Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008359.1 Hibiscus syriacus cultivar Beakdansim tig00111098_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: 1252926
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:254666 original size:27 final size:27
Alignment explanation
Indices: 254614--254667 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
254604 ACCATCACCG
* *
254614 CTTTGAACTTGAAACTCCATAGCATCA
1 CTTTGAACTTGAAACTCCACAACATCA
* *
254641 CTTTGAACTTGAAAGTTCACAACATCA
1 CTTTGAACTTGAAACTCCACAACATCA
254668 AGTCTTCATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (27 bp):
CTTTGAACTTGAAACTCCACAACATCA
Found at i:262875 original size:20 final size:20
Alignment explanation
Indices: 262840--262901 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
262830 TTAACTTTAT
262840 TCTTTTCTTCTTCTTTCTTTC
1 TCTTTTCTT-TTCTTTCTTTC
*
262861 TCTTTTCTTTTCTTTCTTCC
1 TCTTTTCTTTTCTTTCTTTC
* *
262881 TCTTTTCTCTTCTTCCTTTC
1 TCTTTTCTTTTCTTTCTTTC
262901 T
1 T
262902 TTCTTCCTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 28 0.76
21 9 0.24
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
TCTTTTCTTTTCTTTCTTTC
Found at i:262893 original size:16 final size:15
Alignment explanation
Indices: 262843--262909 Score: 61
Period size: 15 Copynumber: 4.6 Consensus size: 15
262833 ACTTTATTCT
*
262843 TTTCTTCTTC-TTTC
1 TTTCTTCCTCTTTTC
**
262857 TTTCTCTTTTCTTTTC
1 TTTCT-TCCTCTTTTC
262873 TTTCTTCCTCTTTTC
1 TTTCTTCCTCTTTTC
262888 TCTTCTT-C-C-TTTC
1 T-TTCTTCCTCTTTTC
262901 TTTCTTCCT
1 TTTCTTCCT
262910 TCTCCTGTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
12 5 0.11
13 6 0.13
14 6 0.13
15 14 0.31
16 14 0.31
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTCTTCCTCTTTTC
Found at i:262908 original size:28 final size:27
Alignment explanation
Indices: 262857--262909 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
262847 TTCTTCTTTC
*
262857 TTTCTCTTTTCTTTTCTTTCTTCCTCT
1 TTTCTCTTTTCCTTTCTTTCTTCCTCT
262884 TTTCTCTTCTTCCTTTCTTTCTTCCT
1 TTTCTCTT-TTCCTTTCTTTCTTCCT
262910 TCTCCTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTCTCTTTTCCTTTCTTTCTTCCTCT
Found at i:262911 original size:16 final size:16
Alignment explanation
Indices: 262843--262911 Score: 53
Period size: 16 Copynumber: 4.7 Consensus size: 16
262833 ACTTTATTCT
262843 TTTCTT-CTT-CTTTC
1 TTTCTTCCTTCCTTTC
* *
262857 TTTC-TCTTTTCTTTTC
1 TTTCTTC-CTTCCTTTC
262873 TTTCTTCC-T-CTTT-
1 TTTCTTCCTTCCTTTC
*
262886 TCTCTT-CTTCCTTTC
1 TTTCTTCCTTCCTTTC
262901 TTTCTTCCTTC
1 TTTCTTCCTTC
262912 TCCTGTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
12 1 0.02
13 7 0.17
14 11 0.27
15 8 0.20
16 12 0.29
17 2 0.05
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTCTTCCTTCCTTTC
Found at i:263163 original size:39 final size:40
Alignment explanation
Indices: 263109--263221 Score: 138
Period size: 39 Copynumber: 2.8 Consensus size: 40
263099 GAGTGCATGT
* * *
263109 AGGAGGGAGATGCATGGAGTGCAATGCATCTTTAAGGGG-
1 AGGAGAGAGACGCATGGAGTGCAATGCGTCTTTAAGGGGA
***
263148 AGGAGAGAGACGCATGGAGTGCAATGCGTCTTCGGGGGGAA
1 AGGAGAGAGACGCATGGAGTGCAATGCGTCTTTAAGGGG-A
* *
263189 AGGGGAGAGACGTATGGAGTGCAATGCGTCTTT
1 AGGAGAGAGACGCATGGAGTGCAATGCGTCTTT
263222 GGTGTGTACT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
39 33 0.52
41 30 0.48
ACGTcount: A:0.27, C:0.12, G:0.42, T:0.19
Consensus pattern (40 bp):
AGGAGAGAGACGCATGGAGTGCAATGCGTCTTTAAGGGGA
Found at i:267490 original size:159 final size:160
Alignment explanation
Indices: 267290--267610 Score: 626
Period size: 159 Copynumber: 2.0 Consensus size: 160
267280 AAAGGTTCCA
*
267290 ATATCCAGGTCCGTTACGTTGGACCCAATCTTTATTTATTTTCCTTCGAATCTGATTTTGCTCAT
1 ATATCCAGGTCAGTTACGTTGGACCCAATCTTTATTTATTTTCCTTCGAATCTGATTTTGCTCAT
267355 GAATGGGTAATGGAAAACAGGCCTTGGCATATTTACAATAAACCTTTAATTCTCAGAC-GTGGGA
66 GAATGGGTAATGGAAAACAGGCCTTGGCATATTTACAATAAACCTTTAATTCTCAGACAGTGGGA
267419 ACCTAATATGCAAAAACTTCACTTTGATTT
131 ACCTAATATGCAAAAACTTCACTTTGATTT
267449 ATATCCAGGTCAGTTACGTTGGACCCAATCTTTATTTATTTTCCTTCGAATCTGATTTTGCTCAT
1 ATATCCAGGTCAGTTACGTTGGACCCAATCTTTATTTATTTTCCTTCGAATCTGATTTTGCTCAT
267514 GAATGGGTAATGGAAAACAGGCCTTGGCATATTTACAATAAACCTTTAATTCTCAGACAGTGGGA
66 GAATGGGTAATGGAAAACAGGCCTTGGCATATTTACAATAAACCTTTAATTCTCAGACAGTGGGA
267579 ACCTAATATGCAAAAACTTCACTTTGATTT
131 ACCTAATATGCAAAAACTTCACTTTGATTT
267609 AT
1 AT
267611 CCAGAATTTC
Statistics
Matches: 160, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
159 122 0.76
160 38 0.24
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (160 bp):
ATATCCAGGTCAGTTACGTTGGACCCAATCTTTATTTATTTTCCTTCGAATCTGATTTTGCTCAT
GAATGGGTAATGGAAAACAGGCCTTGGCATATTTACAATAAACCTTTAATTCTCAGACAGTGGGA
ACCTAATATGCAAAAACTTCACTTTGATTT
Found at i:269788 original size:21 final size:22
Alignment explanation
Indices: 269763--269803 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
269753 ATAAAGAGTC
269763 ATATGAGAA-CAAATATAAGTA
1 ATATGAGAATCAAATATAAGTA
* *
269784 ATATGATAATGAAATATAAG
1 ATATGAGAATCAAATATAAG
269804 ACTGTGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.56, C:0.02, G:0.15, T:0.27
Consensus pattern (22 bp):
ATATGAGAATCAAATATAAGTA
Found at i:270826 original size:25 final size:25
Alignment explanation
Indices: 270798--270858 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
270788 CTATGTGGTC
*
270798 CTTCGG-GACAAATTTCTACGCGGCA
1 CTTCGGTG-CAAAATTCTACGCGGCA
*
270823 CTTCGGTGCAAAATTCTACGTGGCA
1 CTTCGGTGCAAAATTCTACGCGGCA
*
270848 CTACGGTGCAA
1 CTTCGGTGCAA
270859 TTTATACGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 31 0.97
26 1 0.03
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (25 bp):
CTTCGGTGCAAAATTCTACGCGGCA
Found at i:278327 original size:2 final size:2
Alignment explanation
Indices: 278320--278363 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
278310 CAAAATCCAT
278320 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
278362 TA
1 TA
278364 AACTCATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:279661 original size:30 final size:30
Alignment explanation
Indices: 279626--279685 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
279616 GGAAGAATCA
279626 GCTGAAAACCGGAAAAACCGGGGTGAACCG
1 GCTGAAAACCGGAAAAACCGGGGTGAACCG
* **
279656 GCTGAAAACCGGCAAAACCGGTTTGAACCG
1 GCTGAAAACCGGAAAAACCGGGGTGAACCG
279686 CCGGTTCACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.30, T:0.10
Consensus pattern (30 bp):
GCTGAAAACCGGAAAAACCGGGGTGAACCG
Found at i:279940 original size:24 final size:24
Alignment explanation
Indices: 279907--279964 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
279897 ATTAGAAGTT
*
279907 CAATTAAAGCCTAAAATTTGAGCC
1 CAATTGAAGCCTAAAATTTGAGCC
*
279931 CAATTGAAGCCTAAAATTTGAGCT
1 CAATTGAAGCCTAAAATTTGAGCC
279955 CAATTGAAGC
1 CAATTGAAGC
279965 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (24 bp):
CAATTGAAGCCTAAAATTTGAGCC
Found at i:284191 original size:16 final size:16
Alignment explanation
Indices: 284148--284192 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
284138 AATATACATC
284148 GTGATCGATTAAATAA
1 GTGATCGATTAAATAA
* *
284164 GTGACCAATTAAATAA
1 GTGATCGATTAAATAA
*
284180 GTGATCGGTTAAA
1 GTGATCGATTAAA
284193 ATTTAGACAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (16 bp):
GTGATCGATTAAATAA
Found at i:284802 original size:23 final size:23
Alignment explanation
Indices: 284776--284839 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
284766 AACATAAGAA
284776 CTACCTATTACATTATATAAACG
1 CTACCTATTACATTATATAAACG
*
284799 CTACCTATTACATTATATAAGCG
1 CTACCTATTACATTATATAAACG
*
284822 CTACCTATTACATCATAT
1 CTACCTATTACATTATAT
284840 TTTTACCTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (23 bp):
CTACCTATTACATTATATAAACG
Found at i:285285 original size:23 final size:23
Alignment explanation
Indices: 285259--285329 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
285249 ATTTTACAAC
285259 ATAAGAACTACCTATTACATTAT
1 ATAAGAACTACCTATTACATTAT
*
285282 ATAA-ACTCTACCTATTACATTAT
1 ATAAGA-ACTACCTATTACATTAT
** *
285305 ATAAGCGCTACCTATTACATCAT
1 ATAAGAACTACCTATTACATTAT
285328 AT
1 AT
285330 TTTTACTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.02
23 41 0.98
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.35
Consensus pattern (23 bp):
ATAAGAACTACCTATTACATTAT
Found at i:285783 original size:23 final size:23
Alignment explanation
Indices: 285747--285819 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
285737 ATACTTTACA
* *
285747 ATATAAGCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
285770 ATATAAACGTTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
285793 ATATAAGCGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
285816 ATAT
1 ATAT
285820 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.37
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:286141 original size:491 final size:490
Alignment explanation
Indices: 284364--286166 Score: 3360
Period size: 490 Copynumber: 3.7 Consensus size: 490
284354 TTATAATATG
* *
284364 TTGAAAGTGTCTATACTTTTTTATAAAAAATATCGATACTTTTTTGAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCTATAC-TTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
*
284429 TTTAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
65 TTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
284493 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAAAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
284558 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
284623 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
284688 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGGAAAAAAGTATAGACACTTTTATAAAAAGG
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGGAAAAAAGTATAGACACTTTTATAAAAAGG
*
284753 ATAGATACTTTACAACATAAGAACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
390 ATAGATACTTTACAACATAAGAACTACCTATTACATTATATAAACGTTACCTATTACATTATATA
284818 AGCGCTACCTATTACATCATATTTTTACCTATTATA
455 AGCGCTACCTATTACATCATATTTTTACCTATTATA
*
284854 TTGAAAATGTCTATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
284919 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
284984 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
285049 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
285114 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
261 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
285179 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGGAAAAAAGTATAGACACTTTTATAAAAAGGA
326 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGGAAAAAAGTATAGACACTTTTATAAAAAGGA
*
285244 TAGATATTTTACAACATAAGAACTACCTATTACATTATATAAAC-TCTACCTATTACATTATATA
391 TAGATACTTTACAACATAAGAACTACCTATTACATTATATAAACGT-TACCTATTACATTATATA
*
285308 AGCGCTACCTATTACATCATATTTTTACTTATTATA
455 AGCGCTACCTATTACATCATATTTTTACCTATTATA
*
285344 TTGAAAGTGTTTATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
285409 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
285474 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
285539 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
* *
285604 TCGTAACGTAAAAAATAAATCATTACACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
261 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
*
285669 AAAAGATAACCTTAAATTAATGTTTTCCACAG-CGAAAAAAGTATAGACACTTTTATAAAAAAGG
326 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGGAAAAAAGTATAGACACTTTTAT-AAAAAGG
* *
285733 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGTTACCTATTACATTATATA
390 ATAGATACTTTACAACATAAGAACTACCTATTACATTATATAAACGTTACCTATTACATTATATA
*
285798 AGCGCTACCTATTACATTATATTTTTACCTATTATA
455 AGCGCTACCTATTACATCATATTTTTACCTATTATA
* *
285834 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTTAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
285899 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
* *
285964 CAAAAAATTATTTGATTGATTTGATATTATATAAAATAATATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
286029 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
286094 ACCGCAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
286159 CAAAAGAT
325 CAAAAGAT
286167 GTACATACCT
Statistics
Matches: 1281, Mismatches: 27, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
489 73 0.06
490 949 0.74
491 259 0.20
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (490 bp):
TTGAAAGTGTCTATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
AAAAGATAACCTTAAATTAATGTTTTCCACAGTGGAAAAAAGTATAGACACTTTTATAAAAAGGA
TAGATACTTTACAACATAAGAACTACCTATTACATTATATAAACGTTACCTATTACATTATATAA
GCGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:286529 original size:33 final size:33
Alignment explanation
Indices: 286492--286557 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
286482 CATCTTAATA
* *
286492 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACACCAACTTCTTTCACCACT
* *
286525 TCACCCCTCAACACATCTACTTCTTTCACCACT
1 TCACCCCTCAACACACCAACTTCTTTCACCACT
286558 CCATTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.47, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACACCAACTTCTTTCACCACT
Found at i:286616 original size:21 final size:21
Alignment explanation
Indices: 286591--286655 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
286581 CCCCTTATGC
* *
286591 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
286612 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
286633 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
286654 CT
1 CT
286656 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:286808 original size:9 final size:9
Alignment explanation
Indices: 286794--286818 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
286784 CTCCTTTCTT
286794 CTCCTCTGC
1 CTCCTCTGC
286803 CTCCTCTGC
1 CTCCTCTGC
286812 CTCCTCT
1 CTCCTCT
286819 ACATCTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.56, G:0.08, T:0.36
Consensus pattern (9 bp):
CTCCTCTGC
Found at i:288902 original size:17 final size:18
Alignment explanation
Indices: 288880--288922 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
288870 ATATATCCGG
288880 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
288897 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
288917 TATCAT
1 TATCAT
288923 ATTTTTACAT
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:289197 original size:146 final size:147
Alignment explanation
Indices: 288957--289230 Score: 426
Period size: 146 Copynumber: 1.9 Consensus size: 147
288947 GATCGATATA
* *
288957 TTTTTTTAAAGTATCGACACATTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTC
1 TTTTTTAAAAGTATCGACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTC
* *
289022 GATCCTTATATAAAGTATCGACACTTTT-AATATATCCGGTAACGTTTTACCGGTTTTATCATAT
66 GATCCTTATATAAAGTACCGACACTTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATAT
289086 TTTTACCTGGTATATCG
131 TTTTACCTGGTATATCG
* ** *
289103 TTTTTTAAAAGTATCGACACTTTATAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTC
1 TTTTTTAAAAGTATCGACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTC
* * *
289168 GATCCTTATATTAAAGTACCGACAC-TTTAAATGTATCCGGTAGCGCTTTACCGTTTTTATCAT
66 GATCCTTATA-TAAAGTACCGACACTTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCAT
289231 TTCAATACTG
Statistics
Matches: 115, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
146 72 0.63
147 43 0.37
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (147 bp):
TTTTTTAAAAGTATCGACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTC
GATCCTTATATAAAGTACCGACACTTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATAT
TTTTACCTGGTATATCG
Found at i:296726 original size:20 final size:20
Alignment explanation
Indices: 296689--296726 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
296679 AAAATCAAAC
*
296689 AAAATATTAGATGGTAAAAT
1 AAAATATTAGATGCTAAAAT
296709 AAAATATT-GAATGCTAAA
1 AAAATATTAG-ATGCTAAA
296727 CAAAAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (20 bp):
AAAATATTAGATGCTAAAAT
Found at i:296858 original size:31 final size:32
Alignment explanation
Indices: 296766--296863 Score: 98
Period size: 31 Copynumber: 3.1 Consensus size: 32
296756 AAAATTAAGA
*
296766 TAAAAAT-AAT-AATAATAAAGTGAA-ATAATGT
1 TAAAAATAAATAAATAA-AAA-TGAAGAAAATGT
*
296797 TACAAGATAAATAAATAAAAATGAAGAAAATGT
1 TA-AAAATAAATAAATAAAAATGAAGAAAATGT
*
296830 TAAAAATAAA-AAA-AAAAATTTAAGAAAATGT
1 TAAAAATAAATAAATAAAAA-TGAAGAAAATGT
296861 TAA
1 TAA
296864 TTTCTAAAAG
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
30 5 0.09
31 19 0.33
32 15 0.26
33 14 0.24
34 5 0.09
ACGTcount: A:0.65, C:0.01, G:0.09, T:0.24
Consensus pattern (32 bp):
TAAAAATAAATAAATAAAAATGAAGAAAATGT
Found at i:297189 original size:22 final size:20
Alignment explanation
Indices: 297132--297185 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 20
297122 CAAAATACAA
297132 AAATTAAAATAACAGTAACT
1 AAATTAAAATAACAGTAACT
* *
297152 AAATCAGAAATTAACAGTGACT
1 AAATTA-AAA-TAACAGTAACT
297174 AAATTAAAATAA
1 AAATTAAAATAA
297186 AACAACATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 8 0.28
21 6 0.21
22 15 0.52
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.24
Consensus pattern (20 bp):
AAATTAAAATAACAGTAACT
Found at i:298464 original size:84 final size:84
Alignment explanation
Indices: 298262--298634 Score: 461
Period size: 84 Copynumber: 4.5 Consensus size: 84
298252 TTCTTGTTAA
* * * * * *
298262 CAGATAACCCTTCTCGTCTTGAGCTATGCTGTAAATTTGATATGTCC-ATGAGCTGAATGTAATC
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAA--TGATGTG-CCTTTGAGCTGAGTGTAATC
*
298326 GAACTCGAAGG---TTTGCTT-A
63 GAACTCGAAGGTCTTTTG-TTGG
* *
298345 CAGATAACCCTTCTCGCCTTGAGCTATGCTCCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
*
298410 CTCGAAGGTCTTTTATTGG
66 CTCGAAGGTCTTTTGTTGG
* * *
298429 CAGATATCCCTTCTTACCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGAC-GAGTGTAATCGA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAG-CTGAGTGTAATCGA
298493 ACTCGAAGGTCTTTTGTTGG
65 ACTCGAAGGTCTTTTGTTGG
* * *
298513 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCATTTAAGCTAAGTGTAATCGAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* *
298578 CTCGAAGGCCTTCTGTTGG
66 CTCGAAGGTCTTTTGTTGG
* * * *
298597 GAGATAACCCTTTTTTCCTTGAGTTATGCTGCAAATGA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGA
298635 ACACGATATC
Statistics
Matches: 257, Mismatches: 26, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
80 2 0.01
81 32 0.12
83 35 0.14
84 187 0.73
85 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (84 bp):
CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
CTCGAAGGTCTTTTGTTGG
Found at i:298810 original size:124 final size:124
Alignment explanation
Indices: 298636--299001 Score: 572
Period size: 124 Copynumber: 3.0 Consensus size: 124
298626 TGCAAATGAA
* * * *
298636 CACGATAT-CCTTCGTCGTGAAGTTAAAATCGTGGAGGGCCCCTTCGTTGTGAAGTTGAACCTTG
1 CACGAT-TCCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTG
* *
298700 AATTAGATATCCTTCGTCGTGAAGCTGAAATCCAATCTGAAGATGAATGTTGCTGGTAGG
65 AATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATATTGCTGGTAGG
*
298760 CACGATTCCCTTCGTCGTGAAGTTGAAATCGTGGATGGTCCATTCGTTGTGAAGTTGAGCCTTGA
1 CACGATTCCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
* * *
298825 ATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTGAAGATGAATATTGCTGGTGGG
66 ATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATATTGCTGGTAGG
* * *
298884 CACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGA
1 CACGATTCCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
* * *
298949 ATTTGATATCCTTCGTCGTGAAGTTGGAATCCAATCTAAAGATGAATATTGCT
66 ATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATATTGCT
299002 TCGAGTTCAA
Statistics
Matches: 223, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
123 1 0.00
124 222 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (124 bp):
CACGATTCCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
ATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATATTGCTGGTAGG
Found at i:301280 original size:21 final size:21
Alignment explanation
Indices: 301254--301298 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
301244 GATTTCTGGG
* *
301254 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
301275 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
301296 CAA
1 CAA
301299 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:302858 original size:30 final size:30
Alignment explanation
Indices: 302819--302885 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
302809 TCGGGGCCTA
*
302819 TGGACAGTTACCAAGGATCTTTATGACCTC
1 TGGATAGTTACCAAGGATCTTTATGACCTC
*
302849 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCAAGGATCTTTATGACCTC
302879 TGGATAG
1 TGGATAG
302886 GTCCTTCGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (30 bp):
TGGATAGTTACCAAGGATCTTTATGACCTC
Found at i:307157 original size:23 final size:23
Alignment explanation
Indices: 307117--307166 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 23
307107 CCAGATAAAT
307117 AAATAAAAATAAAGAAAATGTTAA
1 AAATAAAAATAAAGAAAAT-TTAA
307141 AAATAAAAAATAAA-AAAATTTAA
1 AAAT-AAAAATAAAGAAAATTTAA
307164 AAA
1 AAA
307167 AATGTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 7 0.28
24 9 0.36
25 9 0.36
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (23 bp):
AAATAAAAATAAAGAAAATTTAA
Found at i:307167 original size:24 final size:25
Alignment explanation
Indices: 307112--307167 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
307102 TGTTACCAGA
307112 TAAATAAATAAAAATAAAGAAAATGT
1 TAAA-AAATAAAAATAAAGAAAATGT
307138 T-AAAAATAAAAAATAAA-AAAAT-T
1 TAAAAAAT-AAAAATAAAGAAAATGT
307161 TAAAAAA
1 TAAAAAA
307168 ATGTTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 2 0.07
24 14 0.50
25 11 0.39
26 1 0.04
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (25 bp):
TAAAAAATAAAAATAAAGAAAATGT
Found at i:307167 original size:25 final size:26
Alignment explanation
Indices: 307112--307169 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
307102 TGTTACCAGA
*
307112 TAAATAAATAAAAATAAAGAAAATGT
1 TAAAAAAATAAAAATAAAGAAAATGT
*
307138 TAAAAATA-AAAAATAAA-AAAAT-T
1 TAAAAAAATAAAAATAAAGAAAATGT
307161 TAAAAAAAT
1 TAAAAAAAT
307170 GTTAATTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 8 0.29
24 5 0.18
25 9 0.32
26 6 0.21
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.22
Consensus pattern (26 bp):
TAAAAAAATAAAAATAAAGAAAATGT
Found at i:307488 original size:22 final size:21
Alignment explanation
Indices: 307458--307498 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
307448 GAAAAAAAAT
307458 AAAATAACAGT-AGCTAAATCA
1 AAAATAACAGTGA-CTAAATCA
307479 AAAATTAACAGTGACTAAAT
1 AAAA-TAACAGTGACTAAAT
307499 TAAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 13 0.72
23 1 0.06
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.22
Consensus pattern (21 bp):
AAAATAACAGTGACTAAATCA
Found at i:308253 original size:288 final size:288
Alignment explanation
Indices: 307737--308313 Score: 1073
Period size: 288 Copynumber: 2.0 Consensus size: 288
307727 TCAATAAATT
*
307737 ATCTTGCCTGCTGCACGTCGTATCTGCCTCTGGTGGCCGTTGGCCACCAAAATTTACCGAGGGAC
1 ATCTTGCCCGCTGCACGTCGTATCTGCCTCTGGTGGCCGTTGGCCACCAAAATTTACCGAGGGAC
307802 TCGTCTCGACGCGGTAGTCATGGATTCGGGCTTCGTTTCGTCAGGGGGTGCTCCGAACGTCGTGA
66 TCGTCTCGACGCGGTAGTCATGGATTCGGGCTTCGTTTCGTCAGGGGGTGCTCCGAACGTCGTGA
*
307867 AATGGATAAAAACCGCTCGGCTTTCCCGGGCTCCGATCTGCGCTGTCTGCCGTTGGATCAAGCTC
131 AATGGATAAAAACCGCTCGGCTTTCCCGGGCTCCGATCTGCGCTGTCCGCCGTTGGATCAAGCTC
*
307932 AAATTTCAGTATGTTACTCCCCTCCTCGAGAAGCTCCTTCTCACCGTTTGGTTCGTCGAGCCGAC
196 AAATTTCAGTATGTTACTCCCCTCCTCGAGAAGCTCCTTCTCACCATTTGGTTCGTCGAGCCGAC
*
307997 CCTCCGACCGCCGGCGAGATTCTGACAG
261 CCTCCGACCGCCGGCAAGATTCTGACAG
* *
308025 ATCTTGCCCGTTGCACGTCGTATCTGCCTCTGGTGGCCGTTGGCCACCAAAATTTACCGGGGGAC
1 ATCTTGCCCGCTGCACGTCGTATCTGCCTCTGGTGGCCGTTGGCCACCAAAATTTACCGAGGGAC
308090 TCGTCTCGACGCGGTAGTCATGGATTCGGGCTTCGTTTCGTCAGGGGGTGCTCCGAACGTCGTGA
66 TCGTCTCGACGCGGTAGTCATGGATTCGGGCTTCGTTTCGTCAGGGGGTGCTCCGAACGTCGTGA
* * *
308155 AATGGATAAAAATCGCTCGGTTTTCCCGGGCTCCGATCTGCGTTGTCCGCCGTTGGATCAAGCTC
131 AATGGATAAAAACCGCTCGGCTTTCCCGGGCTCCGATCTGCGCTGTCCGCCGTTGGATCAAGCTC
308220 AAATTTCAGTATGTTACTCCCCTCCTCGAGAAGCTCCTTCTCACCATTTGGTTCGTCGAGCCGAC
196 AAATTTCAGTATGTTACTCCCCTCCTCGAGAAGCTCCTTCTCACCATTTGGTTCGTCGAGCCGAC
308285 CCTCCGACCGCCGGCAAGATTCTGACAG
261 CCTCCGACCGCCGGCAAGATTCTGACAG
308313 A
1 A
308314 ACGGTAAAAC
Statistics
Matches: 280, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
288 280 1.00
ACGTcount: A:0.17, C:0.30, G:0.27, T:0.26
Consensus pattern (288 bp):
ATCTTGCCCGCTGCACGTCGTATCTGCCTCTGGTGGCCGTTGGCCACCAAAATTTACCGAGGGAC
TCGTCTCGACGCGGTAGTCATGGATTCGGGCTTCGTTTCGTCAGGGGGTGCTCCGAACGTCGTGA
AATGGATAAAAACCGCTCGGCTTTCCCGGGCTCCGATCTGCGCTGTCCGCCGTTGGATCAAGCTC
AAATTTCAGTATGTTACTCCCCTCCTCGAGAAGCTCCTTCTCACCATTTGGTTCGTCGAGCCGAC
CCTCCGACCGCCGGCAAGATTCTGACAG
Found at i:315058 original size:132 final size:132
Alignment explanation
Indices: 314922--315173 Score: 312
Period size: 133 Copynumber: 1.9 Consensus size: 132
314912 AAAAATGTAT
* * * * *
314922 AAAATTATTTAAAAA-ATAAAATATCTT-ATAAAGTTAACAATAATTTTTATATATGATCATCAA
1 AAAATTATTTAAAAACATAAAATAT-TTGAGAAAGTTAACAACAATGTATATATATAATCATCAA
314985 ATTAAACTTTTTAA-TCTAAATAATAATTTTAAAATTTTAATTAATAATTATATATATATATATT
65 ATTAAACTTTTTAACT-TAAATAATAATTTT-AAATTTTAATTAATAATTATATATATATATATT
315049 AACTC
128 AACTC
* * * * *
315054 AAAATTATTTAAAAACTTAAATTATTTGAGAAATTTAAGAACAATGTATATATATAATCATTAAA
1 AAAATTATTTAAAAACATAAAATATTTGAGAAAGTTAACAACAATGTATATATATAATCATCAAA
* * * * * *
315119 TTAAATTTTTTAACTTAAGTAATAATTTTAATTTTTTATTAATGATTTTATATAT
66 TTAAACTTTTTAACTTAAATAATAATTTTAAATTTTAATTAATAATTATATATAT
315174 TTTAAAATTA
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
132 39 0.39
133 61 0.60
134 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (132 bp):
AAAATTATTTAAAAACATAAAATATTTGAGAAAGTTAACAACAATGTATATATATAATCATCAAA
TTAAACTTTTTAACTTAAATAATAATTTTAAATTTTAATTAATAATTATATATATATATATTAAC
TC
Found at i:318125 original size:20 final size:19
Alignment explanation
Indices: 318086--318127 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
318076 TTTCTTCGAT
318086 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
318105 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
318125 ATT
1 ATT
318128 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:318238 original size:120 final size:120
Alignment explanation
Indices: 317992--318231 Score: 297
Period size: 120 Copynumber: 2.0 Consensus size: 120
317982 AAAATATATT
* * * ** * * *
317992 AATTTATATATATATATATATAATATAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTA
1 AATTAATATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAAGGACATCCA
* *
318057 GGTGCCTTAAGACAACTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAAC
65 GGTGCCTTAAGACAACTCATTTCTTCAATATTAAAAAATAAATAAATAATTAAAAC
318113 AATTAATATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCA
1 AATTAATATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCA
* ** ** *
318178 GTTGTTTTAAGACTGC-CATTTCTT-AATATTGAAAAATAAATAAAT-ATTAAAAC
65 GGTGCCTTAAGACAACTCATTTCTTCAATATTAAAAAATAAATAAATAATTAAAAC
318231 A
1 A
318232 GGATTAAAAT
Statistics
Matches: 102, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
118 9 0.09
119 19 0.19
120 45 0.44
121 29 0.28
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (120 bp):
AATTAATATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAG
GTGCCTTAAGACAACTCATTTCTTCAATATTAAAAAATAAATAAATAATTAAAAC
Found at i:318330 original size:3 final size:3
Alignment explanation
Indices: 318322--318351 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
318312 TTTATGGCTA
*
318322 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
318352 TAAAAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:319632 original size:3 final size:3
Alignment explanation
Indices: 319624--319676 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
319614 GGCATGTTTG
**
319624 TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
319669 TAA TAA TA
1 TAA TAA TA
319677 TCAATAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:319650 original size:21 final size:21
Alignment explanation
Indices: 319624--319685 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
319614 GGCATGTTTG
* **
319624 TAATAATAATAATTTTAATAA
1 TAATAATAATAAATAAAATAA
319645 TAATAATAATAAATAAAATAA
1 TAATAATAATAAATAAAATAA
319666 TAATAATAATATCAATAAAA
1 TAATAATAATA--AATAAAA
319686 ATGGGTAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 29 0.81
23 7 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
TAATAATAATAAATAAAATAA
Found at i:319682 original size:18 final size:18
Alignment explanation
Indices: 319624--319683 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
319614 GGCATGTTTG
* *
319624 TAATAATAATAATTTTAA
1 TAATAATAATAATATAAA
319642 TAATAATAATAATAAATAAAA
1 TAATAATAATAAT--AT-AAA
*
319663 TAATAATAATAATATCAA
1 TAATAATAATAATATAAA
319681 TAA
1 TAA
319684 AAATGGGTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 18 0.50
19 2 0.06
20 1 0.03
21 15 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATAATAATAATATAAA
Found at i:320879 original size:3 final size:3
Alignment explanation
Indices: 320871--320923 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
320861 GGCCTGTTTG
**
320871 TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
320916 TAA TAA TA
1 TAA TAA TA
320924 TCAATACAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:320929 original size:18 final size:18
Alignment explanation
Indices: 320871--320929 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
320861 GGCCTGTTTG
* *
320871 TAATAATAATAATTTTAA
1 TAATAATAATAATATAAA
320889 TAATAATAATAATAAATAAAA
1 TAATAATAATAAT--AT-AAA
*
320910 TAATAATAATAATATCAA
1 TAATAATAATAATATAAA
320928 TA
1 TA
320930 CAAAATGGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
18 17 0.49
19 2 0.06
20 1 0.03
21 15 0.43
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATAATAATAATATAAA
Found at i:321517 original size:113 final size:113
Alignment explanation
Indices: 321149--322038 Score: 1072
Period size: 113 Copynumber: 7.8 Consensus size: 113
321139 TGTAATCTAG
* * * *
321149 CAAAAAGTTGAATAAATTCTCCTCTTTATGAACTTCTTC-T--TT-TTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
321210 TTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAA
66 TTATGAACT-TTCTCTGGAAATGCTGATCCATCAAGTGATGAATTCAAA
*
321258 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** *
321323 TTATGAACTTTCTCTGGAAAAATTAATGCTGATCTATCTCCTTCTGTGATAGAA-TCATGA
66 TTATGAACTTTCTCTGG----A--AATGCTGATCCA--T-C--AAGTGAT-GAATTCA-AA
* * * **
321383 -AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGTTTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
321447 TTATGAACTCTAC-CT-GACAATGTTGATCCATCAAATGATGAATTCAAA
66 TTATGAACT-TTCTCTGGA-AATGCTGATCCATCAAGTGATGAATTCAAA
321495 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
321560 TTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAA
66 TTATGAACT-TTCTCTGGAAATGCTGATCCATCAAGTGATGAATTCAAA
*
321608 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * ** *
321673 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGAATTCAAA
** *
321721 CAAAAGGTTGAACAAGCTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
321786 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGCGATGGATT--AA
66 TTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGAATTCAAA
* * * *
321832 GATAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
321897 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATT--AA
66 TTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGAATTCAAA
* * * * * *
321943 GATAAGGTCGAACAAGTTCTTCTCATTATAAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
322008 TTATGAACTCTT-TCTGGAAATGTTGATCCAT
66 TTATGAACT-TTCTCTGGAAATGCTGATCCAT
322039 TGTGATGGAT
Statistics
Matches: 697, Mismatches: 60, Indels: 46
0.87 0.07 0.06
Matches are distributed among these distances:
109 34 0.05
110 1 0.00
111 194 0.28
112 12 0.02
113 347 0.50
114 1 0.00
115 1 0.00
116 1 0.00
118 10 0.01
119 11 0.02
121 1 0.00
122 1 0.00
123 1 0.00
124 76 0.11
125 6 0.01
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGAATTCAAA
Found at i:321661 original size:24 final size:23
Alignment explanation
Indices: 321626--321670 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
321616 TGAACAAATT
321626 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
321650 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
321671 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:325088 original size:114 final size:114
Alignment explanation
Indices: 324892--325114 Score: 401
Period size: 114 Copynumber: 2.0 Consensus size: 114
324882 GACTATCATT
*
324892 AAATTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACTAAACCAGATCAAATAACTCAA
1 AAATTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAAATAACTCAA
* *
324957 AGAACACTTCTAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGC
66 AGAACACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGC
* *
325006 AAATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAA
1 AAATTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAAATAACTCAA
325071 AGAACACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCTACTA
66 AGAACACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCTACTA
325115 CGAGAACGTG
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 104 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (114 bp):
AAATTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAAATAACTCAA
AGAACACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGC
Found at i:327307 original size:14 final size:14
Alignment explanation
Indices: 327288--327329 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
327278 CAATTTTCCT
327288 TTTTTTTCTTTTTA
1 TTTTTTTCTTTTTA
* *
327302 TTTTTTCCTTTTTC
1 TTTTTTTCTTTTTA
327316 TTTTTATTCTTTTT
1 TTTTT-TTCTTTTT
327330 TTCTTCTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTCTTTTTA
Found at i:327308 original size:23 final size:23
Alignment explanation
Indices: 327281--327345 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
327271 CTTGATTCAA
327281 TTTTCCTTTTTTTTCTTTTTATT
1 TTTTCCTTTTTTTTCTTTTTATT
* *
327304 TTTTCCTTTTTCTTT-TTATTCTT
1 TTTTCCTTTTT-TTTCTTTTTATT
* *
327327 TTTTTCTTCTTCTTTCTTT
1 TTTTCCTT-TTTTTTCTTT
327346 GCTGGATGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
23 27 0.79
24 7 0.21
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTCCTTTTTTTTCTTTTTATT
Found at i:327315 original size:20 final size:21
Alignment explanation
Indices: 327290--327328 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
327280 ATTTTCCTTT
327290 TTTTTCTTTTTATT-TTTTCC
1 TTTTTCTTTTTATTCTTTTCC
327310 TTTTTCTTTTTATTCTTTT
1 TTTTTCTTTTTATTCTTTT
327329 TTTCTTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTCTTTTTATTCTTTTCC
Found at i:327336 original size:20 final size:18
Alignment explanation
Indices: 327287--327337 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 18
327277 TCAATTTTCC
327287 TTTTTTTTCTTTTTATTT
1 TTTTTTTTCTTTTTATTT
327305 TTTCCTTTTTCTTTTTATTCT
1 TTT--TTTTTCTTTTTATT-T
327326 TTTTTTCTTCTT
1 TTTTTT-TTCTT
327338 CTTTCTTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.10
19 3 0.10
20 19 0.66
21 4 0.14
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTTTCTTTTTATTT
Found at i:327645 original size:2 final size:2
Alignment explanation
Indices: 327638--327665 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
327628 ACAACAAATG
327638 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
327666 TAAAGGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:329415 original size:15 final size:15
Alignment explanation
Indices: 329397--329435 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
329387 ATAAAAGTAT
329397 AAATGAAAAAATGAA
1 AAATGAAAAAATGAA
* * *
329412 AAATGCAAAGATGCA
1 AAATGAAAAAATGAA
329427 AAATGAAAA
1 AAATGAAAA
329436 TGTATGTATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.67, C:0.05, G:0.15, T:0.13
Consensus pattern (15 bp):
AAATGAAAAAATGAA
Found at i:330932 original size:18 final size:19
Alignment explanation
Indices: 330909--330947 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
330899 TTTAATATCT
*
330909 AAAAATAAAGTAAA-AATA
1 AAAAATAAAGAAAATAATA
330927 AAAAATAAAGAAAATAATA
1 AAAAATAAAGAAAATAATA
330946 AA
1 AA
330948 TATTGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (19 bp):
AAAAATAAAGAAAATAATA
Found at i:330940 original size:16 final size:17
Alignment explanation
Indices: 330909--330949 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
330899 TTTAATATCT
330909 AAAAATAAAGTAAAAATA
1 AAAAATAAAG-AAAAATA
330927 AAAAATAAAG-AAAATA
1 AAAAATAAAGAAAAATA
*
330943 ATAAATA
1 AAAAATA
330950 TTGTGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.55
18 10 0.45
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (17 bp):
AAAAATAAAGAAAAATA
Found at i:331483 original size:23 final size:23
Alignment explanation
Indices: 331457--331510 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
331447 AAATTATAAT
331457 TATAAA-AAATATATTAATGTATA
1 TATAAATAAA-ATATTAATGTATA
* *
331480 TATAAATAAAATATTTATTTATA
1 TATAAATAAAATATTAATGTATA
*
331503 TAGAAATA
1 TATAAATA
331511 TCAGAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 24 0.89
24 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (23 bp):
TATAAATAAAATATTAATGTATA
Found at i:331596 original size:20 final size:19
Alignment explanation
Indices: 331557--331598 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
331547 TTTCTTCGAT
331557 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
331576 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
331596 ATT
1 ATT
331599 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:331776 original size:2 final size:2
Alignment explanation
Indices: 331769--331805 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
331759 TATTATTTAT
331769 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
331806 GGCTAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:333143 original size:3 final size:3
Alignment explanation
Indices: 333135--333181 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
333125 GGCATGTTTG
**
333135 TAA TAA TAA TAA TTT TAA TAA TAA TAAA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
333180 TA
1 TA
333182 TCAATAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:341594 original size:31 final size:31
Alignment explanation
Indices: 341550--341628 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
341540 GTTAACAACG
* *
341550 AGTGACCAATTTGTTATAAATTGATAATGTT
1 AGTGACCAATTTGTTACAAATCGATAATGTT
* *
341581 AGTGATCATTTTGTTACAAATCGATAATGTT
1 AGTGACCAATTTGTTACAAATCGATAATGTT
* * *
341612 CGTGTCTAATTTGTTAC
1 AGTGACCAATTTGTTAC
341629 TTTTTAAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.43
Consensus pattern (31 bp):
AGTGACCAATTTGTTACAAATCGATAATGTT
Found at i:342596 original size:4 final size:4
Alignment explanation
Indices: 342587--342612 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
342577 GGTTTTCTTC
342587 TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT
342613 TAATTTTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:345452 original size:30 final size:30
Alignment explanation
Indices: 345418--345489 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
345408 TCTTTGTTGA
*
345418 AATTTGCTGCAAGCGGGGGCTTTACACATG
1 AATTTGATGCAAGCGGGGGCTTTACACATG
345448 AATTTGATGCAAGCGGGGGCTTTACACATG
1 AATTTGATGCAAGCGGGGGCTTTACACATG
345478 AATTTGATGCAA
1 AATTTGATGCAA
345490 TTATGTTTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (30 bp):
AATTTGATGCAAGCGGGGGCTTTACACATG
Found at i:346445 original size:30 final size:31
Alignment explanation
Indices: 346411--346473 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
346401 AAATATTTAA
346411 ACTCTTATGTTTAATTTAATC-TTTACTATC
1 ACTCTTATGTTTAATTTAATCTTTTACTATC
*
346441 ACTCTTATGTTTAATTTAATCTTTTACTTTC
1 ACTCTTATGTTTAATTTAATCTTTTACTATC
346472 AC
1 AC
346474 CAATAGTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 21 0.68
31 10 0.32
ACGTcount: A:0.25, C:0.17, G:0.03, T:0.54
Consensus pattern (31 bp):
ACTCTTATGTTTAATTTAATCTTTTACTATC
Found at i:349009 original size:2 final size:2
Alignment explanation
Indices: 349002--349031 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
348992 CTCTTTAATA
349002 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
349032 TAAACTCATA
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):
AT
Found at i:356881 original size:114 final size:112
Alignment explanation
Indices: 356662--356899 Score: 386
Period size: 114 Copynumber: 2.1 Consensus size: 112
356652 AACTTTCAAC
** *
356662 AAAGTATCGATATATGTACAAAAAGTATTTATACTTTCAACATATCAGGTAGCTCTTTATCGATT
1 AAAGTATCGATATATGTACAAAAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGATT
*
356727 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACTTGTTATATTGT
66 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * * *
356774 AAAGTATCGATATATTTTTATAAAAAGTATCGATACTTTCAACATATCATGTAGCTCTTTACCGG
1 AAAGTATCGATATA--TGTACAAAAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGA
356839 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
64 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
356888 AAAGTATCGATA
1 AAAGTATCGATA
356900 CTTTCAACAT
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
112 14 0.12
114 102 0.88
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (112 bp):
AAAGTATCGATATATGTACAAAAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGATT
TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
Found at i:356903 original size:91 final size:91
Alignment explanation
Indices: 356797--356991 Score: 363
Period size: 91 Copynumber: 2.1 Consensus size: 91
356787 ATTTTTATAA
*
356797 AAAGTATCGATACTTTCAACATATCATGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTT
1 AAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTT
* *
356862 TGTCATATTTTTACCTGTTATATTGT
66 TGTCATATTTTTACATGTTATATTAT
356888 AAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTT
1 AAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTT
356953 TGTCATATTTTTACATGTTATATTAT
66 TGTCATATTTTTACATGTTATATTAT
356979 AAAGTATCGATAC
1 AAAGTATCGATAC
356992 ATTTTTATAA
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 101 1.00
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (91 bp):
AAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTT
TGTCATATTTTTACATGTTATATTAT
Found at i:357045 original size:112 final size:113
Alignment explanation
Indices: 356887--357126 Score: 374
Period size: 115 Copynumber: 2.1 Consensus size: 113
356877 TGTTATATTG
* * * *
356887 TAAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGG-T
1 TAAAGTATCGATACTTTCAACATATCAAGTAGATATTTACCAGTTTTGTCATAATGAAACTGGTT
356951 TTTGTCATATTTTTACATGTTATATTATAAAGTATCGATACATTTTTA
66 TTTGTCATATTTTTACATGTTATATTATAAAGTATCGATACATTTTTA
* *
356999 TAAAGTATTGATACTTTCAACATATCAAGTAGATATTTATCAGTTTTGTCATAATGAAACTGGTT
1 TAAAGTATCGATACTTTCAACATATCAAGTAGATATTTACCAGTTTTGTCATAATGAAACTGG--
* * *
357064 TTTTTTTCATATTTTTACTTGTTATATTGTAAAGTATCGATACATTTTTA
64 TTTTTGTCATATTTTTACATGTTATATTATAAAGTATCGATACATTTTTA
357114 TAAAGTATCGATA
1 TAAAGTATCGATA
357127 TTTTATAGGC
Statistics
Matches: 115, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
112 57 0.50
115 58 0.50
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (113 bp):
TAAAGTATCGATACTTTCAACATATCAAGTAGATATTTACCAGTTTTGTCATAATGAAACTGGTT
TTTGTCATATTTTTACATGTTATATTATAAAGTATCGATACATTTTTA
Found at i:357133 original size:18 final size:20
Alignment explanation
Indices: 357093--357130 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
357083 TGTTATATTG
357093 TAAAGTATCGATACATTTTTA
1 TAAAGTATCGATA-ATTTTTA
357114 TAAAGTATCGAT-ATTTT
1 TAAAGTATCGATAATTTT
357131 ATAGGCGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
21 12 0.71
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (20 bp):
TAAAGTATCGATAATTTTTA
Found at i:357408 original size:74 final size:72
Alignment explanation
Indices: 357212--357457 Score: 341
Period size: 73 Copynumber: 3.4 Consensus size: 72
357202 CAACATATCT
* * * *
357212 GGTAGGTAGTTTAATGTAATAGGTAGCATATATTTTTTTTTATCGTTTACATTATTAGCAACCTT
1 GGTAGATATTTTAATGTAATAGGTAGCA-CTA-TTTTTTTTACCGTTTACATTATTAGCAACCTT
*
357277 AAAAAAA-T
64 AAAAAAACC
*
357285 GGTAGATATTTTAATGTAATAGGTAGCACTATTTTTTTTACCGTTTACATTATTAGCAACATTCA
1 GGTAGATATTTTAATGTAATAGGTAGCACTATTTTTTTTACCGTTTACATTATTAGCAACCTT-A
357350 AAAAAACC
65 AAAAAACC
* * * *
357358 GGTAGATATTTTAATGTAATATGTAGCGCCTATTTTTTTTACCATTTACATTATTAACAACCTTA
1 GGTAGATATTTTAATGTAATAGGTAGC-ACTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
357423 AAAAAATCC
65 AAAAAA-CC
*
357432 GGTAGGTATTTTAATGTAATAGGTAG
1 GGTAGATATTTTAATGTAATAGGTAG
357458 TTTAAATTTT
Statistics
Matches: 156, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
71 30 0.19
72 9 0.06
73 59 0.38
74 58 0.37
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (72 bp):
GGTAGATATTTTAATGTAATAGGTAGCACTATTTTTTTTACCGTTTACATTATTAGCAACCTTAA
AAAAACC
Found at i:357818 original size:158 final size:158
Alignment explanation
Indices: 357525--357898 Score: 568
Period size: 158 Copynumber: 2.4 Consensus size: 158
357515 AAGTAAGTAA
** * * * *
357525 TTACCTATTTTGTTACATAAGCGTTACCTAATATGTTATTATGTTTGATAATGTTTCCAGTAATT
1 TTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGTTTGATAATGTTTCCAATAATT
* * *
357590 AATCGGTTATGTTATCATTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAA
66 AACCGATTATGTTATCATTGGTAACATTTTAGGCGTTTACCTAATATATTGTAATAACAAATTAA
*
357655 ATAATTAACCTATTTTATTATAAAAGTG
131 ATAATTAACCTATTTTATTATAAAAGCG
*
357683 TTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAATAATT
1 TTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGTTTGATAATGTTTCCAATAATT
*
357748 AACCGATTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATATTGTAATAACAAATTAA
66 AACCGATTATGTTATCATTGGTAACATTTTAGGCGTTTACCTAATATATTGTAATAACAAATTAA
* * *
357813 GTAATTAACTTATTTTATTATATAAGCG
131 ATAATTAACCTATTTTATTATAAAAGCG
* * * * *
357841 CTACCTATTACATTATATAAGTGCTACCTAATATGTTATTGTATTTGATAATATTTCC
1 TTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGTTTGATAATGTTTCC
357899 GGTTGAATGA
Statistics
Matches: 195, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
158 195 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.43
Consensus pattern (158 bp):
TTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGTTTGATAATGTTTCCAATAATT
AACCGATTATGTTATCATTGGTAACATTTTAGGCGTTTACCTAATATATTGTAATAACAAATTAA
ATAATTAACCTATTTTATTATAAAAGCG
Found at i:357879 original size:23 final size:23
Alignment explanation
Indices: 357829--357873 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
357819 AACTTATTTT
*
357829 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
357852 ATTATATAAGTGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
357874 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:361357 original size:21 final size:21
Alignment explanation
Indices: 361331--361377 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
361321 GAAGTATTCA
*
361331 TGCTCCCATGTCATAGCAGCT
1 TGCTCCCATGTCATAACAGCT
361352 TGCTCCCATGTCATAACAGCT
1 TGCTCCCATGTCATAACAGCT
361373 TGCTC
1 TGCTC
361378 TTATACCCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.34, G:0.17, T:0.30
Consensus pattern (21 bp):
TGCTCCCATGTCATAACAGCT
Found at i:362043 original size:6 final size:6
Alignment explanation
Indices: 362034--362059 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
362024 TTATCATCAT
362034 CATAAG CATAAG CATAAG CATAAG CA
1 CATAAG CATAAG CATAAG CATAAG CA
362060 ACAACAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.15
Consensus pattern (6 bp):
CATAAG
Found at i:363651 original size:61 final size:64
Alignment explanation
Indices: 363564--363707 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 64
363554 TGCACTAAGC
*
363564 TTACACTCTAGTGCTAATCTGGATATGACACATAAGGTCGTGCCCACCACCTACA-CTAG-GT-
1 TTACACTCTAGTGCTAATCTAGATATGACACATAAGGTCGTGCCCACCACCTACATCTAGTGTA
* * * * *
363625 TTACACTCTAGTGCTAATCTATATATGACATATAAGGTTGTGCCCTCCACCTACATTTAGTGTCA
1 TTACACTCTAGTGCTAATCTAGATATGACACATAAGGTCGTGCCCACCACCTACATCTAGTGT-A
*
363690 TTACACACTAGTGCTAAT
1 TTACACTCTAGTGCTAAT
363708 ATAAACCTGC
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
61 50 0.69
62 3 0.04
63 2 0.03
65 17 0.24
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (64 bp):
TTACACTCTAGTGCTAATCTAGATATGACACATAAGGTCGTGCCCACCACCTACATCTAGTGTA
Found at i:366840 original size:30 final size:30
Alignment explanation
Indices: 366804--366891 Score: 169
Period size: 29 Copynumber: 3.0 Consensus size: 30
366794 CCTTAAACAT
366804 GACCACCTATTCAGTGTAATTTTTTTTATA
1 GACCACCTATTCAGTGTAATTTTTTTTATA
366834 GACCACCTATTCAGTGTAA-TTTTTTTATA
1 GACCACCTATTCAGTGTAATTTTTTTTATA
366863 GACCACCTATTCAGTGTAATTTTTTTTAT
1 GACCACCTATTCAGTGTAATTTTTTTTAT
366892 TATATACTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 29 0.51
30 28 0.49
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.47
Consensus pattern (30 bp):
GACCACCTATTCAGTGTAATTTTTTTTATA
Found at i:373841 original size:18 final size:18
Alignment explanation
Indices: 373814--373858 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
373804 AACTCATTTA
*
373814 GAGTTTATTTCTCCCTTT
1 GAGTTGATTTCTCCCTTT
373832 GAGTTGATTTCTCCCTTT
1 GAGTTGATTTCTCCCTTT
373850 GAGTTGATT
1 GAGTTGATT
373859 AAGCTCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.13, C:0.18, G:0.18, T:0.51
Consensus pattern (18 bp):
GAGTTGATTTCTCCCTTT
Found at i:380516 original size:37 final size:36
Alignment explanation
Indices: 380454--380576 Score: 133
Period size: 38 Copynumber: 3.3 Consensus size: 36
380444 ATCCCATTAT
* * *
380454 CATTTTTC-AACAAACATCTATCAAACTTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
380489 CTATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
* *
380526 CA-TTTTCAAAAAAAAAACATTTACCAAACTTTGAAAAT
1 CATTTTTC---AAAGAAACATTTACCAAACTTTGAAAAA
380564 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
380577 TTGGTTGCCA
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
35 6 0.08
36 8 0.11
37 27 0.36
38 28 0.38
40 5 0.07
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
Found at i:380529 original size:21 final size:21
Alignment explanation
Indices: 380502--380568 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
380492 TTTTTCAAAG
380502 AAACATTTACCAAACTTTGAA
1 AAACATTTACCAAACTTTGAA
* * **
380523 AACCATTT-TCAAA---AAAA
1 AAACATTTACCAAACTTTGAA
380540 AAACATTTACCAAACTTTGAA
1 AAACATTTACCAAACTTTGAA
*
380561 AATCATTT
1 AAACATTT
380569 TTTCAAAGTT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
17 9 0.27
18 4 0.12
20 4 0.12
21 16 0.48
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.30
Consensus pattern (21 bp):
AAACATTTACCAAACTTTGAA
Found at i:384668 original size:16 final size:17
Alignment explanation
Indices: 384640--384675 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
384630 CGTATCGCTG
384640 ACAAAATTTTACTATTC
1 ACAAAATTTTACTATTC
384657 ACAAAA-TTTACTATTC
1 ACAAAATTTTACTATTC
384673 ACA
1 ACA
384676 TGAATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.36
Consensus pattern (17 bp):
ACAAAATTTTACTATTC
Found at i:385107 original size:36 final size:37
Alignment explanation
Indices: 385050--385167 Score: 149
Period size: 35 Copynumber: 3.3 Consensus size: 37
385040 TCCCATTATC
* *
385050 ATTTTTC-AACAAACATCTACC-AACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACT
385085 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACT
*
385121 ATTTTT-AAAAAAACATTTACCAAACTTT-AAAAA-T
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACT
385155 CATTTTTTCAAAG
1 -A-TTTTTCAAAG
385168 TTGGTTGCCA
Statistics
Matches: 73, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
34 1 0.01
35 33 0.45
36 29 0.40
37 10 0.14
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (37 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACT
Found at i:387550 original size:17 final size:17
Alignment explanation
Indices: 387528--387588 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
387518 AAAAATCATA
387528 TATATTATTTATGAATT
1 TATATTATTTATGAATT
* * *
387545 TATATTCGATTGAAATAAAAT
1 TATATT--ATT--TATGAATT
387566 TATATTATTTATGAATT
1 TATATTATTTATGAATT
387583 TATATT
1 TATATT
387589 TAAAATACGA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 17 0.50
19 6 0.18
21 11 0.32
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (17 bp):
TATATTATTTATGAATT
Found at i:388132 original size:20 final size:20
Alignment explanation
Indices: 388092--388138 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
388082 ACCTCGTTCT
388092 TTATCTTAAATTTTATAATAA
1 TTAT-TTAAATTTTATAATAA
*
388113 -TATTTAAATATTTATTATAA
1 TTATTTAAAT-TTTATAATAA
388133 TTATTT
1 TTATTT
388139 TTTTCTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 6 0.26
20 12 0.52
21 5 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTTAAATTTTATAATAA
Found at i:399262 original size:22 final size:22
Alignment explanation
Indices: 399203--399262 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
399193 ATAGGGCAGA
* * *
399203 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCTTTGAAG
*
399225 GGTAACCGATTCCCCTTTGAAG
1 GGGAACCGATTCCCCTTTGAAG
399247 GGGAACCGATTCCCCT
1 GGGAACCGATTCCCCT
399263 AGGGGAATCG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (22 bp):
GGGAACCGATTCCCCTTTGAAG
Found at i:399268 original size:18 final size:18
Alignment explanation
Indices: 399245--399279 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
399235 TCCCCTTTGA
*
399245 AGGGGAACCGATTCCCCT
1 AGGGGAACCGATACCCCT
*
399263 AGGGGAATCGATACCCC
1 AGGGGAACCGATACCCC
399280 CTGGGGTTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.29, T:0.14
Consensus pattern (18 bp):
AGGGGAACCGATACCCCT
Found at i:405313 original size:3 final size:3
Alignment explanation
Indices: 405305--405339 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
405295 AATGAATAAT
405305 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
405340 TTTAATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:405897 original size:14 final size:14
Alignment explanation
Indices: 405878--405904 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
405868 GACATCAAAC
405878 ATCAAATTAAAAAT
1 ATCAAATTAAAAAT
405892 ATCAAATTAAAAA
1 ATCAAATTAAAAA
405905 CTTTAATTGA
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:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (14 bp):
ATCAAATTAAAAAT
Found at i:406796 original size:50 final size:51
Alignment explanation
Indices: 406720--406819 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 51
406710 ATCCAAACCG
*
406720 AAACTAAAGATAATATTTTAATTCTATCCTAATTCCTAA-AAAATAATAAT
1 AAACTAAAGATAATATTTTAACTCTATCCTAATTCCTAATAAAATAATAAT
* * *
406770 AAACTGAAGATAATGTTTTAACTCTATCTTAATTCCTAATAAAATAATAA
1 AAACTAAAGATAATATTTTAACTCTATCCTAATTCCTAATAAAATAATAA
406820 ATATAATTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 35 0.78
51 10 0.22
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.36
Consensus pattern (51 bp):
AAACTAAAGATAATATTTTAACTCTATCCTAATTCCTAATAAAATAATAAT
Found at i:412943 original size:89 final size:89
Alignment explanation
Indices: 412792--412972 Score: 362
Period size: 89 Copynumber: 2.0 Consensus size: 89
412782 GATTTACCAA
412792 GATCAATAATGACCACTCTCGGGCATTTATGCGAAAGCTTCGTTATTGATACCAATAAACAAGCA
1 GATCAATAATGACCACTCTCGGGCATTTATGCGAAAGCTTCGTTATTGATACCAATAAACAAGCA
412857 TTGCCTTAATTAATTAGAAAACAT
66 TTGCCTTAATTAATTAGAAAACAT
412881 GATCAATAATGACCACTCTCGGGCATTTATGCGAAAGCTTCGTTATTGATACCAATAAACAAGCA
1 GATCAATAATGACCACTCTCGGGCATTTATGCGAAAGCTTCGTTATTGATACCAATAAACAAGCA
412946 TTGCCTTAATTAATTAGAAAACAT
66 TTGCCTTAATTAATTAGAAAACAT
412970 GAT
1 GAT
412973 GCAAGGTTTT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 92 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (89 bp):
GATCAATAATGACCACTCTCGGGCATTTATGCGAAAGCTTCGTTATTGATACCAATAAACAAGCA
TTGCCTTAATTAATTAGAAAACAT
Found at i:414301 original size:51 final size:52
Alignment explanation
Indices: 414182--414421 Score: 290
Period size: 51 Copynumber: 4.6 Consensus size: 52
414172 TACATCAATA
* * * *
414182 TAAGTATGTGTTAAGTGCTACACTTTTTTTATTTTATTTATTTACTTACACTGTTG
1 TAAGTATGTGTTAAGTGTTACACTTTTTTTA---T-TTTATTCACTTACACCGGTG
* * * *
414238 TAAATTTGTGTTAAGTGTTACACTTTTTTTATTTTATTCACTTACACAGATG
1 TAAGTATGTGTTAAGTGTTACACTTTTTTTATTTTATTCACTTACACCGGTG
*
414290 T-AGTATGTGTTAAGTGTTACAC-TTTTTTGTTTTATTCACTTACACCGGTG
1 TAAGTATGTGTTAAGTGTTACACTTTTTTTATTTTATTCACTTACACCGGTG
* * *
414340 TAAGTACGTATTAAGTGTTACAC-TTGTTTATTTTATTCACTTACACCGGTG
1 TAAGTATGTGTTAAGTGTTACACTTTTTTTATTTTATTCACTTACACCGGTG
**
414391 TAAGTATGTGTTAAGTACTACA-TTTTTTTAT
1 TAAGTATGTGTTAAGTGTTACACTTTTTTTAT
414422 AGTATGAATT
Statistics
Matches: 162, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
50 26 0.16
51 89 0.55
52 18 0.11
53 1 0.01
56 28 0.17
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (52 bp):
TAAGTATGTGTTAAGTGTTACACTTTTTTTATTTTATTCACTTACACCGGTG
Found at i:415683 original size:35 final size:35
Alignment explanation
Indices: 415638--415709 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
415628 TTGATATTAT
415638 TTATAATAAGTCATGTCACTTGGTGAATAAATTTA
1 TTATAATAAGTCATGTCACTTGGTGAATAAATTTA
* * *
415673 TTATGATAAGTCATGTCACTTGGTGAGTGAATTTA
1 TTATAATAAGTCATGTCACTTGGTGAATAAATTTA
415708 TT
1 TT
415710 TTTTAGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (35 bp):
TTATAATAAGTCATGTCACTTGGTGAATAAATTTA
Found at i:416354 original size:24 final size:24
Alignment explanation
Indices: 416327--416399 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
416317 CGTTCATTTA
416327 CGTTC-GTGAACGTTCGATTATGTT
1 CGTTCGGT-AACGTTCGATTATGTT
* *
416351 CGTTCGGTTACGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGATTATGTT
* * *
416375 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGATTATGTT
416399 C
1 C
416400 ATTCATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 43 0.96
25 2 0.04
ACGTcount: A:0.11, C:0.16, G:0.25, T:0.48
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGATTATGTT
Found at i:416356 original size:14 final size:14
Alignment explanation
Indices: 416337--416392 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
416327 CGTTCGTGAA
*
416337 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
416351 CGTTCGGTTA----
1 CGTTCGGTTATGTT
*
416361 CGTTCGTTTATGTT
1 CGTTCGGTTATGTT
416375 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
416389 CGTT
1 CGTT
416393 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 9 0.26
14 26 0.74
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:416412 original size:24 final size:24
Alignment explanation
Indices: 416338--416399 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
416328 GTTCGTGAAC
* *
416338 GTTCGATTATGTTCGTTCGGTTAC
1 GTTCGTTTATGTTCGTTCGGTTAT
416362 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
416386 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
416400 ATTCATTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.52
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGTTAT
Found at i:417443 original size:10 final size:10
Alignment explanation
Indices: 417428--417486 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
417418 AGGTCTCTAA
417428 CGTTTATGTT
1 CGTTTATGTT
417438 CGTTTATGTT
1 CGTTTATGTT
417448 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
417459 ATGTTCGTGTT
1 -CGTTTATGTT
417470 CGTTTATGTT
1 CGTTTATGTT
417480 CGTTTAT
1 CGTTTAT
417487 TTATTAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 28 0.72
11 7 0.18
12 4 0.10
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.58
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:417459 original size:16 final size:16
Alignment explanation
Indices: 417434--417490 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
417424 CTAACGTTTA
*
417434 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
417450 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
417466 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
417482 T-TT-ATTTAT
1 TGTTCATTTAT
417491 TAAATGAACG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 5 0.13
15 2 0.05
16 31 0.82
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:422923 original size:23 final size:23
Alignment explanation
Indices: 422897--422957 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
422887 CTCGTATAAA
*
422897 TGCACCTAAGTGCCACGTAGAAT
1 TGCACCAAAGTGCCACGTAGAAT
*
422920 TGCACCAAAGTGTCACGTAGAAT
1 TGCACCAAAGTGCCACGTAGAAT
*
422943 TGCACCGAAGTGCCA
1 TGCACCAAAGTGCCA
422958 TATTAAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.20
Consensus pattern (23 bp):
TGCACCAAAGTGCCACGTAGAAT
Found at i:427979 original size:24 final size:23
Alignment explanation
Indices: 427915--428001 Score: 110
Period size: 24 Copynumber: 3.9 Consensus size: 23
427905 TTTCAATTTC
427915 CCCTTAA-AGTGCATCGATGCAT
1 CCCTTAACAGTGCATCGATGCAT
* *
427937 -TC-T-ACAGTGTATCGATGCAT
1 CCCTTAACAGTGCATCGATGCAT
427957 CCCTTAACATGTGCATCGATGCAT
1 CCCTTAACA-GTGCATCGATGCAT
427981 CCCTTAACATGTGCATCGATG
1 CCCTTAACA-GTGCATCGATG
428002 AACTCCTTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.02
20 15 0.27
21 2 0.04
22 1 0.02
23 3 0.05
24 34 0.61
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (23 bp):
CCCTTAACAGTGCATCGATGCAT
Found at i:429556 original size:2 final size:2
Alignment explanation
Indices: 429549--429605 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
429539 TTTTAGACTC
429549 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
429591 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
429606 ACAAAATACA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:430212 original size:89 final size:88
Alignment explanation
Indices: 430051--430328 Score: 369
Period size: 89 Copynumber: 3.1 Consensus size: 88
430041 AAGAACTGCG
* ** * * *
430051 TCCGTAGGGCTTACCCTAAGCACACAACAAAAAAGAGCCAACCTAAGGATATTCCTTAGGGCCTA
1 TCCGTAGGG-TTACCCTAAGCACATAAC-AAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTA
*
430116 TGGCCTACCCAAGGGTATCCTTAGG
64 TGGCCTACCCAAGGGTATCCTTAGA
* *
430141 TCTGTAGGGTTACCCTAAGGACATAACAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTATA
1 TCCGTAGGGTTACCCTAAGCACATAACAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAT-
430206 GGCCTACCCAAGGGTATCCTTAGA
65 GGCCTACCCAAGGGTATCCTTAGA
* * * * *
430230 TCCGTAGGGTTACCTTAAGCACATAGCAAAGGAAACCAACCTAAGAATATGTCTTGGGGCCTATG
1 TCCGTAGGGTTACCCTAAGCACATAACAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAT-
*
430295 GGCCTACCCAAGGATAT-CTTAGA
65 GGCCTACCCAAGGGTATCCTTAGA
*
430318 TCCGTATGGTT
1 TCCGTAGGGTT
430329 TTACCAGCTA
Statistics
Matches: 168, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
88 48 0.29
89 112 0.67
90 8 0.05
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.22
Consensus pattern (88 bp):
TCCGTAGGGTTACCCTAAGCACATAACAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTATG
GCCTACCCAAGGGTATCCTTAGA
Found at i:431955 original size:88 final size:88
Alignment explanation
Indices: 431806--431986 Score: 353
Period size: 88 Copynumber: 2.1 Consensus size: 88
431796 AATCCAAGAT
*
431806 ATTTACTTAGTTTAGGACATAAGGGTATTTTGGTTATTTTGGTGCTCAGTTTTATTCCAATCATT
1 ATTTACTTAGTCTAGGACATAAGGGTATTTTGGTTATTTTGGTGCTCAGTTTTATTCCAATCATT
431871 TCATAGCTTGATGGTATCCAATC
66 TCATAGCTTGATGGTATCCAATC
431894 ATTTACTTAGTCTAGGACATAAGGGTATTTTGGTTATTTTGGTGCTCAGTTTTATTCCAATCATT
1 ATTTACTTAGTCTAGGACATAAGGGTATTTTGGTTATTTTGGTGCTCAGTTTTATTCCAATCATT
431959 TCATAGCTTGATGGTATCCAATC
66 TCATAGCTTGATGGTATCCAATC
431982 ATTTA
1 ATTTA
431987 TGTGCTTGGT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 92 1.00
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (88 bp):
ATTTACTTAGTCTAGGACATAAGGGTATTTTGGTTATTTTGGTGCTCAGTTTTATTCCAATCATT
TCATAGCTTGATGGTATCCAATC
Found at i:436340 original size:12 final size:12
Alignment explanation
Indices: 436323--436347 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
436313 ATCTTCATTG
436323 TTTTTCTTTTAT
1 TTTTTCTTTTAT
436335 TTTTTCTTTTAT
1 TTTTTCTTTTAT
436347 T
1 T
436348 ATTATTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTCTTTTAT
Found at i:437432 original size:2 final size:2
Alignment explanation
Indices: 437427--437451 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
437417 AAATATTAAA
437427 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
437452 ATTGTATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:438117 original size:29 final size:29
Alignment explanation
Indices: 438074--438197 Score: 162
Period size: 29 Copynumber: 4.3 Consensus size: 29
438064 AAGTCCCTCA
* *
438074 ACTATTCAAAATTACAAAACGATCACTTG
1 ACTATTCAAAATTACAAAATGATCACTCG
438103 ACTATT-AAAAGTTACAAAATGATCACTCG
1 ACTATTCAAAA-TTACAAAATGATCACTCG
* *
438132 ACTATTCAGAATTACAAAATGATCACTAG
1 ACTATTCAAAATTACAAAATGATCACTCG
* *
438161 ACTATT-AAAAGGTGCAAAATGATCACTCG
1 ACTATTCAAAA-TTACAAAATGATCACTCG
438190 ACTATTCA
1 ACTATTCA
438198 TTATGTTCCA
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
28 7 0.08
29 72 0.87
30 4 0.05
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (29 bp):
ACTATTCAAAATTACAAAATGATCACTCG
Found at i:438164 original size:58 final size:58
Alignment explanation
Indices: 438074--438197 Score: 203
Period size: 58 Copynumber: 2.1 Consensus size: 58
438064 AAGTCCCTCA
* *
438074 ACTATTCAAAATTACAAAACGATCACTTGACTATTAAAAGTTACAAAATGATCACTCG
1 ACTATTCAAAATTACAAAACGATCACTAGACTATTAAAAGGTACAAAATGATCACTCG
* * *
438132 ACTATTCAGAATTACAAAATGATCACTAGACTATTAAAAGGTGCAAAATGATCACTCG
1 ACTATTCAAAATTACAAAACGATCACTAGACTATTAAAAGGTACAAAATGATCACTCG
438190 ACTATTCA
1 ACTATTCA
438198 TTATGTTCCA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (58 bp):
ACTATTCAAAATTACAAAACGATCACTAGACTATTAAAAGGTACAAAATGATCACTCG
Found at i:443395 original size:66 final size:65
Alignment explanation
Indices: 443239--443444 Score: 272
Period size: 65 Copynumber: 3.2 Consensus size: 65
443229 ATCACTTATA
* * *
443239 TGACTCATGTACCTTTATGGTGCAT-AAGGTGAAGTGATAATTGAATACTGTACA-AATCACACA
1 TGACTCATGTACCTTTATGGTGCATGAA-GTGGAGTGATAATTGAATACCGTACATAA-CACTCA
*
443302 TA
64 TG
* *
443304 TGACTCATGTACCTTTGTGGTGCATGAAATGGAGTGATAATTGAATACCGTACATAACACTCATT
1 TGACTCATGTACCTTTATGGTGCATGAAGTGGAGTGATAATTGAATACCGTACATAACACTCA-T
443369 G
65 G
* * * * *
443370 TGACTCATGTACTTTTATGGTGCATGAGGTGGAGTGATAATTGAATATCGTACATATCACTTATG
1 TGACTCATGTACCTTTATGGTGCATGAAGTGGAGTGATAATTGAATACCGTACATAACACTCATG
443435 TGACTCATGT
1 TGACTCATGT
443445 GACTTATGTA
Statistics
Matches: 125, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
65 64 0.51
66 61 0.49
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (65 bp):
TGACTCATGTACCTTTATGGTGCATGAAGTGGAGTGATAATTGAATACCGTACATAACACTCATG
Found at i:444404 original size:65 final size:65
Alignment explanation
Indices: 444316--444572 Score: 282
Period size: 65 Copynumber: 3.9 Consensus size: 65
444306 GAGTAATTGC
** * * *
444316 TGAATATAATACAGATCACTCATATGACTCATGTACTTTTGTGGTGCATGAGGTGGAGTTATAAT
1 TGAATATTGTACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAAT
* ** * *
444381 TGAATATTGTACAAATCACTCATATGACTCATGTACCTTTGTGGCGCATGAAATAGAATGATAAT
1 TGAATATTGTACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAAT
** * * * *
444446 TGAATACCGTACAAAACACTCATGTGACTCATGTACCTTTATGGTGCATGAGGTGGACTGATAAT
1 TGAATATTGTACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAAT
**** ** *
444511 TGAATATTGTTTTGATCACTCA-ATGAGACTTGTGTACCTTTGTGGTGCATAAGGTGGAGTGA
1 TGAATATTGTACAAATCACTCATAT--GACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGA
444573 CTATATGATG
Statistics
Matches: 157, Mismatches: 33, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
64 1 0.01
65 125 0.80
66 31 0.20
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33
Consensus pattern (65 bp):
TGAATATTGTACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAAT
Found at i:445558 original size:65 final size:65
Alignment explanation
Indices: 445342--445546 Score: 284
Period size: 65 Copynumber: 3.2 Consensus size: 65
445332 GAGTAATTGC
** * *
445342 TGAATATAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTTATAAT
1 TGAATATTGTACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAAT
* * **
445407 TGAATATTGTACAAATCACTCATATGACTCATGTACTTTTGTGGCGCATGAAATGGAGTGATAAT
1 TGAATATTGTACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAAT
** * * * *
445472 TGAATACCGTACAAAACACTCATGTGACTCATGTACCTTTATGGTGCATGAGGTGGACTGATAAT
1 TGAATATTGTACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAAT
445537 TGAATATTGT
1 TGAATATTGT
445547 TTTGATCACT
Statistics
Matches: 120, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
65 120 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (65 bp):
TGAATATTGTACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAAT
Found at i:445834 original size:23 final size:22
Alignment explanation
Indices: 445783--445836 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
445773 ACAATATAAG
* *
445783 ATATAAAACAATATAAGAGAAA
1 ATATAAGACAAGATAAGAGAAA
445805 ATAATAAGACAAGA-AAGAGAAACA
1 AT-ATAAGACAAGATAAGAG-AA-A
445829 ATATAAGA
1 ATATAAGA
445837 AAAGGAACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 7 0.26
23 17 0.63
24 3 0.11
ACGTcount: A:0.67, C:0.06, G:0.13, T:0.15
Consensus pattern (22 bp):
ATATAAGACAAGATAAGAGAAA
Found at i:453073 original size:30 final size:30
Alignment explanation
Indices: 453037--453096 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
453027 CCACCACCTA
*
453037 CACTAAGTATCATTGCACACTATAGTGTTG
1 CACTAAGTATCATTCCACACTATAGTGTTG
* *
453067 CACTAAGTGTCCTTCCACACTATAGTGTTG
1 CACTAAGTATCATTCCACACTATAGTGTTG
453097 AAACCTGCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (30 bp):
CACTAAGTATCATTCCACACTATAGTGTTG
Found at i:455740 original size:30 final size:30
Alignment explanation
Indices: 455704--455770 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
455694 CAAAACACCT
* * *
455704 AACTTTTGGAAATTGCACTTTTGGTCCCCA
1 AACTTTTGAAAATTACACTTTTGGTACCCA
* *
455734 AACTTTTGAAAATTACCCTTTTGGTACCTA
1 AACTTTTGAAAATTACACTTTTGGTACCCA
455764 AACTTTT
1 AACTTTT
455771 CCAAACTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (30 bp):
AACTTTTGAAAATTACACTTTTGGTACCCA
Found at i:456602 original size:15 final size:16
Alignment explanation
Indices: 456582--456622 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
456572 GTTTACTTCA
*
456582 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
456597 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
456613 GAATGATTCA
1 GAATGATTCA
456623 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:456731 original size:23 final size:23
Alignment explanation
Indices: 456701--456764 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
456691 TACTTAGATG
*
456701 CTGAATCATTCAGCACTGTTTTA
1 CTGAATCAGTCAGCACTGTTTTA
* *
456724 CTGAATCAGTCAACACTGTTTTG
1 CTGAATCAGTCAGCACTGTTTTA
456747 CTGAATCAGTCAGCACTG
1 CTGAATCAGTCAGCACTG
456765 AATCATTCAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (23 bp):
CTGAATCAGTCAGCACTGTTTTA
Found at i:465076 original size:27 final size:26
Alignment explanation
Indices: 465020--465084 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
465010 CGATATATAA
*
465020 TTATATATAAATATATTTAAAAATATT
1 TTATATAT-AATATATTTAAAAATAGT
*
465047 TTATATATAATATGATTT-AAATTAAGT
1 TTATATATAATAT-ATTTAAAAAT-AGT
*
465074 TTATCTATAAT
1 TTATATATAAT
465085 TTAAATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 9 0.27
27 24 0.73
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (26 bp):
TTATATATAATATATTTAAAAATAGT
Found at i:465887 original size:21 final size:22
Alignment explanation
Indices: 465847--465887 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
465837 AGCAATGGCC
* *
465847 ATATTTGTTTGGGTATAAATTT
1 ATATTAGTTTGCGTATAAATTT
465869 ATATTAGTTTGCG-ATAAAT
1 ATATTAGTTTGCGTATAAAT
465888 ATGATCTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (22 bp):
ATATTAGTTTGCGTATAAATTT
Found at i:466545 original size:20 final size:20
Alignment explanation
Indices: 466520--466568 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
466510 GGTTACCTGT
466520 GCTGCATTCTCTAGCACATA
1 GCTGCATTCTCTAGCACATA
466540 GCTGCATTCTCTAGCACATA
1 GCTGCATTCTCTAGCACATA
466560 GCTGCATTC
1 GCTGCATTC
466569 ACAAGGTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (20 bp):
GCTGCATTCTCTAGCACATA
Found at i:471285 original size:17 final size:18
Alignment explanation
Indices: 471246--471285 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
471236 ATATTATGTC
471246 ATTTGTTTTTCTTTTTTCT
1 ATTT-TTTTTCTTTTTTCT
471265 -TTTTTTTTCTTTTTT-T
1 ATTTTTTTTCTTTTTTCT
471281 ATTTT
1 ATTTT
471286 GTTTAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.05
17 16 0.80
18 3 0.15
ACGTcount: A:0.05, C:0.07, G:0.03, T:0.85
Consensus pattern (18 bp):
ATTTTTTTTCTTTTTTCT
Found at i:471863 original size:3 final size:3
Alignment explanation
Indices: 471855--471890 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
471845 TCGGTCACGT
*
471855 CAA CAA CAA CAA CAA CAA TAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
471891 AACTCAATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.67, C:0.31, G:0.00, T:0.03
Consensus pattern (3 bp):
CAA
Found at i:473745 original size:2 final size:2
Alignment explanation
Indices: 473738--473768 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
473728 ATACTATCAT
473738 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
473769 GAATCCACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:478478 original size:2 final size:2
Alignment explanation
Indices: 478473--478518 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
478463 TGGTGGTGTG
478473 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
478515 TA TA
1 TA TA
478519 CTCTCTCAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:483809 original size:15 final size:15
Alignment explanation
Indices: 483789--483845 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
483779 AACCGGGTAT
*
483789 CGGGTACTCGATTAC
1 CGGGTACCCGATTAC
**
483804 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
*
483821 CAGGTACCCGATTAC
1 CGGGTACCCGATTAC
483836 CGGGTACCCG
1 CGGGTACCCG
483846 TAACATCCGG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 19 0.58
16 4 0.12
17 10 0.30
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:485318 original size:23 final size:23
Alignment explanation
Indices: 485288--485350 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
485278 AATATAAGAC
485288 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
485311 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
485334 TACCTATTACATCATAT
1 TACCTATTACATTATAT
485351 TTTTACATAT
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
Done.