Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold193
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: 443907
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:245787 original size:27 final size:27
Alignment explanation
Indices: 245746--245797 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
245736 TCATTGAAGC
* *
245746 ATCTTCATTGCTGTCCATGCATGTATT
1 ATCTTCAATGATGTCCATGCATGTATT
245773 ATCTTCAATGATGTCCATGCATGTA
1 ATCTTCAATGATGTCCATGCATGTA
245798 CCTACAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.40
Consensus pattern (27 bp):
ATCTTCAATGATGTCCATGCATGTATT
Found at i:247408 original size:40 final size:40
Alignment explanation
Indices: 247324--247507 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
247314 TTGAATGCTG
* * * *
247324 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
247363 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
247404 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
247444 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
247484 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
247508 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:247461 original size:80 final size:81
Alignment explanation
Indices: 247324--247504 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
247314 TTGAATGCTG
* * *
247324 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
247388 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
247404 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
247465 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
247484 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
247505 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:247528 original size:39 final size:38
Alignment explanation
Indices: 247405--247554 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
247395 GTTATTAATT
* ** * *
247405 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
247445 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
247484 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
247524 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
247555 GAGCTAAATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:255257 original size:40 final size:40
Alignment explanation
Indices: 255173--255356 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
255163 TTGAATGCTG
* * * *
255173 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
255212 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
255253 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
255293 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
255333 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
255357 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:255310 original size:80 final size:81
Alignment explanation
Indices: 255173--255353 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
255163 TTGAATGCTG
* * *
255173 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
255237 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
255253 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
255314 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
255333 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
255354 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:255377 original size:39 final size:38
Alignment explanation
Indices: 255254--255403 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
255244 GTTATTAATT
* ** * *
255254 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
255294 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
255333 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
255373 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
255404 GAGCTAAATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:260605 original size:23 final size:22
Alignment explanation
Indices: 260579--260633 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
260569 AAGTACAAGA
260579 AAAAAAGATTGA-AAAAGAGAAAG
1 AAAAAAGA-TGATAAAA-AGAAAG
260602 AAAAAA-ATGATAAAAAGAAAG
1 AAAAAAGATGATAAAAAGAAAG
*
260623 GAAAAAG-TGAT
1 AAAAAAGATGAT
260634 GGAGTGGAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 18 0.62
22 5 0.17
23 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (22 bp):
AAAAAAGATGATAAAAAGAAAG
Found at i:262916 original size:20 final size:20
Alignment explanation
Indices: 262893--262939 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
262883 GGGTTAAGAT
*
262893 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
262913 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
262933 TGAGCTG
1 TGAGCTG
262940 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:274756 original size:45 final size:45
Alignment explanation
Indices: 274688--274894 Score: 351
Period size: 45 Copynumber: 4.6 Consensus size: 45
274678 AAGAGGTGGA
** * * *
274688 CAACATCATGCATAATTTGTGGAACAAATTAAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
274733 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
*
274778 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
*
274823 CAACATCATGCATAATTCATGAAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
274868 CAACATCATGCATAATTCATGGAAGAA
1 CAACATCATGCATAATTCATGGAAGAA
274895 CCTTGAATTA
Statistics
Matches: 153, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 153 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
Found at i:281008 original size:45 final size:45
Alignment explanation
Indices: 280940--281146 Score: 360
Period size: 45 Copynumber: 4.6 Consensus size: 45
280930 AAGAGGTGGA
** * * *
280940 CAACATCATGCATAATTTGTGGAACAAATTAAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
280985 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
*
281030 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
281075 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
281120 CAACATCATGCATAATTCATGGAAGAA
1 CAACATCATGCATAATTCATGGAAGAA
281147 CCTTGAATTA
Statistics
Matches: 155, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 155 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
Found at i:297805 original size:19 final size:18
Alignment explanation
Indices: 297769--297808 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
297759 TTTCCACTCG
*
297769 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
297787 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
297806 TTT
1 TTT
297809 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:298874 original size:16 final size:17
Alignment explanation
Indices: 298853--298897 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
298843 AAACTAGCTC
298853 TTTTTTTTTTCAC-AAA
1 TTTTTTTTTTCACAAAA
298869 TTTTTTTTTTCACAAAA
1 TTTTTTTTTTCACAAAA
298886 TTTTTTTTTTCA
1 TTTTTTTTTTCA
298898 ACTTGATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTTTTTTCACAAAA
Found at i:298954 original size:11 final size:11
Alignment explanation
Indices: 298938--298982 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
298928 GAAACCATTT
298938 TTTTTTTTGAA
1 TTTTTTTTGAA
298949 TTTTTTTTGAA
1 TTTTTTTTGAA
*
298960 TTTTTTTTCAAA
1 TTTTTTTT-GAA
298972 TTTTTTTTGAA
1 TTTTTTTTGAA
298983 GAAACTACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 21 0.68
12 10 0.32
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.71
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:298954 original size:12 final size:12
Alignment explanation
Indices: 298937--298979 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
298927 GGAAACCATT
298937 TTTTTTTTTGAA
1 TTTTTTTTTGAA
298949 -TTTTTTTTGAA
1 TTTTTTTTTGAA
**
298960 TTTTTTTTCAAA
1 TTTTTTTTTGAA
298972 TTTTTTTT
1 TTTTTTTT
298980 GAAGAAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 11 0.39
12 17 0.61
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:298963 original size:23 final size:23
Alignment explanation
Indices: 298937--298982 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
298927 GGAAACCATT
**
298937 TTTTTTTTTGAATTTTTTTTGAA
1 TTTTTTTTCAAATTTTTTTTGAA
298960 TTTTTTTTCAAATTTTTTTTGAA
1 TTTTTTTTCAAATTTTTTTTGAA
298983 GAAACTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.72
Consensus pattern (23 bp):
TTTTTTTTCAAATTTTTTTTGAA
Found at i:308283 original size:25 final size:24
Alignment explanation
Indices: 308255--308333 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 24
308245 TCTTGTACAT
308255 GTATGCTTATACGAGCTGTAAATCG
1 GTATGCTTATA-GAGCTGTAAATCG
* * *
308280 GTATGCTTACATGAGCTATAAATTG
1 GTATGCTTATA-GAGCTGTAAATCG
308305 GTATGCTCTCATA-AGCTGTAAATCG
1 GTATGCT-T-ATAGAGCTGTAAATCG
308330 GTAT
1 GTAT
308334 ATTTTCACGA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
25 42 0.93
26 1 0.02
27 2 0.04
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (24 bp):
GTATGCTTATAGAGCTGTAAATCG
Found at i:311843 original size:11 final size:11
Alignment explanation
Indices: 311827--311856 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
311817 GACACGGTTG
*
311827 TAGAAATACCT
1 TAGAAACACCT
311838 TAGAAACACCT
1 TAGAAACACCT
311849 TAGAAACA
1 TAGAAACA
311857 ATTTAGGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.20, G:0.10, T:0.20
Consensus pattern (11 bp):
TAGAAACACCT
Found at i:312852 original size:14 final size:15
Alignment explanation
Indices: 312833--312861 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
312823 TACATATTAA
312833 CATATCAATC-TCAT
1 CATATCAATCATCAT
312847 CATATCAATCATCAT
1 CATATCAATCATCAT
312862 AATAATCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (15 bp):
CATATCAATCATCAT
Found at i:313650 original size:54 final size:54
Alignment explanation
Indices: 313532--313641 Score: 157
Period size: 54 Copynumber: 2.0 Consensus size: 54
313522 ACTTACTTGG
* * * *
313532 TATCCTTATTTACCGATTTTTACCGATCTCTGTGAATACACTCGTATTCACACA
1 TATCCTTATTTACCAATTTTTACCAATCTCTATGAATACACTCATATTCACACA
* * *
313586 TATCCTTATTTATCAATTTTTACTAATCTCTATGAATACGCTCATATTCACACA
1 TATCCTTATTTACCAATTTTTACCAATCTCTATGAATACACTCATATTCACACA
313640 TA
1 TA
313642 CTTATATTTC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (54 bp):
TATCCTTATTTACCAATTTTTACCAATCTCTATGAATACACTCATATTCACACA
Found at i:313716 original size:21 final size:21
Alignment explanation
Indices: 313687--313726 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
313677 CATTTAAAAT
* *
313687 ATCACTATTATTTATTATTTA
1 ATCAATATTATTAATTATTTA
313708 ATCAATATTATTAATTATT
1 ATCAATATTATTAATTATT
313727 ATCAAGAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
ATCAATATTATTAATTATTTA
Found at i:316030 original size:35 final size:35
Alignment explanation
Indices: 315973--316089 Score: 123
Period size: 35 Copynumber: 3.3 Consensus size: 35
315963 AATCCAACCA
*
315973 AAACACACCAGATGCTCATAAGAGCCAAT-CCAAT-TG
1 AAACACACCA-ATGCTCATAAGAGCCAATACC--TCCG
*
316009 AAACACACCAATGCTCATAAGAGCTAATACCTCCG
1 AAACACACCAATGCTCATAAGAGCCAATACCTCCG
* * * *
316044 GAACACACCAATGCTCATAAGAGCTAATTCACT-CA
1 AAACACACCAATGCTCATAAGAGCCAATAC-CTCCG
316079 AAACACACCAA
1 AAACACACCAA
316090 ACAGAGAGTA
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
34 1 0.01
35 57 0.79
36 14 0.19
ACGTcount: A:0.43, C:0.30, G:0.11, T:0.16
Consensus pattern (35 bp):
AAACACACCAATGCTCATAAGAGCCAATACCTCCG
Found at i:317833 original size:27 final size:27
Alignment explanation
Indices: 317803--317893 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 27
317793 CTTTATAATT
* *
317803 CGCCATAAAGGCATTCTTTTCATATTC
1 CGCCACAAAGGCATTCTTTTCATATTA
* *
317830 CGCCACAAAGG-GTTTTCTTTCATATTA
1 CGCCACAAAGGCATTCT-TTTCATATTA
* *
317857 CGCCACAAAGTCTTTC-TTTCATATTA
1 CGCCACAAAGGCATTCTTTTCATATTA
*
317883 TGCCACAAAGG
1 CGCCACAAAGG
317894 TTATCATTGC
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
26 22 0.42
27 29 0.55
28 2 0.04
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.34
Consensus pattern (27 bp):
CGCCACAAAGGCATTCTTTTCATATTA
Found at i:321484 original size:58 final size:58
Alignment explanation
Indices: 321394--321509 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
321384 ACCCACTTCA
321394 AACATCATTCCATCCATTGTCGAGGATCTGCAAAACCAAAACTTTCCATTTTTTGTCT
1 AACATCATTCCATCCATTGTCGAGGATCTGCAAAACCAAAACTTTCCATTTTTTGTCT
321452 AACATCATTCCATCCATTGTCGAGGATCTGCAAAACCAAAACTTTCCATTTTTTGTCT
1 AACATCATTCCATCCATTGTCGAGGATCTGCAAAACCAAAACTTTCCATTTTTTGTCT
321510 TTTGAAAAGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.34
Consensus pattern (58 bp):
AACATCATTCCATCCATTGTCGAGGATCTGCAAAACCAAAACTTTCCATTTTTTGTCT
Found at i:333946 original size:20 final size:21
Alignment explanation
Indices: 333921--333970 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
333911 AGCTAATTGC
333921 TTGTATTTT-GGTACATTT-AG
1 TTGTATTTTAGG-ACATTTCAG
*
333941 TTGTATTTTAGGACATTTCAT
1 TTGTATTTTAGGACATTTCAG
333962 TTGTATTTT
1 TTGTATTTT
333971 CATCATTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.20, C:0.06, G:0.16, T:0.58
Consensus pattern (21 bp):
TTGTATTTTAGGACATTTCAG
Found at i:339034 original size:20 final size:20
Alignment explanation
Indices: 339009--339115 Score: 81
Period size: 20 Copynumber: 5.4 Consensus size: 20
338999 TTCAGGTCAC
*
339009 TCGAGCTTAAGTCAACTCAT
1 TCGAGCTCAAGTCAACTCAT
* *
339029 TCGAGCTCAAGTCAGCTCAC
1 TCGAGCTCAAGTCAACTCAT
* * * *
339049 ACGAGCTCAATTCAGCTCAC
1 TCGAGCTCAAGTCAACTCAT
* * * *
339069 ACGAGCTCAATTCAGCTCAC
1 TCGAGCTCAAGTCAACTCAT
* * *
339089 ACGAGCTCAATTCAGCTCAT
1 TCGAGCTCAAGTCAACTCAT
339109 T-GAGCTC
1 TCGAGCTC
339116 GTTATTAGCT
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
19 6 0.08
20 74 0.93
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (20 bp):
TCGAGCTCAAGTCAACTCAT
Found at i:339126 original size:40 final size:40
Alignment explanation
Indices: 339030--339107 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
339020 TCAACTCATT
*
339030 CGAGCTCAAGTCAGCTCACACGAGCTCAATTCAGCTCACA
1 CGAGCTCAATTCAGCTCACACGAGCTCAATTCAGCTCACA
339070 CGAGCTCAATTCAGCTCACACGAGCTCAATTCAGCTCA
1 CGAGCTCAATTCAGCTCACACGAGCTCAATTCAGCTCA
339108 TTGAGCTCGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.29, C:0.35, G:0.17, T:0.19
Consensus pattern (40 bp):
CGAGCTCAATTCAGCTCACACGAGCTCAATTCAGCTCACA
Found at i:342948 original size:20 final size:20
Alignment explanation
Indices: 342899--342940 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
342889 CTATCTAGGG
342899 AGATAGGAACCTCGGTATGA
1 AGATAGGAACCTCGGTATGA
342919 AGATAGGAACCTCGGTATGA
1 AGATAGGAACCTCGGTATGA
342939 AG
1 AG
342941 GTTTGAACGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.31, T:0.19
Consensus pattern (20 bp):
AGATAGGAACCTCGGTATGA
Found at i:349084 original size:50 final size:52
Alignment explanation
Indices: 348974--349093 Score: 190
Period size: 50 Copynumber: 2.3 Consensus size: 52
348964 ATGAACAAAT
* * *
348974 GAGTTACTTAATGCATGACTTAATTTAATGATGCAAACTTTAACTAACATGG
1 GAGTTACATAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
*
349026 GAGTTACATAATGCATGTCATAATTT-ATGATGCAAAC-TTAACTAACATGA
1 GAGTTACATAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
349076 GAGTTACATAATGCATGA
1 GAGTTACATAATGCATGA
349094 ATTTATTAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 29 0.46
51 11 0.17
52 23 0.37
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (52 bp):
GAGTTACATAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
Found at i:360001 original size:11 final size:12
Alignment explanation
Indices: 359985--360018 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
359975 AAAAGTACAA
*
359985 GAAAAATAGATT
1 GAAAAAGAGATT
359997 GAAAAAGAGATT
1 GAAAAAGAGATT
360009 GAAAAAGAGA
1 GAAAAAGAGA
360019 AAGAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.15
Consensus pattern (12 bp):
GAAAAAGAGATT
Found at i:361945 original size:24 final size:23
Alignment explanation
Indices: 361918--361999 Score: 89
Period size: 24 Copynumber: 3.6 Consensus size: 23
361908 GCTGCTGAAT
*
361918 TTTAAAGGATGTATAATGCTCTCC
1 TTTAAATGATGTATAA-GCTCTCC
*
361942 TTTAATTGATGTA-ACAG--CTCC
1 TTTAAATGATGTATA-AGCTCTCC
361963 TTTAAATGATGTATAAAGCTCTCC
1 TTTAAATGATGTAT-AAGCTCTCC
*
361987 TTTAATTGATGTA
1 TTTAAATGATGTA
362000 ACAGCCCCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
21 16 0.33
22 2 0.04
23 3 0.06
24 28 0.57
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (23 bp):
TTTAAATGATGTATAAGCTCTCC
Found at i:361964 original size:21 final size:21
Alignment explanation
Indices: 361938--362009 Score: 90
Period size: 21 Copynumber: 3.3 Consensus size: 21
361928 GTATAATGCT
361938 CTCCTTTAATTGATGTAACAG
1 CTCCTTTAATTGATGTAACAG
* *
361959 CTCCTTTAAATGATGTATAAAG
1 CTCCTTTAATTGATGTA-ACAG
361981 CTCTCCTTTAATTGATGTAACAG
1 --CTCCTTTAATTGATGTAACAG
*
362004 CCCCTT
1 CTCCTT
362010 GTATGTAACT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 21 0.49
22 3 0.07
23 3 0.07
24 16 0.37
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (21 bp):
CTCCTTTAATTGATGTAACAG
Found at i:361984 original size:45 final size:45
Alignment explanation
Indices: 361918--362009 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
361908 GCTGCTGAAT
* *
361918 TTTAAAGGATGTATAATGCTCTCCTTTAATTGATGTAACAGCTCC
1 TTTAAAGGATGTATAAAGCTCTCCTTTAATTGATGTAACAGCCCC
*
361963 TTTAAATGATGTATAAAGCTCTCCTTTAATTGATGTAACAGCCCC
1 TTTAAAGGATGTATAAAGCTCTCCTTTAATTGATGTAACAGCCCC
362008 TT
1 TT
362010 GTATGTAACT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (45 bp):
TTTAAAGGATGTATAAAGCTCTCCTTTAATTGATGTAACAGCCCC
Found at i:362266 original size:40 final size:40
Alignment explanation
Indices: 362220--362305 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
362210 GTTTAATAAA
** *
362220 AATAAAGTGTAACAACTTAATTATTAACTAAGATGAGTTT
1 AATAAAGTCCAACAACTCAATTATTAACTAAGATGAGTTT
*
362260 AATAAAGTCCAGCAACTCAATTATTAACTAAGATGAGTTT
1 AATAAAGTCCAACAACTCAATTATTAACTAAGATGAGTTT
362300 AATAAA
1 AATAAA
362306 ATTAAAGTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (40 bp):
AATAAAGTCCAACAACTCAATTATTAACTAAGATGAGTTT
Found at i:364574 original size:20 final size:19
Alignment explanation
Indices: 364530--364578 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
364520 TTGTTCAATT
* *
364530 TCAATCTCATTTTTCTTTT
1 TCAATTTCATTTTTCTTTC
364549 TC--TTTCATTTTTCTTCTC
1 TCAATTTCATTTTTCTT-TC
364567 TCAATTTCATTT
1 TCAATTTCATTT
364579 CATGTTCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 12 0.48
18 3 0.12
19 2 0.08
20 8 0.32
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.63
Consensus pattern (19 bp):
TCAATTTCATTTTTCTTTC
Found at i:366397 original size:24 final size:24
Alignment explanation
Indices: 366340--366400 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
366330 GCTGCTAAAT
* *
366340 TTTAAAGGATGAATAATGCTCTCC
1 TTTAAATGATGTATAATGCTCTCC
366364 TTTAAATGATGTATAATGCTCTCC
1 TTTAAATGATGTATAATGCTCTCC
*
366388 TTTAATTGATGTA
1 TTTAAATGATGTA
366401 ACAGCCCCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (24 bp):
TTTAAATGATGTATAATGCTCTCC
Found at i:366711 original size:40 final size:40
Alignment explanation
Indices: 366630--366713 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
366620 GTTTAATAAA
* * * *
366630 AATAAATTCCAACAACTCAATTATTAACTAAGTTGAGTTT
1 AATAAAGTCCAACAACTCAATTATTAACTAAGATAAATTT
* *
366670 AATAAAGTCCAGCAACTCGATTATTAACTAAGATAAATTT
1 AATAAAGTCCAACAACTCAATTATTAACTAAGATAAATTT
366710 AATA
1 AATA
366714 GAATTAAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.32
Consensus pattern (40 bp):
AATAAAGTCCAACAACTCAATTATTAACTAAGATAAATTT
Found at i:366984 original size:21 final size:21
Alignment explanation
Indices: 366958--367013 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
366948 AATAGTGGTG
*
366958 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
366979 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
367000 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
367014 AGCAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:372285 original size:27 final size:27
Alignment explanation
Indices: 372255--372432 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
372245 ATATTGAGCC
* * *
372255 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
372282 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* * * *
372309 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACACAATCA-AAT
** *** *
372337 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACACAATCAAAT
* * **
372364 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * * *
372391 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTACACAATCAAAT
372418 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
372433 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:372348 original size:55 final size:55
Alignment explanation
Indices: 372255--372432 Score: 204
Period size: 54 Copynumber: 3.3 Consensus size: 55
372245 ATATTGAGCC
* * *
372255 CGCACACTCAGTGCTATACA-A-TCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAT-CATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * *
372309 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATA-TTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
** * *
372364 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
372418 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
372433 GTACAATTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 56 0.54
55 45 0.43
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:372394 original size:82 final size:81
Alignment explanation
Indices: 372276--372431 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
372266 TGCTATACAA
* * *
372276 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA
372341 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
372358 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA
372422 CACTTAGTGC
65 CACTTAGTGC
372432 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.31
82 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:383132 original size:265 final size:265
Alignment explanation
Indices: 382659--383190 Score: 1019
Period size: 265 Copynumber: 2.0 Consensus size: 265
382649 CCCCAAGTGT
* *
382659 TTGTTTTCTTTGATTAGGAGTTTCATGAGAAGGGTTTGAGGGTACCTCATTAGGAGGACTACCTT
1 TTGTTTTCTTTGATTAGGAGTTTCATGAAAAGGGTTTGAGGGCACCTCATTAGGAGGACTACCTT
382724 CATTCTCATTACTATGTTCATCTAAATCACCAAATCCCTCATTAGGTGTATCATCTCCCATAGGA
66 CATTCTCATTACTATGTTCATCTAAATCACCAAATCCCTCATTAGGTGTATCATCTCCCATAGGA
*
382789 ACCCCACTTGGAAGAACACCAGACGAATGTGCCCATGCATTCTCTCCAGTAGCTACAATGCCACC
131 ACCCCACTTGAAAGAACACCAGACGAATGTGCCCATGCATTCTCTCCAGTAGCTACAATGCCACC
382854 AAACATTTGCCACATTAACTCATTCAATCGTGGTTCAATTCCTTTCTTCTTAAATCCTTTAAAAT
196 AAACATTTGCCACATTAACTCATTCAATCGTGGTTCAATTCCTTTCTTCTTAAATCCTTTAAAAT
382919 CAAGA
261 CAAGA
382924 TTGTTTTCTTTGATTAGGAGTTTCATGAAAAGGGTTTGAGGGCACCTCATTAGGAGGACTACCTT
1 TTGTTTTCTTTGATTAGGAGTTTCATGAAAAGGGTTTGAGGGCACCTCATTAGGAGGACTACCTT
382989 CATTCTCATTACTATGTTCATCTAAATCACCAAATCCCTCATTAGGTGTATCATCTCCCATAGGA
66 CATTCTCATTACTATGTTCATCTAAATCACCAAATCCCTCATTAGGTGTATCATCTCCCATAGGA
*
383054 ACCCCACTTGAAAGAACATCAGACGAATGTGCCCATGCATTCTCTCCAGTAGCTACAATGCCACC
131 ACCCCACTTGAAAGAACACCAGACGAATGTGCCCATGCATTCTCTCCAGTAGCTACAATGCCACC
*
383119 AAATATTTGCCACATTAACTCATTCAATCGTGGTTCAATTCCTTTCTTCTTAAATCCTTTAAAAT
196 AAACATTTGCCACATTAACTCATTCAATCGTGGTTCAATTCCTTTCTTCTTAAATCCTTTAAAAT
383184 CAAGA
261 CAAGA
383189 TT
1 TT
383191 TTCCTACATA
Statistics
Matches: 262, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
265 262 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.33
Consensus pattern (265 bp):
TTGTTTTCTTTGATTAGGAGTTTCATGAAAAGGGTTTGAGGGCACCTCATTAGGAGGACTACCTT
CATTCTCATTACTATGTTCATCTAAATCACCAAATCCCTCATTAGGTGTATCATCTCCCATAGGA
ACCCCACTTGAAAGAACACCAGACGAATGTGCCCATGCATTCTCTCCAGTAGCTACAATGCCACC
AAACATTTGCCACATTAACTCATTCAATCGTGGTTCAATTCCTTTCTTCTTAAATCCTTTAAAAT
CAAGA
Found at i:386112 original size:12 final size:11
Alignment explanation
Indices: 386095--386137 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
386085 GTAGTTTCTT
386095 GAAAAAAAACTC
1 GAAAAAAAA-TC
* *
386107 GAAAAAATATT
1 GAAAAAAAATC
386118 GAAAAAAAATTC
1 GAAAAAAAA-TC
386130 GAAAAAAA
1 GAAAAAAA
386138 CTAGTTTCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.70, C:0.07, G:0.09, T:0.14
Consensus pattern (11 bp):
GAAAAAAAATC
Found at i:386123 original size:23 final size:23
Alignment explanation
Indices: 386093--386136 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
386083 TAGTAGTTTC
386093 TTGAAAAAAAACTCGAAAAAATA
1 TTGAAAAAAAACTCGAAAAAATA
*
386116 TTGAAAAAAAATTCGAAAAAA
1 TTGAAAAAAAACTCGAAAAAA
386137 ACTAGTTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.66, C:0.07, G:0.09, T:0.18
Consensus pattern (23 bp):
TTGAAAAAAAACTCGAAAAAATA
Found at i:386209 original size:14 final size:14
Alignment explanation
Indices: 386175--386227 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
386165 GGATATCAAG
386175 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
**
386189 -T-CAAAAAAAAAA
1 TTGTGAAAAAAAAA
386201 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
386215 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
386228 GAGCTAGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 9 0.27
13 2 0.06
14 22 0.67
ACGTcount: A:0.68, C:0.02, G:0.11, T:0.19
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:400433 original size:33 final size:33
Alignment explanation
Indices: 400391--400457 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
400381 ATAGTTACTG
*
400391 TTACTTAGGCCTAGAATTTCAAGAGTTTGTGCT
1 TTACTTAGGCCTAAAATTTCAAGAGTTTGTGCT
400424 TTACTTAGGCCTAAAATTTCAAGAGTTTGTGCT
1 TTACTTAGGCCTAAAATTTCAAGAGTTTGTGCT
400457 T
1 T
400458 AGTGATTAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.40
Consensus pattern (33 bp):
TTACTTAGGCCTAAAATTTCAAGAGTTTGTGCT
Found at i:402397 original size:20 final size:20
Alignment explanation
Indices: 402374--402420 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
402364 GGGTTAAGAT
402374 TGAGCTGAATTAAGCTCGAA-
1 TGAGCTGAATTAAGCTC-AAG
* *
402394 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTAAGCTCAAG
402414 TGAGCTG
1 TGAGCTG
402421 GAAATGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTAAGCTCAAG
Found at i:404324 original size:12 final size:12
Alignment explanation
Indices: 404291--404356 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
404281 TTTCCACTCG
404291 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
404302 AGCTCTCTTTCA
1 ATTTCTTTTTCA
*
404314 ATTTCTTTTTCC
1 ATTTCTTTTTCA
*
404326 A---CTATTTCA
1 ATTTCTTTTTCA
404335 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
404347 ATCTCTTTTT
1 ATTTCTTTTT
404357 GCTTTTCACT
Statistics
Matches: 40, Mismatches: 11, Indels: 7
0.69 0.19 0.12
Matches are distributed among these distances:
9 7 0.17
11 3 0.08
12 30 0.75
ACGTcount: A:0.17, C:0.23, G:0.02, T:0.59
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:404409 original size:15 final size:15
Alignment explanation
Indices: 404386--404427 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
404376 TTTTGAAATC
404386 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
404401 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
404416 TCATTTTCATTT
1 TCATTTTCATTT
404428 TCATTATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 2 0.08
15 22 0.92
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:405493 original size:8 final size:9
Alignment explanation
Indices: 405479--405503 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
405469 TTTCACTTCT
405479 TTTTTTTAC
1 TTTTTTTAC
405488 TTTTTTTAC
1 TTTTTTTAC
405497 TTTTTTT
1 TTTTTTT
405504 TTTGCTCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAC
Found at i:407111 original size:20 final size:20
Alignment explanation
Indices: 407082--407125 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
407072 TTAAGATTGT
407082 GCTGAATTGAGCTCGAA-TGA
1 GCTGAATTGAGCTC-AAGTGA
*
407102 GCTGACTTGAGCTCAAGTGA
1 GCTGAATTGAGCTCAAGTGA
407122 GCTG
1 GCTG
407126 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (20 bp):
GCTGAATTGAGCTCAAGTGA
Found at i:408508 original size:18 final size:18
Alignment explanation
Indices: 408487--408541 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 18
408477 GCTGTTGAGA
*
408487 AGGAAGTTGCTACAGAAG
1 AGGAAGTTGCTAAAGAAG
408505 AGGAAGTTGTTGCTAAAGAAG
1 AGGAA---GTTGCTAAAGAAG
* *
408526 AAGAAGTTGCTGAAGA
1 AGGAAGTTGCTAAAGA
408542 TGAAAAGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 15 0.48
21 16 0.52
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (18 bp):
AGGAAGTTGCTAAAGAAG
Found at i:408518 original size:21 final size:21
Alignment explanation
Indices: 408492--408534 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
408482 TGAGAAGGAA
* *
408492 GTTGCTACAGAAGAGGAAGTT
1 GTTGCTAAAGAAGAAGAAGTT
408513 GTTGCTAAAGAAGAAGAAGTT
1 GTTGCTAAAGAAGAAGAAGTT
408534 G
1 G
408535 CTGAAGATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (21 bp):
GTTGCTAAAGAAGAAGAAGTT
Found at i:414289 original size:24 final size:23
Alignment explanation
Indices: 414249--414315 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
414239 AAAAATCAAA
**
414249 AGAAAAAGAACCAAAAAAAAGATTG
1 AGAAAAAGAAAGAAAAAAAA-A-TG
414274 A-AAAAGAGAAAGAAAAGAAAAATG
1 AGAAAA-AGAAAGAAAA-AAAAATG
*
414298 AGAAAAAGAAAGGAAAAA
1 AGAAAAAGAAAGAAAAAA
414316 GTGAGAGAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 2 0.06
24 16 0.44
25 14 0.39
26 4 0.11
ACGTcount: A:0.73, C:0.03, G:0.19, T:0.04
Consensus pattern (23 bp):
AGAAAAAGAAAGAAAAAAAAATG
Found at i:414307 original size:20 final size:21
Alignment explanation
Indices: 414282--414321 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
414272 TGAAAAAGAG
414282 AAAGAAAAGAAAAA-TGAGAA
1 AAAGAAAAGAAAAAGTGAGAA
*
414302 AAAGAAAGGAAAAAGTGAGA
1 AAAGAAAAGAAAAAGTGAGA
414322 GAGTGGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (21 bp):
AAAGAAAAGAAAAAGTGAGAA
Found at i:428220 original size:44 final size:44
Alignment explanation
Indices: 428157--428241 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
428147 GTATGAAAAG
428157 GAAAATAATGGTAAGTGTTGAAATGAACTATGTATTGTAATTAT
1 GAAAATAATGGTAAGTGTTGAAATGAACTATGTATTGTAATTAT
*
428201 GAAAATAATGGTAAGTGTTGAAATGAACTATGTCTTGTAAT
1 GAAAATAATGGTAAGTGTTGAAATGAACTATGTATTGTAAT
428242 GATGCGATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (44 bp):
GAAAATAATGGTAAGTGTTGAAATGAACTATGTATTGTAATTAT
Found at i:430098 original size:14 final size:14
Alignment explanation
Indices: 430078--430118 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
430068 TTGGCCTCTC
430078 CATTTTTACT-TTTT
1 CATTTTT-CTATTTT
*
430092 TATTTTTCTATTTT
1 CATTTTTCTATTTT
430106 CATTTTT-TATTTT
1 CATTTTTCTATTTT
430119 TACGACTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.76
Consensus pattern (14 bp):
CATTTTTCTATTTT
Found at i:430846 original size:9 final size:9
Alignment explanation
Indices: 430814--430845 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
430804 TATTTTAATT
430814 TTTTTTGAA
1 TTTTTTGAA
430823 TTTTTTGAA
1 TTTTTTGAA
430832 TTTTTTG-A
1 TTTTTTGAA
430840 TTTTTT
1 TTTTTT
430846 TTTGATCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.75
Consensus pattern (9 bp):
TTTTTTGAA
Found at i:441346 original size:16 final size:16
Alignment explanation
Indices: 441327--441365 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
441317 TTATGGGAGC
*
441327 ATACATGAATGGCTGG
1 ATACATGAATGACTGG
*
441343 ATACATGGATGACTGG
1 ATACATGAATGACTGG
*
441359 ATTCATG
1 ATACATG
441366 GATATGGCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (16 bp):
ATACATGAATGACTGG
Found at i:443094 original size:14 final size:14
Alignment explanation
Indices: 443075--443103 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
443065 GTTATAATAT
443075 ATGAGAAATGGTTG
1 ATGAGAAATGGTTG
443089 ATGAGAAATGGTTG
1 ATGAGAAATGGTTG
443103 A
1 A
443104 ATATGAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (14 bp):
ATGAGAAATGGTTG
Found at i:443413 original size:51 final size:51
Alignment explanation
Indices: 443358--443541 Score: 212
Period size: 51 Copynumber: 3.6 Consensus size: 51
443348 TATAAAAATG
* * *
443358 TGTGTAGTACTAAGTGCAGGCTACTCCGTGTATC-GATA-GATAATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-AGGAT-ATGGTCACA
* *
443409 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGAAGGATTTGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAGGATATGGTCACA
* * * * * *
443460 TGTGTAGTACTATGTGCAGGCTACTACGTGAACCGGAAAG-TTTGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAGGATATGGTCACA
* *
443510 TGTGTAGTACTATGTGAAGGCTTCTACGTGTA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTA
443542 TCGAATGATA
Statistics
Matches: 117, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
50 37 0.32
51 75 0.64
52 5 0.04
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAGGATATGGTCACA
Found at i:443541 original size:101 final size:102
Alignment explanation
Indices: 443358--443541 Score: 246
Period size: 101 Copynumber: 1.8 Consensus size: 102
443348 TATAAAAATG
* * * * *
443358 TGTGTAGTACTAAGTGCAGGCTACTCCGTGTATCGATAGATAATGGTCACATGTGTAGTACTATG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGAAAGATAATGATCACATGTGTAGTACTATG
* *
443423 TGCAGGCTACTATGTGTACCAGAAGGATTTGGTCACA
66 TGAAGGCTACTACGTGTACCAGAAGGATTTGGTCACA
* * *
443460 TGTGTAGTACTATGTGCAGGCTACTACGTGAACCGGAAAG-T-TTGATCACGTGTGTAGTACTAT
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGAACC-GAAAGATAATGATCACATGTGTAGTACTAT
*
443523 GTGAAGGCTTCTACGTGTA
65 GTGAAGGCTACTACGTGTA
443542 TCGAATGATA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
101 35 0.50
102 31 0.44
103 4 0.06
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (102 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGAAAGATAATGATCACATGTGTAGTACTATG
TGAAGGCTACTACGTGTACCAGAAGGATTTGGTCACA
Done.