAGA
6537537 CAAAATTT
1 CAAAATTT
6537545 ATTTTTTTAA
Statistics
Matches: 90, Mismatches: 8, Indels: 29
0.71 0.06 0.23
Matches are distributed among these distances:
29 7 0.08
30 15 0.17
31 1 0.01
32 1 0.01
33 2 0.02
34 2 0.02
35 1 0.01
36 5 0.06
37 42 0.47
38 10 0.11
39 4 0.04
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (38 bp):
CAAAATTTTAGTTTCAAGAGAAACTGTCTCAAGAGAGA
Found at i:6545717 original size:15 final size:16
Alignment explanation
Indices: 6545697--6545727 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
6545687 CAATCTTATG
6545697 TATATAATA-AAGTAA
1 TATATAATACAAGTAA
6545712 TATATAATACAAGTAA
1 TATATAATACAAGTAA
6545728 AATAAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.32
Consensus pattern (16 bp):
TATATAATACAAGTAA
Found at i:6553809 original size:23 final size:23
Alignment explanation
Indices: 6553783--6553830 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
6553773 ATAAAGTACA
* *
6553783 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
**
6553806 ATAATGTAATAGATAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
6553829 AT
1 AT
6553831 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGATAGCGCTTAT
Found at i:6554287 original size:23 final size:23
Alignment explanation
Indices: 6554261--6554319 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
6554251 AACCACTACA
6554261 TATTACATTATATAAATGATACC
1 TATTACATTATATAAATGATACC
* *
6554284 TATTACATTATATAAGTGCTACC
1 TATTACATTATATAAATGATACC
*
6554307 TATTACATCATAT
1 TATTACATTATAT
6554320 TTTTACCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (23 bp):
TATTACATTATATAAATGATACC
Found at i:6554485 original size:431 final size:430
Alignment explanation
Indices: 6553897--6554954 Score: 1922
Period size: 431 Copynumber: 2.5 Consensus size: 430
6553887 TATTACATTA
6553897 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
6553962 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
6554027 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
131 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
6554092 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
196 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
*
6554157 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
261 TTAAAACTCACTCAAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
*
6554222 TTATAAAAAGGATAGACACTTTACAATATAACCACTACATATTACATTATATAAATGATACCTAT
326 TTATAAAAAGGATAGACACTTTACAATATAACCACTACATATTACATTATATAAACGATACCTAT
* *
6554287 TACATTATATAAGTGCTACCTATTACATCATATTTTTACC
391 TACATTATATAAGCGCTACCTATTACATCATATGTTTACC
* *
6554327 TATTATATTGAAAATGTCCATATTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
6554392 TTATGTTTCAATTTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTT
66 TTATGTTTCAA-TTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTT
6554457 CATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
130 CATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
6554522 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
195 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
*
6554587 CTTGAAACTCACTCAAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
260 CTTAAAACTCACTCAAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
*
6554652 TTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
325 TTTATAAAAAGGATAGACACTTTACAATATAACCACTACATATTACATTATATAAACGATACCTA
6554717 TTACATTATATAAGCGCTACCTATTACATCATATGTTTACC
390 TTACATTATATAAGCGCTACCTATTACATCATATGTTTACC
*
6554758 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTTAAAAGTTATGTA
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTCTTTT-AAAGTTATGTA
* *
6554823 ATTTATGTTTCAA-TTTTTTTAACAGTGTTTCATATTTTCCACCTACAATATTAATTTAATAATT
64 ATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATT
* * * * *
6554887 TCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTATAA-TTTAAAT
129 TCATTTGCACAAAAAATTATTTGATT-ATTTGATATTTTATAAAATATTATTTAGAATTTTTAAT
6554951 TTAA
193 TTAA
6554955 CAACATTAAC
Statistics
Matches: 606, Mismatches: 18, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
430 74 0.12
431 475 0.78
432 33 0.05
433 24 0.04
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.42
Consensus pattern (430 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
TTAAAACTCACTCAAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
TTATAAAAAGGATAGACACTTTACAATATAACCACTACATATTACATTATATAAACGATACCTAT
TACATTATATAAGCGCTACCTATTACATCATATGTTTACC
Found at i:6554714 original size:23 final size:23
Alignment explanation
Indices: 6554688--6554750 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
6554678 ATATAACCAC
6554688 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
6554711 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
6554734 TACCTATTACATCATAT
1 TACCTATTACATTATAT
6554751 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:6555226 original size:39 final size:39
Alignment explanation
Indices: 6555172--6555257 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
6555162 CAAGTTGTAG
*
6555172 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
6555211 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
6555250 ATTTTGAT
1 ATTTTGAT
6555258 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:6555997 original size:23 final size:23
Alignment explanation
Indices: 6555971--6556033 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
6555961 ATATAACCAC
6555971 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
6555994 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
6556017 TACCTATTACATCATAT
1 TACCTATTACATTATAT
6556034 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:6556074 original size:21 final size:22
Alignment explanation
Indices: 6556049--6556098 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
6556039 CCTATTATAT
6556049 TAAAAGTG-TCCATACTTTTTA
1 TAAAAGTGATCCATACTTTTTA
*
6556070 TAAAAAG-GATCGATACTTTTTA
1 T-AAAAGTGATCCATACTTTTTA
6556092 TAAAAGT
1 TAAAAGT
6556099 TATGTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (22 bp):
TAAAAGTGATCCATACTTTTTA
Found at i:6559815 original size:17 final size:18
Alignment explanation
Indices: 6559793--6559835 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
6559783 ATATATCCGA
6559793 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
6559810 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
6559830 TATCAT
1 TATCAT
6559836 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:6559853 original size:20 final size:19
Alignment explanation
Indices: 6559798--6559844 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
6559788 TCCGATATCA
6559798 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
6559817 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
6559838 TTTTACC
1 TTTTACC
6559845 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:6560006 original size:20 final size:20
Alignment explanation
Indices: 6559979--6560025 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
6559969 TCCGGTAACG
6559979 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
6559998 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
6560019 TTTTACC
1 TTTTACC
6560026 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:6560069 original size:181 final size:182
Alignment explanation
Indices: 6559765--6560237 Score: 680
Period size: 181 Copynumber: 2.6 Consensus size: 182
6559755 CGTACTTACG
* * * *
6559765 AAAGTATCGACACTTTCAATATATCCGATATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
6559830 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
6559895 AGGCGCTATAACTGCCTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCCTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
6559946 AAAGTATCGACACTTTGAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
6560011 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** * * *
6560076 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCTTTATATT
131 AGGAGCTAAAACTGCCTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * *
6560128 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACCGGTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* * * *
6560192 TTGTCATAGTTTTACCTATTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
6560238 AATTTGGATC
Statistics
Matches: 261, Mismatches: 29, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
181 163 0.62
182 97 0.37
183 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCCTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:6560705 original size:229 final size:228
Alignment explanation
Indices: 6560304--6560790 Score: 866
Period size: 229 Copynumber: 2.1 Consensus size: 228
6560294 ACCTACTTTT
6560304 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
6560369 ATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
66 ATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
*
6560434 ATATTATTTGATTATTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
131 AAATTATTTGATTATTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
* *
6560499 CAAATATAATAATAAATATGTTTTCAACAGTGAA
196 CAAAGATAATAATAAATATATTTTC-ACAGTGAA
**
6560533 ATAAGTATAAACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
* *
6560598 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
66 ATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
* *
6560663 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGATTTTAAATTTAACAATATTAAC
131 AAATTATTTGATTATTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
*
6560728 TAAAGATAATAATAAATATATTTTCACAGTGAA
196 CAAAGATAATAATAAATATATTTTCACAGTGAA
*
6560761 ATAAGTATGGACACTTTTATAAAAAGGATA
1 ATAAGTATGGACACTTTTATAAAAATGATA
6560791 AATAATTTAC
Statistics
Matches: 245, Mismatches: 13, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
228 35 0.14
229 210 0.86
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.44
Consensus pattern (228 bp):
ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
ATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
AAATTATTTGATTATTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
CAAAGATAATAATAAATATATTTTCACAGTGAA
Found at i:6566705 original size:23 final size:23
Alignment explanation
Indices: 6566679--6566726 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
6566669 ATAAAGTACA
* *
6566679 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
**
6566702 ATAATGTAATAGATAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
6566725 AT
1 AT
6566727 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGATAGCGCTTAT
Found at i:6567183 original size:23 final size:23
Alignment explanation
Indices: 6567157--6567215 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
6567147 AACCACTACA
6567157 TATTACATTATATAAACGATACC
1 TATTACATTATATAAACGATACC
** *
6567180 TATTACATTATATAAGTGCTACC
1 TATTACATTATATAAACGATACC
*
6567203 TATTACATCATAT
1 TATTACATTATAT
6567216 TTTTACTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (23 bp):
TATTACATTATATAAACGATACC
Found at i:6567381 original size:431 final size:430
Alignment explanation
Indices: 6566793--6567849 Score: 1929
Period size: 431 Copynumber: 2.5 Consensus size: 430
6566783 TATTACATTA
6566793 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
6566858 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
6566923 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
131 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
6566988 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
196 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
*
6567053 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
261 TTAAAACTCACTCAAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
6567118 TTATAAAAAGGATAGACACTTTACAATATAACCACTACATATTACATTATATAAACGATACCTAT
326 TTATAAAAAGGATAGACACTTTACAATATAACCACTACATATTACATTATATAAACGATACCTAT
* * *
6567183 TACATTATATAAGTGCTACCTATTACATCATATTTTTACT
391 TACATTATATAAGCGCTACCTATTACATCATATGTTTACC
*
6567223 TATTATATTGAAAATGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
6567288 TTATGTTTCAATTTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTT
66 TTATGTTTCAA-TTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTT
*
6567353 CATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATATAGAATTTTTAATTT
130 CATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
6567418 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
195 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
*
6567483 CTTGAAACTCACTCAAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
260 CTTAAAACTCACTCAAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
*
6567548 TTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
325 TTTATAAAAAGGATAGACACTTTACAATATAACCACTACATATTACATTATATAAACGATACCTA
6567613 TTACATTATATAAGCGCTACCTATTACATCATATGTTTACC
390 TTACATTATATAAGCGCTACCTATTACATCATATGTTTACC
*
6567654 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAA
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTT-AAAGTTATGTAA
* *
6567719 TTTATGTTTCAA-TTTTTTTAACAGTGTTTCATATTTTCCACCTACAATATTAATTTAATAATTT
65 TTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTT
* * * * *
6567783 CATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTATAA-TTTAAATT
130 CATTTGCACAAAAAATTATTTGATT-ATTTGATATTTTATAAAATATTATTTAGAATTTTTAATT
6567847 TAA
194 TAA
6567850 CAACATTAAC
Statistics
Matches: 606, Mismatches: 18, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
430 159 0.26
431 423 0.70
432 24 0.04
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.42
Consensus pattern (430 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
TTAAAACTCACTCAAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
TTATAAAAAGGATAGACACTTTACAATATAACCACTACATATTACATTATATAAACGATACCTAT
TACATTATATAAGCGCTACCTATTACATCATATGTTTACC
Found at i:6567610 original size:23 final size:23
Alignment explanation
Indices: 6567584--6567646 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
6567574 ATATAACCAC
6567584 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
6567607 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
6567630 TACCTATTACATCATAT
1 TACCTATTACATTATAT
6567647 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:6568123 original size:39 final size:39
Alignment explanation
Indices: 6568069--6568154 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
6568059 CAAGTTGTAG
*
6568069 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
6568108 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
6568147 ATTTTGAT
1 ATTTTGAT
6568155 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:6580267 original size:33 final size:30
Alignment explanation
Indices: 6580201--6580288 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 30
6580191 TAAATAGTTG
6580201 TTATATTTTTATTAATATAATTATATAAATA
1 TTAT-TTTTTATTAATATAATTATATAAATA
* *
6580232 TTATTTTTTATTAAAATAATATTTATATAATTA
1 TTATTTTTTATT--AAT-ATAATTATATAAATA
6580265 TTATTTATTTAAATTAAT-TAATTA
1 TTATTT-TTT--ATTAATATAATTA
6580289 ATTATTATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
30 8 0.17
31 4 0.08
32 8 0.17
33 19 0.40
34 6 0.12
36 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TTATTTTTTATTAATATAATTATATAAATA
Found at i:6580296 original size:31 final size:30
Alignment explanation
Indices: 6580204--6580297 Score: 77
Period size: 30 Copynumber: 3.1 Consensus size: 30
6580194 ATAGTTGTTA
* * *
6580204 TATT-TTTATTAATATAATTA-TATAAATAT
1 TATTATTTATTAAAATAATAATTAT-ATTAT
* * *
6580233 TATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTATTAAAATAATAATTATATTAT
*
6580263 TATTATTTATTTAAATTAATTAATTA-ATTAT
1 TATTATTTA-TTAAAATAA-TAATTATATTAT
6580294 TATT
1 TATT
6580298 TGTGCTAATT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
29 4 0.08
30 24 0.46
31 19 0.37
32 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TATTATTTATTAAAATAATAATTATATTAT
Found at i:6590643 original size:11 final size:11
Alignment explanation
Indices: 6590627--6590651 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6590617 GAATTTGTTC
6590627 AAAGTTTTCAA
1 AAAGTTTTCAA
6590638 AAAGTTTTCAA
1 AAAGTTTTCAA
6590649 AAA
1 AAA
6590652 TAATTCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (11 bp):
AAAGTTTTCAA
Found at i:6596727 original size:18 final size:19
Alignment explanation
Indices: 6596693--6596734 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
6596683 GAAACTATAT
*
6596693 TATAAAATTATTCTAATA-
1 TATAAAAGTATTCTAATAC
6596711 TATAAAAGTATAT-TAATAC
1 TATAAAAGTAT-TCTAATAC
6596730 TATAA
1 TATAA
6596735 TTAGTCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
TATAAAAGTATTCTAATAC
Found at i:6598024 original size:2 final size:2
Alignment explanation
Indices: 6597996--6598064 Score: 87
Period size: 2 Copynumber: 37.5 Consensus size: 2
6597986 ATAAATAATA
*
6597996 AT AT TT AT A- AT AT A- AT AT -T AT -T AT AT AT A- 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
6598033 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6598065 ATAATCATCA
Statistics
Matches: 59, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
1 6 0.10
2 53 0.90
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6598026 original size:29 final size:32
Alignment explanation
Indices: 6597985--6598067 Score: 113
Period size: 29 Copynumber: 2.8 Consensus size: 32
6597975 CTTCGGCCTT
* *
6597985 TATAAATA-ATAATATTTATAATATA-ATAT-
1 TATATATATATAATATATATAATATATATATA
6598014 TAT-TATATATAATATATAT-ATATATATATA
1 TATATATATATAATATATATAATATATATATA
6598044 TATATATATATAATATATATAATA
1 TATATATATATAATATATATAATA
6598068 ATCATCACTC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
28 8 0.17
29 17 0.36
30 3 0.06
31 16 0.34
32 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
TATATATATATAATATATATAATATATATATA
Found at i:6598745 original size:20 final size:20
Alignment explanation
Indices: 6598720--6598763 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
6598710 AGACTTATAG
6598720 ATGACCCAAAGGATTTACAA
1 ATGACCCAAAGGATTTACAA
* *
6598740 ATGACCCGAAGGTTTTACAA
1 ATGACCCAAAGGATTTACAA
6598760 ATGA
1 ATGA
6598764 TCTGGAGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (20 bp):
ATGACCCAAAGGATTTACAA
Found at i:6604100 original size:15 final size:15
Alignment explanation
Indices: 6604062--6604100 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
6604052 ATTTTAAAAG
6604062 CTTCCTTGAGATATC
1 CTTCCTTGAGATATC
*
6604077 ATTCCTTGAGATATC
1 CTTCCTTGAGATATC
*
6604092 CTTCTTTGA
1 CTTCCTTGA
6604101 CTGCTTCACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.44
Consensus pattern (15 bp):
CTTCCTTGAGATATC
Found at i:6605449 original size:18 final size:19
Alignment explanation
Indices: 6605415--6605456 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
6605405 GAAACTATAT
*
6605415 TATAAAATTATTCTAATA-
1 TATAAAAGTATTCTAATAC
6605433 TATAAAAGTATAT-TAATAC
1 TATAAAAGTAT-TCTAATAC
6605452 TATAA
1 TATAA
6605457 TTAGTCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
TATAAAAGTATTCTAATAC
Found at i:6606731 original size:14 final size:14
Alignment explanation
Indices: 6606702--6606762 Score: 52
Period size: 14 Copynumber: 4.0 Consensus size: 14
6606692 GCCTTCGGGC
6606702 TTTATAAATAATAATA
1 TTTAT-AAT-ATAATA
6606718 TTTATAATATAATA
1 TTTATAATATAATA
6606732 TTATTATATATATAATAA
1 -T-TTATA-ATATAAT-A
*
6606750 TGTAT-ATATAATA
1 TTTATAATATAATA
6606763 ATCGTCACTC
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
13 1 0.03
14 13 0.32
15 4 0.10
16 13 0.32
17 8 0.20
18 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
TTTATAATATAATA
Found at i:6606731 original size:17 final size:17
Alignment explanation
Indices: 6606702--6606750 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
6606692 GCCTTCGGGC
6606702 TTTATAA-ATAATAATA
1 TTTATAATATAATAATA
*
6606718 TTTATAATATAATATTA
1 TTTATAATATAATAATA
6606735 -TTATATATATAATAAT
1 TTTATA-ATATAATAAT
6606751 GTATATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 12 0.41
17 17 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTATAATATAATAATA
Found at i:6606759 original size:20 final size:16
Alignment explanation
Indices: 6606703--6606762 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 16
6606693 CCTTCGGGCT
*
6606703 TTATAA-ATAATAATA
1 TTATAATATAATATTA
6606718 TTTATAATATAATATTA
1 -TTATAATATAATATTA
6606735 TTATATATATAATAATGTA
1 TTATA-ATATAAT-AT-TA
6606754 TATATAATA
1 T-TATAATA
6606763 ATCGTCACTC
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
16 11 0.29
17 15 0.39
18 2 0.05
19 6 0.16
20 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TTATAATATAATATTA
Found at i:6606763 original size:14 final size:14
Alignment explanation
Indices: 6606738--6606764 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6606728 AATATTATTA
6606738 TATATATAATAATG
1 TATATATAATAATG
6606752 TATATATAATAAT
1 TATATATAATAAT
6606765 CGTCACTCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
TATATATAATAATG
Found at i:6615827 original size:33 final size:35
Alignment explanation
Indices: 6615763--6615827 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 35
6615753 AATTAATTTA
**
6615763 TATATTTTCTTTAAAAAATTTAAATTCATAAAATT
1 TATATTTTCTTTAAAAAATTTAAAAACATAAAATT
* *
6615798 TATATTTT-TTTACAAAA-TTAAAAAGATAAA
1 TATATTTTCTTTAAAAAATTTAAAAACATAAA
6615828 TATGTTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 10 0.38
34 8 0.31
35 8 0.31
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.45
Consensus pattern (35 bp):
TATATTTTCTTTAAAAAATTTAAAAACATAAAATT
Found at i:6616891 original size:15 final size:15
Alignment explanation
Indices: 6616871--6616900 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6616861 TATTATTTTT
6616871 CTCCAGAAATTCCCG
1 CTCCAGAAATTCCCG
*
6616886 CTCCAGAAGTTCCCG
1 CTCCAGAAATTCCCG
6616901 TGACTATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.40, G:0.17, T:0.20
Consensus pattern (15 bp):
CTCCAGAAATTCCCG
Found at i:6619059 original size:2 final size:2
Alignment explanation
Indices: 6619052--6619120 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
6619042 TAATGCACAA
6619052 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
*
6619094 AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6619121 CACTAATGCA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6620804 original size:53 final size:53
Alignment explanation
Indices: 6620712--6621015 Score: 364
Period size: 53 Copynumber: 5.8 Consensus size: 53
6620702 GTGACTGGTC
* * ****
6620712 CGCTCCCTCTT-GTTCAGGGATTAAGGAACTCGAACAATCTTCTAAAAACGGGTT
1 CGCTCCCTCTTACTTCAGGGAGT-A-GAACTCGAACAATCTTCTGCCTACGGGTT
* * * * *
6620766 CACTCCCTATTACTTCAGAGAGTAGAACTCGAATAATCTTCTGCTTACGGGTT
1 CGCTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
* *
6620819 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCCTACGGGTT
1 CGCTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
* *
6620872 CGCTCCCTCTTACTTCAGGGAGTATAACTCGAACAATCTTCTGTCTACGGGTT
1 CGCTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
* * * *
6620925 TGTTCCCTCTTACTTCAGGGAGTAGAACTCGGACAATCTTCTGCCTAC-AG-T
1 CGCTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
* * *
6620976 C-CTCCCTCTTGCTTAAGGGAGTAAAACTCGAACAATCTTC
1 CGCTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTTC
6621016 GGGTGTGATT
Statistics
Matches: 218, Mismatches: 31, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
50 34 0.16
51 1 0.00
52 1 0.00
53 164 0.75
54 10 0.05
55 8 0.04
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (53 bp):
CGCTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
Found at i:6621553 original size:41 final size:42
Alignment explanation
Indices: 6621508--6621595 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
6621498 TTGGTGAAGG
* *
6621508 CTTACAAATTACCCGAA-GATTTAATCATCATGCTCGAAAGA
1 CTTACAAATGACCCGAAGGACTTAATCATCATGCTCGAAAGA
** * * *
6621549 CTTACTGATGGCCCGAAGGACTTCATCATGATGCTCGAAAGA
1 CTTACAAATGACCCGAAGGACTTAATCATCATGCTCGAAAGA
6621591 CTTAC
1 CTTAC
6621596 TGATGGGTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 13 0.33
42 26 0.67
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (42 bp):
CTTACAAATGACCCGAAGGACTTAATCATCATGCTCGAAAGA
Found at i:6621570 original size:20 final size:20
Alignment explanation
Indices: 6621542--6621601 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 20
6621532 TCATCATGCT
6621542 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTGATGGCC
* *
6621562 CGAAGGACTTCATCATGAT-GCT
1 CGAAAGACTT-A-C-TGATGGCC
6621584 CGAAAGACTTACTGATGG
1 CGAAAGACTTACTGATGG
6621602 GTTTGTTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
19 4 0.12
20 11 0.33
21 2 0.06
22 12 0.36
23 4 0.12
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (20 bp):
CGAAAGACTTACTGATGGCC
Found at i:6621575 original size:121 final size:122
Alignment explanation
Indices: 6621373--6621723 Score: 447
Period size: 121 Copynumber: 2.9 Consensus size: 122
6621363 TTGCTCTAAC
* * * ** * **
6621373 ACTCTTCCGAGAATGCTTA-AAATTGCCCGAAGGACAT-ATCATCTTGCTCAAAAGACTTACAAA
1 ACTCTTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCAAAAGACTTACTGA
*
6621436 TGACCCAAAGGATTTCATCATCATGCTCGAAAGACTTATTGATGGATTTGCTTCACT
66 TGGCCCAAAGGATTTCATCATCATGCTCGAAAGACTTATTGATGGATTTGCTTCACT
** *
6621493 ACTCTTTGGTGAAGGCTTACAAATTACCCGAA-GATTTAATCATCATGCTCGAAAGACTTACTGA
1 ACTCTTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCAAAAGACTTACTGA
* * * * * *
6621557 TGGCCCGAAGGACTTCATCATGATGCTCGAAAGACTTACTGATGGGTTTGTTTCACT
66 TGGCCCAAAGGATTTCATCATCATGCTCGAAAGACTTATTGATGGATTTGCTTCACT
* * * *
6621614 ACTCTTCCGTGAAGGCTTATAAATTACCCGAAGGATTTAATCATTATACTCTAAAGACTTACTGA
1 ACTCTTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCAAAAGACTTACTGA
* * * *
6621679 TGGCACTAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG
66 TGGCCCAAAGGATTTCATCATCATGCTCGAAAGACTTATTGATGG
6621724 CCCGAAGGAC
Statistics
Matches: 197, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
120 18 0.09
121 112 0.57
122 67 0.34
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (122 bp):
ACTCTTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCAAAAGACTTACTGA
TGGCCCAAAGGATTTCATCATCATGCTCGAAAGACTTATTGATGGATTTGCTTCACT
Found at i:6621732 original size:42 final size:42
Alignment explanation
Indices: 6621640--6621732 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
6621630 TTATAAATTA
* * *
6621640 CCCGAAGGATTTAATCATTATACTCTAAAGACTTACTGATGG
1 CCCGAAGGATTTAAGCATCATACTCGAAAGACTTACTGATGG
* * * *
6621682 CACTAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG
1 CCCGAAGGATTTAAGCATCATACTCGAAAGACTTACTGATGG
6621724 CCCGAAGGA
1 CCCGAAGGA
6621733 CTTACTAAGT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (42 bp):
CCCGAAGGATTTAAGCATCATACTCGAAAGACTTACTGATGG
Found at i:6621933 original size:42 final size:41
Alignment explanation
Indices: 6621852--6621952 Score: 148
Period size: 42 Copynumber: 2.4 Consensus size: 41
6621842 ATGTCTTATG
* * *
6621852 GATGACCCGAAGGACTTATCATCTTGCTTTAAAGGCTTACA
1 GATGACCCGAAGGACTTATCATCATGCTTGAAAGACTTACA
* *
6621893 GATGACCCGAAGGATTTCATCATCATGCTTGAAAGACTTACT
1 GATGACCCGAAGGACTT-ATCATCATGCTTGAAAGACTTACA
6621935 GATGACCCGAAGGACTTA
1 GATGACCCGAAGGACTTA
6621953 AATTGTTTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 17 0.32
42 36 0.68
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCATGCTTGAAAGACTTACA
Found at i:6629183 original size:67 final size:69
Alignment explanation
Indices: 6629097--6629249 Score: 211
Period size: 68 Copynumber: 2.2 Consensus size: 69
6629087 ACCCATTCAA
* * * *
6629097 GGGGAACCGATACCTCCTCAACG-AAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCC-C
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCTA
6629160 AGGG
66 AGGG
* * * *
6629164 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCTA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCTA
6629229 AGGG
66 AGGG
*
6629233 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
6629250 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
67 21 0.28
68 34 0.45
69 20 0.27
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCTA
AGGG
Found at i:6629586 original size:29 final size:29
Alignment explanation
Indices: 6629552--6629623 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
6629542 CATATTATGA
**
6629552 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
6629581 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
6629610 TACATGACATGAAT
1 TACATGACATGAAT
6629624 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:6629990 original size:22 final size:22
Alignment explanation
Indices: 6629916--6629980 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
6629906 TTATGGACAT
*
6629916 AATTCTATGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
6629938 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
6629960 AATTCTACGGGCACTTCGGTG
1 AATTCTACGGGCACTTCGGTG
6629981 TATTTATACG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.29
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:6636173 original size:68 final size:68
Alignment explanation
Indices: 6636046--6636197 Score: 209
Period size: 68 Copynumber: 2.2 Consensus size: 68
6636036 ACCCATTCAA
* * *
6636046 GGGGAACCGATA-CCCCTCAACGAAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCC-CA
1 GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCTAA
6636109 GGG
66 GGG
* * * *
6636112 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCTA
1 GGGGAACCGATACCCCCTCAACG-AAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCTA
6636177 AGGG
65 AGGG
*
6636181 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
6636198 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
66 12 0.16
67 9 0.12
68 34 0.45
69 20 0.27
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCTAA
GGG
Found at i:6636534 original size:29 final size:29
Alignment explanation
Indices: 6636500--6636571 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
6636490 CATATTATGA
**
6636500 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
6636529 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
6636558 TACATGACATGAAT
1 TACATGACATGAAT
6636572 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:6636939 original size:22 final size:22
Alignment explanation
Indices: 6636865--6636931 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
6636855 TTATGGACAT
6636865 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
6636887 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
6636909 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
6636931 A
1 A
6636932 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:6638844 original size:17 final size:17
Alignment explanation
Indices: 6638822--6638868 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
6638812 ACGTTTTGTC
6638822 ATTTTAAATAAAAATTA
1 ATTTTAAATAAAAATTA
6638839 ATTTTAAATAAAAATTA
1 ATTTTAAATAAAAATTA
*
6638856 ATTTTAATTAAAA
1 ATTTTAAATAAAA
6638869 CAACAAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTTAAATAAAAATTA
Found at i:6641628 original size:39 final size:40
Alignment explanation
Indices: 6641583--6641679 Score: 108
Period size: 42 Copynumber: 2.4 Consensus size: 40
6641573 TATAGAGTGT
**
6641583 ATAATTAATGGCGTTTATGA-GAAAAACGTCACTATATAC
1 ATAATTAATGGCGTTTATGAGGAAAAACAACACTATATAC
* *
6641622 ATAATTATTAGTGGCGTTTGTGAGGAAAAACAACATTATATAC
1 ATAATTA--A-TGGCGTTTATGAGGAAAAACAACACTATATAC
*
6641665 -TTATTAATGGCGTTT
1 ATAATTAATGGCGTTT
6641680 GTAACAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
39 15 0.31
40 1 0.02
41 1 0.02
42 16 0.33
43 16 0.33
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (40 bp):
ATAATTAATGGCGTTTATGAGGAAAAACAACACTATATAC
Found at i:6641680 original size:39 final size:41
Alignment explanation
Indices: 6641586--6641690 Score: 108
Period size: 39 Copynumber: 2.6 Consensus size: 41
6641576 AGAGTGTATA
* *
6641586 ATTAATGGCGTTTATGAGAAAAACGTCACTATATACATAATT
1 ATTAATGGCGTTTGTGAGAAAAACG-AACTATATACATAATT
* * *
6641628 ATTAGTGGCGTTTGTGAGGAAAAAC-AAC-AT-TATATACTT
1 ATTAATGGCGTTTGTGA-GAAAAACGAACTATATACATAATT
* *
6641667 ATTAATGGCGTTTGTAACAAAAAC
1 ATTAATGGCGTTTGTGAGAAAAAC
6641691 ACCGCACCGC
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
38 6 0.11
39 22 0.41
40 2 0.04
41 2 0.04
42 15 0.28
43 7 0.13
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.32
Consensus pattern (41 bp):
ATTAATGGCGTTTGTGAGAAAAACGAACTATATACATAATT
Found at i:6653111 original size:2 final size:2
Alignment explanation
Indices: 6653104--6653133 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6653094 TGCTTGTCAG
6653104 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6653134 AATCCAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6654565 original size:17 final size:18
Alignment explanation
Indices: 6654543--6654588 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
6654533 TATAGAATTG
6654543 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTGACA
*
6654560 GATTCCAATTCCTTTACA
1 GATTCCAATTCCTTGACA
6654578 GATTCCAATTC
1 GATTCCAATTC
6654589 TCTCAGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTGACA
Found at i:6654760 original size:2 final size:2
Alignment explanation
Indices: 6654749--6654778 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6654739 TTATAATCTC
6654749 TA TA -A 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
6654779 GCCTTTCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6655026 original size:25 final size:26
Alignment explanation
Indices: 6654991--6655041 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
6654981 TCTCCTAAAA
6654991 ATTTTAAATTTAT-ATATATTTTTAT
1 ATTTTAAATTTATAATATATTTTTAT
* *
6655016 ATTTTATATTTATAATCTATTTTTAT
1 ATTTTAAATTTATAATATATTTTTAT
6655042 CCTTTAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (26 bp):
ATTTTAAATTTATAATATATTTTTAT
Found at i:6655047 original size:26 final size:25
Alignment explanation
Indices: 6654993--6655058 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
6654983 TCCTAAAAAT
*
6654993 TTTAAATTTATATATATTTTTATAT
1 TTTAAATTTATATATATTTTTATAC
* * *
6655018 TTTATATTTATAATCTATTTTTATCC
1 TTTAAATTTAT-ATATATTTTTATAC
*
6655044 TTTAAGATTTTTATA
1 TTTAA-ATTTATATA
6655059 GACCCTTTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
25 10 0.31
26 17 0.53
27 5 0.16
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTAAATTTATATATATTTTTATAC
Found at i:6657839 original size:3 final size:3
Alignment explanation
Indices: 6657831--6657885 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
6657821 ATGTAAAATA
* * *
6657831 AAT AAT AAT AAT AAT AAT AAT AAC AAT GAT AAT GAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6657878 AAAT AAT A
1 -AAT AAT A
6657886 TTTTTTAGAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6660048 original size:201 final size:199
Alignment explanation
Indices: 6659715--6660240 Score: 580
Period size: 201 Copynumber: 2.6 Consensus size: 199
6659705 ATTTTTGGAC
* * ** ** **
6659715 AGTTAATCTAAAAATGTTT-GTAATTTATAAGATTATAGGCATAGTATTGAAAAAAAAATTTCAA
1 AGTTAATCT-AAAAT-TTTCGT-ATTTATAAGATTAGAGGCGTAGTATTGGTAATTATGTTTCAA
* * * * * *
6659779 ATGAGGCCAATATCGACACATATGAGATATTGTAAGTGGAT-TTAAAATCGCATTGAAAAA-GGT
63 TTGAGGCTAGTATCGACACATATGAGACATTGTAAGCGG-TGTTAAAATCGCATT-AAAAATGAT
* * * * * *
6659842 TCCAAATATT-GTTTTATGTATGAAGAAAAAGCTAAAATGGTTTGATAGGCATATTC-GAGGGTT
126 TCCAAAGATTGGTTTTAAGCATGAAGAAAAAGCTAAAATGGCTTCATAGGCATATTCGGAGAG-T
* *
6659905 TTTTTCCGA-GT
190 ATTTT-C-ATGA
*
6659916 AGTTAATCTAATAATTTTCGTAGTTTATAAGATTAGAGGCGTAATATTGGTAATTATGTTTCAAT
1 AGTTAATCTAA-AATTTTCGTA-TTTATAAGATTAGAGGCGTAGTATTGGTAATTATGTTTCAAT
* *
6659981 TGAGGCTAGTATCGACACATATGAGACATTGTAAGCGGTGTAAAAACCGCATTAAAAATGATTCC
64 TGAGGCTAGTATCGACACATATGAGACATTGTAAGCGGTGTTAAAATCGCATTAAAAATGATTCC
* * *
6660046 AAAGCTTGGTTTTAAGCATGAAGAATAAGCTAAAATGGCTTCATAGGCATGTTCGGAGAGTATTT
129 AAAGATTGGTTTTAAGCATGAAGAAAAAGCTAAAATGGCTTCATAGGCATATTCGGAGAGTATTT
6660111 TCATGA
194 TCATGA
* * *
6660117 AGTTAATCTGAAAATTTTCGTAATTATAAGATTAGAGGTGTAGTATTGGTACTTATGTTTCAATT
1 AGTTAATCT-AAAATTTTCGTATTTATAAGATTAGAGGCGTAGTATTGGTAATTATGTTTCAATT
** **
6660182 GAGGCTAGTATC-AGCACATACAAGACATTGTAAGCGGTGTTAAAATCATATTAAAAATG
65 GAGGCTAGTATCGA-CACATATGAGACATTGTAAGCGGTGTTAAAATCGCATTAAAAATG
6660241 GTTCAAAACC
Statistics
Matches: 277, Mismatches: 38, Indels: 21
0.82 0.11 0.06
Matches are distributed among these distances:
199 1 0.00
200 103 0.37
201 122 0.44
202 47 0.17
203 4 0.01
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.34
Consensus pattern (199 bp):
AGTTAATCTAAAATTTTCGTATTTATAAGATTAGAGGCGTAGTATTGGTAATTATGTTTCAATTG
AGGCTAGTATCGACACATATGAGACATTGTAAGCGGTGTTAAAATCGCATTAAAAATGATTCCAA
AGATTGGTTTTAAGCATGAAGAAAAAGCTAAAATGGCTTCATAGGCATATTCGGAGAGTATTTTC
ATGA
Found at i:6660210 original size:200 final size:201
Alignment explanation
Indices: 6659773--6660240 Score: 547
Period size: 200 Copynumber: 2.3 Consensus size: 201
6659763 GAAAAAAAAA
* * * ** * * *
6659773 TTTCAAATGAGGCCAATATCGACACATATGAGATATTGTAAGTGGAT-TTAAAATCGCATTGAAA
1 TTTCAATTGAGGCTAGTATCGACACATACAAGACATTGTAAGCGG-TGTAAAAATCGCATT-AAA
* * * * * *
6659837 AA-GGTTCCAAATATTGTTTTATGTATGAAGAAAAAGCTAAAATGGTTTGATAGGCATATTCGAG
64 AATGATTCCAAAGATTGTTTTAAGCATGAAGAAAAAGCTAAAATGGCTTCATAGGCATATTCGAG
* * * *
6659901 GGTTTTTTTCCGAGTAGTTAATCTAATAATTTTCGTAGTTTATAAGATTAGAGGCGTAATATTGG
129 AGTTATTTTCCGAGAAGTTAATCTAATAATTTTCGTAGATTATAAGATTAGAGGCGTAATATTGG
6659966 TAATTATG
194 TAATTATG
** *
6659974 TTTCAATTGAGGCTAGTATCGACACATATGAGACATTGTAAGCGGTGTAAAAACCGCATTAAAAA
1 TTTCAATTGAGGCTAGTATCGACACATACAAGACATTGTAAGCGGTGTAAAAATCGCATTAAAAA
* * *
6660039 TGATTCCAAAGCTTGGTTTTAAGCATGAAGAATAAGCTAAAATGGCTTCATAGGCATGTTCGGAG
66 TGATTCCAAAGATT-GTTTTAAGCATGAAGAAAAAGCTAAAATGGCTTCATAGGCATATTC-GAG
* *
6660104 AG-TATTTT-C-ATGAAGTTAATCTGAA-AATTTTCGTA-ATTATAAGATTAGAGGTGTAGTATT
129 AGTTATTTTCCGA-GAAGTTAATCT-AATAATTTTCGTAGATTATAAGATTAGAGGCGTAATATT
*
6660164 GGTACTTATG
192 GGTAATTATG
* **
6660174 TTTCAATTGAGGCTAGTATC-AGCACATACAAGACATTGTAAGCGGTGTTAAAATCATATTAAAA
1 TTTCAATTGAGGCTAGTATCGA-CACATACAAGACATTGTAAGCGGTGTAAAAATCGCATTAAAA
6660238 ATG
65 ATG
6660241 GTTCAAAACC
Statistics
Matches: 231, Mismatches: 29, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
199 1 0.00
200 97 0.42
201 82 0.35
202 47 0.20
203 4 0.02
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.34
Consensus pattern (201 bp):
TTTCAATTGAGGCTAGTATCGACACATACAAGACATTGTAAGCGGTGTAAAAATCGCATTAAAAA
TGATTCCAAAGATTGTTTTAAGCATGAAGAAAAAGCTAAAATGGCTTCATAGGCATATTCGAGAG
TTATTTTCCGAGAAGTTAATCTAATAATTTTCGTAGATTATAAGATTAGAGGCGTAATATTGGTA
ATTATG
Found at i:6660929 original size:21 final size:21
Alignment explanation
Indices: 6660905--6660956 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
6660895 CCCTTCAAAT
6660905 TAAAAAAATTAAATTACTAAA
1 TAAAAAAATTAAATTACTAAA
6660926 TAAAAAAATT--A--ACTAAA
1 TAAAAAAATTAAATTACTAAA
6660943 T-AAAAAATTAAATT
1 TAAAAAAATTAAATT
6660957 TACCTCAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
16 8 0.30
17 7 0.26
18 1 0.04
19 1 0.04
21 10 0.37
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAAAATTAAATTACTAAA
Found at i:6660936 original size:16 final size:17
Alignment explanation
Indices: 6660915--6660953 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
6660905 TAAAAAAATT
6660915 AAATT-ACTAAATAAAA
1 AAATTAACTAAATAAAA
6660931 AAATTAACTAAAT-AAA
1 AAATTAACTAAATAAAA
6660947 AAATTAA
1 AAATTAA
6660954 ATTTACCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATTAACTAAATAAAA
Found at i:6663373 original size:31 final size:31
Alignment explanation
Indices: 6663327--6663389 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
6663317 TAGTCGAGGG
*
6663327 TTACCTATGTCTTTCGAGACATATGGACAGT
1 TTACCTAAGTCTTTCGAGACATATGGACAGT
* * *
6663358 TTACCTAAGTTTTTCGGGACCTATGGACAGT
1 TTACCTAAGTCTTTCGAGACATATGGACAGT
6663389 T
1 T
6663390 GCCGAGGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTAAGTCTTTCGAGACATATGGACAGT
Found at i:6663431 original size:29 final size:30
Alignment explanation
Indices: 6663375--6663446 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
6663365 AGTTTTTCGG
* * * *
6663375 GACCTATGGACAGTTGCCGAGGTTCTTTAT
1 GACCTCTGGATAGTTACCGAGGGTCTTTAT
*
6663405 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGATAGTTACCGAGGGTCTTTAT
*
6663434 GACATCTGGATAG
1 GACCTCTGGATAG
6663447 GTCCTTCGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 20 0.56
30 16 0.44
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGGTCTTTAT
Found at i:6665976 original size:16 final size:16
Alignment explanation
Indices: 6665955--6665991 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
6665945 AGAACTTTAG
6665955 AAGATATATTTCTATC
1 AAGATATATTTCTATC
*
6665971 AAGATATGTTTCTATC
1 AAGATATATTTCTATC
6665987 AAGAT
1 AAGAT
6665992 GTCCAGTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (16 bp):
AAGATATATTTCTATC
Found at i:6667639 original size:30 final size:31
Alignment explanation
Indices: 6667578--6667640 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
6667568 ACCTATGTCT
*
6667578 TTCGAGACATATGGACAGTTTACCTAGGTTC
1 TTCGAGACATATGGACAGTTTACCGAGGTTC
* * *
6667609 TTCGGGACCTATGGACAG-TTGCCGAGGTTC
1 TTCGAGACATATGGACAGTTTACCGAGGTTC
6667639 TT
1 TT
6667641 TATAACCTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 12 0.43
31 16 0.57
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.32
Consensus pattern (31 bp):
TTCGAGACATATGGACAGTTTACCGAGGTTC
Found at i:6668003 original size:2 final size:2
Alignment explanation
Indices: 6667957--6667992 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6667947 ATGCGTGGAT
6667957 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6667993 GATGAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6668835 original size:50 final size:51
Alignment explanation
Indices: 6668742--6668868 Score: 161
Period size: 50 Copynumber: 2.5 Consensus size: 51
6668732 TTTAAATTAG
* *
6668742 GAATTTTTTA-ATTAAGA-TATTTAAAAAAAATAAGATTCTTTATAATTTA
1 GAATTTTTTAGATTAAGATTTTTTTAAAAAAATAAGATTCTTTATAATTTA
* *
6668791 -AATTTTTTAGATTAAGATTTTTTTAAAAAAGTAAGATTTTTTATAATTTA
1 GAATTTTTTAGATTAAGATTTTTTTAAAAAAATAAGATTCTTTATAATTTA
*
6668841 GATTTTCTTTTAGATTAAGATATTTTTT
1 GA-ATT-TTTTAGATTAAGAT-TTTTTT
6668869 TAAATTAGAA
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
48 9 0.13
49 7 0.10
50 28 0.42
51 1 0.01
52 2 0.03
53 14 0.21
54 6 0.09
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (51 bp):
GAATTTTTTAGATTAAGATTTTTTTAAAAAAATAAGATTCTTTATAATTTA
Found at i:6668869 original size:18 final size:17
Alignment explanation
Indices: 6668793--6668875 Score: 69
Period size: 18 Copynumber: 4.7 Consensus size: 17
6668783 ATAATTTAAA
*
6668793 TTTTTTAGATTAAGATT
1 TTTTTTAAATTAAGATT
* *
6668810 TTTTTAAAAAAGTAAGATT
1 TTTTT--TAAATTAAGATT
* *
6668829 TTTTAT-AATTTAGATT
1 TTTTTTAAATTAAGATT
*
6668845 TTCTTTTAGATTAAGATAT
1 TT-TTTTAAATTAAGAT-T
6668864 TTTTTTAAATTA
1 TTTTTTAAATTA
6668876 GAATATTTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
16 10 0.20
17 8 0.16
18 16 0.32
19 16 0.32
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.55
Consensus pattern (17 bp):
TTTTTTAAATTAAGATT
Found at i:6668881 original size:18 final size:18
Alignment explanation
Indices: 6668807--6668887 Score: 60
Period size: 18 Copynumber: 4.4 Consensus size: 18
6668797 TTAGATTAAG
** *
6668807 ATTTTTTTAAAAAAGTAAG
1 ATTTTTTTAAATTAG-AAT
*
6668826 ATTTTTTATAATTTAG-AT
1 ATTTTTT-TAAATTAGAAT
*
6668844 -TTTCTTTTAGATTA-AGAT
1 ATTT-TTTTAAATTAGA-AT
6668862 ATTTTTTTAAATTAGAAT
1 ATTTTTTTAAATTAGAAT
6668880 ATTTTTTT
1 ATTTTTTT
6668888 TTTCTAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
17 8 0.16
18 25 0.51
19 11 0.22
20 5 0.10
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.57
Consensus pattern (18 bp):
ATTTTTTTAAATTAGAAT
Found at i:6672517 original size:26 final size:27
Alignment explanation
Indices: 6672462--6672521 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
6672452 ATTATTATTT
*
6672462 TTAATTTAAATTTATAATGAATTTATA
1 TTAATTTAAATTTATAATGAATGTATA
*
6672489 TTAATTATAAATTT-TTAT-AATGTATA
1 TTAATT-TAAATTTATAATGAATGTATA
6672515 TT-ATTTA
1 TTAATTTA
6672522 GGAAACTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 2 0.07
25 3 0.10
26 9 0.30
27 9 0.30
28 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (27 bp):
TTAATTTAAATTTATAATGAATGTATA
Found at i:6674144 original size:21 final size:21
Alignment explanation
Indices: 6674099--6674164 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
6674089 ATCTTTGTAG
*
6674099 GGTTACATTCCTAG-CCTCAA
1 GGTTACATTCCTAGCCCGCAA
*
6674119 GGTTACATTCCTAGCCCGCCA
1 GGTTACATTCCTAGCCCGCAA
* * *
6674140 GGTTATATGCCTAGCCCGCAG
1 GGTTACATTCCTAGCCCGCAA
6674161 GGTT
1 GGTT
6674165 TTATGACACC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 14 0.36
21 25 0.64
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (21 bp):
GGTTACATTCCTAGCCCGCAA
Found at i:6674873 original size:14 final size:14
Alignment explanation
Indices: 6674854--6674896 Score: 86
Period size: 14 Copynumber: 3.1 Consensus size: 14
6674844 TTTTATCCTT
6674854 AACATATACATTAA
1 AACATATACATTAA
6674868 AACATATACATTAA
1 AACATATACATTAA
6674882 AACATATACATTAA
1 AACATATACATTAA
6674896 A
1 A
6674897 CCAACTTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:6675035 original size:63 final size:63
Alignment explanation
Indices: 6674963--6675153 Score: 328
Period size: 63 Copynumber: 3.0 Consensus size: 63
6674953 TTTCAATGTC
* * *
6674963 ACAACCAACTTTTCACTTCACATTTATTCAATTTATCTATAACATTTTATCCAATTTATTTAA
1 ACAACCAACTTATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCAA
* *
6675026 ACAACCAACTTGTCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAA
1 ACAACCAACTTATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCAA
*
6675089 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCAA
1 ACAACCAACTTATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCAA
6675152 AC
1 AC
6675154 TTCACATAAC
Statistics
Matches: 121, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 121 1.00
ACGTcount: A:0.36, C:0.23, G:0.01, T:0.40
Consensus pattern (63 bp):
ACAACCAACTTATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCAA
Found at i:6675080 original size:23 final size:22
Alignment explanation
Indices: 6674982--6675147 Score: 73
Period size: 23 Copynumber: 7.8 Consensus size: 22
6674972 TTTTCACTTC
* *
6674982 ACATTTATTCAATTTATCTATA
1 ACATTTATCCAATTTATCCATA
**
6675004 ACATTTTATCCAATTTATTTA-A
1 ACA-TTTATCCAATTTATCCATA
* * * *
6675026 ACA---A-CCAACTTGTCACTTC
1 ACATTTATCCAATTTATC-CATA
*
6675045 ACATTTATTCAATTTATCCATA
1 ACATTTATCCAATTTATCCATA
* *
6675067 ACATTTTATCCAATATATTCA-A
1 ACA-TTTATCCAATTTATCCATA
* * * *
6675089 ACA---A-CCAACTGATCACTTC
1 ACATTTATCCAATTTATC-CATA
*
6675108 ACATTTATTCAATTTATCCATA
1 ACATTTATCCAATTTATCCATA
6675130 ACATTTTATCCAATTTAT
1 ACA-TTTATCCAATTTAT
6675148 TCAAACTTCA
Statistics
Matches: 101, Mismatches: 28, Indels: 29
0.64 0.18 0.18
Matches are distributed among these distances:
17 13 0.13
18 3 0.03
19 6 0.06
22 23 0.23
23 56 0.55
ACGTcount: A:0.36, C:0.21, G:0.01, T:0.42
Consensus pattern (22 bp):
ACATTTATCCAATTTATCCATA
Found at i:6675880 original size:233 final size:234
Alignment explanation
Indices: 6675289--6675970 Score: 906
Period size: 233 Copynumber: 2.9 Consensus size: 234
6675279 ATCTATAGTT
* *
6675289 CCCCGGGGGACATGAGTGACATAATAGGACAATGATAACATATTCTCTGACAAAATAAT-GAAAG
1 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAG-AAG
* * * * *
6675353 GCGCGCCCCCGGGAACGCGCTTTCAAGTCCCCTCAGAAATAATAGGTACTGACATGAATAGT-TC
65 GCGCACCCCCGAGAACGCGCTTTC-A--CCACT------T--TGGGTACTGACATGAATAGTGCC
* * * * *
6675417 CTCGGGGGACATGAGTGACATAATAGGGCAATGATAATATATTCTCTGACAAAACAATCGAAGGC
119 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGC
* * * *
6675482 ACG-CCCCGGGAACGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGC
184 GCGCCCCCGGGAACGCGCTTTCACCACTTTGGGCACTGACATAAATAGTAC
* * *
6675532 CCCTGAGTGACATGAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATAGAAGG
1 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAGAAGG
* *
6675597 CGCACCCCCGAGAACGCGCTTTCACCACCTTGGGTGCTGACATGAATAGTGCCCCCGAGGGACAT
66 CGCACCCCCGAGAACGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACAT
6675662 GAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGA
131 GAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGA
6675727 ACGCGCTTTCACCACTTTGGGCACTGACATAAATAGTAC
196 ACGCGCTTTCACCACTTTGGGCACTGACATAAATAGTAC
* *
6675766 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGATAAAATAATAGAAGG
1 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAGAAGG
* ** *
6675831 CGC-CCCCCAAGAATACGCTTTCACCACTTTGGGTACTGACATAAATAGTGCCCCCGAGGGACAT
66 CGCACCCCCGAGAACGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACAT
* * * * * *
6675895 GAGTGATATAATAGGGCAATGGTAACATATTATCTGATAAAATAATGGAATGCGC-CCCCCAGGA
131 GAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGA
* *
6675959 ACGTGCCTTCAC
196 ACGCGCTTTCAC
6675971 TTGAATAGTA
Statistics
Matches: 396, Mismatches: 40, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
232 36 0.09
233 168 0.42
234 108 0.27
240 3 0.01
242 1 0.00
243 79 0.20
244 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (234 bp):
CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAGAAGG
CGCACCCCCGAGAACGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACAT
GAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGA
ACGCGCTTTCACCACTTTGGGCACTGACATAAATAGTAC
Found at i:6675955 original size:116 final size:116
Alignment explanation
Indices: 6675397--6675954 Score: 812
Period size: 117 Copynumber: 4.8 Consensus size: 116
6675387 AGAAATAATA
* * * *
6675397 GGTACTGACATGAATAGT-TCCTCGGGGGACATGAGTGACATAATAGGGCAATGATAATATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * * * *
6675461 TCTGACAAAACAATCGAAGGCACGCCCCGGGAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATAGAAGGCGCCCCCCGAGAACGCGCTTTCACCACTTTG
* * *
6675512 GGTACTGACATGAATAGTGCCCCTGAGTGACATGAGTGACATAATAGGGTAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
6675577 TCTGACAAAATAATAGAAGGCGCACCCCCGAGAACGCGCTTTCACCACCTTG
66 TCTGACAAAATAATAGAAGGCGC-CCCCCGAGAACGCGCTTTCACCACTTTG
*
6675629 GGTGCTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* *
6675694 TCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATAGAAGGCGC-CCCCCGAGAACGCGCTTTCACCACTTTG
* * * *
6675746 GGCACTGACATAAATAGTACCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTA
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * **
6675811 TCTGATAAAATAATAGAAGGCGCCCCCCAAGAATACGCTTTCACCACTTTG
66 TCTGACAAAATAATAGAAGGCGCCCCCCGAGAACGCGCTTTCACCACTTTG
* * * *
6675862 GGTACTGACATAAATAGTGCCCCCGAGGGACATGAGTGATATAATAGGGCAATGGTAACATATTA
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * *
6675927 TCTGATAAAATAATGGAATGCGCCCCCC
66 TCTGACAAAATAATAGAAGGCGCCCCCC
6675955 AGGAACGTGC
Statistics
Matches: 403, Mismatches: 38, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
115 18 0.04
116 170 0.42
117 215 0.53
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.22
Consensus pattern (116 bp):
GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
TCTGACAAAATAATAGAAGGCGCCCCCCGAGAACGCGCTTTCACCACTTTG
Found at i:6679163 original size:21 final size:21
Alignment explanation
Indices: 6679137--6679178 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6679127 AATAATTAAT
*
6679137 ATTATTTATTATAAAAAATTA
1 ATTATTAATTATAAAAAATTA
* *
6679158 ATTATTAATTTTAAAATATTA
1 ATTATTAATTATAAAAAATTA
6679179 TAATAATTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATTATAAAAAATTA
Found at i:6679860 original size:16 final size:16
Alignment explanation
Indices: 6679836--6679868 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6679826 TTGAAACTCG
6679836 ACTCGAATTCAAAAAA
1 ACTCGAATTCAAAAAA
*
6679852 ACTCTAATTCAAAAAA
1 ACTCGAATTCAAAAAA
6679868 A
1 A
6679869 TATCAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.18, G:0.03, T:0.21
Consensus pattern (16 bp):
ACTCGAATTCAAAAAA
Found at i:6679953 original size:22 final size:22
Alignment explanation
Indices: 6679906--6679961 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
6679896 ATTCAACTCA
*
6679906 ATTCAAGCTCAATTATGAGCTTG
1 ATTCAAGCTC-ATTATGAGCTCG
* *
6679929 ATTCAAACTCATTTTGAGCTCG
1 ATTCAAGCTCATTATGAGCTCG
6679951 ATTCAAGCTCA
1 ATTCAAGCTCA
6679962 AGGCCTAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.34
Consensus pattern (22 bp):
ATTCAAGCTCATTATGAGCTCG
Found at i:6681647 original size:7 final size:7
Alignment explanation
Indices: 6681541--6681647 Score: 83
Period size: 7 Copynumber: 15.4 Consensus size: 7
6681531 AATCAAATTA
6681541 AGGGTTT
1 AGGGTTT
*
6681548 AGTGTTT
1 AGGGTTT
*
6681555 AGTGTTT
1 AGGGTTT
6681562 A-GGTTT
1 AGGGTTT
* *
6681568 ATGATTT
1 AGGGTTT
*
6681575 ATGGTTT
1 AGGGTTT
6681582 AGGGTTT
1 AGGGTTT
**
6681589 ATAGTTT
1 AGGGTTT
*
6681596 AGGGTTC
1 AGGGTTT
*
6681603 AGGGGTT
1 AGGGTTT
6681610 -GAGGTTT
1 AG-GGTTT
*
6681617 AGAGTTT
1 AGGGTTT
*
6681624 ATGGTTT
1 AGGGTTT
*
6681631 AGAGTTT
1 AGGGTTT
6681638 AGGGTTT
1 AGGGTTT
6681645 AGG
1 AGG
6681648 ATTCATTGCA
Statistics
Matches: 78, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
6 6 0.08
7 71 0.91
8 1 0.01
ACGTcount: A:0.19, C:0.01, G:0.35, T:0.46
Consensus pattern (7 bp):
AGGGTTT
Found at i:6681787 original size:11 final size:11
Alignment explanation
Indices: 6681771--6681833 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
6681761 GTATTATAGA
6681771 ATTTTTAATAT
1 ATTTTTAATAT
6681782 ATTTTTAA-A-
1 ATTTTTAATAT
6681791 ATTTTATAAT-T
1 ATTTT-TAATAT
*** * *
6681802 ATCAATAGTGT
1 ATTTTTAATAT
6681813 ATTTTTAATAT
1 ATTTTTAATAT
6681824 ATTTTTAATA
1 ATTTTTAATA
6681834 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:6682219 original size:60 final size:61
Alignment explanation
Indices: 6682155--6682287 Score: 205
Period size: 60 Copynumber: 2.2 Consensus size: 61
6682145 AGAACTCATA
* * * *
6682155 TAAAGCGCGTCTCCGGGGATGCGCCTTACACGTATGGCATCCCAGTCAGCATAAA-CCAAG
1 TAAAGCGCGTCCCCGGGGATACGCCTTACAAGCATGGCATCCCAGTCAGCATAAACCCAAG
* *
6682215 TAAAGCACGTCCCCGGGGATACGCCTTACAAGCATGGCATCCTAGTCAGCATAAACCCAAG
1 TAAAGCGCGTCCCCGGGGATACGCCTTACAAGCATGGCATCCCAGTCAGCATAAACCCAAG
6682276 TAAAGCGCGTCC
1 TAAAGCGCGTCC
6682288 TCGGAATTCA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
60 49 0.75
61 16 0.25
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (61 bp):
TAAAGCGCGTCCCCGGGGATACGCCTTACAAGCATGGCATCCCAGTCAGCATAAACCCAAG
Found at i:6694237 original size:25 final size:25
Alignment explanation
Indices: 6694176--6694261 Score: 102
Period size: 25 Copynumber: 3.4 Consensus size: 25
6694166 CAAAAAAAAA
6694176 TGTGCAGAAAAGTAAAAAAGATAAAAGG
1 TGTGCAGAAAAGT---AAAGATAAAAGG
* *
6694204 TGTGAAGAAAAGTAAAGATAAAGGG
1 TGTGCAGAAAAGTAAAGATAAAAGG
* *
6694229 TATGCAGAAAAGTAAA-AAAAAAGG
1 TGTGCAGAAAAGTAAAGATAAAAGG
6694253 TGTGCAGAA
1 TGTGCAGAA
6694262 TTTTTAAGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
24 14 0.27
25 25 0.49
28 12 0.24
ACGTcount: A:0.55, C:0.03, G:0.27, T:0.15
Consensus pattern (25 bp):
TGTGCAGAAAAGTAAAGATAAAAGG
Found at i:6704569 original size:91 final size:91
Alignment explanation
Indices: 6704409--6704590 Score: 249
Period size: 91 Copynumber: 2.0 Consensus size: 91
6704399 TGGTAGAAAT
* * * *
6704409 CATTTCCAGCGGGGAGTTCATAATGAGAATAACTCATCCGACGAGGAAGAAGAAGTTCATAATGA
1 CATTTCCAGAGGAGAGTTCATAATAAGAAGAACTCATCCGACGAGGAAGAAGAAGTTCATAATGA
*
6704474 GAAGAGCATGTTCAACATTGGATCAA
66 GAAGAACATGTTCAACATTGGATCAA
* *
6704500 CATTTCCAGAGGAGAGTTCATAATAAGAAGAACTCATCC-AGCGAGGGAGAAGAATTTCATAATG
1 CATTTCCAGAGGAGAGTTCATAATAAGAAGAACTCATCCGA-CGAGGAAGAAGAAGTTCATAATG
* * * *
6704564 TGAAGAACTTGTTCAACCTTGGTTCAA
65 AGAAGAACATGTTCAACATTGGATCAA
6704591 TTTCATAACA
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
90 1 0.01
91 78 0.99
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (91 bp):
CATTTCCAGAGGAGAGTTCATAATAAGAAGAACTCATCCGACGAGGAAGAAGAAGTTCATAATGA
GAAGAACATGTTCAACATTGGATCAA
Found at i:6708831 original size:25 final size:26
Alignment explanation
Indices: 6708803--6708851 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
6708793 TCGCGCCTTG
* *
6708803 TATAATTACACTAAC-TCCTCTCAGT
1 TATAAATACACCAACTTCCTCTCAGT
*
6708828 TATAAATACCCCAACTTCCTCTCA
1 TATAAATACACCAACTTCCTCTCA
6708852 ACCGAAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.33
Consensus pattern (26 bp):
TATAAATACACCAACTTCCTCTCAGT
Found at i:6711623 original size:35 final size:33
Alignment explanation
Indices: 6711557--6711640 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 33
6711547 AATATAATTT
*
6711557 TAAATACAAAAAACTTACAATAAGTATTAAATGG
1 TAAATA-AAAAAAATTACAATAAGTATTAAATGG
6711591 TAAATAAAAAAAATTACAATAACTGGTA-TAAATGG
1 TAAATAAAAAAAATTACAATAA---GTATTAAATGG
*
6711626 T-AATAAACAAAATTA
1 TAAATAAAAAAAATTA
6711641 ATTAACAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
33 15 0.33
34 19 0.42
35 8 0.18
36 3 0.07
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.26
Consensus pattern (33 bp):
TAAATAAAAAAAATTACAATAAGTATTAAATGG
Found at i:6714029 original size:10 final size:10
Alignment explanation
Indices: 6714014--6714053 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
6714004 ATACCTTAAG
6714014 TTGAGAGGAT
1 TTGAGAGGAT
* *
6714024 TTGAGAGAAG
1 TTGAGAGGAT
6714034 TTGAGAGGAT
1 TTGAGAGGAT
6714044 TTGAGAGGAT
1 TTGAGAGGAT
6714054 GAAAATTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.40, T:0.28
Consensus pattern (10 bp):
TTGAGAGGAT
Found at i:6714036 original size:20 final size:20
Alignment explanation
Indices: 6714011--6714050 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
6714001 AATATACCTT
6714011 AAGTTGAGAGGATTTGAGAG
1 AAGTTGAGAGGATTTGAGAG
6714031 AAGTTGAGAGGATTTGAGAG
1 AAGTTGAGAGGATTTGAGAG
6714051 GATGAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.40, T:0.25
Consensus pattern (20 bp):
AAGTTGAGAGGATTTGAGAG
Found at i:6715084 original size:19 final size:17
Alignment explanation
Indices: 6715062--6715112 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
6715052 AAGATGAATG
6715062 AAATAAAGAAAGTAATAT
1 AAATAAAGAAAGTAA-AT
*
6715080 AAAATAAAGAAAATAAAT
1 -AAATAAAGAAAGTAAAT
*
6715098 GAATAAA-AAAGTAAA
1 AAATAAAGAAAGTAAA
6715113 GATAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 7 0.24
17 6 0.21
18 2 0.07
19 14 0.48
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.18
Consensus pattern (17 bp):
AAATAAAGAAAGTAAAT
Found at i:6715657 original size:25 final size:23
Alignment explanation
Indices: 6715601--6715650 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
6715591 GAATATAAAA
*
6715601 AATACATAAATAAATATAATATAT
1 AATA-ATAAATAAAAATAATATAT
*
6715625 AATAATAAATAAAAAT-ATATGT
1 AATAATAAATAAAAATAATATAT
6715647 AATA
1 AATA
6715651 GTAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.38
23 11 0.46
24 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
AATAATAAATAAAAATAATATAT
Found at i:6716858 original size:15 final size:15
Alignment explanation
Indices: 6716840--6716870 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6716830 GTTTATAATA
6716840 ATATAATACAATATT
1 ATATAATACAATATT
*
6716855 ATATAATATAATATT
1 ATATAATACAATATT
6716870 A
1 A
6716871 ATCTGTCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATAATACAATATT
Found at i:6717911 original size:106 final size:106
Alignment explanation
Indices: 6717771--6718941 Score: 1776
Period size: 106 Copynumber: 11.0 Consensus size: 106
6717761 TGTATTGCTC
* * * *
6717771 CGAGTCCAATATCC-TC-CATCGTGAAGTAGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGA
1 CGAGTCCAATATCCTTCGC-T-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGA
** * * * **
6717834 CAGTCAGCCGCCCCTTCG-CTGTGAAGTTGAGCTTATGTTGTCT
64 CAACCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCT
* * * * *
6717877 CGAGTCTAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAAATCGGGAAGTTGTTTGTTGAAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * *
6717942 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
6717983 CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
6718048 ACCAGCGGTCCCTTCGTCGTGAAGATGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
6718089 AGAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * *
6718154 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
6718195 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
6718260 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
6718301 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
6718366 ACTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
6718407 -GAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGAC
1 CG-AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGAC
*
6718471 AACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
6718513 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* *
6718578 ACCAGTGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
6718619 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
6718684 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
6718725 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
6718790 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
6718831 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * *
6718896 ACCAGTC-GTCCCTTCGTTGTGAAGTTAAACTTGTGTTGTCT
66 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
6718937 CGAGT
1 CGAGT
6718942 GGTACGATAT
Statistics
Matches: 990, Mismatches: 69, Indels: 12
0.92 0.06 0.01
Matches are distributed among these distances:
105 1 0.00
106 983 0.99
107 5 0.01
108 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:6720529 original size:22 final size:19
Alignment explanation
Indices: 6720501--6720545 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 19
6720491 TGCATGTGCT
6720501 TTTTTGTCCATTTTTCTTTTG
1 TTTTTGTCC-TTTTT-TTTTG
*
6720522 ATTTTTGTTCTTTTTTTTTG
1 -TTTTTGTCCTTTTTTTTTG
6720542 TTTT
1 TTTT
6720546 CTTCTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 5 0.23
21 5 0.23
22 8 0.36
ACGTcount: A:0.04, C:0.09, G:0.09, T:0.78
Consensus pattern (19 bp):
TTTTTGTCCTTTTTTTTTG
Found at i:6720532 original size:15 final size:13
Alignment explanation
Indices: 6720523--6720570 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 13
6720513 TTTCTTTTGA
6720523 TTTTTGTTCTTTT
1 TTTTTGTTCTTTT
*
6720536 TTTTTGTTTTCTTCT
1 TTTTTG--TTCTTTT
6720551 TTTTTGTTTCTTTT
1 TTTTTG-TTCTTTT
6720565 CTTTTT
1 -TTTTT
6720571 TATTTTTGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 6 0.20
14 7 0.23
15 17 0.57
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.83
Consensus pattern (13 bp):
TTTTTGTTCTTTT
Found at i:6720545 original size:18 final size:18
Alignment explanation
Indices: 6720524--6720578 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
6720514 TTCTTTTGAT
*
6720524 TTTTGTTCTTTTTTTTTG
1 TTTTCTTCTTTTTTTTTG
*
6720542 TTTTCTTCTTTTTTGTTTC
1 TTTTCTTCTTTTTT-TTTG
6720561 TTTTCTT-TTTTATTTTTG
1 TTTTCTTCTTTT-TTTTTG
6720579 CCCTTTTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 20 0.62
19 12 0.38
ACGTcount: A:0.02, C:0.09, G:0.07, T:0.82
Consensus pattern (18 bp):
TTTTCTTCTTTTTTTTTG
Found at i:6724025 original size:19 final size:20
Alignment explanation
Indices: 6723997--6724034 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
6723987 TGCAGATGAT
*
6723997 GGAAATAAAAT-AAAAGAGA
1 GGAAAAAAAATGAAAAGAGA
6724016 GGAAAAAAAATGAAAAGAG
1 GGAAAAAAAATGAAAAGAG
6724035 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (20 bp):
GGAAAAAAAATGAAAAGAGA
Found at i:6725152 original size:19 final size:17
Alignment explanation
Indices: 6725130--6725180 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
6725120 AAGATGAATG
6725130 AAATAAAGAAAGTAATAT
1 AAATAAAGAAAGTAA-AT
*
6725148 AAAATAAAGAAAATAAAT
1 -AAATAAAGAAAGTAAAT
*
6725166 GAATAAA-AAAGTAAA
1 AAATAAAGAAAGTAAA
6725181 GATAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 7 0.24
17 6 0.21
18 2 0.07
19 14 0.48
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.18
Consensus pattern (17 bp):
AAATAAAGAAAGTAAAT
Found at i:6725677 original size:25 final size:23
Alignment explanation
Indices: 6725621--6725670 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
6725611 GAATATAAAA
*
6725621 AATACATAAATAAATATAATATAT
1 AATA-ATAAATAAAAATAATATAT
*
6725645 AATAATAAATAAAAAT-ATATGT
1 AATAATAAATAAAAATAATATAT
6725667 AATA
1 AATA
6725671 GTAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.38
23 11 0.46
24 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
AATAATAAATAAAAATAATATAT
Found at i:6733117 original size:55 final size:55
Alignment explanation
Indices: 6732723--6733115 Score: 606
Period size: 55 Copynumber: 7.1 Consensus size: 55
6732713 GAACTTGAAG
* * * *
6732723 AATCTTCATCAATCGAGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACTTGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
6732778 CATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACCCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
6732833 AATCTTCATCAATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
6732888 AATCTTCATCAATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACCCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
6732943 AATCTTCATCAATCGTGCCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
6732998 AATCTTCAACAGTCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
6733053 AATCTTCAACAGTCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
6733108 AATCTTCA
1 AATCTTCA
6733116 ACGATCGCTG
Statistics
Matches: 315, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 315 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.29
Consensus pattern (55 bp):
AATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
Found at i:6734152 original size:7 final size:8
Alignment explanation
Indices: 6734120--6734179 Score: 58
Period size: 8 Copynumber: 7.9 Consensus size: 8
6734110 TCTTGAACCC
6734120 TCATTTTT
1 TCATTTTT
6734128 TCATTTTT
1 TCATTTTT
6734136 TCA----T
1 TCATTTTT
6734140 TCATTTTT
1 TCATTTTT
6734148 T-ATTTATTT
1 TCA-TT-TTT
*
6734157 TTATTTTT
1 TCATTTTT
6734165 TCATTTTT
1 TCATTTTT
6734173 TCATTTT
1 TCATTTT
6734180 CACTCATTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
4 4 0.09
7 1 0.02
8 32 0.73
9 6 0.14
10 1 0.02
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (8 bp):
TCATTTTT
Found at i:6737705 original size:8 final size:8
Alignment explanation
Indices: 6737692--6737719 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
6737682 AAAAGAAAAT
6737692 ATATATAC
1 ATATATAC
6737700 ATATATAC
1 ATATATAC
6737708 ATATATAC
1 ATATATAC
6737716 ATAT
1 ATAT
6737720 GGGAGAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:6744195 original size:16 final size:16
Alignment explanation
Indices: 6744170--6744207 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
6744160 AACCTTATTC
6744170 ACATGATATCTACCCA
1 ACATGATATCTACCCA
*
6744186 ACATGGTATCTACCCA
1 ACATGATATCTACCCA
6744202 ATCATG
1 A-CATG
6744208 CTTTAGTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.26
Consensus pattern (16 bp):
ACATGATATCTACCCA
Found at i:6747578 original size:2 final size:2
Alignment explanation
Indices: 6747516--6747564 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
6747506 ATTTATTGCC
6747516 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6747558 TA TA TA T
1 TA TA TA T
6747565 TAATTAATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6748463 original size:17 final size:19
Alignment explanation
Indices: 6748423--6748462 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
6748413 ATTTTTAATA
6748423 AAAATATATATATAAATTT
1 AAAATATATATATAAATTT
*
6748442 AAAATATAT-TATAATTTT
1 AAAATATATATATAAATTT
6748460 AAA
1 AAA
6748463 TTTTTTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATATATATATAAATTT
Found at i:6749968 original size:11 final size:12
Alignment explanation
Indices: 6749945--6749974 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
6749935 TTCAGAAATA
6749945 TCTTCTCTCTTT
1 TCTTCTCTCTTT
6749957 TCTTCT-TCTTT
1 TCTTCTCTCTTT
6749968 TCTTCTC
1 TCTTCTC
6749975 CACGTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (12 bp):
TCTTCTCTCTTT
Found at i:6751459 original size:31 final size:30
Alignment explanation
Indices: 6751421--6751540 Score: 88
Period size: 31 Copynumber: 3.9 Consensus size: 30
6751411 GAGTCGAGGG
6751421 TACCTATGTTTACGGAACATATGGACAGAAT
1 TACCTATGTTTACGGAACATATGGACAG-AT
* *
6751452 TACCTATGTCTTTC-AAGACATATGGACAG-T
1 TACCTATGT-TTACGGA-ACATATGGACAGAT
*
6751482 ATACCTATGTTCTAAGG-A-ATATGGACAG-T
1 -TACCTATGTT-TACGGAACATATGGACAGAT
* * *
6751511 TCACCTAGGTTTTTCGGAACCTATGGACAG
1 T-ACCTATG-TTTACGGAACATATGGACAG
6751541 TTGCCGAGGA
Statistics
Matches: 71, Mismatches: 9, Indels: 18
0.72 0.09 0.18
Matches are distributed among these distances:
28 1 0.01
29 20 0.28
30 6 0.08
31 29 0.41
32 15 0.21
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (30 bp):
TACCTATGTTTACGGAACATATGGACAGAT
Found at i:6751580 original size:30 final size:30
Alignment explanation
Indices: 6751529--6751600 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
6751519 GTTTTTCGGA
* * *
6751529 ACCTATGGACAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
*
6751559 ACCTCTGGATAGTTACCGAGGATTTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
6751589 ACCTCTGGATAG
1 ACCTCTGGATAG
6751601 GTCCTGTGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:6752642 original size:27 final size:27
Alignment explanation
Indices: 6752604--6752667 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
6752594 TCTTTTTTCA
*
6752604 ATTCATTTGACATTAGACACTAGTTCG
1 ATTCGTTTGACATTAGACACTAGTTCG
6752631 ATTCGTTTGACATTAGACACTAGTTCG
1 ATTCGTTTGACATTAGACACTAGTTCG
*
6752658 ATTTGTTTGA
1 ATTCGTTTGA
6752668 ATTCAATTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.41
Consensus pattern (27 bp):
ATTCGTTTGACATTAGACACTAGTTCG
Found at i:6753812 original size:15 final size:15
Alignment explanation
Indices: 6753792--6753829 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
6753782 TTATATATAT
6753792 AAAAGGAAATTAGAA
1 AAAAGGAAATTAGAA
6753807 AAAAGGAAATTAGAA
1 AAAAGGAAATTAGAA
6753822 AAAAGGAA
1 AAAAGGAA
6753830 TAATGCATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.11
Consensus pattern (15 bp):
AAAAGGAAATTAGAA
Found at i:6762417 original size:21 final size:21
Alignment explanation
Indices: 6762391--6762438 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
6762381 GTAGACAACC
6762391 TATTCAAGAAAAATAATTTCT
1 TATTCAAGAAAAATAATTTCT
6762412 TATTCAAGAAAAATAATTTCT
1 TATTCAAGAAAAATAATTTCT
6762433 TATTCA
1 TATTCA
6762439 CTATATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (21 bp):
TATTCAAGAAAAATAATTTCT
Found at i:6766420 original size:20 final size:20
Alignment explanation
Indices: 6766373--6766420 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
6766363 AATCTGATCC
*
6766373 AAAAAAATAATCGAAAACCG
1 AAAAAAAAAATCGAAAACCG
*** *
6766393 ATCCAAAAAATCGATAACCG
1 AAAAAAAAAATCGAAAACCG
6766413 AAAAAAAA
1 AAAAAAAA
6766421 GAAATCGATT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.17, G:0.08, T:0.10
Consensus pattern (20 bp):
AAAAAAAAAATCGAAAACCG
Found at i:6770392 original size:20 final size:20
Alignment explanation
Indices: 6770298--6770626 Score: 430
Period size: 20 Copynumber: 16.4 Consensus size: 20
6770288 GATTTTCCAT
* ** *
6770298 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
6770318 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
6770338 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
6770358 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
6770378 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
6770398 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
6770418 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
6770438 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
6770458 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
6770478 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
6770498 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
6770518 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
6770538 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
6770558 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
6770578 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
6770598 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
6770618 AATCACAAC
1 AATCGCAAC
6770627 ACTGAAATTT
Statistics
Matches: 273, Mismatches: 30, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 267 0.98
21 3 0.01
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Done.