Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 99 of 153
Found at i:31252983 original size:708 final size:708
Alignment explanation
Indices: 31251589--31252987 Score: 1722
Period size: 708 Copynumber: 2.0 Consensus size: 708
31251579 ATCAAGTCAC
* * *
31251589 TCATCACAAAGACGAACAACATGTGGCTACTTTTACTTTTCATCAATCATGTAATGCCAATGAGA
1 TCATCACAAAGACGAACAACATGTGGCTAATTTTACTTTTCATCAACCATGTAATGCCAATGAAA
* ** * * **
31251654 GGATATCATTTACCCATGTCTCAGGCTATGAAATACGTTGTTTTAAATGATGTTACATACTACAG
66 GGATATCATTTACCCATGTCTCAGGCAATGAAATACACTATTGTAAATGACATTACATACTACAG
* *
31251719 AAGTCGTATACCCAACGCATCAACTTTCAATTCCTTTTCCATTTGAACTCAGGCTTTTACTTACA
131 AAGTCGTATACCCAACGCATCAACCTTCAATTCCTTATCCATTTGAACTCAGGCTTTTACTTACA
*
31251784 TCAAAGTATACAAGTCACGCATACATAGTCTACCATCCACTCAGAATTAAGGTATGTCACACTTT
196 TCAAAGTATACAAGTCACGCATACATAGTCTACCATCCACTCAGAATTAAGGTATGCCACACTTT
* * * * *
31251849 TAATCTCACAAGTGAATAAATCCATAAGAGCATTTAGGATCTCTTCTTCTTAGGTCTAGTCTCAT
261 AAATCTCACAAGTGAATAAATCCATAAAAGCATTCAGGATCTCTTCTTCTTAGGTCCAGTCTAAT
* * *
31251914 GTACTATCAGTCCAGCTAGTCACATTCATTCATCACAAAGACAAACACCCCGTGGCCACGCATAC
326 GAACCATCAGTCCAGCTAGTCACATTCATTCATCACAAAAACAAACACCCCGTGGCCACGCATAC
* * * * *
31251979 TTTTTATCAAACATGTAATTCGAATAAAAGGATATCATTTACCCATGTCTTAGGGATTGAATTCT
391 TTTTTATCAAACATGTAATGCCAATAAAAGCATATCATTTACCCATGTCTTAGGGAATAAATTCT
* ** * * *
31252044 ATTATTGTGAATGACGTTACATATTGTAGAAGTCGTATACCCAATCCTCCAGCTTTCAATTCCTT
456 ACTATTGTGAATGACGTTACATATTACAGAAGTCGTATACCCAATCCACCAACCTTCAATTCCTT
* * * ** *
31252109 ATTTGTTTGAACTCAGGCATTTACTTACATCAATATATACGAGTCATGCATACATAGCCCGTCAT
521 ATCTATTTGAACTCAGGCATTTACTTACATCAATATATACAAGTCACACATACATAGCCAGTCAT
* * * * *
31252174 CCACTCAATATTAAGGTATGCCAAACTTTGAATGTCACAAGTGTATAAATCCATAAACGGATTTA
586 CCACTCAAGATTAAGGTATGCCAAAATTTGAATGTCACAAGTGAATAAACCCATAAACGGATTCA
* * *
31252239 GGATATCTTCTTCTTAGGTCCAGTCTAATTTACTATCAGTCTAGCCACTCACATTCAT
651 AGATATCTTCTTCTTAGGTCCAATCTAATCTACTATCAGTCTAGCCACTCACATTCAT
* * *
31252297 TCATCACAAAGACGAACGACCTGTGGC-AATGTTTACTTTTTATCAACCATGTAATGCCAATGAA
1 TCATCACAAAGACGAACAACATGTGGCTAAT-TTTACTTTTCATCAACCATGTAATGCCAATGAA
* * * * * * * *
31252361 AGGATATCGTTTACTCATGTCTC-GAGCAATGAATTCCACTATTGTGAATGGCATTACATATTGC
65 AGGATATCATTTACCCATGTCTCAG-GCAATGAAATACACTATTGTAAATGACATTACATACTAC
* * * * *
31252425 AGAAGTCGTATACCCAATGCA-CTAGCCTTCAATTCCTTATCTATTTGAACTGAGGCTTTTATTT
129 AGAAGTCGTATACCCAACGCATC-AACCTTCAATTCCTTATCCATTTGAACTCAGGCTTTTACTT
** * * *** * *
31252489 ACATCAATA-TATATGAGTCATGCATACGTAG-CTTGTGATCCACTCAGGATTAAGGTATGCCAT
193 ACATCAA-AGTATACAAGTCACGCATACATAGTC-TACCATCCACTCAGAATTAAGGTATGCCAC
* * *
31252552 ACTTTAAATGTCACAAGTGAATAAATCTA-AAAATGGATTCAGGATCTCTTCTTCTTAGGTCCAG
256 ACTTTAAATCTCACAAGTGAATAAATCCATAAAA-GCATTCAGGATCTCTTCTTCTTAGGTCCAG
* * * * **
31252616 TTTAATGAACCATCAGTCTAGTTAGTCACATTCATTCATCATAAAAATGAACGA-CCCGTGGCCA
320 TCTAATGAACCATCAGTCCAGCTAGTCACATTCATTCATCACAAAAACAAAC-ACCCCGTGGCCA
** * * *
31252680 CGTTTACTTTTTATCAACCATGTAATGCCAATGAAAGCATATCATTTACCCATGTC-TCGGGTAA
384 CGCATACTTTTTATCAAACATGTAATGCCAATAAAAGCATATCATTTACCCATGTCTTAGGG-AA
* *
31252744 TAAATT-TCACTATTGTGAATGAC-TCTACATATTACAGAAGTTGTATACCCAATGCACCAACCT
448 TAAATTCT-ACTATTGTGAATGACGT-TACATATTACAGAAGTCGTATACCCAATCCACCAACCT
* * * *
31252807 TCAATTCCTTATCTATTTGAACTCA-GTATTTTACTTACTTCAGTGTATACAAGTCACACATACA
511 TCAATTCCTTATCTATTTGAACTCAGGCA-TTTACTTACATCAATATATACAAGTCACACATACA
* * * *
31252871 TAGTCAGTCATCTACTTAGGATTAAGGTATGCCAAAATTTGAATGTCACAAGTGAATAAACCCAT
575 TAGCCAGTCATCCACTCAAGATTAAGGTATGCCAAAATTTGAATGTCACAAGTGAATAAACCCAT
* * * * *
31252936 AAATGGATTCAAGATCTCTTTTTCTTGGGTCCAATCTGATCTACTATCAGTC
640 AAACGGATTCAAGATATCTTCTTCTTAGGTCCAATCTAATCTACTATCAGTC
31252988 CAATCAGTCA
Statistics
Matches: 580, Mismatches: 100, Indels: 22
0.83 0.14 0.03
Matches are distributed among these distances:
707 16 0.03
708 562 0.97
709 2 0.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (708 bp):
TCATCACAAAGACGAACAACATGTGGCTAATTTTACTTTTCATCAACCATGTAATGCCAATGAAA
GGATATCATTTACCCATGTCTCAGGCAATGAAATACACTATTGTAAATGACATTACATACTACAG
AAGTCGTATACCCAACGCATCAACCTTCAATTCCTTATCCATTTGAACTCAGGCTTTTACTTACA
TCAAAGTATACAAGTCACGCATACATAGTCTACCATCCACTCAGAATTAAGGTATGCCACACTTT
AAATCTCACAAGTGAATAAATCCATAAAAGCATTCAGGATCTCTTCTTCTTAGGTCCAGTCTAAT
GAACCATCAGTCCAGCTAGTCACATTCATTCATCACAAAAACAAACACCCCGTGGCCACGCATAC
TTTTTATCAAACATGTAATGCCAATAAAAGCATATCATTTACCCATGTCTTAGGGAATAAATTCT
ACTATTGTGAATGACGTTACATATTACAGAAGTCGTATACCCAATCCACCAACCTTCAATTCCTT
ATCTATTTGAACTCAGGCATTTACTTACATCAATATATACAAGTCACACATACATAGCCAGTCAT
CCACTCAAGATTAAGGTATGCCAAAATTTGAATGTCACAAGTGAATAAACCCATAAACGGATTCA
AGATATCTTCTTCTTAGGTCCAATCTAATCTACTATCAGTCTAGCCACTCACATTCAT
Found at i:31252999 original size:354 final size:354
Alignment explanation
Indices: 31251589--31253000 Score: 1543
Period size: 354 Copynumber: 4.0 Consensus size: 354
31251579 ATCAAGTCAC
* ** * * * * *
31251589 TCATCACAAAGACGAACAACATGTGGCTACTTTTACTTTTCATCAATCATGTAATGCCAATGAGA
1 TCATCACAAAGACGAACGACCCGTGGCCACGTTTACTTTTTATCAACCATGTAATGCCAATGAAA
* * ** * * * ** *
31251654 GGATATCATTTACCCATGTCTCAGGCT-ATGAAATACGTTGTTTTAAATGATGTTACATACTACA
66 GGATATCATTTACCCATGTCTC-GGGTAAT-AAATTCACTATTGTGAATGACATTACATATTACA
* * * * * *
31251718 GAAGTCGTATACCCAACGCATCAACTTTCAATTCCTTTTCCATTTGAACTCAGGCTTTTACTTAC
129 GAAGTCGTATACCCAATGCACCAACCTTCAATTCCTTATCTATTTGAACTCAGGATTTTACTTAC
* * * *
31251783 ATCAA-AGTATACAAGTCACGCATACATAGTCTA-CCATCCACTCAGAATTAAGGTATGTCACAC
194 ATCAATA-TATACAAGTCACGCATACATAGTCTAGTCATCCACTCAGGATTAAGGTATGCCAAAC
* * * * *
31251846 TTTTAATCTCACAAGTGAATAAATCCATAAGA-GCATTTAGGATCTCTTCTTCTTAGGTCTAGTC
258 TTTGAATGTCACAAGTGAATAAATCCATAA-ATGGATTCAGGATCTCTTCTTCTTAGGTCCAGTC
* *
31251910 TCATGTACTATCAGTCC-AGCTAGTCACATTCAT
322 TAATGTACTATCAGTCCAATC-AGTCACATTCAT
* ** * * * *
31251943 TCATCACAAAGACAAAC-ACCCCGTGGCCACGCATACTTTTTATCAAACATGTAATTCGAATAAA
1 TCATCACAAAGACGAACGA-CCCGTGGCCACGTTTACTTTTTATCAACCATGTAATGCCAATGAA
* * * * * **
31252007 AGGATATCATTTACCCATGTCTTAGGG-ATTGAATTCTATTATTGTGAATGACGTTACATATTGT
65 AGGATATCATTTACCCATGTC-TCGGGTAATAAATTC-ACTATTGTGAATGACATTACATATTAC
* * * * * *
31252071 AGAAGTCGTATACCCAATCCTCCAGCTTTCAATTCCTTATTTGTTTGAACTCAGGCA-TTTACTT
128 AGAAGTCGTATACCCAATGCACCAACCTTCAATTCCTTATCTATTTGAACTCAGG-ATTTTACTT
* * ** **
31252135 ACATCAATATATACGAGTCATGCATACATAG-CCCGTCATCCACTCAATATTAAGGTATGCCAAA
192 ACATCAATATATACAAGTCACGCATACATAGTCTAGTCATCCACTCAGGATTAAGGTATGCCAAA
* * * *
31252199 CTTTGAATGTCACAAGTGTATAAATCCATAAACGGATTTAGGATATCTTCTTCTTAGGTCCAGTC
257 CTTTGAATGTCACAAGTGAATAAATCCATAAATGGATTCAGGATCTCTTCTTCTTAGGTCCAGTC
* * ** *
31252264 TAATTTACTATCAGTCTAGCCACTCACATTCAT
322 TAATGTACTATCAGTCCAATCAGTCACATTCAT
* * *
31252297 TCATCACAAAGACGAACGACCTGTGGCAATGTTTACTTTTTATCAACCATGTAATGCCAATGAAA
1 TCATCACAAAGACGAACGACCCGTGGCCACGTTTACTTTTTATCAACCATGTAATGCCAATGAAA
* * * * * * *
31252362 GGATATCGTTTACTCATGTCTCGAGCAATGAATTCCACTATTGTGAATGGCATTACATATTGCAG
66 GGATATCATTTACCCATGTCTCGGGTAATAAATT-CACTATTGTGAATGACATTACATATTACAG
* * * * *
31252427 AAGTCGTATACCCAATGCACTAGCCTTCAATTCCTTATCTATTTGAACTGAGGCTTTTATTTACA
130 AAGTCGTATACCCAATGCACCAACCTTCAATTCCTTATCTATTTGAACTCAGGATTTTACTTACA
** * * * * *
31252492 TCAATATATATGAGTCATGCATACGTAG-CTTGTGATCCACTCAGGATTAAGGTATGCCATACTT
195 TCAATATATACAAGTCACGCATACATAGTCTAGTCATCCACTCAGGATTAAGGTATGCCAAACTT
* * * *
31252556 TAAATGTCACAAGTGAATAAATCTAAAAATGGATTCAGGATCTCTTCTTCTTAGGTCCAGTTTAA
260 TGAATGTCACAAGTGAATAAATCCATAAATGGATTCAGGATCTCTTCTTCTTAGGTCCAGTCTAA
* * * * *
31252621 TGAACCATCAGTCTAGTTAGTCACATTCAT
325 TGTACTATCAGTCCAATCAGTCACATTCAT
* * *
31252651 TCATCATAAAAATGAACGACCCGTGGCCACGTTTACTTTTTATCAACCATGTAATGCCAATGAAA
1 TCATCACAAAGACGAACGACCCGTGGCCACGTTTACTTTTTATCAACCATGTAATGCCAATGAAA
*
31252716 GCATATCATTTACCCATGTCTCGGGTAATAAATTTCACTATTGTGAATGAC-TCTACATATTACA
66 GGATATCATTTACCCATGTCTCGGGTAATAAA-TTCACTATTGTGAATGACAT-TACATATTACA
* *
31252780 GAAGTTGTATACCCAATGCACCAACCTTCAATTCCTTATCTATTTGAACTCAGTATTTTACTTAC
129 GAAGTCGTATACCCAATGCACCAACCTTCAATTCCTTATCTATTTGAACTCAGGATTTTACTTAC
* * * * * * *
31252845 TTCAGTGTATACAAGTCACACATACATAGTC-AGTCATCTACTTAGGATTAAGGTATGCCAAAAT
194 ATCAATATATACAAGTCACGCATACATAGTCTAGTCATCCACTCAGGATTAAGGTATGCCAAACT
* * * * * *
31252909 TTGAATGTCACAAGTGAATAAACCCATAAATGGATTCAAGATCTCTTTTTCTTGGGTCCAATCTG
259 TTGAATGTCACAAGTGAATAAATCCATAAATGGATTCAGGATCTCTTCTTCTTAGGTCCAGTCTA
*
31252974 ATCTACTATCAGTCCAATCAGTCACAT
324 ATGTACTATCAGTCCAATCAGTCACAT
31253001 CTAAGTCTCT
Statistics
Matches: 884, Mismatches: 158, Indels: 32
0.82 0.15 0.03
Matches are distributed among these distances:
353 11 0.01
354 865 0.98
355 8 0.01
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.33
Consensus pattern (354 bp):
TCATCACAAAGACGAACGACCCGTGGCCACGTTTACTTTTTATCAACCATGTAATGCCAATGAAA
GGATATCATTTACCCATGTCTCGGGTAATAAATTCACTATTGTGAATGACATTACATATTACAGA
AGTCGTATACCCAATGCACCAACCTTCAATTCCTTATCTATTTGAACTCAGGATTTTACTTACAT
CAATATATACAAGTCACGCATACATAGTCTAGTCATCCACTCAGGATTAAGGTATGCCAAACTTT
GAATGTCACAAGTGAATAAATCCATAAATGGATTCAGGATCTCTTCTTCTTAGGTCCAGTCTAAT
GTACTATCAGTCCAATCAGTCACATTCAT
Found at i:31254230 original size:15 final size:15
Alignment explanation
Indices: 31254210--31254238 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31254200 TGTGGCAAAG
31254210 TTTGATATGTCATAA
1 TTTGATATGTCATAA
31254225 TTTGATATGTCATA
1 TTTGATATGTCATA
31254239 GTTTTTCGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.48
Consensus pattern (15 bp):
TTTGATATGTCATAA
Found at i:31254582 original size:21 final size:19
Alignment explanation
Indices: 31254536--31254583 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
31254526 ACACGCATTG
31254536 CCTGTGTTACAACACACAC
1 CCTGTGTTACAACACACAC
*
31254555 CTTGTGTTGAC-ACACAGCAGC
1 CCTGTGTT-ACAACACA-CA-C
31254576 CCTGTGTT
1 CCTGTGTT
31254584 CATCCATAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 12 0.50
20 4 0.17
21 8 0.33
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (19 bp):
CCTGTGTTACAACACACAC
Found at i:31266847 original size:15 final size:15
Alignment explanation
Indices: 31266827--31266855 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31266817 TGTGGGAGAG
31266827 TTTGATATGTCATAA
1 TTTGATATGTCATAA
31266842 TTTGATATGTCATA
1 TTTGATATGTCATA
31266856 GTTTTTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.48
Consensus pattern (15 bp):
TTTGATATGTCATAA
Found at i:31272043 original size:9 final size:9
Alignment explanation
Indices: 31272026--31272062 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
31272016 TGAGTTTTCG
31272026 AATTCGAAT
1 AATTCGAAT
*
31272035 AACTCGAAT
1 AATTCGAAT
*
31272044 AATTTGAAT
1 AATTCGAAT
31272053 AATTCGAAT
1 AATTCGAAT
31272062 A
1 A
31272063 TCAAACTACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:31289550 original size:110 final size:110
Alignment explanation
Indices: 31289369--31289946 Score: 1014
Period size: 110 Copynumber: 5.3 Consensus size: 110
31289359 GTTTATCAGA
* * * *
31289369 TTTCTAAACGTAAAACATTGCCTTATTTTGAAATTTTTTTAAAGGATATTTAGCCATTTGGTTGA
1 TTTCCAAACGCAAAACATTGCCTTATTTT-AAATTTTTTAAAAGGATATTAAGCCATTTGGTTGA
*
31289434 ATGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAAT
65 ACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAAT
*
31289480 TTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAA
1 TTTCCAAACGCAAAACATTGCCTTATTTTAAATTTTTTAAAAGGATATTAAGCCATTTGGTTGAA
31289545 CGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAAT
66 CGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAAT
*
31289590 TTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAA
1 TTTCCAAACGCAAAACATTGCCTTATTTTAAATTTTTTAAAAGGATATTAAGCCATTTGGTTGAA
31289655 CGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAAT
66 CGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAAT
* *
31289700 TTCCCAAACGCAAAACATTGCCTTATTTTAAATTTTTTAAAAGGATATTAAGTCATTTGGTTGAA
1 TTTCCAAACGCAAAACATTGCCTTATTTTAAATTTTTTAAAAGGATATTAAGCCATTTGGTTGAA
31289765 CGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAAT
66 CGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAAT
* *
31289810 TTCCCAAACGCAAAACATTGCCTTATTTTAAATTTTTTAAAAGGATATTAAGTCATTTGGTTGAA
1 TTTCCAAACGCAAAACATTGCCTTATTTTAAATTTTTTAAAAGGATATTAAGCCATTTGGTTGAA
*
31289875 CGAGAAAAATCGACACCCAGCACCTTAGGGCATATTTTCTCGAA-
66 CGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAAT
* *
31289919 TTTCCAAACGCAAAATATTACCTTATTT
1 TTTCCAAACGCAAAACATTGCCTTATTT
31289947 AGGAAAAAAG
Statistics
Matches: 454, Mismatches: 13, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
109 25 0.06
110 402 0.89
111 27 0.06
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Consensus pattern (110 bp):
TTTCCAAACGCAAAACATTGCCTTATTTTAAATTTTTTAAAAGGATATTAAGCCATTTGGTTGAA
CGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAAT
Found at i:31290545 original size:20 final size:20
Alignment explanation
Indices: 31290481--31290546 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
31290471 TGTATGCATA
* *
31290481 TATGTAAAAATTTAAGATGTA
1 TATGTAAAAATATAA-ATGTG
* * * *
31290502 TATAT-AAATTATATATGAG
1 TATGTAAAAATATAAATGTG
*
31290521 AATGTAAAAATATAAATGTG
1 TATGTAAAAATATAAATGTG
31290541 TATGTA
1 TATGTA
31290547 TTTATAAAAA
Statistics
Matches: 32, Mismatches: 12, Indels: 3
0.68 0.26 0.06
Matches are distributed among these distances:
19 6 0.19
20 22 0.69
21 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (20 bp):
TATGTAAAAATATAAATGTG
Found at i:31291635 original size:14 final size:14
Alignment explanation
Indices: 31291616--31291659 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
31291606 AAATAGTTAG
31291616 AAGAGAAAAAAATA
1 AAGAGAAAAAAATA
31291630 AAGAGAAAAAAA-A
1 AAGAGAAAAAAATA
*
31291643 AAGAAAAAGAAAATA
1 AAGAGAAA-AAAATA
31291658 AA
1 AA
31291660 TATACCGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 8 0.30
14 16 0.59
15 3 0.11
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05
Consensus pattern (14 bp):
AAGAGAAAAAAATA
Found at i:31291643 original size:17 final size:17
Alignment explanation
Indices: 31291621--31291655 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31291611 GTTAGAAGAG
* *
31291621 AAAAAAATAAAGAGAAA
1 AAAAAAAGAAAAAGAAA
31291638 AAAAAAAGAAAAAGAAA
1 AAAAAAAGAAAAAGAAA
31291655 A
1 A
31291656 TAAATATACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAAAAAGAAA
Found at i:31294667 original size:54 final size:47
Alignment explanation
Indices: 31294548--31294679 Score: 156
Period size: 47 Copynumber: 2.7 Consensus size: 47
31294538 AAGAAAGGAT
*
31294548 CAAGGTGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAAAGAC
1 CAAGGTGAAAACCCGCAAAGGGCGCCTTGAGTCCTAAAAAAAAAGAC
* * *
31294595 CAAAGTGAAAACCTGCAAAGGGTGCCTTGAGTCCTAAAAAAAAAAGAAAGAGGC
1 CAAGGTGAAAACCCGCAAAGGGCGCCTTGAGTCCT----AAAAAA-AAAGA--C
*
31294649 CAAGGTGAAAACCCGCAAATGGCGCCTTGAG
1 CAAGGTGAAAACCCGCAAAGGGCGCCTTGAG
31294680 ACCAAAGGGG
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
47 31 0.44
51 6 0.09
52 5 0.07
54 28 0.40
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.13
Consensus pattern (47 bp):
CAAGGTGAAAACCCGCAAAGGGCGCCTTGAGTCCTAAAAAAAAAGAC
Found at i:31296691 original size:43 final size:42
Alignment explanation
Indices: 31296643--31296769 Score: 172
Period size: 46 Copynumber: 3.0 Consensus size: 42
31296633 AGGGTAAATC
31296643 CAACAACCCAAGATTACCTTCTCCTCTTTTTAAATTCTTTTTT
1 CAACAACCCAAGATTA-CTTCTCCTCTTTTTAAATTCTTTTTT
31296686 CAACAACCCAAGATTATTATCTTCTCCTCTTTTTAAATTCTTTTTT
1 CAACAACCCAAG---ATTA-CTTCTCCTCTTTTTAAATTCTTTTTT
*
31296732 CAACAACCCAAGATTA----TCCTCTTTTTAAATTTTTTTTT
1 CAACAACCCAAGATTACTTCTCCTCTTTTTAAATTCTTTTTT
31296770 TCTAAGATAA
Statistics
Matches: 79, Mismatches: 2, Indels: 11
0.86 0.02 0.12
Matches are distributed among these distances:
38 21 0.27
43 16 0.20
46 42 0.53
ACGTcount: A:0.27, C:0.24, G:0.02, T:0.46
Consensus pattern (42 bp):
CAACAACCCAAGATTACTTCTCCTCTTTTTAAATTCTTTTTT
Found at i:31296721 original size:46 final size:46
Alignment explanation
Indices: 31296643--31296748 Score: 182
Period size: 46 Copynumber: 2.4 Consensus size: 46
31296633 AGGGTAAATC
31296643 CAACAACCCAAG---ATTACCTTCTCCTCTTTTTAAATTCTTTTTT
1 CAACAACCCAAGATTATTACCTTCTCCTCTTTTTAAATTCTTTTTT
*
31296686 CAACAACCCAAGATTATTATCTTCTCCTCTTTTTAAATTCTTTTTT
1 CAACAACCCAAGATTATTACCTTCTCCTCTTTTTAAATTCTTTTTT
31296732 CAACAACCCAAGATTAT
1 CAACAACCCAAGATTAT
31296749 CCTCTTTTTA
Statistics
Matches: 59, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
43 12 0.20
46 47 0.80
ACGTcount: A:0.29, C:0.26, G:0.03, T:0.42
Consensus pattern (46 bp):
CAACAACCCAAGATTATTACCTTCTCCTCTTTTTAAATTCTTTTTT
Found at i:31308176 original size:15 final size:15
Alignment explanation
Indices: 31308156--31308189 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
31308146 AATGTTACAA
31308156 TTTTCACTTTGATAC
1 TTTTCACTTTGATAC
31308171 TTTTCACTTTGATAC
1 TTTTCACTTTGATAC
31308186 TTTT
1 TTTT
31308190 ATCATGGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59
Consensus pattern (15 bp):
TTTTCACTTTGATAC
Found at i:31309018 original size:20 final size:20
Alignment explanation
Indices: 31308993--31309035 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
31308983 GGGGAGGAGT
* *
31308993 TAACATGTACCCATGATACA
1 TAACATCTACCAATGATACA
*
31309013 TAACATCTATCAATGATACA
1 TAACATCTACCAATGATACA
31309033 TAA
1 TAA
31309036 GTATTAGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (20 bp):
TAACATCTACCAATGATACA
Found at i:31317090 original size:15 final size:15
Alignment explanation
Indices: 31317066--31317096 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31317056 GTAAGATGAA
31317066 ATTTTAAATTTTGTT
1 ATTTTAAATTTTGTT
*
31317081 ATTTTTAATTTTGTT
1 ATTTTAAATTTTGTT
31317096 A
1 A
31317097 AATTTAATTA
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:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
ATTTTAAATTTTGTT
Found at i:31317102 original size:15 final size:15
Alignment explanation
Indices: 31317072--31317105 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
31317062 TGAAATTTTA
**
31317072 AATTTTGTTATTTTT
1 AATTTTGTTAAATTT
31317087 AATTTTGTTAAATTT
1 AATTTTGTTAAATTT
31317102 AATT
1 AATT
31317106 AATTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
AATTTTGTTAAATTT
Found at i:31319036 original size:16 final size:17
Alignment explanation
Indices: 31319005--31319038 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
31318995 CCCCGATGAG
31319005 ACGATTGATGTATTTTTT
1 ACGATTGA-GTATTTTTT
31319023 ACGATTGA-TATTTTTT
1 ACGATTGAGTATTTTTT
31319039 TTCTAAATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56
Consensus pattern (17 bp):
ACGATTGAGTATTTTTT
Found at i:31319040 original size:18 final size:18
Alignment explanation
Indices: 31319005--31319039 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31318995 CCCCGATGAG
*
31319005 ACGATTGATGTATTTTTT
1 ACGATTGATATATTTTTT
31319023 ACGATTGATAT-TTTTTT
1 ACGATTGATATATTTTTT
31319040 TCTAAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.23, C:0.06, G:0.14, T:0.57
Consensus pattern (18 bp):
ACGATTGATATATTTTTT
Found at i:31325175 original size:44 final size:44
Alignment explanation
Indices: 31325086--31325176 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 44
31325076 CGCTATATTG
*
31325086 GAATAGAGGCGTAATAGCAAATTAATTGTTTGGTTGAATGTAATA
1 GAATAGAGGCGTAATAG-AAATTAATTGTTTGGTTGAATGGAATA
* **
31325131 GAATAGAGGCGTAATAG-TATTCTTGTGTTTGGTTGAATGGAATA
1 GAATAGAGGCGTAATAGAAATTAAT-TGTTTGGTTGAATGGAATA
31325175 GA
1 GA
31325177 GGTGTAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
43 4 0.10
44 20 0.49
45 17 0.41
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (44 bp):
GAATAGAGGCGTAATAGAAATTAATTGTTTGGTTGAATGGAATA
Found at i:31325362 original size:14 final size:15
Alignment explanation
Indices: 31325323--31325364 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
31325313 TTTTAACATA
*
31325323 ATTATTATTAAATAT
1 ATTATAATTAAATAT
31325338 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
31325352 A-TATAATTTAATA
1 ATTATAATTAAATA
31325365 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:31325473 original size:16 final size:16
Alignment explanation
Indices: 31325429--31325475 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
31325419 TACAATAAAA
*
31325429 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
31325445 TATTATT-AAATATAT
1 TATAATTAAAATATAT
31325460 TATAATTAAAATATAT
1 TATAATTAAAATATAT
31325476 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:31325595 original size:18 final size:17
Alignment explanation
Indices: 31325574--31325608 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31325564 TTATTATTAA
*
31325574 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
31325592 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
31325609 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:31325738 original size:120 final size:120
Alignment explanation
Indices: 31325314--31325729 Score: 735
Period size: 120 Copynumber: 3.5 Consensus size: 120
31325304 TTAATCATAT
31325314 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* *
31325379 CAATATTCTTATATGAGTTTACTCAAATCATAATATATGATACAATAAAATATAA
66 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
31325434 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* *
31325499 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAA
66 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
*
31325554 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
*
31325619 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
* * *
31325674 TTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
31325730 TAAAATAATT
Statistics
Matches: 285, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
120 283 0.99
121 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
Found at i:31325780 original size:47 final size:46
Alignment explanation
Indices: 31325711--31325878 Score: 143
Period size: 47 Copynumber: 3.7 Consensus size: 46
31325701 TTAATTAAAA
*
31325711 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTTTCT
* * *
31325758 TATATGAATTTGTATAATTTAAAATAATTAT--TATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAAT-T-TTCT
* * * *
31325803 TA-AT-AATAATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
*
31325849 TATATGAATTTATACAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
31325879 ATATTAAATA
Statistics
Matches: 95, Mismatches: 14, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
43 3 0.03
44 22 0.23
45 9 0.09
46 8 0.08
47 46 0.48
48 7 0.07
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.46
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTTTCT
Found at i:31325783 original size:101 final size:93
Alignment explanation
Indices: 31325668--31325952 Score: 346
Period size: 91 Copynumber: 3.0 Consensus size: 93
31325658 ATACTATAAA
* * * *
31325668 ATATAATTTGAAATAATTAATATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATTTA
1 ATATAATTTAAAATAATTAATATTAAATATAATTTAA-TAATAATATATAATTTCATAAAATTT-
*
31325732 AAATAATTATAACTAATAAATTTTCTTATATGAATTT
64 ---T--CT-TAA-TAATAAATTTTCTTATATGAATTT
* *
31325769 GTATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAA--TTC
1 ATATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTC
*
31325832 TTGATAATAAATTTTCTTATATGAATTT
66 TTAATAATAAATTTTCTTATATGAATTT
* *
31325860 ATACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAA--TTC
1 ATATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTC
*
31325923 TTAATAATAAAATGTTCTTATATGAATTT
66 TTAATAAT-AAATTTTCTTATATGAATTT
31325952 A
1 A
31325953 CTAAAATCAA
Statistics
Matches: 168, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
91 90 0.54
92 22 0.13
93 1 0.01
95 1 0.01
99 1 0.01
100 3 0.02
101 50 0.30
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (93 bp):
ATATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTC
TTAATAATAAATTTTCTTATATGAATTT
Found at i:31325820 original size:44 final size:43
Alignment explanation
Indices: 31325770--31325912 Score: 130
Period size: 44 Copynumber: 3.2 Consensus size: 43
31325760 TATGAATTTG
31325770 TATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATA
1 TATAATTTAAAATAATTATTATTAAATATAATTTAATAAT-ATA
* * * *
31325814 TATAATTTCATAA-AATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAATTT-AAAATAATTATT-AT--TAAATATAAT-TTA-AT-AATATA
* *
31325861 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTATTATTAAATATAATTTAATAAT-ATA
31325905 TATAATTT
1 TATAATTT
31325913 CATAAAATTC
Statistics
Matches: 77, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
43 3 0.04
44 30 0.39
45 10 0.13
46 10 0.13
47 21 0.27
48 3 0.04
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTATTATTAAATATAATTTAATAATATA
Found at i:31325841 original size:91 final size:91
Alignment explanation
Indices: 31325745--31325952 Score: 353
Period size: 91 Copynumber: 2.3 Consensus size: 91
31325735 TAATTATAAC
* * *
31325745 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
31325810 AATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTAA
31325836 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
31325901 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
31325927 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
31325953 CTAAAATCAA
Statistics
Matches: 110, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
91 90 0.82
92 20 0.18
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:31325927 original size:47 final size:47
Alignment explanation
Indices: 31325792--31325933 Score: 143
Period size: 47 Copynumber: 3.1 Consensus size: 47
31325782 TAATTATTAT
* *
31325792 TAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAA
1 TAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAA
* * * ** *
31325839 TAAAT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATAT
1 TAAATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAA
31325883 TAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAA
1 TAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAA
31325930 TAAA
1 TAAA
31325934 ATGTTCTTAT
Statistics
Matches: 72, Mismatches: 14, Indels: 18
0.69 0.13 0.17
Matches are distributed among these distances:
44 20 0.28
45 13 0.18
46 13 0.18
47 26 0.36
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (47 bp):
TAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAA
Found at i:31329394 original size:96 final size:96
Alignment explanation
Indices: 31329230--31329548 Score: 638
Period size: 96 Copynumber: 3.3 Consensus size: 96
31329220 AAGAGATCGA
31329230 ATGTTTCGTATTTGTATCATTGACAGTTAATTTCTTTGTATGGTCACAGAAATCTTATTTAACAA
1 ATGTTTCGTATTTGTATCATTGACAGTTAATTTCTTTGTATGGTCACAGAAATCTTATTTAACAA
31329295 ATATTAATTTCTTTACCATTCGACTCAACAG
66 ATATTAATTTCTTTACCATTCGACTCAACAG
31329326 ATGTTTCGTATTTGTATCATTGACAGTTAATTTCTTTGTATGGTCACAGAAATCTTATTTAACAA
1 ATGTTTCGTATTTGTATCATTGACAGTTAATTTCTTTGTATGGTCACAGAAATCTTATTTAACAA
31329391 ATATTAATTTCTTTACCATTCGACTCAACAG
66 ATATTAATTTCTTTACCATTCGACTCAACAG
31329422 ATGTTTCGTATTTGTATCATTGACAGTTAATTTCTTTGTATGGTCACAGAAATCTTATTTAACAA
1 ATGTTTCGTATTTGTATCATTGACAGTTAATTTCTTTGTATGGTCACAGAAATCTTATTTAACAA
31329487 ATATTAATTTCTTTACCATTCGACTCAACAG
66 ATATTAATTTCTTTACCATTCGACTCAACAG
31329518 ATGTTTCGTATTTGTATCATTGACAGTTAAT
1 ATGTTTCGTATTTGTATCATTGACAGTTAAT
31329549 AAACTGATGG
Statistics
Matches: 223, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 223 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (96 bp):
ATGTTTCGTATTTGTATCATTGACAGTTAATTTCTTTGTATGGTCACAGAAATCTTATTTAACAA
ATATTAATTTCTTTACCATTCGACTCAACAG
Found at i:31329422 original size:47 final size:47
Alignment explanation
Indices: 31329371--31329518 Score: 117
Period size: 47 Copynumber: 3.1 Consensus size: 47
31329361 TTGTATGGTC
31329371 ACAGAAATCTTATTTAACAAATATTAATTTCTTTACCATTCGACTCA
1 ACAGAAATCTTATTTAACAAATATTAATTTCTTTACCATTCGACTCA
** * * * * ** *
31329418 ACAGATGTTTCGTATTTGTATCATTGACAGTTAATTTCTTT-GTA-T-G-GTC-
1 ACAGA--AATCTTA-TT-TAACA--AATA-TTAATTTCTTTACCATTCGACTCA
31329467 ACAGAAATCTTATTTAACAAATATTAATTTCTTTACCATTCGACTCA
1 ACAGAAATCTTATTTAACAAATATTAATTTCTTTACCATTCGACTCA
31329514 ACAGA
1 ACAGA
31329519 TGTTTCGTAT
Statistics
Matches: 71, Mismatches: 18, Indels: 24
0.63 0.16 0.21
Matches are distributed among these distances:
42 11 0.15
43 3 0.04
44 1 0.01
45 5 0.07
46 4 0.06
47 14 0.20
49 9 0.13
50 4 0.06
51 5 0.07
52 1 0.01
53 3 0.04
54 11 0.15
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (47 bp):
ACAGAAATCTTATTTAACAAATATTAATTTCTTTACCATTCGACTCA
Found at i:31334332 original size:21 final size:20
Alignment explanation
Indices: 31334308--31334348 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
31334298 AAAAATATTA
31334308 TGAAAAAATATTGGTTCAAAC
1 TGAAAAAATATT-GTTCAAAC
**
31334329 TGAATCAATATTGTTCAAAC
1 TGAAAAAATATTGTTCAAAC
31334349 ATTACACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (20 bp):
TGAAAAAATATTGTTCAAAC
Found at i:31334994 original size:187 final size:187
Alignment explanation
Indices: 31334679--31335053 Score: 651
Period size: 187 Copynumber: 2.0 Consensus size: 187
31334669 GCAAAAATCC
* * * *
31334679 AAAATTTATGGGCCAAGTTCTTTGATAAATTCCATCCAGAATTAGACCAAAAACACATATACAAA
1 AAAATTTATGGCCCAAGTTATTTGATAAATTCCATCCAGAATCAGACCAAAAACACATACACAAA
* * *
31334744 ATAATCTATTTCTTTTCAAATTTGTGTATTTCTTGGATTTTTTCCTAGAATTATGCTTATGAACA
66 ACAATCTATTTCTTTTCAAATTTGTGTATCTCTTGGATTGTTTCCTAGAATTATGCTTATGAACA
31334809 AGATCCATACATGAGAATCCTATTGTTAGTTCAAAATTTTAGAACGAAATGGTGGGA
131 AGATCCATACATGAGAATCCTATTGTTAGTTCAAAATTTTAGAACGAAATGGTGGGA
*
31334866 AAAATTTATGGCCCAAGTTATTTGATAAATTCCATCTAGAATCAGACCAAAAACACATACACAAA
1 AAAATTTATGGCCCAAGTTATTTGATAAATTCCATCCAGAATCAGACCAAAAACACATACACAAA
31334931 ACAATCTATTTCTTTTCAAATTTGTGTATCTCTTGGATTGTTTCCTAGAATTATGCTTATGAACA
66 ACAATCTATTTCTTTTCAAATTTGTGTATCTCTTGGATTGTTTCCTAGAATTATGCTTATGAACA
* * *
31334996 AGATTCATACATGAGAATCTTATTGTTAGTTCAAAATTTTAGAAGGAAATGGTGGGA
131 AGATCCATACATGAGAATCCTATTGTTAGTTCAAAATTTTAGAACGAAATGGTGGGA
31335053 A
1 A
31335054 TCCTATTGTA
Statistics
Matches: 177, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
187 177 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (187 bp):
AAAATTTATGGCCCAAGTTATTTGATAAATTCCATCCAGAATCAGACCAAAAACACATACACAAA
ACAATCTATTTCTTTTCAAATTTGTGTATCTCTTGGATTGTTTCCTAGAATTATGCTTATGAACA
AGATCCATACATGAGAATCCTATTGTTAGTTCAAAATTTTAGAACGAAATGGTGGGA
Found at i:31335864 original size:22 final size:22
Alignment explanation
Indices: 31335836--31335912 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
31335826 CCAAAAAATT
31335836 ATCTCCTAAATTTTAGCATCTA
1 ATCTCCTAAATTTTAGCATCTA
** * * *
31335858 ATCTCCT-AATTAAACCAAAACATT
1 ATCTCCTAAATTTTAGC--ATC-TA
*
31335882 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAATTTTAGCATCTA
31335904 ATCTCCTAA
1 ATCTCCTAA
31335913 TTAAAAGAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
21 6 0.15
22 17 0.43
23 4 0.10
24 8 0.20
25 5 0.12
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (22 bp):
ATCTCCTAAATTTTAGCATCTA
Found at i:31335873 original size:46 final size:46
Alignment explanation
Indices: 31335823--31335917 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
31335813 ACAAAGATAG
*
31335823 AAACCAAAAAATTATCTCCTAAATTTTAGCATCTAATCTCCTAATT
1 AAACCAAAAAATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
*
31335869 AAACCAAAACATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAAAATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
31335915 AAA
1 AAA
31335918 AGAAAAGAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.33
Consensus pattern (46 bp):
AAACCAAAAAATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
Found at i:31339862 original size:46 final size:46
Alignment explanation
Indices: 31339811--31339905 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
31339801 ACAAAGATAG
*
31339811 AAACCAAAAAATTATCTCCTAAATTTTAGCATCTAATCTCCTAATT
1 AAACCAAAAAATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
* *
31339857 AAACCAAAACATTTTCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAAAATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
31339903 AAA
1 AAA
31339906 AGAAAAGAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.41, C:0.23, G:0.02, T:0.34
Consensus pattern (46 bp):
AAACCAAAAAATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
Found at i:31344965 original size:23 final size:21
Alignment explanation
Indices: 31344939--31344980 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
31344929 AATGCAATAT
31344939 TAAAAATGCTAACTAAAATGTCA
1 TAAAAATGC-AAC-AAAATGTCA
31344962 TAAAAATGCAACAAAATGT
1 TAAAAATGCAACAAAATGT
31344981 TACGTAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 3 0.16
23 9 0.47
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.24
Consensus pattern (21 bp):
TAAAAATGCAACAAAATGTCA
Found at i:31347954 original size:32 final size:32
Alignment explanation
Indices: 31347917--31347979 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
31347907 TATAATAAAG
*
31347917 TAGTTAGACTAATGTCGTTATAAAAGTTGAGA
1 TAGTTAAACTAATGTCGTTATAAAAGTTGAGA
31347949 TAGTTAAACTAATGTCGTTATAAAAGTTGAG
1 TAGTTAAACTAATGTCGTTATAAAAGTTGAG
31347980 GTACCAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (32 bp):
TAGTTAAACTAATGTCGTTATAAAAGTTGAGA
Found at i:31348795 original size:122 final size:122
Alignment explanation
Indices: 31348575--31348947 Score: 638
Period size: 122 Copynumber: 3.0 Consensus size: 122
31348565 TTAGGGTTTT
* * * * *
31348575 TAGGTCTTGGAAAAAATAATTTTGAGTTGATGTTTCTAATCAAATATTATAAAATCGCTTCTAGC
1 TAGGTCATGG-AAAAATAATTTT--TTTGAAGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGC
31348640 AGGATGCTATTTAAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGATTTTGCTACAG
63 AGGATGCTATTTAAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGATTTTGCTACAG
31348700 TAGGTCATGGAAAAATAATTTTTTTGAAGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCAGG
1 TAGGTCATGGAAAAATAATTTTTTTGAAGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCAGG
31348765 ATGCTATTTAAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGATTTTGCTACAG
66 ATGCTATTTAAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGATTTTGCTACAG
31348822 TAGGTCATGGAAAAATAATTTTTTTGAAGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCAGG
1 TAGGTCATGGAAAAATAATTTTTTTGAAGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCAGG
* * *
31348887 ATGCTATTTGAGAAGAATTTGTGAAAATCACGCCCTCGTGGACGCGCTTTTGCTACAG
66 ATGCTATTTAAGAAGAATTTGTG-AAATCGCGCCCTCGTGGACGCGATTTTGCTACAG
31348945 TAG
1 TAG
31348948 CATGTTTGGG
Statistics
Matches: 239, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
122 183 0.77
123 35 0.15
124 12 0.05
125 9 0.04
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (122 bp):
TAGGTCATGGAAAAATAATTTTTTTGAAGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCAGG
ATGCTATTTAAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGATTTTGCTACAG
Found at i:31352161 original size:115 final size:115
Alignment explanation
Indices: 31351958--31352431 Score: 849
Period size: 115 Copynumber: 4.1 Consensus size: 115
31351948 TAAGTTTGTG
* *
31351958 AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAA
1 AAATTAGTAATTGATAAATTGTATTAATGATTAGT-AAAATTATCAAATTATATAAAATTATTAA
31352023 TTTTTAGTACCAGTCAAAACATTTTTCTAAATCTAACATTATGTGAATGTA
65 TTTTTAGTACCAGTCAAAACATTTTTCTAAATCTAACATTATGTGAATGTA
31352074 AAATTAGTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAAT
1 AAATTAGTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAAT
31352139 TTTTAGTACCAGTCAAAACATTTTTCTAAATCTAACATTATGTGAATGTA
66 TTTTAGTACCAGTCAAAACATTTTTCTAAATCTAACATTATGTGAATGTA
31352189 AAATTAGTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAAT
1 AAATTAGTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAAT
31352254 TTTTAGTACCAGTCAAAACATTTTTCTAAATCTAACATTATGTGAATGTA
66 TTTTAGTACCAGTCAAAACATTTTTCTAAATCTAACATTATGTGAATGTA
31352304 AAATTAGTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAAT
1 AAATTAGTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAAT
* * ** * *
31352369 TGTCAGTACCAGGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
66 TTTTAGTACCA-GTCAAAACATTTTTCTAAATCTAACATTATGTGAATGTA
*
31352420 AAATTATTAATT
1 AAATTAGTAATT
31352432 TAGTTTAGGG
Statistics
Matches: 348, Mismatches: 9, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
115 269 0.77
116 79 0.23
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (115 bp):
AAATTAGTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAAT
TTTTAGTACCAGTCAAAACATTTTTCTAAATCTAACATTATGTGAATGTA
Found at i:31352457 original size:23 final size:23
Alignment explanation
Indices: 31352425--31353000 Score: 335
Period size: 23 Copynumber: 24.1 Consensus size: 23
31352415 AAGTAAAATT
* *
31352425 ATTAATTTAGTTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
31352448 ATTAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
* *
31352471 ATTTAATTAGATTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
*** *
31352494 AGTT-AAGGGGGTCAGGGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
* **
31352517 AGT---TTAGGGTTTAAAGTTTTTA
1 ATTAAATTA-GG-TTAGGGTTTTTA
*
31352539 ATTTAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
* *
31352562 ATTTAATTAGGTTAGTGTTTTTAA
1 ATTAAATTAGGTTAGGGTTTTT-A
31352586 ATT-AATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
* *
31352608 ATTTAATTAAGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
** *
31352631 AGTTTAGGGTTTTTAAGTTTAGGG-TTTTA
1 A--TTA----AATT-AGGTTAGGGTTTTTA
31352660 ATTAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
* *
31352683 AGT---TTAGGGTTTAGAGTTTTTA
1 ATTAAATTA-GG-TTAGGGTTTTTA
31352705 ATTAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
*
31352728 ATTTAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
31352751 AGTTAAGGGTAAATTAGGTTAGGGTTTTTA
1 A--T-----TAAATTAGGTTAGGGTTTTTA
** *
31352781 AGTTTAGGGTTTTTAAGTTTAGGG-TTTTA
1 A--TTA----AATT-AGGTTAGGGTTTTTA
31352810 ATTAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
** *
31352833 AGTTTAGGGTTTTTAAGTTTAGGG-TTTTA
1 A--TTA----AATT-AGGTTAGGGTTTTTA
31352862 ATTAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
*
31352885 AGT---TTAGAGTTTAGGGTTTTTA
1 ATTAAATTAG-G-TTAGGGTTTTTA
* *
31352907 AGTT-AATCAGGTTAGTGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
*** *
31352930 AGTT-AAGGGGGCTAGGGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
*
31352953 AGT---TTAGGGTTTAGGGTTTTTA
1 ATTAAATTA-GG-TTAGGGTTTTTA
31352975 ATTAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
31352998 ATT
1 ATT
31353001 TAAGGGTATT
Statistics
Matches: 438, Mismatches: 63, Indels: 104
0.72 0.10 0.17
Matches are distributed among these distances:
20 7 0.02
21 7 0.02
22 80 0.18
23 231 0.53
24 13 0.03
25 20 0.05
27 9 0.02
29 24 0.05
30 47 0.11
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (23 bp):
ATTAAATTAGGTTAGGGTTTTTA
Found at i:31352639 original size:15 final size:15
Alignment explanation
Indices: 31352614--31352860 Score: 122
Period size: 15 Copynumber: 16.1 Consensus size: 15
31352604 TTTAATTTAA
31352614 TTAAG-TTAGGGTTT
1 TTAAGTTTAGGGTTT
31352628 TTAAGTTTAGGGTTT
1 TTAAGTTTAGGGTTT
31352643 TTAAGTTTAGGGTTTT
1 TTAAGTTTAGGG-TTT
*
31352659 AATTAAATTAGGTTAGGGTTT
1 --TT--A--AGTTTAGGGTTT
31352680 TTAAGTTTAGGG--T
1 TTAAGTTTAGGGTTT
**** *
31352693 TTAGAGTTTTTAATTAAA
1 TTA-AGTTTAGGGTT--T
*
31352711 TT-AGGTTAGGGTTT
1 TTAAGTTTAGGGTTT
*
31352725 TTAA-TTTA-----A
1 TTAAGTTTAGGGTTT
*
31352734 TT-AGGTTAGGGTTT
1 TTAAGTTTAGGGTTT
* **
31352748 TTAAGTTAAGGGTAAA
1 TTAAGTTTAGGGT-TT
*
31352764 TT-AGGTTAGGGTTT
1 TTAAGTTTAGGGTTT
31352778 TTAAGTTTAGGGTTT
1 TTAAGTTTAGGGTTT
31352793 TTAAGTTTAGGGTTTT
1 TTAAGTTTAGGG-TTT
*
31352809 AATTAAATTAGGTTAGGGTTT
1 --TT--A--AGTTTAGGGTTT
31352830 TTAAGTTTAGGGTTT
1 TTAAGTTTAGGGTTT
31352845 TTAAGTTTAGGGTTT
1 TTAAGTTTAGGGTTT
31352860 T
1 T
31352861 AATTAAATTA
Statistics
Matches: 175, Mismatches: 28, Indels: 59
0.67 0.11 0.23
Matches are distributed among these distances:
8 1 0.01
9 5 0.03
13 4 0.02
14 19 0.11
15 96 0.55
16 14 0.08
17 2 0.01
18 6 0.03
19 4 0.02
20 2 0.01
21 6 0.03
22 16 0.09
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (15 bp):
TTAAGTTTAGGGTTT
Found at i:31352668 original size:52 final size:52
Alignment explanation
Indices: 31352596--31352896 Score: 369
Period size: 52 Copynumber: 5.9 Consensus size: 52
31352586 ATTAATTAGG
* *
31352596 TTAGGGTTTTTAATTTAATTAAGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGT
1 TTAGGG-TTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGT
31352649 TTAGGGTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGG--TTT-AG-
1 TTAGGGTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGT
* * *
31352697 --A-GTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTTA-----ATT-AGG
1 TTAGGGTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGT
31352739 TTAGGGTTTTTAAGTTAAGGGTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGT
1 TTAGGG-TTTTAA--T-----TAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGT
31352799 TTAGGGTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGT
1 TTAGGGTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGT
*
31352851 TTAGGGTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGAGTTT
1 TTAGGGTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTT
31352897 AGGGTTTTTA
Statistics
Matches: 221, Mismatches: 8, Indels: 39
0.82 0.03 0.15
Matches are distributed among these distances:
41 4 0.02
44 5 0.02
45 31 0.14
46 7 0.03
48 1 0.00
49 2 0.01
50 3 0.01
52 119 0.54
53 28 0.13
54 4 0.02
57 1 0.00
59 8 0.04
60 8 0.04
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.50
Consensus pattern (52 bp):
TTAGGGTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGT
Found at i:31352704 original size:166 final size:161
Alignment explanation
Indices: 31352426--31353003 Score: 184
Period size: 166 Copynumber: 3.5 Consensus size: 161
31352416 AGTAAAATTA
* * *
31352426 TTAATTTAGTTTAGGGTTTTT-AATTAAATTAGGTTAGGGTTTTTAATTTAATT-AGATTAGGGT
1 TTAA-TTAGGTTAGGGTTTTTAAATTAATTTAGGTTAGGGTTTTTAATTAAATTAAG-TTAGGGT
* *** * * * * * ** *
31352489 TTTTAAGTTAAGGGGGTCAGGGTTTTTAAGTTTAGG-GTTTAAAGTTTTTAA-TTTAATTAGG-T
64 TTTTAATTTAATTAGATTAGGGTTTTTAAGTTAAGGAGGTCAGGGTTTTTAAGTTT-A--GGGTT
** * * *
31352551 TAGGGTTTTTAATTTAATTAGGTTAGTGTTTTTAAA
126 TAAAGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT
* * **
31352587 TTAATTAGGTTAGGGTTTTTAATTTAA-TTAAGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGTTT
1 TTAATTAGGTTAGGGTTTTTAAATTAATTTAGGTTAGGGTTTTTAA--TTA----AATTAAG-TT
* * * * * * *
31352651 AGGG-TTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG-GTTTAGAGTTTTTAATTAAATTA
59 AGGGTTTTTAATTTAATTAGATTAGGGTTTTTAAGTTAAGGAGGTCAGGGTTTTTAAGT---TTA
** *
31352714 -GG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGT
121 GGGTTTAAAGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-T
* * *
31352754 TAAGGGTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGTTTAGGG-TTTTAATTAAATT
1 T-----T-AATTAGGTTAGGGTTTTTAA-ATTA----ATTT-AGGTTAGGGTTTTTAATTAAATT
* * * ** *
31352818 AGGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGTTTAGGG-TTTTAA-TTAAATTAGGTTAGGGTT
54 AAGTTAGGGTTTTTAA-TTTA-----ATT-AGATTAGGGTTTTTAAGTT-AAGGAGGTCAGGGTT
* ** * * *
31352881 TTTAAGTTTAGAGTTTAGGGTTTTTAAGTT-AATCAGGTTAGTGTTTTTAAG
111 TTTAAGTTTAGGGTTTAAAGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAT
*** * * *
31352932 TTAAGGGGGCTAGGGTTTTT--A--AGTTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAATTAGGTTAGGGTTTTTAAATTAATTTA-GG-TTAGGGTTTTTAATTAAATTAAGTTAGGGT
31352993 TTTTAATTTAA
64 TTTTAATTTAA
31353004 GGGTATTAAT
Statistics
Matches: 332, Mismatches: 43, Indels: 86
0.72 0.09 0.19
Matches are distributed among these distances:
160 32 0.10
161 9 0.03
162 3 0.01
163 4 0.01
164 10 0.03
165 29 0.09
166 83 0.25
167 11 0.03
169 1 0.00
170 2 0.01
172 21 0.06
173 31 0.09
174 7 0.02
177 6 0.02
178 4 0.01
179 48 0.14
180 31 0.09
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (161 bp):
TTAATTAGGTTAGGGTTTTTAAATTAATTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTT
TTAATTTAATTAGATTAGGGTTTTTAAGTTAAGGAGGTCAGGGTTTTTAAGTTTAGGGTTTAAAG
TTTTTAATTAAATTAGGTTAGGGTTTTTAAT
Found at i:31352728 original size:82 final size:89
Alignment explanation
Indices: 31352634--31352851 Score: 216
Period size: 98 Copynumber: 2.3 Consensus size: 89
31352624 GTTTTTAAGT
31352634 TTAGGGTTTTTAAGTTTAGGGTTTTAA-TT-A-AATTAGGTTAGGGTTTTTAAGTTTAGGG-TTT
1 TTAGGGTTTTTAAGTTTAGGGTTTTAAGTTAAGAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTT
*
31352695 -AG-A-GTTTTTAATTAAATTAGG
66 AAGTAGGGTTTTAATTAAATTAGG
*
31352716 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTAAATTAGGTTAGGGTTTTTA
1 TTAGGG---TT--TTT-A--AGTTTAGGG-TTTTAAGTTAA--G--AATTAGGTTAGGGTTTTTA
31352781 AGTTTAGGGTTTTTAAGTTTAGGGTTTTAATTAAATTAGG
53 AGTTTAGGG-TTTTAAG--TAGGGTTTTAATTAAATTAGG
31352821 TTAGGGTTTTTAAGTTTAGGGTTTTTAAGTT
1 TTAGGGTTTTTAAGTTTAGGG-TTTTAAGTT
31352852 TAGGGTTTTA
Statistics
Matches: 110, Mismatches: 3, Indels: 31
0.76 0.02 0.22
Matches are distributed among these distances:
82 6 0.05
85 2 0.02
87 3 0.03
88 1 0.01
90 8 0.07
91 6 0.05
92 2 0.02
93 1 0.01
97 18 0.16
98 28 0.25
99 1 0.01
100 6 0.05
101 2 0.02
102 2 0.02
104 1 0.01
105 23 0.21
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (89 bp):
TTAGGGTTTTTAAGTTTAGGGTTTTAAGTTAAGAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTT
AAGTAGGGTTTTAATTAAATTAGG
Found at i:31352848 original size:202 final size:193
Alignment explanation
Indices: 31352459--31353000 Score: 612
Period size: 202 Copynumber: 2.8 Consensus size: 193
31352449 TTAAATTAGG
* * * * * *
31352459 TTAGGGTTTTTAATTTAATTAGATTAGGGTTTTTAAGTTAAGGGGGTCAGGGTTTTTAAGT--TT
1 TTAGGG-TTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTA-GGGTTTAGGGTTTTTAATTAATT
* *
31352522 AGGGTTTAAAGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TT----TAATTAGGTTAGTGTTT
64 A-GG-TTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAGGGTAATTAGGTTAGGGTTT
*
31352582 TTAAATTAATTAGGTTAGGGTTTTTAATTTAATTAAGTTAGGGTTTTTAAGTTTAGGGTTTTTAA
127 TTAAATTAATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTTAAGTTTAGGGTTTTTAA
31352647 GT
192 GT
*
31352649 TTAGGGTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAGAGTTTTTAATTAAATTA
1 TTAGGGTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAATT-AATTA
*
31352714 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTAAATTAGGTTAGGGTTTT
65 GGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTT-AGGGT-AATTAGGTTAGGGTTTT
* * * *
31352779 TAAGTTTAGGGTTTTTAAGTTTAGGG-TTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGT
128 TAA-ATTA-----ATT-AGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTTAAGTTTAGGGT
31352843 TTTTAAGT
186 TTTTAAGT
* *
31352851 TTAGGGTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGAGTTTAGGGTTTTTAAGTTAATCA
1 TTAGGGTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAA-TTAATTA
* * *** *
31352916 GGTTAGTGTTTTTAAGTTAAGGGGGCTAGGGTTTTTAAGTTTAGGG----T---TTAGGGTTTTT
65 GGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAAG-TTAGGGTAATTAGGTTAGGGTTTTT
31352974 -AATTAAATTAGGTTAGGGTTTTTAATT
129 AAATT-AATTAGGTTAGGGTTTTTAATT
31353001 TAAGGGTATT
Statistics
Matches: 304, Mismatches: 27, Indels: 44
0.81 0.07 0.12
Matches are distributed among these distances:
187 8 0.03
188 25 0.08
189 65 0.21
190 10 0.03
191 3 0.01
192 2 0.01
193 2 0.01
194 11 0.04
195 1 0.00
196 19 0.06
197 4 0.01
202 142 0.47
203 12 0.04
ACGTcount: A:0.26, C:0.01, G:0.25, T:0.49
Consensus pattern (193 bp):
TTAGGGTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAATTAATTAG
GTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAGGGTAATTAGGTTAGGGTTTTTAA
ATTAATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGT
Found at i:31352966 original size:68 final size:68
Alignment explanation
Indices: 31352874--31353006 Score: 214
Period size: 68 Copynumber: 2.0 Consensus size: 68
31352864 TAAATTAGGT
*
31352874 TAGGGTTTTTAAGTTTAGAGTTTAGGGTTTTTAAGTT-AATCAGGTTAGTGTTTTTAAGTTAAGG
1 TAGGGTTTTTAAGTTTAGAGTTTAGGGTTTTTAA-TTAAATCAGGTTAGGGTTTTTAAGTTAAGG
31352938 GGGC
65 GGGC
* * *
31352942 TAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGGG
1 TAGGGTTTTTAAGTTTAGAGTTTAGGGTTTTTAATTAAATCAGGTTAGGGTTTTTAAGTTAAGGG
31353007 TATTAATGGT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 2 0.03
68 58 0.97
ACGTcount: A:0.24, C:0.02, G:0.29, T:0.46
Consensus pattern (68 bp):
TAGGGTTTTTAAGTTTAGAGTTTAGGGTTTTTAATTAAATCAGGTTAGGGTTTTTAAGTTAAGGG
GGC
Found at i:31353075 original size:25 final size:25
Alignment explanation
Indices: 31353046--31353093 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
31353036 TATAAAAAAT
31353046 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
31353071 TTCTATTTTATTACATCAAATAA
1 TTCTATTTTATTACATCAAATAA
31353094 TATCAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.46
Consensus pattern (25 bp):
TTCTATTTTATTACATCAAATAAAC
Found at i:31353095 original size:28 final size:26
Alignment explanation
Indices: 31353037--31353093 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 26
31353027 CTCAAATAAT
* *
31353037 ATAAAAAATTTCTATTTTATTACATC
1 ATAATAAACTTCTATTTTATTACATC
31353063 A-AATAAACTTCTATTTTATTACATC
1 ATAATAAACTTCTATTTTATTACATC
31353088 A-AATAA
1 ATAATAA
31353094 TATCAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 28 0.97
26 1 0.03
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (26 bp):
ATAATAAACTTCTATTTTATTACATC
Found at i:31353547 original size:18 final size:18
Alignment explanation
Indices: 31353524--31353561 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
31353514 CTCGAAAAAT
*
31353524 GATACATATAAGGGTTAG
1 GATACATATAAGGGCTAG
31353542 GATACATATAAGGGCTAG
1 GATACATATAAGGGCTAG
31353560 GA
1 GA
31353562 AACGCACCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.08, G:0.29, T:0.24
Consensus pattern (18 bp):
GATACATATAAGGGCTAG
Found at i:31354222 original size:7 final size:7
Alignment explanation
Indices: 31354212--31354236 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31354202 TTATATACAT
31354212 AATACTA
1 AATACTA
31354219 AATACTA
1 AATACTA
31354226 AATACTA
1 AATACTA
31354233 AATA
1 AATA
31354237 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:31354444 original size:20 final size:20
Alignment explanation
Indices: 31354407--31354444 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31354397 TTTATTTTTA
*
31354407 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
31354427 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
31354445 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:31355379 original size:12 final size:11
Alignment explanation
Indices: 31355337--31355379 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
31355327 ATTTTTACGG
*
31355337 TTTAAAAAAAA
1 TTTAAAAAATA
31355348 TTTAAAAAATA
1 TTTAAAAAATA
* *
31355359 TTTTTAAAATTA
1 -TTTAAAAAATA
31355371 TTTAAAAAA
1 TTTAAAAAA
31355380 AGAGAGTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TTTAAAAAATA
Found at i:31355402 original size:11 final size:11
Alignment explanation
Indices: 31355386--31355416 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
31355376 AAAAAGAGAG
31355386 TTAAGAGAAAC
1 TTAAGAGAAAC
*
31355397 TTAAGAGGAAC
1 TTAAGAGAAAC
31355408 TTAAGAGAA
1 TTAAGAGAA
31355417 TTTTTTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (11 bp):
TTAAGAGAAAC
Found at i:31355458 original size:12 final size:11
Alignment explanation
Indices: 31355424--31355459 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
31355414 GAATTTTTTA
*
31355424 AGGAAATTGGG
1 AGGAAATTGAG
31355435 AGGAAATTGAG
1 AGGAAATTGAG
31355446 AGGAAATTTGAG
1 AGGAAA-TTGAG
31355458 AG
1 AG
31355460 AGGATTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.39, T:0.19
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:31362322 original size:5 final size:5
Alignment explanation
Indices: 31362305--31362336 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
31362295 TATTGCAAAT
31362305 AATTA AA-TA AATTA AATTA AATTA AATTA AAT
1 AATTA AATTA AATTA AATTA AATTA AATTA AAT
31362337 AGATAAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATTA
Found at i:31362874 original size:20 final size:19
Alignment explanation
Indices: 31362849--31362931 Score: 66
Period size: 17 Copynumber: 4.4 Consensus size: 19
31362839 TACATAATTT
31362849 AAAATATTACAAAATTATTA
1 AAAATATTA-AAAATTATTA
31362869 AAAATATTTAAAAA-TA-TA
1 AAAATA-TTAAAAATTATTA
* *
31362887 AAAAAATTATTAAAATCATTA
1 AAAATATTA--AAAATTATTA
**
31362908 AAAA-GGT-AAAATTATTA
1 AAAATATTAAAAATTATTA
31362925 AAAATAT
1 AAAATAT
31362932 ATTAAAATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
17 16 0.32
18 7 0.14
19 6 0.12
20 12 0.24
21 9 0.18
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAATATTAAAAATTATTA
Found at i:31362890 original size:8 final size:9
Alignment explanation
Indices: 31362849--31362931 Score: 62
Period size: 10 Copynumber: 8.8 Consensus size: 9
31362839 TACATAATTT
31362849 AAAATATTA
1 AAAATATTA
31362858 CAAAATTATTA
1 -AAAA-TATTA
31362869 AAAATATTTA
1 AAAATA-TTA
31362879 AAAATA-TA
1 AAAATATTA
*
31362887 AAAAAATTA
1 AAAATATTA
31362896 TTAAAATCATTA
1 --AAAAT-ATTA
**
31362908 AAAA-GGTA
1 AAAATATTA
*
31362916 AAATTATTA
1 AAAATATTA
31362925 AAAATAT
1 AAAATAT
31362932 ATTAAAATGT
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
8 12 0.21
9 12 0.21
10 21 0.36
11 9 0.16
12 4 0.07
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAATATTA
Found at i:31363650 original size:30 final size:32
Alignment explanation
Indices: 31363615--31363685 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
31363605 GTCAAATAAT
*
31363615 ATTAAAA-TAATT-TAGACTAATCAGAGTTTG
1 ATTAAAACAAATTCTAGACTAATCAGAGTTTG
31363645 ATTAAAACAAATTCTAGACTAATCAGAGTTTG
1 ATTAAAACAAATTCTAGACTAATCAGAGTTTG
*
31363677 ATTGAAACA
1 ATTAAAACA
31363686 GATAAACAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 7 0.19
31 4 0.11
32 26 0.70
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (32 bp):
ATTAAAACAAATTCTAGACTAATCAGAGTTTG
Found at i:31366261 original size:29 final size:30
Alignment explanation
Indices: 31366222--31366300 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
31366212 CTTAATAATC
31366222 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
31366252 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
31366281 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
31366301 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:31366478 original size:29 final size:30
Alignment explanation
Indices: 31366439--31366517 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
31366429 CTTAATAATC
31366439 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
31366469 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
31366498 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
31366518 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:31366491 original size:217 final size:217
Alignment explanation
Indices: 31366116--31366532 Score: 798
Period size: 217 Copynumber: 1.9 Consensus size: 217
31366106 AACTCAAGGT
*
31366116 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
31366181 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
31366246 ACTTTAAACTCGCACACTTAGTGCTGTACAATTTAAACCCGCACACTTAGTGCCAATCTCATGAC
131 ACTTTAAACTCGCACACTTAGTGCTGTACAATTTAAACCCGCACACTTAGTGCCAATCTCATGAC
31366311 CGTGAGCATTTCAAGTTCGCAC
196 CGTGAGCATTTCAAGTTCGCAC
* * *
31366333 ACTTACCTTTTCTGTTGTCCAAAATTGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
31366398 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
31366463 ACTTTAAACTCGCACACTTAGTGCTGTACAATTTAAACCCGCACACTTAGTGCCAATCTCATGAC
131 ACTTTAAACTCGCACACTTAGTGCTGTACAATTTAAACCCGCACACTTAGTGCCAATCTCATGAC
31366528 CGTGA
196 CGTGA
31366533 ACACTTATTG
Statistics
Matches: 196, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
217 196 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (217 bp):
ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
ACTTTAAACTCGCACACTTAGTGCTGTACAATTTAAACCCGCACACTTAGTGCCAATCTCATGAC
CGTGAGCATTTCAAGTTCGCAC
Found at i:31369141 original size:21 final size:21
Alignment explanation
Indices: 31369115--31369154 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
31369105 GAGTACATGG
31369115 ATAAA-TTTTAGATAACTTTGT
1 ATAAATTTTTA-ATAACTTTGT
31369136 ATAAATTTTTAATAACTTT
1 ATAAATTTTTAATAACTTT
31369155 TTAATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (21 bp):
ATAAATTTTTAATAACTTTGT
Found at i:31369155 original size:11 final size:11
Alignment explanation
Indices: 31369120--31369161 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
31369110 CATGGATAAA
31369120 TTTTAGATAACT
1 TTTTA-ATAACT
* *
31369132 TTGT-ATAAAT
1 TTTTAATAACT
31369142 TTTTAATAACT
1 TTTTAATAACT
31369153 TTTTAATAA
1 TTTTAATAA
31369162 TTTCATAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 8 0.32
11 14 0.56
12 3 0.12
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (11 bp):
TTTTAATAACT
Found at i:31369163 original size:21 final size:21
Alignment explanation
Indices: 31369115--31369164 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
31369105 GAGTACATGG
*
31369115 ATAAATTTTAGATAACTTTGT
1 ATAATTTTTAGATAACTTTGT
*
31369136 ATAAATTTTTA-ATAACTTTTT
1 AT-AATTTTTAGATAACTTTGT
31369157 AATAATTT
1 -ATAATTT
31369165 CATAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (21 bp):
ATAATTTTTAGATAACTTTGT
Found at i:31371064 original size:24 final size:23
Alignment explanation
Indices: 31371037--31371096 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
31371027 GGAGTTTGCA
*
31371037 GATAAAAGCTGCCAGTAATTTGTG
1 GATAAAA-CCGCCAGTAATTTGTG
31371061 GAT-AAACCGCCAGTAATTTGTG
1 GATAAAACCGCCAGTAATTTGTG
*
31371083 GAT-AAACCACCAGT
1 GATAAAACCGCCAGT
31371097 GTTTGTAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 28 0.82
23 3 0.09
24 3 0.09
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (23 bp):
GATAAAACCGCCAGTAATTTGTG
Found at i:31371075 original size:22 final size:22
Alignment explanation
Indices: 31371047--31371096 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
31371037 GATAAAAGCT
31371047 GCCAGTAATTTGTGGATAAACC
1 GCCAGTAATTTGTGGATAAACC
31371069 GCCAGTAATTTGTGGATAAACC
1 GCCAGTAATTTGTGGATAAACC
*
31371091 ACCAGT
1 GCCAGT
31371097 GTTTGTAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (22 bp):
GCCAGTAATTTGTGGATAAACC
Found at i:31387547 original size:15 final size:16
Alignment explanation
Indices: 31387521--31387550 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31387511 ATAAATTTTA
31387521 TTTTACTTTACTTAAG
1 TTTTACTTTACTTAAG
31387537 TTTTA-TTTACTTAA
1 TTTTACTTTACTTAA
31387551 TTACTAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.10, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTTACTTTACTTAAG
Found at i:31394272 original size:20 final size:20
Alignment explanation
Indices: 31394247--31394289 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
31394237 TTGGTTGTAA
31394247 AAATAGTAAAAGTTCAAGTT
1 AAATAGTAAAAGTTCAAGTT
*
31394267 AAATAGTAAAAGTTTAAGTT
1 AAATAGTAAAAGTTCAAGTT
31394287 AAA
1 AAA
31394290 GCCAAATTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.02, G:0.14, T:0.30
Consensus pattern (20 bp):
AAATAGTAAAAGTTCAAGTT
Found at i:31398575 original size:15 final size:15
Alignment explanation
Indices: 31398551--31398582 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31398541 TAGCTCTGAT
31398551 ACCACAAAAAGTAAC
1 ACCACAAAAAGTAAC
*
31398566 ACCACTAAAAGTAAC
1 ACCACAAAAAGTAAC
31398581 AC
1 AC
31398583 TGGATTAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.28, G:0.06, T:0.09
Consensus pattern (15 bp):
ACCACAAAAAGTAAC
Found at i:31408910 original size:39 final size:39
Alignment explanation
Indices: 31408802--31408917 Score: 160
Period size: 39 Copynumber: 3.0 Consensus size: 39
31408792 AATTTAGTTT
* * *
31408802 GAGTCTTCAATTATGTCATAATTTGAAAATCATTAATAT
1 GAGTCTTTAATTATGTCATAATTTGAACATCATTAATAA
* *
31408841 GAGTTTTTAATTATGTCATAATCTGAACATCATTAATAA
1 GAGTCTTTAATTATGTCATAATTTGAACATCATTAATAA
* * *
31408880 GAGTCTTTAATTATGTCATAGTTTGGACATCTTTAATA
1 GAGTCTTTAATTATGTCATAATTTGAACATCATTAATA
31408918 CATGTTTTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 67 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (39 bp):
GAGTCTTTAATTATGTCATAATTTGAACATCATTAATAA
Found at i:31412214 original size:15 final size:15
Alignment explanation
Indices: 31412196--31412232 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
31412186 GGAAAAAGTG
31412196 AGAAAGAAAAAAAAA
1 AGAAAGAAAAAAAAA
*
31412211 AGAAATCAAAAAAAAA
1 AGAAA-GAAAAAAAAA
31412227 AGAAAG
1 AGAAAG
31412233 GAAAGGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.03
Consensus pattern (15 bp):
AGAAAGAAAAAAAAA
Found at i:31415954 original size:19 final size:20
Alignment explanation
Indices: 31415922--31415962 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
31415912 CTGAATTTTA
31415922 TTTTATTTGGTTTTATTTATT
1 TTTTATTT-GTTTTATTTATT
*
31415943 TTTTATTT-TTTTGTTTATT
1 TTTTATTTGTTTTATTTATT
31415962 T
1 T
31415963 AATCTGCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
21 8 0.42
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.80
Consensus pattern (20 bp):
TTTTATTTGTTTTATTTATT
Found at i:31418247 original size:39 final size:39
Alignment explanation
Indices: 31418133--31418248 Score: 169
Period size: 39 Copynumber: 3.0 Consensus size: 39
31418123 AATTTAGCTT
* *
31418133 GAGTCTTTAATTATGTCATAATTTGAACATCATTAACAT
1 GAGTCTTTAATTATGTCATAATTTGAACATCATTAATAA
* *
31418172 GAGTTTTTAATTATGTCATAATCTGAACATCATTAATAA
1 GAGTCTTTAATTATGTCATAATTTGAACATCATTAATAA
* * *
31418211 GAGTCTTTAATTATGTCATAGTTTGGACATCTTTAATA
1 GAGTCTTTAATTATGTCATAATTTGAACATCATTAATA
31418249 CATGTTTTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 68 1.00
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (39 bp):
GAGTCTTTAATTATGTCATAATTTGAACATCATTAATAA
Found at i:31424041 original size:28 final size:28
Alignment explanation
Indices: 31424009--31424080 Score: 135
Period size: 28 Copynumber: 2.6 Consensus size: 28
31423999 TTTAATAAGT
31424009 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
31424037 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
*
31424065 TCGTACACTTAGTGCT
1 TCGCACACTTAGTGCT
31424081 AATCTCTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTTACAATTAAAC
Found at i:31430869 original size:39 final size:37
Alignment explanation
Indices: 31430807--31430879 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
31430797 GTTATACATA
* *
31430807 AATTTTGATTCAATATGCAATTTAATATATAAATTTT
1 AATTTTGATTCAATATGCAATTTAAAAAATAAATTTT
*
31430844 AATTTTGATTCAATTATGTATATTTAAAAAATAAAT
1 AATTTTGATTCAA-TATGCA-ATTTAAAAAATAAAT
31430880 ATATCAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 13 0.42
38 5 0.16
39 13 0.42
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (37 bp):
AATTTTGATTCAATATGCAATTTAAAAAATAAATTTT
Found at i:31433116 original size:104 final size:105
Alignment explanation
Indices: 31432937--31433203 Score: 432
Period size: 105 Copynumber: 2.6 Consensus size: 105
31432927 TAACCGTTAT
* ** *
31432937 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGG-ATCAGCACTTAGCAACCCTTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
31433001 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
*
31433040 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
31433105 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* **
31433145 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
31433204 TTATATACAA
Statistics
Matches: 152, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
103 34 0.22
104 46 0.30
105 71 0.47
106 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (105 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:31433980 original size:19 final size:19
Alignment explanation
Indices: 31433956--31434008 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
31433946 GTTCGATAAA
31433956 TTATATTTTTTAAATTAAT
1 TTATATTTTTTAAATTAAT
* ** *
31433975 TTATATTTTTAAAAAGATT
1 TTATATTTTTTAAATTAAT
31433994 TTA-ATTTTTTAAATT
1 TTATATTTTTTAAATT
31434009 TATGTCTGCC
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTATATTTTTTAAATTAAT
Found at i:31435174 original size:37 final size:38
Alignment explanation
Indices: 31435079--31435176 Score: 90
Period size: 40 Copynumber: 2.6 Consensus size: 38
31435069 ACACACCAGT
* **
31435079 TTGGCACCCAATGCCTCATCAGATAATTCGAAGTAATAAA
1 TTGGCACCCAATGCCTCATCGGATAACCCGAAG--ATAAA
* * * * * *
31435119 TTGACAACTAGTGTCTCATCGGCTAACCCGAAG-TAAA
1 TTGGCACCCAATGCCTCATCGGATAACCCGAAGATAAA
31435156 TTGGCACCCAATGCCTCATCG
1 TTGGCACCCAATGCCTCATCG
31435177 AATTAATCTA
Statistics
Matches: 44, Mismatches: 14, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
37 20 0.45
40 24 0.55
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (38 bp):
TTGGCACCCAATGCCTCATCGGATAACCCGAAGATAAA
Found at i:31436237 original size:15 final size:15
Alignment explanation
Indices: 31436187--31436237 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
31436177 TTTGTTTTAT
*
31436187 TATTATTATAATATA
1 TATTAATATAATATA
31436202 TATTAAGTA-AACT-TA
1 TATTAA-TATAA-TATA
*
31436217 TTTTAATATAATATA
1 TATTAATATAATATA
31436232 TATTAA
1 TATTAA
31436238 ATTCTCCTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
14 3 0.10
15 23 0.79
16 3 0.10
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
TATTAATATAATATA
Found at i:31437260 original size:3 final size:3
Alignment explanation
Indices: 31437252--31437289 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
31437242 GGAAAAAACT
31437252 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31437290 TCAACTCTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31445088 original size:23 final size:23
Alignment explanation
Indices: 31445069--31445122 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
31445059 TGTATACACG
31445069 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATATATACTAA
* *
31445092 TACATAATAATAATA-ATAGTAA
1 TACATAATAAAAATATATACTAA
31445114 TAC-TAATAA
1 TACATAATAA
31445123 TACTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (23 bp):
TACATAATAAAAATATATACTAA
Found at i:31445103 original size:3 final size:3
Alignment explanation
Indices: 31445072--31445142 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
31445062 ATACACGTAC
* * * *
31445072 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
31445119 ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
31445143 CAAGGATATT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:31445595 original size:90 final size:91
Alignment explanation
Indices: 31445429--31445608 Score: 353
Period size: 90 Copynumber: 2.0 Consensus size: 91
31445419 CATAAATATC
31445429 CCATTCAAACGAAAACACGCGGATCCTCTAGCGGGTCGGGTCGGATGGGTCGGGCAATGGTCAAA
1 CCATTCAAACGAAAACACGCGGATCCTCTAGCGGGTCGGGTCGGATGGGTCGGGCAATGGTCAAA
31445494 ACGACGTCGTTTTGAGGCTTAAGTGA
66 ACGACGTCGTTTTGAGGCTTAAGTGA
31445520 CCATTCAAACGAAAACACGCGGATCCTCTAGCGGGTC-GGTCGGATGGGTCGGGCAATGGTCAAA
1 CCATTCAAACGAAAACACGCGGATCCTCTAGCGGGTCGGGTCGGATGGGTCGGGCAATGGTCAAA
31445584 ACGACGTCGTTTTGAGGCTTAAGTG
66 ACGACGTCGTTTTGAGGCTTAAGTG
31445609 TAGCCCCCAA
Statistics
Matches: 89, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
90 52 0.58
91 37 0.42
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.21
Consensus pattern (91 bp):
CCATTCAAACGAAAACACGCGGATCCTCTAGCGGGTCGGGTCGGATGGGTCGGGCAATGGTCAAA
ACGACGTCGTTTTGAGGCTTAAGTGA
Found at i:31445717 original size:11 final size:12
Alignment explanation
Indices: 31445697--31445734 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
31445687 AGAAAAAAAA
31445697 GAAGAGAGAGAGG
1 GAAGAGAGA-AGG
31445710 GAAGAGAGAAGG
1 GAAGAGAGAAGG
31445722 G-AGAGAGAAGG
1 GAAGAGAGAAGG
31445733 GA
1 GA
31445735 GGGGGAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.46
12 4 0.17
13 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:31446217 original size:8 final size:8
Alignment explanation
Indices: 31446204--31446228 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
31446194 GGTGTTCGGC
31446204 GCAAGTGG
1 GCAAGTGG
31446212 GCAAGTGG
1 GCAAGTGG
31446220 GCAAGTGG
1 GCAAGTGG
31446228 G
1 G
31446229 GGGGTAGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.52, T:0.12
Consensus pattern (8 bp):
GCAAGTGG
Found at i:31456313 original size:33 final size:30
Alignment explanation
Indices: 31456234--31456333 Score: 155
Period size: 33 Copynumber: 3.2 Consensus size: 30
31456224 GGTACCTCTC
31456234 TTTTTTTTGTAATGATGTTAAGATAAACTGA
1 TTTTTTTT-TAATGATGTTAAGATAAACTGA
31456265 TTTTTTTTTAATGATGTTAAGATAAACTGCAA
1 TTTTTTTTTAATGATGTTAAGATAAACTG--A
*
31456297 TTTTTGTTTTAGTGATGTTAAGATAAACTGA
1 TTTTT-TTTTAATGATGTTAAGATAAACTGA
31456328 TTTTTT
1 TTTTTT
31456334 AAACCCATTT
Statistics
Matches: 65, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
30 22 0.34
31 14 0.22
32 6 0.09
33 23 0.35
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.51
Consensus pattern (30 bp):
TTTTTTTTTAATGATGTTAAGATAAACTGA
Found at i:31460057 original size:69 final size:68
Alignment explanation
Indices: 31459889--31460175 Score: 222
Period size: 69 Copynumber: 4.2 Consensus size: 68
31459879 CGCAAACTAG
* ** * *
31459889 GTTGGAGGCTGCGATTTTTATCTTGTTAGCCCTAGTATGACAGTTGGGAGCTTT-CTTCTCGCTA
1 GTTGGAGGCTGCGATTTTTA-CCTGCAAGCCCTAGTATTACAGCTGGGAGCTTTGC-TCTCGCTA
31459953 ACTA-T
64 AC-AGT
* * * * * * * * *
31459958 GTTAGATGTTGCGATTTTTCACTTGTAAGCCCTAGTATTATAGTTGGGAGCTTTGTTCTCACTAA
1 GTTGGAGGCTGCGATTTTT-ACCTGCAAGCCCTAGTATTACAGCTGGGAGCTTTGCTCTCGCTAA
31460023 CAGT
65 CAGT
* * * *
31460027 GTTGGAGGCTGTGACTTTTTACCTGCAAGCCTTA--ATTGACAGCTAGGAGCTTTGCTCTTGCTA
1 GTTGGAGGCTGCGA-TTTTTACCTGCAAGCCCTAGTATT-ACAGCTGGGAGCTTTGCTCTCGCTA
*
31460090 ACTGT
64 ACAGT
* * * * * * * * *
31460095 GTTAGAGGCTGCGGCTCTTCACCTACGAGCCTTAATATTACAGCTGGGAGTTTTGCTCTCGCTAA
1 GTTGGAGGCTGC-GATTTTTACCTGCAAGCCCTAGTATTACAGCTGGGAGCTTTGCTCTCGCTAA
*
31460160 CTGT
65 CAGT
31460164 GTTGGAGGCTGC
1 GTTGGAGGCTGC
31460176 AACTCTTCCT
Statistics
Matches: 177, Mismatches: 33, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
67 3 0.02
68 49 0.28
69 116 0.66
70 9 0.05
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (68 bp):
GTTGGAGGCTGCGATTTTTACCTGCAAGCCCTAGTATTACAGCTGGGAGCTTTGCTCTCGCTAAC
AGT
Found at i:31460182 original size:69 final size:69
Alignment explanation
Indices: 31459928--31460201 Score: 232
Period size: 69 Copynumber: 4.0 Consensus size: 69
31459918 CCCTAGTATG
* * * * * * * * ** *
31459928 ACAGTTGGGAGCTTT-CTTCTCGCTAACTATGTTAGATGTTGCGATTTTTCACTTGTAAGCCCTA
1 ACAGCTGGGAGCTTTGC-TCTCGCTAACTGTGTTGGAGGCTGCGACTCTTCACCTACAAGCCTTA
*
31459992 GTATT
65 ATATT
* * * * * * * * *
31459997 ATAGTTGGGAGCTTTGTTCTCACTAACAGTGTTGGAGGCTGTGACTTTTTACCTGCAAGCCTTAA
1 ACAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGACTCTTCACCTACAAGCCTTAA
*
31460062 T-TG
66 TATT
* * * * *
31460065 ACAGCTAGGAGCTTTGCTCTTGCTAACTGTGTTAGAGGCTGCGGCTCTTCACCTACGAGCCTTAA
1 ACAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGACTCTTCACCTACAAGCCTTAA
31460130 TATT
66 TATT
* *
31460134 ACAGCTGGGAGTTTTGCTCTCGCTAACTGTGTTGGAGGCTGCAACTCTTC-CTCTGA-AAGCCTT
1 ACAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGACTCTTCAC-CT-ACAAGCCTT
31460197 AATAT
64 AATAT
31460202 GACATAAATG
Statistics
Matches: 163, Mismatches: 38, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
68 54 0.33
69 108 0.66
70 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.35
Consensus pattern (69 bp):
ACAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGACTCTTCACCTACAAGCCTTAA
TATT
Found at i:31460291 original size:45 final size:44
Alignment explanation
Indices: 31460220--31460306 Score: 102
Period size: 45 Copynumber: 2.0 Consensus size: 44
31460210 TGTTGTTAGA
* * *
31460220 GAAAGATTCTTCATTCACAGGATAAGGGTTTAAACATGATACNGG
1 GAAAGATTCTTCATTAACAGGATAAGGATTTAAACATAATAC-GG
* * * *
31460265 GAAAGATTCTTTATTAATAGGGTAAGGATTTACACATAATAC
1 GAAAGATTCTTCATTAACAGGATAAGGATTTAAACATAATAC
31460307 TTTTTGAGAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.30
Consensus pattern (44 bp):
GAAAGATTCTTCATTAACAGGATAAGGATTTAAACATAATACGG
Found at i:31466809 original size:17 final size:17
Alignment explanation
Indices: 31466787--31466824 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
31466777 GATTGAAACC
31466787 TAAAACCCCAT-TTAATT
1 TAAAA-CCCATATTAATT
*
31466804 TAAAACCCTTATTAATT
1 TAAAACCCATATTAATT
31466821 TAAA
1 TAAA
31466825 TAATTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAAACCCATATTAATT
Found at i:31466912 original size:89 final size:89
Alignment explanation
Indices: 31466750--31466919 Score: 259
Period size: 89 Copynumber: 1.9 Consensus size: 89
31466740 TACAAAGCCT
* *
31466750 TAACAATCGACGAGGTTAATTCGGAATGATTGAAACCTAAAACCCCATTTAATTTAAAACCCTTA
1 TAACAATCGACGAGGTTAATTCGGAATGATTGAAACCCAAAACCCCATTTAATTTAAAACCCGTA
*
31466815 TTAATTTAAATAATTATAAAATCC
66 ATAATTTAAATAATTATAAAATCC
* * * *
31466839 TAACAATCGAGGAGGTTAGTTCGGATTGATTGAAACCCAAAACCCCATTTAATTTGAAACCCGTA
1 TAACAATCGACGAGGTTAATTCGGAATGATTGAAACCCAAAACCCCATTTAATTTAAAACCCGTA
* *
31466904 ATAGTTTAAATGATTA
66 ATAATTTAAATAATTA
31466920 AACCCAAAAC
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 72 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (89 bp):
TAACAATCGACGAGGTTAATTCGGAATGATTGAAACCCAAAACCCCATTTAATTTAAAACCCGTA
ATAATTTAAATAATTATAAAATCC
Found at i:31468044 original size:3 final size:3
Alignment explanation
Indices: 31468036--31468061 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31468026 ATTGAGATTG
31468036 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
31468062 TGTGATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:31468580 original size:21 final size:21
Alignment explanation
Indices: 31468554--31468601 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
31468544 GACTGCTAAC
31468554 TTTATTGAGTACATAATAATA
1 TTTATTGAGTACATAATAATA
* * *
31468575 TTTATTGATTATATAATAGTA
1 TTTATTGAGTACATAATAATA
31468596 TTTATT
1 TTTATT
31468602 TTAGATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (21 bp):
TTTATTGAGTACATAATAATA
Found at i:31468614 original size:24 final size:21
Alignment explanation
Indices: 31468554--31468615 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
31468544 GACTGCTAAC
* *
31468554 TTTATTGAGTACATAATAATA
1 TTTATTGATTAAATAATAATA
* *
31468575 TTTATTGATTATATAATAGTA
1 TTTATTGATTAAATAATAATA
31468596 TTTATTTTAGATTAAATAAT
1 TTTA--TT-GATTAAATAAT
31468616 TTAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 22 0.65
23 2 0.06
24 10 0.29
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (21 bp):
TTTATTGATTAAATAATAATA
Found at i:31471935 original size:50 final size:50
Alignment explanation
Indices: 31471860--31471954 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 50
31471850 CTCTAGTCTA
* * * * *
31471860 TGTGACTCTAAATCCAATAGAGTGAGTTATACGGCCTAGACACACACCCG
1 TGTGACCCTAAAGCCAAAACAGTGAGTTACACGGCCTAGACACACACCCG
* *
31471910 TGTGACCCTAAAGCCAAAACAGTGAGTTACACGGCTTGGACACAC
1 TGTGACCCTAAAGCCAAAACAGTGAGTTACACGGCCTAGACACAC
31471955 GCCTGTATCC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (50 bp):
TGTGACCCTAAAGCCAAAACAGTGAGTTACACGGCCTAGACACACACCCG
Found at i:31472015 original size:63 final size:63
Alignment explanation
Indices: 31471910--31472055 Score: 202
Period size: 63 Copynumber: 2.3 Consensus size: 63
31471900 CACACACCCG
* * * * * * * *
31471910 TGTGACCCTAAAGCCAAAACAGTGAGTTACACGGCTTGGACACACGCCTGTATCCTTGGCCCA
1 TGTGACCCTAAAGCCAAAACAATGAGTTACACGACCTAGACACACACATATATCCCTGGCCCA
* *
31471973 TGTGACCTTAAAGCCAAAACAATGAGTTACACGACCTAGACACACACATATGTCCCTGGCCCA
1 TGTGACCCTAAAGCCAAAACAATGAGTTACACGACCTAGACACACACATATATCCCTGGCCCA
31472036 TGTGACCCTAAAGCCAAAAC
1 TGTGACCCTAAAGCCAAAAC
31472056 CATACGACCA
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 72 1.00
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.19
Consensus pattern (63 bp):
TGTGACCCTAAAGCCAAAACAATGAGTTACACGACCTAGACACACACATATATCCCTGGCCCA
Found at i:31476784 original size:12 final size:12
Alignment explanation
Indices: 31476691--31476788 Score: 53
Period size: 12 Copynumber: 8.1 Consensus size: 12
31476681 ATCTTGTAGA
*
31476691 TAAATATTAAAC
1 TAAATATTAAAT
31476703 TAAAT-TTAATAT
1 TAAATATTAA-AT
* *
31476715 TAAGATAATCAAT
1 TAA-ATATTAAAT
*
31476728 TTAATATTAAAT
1 TAAATATTAAAT
**
31476740 TAATATAGTTGTAT
1 TAA-ATA-TTAAAT
31476754 T-AATA-TAAGTAT
1 TAAATATTAA--AT
31476766 T-AA-ATTAAAT
1 TAAATATTAAAT
31476776 TAAATATTAAAT
1 TAAATATTAAAT
31476788 T
1 T
31476789 TATTAAAATA
Statistics
Matches: 65, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
10 4 0.06
11 7 0.11
12 37 0.57
13 10 0.15
14 7 0.11
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:31476798 original size:17 final size:17
Alignment explanation
Indices: 31476691--31476788 Score: 62
Period size: 17 Copynumber: 5.8 Consensus size: 17
31476681 ATCTTGTAGA
*
31476691 TAAATATTAAACTAAAT
1 TAAATATTAAATTAAAT
*
31476708 TTAATATTAAGA-T-AA-
1 TAAATATTAA-ATTAAAT
*
31476723 TCAAT-TTAATATTAAAT
1 TAAATATTAA-ATTAAAT
**
31476740 TAATATAGTTGTATT-AAT
1 TAA-ATA-TTAAATTAAAT
*
31476758 ATAAGTATTAAATTAAAT
1 -TAAATATTAAATTAAAT
31476776 TAAATATTAAATT
1 TAAATATTAAATT
31476789 TATTAAAATA
Statistics
Matches: 62, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
14 5 0.08
15 5 0.08
16 4 0.06
17 29 0.47
18 11 0.18
19 6 0.10
20 2 0.03
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (17 bp):
TAAATATTAAATTAAAT
Found at i:31482912 original size:265 final size:265
Alignment explanation
Indices: 31481960--31484040 Score: 2476
Period size: 265 Copynumber: 7.9 Consensus size: 265
31481950 TGTTGTGCAT
* * * * * *
31481960 GTGCCTTTATGTTGATCATTACAAATCTTATTCTAACCTTGTTTTGCTAGTTGTTGTTTCTCCAT
1 GTGCCTTCACGTTGATCATTACAAATCTTATTCTAATCTTTTTTTGCCAGTTGTTGTTGCTCCAT
* * *
31482025 AAGGGTAATGATTCCTCATACTTTATGCGGTGTGCTTACGTATTTG-CCTTAATATAATACTGAA
66 AAGGGTAATGATTCCTCATACTTTATGCGGTGTGTTTACGTATTTGCCCTTAACATAATACTGAG
* ** * * * *
31482089 GGAACCTCTCTTTACTTTTCACACGTTCAATCGAAATTTGAGGGAATAAGAACATAATTACACAT
131 GGAACCTCCCTTTGTTTTTCACACGTTCAACCAAAATTTGAGGGAAGAAGAACATAATTACACAG
* * * * * *
31482154 GTGAAATTCAGTATTGATAACTTATTGAGACCAAATGTTGTGCAAGCGTGATTTATAGCCCGAGA
196 GTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATTTATAGTCCAAGA
31482219 CATAC
261 CATAC
* * *
31482224 GTGGCTTCACATTGATCATTACAAATCTTATTCTAATC-TTTTTTGTCAGTTGTTGTTGCTCCAT
1 GTGCCTTCACGTTGATCATTACAAATCTTATTCTAATCTTTTTTTGCCAGTTGTTGTTGCTCCAT
* * * *
31482288 AAGGGTAATGATGCCTCATACTTTATGCAGCGTGTTTACGTATTTGCCCTTAATATAATACTGAG
66 AAGGGTAATGATTCCTCATACTTTATGCGGTGTGTTTACGTATTTGCCCTTAACATAATACTGAG
* * ** * *
31482353 GGAAGCTCCCTTTGTTTTTCACACGTTCAACCAAAATTTGAGCGAACTAGAAAATAATTCCACAG
131 GGAACCTCCCTTTGTTTTTCACACGTTCAACCAAAATTTGAGGGAAGAAGAACATAATTACACAG
* * * * **
31482418 GTGAAATTAAGTATTGATAACTTCTTAAGGTCAAATGTTGTACAAGTATGATTTATAGTCTGAGA
196 GTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATTTATAGTCCAAGA
**
31482483 TTTAC
261 CATAC
* * * * **
31482488 GTGCCTTCACGTTCATCATTAAAAATCTTATTCTAAT-TTTTTTTACCAATTGTTGTT-CTTTTA
1 GTGCCTTCACGTTGATCATTACAAATCTTATTCTAATCTTTTTTTGCCAGTTGTTGTTGC-TCCA
* * * **
31482551 TAAGGGTGATGGTTCTTCATACTTTATGCGGTGTGTTCCCGTATTTGCCCTTAACATAATACTGA
65 TAAGGGTAATGATTCCTCATACTTTATGCGGTGTGTTTACGTATTTGCCCTTAACATAATACTGA
* * * *
31482616 GGGGACCT-CCTATTGATTTTCACATGTTCAACCAAAATTT-AGAGGAAGAAGAACATAGTTACA
130 GGGAACCTCCCT-TTGTTTTTCACACGTTCAACCAAAATTTGAG-GGAAGAAGAACATAATTACA
* * * * *
31482679 CATGTGAAAGTAAGTATTGATAACTTTTTGAGGCCAAATGTTGTGCAAACATGATTTATAGTTCA
193 CAGGTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATTTATAGTCCA
31482744 AGACATAC
258 AGACATAC
* * *
31482752 GTGTCTTCACGTTGATCATTACAAATCCTATTCTAATCTTTTTTTGCCAGTTGTTGTTGCTCTAT
1 GTGCCTTCACGTTGATCATTACAAATCTTATTCTAATCTTTTTTTGCCAGTTGTTGTTGCTCCAT
** * * * * *
31482817 AAGGGTAATGATTATTTATACTTTATGCGGTGTGTTTATGTATTTGCTCTTAACATAATTCTGAA
66 AAGGGTAATGATTCCTCATACTTTATGCGGTGTGTTTACGTATTTGCCCTTAACATAATACTGAG
* * * * *
31482882 GGAACCTCCCTTTATTTTTCACATGTTCAACCGAAATTTGAGGGAAGAAGAACGTAATTACACAA
131 GGAACCTCCCTTTGTTTTTCACACGTTCAACCAAAATTTGAGGGAAGAAGAACATAATTACACAG
* * *
31482947 GTGAAATTAAGTATTGATAACTTCTTGAGGCTAAATATTGTGCAAGCATGATGTATAGTCCAAGA
196 GTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATTTATAGTCCAAGA
31483012 CATAC
261 CATAC
* * * * * * *
31483017 GTGTCTTCACATTCATGATTACAAATTTTATTCTAAT-TTTTTTTGGCA---ATTGTTGCTCCAT
1 GTGCCTTCACGTTGATCATTACAAATCTTATTCTAATCTTTTTTTGCCAGTTGTTGTTGCTCCAT
* * * * * *
31483078 AAGGGCAATGATTCCTCATACTTTATGAGATATATTTACATATTT-CCCTTAACATAATACTGAG
66 AAGGGTAATGATTCCTCATACTTTATGCGGTGTGTTTACGTATTTGCCCTTAACATAATACTGAG
* * * * *
31483142 GGAACCTCCATTTGTTTTTTACACATTCAACTAGAAA-TTGAGGGAAAAAGAACATAATTACACA
131 GGAACCTCCCTTTGTTTTTCACACGTTCAACCA-AAATTTGAGGGAAGAAGAACATAATTACACA
31483206 GGTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATTTATAGTCCAAG
195 GGTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATTTATAGTCCAAG
31483271 ACATAC
260 ACATAC
* * * * * * * *
31483277 GTGCTTTCATGTTGATCATTACAAATCTTGTTCTAATCTTGTTTTACTAGTTTTTGTTGCTCTAT
1 GTGCCTTCACGTTGATCATTACAAATCTTATTCTAATCTTTTTTTGCCAGTTGTTGTTGCTCCAT
** * ** * * * *
31483342 AAAAGTAATGATTCGTCATACTTTATGCAATGTGTTTACATACTCGCCCTTAACATAATATTGAG
66 AAGGGTAATGATTCCTCATACTTTATGCGGTGTGTTTACGTATTTGCCCTTAACATAATACTGAG
* * *
31483407 GGAACCTCCCTTCGCTTTTCACACGTTCAACCGAAATTTGAGGGAAGAAGAACATAATTACACAG
131 GGAACCTCCCTTTGTTTTTCACACGTTCAACCAAAATTTGAGGGAAGAAGAACATAATTACACAG
* * *
31483472 GTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTATGCAAGCATGATTTATAATGCAAGA
196 GTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATTTATAGTCCAAGA
*
31483537 CATAT
261 CATAC
* * * * **
31483542 GTGCCTTCATGATGATCATTACAAATCTTGTTTTAATCTTTTTTTGTTAGTTGTTGTTGC-CCTA
1 GTGCCTTCACGTTGATCATTACAAATCTTATTCTAATCTTTTTTTGCCAGTTGTTGTTGCTCC-A
* * * * *
31483606 GAAGGGTAATGATTTCTTATACTTTATGCAGTGTGTTTTCGTATTTGCCCTTAACATAATACTGA
65 TAAGGGTAATGATTCCTCATACTTTATGCGGTGTGTTTACGTATTTGCCCTTAACATAATACTGA
* * * * ** * * * * *
31483671 AGGAACCTACTTTTGCTTTTCACACGTTCAACTGAAATTTGAGTGAAGGAGAATATAAATCCACA
130 GGGAACCTCCCTTTGTTTTTCACACGTTCAACCAAAATTTGAGGGAAGAAGAACATAATTACACA
**
31483736 GGTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTATAAGC-------ATAGTCCGAA
195 GGTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATTTATAGTCC-AA
*
31483794 -ACACAC
259 GACATAC
* * * *
31483800 ATGCCTTCACATTGATCATCACAAATCTTATTCTAATCTTTTTTTGCTAGTTGTTGTTGCTCCAT
1 GTGCCTTCACGTTGATCATTACAAATCTTATTCTAATCTTTTTTTGCCAGTTGTTGTTGCTCCAT
* * * * * *
31483865 AAGGGTAATGATTCCTTATACTTTATGCGATGTTTTTATGTATTTACCCTTAATATAATACTGAG
66 AAGGGTAATGATTCCTCATACTTTATGCGGTGTGTTTACGTATTTGCCCTTAACATAATACTGAG
* * **
31483930 GGAAGCTCCATTTGTTTTTCACACGTTCAACCAAAATTTGAGGGAAGAAGAATGTAATTACACAG
131 GGAACCTCCCTTTGTTTTTCACACGTTCAACCAAAATTTGAGGGAAGAAGAACATAATTACACAG
* * *
31483995 GTGAAATTAAGTATTGATAAGTTCTTGAGGCTAAATGTTATGCAAG
196 GTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAG
31484041 GGAGATTCTA
Statistics
Matches: 1546, Mismatches: 252, Indels: 44
0.84 0.14 0.02
Matches are distributed among these distances:
258 213 0.14
259 4 0.00
260 163 0.11
261 56 0.04
263 70 0.05
264 467 0.30
265 567 0.37
266 6 0.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (265 bp):
GTGCCTTCACGTTGATCATTACAAATCTTATTCTAATCTTTTTTTGCCAGTTGTTGTTGCTCCAT
AAGGGTAATGATTCCTCATACTTTATGCGGTGTGTTTACGTATTTGCCCTTAACATAATACTGAG
GGAACCTCCCTTTGTTTTTCACACGTTCAACCAAAATTTGAGGGAAGAAGAACATAATTACACAG
GTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATTTATAGTCCAAGA
CATAC
Found at i:31483507 original size:790 final size:789
Alignment explanation
Indices: 31481960--31484040 Score: 2657
Period size: 790 Copynumber: 2.6 Consensus size: 789
31481950 TGTTGTGCAT
* * * * * *
31481960 GTGCCTTTATGTTGATCATTACAAATCTTATTCTAACCTTGTTTTGCTAGTTGTTGTTTCTCCAT
1 GTGCCTTCACGTTGATCATTACAAATCTTATTCTAATCTTTTTTTGCTAGTTGTTGTTGCTCTAT
* * * * *
31482025 AAGGGTAATGATTCCTCATACTTTATGCGGTGTGCTTACGTATTTGCCTTAATATAATACTGAAG
66 AAGGGTAATGATT-TTTATACTTTATGCGGTGTGTTTATGTATTTGCCTTAACATAATACTGAAG
* * * *
31482090 GAACCTCTCTTTACTTTTCACACGTTCAATCGAAATTTGAGGGAATAAGAACATAATTACACATG
130 GAACCTCCCTTTACTTTTCACACGTTCAACCGAAATTTGAGGGAAGAAGAACATAATTACACAAG
* * * * * * *
31482155 TGAAATTCAGTATTGATAACTTATTGAGACCAAATGTTGTGCAAGCGTGATTTATAGCCCGAGAC
195 TGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATGTATAGTCCAAGAC
* * *
31482220 ATACGTGGCTTCACATTGATCATTACAAATCTTATTCTAATCTTTTTTGTCAGTTGTTGTTGCTC
260 ATACGTGCCTTCACATTGATCATTACAAATCTTATTCTAATTTTTTTTGGCA--TGTTGTTGCTC
* * * *
31482285 CATAAGGGTAATGATGCCTCATACTTTATGCAG-CGTGTTTACGTATTTGCCCTTAATATAATAC
323 CATAAGGGTAATGATTCCTCATACTTTATG-AGATGTATTTACGTATTTACCCTTAATATAATAC
* * ** *
31482349 TGAGGGAAGCTCCCTTTGTTTTTCACACGTTCAACCAAAATTTGAGCGAACTAGAAAATAATTCC
387 TGAGGGAAGCTCCATTTGTTTTTCACACGTTCAACCAAAATTTGAGGGAAAAAGAAAATAATTAC
* * * * *
31482414 ACAGGTGAAATTAAGTATTGATAACTTCTTAAGGTCAAATGTTGTACAAGTATGATTTATAGTCT
452 ACAGGTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATTTATAGTCC
* ** *
31482479 GAGATTTACGTGCCTTCACGTTCATCATTAAAAATCTTATTCTAATTTTTTTTACCAATTGTTGT
517 AAGACATACGTGCCTTCACGTTCATCATTAAAAATCTTATTCTAATTTGTTTTACCAATTGTTGT
* ** * * * ** * * * *
31482544 TCTTTTATAAGGGTGATGGTTCTTCATACTTTATGCGGTGTGTTCCCGTATTTGCCCTTAACATA
582 TCTTCTATAAAAGTAATGATTCGTCATACTTTATGCAATGTGTTCACATACTCGCCCTTAACATA
* * * *
31482609 ATACTGAGGGGACCTCCTATTGATTTTCACATGTTCAACCAAAATTTAGAGGAAGAAGAACATAG
647 ATACTGAGGGAACCTCCTATCGATTTTCACACGTTCAACCAAAATTTAGAGGAAGAAGAACATAA
* * *
31482674 TTACACATGTGAAAGTAAGTATTGATAACTTTTTGAGGCCAAATGTTGTGCAAACATGATTTATA
712 TTACACAGGTGAAAGTAAGTATTGATAACTTCTTGAGGCCAAATGTTATGCAAACATGATTTATA
* *
31482739 GTTCAAGACATAC
777 ATGCAAGACATAC
* * *
31482752 GTGTCTTCACGTTGATCATTACAAATCCTATTCTAATCTTTTTTTGCCAGTTGTTGTTGCTCTAT
1 GTGCCTTCACGTTGATCATTACAAATCTTATTCTAATCTTTTTTTGCTAGTTGTTGTTGCTCTAT
*
31482817 AAGGGTAATGATTATTTATACTTTATGCGGTGTGTTTATGTATTTGCTCTTAACATAATTCTGAA
66 AAGGGTAATGATT-TTTATACTTTATGCGGTGTGTTTATGTATTTGC-CTTAACATAATACTGAA
* * *
31482882 GGAACCTCCCTTTATTTTTCACATGTTCAACCGAAATTTGAGGGAAGAAGAACGTAATTACACAA
129 GGAACCTCCCTTTACTTTTCACACGTTCAACCGAAATTTGAGGGAAGAAGAACATAATTACACAA
* *
31482947 GTGAAATTAAGTATTGATAACTTCTTGAGGCTAAATATTGTGCAAGCATGATGTATAGTCCAAGA
194 GTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATGTATAGTCCAAGA
* * * * *
31483012 CATACGTGTCTTCACATTCATGATTACAAATTTTATTCTAATTTTTTTTGGCA-ATTGTTGCTCC
259 CATACGTGCCTTCACATTGATCATTACAAATCTTATTCTAATTTTTTTTGGCATGTTGTTGCTCC
* * * *
31483076 ATAAGGGCAATGATTCCTCATACTTTATGAGATATATTTACATATTT-CCCTTAACATAATACTG
324 ATAAGGGTAATGATTCCTCATACTTTATGAGATGTATTTACGTATTTACCCTTAATATAATACTG
* * * * *
31483140 AGGGAACCTCCATTTGTTTTTTACACATTCAACTAGAAA-TTGAGGGAAAAAGAACATAATTACA
389 AGGGAAGCTCCATTTGTTTTTCACACGTTCAACCA-AAATTTGAGGGAAAAAGAAAATAATTACA
31483204 CAGGTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATTTATAGTCCA
453 CAGGTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATTTATAGTCCA
* * * * * * * *
31483269 AGACATACGTGCTTTCATGTTGATCATTACAAATCTTGTTCTAATCTTGTTTTACTAGTTTTTGT
518 AGACATACGTGCCTTCACGTTCATCATTAAAAATCTTATTCTAAT-TTGTTTTACCAATTGTTGT
*
31483334 TGC-TCTATAAAAGTAATGATTCGTCATACTTTATGCAATGTGTTTACATACTCGCCCTTAACAT
582 T-CTTCTATAAAAGTAATGATTCGTCATACTTTATGCAATGTGTTCACATACTCGCCCTTAACAT
* * *
31483398 AATATTGAGGGAACCTCCCT-TCGCTTTTCACACGTTCAACCGAAATTT-GAGGGAAGAAGAACA
646 AATACTGAGGGAACCT-CCTATCGATTTTCACACGTTCAACCAAAATTTAGA-GGAAGAAGAACA
* *
31483461 TAATTACACAGGTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTATGCAAGCATGATTT
709 TAATTACACAGGTGAAAGTAAGTATTGATAACTTCTTGAGGCCAAATGTTATGCAAACATGATTT
*
31483526 ATAATGCAAGACATAT
774 ATAATGCAAGACATAC
* * * * * * *
31483542 GTGCCTTCATGATGATCATTACAAATCTTGTTTTAATCTTTTTTTGTTAGTTGTTGTTGCCCTAG
1 GTGCCTTCACGTTGATCATTACAAATCTTATTCTAATCTTTTTTTGCTAGTTGTTGTTGCTCTAT
*
31483607 AAGGGTAATGATTTCTTATACTTTATGCAGTGTGTTT-TCGTATTTGCCCTTAACATAATACTGA
66 AAGGGTAATGATTT-TTATACTTTATGCGGTGTGTTTAT-GTATTTG-CCTTAACATAATACTGA
* * * * * * * * *
31483671 AGGAACCTACTTTTGCTTTTCACACGTTCAACTGAAATTTGAGTGAAGGAGAATATAAATCCACA
128 AGGAACCTCCCTTTACTTTTCACACGTTCAACCGAAATTTGAGGGAAGAAGAACATAATTACACA
* * *
31483736 GGTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGT------AT-AAGCATAGTCCGAA
193 AGTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATGTATAGTCC-AA
* * *
31483794 -ACACACATGCCTTCACATTGATCATCACAAATCTTATTCTAATCTTTTTTT-GCTAGTTGTTGT
257 GACATACGTGCCTTCACATTGATCATTACAAATCTTATTCTAAT-TTTTTTTGGC-A--TGTTGT
* * * *
31483857 TGCTCCATAAGGGTAATGATTCCTTATACTTTATGCGATGTTTTTATGTATTTACCCTTAATATA
318 TGCTCCATAAGGGTAATGATTCCTCATACTTTATGAGATGTATTTACGTATTTACCCTTAATATA
* **
31483922 ATACTGAGGGAAGCTCCATTTGTTTTTCACACGTTCAACCAAAATTTGAGGGAAGAAGAATGTAA
383 ATACTGAGGGAAGCTCCATTTGTTTTTCACACGTTCAACCAAAATTTGAGGGAAAAAGAAAATAA
* * *
31483987 TTACACAGGTGAAATTAAGTATTGATAAGTTCTTGAGGCTAAATGTTATGCAAG
448 TTACACAGGTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAG
31484041 GGAGATTCTA
Statistics
Matches: 1115, Mismatches: 156, Indels: 40
0.85 0.12 0.03
Matches are distributed among these distances:
783 47 0.04
784 12 0.01
787 53 0.05
788 115 0.10
789 169 0.15
790 440 0.39
791 5 0.00
792 98 0.09
793 176 0.16
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (789 bp):
GTGCCTTCACGTTGATCATTACAAATCTTATTCTAATCTTTTTTTGCTAGTTGTTGTTGCTCTAT
AAGGGTAATGATTTTTATACTTTATGCGGTGTGTTTATGTATTTGCCTTAACATAATACTGAAGG
AACCTCCCTTTACTTTTCACACGTTCAACCGAAATTTGAGGGAAGAAGAACATAATTACACAAGT
GAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATGTATAGTCCAAGACA
TACGTGCCTTCACATTGATCATTACAAATCTTATTCTAATTTTTTTTGGCATGTTGTTGCTCCAT
AAGGGTAATGATTCCTCATACTTTATGAGATGTATTTACGTATTTACCCTTAATATAATACTGAG
GGAAGCTCCATTTGTTTTTCACACGTTCAACCAAAATTTGAGGGAAAAAGAAAATAATTACACAG
GTGAAATTAAGTATTGATAACTTCTTGAGGCCAAATGTTGTGCAAGCATGATTTATAGTCCAAGA
CATACGTGCCTTCACGTTCATCATTAAAAATCTTATTCTAATTTGTTTTACCAATTGTTGTTCTT
CTATAAAAGTAATGATTCGTCATACTTTATGCAATGTGTTCACATACTCGCCCTTAACATAATAC
TGAGGGAACCTCCTATCGATTTTCACACGTTCAACCAAAATTTAGAGGAAGAAGAACATAATTAC
ACAGGTGAAAGTAAGTATTGATAACTTCTTGAGGCCAAATGTTATGCAAACATGATTTATAATGC
AAGACATAC
Found at i:31488230 original size:17 final size:17
Alignment explanation
Indices: 31488210--31488242 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
31488200 TAGAATTAGG
31488210 TTGAGAAAATAATTTAA
1 TTGAGAAAATAATTTAA
*
31488227 TTGAGAAATTAATTTA
1 TTGAGAAAATAATTTA
31488243 GTTAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (17 bp):
TTGAGAAAATAATTTAA
Found at i:31488249 original size:9 final size:9
Alignment explanation
Indices: 31488233--31488309 Score: 86
Period size: 9 Copynumber: 8.7 Consensus size: 9
31488223 TTAATTGAGA
31488233 AATTAATTT
1 AATTAATTT
*
31488242 AGTTAATTT
1 AATTAATTT
*
31488251 AATTAATTA
1 AATTAATTT
*
31488260 AATTAATTA
1 AATTAATTT
31488269 AATTAATTT
1 AATTAATTT
*
31488278 AGTTAATTT
1 AATTAATTT
*
31488287 TATTAA-TT
1 AATTAATTT
31488295 AATTTAATTT
1 AA-TTAATTT
31488305 -ATTAA
1 AATTAA
31488310 ATAAATAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
8 7 0.12
9 49 0.84
10 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
AATTAATTT
Found at i:31488308 original size:13 final size:13
Alignment explanation
Indices: 31488244--31488309 Score: 69
Period size: 13 Copynumber: 4.9 Consensus size: 13
31488234 ATTAATTTAG
31488244 TTAATTTAATTAAT
1 TTAATTT-ATTAAT
* * *
31488258 TAAATTAATTAAA
1 TTAATTTATTAAT
31488271 TTAATTTAGTTAAT
1 TTAATTTA-TTAAT
* *
31488285 TTTATTAATTAAT
1 TTAATTTATTAAT
31488298 TTAATTTATTAA
1 TTAATTTATTAA
31488310 ATAAATAATA
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
13 26 0.63
14 15 0.37
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (13 bp):
TTAATTTATTAAT
Found at i:31495696 original size:16 final size:16
Alignment explanation
Indices: 31495677--31495709 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
31495667 GCCGTGTAAC
31495677 TCTCTAACTTAGGTTA
1 TCTCTAACTTAGGTTA
31495693 TCTCTAACTTAGGTTA
1 TCTCTAACTTAGGTTA
31495709 T
1 T
31495710 ATGGCCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (16 bp):
TCTCTAACTTAGGTTA
Found at i:31497148 original size:26 final size:25
Alignment explanation
Indices: 31497077--31497159 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 25
31497067 CTGTATAACG
* *
31497077 GGAAGTTCATAAAAGCC-TAAATCA
1 GGAAGCTCATAAAAGCCTTTAATCA
* * * *
31497101 GGAAGTTCACAAAGAACTTTTAATCA
1 GGAAGCTCATAAA-AGCCTTTAATCA
31497127 GGAAGCTCATGAAAAGCCTTTAATCA
1 GGAAGCTCAT-AAAAGCCTTTAATCA
31497153 GG-AGCTC
1 GGAAGCTC
31497160 CGGATAGCCA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
24 12 0.25
25 7 0.15
26 26 0.54
27 3 0.06
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (25 bp):
GGAAGCTCATAAAAGCCTTTAATCA
Found at i:31500797 original size:28 final size:29
Alignment explanation
Indices: 31500759--31500825 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
31500749 AATAAACACC
*
31500759 AAAAATTTATTTTAAAAATA-AAAAAATA
1 AAAAAATTATTTTAAAAATATAAAAAATA
*
31500787 AAAAAATTATTTTAAAAATATTTTAAAAATA
1 AAAAAATTATTTTAAAAATA--TAAAAAATA
31500818 AAAAAATT
1 AAAAAATT
31500826 TATTATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 19 0.56
31 15 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (29 bp):
AAAAAATTATTTTAAAAATATAAAAAATA
Found at i:31500805 original size:12 final size:12
Alignment explanation
Indices: 31500788--31500816 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
31500778 AAAAAAATAA
31500788 AAAAATTATTTT
1 AAAAATTATTTT
31500800 AAAAA-TATTTT
1 AAAAATTATTTT
31500811 AAAAAT
1 AAAAAT
31500817 AAAAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAAATTATTTT
Found at i:31505116 original size:22 final size:21
Alignment explanation
Indices: 31505083--31505125 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
31505073 AATTTGTAAA
*
31505083 AAAATTATTATAAAAATAATT
1 AAAATTAATATAAAAATAATT
**
31505104 AAAATTAAATATATTAATAATT
1 AAAATT-AATATAAAAATAATT
31505126 TAAGTACAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATTAATATAAAAATAATT
Found at i:31505157 original size:27 final size:28
Alignment explanation
Indices: 31505105--31505157 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
31505095 AAAATAATTA
*
31505105 AAATTAAATATATTAATAATTTAAGTAC
1 AAATTAAATATATTAATAATTAAAGTAC
* *
31505133 AAATTAATTAT-TTTATAATTAAAGT
1 AAATTAAATATATTAATAATTAAAGT
31505158 GTGAATTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (28 bp):
AAATTAAATATATTAATAATTAAAGTAC
Found at i:31508054 original size:18 final size:18
Alignment explanation
Indices: 31508033--31508102 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 18
31508023 GTATGCACTC
31508033 CATGCATTCCATGCAAAA
1 CATGCATTCCATGCAAAA
**
31508051 CATGCATTCCATGCAACC
1 CATGCATTCCATGCAAAA
* * * *
31508069 CATGTATTTCATACAAAT
1 CATGCATTCCATGCAAAA
*
31508087 CATGCATCCCATGCAA
1 CATGCATTCCATGCAA
31508103 TGTGCTGCAT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.34, C:0.30, G:0.10, T:0.26
Consensus pattern (18 bp):
CATGCATTCCATGCAAAA
Found at i:31508072 original size:36 final size:36
Alignment explanation
Indices: 31508032--31508102 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
31508022 GGTATGCACT
* *
31508032 CCATGCATTCCATGCAAAACATGCATTCCATGCAAC
1 CCATGCATTCCATACAAAACATGCATCCCATGCAAC
* * *
31508068 CCATGTATTTCATACAAATCATGCATCCCATGCAA
1 CCATGCATTCCATACAAAACATGCATCCCATGCAA
31508103 TGTGCTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.34, C:0.31, G:0.10, T:0.25
Consensus pattern (36 bp):
CCATGCATTCCATACAAAACATGCATCCCATGCAAC
Found at i:31513572 original size:8 final size:8
Alignment explanation
Indices: 31513561--31513603 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
31513551 GAAAATACAA
31513561 AAAAAAAG
1 AAAAAAAG
31513569 AAAAAAA-
1 AAAAAAAG
* *
31513576 CAAAAAAC
1 AAAAAAAG
31513584 AAAAAAAG
1 AAAAAAAG
*
31513592 AAAAAAAT
1 AAAAAAAG
31513600 AAAA
1 AAAA
31513604 TAATATGTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.88, C:0.05, G:0.05, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:31514698 original size:21 final size:21
Alignment explanation
Indices: 31514652--31514699 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
31514642 CTAATTGTCA
*
31514652 CTTTCGTTCATCAATTCTTTT
1 CTTTTGTTCATCAATTCTTTT
*
31514673 ATTTTGTTCATCAATT-TTCTT
1 CTTTTGTTCATCAATTCTT-TT
31514694 CTTTTG
1 CTTTTG
31514700 CTCCATTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (21 bp):
CTTTTGTTCATCAATTCTTTT
Found at i:31518100 original size:850 final size:850
Alignment explanation
Indices: 31516460--31518162 Score: 2971
Period size: 850 Copynumber: 2.0 Consensus size: 850
31516450 TCGTTTTAGG
* * * *
31516460 ATCACTTCAGTGGTCAATGTAACTTCTGAAATTCGGCTGAAACTTCTAGGTTGGGTTTTGGGGTG
1 ATCACTTCAGTGGTCAATGTAACTTCTGAAATCCGACTGAAACTTATAGGTTGGGTTTTGAGGTG
* *
31516525 CTATAATAAGGTTGATTAGCCTCGTCTTCATGTAAATAATGCTCAACGTGTGTCTCGTGCAAATG
66 CTACAATAAGGTTGATCAGCCTCGTCTTCATGTAAATAATGCTCAACGTGTGTCTCGTGCAAATG
31516590 ATGAGACTTTGGTTATTAATGACTGTATGCAACATTTTTAGCTAAACCAAAGTTCAACAATCCAC
131 ATGAGACTTTGGTTATTAATGACTGTATGCAACATTTTTAGCTAAACCAAAGTTCAACAATCCAC
31516655 CATTTCGAGGGACGTATGATCCCAAAGCATATTGTGAGTGGGAATAGAAAATTGAACTTATGTTT
196 CATTTCGAGGGACGTATGATCCCAAAGCATATTGTGAGTGGGAATAGAAAATTGAACTTATGTTT
*
31516720 CGTTACTATAAATTTTGGGAAGAGGAAAAAGTCCAATTGACGACCCTTGGATTTTAAGATTATGC
261 CGTTACTATAAATTTTGGGAAGAGGAAAAAGTCCAATTGACGACCCTTGGATTTTAAGATCATGC
* *
31516785 ATTGAGTTGGTGGATTCAACTAGGAATTGATCGTCAAAGAAACCACGAAAGGGTAATTGAAACAT
326 ATTGAGTTAGTGGATTCAACTAGGAATTGATCATCAAAGAAACCACGAAAGGGTAATTGAAACAT
* * *
31516850 GGGACAAGTTGAAGCAAATGATATGAAAGCGTTATGTTCTTCCTCATTACTATAGAGAGGTCTCA
391 GGGACAAGTTGAAGCAAATGATACGAAAGCGTTACGTTCTTCCTCATTACCATAGAGAGGTCTCA
* *
31516915 ACGAGACTTCAACACCTTGTTAAAGGTAATCGATCTCTTGATGAGTACTTTAAGGAGATAAAGAT
456 ACGAGACTTCAACACCTTGTTAAAGGTAATCGATCTCTTGATGAGTACTTTAAAGACATAAAGAT
* * *
31516980 GCTTATGCAAAGAGAAAATATACGAGAGGATGAAGAAACTACCATCGTGTAATTTATAGATGGCT
521 GCTTATGCAAAGAGAAAATATACGAGAGGACGAAGAAAATACCATCGTGCAATTTATAGATGGCT
* *
31517045 TGAATATTTTGATAGCCAATGCTCTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGTACAC
586 TGAATAGTTCGATAGCCAATGCTCTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGTACAC
*
31517110 AAGACAATTGAGATTGAGCAACAATTTCAGCAACATTAATCTCGTCCATTTGGCGCATCACACTA
651 AAGACAATTGAGATTGAGCAACAATTTCAGCAACATCAATCTCGTCCATTTGGCGCATCACACTA
31517175 TTATCGAGGTACAAGTTCTAATTCTAATTTCAACAATTTGAAACCTTCTTATGCTATTAATAAGT
716 TTATCGAGGTACAAGTTCTAATTCTAATTTCAACAATTTGAAACCTTCTTATGCTATTAATAAGT
*
31517240 TATTTCCAAAACATGCTGAGACTAAACCTTTTGAGTAGAAAAGTGGAGCTCTTACAAAACATTCT
781 TATTTCCAAAACATGCTGAGACTAAACCTTTTGAGTAGAAAAGTGGAGCTCCTACAAAACATTCT
31517305 ACTAC
846 ACTAC
* *
31517310 ATCACTTTAGTGGTCAATGTAACCTT-TGAGATCCGACTGAAACTTATAGGTTGGGTTTTGAGGT
1 ATCACTTCAGTGGTCAATGTAA-CTTCTGAAATCCGACTGAAACTTATAGGTTGGGTTTTGAGGT
*
31517374 GTTACAATAAGGTTGATCAGCCTCGTCTTCATGTAAATAATGCTCAACGTGTGTCTCGTGCAAAT
65 GCTACAATAAGGTTGATCAGCCTCGTCTTCATGTAAATAATGCTCAACGTGTGTCTCGTGCAAAT
31517439 GATGAGACTTTGGTTATTAATGACTGTATGCAACATTTTTAGCTAAACCAAAGTTCAACAATCCA
130 GATGAGACTTTGGTTATTAATGACTGTATGCAACATTTTTAGCTAAACCAAAGTTCAACAATCCA
31517504 CCATTTCGAGGGACGTATGATCCCAAAGCATATTGTGAGTGGGAATAGAAAATTGAACTTATGTT
195 CCATTTCGAGGGACGTATGATCCCAAAGCATATTGTGAGTGGGAATAGAAAATTGAACTTATGTT
*
31517569 TCGTTACTATAAATTTTGGGAAGAGGAAAAAGTCCAATTGGCGACCCTTGGATTTTAAGATCATG
260 TCGTTACTATAAATTTTGGGAAGAGGAAAAAGTCCAATTGACGACCCTTGGATTTTAAGATCATG
* * * *
31517634 CATTGAGTTAGTGGATTTAACTTGGAATTGATCATCAAAGAAACCGCTAAAGGGTAATTGAAACA
325 CATTGAGTTAGTGGATTCAACTAGGAATTGATCATCAAAGAAACCACGAAAGGGTAATTGAAACA
*
31517699 TGGGACAAGTTGAAGCAAGTGATACGAAAGCGTTACGTTCCTT-CTCATTACCATAGAGAGGTCT
390 TGGGACAAGTTGAAGCAAATGATACGAAAGCGTTACGTT-CTTCCTCATTACCATAGAGAGGTCT
* *
31517763 CAACGAGACTTCAACACCTTGTTCAAGGTAATCGATCTGTTGATGAGTACTTTAAAGACATAAAG
454 CAACGAGACTTCAACACCTTGTTAAAGGTAATCGATCTCTTGATGAGTACTTTAAAGACATAAAG
* * * *
31517828 ATGCTTATGCAAAGGGCAAATATACGAGAGGACGAAGAAAATAGCA-CGGTGCAATTTGTAGATG
519 ATGCTTATGCAAAGAGAAAATATACGAGAGGACGAAGAAAATACCATC-GTGCAATTTATAGATG
*
31517892 GCTTGAATGGTTCGATAGCCAATGCTCTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGTA
583 GCTTGAATAGTTCGATAGCCAATGCTCTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGTA
* * *
31517957 CACAAGACAATTGAGTTTGAGCAACAATTTCAGCAACGTCAATGTCGTCCATTTGGCGCATCACA
648 CACAAGACAATTGAGATTGAGCAACAATTTCAGCAACATCAATCTCGTCCATTTGGCGCATCACA
*
31518022 CTATTATCGAGGTACAAGTTCTAATTCTACTTTCAACAATTTGAAACCTTCTTATGCTATTAATA
713 CTATTATCGAGGTACAAGTTCTAATTCTAATTTCAACAATTTGAAACCTTCTTATGCTATTAATA
*
31518087 AGTTATTTCCAAAACATGCTGAGACTAAACCTTTTGAGTGGAAAAGTGGAGCTCCTACAAAACAT
778 AGTTATTTCCAAAACATGCTGAGACTAAACCTTTTGAGTAGAAAAGTGGAGCTCCTACAAAACAT
*
31518152 TCTTCTAC
843 TCTACTAC
31518160 ATC
1 ATC
31518163 TTTCAAGGAA
Statistics
Matches: 807, Mismatches: 43, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
849 1 0.00
850 800 0.99
851 6 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (850 bp):
ATCACTTCAGTGGTCAATGTAACTTCTGAAATCCGACTGAAACTTATAGGTTGGGTTTTGAGGTG
CTACAATAAGGTTGATCAGCCTCGTCTTCATGTAAATAATGCTCAACGTGTGTCTCGTGCAAATG
ATGAGACTTTGGTTATTAATGACTGTATGCAACATTTTTAGCTAAACCAAAGTTCAACAATCCAC
CATTTCGAGGGACGTATGATCCCAAAGCATATTGTGAGTGGGAATAGAAAATTGAACTTATGTTT
CGTTACTATAAATTTTGGGAAGAGGAAAAAGTCCAATTGACGACCCTTGGATTTTAAGATCATGC
ATTGAGTTAGTGGATTCAACTAGGAATTGATCATCAAAGAAACCACGAAAGGGTAATTGAAACAT
GGGACAAGTTGAAGCAAATGATACGAAAGCGTTACGTTCTTCCTCATTACCATAGAGAGGTCTCA
ACGAGACTTCAACACCTTGTTAAAGGTAATCGATCTCTTGATGAGTACTTTAAAGACATAAAGAT
GCTTATGCAAAGAGAAAATATACGAGAGGACGAAGAAAATACCATCGTGCAATTTATAGATGGCT
TGAATAGTTCGATAGCCAATGCTCTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGTACAC
AAGACAATTGAGATTGAGCAACAATTTCAGCAACATCAATCTCGTCCATTTGGCGCATCACACTA
TTATCGAGGTACAAGTTCTAATTCTAATTTCAACAATTTGAAACCTTCTTATGCTATTAATAAGT
TATTTCCAAAACATGCTGAGACTAAACCTTTTGAGTAGAAAAGTGGAGCTCCTACAAAACATTCT
ACTAC
Found at i:31520121 original size:11 final size:11
Alignment explanation
Indices: 31520105--31520130 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
31520095 TTCGATGTCT
31520105 TATTATTCTAA
1 TATTATTCTAA
31520116 TATTATTCTAA
1 TATTATTCTAA
31520127 TATT
1 TATT
31520131 TGATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTATTCTAA
Found at i:31520157 original size:14 final size:13
Alignment explanation
Indices: 31520134--31520175 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
31520124 TAATATTTGA
31520134 TTTATTATTTTAT
1 TTTATTATTTTAT
31520147 TTTAGTTA-TTTAT
1 TTTA-TTATTTTAT
*
31520160 TTTAATTGTTTTAT
1 TTT-ATTATTTTAT
31520174 TT
1 TT
31520176 AACTTGGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTATTATTTTAT
Found at i:31524038 original size:22 final size:20
Alignment explanation
Indices: 31523989--31524038 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
31523979 GTTCACTTTT
31523989 ATATC-TTAAAATATAAAAA
1 ATATCATTAAAATATAAAAA
*
31524008 ATATTATTAAAATATAAAAAA
1 ATATCATTAAAATAT-AAAAA
31524029 ATATACATTA
1 ATAT-CATTA
31524039 GTCAAACCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.15
20 9 0.35
21 9 0.35
22 4 0.15
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (20 bp):
ATATCATTAAAATATAAAAA
Found at i:31524154 original size:19 final size:21
Alignment explanation
Indices: 31524113--31524154 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 21
31524103 AATGTGATAT
* *
31524113 TTAAAACTATACAAATTATCA
1 TTAAAACTATACAAATAAGCA
31524134 TTAAAA-TATA-AAATAAGCA
1 TTAAAACTATACAAATAAGCA
31524153 TT
1 TT
31524155 CACTACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.47
20 4 0.21
21 6 0.32
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (21 bp):
TTAAAACTATACAAATAAGCA
Found at i:31524172 original size:120 final size:120
Alignment explanation
Indices: 31523946--31524176 Score: 268
Period size: 120 Copynumber: 1.9 Consensus size: 120
31523936 TTCGTAATCC
* * * * * * * *
31523946 ACACAAATCTAATTATTCAAACAAACATATAATGTTCACTTTTATATCTTAAAATATAAAAAATA
1 ACACAAATATAATCATTCAAACAAAAATATAATGATAAATGTGATATCTTAAAATATAAAAAATA
* * * * *
31524011 TTATTAAAATATAAAAAAATATACATTAGTCAAACCAATCTTAATATCACTTTCA
66 TCATTAAAATATAAAAAAACATACACTAGCCAAAACAATCTTAATATCACTTTCA
* *
31524066 ACACAAATATAATCATTCAAACAAAAATATAATGATAAATGTGATAT-TTAAAACTATACAAATT
1 ACACAAATATAATCATTCAAACAAAAATATAATGATAAATGTGATATCTTAAAA-TATAAAAAAT
* * *
31524130 ATCATTAAAATATAAAATAAGCATTCACTA-CCAAAACTATCTTAATA
65 ATCATTAAAATATAAAA-AAACATACACTAGCCAAAACAATCTTAATA
31524177 CACAATTCTA
Statistics
Matches: 91, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
119 6 0.07
120 77 0.85
121 8 0.09
ACGTcount: A:0.52, C:0.14, G:0.03, T:0.32
Consensus pattern (120 bp):
ACACAAATATAATCATTCAAACAAAAATATAATGATAAATGTGATATCTTAAAATATAAAAAATA
TCATTAAAATATAAAAAAACATACACTAGCCAAAACAATCTTAATATCACTTTCA
Done.