Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007492.1 Hibiscus syriacus cultivar Beakdansim tig00020714_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 152177
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1927 original size:288 final size:285
Alignment explanation
Indices: 1418--2176 Score: 949
Period size: 286 Copynumber: 2.7 Consensus size: 285
1408 TAAATTGGAT
* * * * *
1418 AAAC-TAATAATTACAAATTGAAATTTAAATTAATTAAACAACATAC-GAGATCAAAATGAAACA
1 AAACATAA-AATTACAAAATGAAATTTAAATAAATTAAACAACACACAAAGATCAAATTGAAACA
* *
1481 ATTGTAAAAT-ATAAAGATAAAATTAATATCAAAATGGACTAAATTGCATTCATTTGAAAAGTTG
65 ATTGTAAAATGA-AAAGATGAAATTAATATCAAATTGGACTAAATTGCATTCATTTGAAAAGTTG
* * * * * * *
1545 GTGAACAAAAGTTTATAAAATTTGGAGATAATGATATAATTTATAGAGTTTAAAATGACGTTTAT
129 GTGAAC-AAAGTTTATAGAATTTGGAGATTATGATATAATTTATAGTGTTTGAAATAAAGCTTAT
* * * **
1610 GGTGTAATTTATAGGTTTTGGAGTAAATTACAAAAAATAGAAATAGTTAT-AGGTCAATTTTGGA
193 GGTGTAATTTATAGGGTTTGGAATAAATTACAAAAAAT--AAATAATTATGACCT-AATTTTGGA
1674 TAAAAATATAATTTTAAGGACTAAATTCAAC
255 TAAAAATATAATTTTAAGGACTAAATTCAAC
* *
1705 AAACATAAAATTATAAACTGAAATTTAAATAAATTAAACAACACACAAAGATCAAATTGAAACAA
1 AAACATAAAATTACAAAATGAAATTTAAATAAATTAAACAACACACAAAGATCAAATTGAAACAA
* * ** * *
1770 TTGTAAAATGAAAAGCTGAAATTAATATCAAATTGGACTAAGTTATATTCACTTAAAAAGTTGGT
66 TTGTAAAATGAAAAGATGAAATTAATATCAAATTGGACTAAATTGCATTCATTTGAAAAGTTGGT
*
1835 TAACGAAAGTTTATAGAATTTGGAGATTATGATATAATTTATAGTGTTTGAAATAAAGCTTA-GG
131 GAAC-AAAGTTTATAGAATTTGGAGATTATGATATAATTTATAGTGTTTGAAATAAAGCTTATGG
* *
1899 ATGTGATTTATAGGGTTTGGAATAAATTACAAAAAATATATAATTATGACCTAATTTTGGATAAA
195 -TGTAATTTATAGGGTTTGGAATAAATTACAAAAAATAAATAATTATGACCTAATTTTGGATAAA
* * *
1964 AATATAATTTTAAGGATTAAATTGAAT
259 AATATAATTTTAAGGACTAAATTCAAC
* * * * *
1991 AAACATAAAATTACAAAATAAAATTTGAATAAATCAAACAACACACAAGGTTCAAATTGAAACAA
1 AAACATAAAATTACAAAATGAAATTTAAATAAATTAAACAACACACAAAGATCAAATTGAAACAA
* * * * *
2056 TTGTAAAATGTAAAGTTGAAATTAATATCAAATTGAACTAAATTGCATTCATTTGAAAATTTGAT
66 TTGTAAAATGAAAAGATGAAATTAATATCAAATTGGACTAAATTGCATTCATTTGAAAAGTTGGT
* * * *
2121 GAA-AAAGTTGATATG-ATTTAGAGATTGTGATATAATTTATAAGT-CTTGAAATAAAG
131 GAACAAAGTTTATA-GAATTTGGAGATTATGATATAATTTAT-AGTGTTTGAAATAAAG
2177 TGAATGATGT
Statistics
Matches: 410, Mismatches: 55, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
284 43 0.10
285 4 0.01
286 160 0.39
287 42 0.10
288 160 0.39
289 1 0.00
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.33
Consensus pattern (285 bp):
AAACATAAAATTACAAAATGAAATTTAAATAAATTAAACAACACACAAAGATCAAATTGAAACAA
TTGTAAAATGAAAAGATGAAATTAATATCAAATTGGACTAAATTGCATTCATTTGAAAAGTTGGT
GAACAAAGTTTATAGAATTTGGAGATTATGATATAATTTATAGTGTTTGAAATAAAGCTTATGGT
GTAATTTATAGGGTTTGGAATAAATTACAAAAAATAAATAATTATGACCTAATTTTGGATAAAAA
TATAATTTTAAGGACTAAATTCAAC
Found at i:2079 original size:286 final size:285
Alignment explanation
Indices: 1406--2176 Score: 971
Period size: 288 Copynumber: 2.7 Consensus size: 285
1396 ATACCAAAGT
* * * * *
1406 ACTAAATTGGATAAAC-TAATAATTACAAATTGAAATTTAAATTAATTAAACAACATACGAGATC
1 ACTAAATTGAATAAACATAA-AATTACAAAATGAAATTTAAATAAATTAAACAACACACAAGATC
* * * *
1470 AAAATGAAACAATTGTAAAATATAAAGATAAAATTAATATCAAAATGGACTAAATTGCATTCATT
65 AAATTGAAACAATTGTAAAATGTAAAGATGAAATTAATATCAAATTGGACTAAATTGCATTCATT
* * * *
1535 TGAAAAGTTGGTGAACAAAAGTTTATAAAATTTGGAGATAATGATATAATTTATAGAGTTTAAAA
130 TGAAAAGTTGGTGAAC-AAAGTTTATAGAATTTGGAGATTATGATATAATTTATAGTGTTTGAAA
* * * * * * **
1600 TGACGTTTATGGTGTAATTTATAGGTTTTGGAGTAAATTACAAAAAATAGAAATAGTTATAGGTC
194 TAAAGCTTATGGTGTAATTTATAGGGTTTGGAATAAATTACAAAAAATA-AAATAATTATACCTC
1665 AATTTTGGATAAAAATATAATTTTAAGG
258 AATTTTGGATAAAAATATAATTTTAAGG
* * * *
1693 ACTAAATTCAACAAACATAAAATTATAAACTGAAATTTAAATAAATTAAACAACACACAAAGATC
1 ACTAAATTGAATAAACATAAAATTACAAAATGAAATTTAAATAAATTAAACAACACAC-AAGATC
* * * ** *
1758 AAATTGAAACAATTGTAAAATGAAAAGCTGAAATTAATATCAAATTGGACTAAGTTATATTCACT
65 AAATTGAAACAATTGTAAAATGTAAAGATGAAATTAATATCAAATTGGACTAAATTGCATTCATT
* *
1823 TAAAAAGTTGGTTAACGAAAGTTTATAGAATTTGGAGATTATGATATAATTTATAGTGTTTGAAA
130 TGAAAAGTTGGTGAAC-AAAGTTTATAGAATTTGGAGATTATGATATAATTTATAGTGTTTGAAA
* *
1888 TAAAGCTTA-GGATGTGATTTATAGGGTTTGGAATAAATTACAAAAAAT-ATATAATTATGACCT
194 TAAAGCTTATGG-TGTAATTTATAGGGTTTGGAATAAATTACAAAAAATAAAATAATTAT-ACCT
1951 -AATTTTGGATAAAAATATAATTTTAAGG
257 CAATTTTGGATAAAAATATAATTTTAAGG
* * * * *
1979 ATTAAATTGAATAAACATAAAATTACAAAATAAAATTTGAATAAATCAAACAACACACAAGGTTC
1 ACTAAATTGAATAAACATAAAATTACAAAATGAAATTTAAATAAATTAAACAACACACAA-GATC
* *
2044 AAATTGAAACAATTGTAAAATGTAAAGTTGAAATTAATATCAAATTGAACTAAATTGCATTCATT
65 AAATTGAAACAATTGTAAAATGTAAAGATGAAATTAATATCAAATTGGACTAAATTGCATTCATT
* * * * * *
2109 TGAAAATTTGATGAA-AAAGTTGATATG-ATTTAGAGATTGTGATATAATTTATAAGT-CTTGAA
130 TGAAAAGTTGGTGAACAAAGTTTATA-GAATTTGGAGATTATGATATAATTTAT-AGTGTTTGAA
2171 ATAAAG
193 ATAAAG
2177 TGAATGATGT
Statistics
Matches: 418, Mismatches: 59, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
284 43 0.10
285 6 0.01
286 158 0.38
287 51 0.12
288 160 0.38
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (285 bp):
ACTAAATTGAATAAACATAAAATTACAAAATGAAATTTAAATAAATTAAACAACACACAAGATCA
AATTGAAACAATTGTAAAATGTAAAGATGAAATTAATATCAAATTGGACTAAATTGCATTCATTT
GAAAAGTTGGTGAACAAAGTTTATAGAATTTGGAGATTATGATATAATTTATAGTGTTTGAAATA
AAGCTTATGGTGTAATTTATAGGGTTTGGAATAAATTACAAAAAATAAAATAATTATACCTCAAT
TTTGGATAAAAATATAATTTTAAGG
Found at i:3857 original size:127 final size:126
Alignment explanation
Indices: 3617--3939 Score: 389
Period size: 125 Copynumber: 2.5 Consensus size: 126
3607 ATAATTTTAA
** * * *
3617 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTTATGCCTTAAAACA
1 GAGAGAAAATAATAATATCTAATTATTTCCAATC-AGAATAAATGACCTCTAATGCCTT-AAA-G
* * * * * *
3682 ATAATTTATTACCCCAATTGAAATGAAGAGATATCACTATTTCGTCTTAAAATTCAATATTGATT
63 A-AGTTTATAACCCCAATAGAAATGAAGAGATATCACTATTCCATCTTAAAA-TCAATATTGACT
3747 C
126 C
* * *
3748 GAGTGAAAATAATAATATCTAATGATTTCCAATCAGAATAAATGACCTCTCATGCCTTAAAGAAG
1 GAGAGAAAATAATAATATCTAATTATTTCCAATCAGAATAAATGACCTCTAATGCCTTAAAGAAG
*
3813 TTTATAACTCCAATAGAAATGAAGAGATATCACTATTCCATCTTAAAATCAATATTGACTC
66 TTTATAACCCCAATAGAAATGAAGAGATATCACTATTCCATCTTAAAATCAATATTGACTC
** * * * *
3874 GAGAGAAAATGGT-ATATCTGATTATTTCCAAT-TGAGATAAATGACCTCTAATGCTTTAAAGTA
1 GAGAGAAAATAATAATATCTAATTATTTCCAATCAGA-ATAAATGACCTCTAATGCCTTAAAGAA
3937 GTT
65 GTT
3940 AATTATTACC
Statistics
Matches: 168, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
124 2 0.01
125 44 0.26
126 22 0.13
127 44 0.26
128 1 0.01
129 3 0.02
130 22 0.13
131 30 0.18
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (126 bp):
GAGAGAAAATAATAATATCTAATTATTTCCAATCAGAATAAATGACCTCTAATGCCTTAAAGAAG
TTTATAACCCCAATAGAAATGAAGAGATATCACTATTCCATCTTAAAATCAATATTGACTC
Found at i:5000 original size:20 final size:21
Alignment explanation
Indices: 4975--5032 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
4965 CCGTTAAACA
4975 GGGGGGAATC-GATACCCCCT
1 GGGGGGAATCTGATACCCCCT
*
4995 GGGGGGAATCTGTTACCCCCT
1 GGGGGGAATCTGATACCCCCT
*
5016 -AGGGGAATCTG-TACCCC
1 GGGGGGAATCTGATACCCC
5033 TGAACAATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 6 0.17
20 20 0.57
21 9 0.26
ACGTcount: A:0.19, C:0.29, G:0.33, T:0.19
Consensus pattern (21 bp):
GGGGGGAATCTGATACCCCCT
Found at i:8565 original size:21 final size:21
Alignment explanation
Indices: 8540--8581 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
8530 CCGTTAAACA
8540 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
8561 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
8582 ACAATCTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.29, G:0.43, T:0.14
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:9153 original size:28 final size:28
Alignment explanation
Indices: 9121--9191 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 28
9111 TACAAAGAAA
9121 TAAAATAAATAAAACATG-A-GGACCAAAT
1 TAAAATAAATAAAA-ATGCATGG-CCAAAT
9149 TAAAATAAA-ATAAAATGCATGGCCAAAT
1 TAAAATAAATA-AAAATGCATGGCCAAAT
*
9177 TAAATTAAATAAAAA
1 TAAAATAAATAAAAA
9192 ATAGATTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
27 4 0.11
28 31 0.82
29 3 0.08
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.21
Consensus pattern (28 bp):
TAAAATAAATAAAAATGCATGGCCAAAT
Found at i:10849 original size:135 final size:134
Alignment explanation
Indices: 10673--11226 Score: 639
Period size: 135 Copynumber: 4.1 Consensus size: 134
10663 TTCGTCATAA
* * * * *
10673 AAGATTGAATTGAGGCAGACTTGTTCCAGTGTTCCTCAGGGAAGATCAAATCTGGAAAAAAGAGG
1 AAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGGGAAGATCAAATCTAG-AAAAAGAGG
* * * *
10738 GATCTGTTCCGCTGCTTCTTAAGGGAAAATCAGATCTAGAAATGTTAATTCATTCCACTATTCTT
65 GATATGTTCCACTACTTCTTAAGGGAAAATCAGATCTAGAAATGTTGATTCATTCCACTATTCTT
10803 CAGGG
130 CAGGG
* * * * * * *
10808 AAGATTAAATCAAGGCAAACTTGTTCCACTGCTACTTAGGGAATATCAAATCTGGAAAGAGATGG
1 AAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGGGAAGATCAAATCTAGAAAAAGA-GG
* * * * * *
10873 GATATGTTCCACTATTTCTTCAA-GGAAAATTAGATATGGGAATGTTGATTCATTCCACTGTTCT
65 GATATGTTCCACTACTTCTT-AAGGGAAAATCAGATCTAGAAATGTTGATTCATTCCACTATTCT
*
10937 TCAAGG
129 TCAGGG
* * * * *
10943 AAGATTGAATTGAGGCATACTTGTTCAACTGATACTCAGGGAAGATCAAATCTAGAAAGAGAGGG
1 AAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGGGAAGATCAAATCTAGAAAAAGAGGG
* * * *
11008 CATTTGTTCTGACGT--TTTTTCAGGGAAAATCAGATCTAGAAATGTTGATTCATTCCACTATTC
66 -ATATGTTC-CAC-TACTTCTTAAGGGAAAATCAGATCTAGAAATGTTGATTCATTCCACTATTC
11071 TTCAGGG
128 TTCAGGG
* * * *
11078 AAGATTGAATCGAGGTAAACTTGTTCCATTGTTCCTCATGGAAGATCAAATCTAGAAAAAAGAGG
1 AAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGGGAAGATCAAATCTAG-AAAAAGAGG
* * * * *
11143 GATAT-TCTCTACTACTTCTTGAGGGAAAATCATATCTGGAAATGTTGATTCTTTCCACTATTCT
65 GATATGT-TCCACTACTTCTTAAGGGAAAATCAGATCTAGAAATGTTGATTCATTCCACTATTCT
11207 TCAGGG
129 TCAGGG
11213 AAGATTGAATCGAG
1 AAGATTGAATCGAG
11227 TTCGACTCAC
Statistics
Matches: 353, Mismatches: 56, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
133 1 0.00
134 13 0.04
135 325 0.92
136 13 0.04
137 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (134 bp):
AAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGGGAAGATCAAATCTAGAAAAAGAGGG
ATATGTTCCACTACTTCTTAAGGGAAAATCAGATCTAGAAATGTTGATTCATTCCACTATTCTTC
AGGG
Found at i:11100 original size:270 final size:270
Alignment explanation
Indices: 10647--11222 Score: 730
Period size: 270 Copynumber: 2.1 Consensus size: 270
10637 TCAAGAAACA
* * * * * * *
10647 TTGATTAATTCCACTGTTCGTCATA-AAAGATTGAATTGAGGCAGACTTGTTCCAGTGTTCCTCA
1 TTGATTCATTCCACTGTTCTTCA-AGGAAGATTGAATTGAGGCAGACTTGTTCAACTGATACTCA
*
10711 GGGAAGATCAAATCTGGAAAAAAGAGGGATCTGTTCCGCTGCTTCTTAAGGGAAAATCAGATCTA
65 GGGAAGATCAAATCTAGAAAAAAGAGGGATCTGTTCCGCTGCTTCTTAAGGGAAAATCAGATCTA
10776 GAAATGTTAATTCATTCCACTATTCTTCAGGGAAGATTAAATCAAGGCAAACTTGTTCCACTGCT
130 GAAATGTTAATTCATTCCACTATTCTTCAGGGAAGATTAAATCAAGGCAAACTTGTTCCACTGCT
* * * * * *
10841 ACTTAGGGAATATCAAATCT-GGAAAGAGATGGGATATGT-TCCACTATTTCTTCAAGGAAAATT
195 ACTCAGGGAAGATCAAATCTAGAAAAAAGA-GGGATAT-TCTCCACTACTTCTTCAAGGAAAATC
*
10904 AGATATGGGAATG
258 AGATATGGAAATG
*
10917 TTGATTCATTCCACTGTTCTTCAAGGAAGATTGAATTGAGGCATACTTGTTCAACTGATACTCAG
1 TTGATTCATTCCACTGTTCTTCAAGGAAGATTGAATTGAGGCAGACTTGTTCAACTGATACTCAG
* * * * * *
10982 GGAAGATCAAATCTAG-AAAGAGAGGGCATTTGTTCTGAC-GTTTTTTCAGGGAAAATCAGATCT
66 GGAAGATCAAATCTAGAAAAAAGAGGG-ATCTGTTCCG-CTGCTTCTTAAGGGAAAATCAGATCT
* * * * * *
11045 AGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGTAAACTTGTTCCATTGT
129 AGAAATGTTAATTCATTCCACTATTCTTCAGGGAAGATTAAATCAAGGCAAACTTGTTCCACTGC
* * * * *
11110 TCCTCATGGAAGATCAAATCTAGAAAAAAGAGGGATATTCTCTACTACTTCTTGAGGGAAAATCA
194 TACTCAGGGAAGATCAAATCTAGAAAAAAGAGGGATATTCTCCACTACTTCTTCAAGGAAAATCA
* *
11175 TATCTGGAAATG
259 GATATGGAAATG
* * *
11187 TTGATTCTTTCCACTATTCTTCAGGGAAGATTGAAT
1 TTGATTCATTCCACTGTTCTTCAAGGAAGATTGAAT
11223 CGAGTTCGAC
Statistics
Matches: 263, Mismatches: 38, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
269 11 0.04
270 244 0.93
271 8 0.03
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (270 bp):
TTGATTCATTCCACTGTTCTTCAAGGAAGATTGAATTGAGGCAGACTTGTTCAACTGATACTCAG
GGAAGATCAAATCTAGAAAAAAGAGGGATCTGTTCCGCTGCTTCTTAAGGGAAAATCAGATCTAG
AAATGTTAATTCATTCCACTATTCTTCAGGGAAGATTAAATCAAGGCAAACTTGTTCCACTGCTA
CTCAGGGAAGATCAAATCTAGAAAAAAGAGGGATATTCTCCACTACTTCTTCAAGGAAAATCAGA
TATGGAAATG
Found at i:21949 original size:130 final size:131
Alignment explanation
Indices: 21707--22045 Score: 420
Period size: 130 Copynumber: 2.6 Consensus size: 131
21697 AATAATTTTA
* * * *
21707 AGAGAGAAAATGATAATATCTAATTTTTTCCATTCAAGAATAAATGACCTTTCATGCCTTAAAAC
1 AGAGAGAAAATGATAATATCTAA-TATTTCCAATCGAGAATAAATGACCTTTCATGCCTT-AAAG
* *
21772 T-GTCATTTATTACCCTAATTGAAATGAAGAGATATCACTATTTTGTCTT-AATATTCAATATTG
64 TAGTCATTTATTACCCTAATTGAAATGAAGAGATATCACTATTCTGTCTTAAAAATT-AATATTG
*
21835 A-TT
128 ACTC
* * *
21838 AGAGTGAAAATAATAATATCTAATATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGTA
1 AGAGAGAAAATGATAATATCTAATATTTCCAATCGAGAATAAATGACCTTTCATGCCTTAAAGTA
* *
21903 ATCATTTATTA-CTTCAATTGAAATGAAGAGATATCACTATTCTGTCTTAAAAATTAATATTGAC
66 GTCATTTATTACCCT-AATTGAAATGAAGAGATATCACTATTCTGTCTTAAAAATTAATATTGAC
21967 TC
130 TC
* * * *
21969 A-AGAGAAAACGGTAATATCTTTATTATTTCCAA-CTGAGAATAAATGACCTTTGATGCCTTAAA
1 AGAGAGAAAATGATAATATC--TAATATTTCCAATC-GAGAATAAATGACCTTTCATGCCTTAAA
*
22032 GCAGTCATTTATTA
63 GTAGTCATTTATTA
22046 AATTAGTTTA
Statistics
Matches: 180, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
129 6 0.03
130 96 0.53
131 29 0.16
132 49 0.27
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.36
Consensus pattern (131 bp):
AGAGAGAAAATGATAATATCTAATATTTCCAATCGAGAATAAATGACCTTTCATGCCTTAAAGTA
GTCATTTATTACCCTAATTGAAATGAAGAGATATCACTATTCTGTCTTAAAAATTAATATTGACT
C
Found at i:23757 original size:3 final size:3
Alignment explanation
Indices: 23751--23803 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
23741 AAAATAATAT
23751 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
23799 TAC TA
1 TAC TA
23804 TAATAATAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:23809 original size:3 final size:3
Alignment explanation
Indices: 23803--23868 Score: 125
Period size: 3 Copynumber: 22.3 Consensus size: 3
23793 TACTACTACT
23803 ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
23850 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
23869 GGGGATGAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 60 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25467 original size:20 final size:20
Alignment explanation
Indices: 25442--25479 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25432 ATTTTTTATA
25442 GAGTATCAATACCCAAGGTG
1 GAGTATCAATACCCAAGGTG
* *
25462 GAGTATCGATACTCAAGG
1 GAGTATCAATACCCAAGG
25480 ATTAATACTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.21
Consensus pattern (20 bp):
GAGTATCAATACCCAAGGTG
Found at i:31570 original size:19 final size:19
Alignment explanation
Indices: 31546--31613 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 19
31536 AACTTTTTTT
31546 GTATCGATACTCATAGAGA
1 GTATCGATACTCATAGAGA
31565 GTATCG-TAC-CA-AGGGTAGA
1 GTATCGATACTCATA--G-AGA
31584 GTATCGATACTACCAATAG-GA
1 GTATCGATACT--C-ATAGAGA
31605 GTATCGATA
1 GTATCGATA
31614 TTGAGGTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
16 1 0.03
17 2 0.05
18 4 0.10
19 15 0.38
20 3 0.08
21 11 0.28
23 2 0.05
24 1 0.03
25 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (19 bp):
GTATCGATACTCATAGAGA
Found at i:33865 original size:14 final size:14
Alignment explanation
Indices: 33846--33874 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
33836 GTCCTCAAGC
33846 AATGTACAATAGCT
1 AATGTACAATAGCT
33860 AATGTACAATAGCT
1 AATGTACAATAGCT
33874 A
1 A
33875 GAAGAAAATC
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:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (14 bp):
AATGTACAATAGCT
Found at i:38413 original size:21 final size:21
Alignment explanation
Indices: 38387--38436 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
38377 AGATGAACAA
*
38387 TGGCTTTGCAAAAGTGTTGCT
1 TGGCTTTGCAAAAGTGTTGAT
38408 TGGCTTTGCAAAAGTGTTGAT
1 TGGCTTTGCAAAAGTGTTGAT
38429 TGGCTTTG
1 TGGCTTTG
38437 TAACAAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.18, C:0.12, G:0.30, T:0.40
Consensus pattern (21 bp):
TGGCTTTGCAAAAGTGTTGAT
Found at i:38520 original size:21 final size:20
Alignment explanation
Indices: 38487--38529 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
38477 TGTATCAAGG
* *
38487 TCTTTGTGGAGGCCATGAAT
1 TCTTTGTCGAGGCCATAAAT
38507 TCTTTCGTCGAGGCCATAAAT
1 TCTTT-GTCGAGGCCATAAAT
38528 TC
1 TC
38530 CTACAATGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (20 bp):
TCTTTGTCGAGGCCATAAAT
Found at i:41989 original size:21 final size:20
Alignment explanation
Indices: 41956--41998 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
41946 TGTATCAAGG
*
41956 TCTTTGTAGAGGCCATGAAT
1 TCTTTGTAGAGGCCATAAAT
*
41976 TCTTTCGTCGAGGCCATAAAT
1 TCTTT-GTAGAGGCCATAAAT
41997 TC
1 TC
41999 CTACAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (20 bp):
TCTTTGTAGAGGCCATAAAT
Found at i:49037 original size:64 final size:64
Alignment explanation
Indices: 48960--49112 Score: 231
Period size: 64 Copynumber: 2.4 Consensus size: 64
48950 CACTCACCAT
* *
48960 ATCGAATGCATTTTATGCATCGATGCAC-TACCATGCATCGATGCACTC-AGGTT-TTATGAAAA
1 ATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAAGCTTGTT-TG--AA
49022 AC
63 AC
*
49024 ATCGAATGCATTTTATGTATCGATGCACAGACCATGCATCGATGCACTCAAGCTTGTTTGAAAC
1 ATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAAGCTTGTTTGAAAC
49088 ATCGAATGCATTTTATGCATCGATG
1 ATCGAATGCATTTTATGCATCGATG
49113 TACTCTTAGT
Statistics
Matches: 82, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
64 55 0.67
65 19 0.23
66 6 0.07
67 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (64 bp):
ATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAAGCTTGTTTGAAAC
Found at i:55184 original size:19 final size:20
Alignment explanation
Indices: 55162--55199 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
55152 CTACATCTTC
*
55162 AAATCCTGC-TAACATCATT
1 AAATCCTGCAAAACATCATT
*
55181 AAATCGTGCAAAACATCAT
1 AAATCCTGCAAAACATCAT
55200 CACAATCCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (20 bp):
AAATCCTGCAAAACATCATT
Found at i:56908 original size:21 final size:21
Alignment explanation
Indices: 56882--56930 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
56872 AGAGTGAACT
56882 GATTCCCCCCTTGAGGGTACC
1 GATTCCCCCCTTGAGGGTACC
*
56903 GATTCCCCCCTTGAGGGTATC
1 GATTCCCCCCTTGAGGGTACC
56924 GATTCCC
1 GATTCCC
56931 TCACTGTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.14, C:0.37, G:0.22, T:0.27
Consensus pattern (21 bp):
GATTCCCCCCTTGAGGGTACC
Found at i:56996 original size:21 final size:21
Alignment explanation
Indices: 56970--57009 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
56960 ATTTGAATAT
*
56970 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
56991 TATGAAGGGGTACCGATTC
1 TATGAAGGGGTACCGATTC
57010 TCCCCATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:58592 original size:20 final size:20
Alignment explanation
Indices: 58567--58604 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
58557 TTTGTGAAGG
58567 GATGCACCGATGCACTCATT
1 GATGCACCGATGCACTCATT
*
58587 GATGCATCGATGCACTCA
1 GATGCACCGATGCACTCA
58605 CCATATCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (20 bp):
GATGCACCGATGCACTCATT
Found at i:58702 original size:64 final size:63
Alignment explanation
Indices: 58588--58729 Score: 182
Period size: 64 Copynumber: 2.2 Consensus size: 63
58578 GCACTCATTG
*
58588 ATGCATCGATGCACTCACCATATCGAATGCACTCAGGTTTTATGAAAAACATCGAATACATTTT
1 ATGCATCGATGCACACACCATATCGAATGCACTCAGGTTTTATG-AAAACATCGAATACATTTT
* *
58652 ATGCATCGATGCACAGACCATGCATCG-ATGCACTCAGGCTTCTT-TG-AAACATCGAATGCATT
1 ATGCATCGATGCACACACCAT--ATCGAATGCACTCAGG-TT-TTATGAAAACATCGAATACATT
58714 TT
62 TT
*
58716 TTGCATCGATGCAC
1 ATGCATCGATGCAC
58730 TCTTAGTGCA
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
64 49 0.70
65 11 0.16
66 8 0.11
67 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (63 bp):
ATGCATCGATGCACACACCATATCGAATGCACTCAGGTTTTATGAAAACATCGAATACATTTT
Found at i:61463 original size:3 final size:3
Alignment explanation
Indices: 61455--61540 Score: 113
Period size: 3 Copynumber: 29.0 Consensus size: 3
61445 ACCATTATCC
* * *
61455 ATT ATT ATT ATT ATC ATT ATT ATT GTT ATT ATT ATC ATT ATT CATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
*
61501 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-A ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
61541 TCAGATCCAA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
2 3 0.04
3 66 0.92
4 3 0.04
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:62830 original size:21 final size:23
Alignment explanation
Indices: 62784--62842 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 23
62774 TCATTGTTTA
*
62784 TTTATAT-TTTAATT-TAATATG
1 TTTATATATTTAATTATTATATG
62805 TTTATATATTTAATTATTAT-TG
1 TTTATATATTTAATTATTATATG
62827 -TTAT-TA-TT-ATTATTAT
1 TTTATATATTTAATTATTAT
62843 GTAGTCATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
18 8 0.23
19 2 0.06
20 2 0.06
21 11 0.31
22 9 0.26
23 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.64
Consensus pattern (23 bp):
TTTATATATTTAATTATTATATG
Found at i:64328 original size:46 final size:47
Alignment explanation
Indices: 64267--64358 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 47
64257 TGATTTCATT
* * *
64267 TTTTTCTAAACAAAGCATGGAACTAGAAATCATGCGGTTA-GATTTA
1 TTTTTCCAAACAAAGCATGGAACTAGAAAGCATGAGGTTAGGATTTA
64313 TTTTTCCAAACAAAGCATGGAACTAGAAAGCATGAGGTTAGGATTT
1 TTTTTCCAAACAAAGCATGGAACTAGAAAGCATGAGGTTAGGATTT
64359 TTATATCAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 37 0.88
47 5 0.12
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (47 bp):
TTTTTCCAAACAAAGCATGGAACTAGAAAGCATGAGGTTAGGATTTA
Found at i:68143 original size:2 final size:2
Alignment explanation
Indices: 68127--68176 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
68117 ATCCTTTCAA
* *
68127 AT AT AT GT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68169 AT AT AT AT
1 AT AT AT AT
68177 CCCTTGTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68493 original size:10 final size:10
Alignment explanation
Indices: 68478--68515 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
68468 CTCATTCATC
68478 AGAAAAAAAA
1 AGAAAAAAAA
68488 AG-AAAAAAA
1 AGAAAAAAAA
68497 AGAAAAAAAA
1 AGAAAAAAAA
68507 AGGAAAAAA
1 A-GAAAAAA
68516 TTGAATCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.35
10 10 0.38
11 7 0.27
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:68502 original size:19 final size:20
Alignment explanation
Indices: 68478--68515 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
68468 CTCATTCATC
68478 AGAAAAAAAAA-GAAAAAAA
1 AGAAAAAAAAAGGAAAAAAA
68497 AGAAAAAAAAAGGAAAAAA
1 AGAAAAAAAAAGGAAAAAA
68516 TTGAATCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (20 bp):
AGAAAAAAAAAGGAAAAAAA
Found at i:68515 original size:9 final size:9
Alignment explanation
Indices: 68481--68506 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
68471 ATTCATCAGA
68481 AAAAAAAAG
1 AAAAAAAAG
68490 AAAAAAAAG
1 AAAAAAAAG
68499 AAAAAAAA
1 AAAAAAAA
68507 AGGAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:72763 original size:22 final size:22
Alignment explanation
Indices: 72738--72838 Score: 168
Period size: 22 Copynumber: 4.6 Consensus size: 22
72728 ACATCTACAT
72738 TCTTCAAAGATGATAGATTCAT-
1 TCTTCAAAGATGATAGATTC-TC
72760 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
72782 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
72804 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
72826 TTTTCAAATATGA
1 TCTTCAAAGATGA
72839 ACGCTTTATT
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
21 1 0.01
22 75 0.99
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:73578 original size:45 final size:45
Alignment explanation
Indices: 73509--74504 Score: 1649
Period size: 45 Copynumber: 22.2 Consensus size: 45
73499 TATTTCCCAT
* * * *
73509 ATCTGTAAGACCTTCAGTGTATGATGTTTTCAAAACATTCAGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* * **
73554 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAATCCTCCATGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
73599 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
73644 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* *
73689 ATCTATAAGCCCTTCAGTGCATGATGTTTTCAAATCCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
73734 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
73779 ATCCGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
73824 ATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* * *
73869 ATCTGTAAGCCCTTCAGTGCATTATATTTTCAAAATCTCTAC--GTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA-C-CTTCGGGTC
*
73914 ATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
73959 ATCTGTAAGCCCGTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
74004 ACCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
74049 ATCTGTAAGCCCTTCAGT-CATGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
74093 ATCTGTAAGCCCTTCAGT-CATGATGTTTTCAAAACCTTTGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
74137 ATCTGTAAGCCCATCAGTGCATGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* *
74182 ATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACTTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* *
74227 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAATCTACGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* * * *
74272 ATCTGTAAGCCCTTCCGTGCATAATGTTTTCAAAACCTCCGCGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
74317 ATCTGCAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
74362 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAATCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
*
74407 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* *
74452 ATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
74497 ATCTGTAA
1 ATCTGTAA
74505 ACCTTCTGAG
Statistics
Matches: 889, Mismatches: 57, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
43 3 0.00
44 87 0.10
45 795 0.89
46 1 0.00
47 3 0.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (45 bp):
ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
Found at i:73637 original size:25 final size:25
Alignment explanation
Indices: 73609--73683 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
73599 ATCTGTAAGC
73609 CCTTCAGTGCATGATGTTTTCAAAA
1 CCTTCAGTGCATGATGTTTTCAAAA
* * **
73634 CCTTC-GGGTCAT-CTG---T-AAGC
1 CCTTCAGTG-CATGATGTTTTCAAAA
73654 CCTTCAGTGCATGATGTTTTCAAAA
1 CCTTCAGTGCATGATGTTTTCAAAA
73679 CCTTC
1 CCTTC
73684 GGGTCATCTA
Statistics
Matches: 35, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
20 10 0.29
21 5 0.14
24 5 0.14
25 15 0.43
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (25 bp):
CCTTCAGTGCATGATGTTTTCAAAA
Found at i:74703 original size:3 final size:3
Alignment explanation
Indices: 74695--74763 Score: 102
Period size: 3 Copynumber: 22.7 Consensus size: 3
74685 TCCATTATCC
* * *
74695 TTA TTA TTA TTA TCA TTA TTA TTG TTA TTA TTA TCA TTA TTCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
74741 TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
74764 TGATTTGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:82711 original size:21 final size:20
Alignment explanation
Indices: 82683--82721 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
82673 TACTGTAGGA
*
82683 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
82703 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
82722 GACTTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:92177 original size:21 final size:21
Alignment explanation
Indices: 92151--92204 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
92141 TCACATTAGT
92151 AGTATTGATACTTCTTGATGG
1 AGTATTGATACTTCTTGATGG
92172 AGTATTGATACTTCTTGATGG
1 AGTATTGATACTTCTTGATGG
*
92193 AGTATCGATACT
1 AGTATTGATACT
92205 CTCCTCACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (21 bp):
AGTATTGATACTTCTTGATGG
Found at i:95242 original size:21 final size:21
Alignment explanation
Indices: 95218--95263 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
95208 TTCAATCCAA
* *
95218 AAAAATTCTTTAAAATATATT
1 AAAAATTATCTAAAATATATT
*
95239 AAAAATTATCTAATATATATT
1 AAAAATTATCTAAAATATATT
95260 AAAA
1 AAAA
95264 GACATTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAATTATCTAAAATATATT
Found at i:95411 original size:19 final size:20
Alignment explanation
Indices: 95368--95412 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
95358 AAATTATTTT
*
95368 TAATTTATCTAAATTTTCTA
1 TAATTTTTCTAAATTTTCTA
95388 T-ATTTTTCT-AATTTT-TAA
1 TAATTTTTCTAAATTTTCT-A
95406 TAATTTT
1 TAATTTT
95413 GTTTAGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 1 0.05
18 8 0.36
19 12 0.55
20 1 0.05
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (20 bp):
TAATTTTTCTAAATTTTCTA
Found at i:98322 original size:46 final size:46
Alignment explanation
Indices: 98261--98509 Score: 362
Period size: 46 Copynumber: 5.5 Consensus size: 46
98251 TCATTTATCC
98261 CATAAGCTCAG-AAGCTTATTTTACCAATATACTTACCATTTAATAT
1 CATAAGCTC-GTAAGCTTATTTTACCAATATACTTACCATTTAATAT
** * *
98307 CATAAGCTTTTAAGCTTATTTTACCAATATACTTACCATTTCATCT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATAT
* *
98353 CATAAGCTCGTAAGCTTTTTTTACCAATATATTTACCATTTAATAT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATAT
* *
98399 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATTTAATCT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATAT
*
98445 CATAAGCTCGTAAGCTTATTTTACCAATATACTTTCCA-TT-AT-T
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATAT
*
98488 CCATAAGCTCGTTAGCTTATTT
1 -CATAAGCTCGTAAGCTTATTT
98510 GCCACTTTAT
Statistics
Matches: 184, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
43 1 0.01
44 22 0.12
45 2 0.01
46 159 0.86
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (46 bp):
CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATAT
Found at i:98670 original size:40 final size:40
Alignment explanation
Indices: 98596--98671 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
98586 AGTCAATTGT
* * *
98596 TGCACCGAAGTGCTGAGGTCGAGCTTTGCTCACCTAATAA
1 TGCACCGAAGTGCTGAGGTCGAGATTTACCCACCTAATAA
* *
98636 TGCACCGTAGTGCTGAGGTCGGGATTTACCCACCTA
1 TGCACCGAAGTGCTGAGGTCGAGATTTACCCACCTA
98672 GTACGCCATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.25
Consensus pattern (40 bp):
TGCACCGAAGTGCTGAGGTCGAGATTTACCCACCTAATAA
Found at i:102494 original size:6 final size:6
Alignment explanation
Indices: 102475--102556 Score: 118
Period size: 6 Copynumber: 14.0 Consensus size: 6
102465 ATTTTTTTTC
102475 TTTC-T TTT-TT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
102521 TTTCTT TTTCTT CTTT-TT TTTCTT TCTT-TT TTTCTT
1 TTTCTT TTTCTT -TTTCTT TTTCTT T-TTCTT TTTCTT
102557 ATATAATATT
Statistics
Matches: 71, Mismatches: 0, Indels: 11
0.87 0.00 0.13
Matches are distributed among these distances:
5 12 0.17
6 54 0.76
7 5 0.07
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:102572 original size:1 final size:1
Alignment explanation
Indices: 102466--102553 Score: 59
Period size: 1 Copynumber: 88.0 Consensus size: 1
102456 TTTAGTCTCA
* * * * * * * * * *
102466 TTTTTTTTCTTTCTTTTTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
102531 TTCTTTTTTTTCTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTT
102554 CTTATATAAT
Statistics
Matches: 61, Mismatches: 26, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (1 bp):
T
Found at i:104956 original size:17 final size:16
Alignment explanation
Indices: 104934--105002 Score: 70
Period size: 15 Copynumber: 4.3 Consensus size: 16
104924 CCGTGTCTCG
*
104934 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
104951 ACCCGG-TATTCGGGT
1 ACCCGGATATTCGGGT
*
104966 ACCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
* *
104983 ACCCAG-TAATCGGGT
1 ACCCGGATATTCGGGT
104998 ACCCG
1 ACCCG
105003 ATACCCGGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
15 20 0.45
16 8 0.18
17 16 0.36
ACGTcount: A:0.17, C:0.28, G:0.32, T:0.23
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:104970 original size:32 final size:32
Alignment explanation
Indices: 104934--105002 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
104924 CCGTGTCTCG
* *
104934 ACCCGGATGTTACGGGTACCCGGTATTCGGGT
1 ACCCGGATGTTACGGGTACCCAGTAATCGGGT
* *
104966 ACCCGGATTTTGCGGGTACCCAGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCAGTAATCGGGT
104998 ACCCG
1 ACCCG
105003 ATACCCGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.17, C:0.28, G:0.32, T:0.23
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCAGTAATCGGGT
Found at i:105948 original size:46 final size:45
Alignment explanation
Indices: 105886--106135 Score: 358
Period size: 46 Copynumber: 5.5 Consensus size: 45
105876 ATTATTTATC
* *
105886 CCATAAGCTTGGAAGCTTATTTTACCAATATACTTACCATTTAAT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAAT
**
105931 ACCATAAGCTTTTAAGCTTATTTTACCAATATACTTACCATTTAAT
1 -CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAAT
* * *
105977 CTCATAAGCTCGTAAGGTTTTTTTACCAATATATTTACCATTTAATT
1 C-CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAA-T
*
106024 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCATTTAAT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAAT
* * *
106069 CTCATAAGCTCGTAAGATTATTTTACCAATATACTTGCCA-TTATT
1 C-CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAAT
106114 CCATAAGCTCGTAAGCTTATTT
1 CCATAAGCTCGTAAGCTTATTT
106136 GCCAATTTAT
Statistics
Matches: 187, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
44 20 0.11
45 8 0.04
46 157 0.84
47 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (45 bp):
CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAAT
Found at i:108977 original size:27 final size:27
Alignment explanation
Indices: 108939--108993 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
108929 AGACTTAAAC
108939 TTCCATTTAATAAATAAATGTTGCTGA
1 TTCCATTTAATAAATAAATGTTGCTGA
108966 TTCCATTTAATAAATAAATGTTGCTGA
1 TTCCATTTAATAAATAAATGTTGCTGA
108993 T
1 T
108994 GTAAAATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (27 bp):
TTCCATTTAATAAATAAATGTTGCTGA
Found at i:110283 original size:194 final size:193
Alignment explanation
Indices: 109926--110317 Score: 444
Period size: 194 Copynumber: 2.0 Consensus size: 193
109916 TGTGTTTTGC
** *
109926 ACAATATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATTTGTGACAATATAAATTATCA
1 ACAATATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATACGTGACAATATAAATCATCA
** **
109991 ATAACGAAATCTTATTTAATTTAATGATGTAACCAACTGTAATAGAATATAAATTATAAAGTGAC
66 ATAACGAAATCTTACATAATTTAATGACATAACCAACTGTAATAGAATATAAATTATAAAGTGAC
* ** ** *
110056 ATTATGCATAAACGTCATTCATAATTTTATTAGGTAAC-ATTTATATTATGTCACTAAAAATGTG
131 ATTATACATAAACGTCACCCATAATACTATTAGGTAACGA--TATACTATGTCACTAAAAATGTG
* * *
110120 ACAATATCTCTTTCGTCACATATAGGTTGATTTTAATGTATTATACGTGACGATATAAATCATCA
1 ACAATATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATACGTGACAATATAAATCATCA
* * ** ** * * * *
110185 ATAACGAAATTTTACATAATTTAGTGACATAATTAGTTGTCATTGAATATTAATTATATAGTGAC
66 ATAACGAAATCTTACATAATTTAATGACATAACCAACTGTAATAGAATATAAATTATAAAGTGAC
* * ** ** * * *
110250 GTTATATATAAGTGTCACCCATGCTACTATTAGGTGACGATATACTATGTTACTAACAATGTG
131 ATTATACATAAACGTCACCCATAATACTATTAGGTAACGATATACTATGTCACTAAAAATGTG
110313 ACAAT
1 ACAAT
110318 TTTCTTTTCG
Statistics
Matches: 162, Mismatches: 35, Indels: 3
0.81 0.17 0.01
Matches are distributed among these distances:
193 25 0.15
194 136 0.84
195 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (193 bp):
ACAATATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATACGTGACAATATAAATCATCA
ATAACGAAATCTTACATAATTTAATGACATAACCAACTGTAATAGAATATAAATTATAAAGTGAC
ATTATACATAAACGTCACCCATAATACTATTAGGTAACGATATACTATGTCACTAAAAATGTG
Found at i:115561 original size:32 final size:33
Alignment explanation
Indices: 115515--115576 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 33
115505 GGATACCTAA
*
115515 TGTTTACTTTTTGTTTCA-TTTTAGTACCTCAT
1 TGTTAACTTTTTGTTTCATTTTTAGTACCTCAT
115547 TGTTAACTTTTTGTTTCATTTTTAGTACCT
1 TGTTAACTTTTTGTTTCATTTTTAGTACCT
115577 AAATTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.16, C:0.15, G:0.10, T:0.60
Consensus pattern (33 bp):
TGTTAACTTTTTGTTTCATTTTTAGTACCTCAT
Found at i:115900 original size:13 final size:13
Alignment explanation
Indices: 115858--115906 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
115848 ATAAATATAC
*
115858 GACGCACATTTAT
1 GACGCGCATTTAT
*
115871 GACACGCATTTAT
1 GACGCGCATTTAT
*
115884 GACGTGCATTTAT
1 GACGCGCATTTAT
*
115897 GACGCTCATT
1 GACGCGCATT
115907 GCGCGTCATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (13 bp):
GACGCGCATTTAT
Found at i:117602 original size:2 final size:2
Alignment explanation
Indices: 117590--117669 Score: 144
Period size: 2 Copynumber: 40.0 Consensus size: 2
117580 TATTTGGTGC
117590 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
117633 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
117670 GTCCGCCAAG
Statistics
Matches: 76, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.01
2 73 0.96
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:120676 original size:8 final size:8
Alignment explanation
Indices: 120660--120694 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
120650 AGATTGATAC
120660 AAAGAGAA
1 AAAGAGAA
*
120668 AAAGGGAA
1 AAAGAGAA
120676 AAAGAGAA
1 AAAGAGAA
120684 AAAGAGAA
1 AAAGAGAA
120692 AAA
1 AAA
120695 AGAGGAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (8 bp):
AAAGAGAA
Found at i:121016 original size:15 final size:14
Alignment explanation
Indices: 120983--121028 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 14
120973 TTGTAGTGAA
120983 AAAATCTTATAAATAT
1 AAAAT-TTATAAAT-T
120999 AAAATTTATGAAATT
1 AAAATTTAT-AAATT
121014 AAAATTTATAAATT
1 AAAATTTATAAATT
121028 A
1 A
121029 TCATGAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.21
15 14 0.48
16 9 0.31
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (14 bp):
AAAATTTATAAATT
Found at i:125336 original size:33 final size:33
Alignment explanation
Indices: 125292--125380 Score: 97
Period size: 39 Copynumber: 2.5 Consensus size: 33
125282 AACAAGATTA
* *
125292 ATCTCGGTTGAGATAGTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTCGAAACAAAAGATTTT
125325 ATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTTT
1 ATCTCGCTTGAGATAG------TCGAAACAAAAGATTTT
*
125364 ATCTTGCTTGAGATAGT
1 ATCTCGCTTGAGATAGT
125381 TTCACTCGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
33 16 0.34
39 31 0.66
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (33 bp):
ATCTCGCTTGAGATAGTCGAAACAAAAGATTTT
Found at i:125362 original size:39 final size:38
Alignment explanation
Indices: 125308--125714 Score: 325
Period size: 39 Copynumber: 10.9 Consensus size: 38
125298 GTTGAGATAG
125308 TCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCAC
1 TCGAAACAGAAGA-TTTATCTCGCTTGAGATAGTTTCAC
* *
125347 TCGAAACAAAAGATTTTATCTTGCTTGAGATAGTTTCAC
1 TCGAAACAGAAGA-TTTATCTCGCTTGAGATAGTTTCAC
* * * **
125386 TCGAAACAGAGGATTTATCTCACTTGAGATTGTTTTTC
1 TCGAAACAGAAGATTTATCTCGCTTGAGATAGTTTCAC
* * * * *
125424 T-TAAA-ACAATATTAATCTCGGTTGAGATAG--T---
1 TCGAAACAGAAGATTTATCTCGCTTGAGATAGTTTCAC
* * *
125455 T-GAAATAGGAGATTTTATCTCGCTTGAGATAGTTTTAC
1 TCGAAACAGAAGA-TTTATCTCGCTTGAGATAGTTTCAC
* * * *
125493 TCGAAATAGAAGATTTTATCTAGATTTAGATAGTTTCAC
1 TCGAAACAGAAGA-TTTATCTCGCTTGAGATAGTTTCAC
* * * * **
125532 TCGAAACATAAGATTTAGCTCACTTGAGATTGTTTTTC
1 TCGAAACAGAAGATTTATCTCGCTTGAGATAGTTTCAC
* * *
125570 T-TAAA-ACAAGATTCATCTCGCTTGAGATAGTTTCAC
1 TCGAAACAGAAGATTTATCTCGCTTGAGATAGTTTCAC
* * * **
125606 TCAAAACAGAAGATTTATCTCACTTGAGATTGTTTTTC
1 TCGAAACAGAAGATTTATCTCGCTTGAGATAGTTTCAC
* * *
125644 T-TAAA-ACAAGATTTATCTCTCTTGAGATAGTTTCAC
1 TCGAAACAGAAGATTTATCTCGCTTGAGATAGTTTCAC
* * ** *
125680 TTGAAATAGAAGATTTATCTAACTTGAGATTGTTT
1 TCGAAACAGAAGATTTATCTCGCTTGAGATAGTTT
125715 TTCTTAAAAC
Statistics
Matches: 292, Mismatches: 64, Indels: 25
0.77 0.17 0.07
Matches are distributed among these distances:
31 4 0.01
32 3 0.01
33 17 0.06
34 1 0.00
35 1 0.00
36 70 0.24
37 15 0.05
38 90 0.31
39 91 0.31
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (38 bp):
TCGAAACAGAAGATTTATCTCGCTTGAGATAGTTTCAC
Found at i:125487 original size:146 final size:145
Alignment explanation
Indices: 125245--125726 Score: 639
Period size: 146 Copynumber: 3.3 Consensus size: 145
125235 CTCATTTAAT
* *
125245 ACAGAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTAATCTCGGTTGAGATAGTC
1 ACAGAAGATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTAATCTCGGTTGAGATAGTT
*
125310 GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTTTATCTTGCTTGA
66 GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTTACTCGAAA-AAAAGATTTTATCTTGCTTGA
125375 GATAGTTTCACTCGAA
130 GATAGTTTCACTCGAA
* *
125391 ACAGAGGATTTATCTCACTTGAGATTGTTTTTCTTAAAACAATATTAATCTCGGTTGAGATAGTT
1 ACAGAAGATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTAATCTCGGTTGAGATAGTT
* * * * * *
125456 GAAATAGGAGATTTTATCTCGCTTGAGATAGTTTTACTCGAAATAGAAGATTTTATCTAGATTTA
66 GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTTACTCGAAA-AAAAGATTTTATCTTGCTTGA
125521 GATAGTTTCACTCGAA
130 GATAGTTTCACTCGAA
* * * *
125537 ACATAAGATTTAGCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTT
1 ACAGAAGATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTAATCTCGGTTGAGATAG--
* * * * * *
125602 TCACTCAAAACAGAAGA-TTTATCTCACTTGAGATTGTTTTTCT-TAAAACAAGA-TTTATCTCT
64 T---T-GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTTACTCGAAAAAAAGATTTTATCT-T
*
125664 -CTTGAGATAGTTTCACTTGAA
124 GCTTGAGATAGTTTCACTCGAA
* *
125685 ATAGAAGATTTATCTAACTTGAGATTGTTTTTCTTAAAACAA
1 ACAGAAGATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
125727 ACTTGTTGAA
Statistics
Matches: 295, Mismatches: 34, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
146 191 0.65
148 64 0.22
149 5 0.02
150 3 0.01
151 24 0.08
152 8 0.03
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (145 bp):
ACAGAAGATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTAATCTCGGTTGAGATAGTT
GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTTACTCGAAAAAAAGATTTTATCTTGCTTGAG
ATAGTTTCACTCGAA
Found at i:125594 original size:36 final size:36
Alignment explanation
Indices: 125252--125726 Score: 234
Period size: 38 Copynumber: 13.0 Consensus size: 36
125242 AATACAGAAA
125252 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAG
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAG
* ** * * *
125288 ATTAATCTCGGTTGAGATAG----TC-GAAACAGAAG
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAA-ACAAG
* * ** * *
125320 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAG
1 A-TTTATCTCACTTGAGATTGTTTTTCT-TAAA-ACAAG
** * ** **
125359 ATTTTATCTTGCTTGAGATAGTTTCACTCGAAACAGAGG
1 A-TTTATCTCACTTGAGATTGTTTTTCTTAAAACA-A-G
*
125398 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAT
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAG
* ** * * **
125434 ATTAATCTCGGTTGAGATAG----T-TGAAATAGGAG
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAA-ACAAG
* * * * *
125466 ATTTTATCTCGCTTGAGATAGTTTTACTCGAAATAGAAG
1 A-TTTATCTCACTTGAGATTGTTTTTCT-TAAA-ACAAG
* * * ** * *
125505 ATTTTATCT-AGATTTAGATAGTTTCACTCGAAACATAAG
1 A-TTTATCTCA-CTTGAGATTGTTTTTCT-TAAA-ACAAG
*
125544 ATTTAGCTCACTTGAGATTGTTTTTCTTAAAACAAG
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAG
* * * ** *
125580 ATTCATCTCGCTTGAGATAGTTTCACTCAAAACAGAAG
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAAC--AAG
125618 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAG
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAG
* * ** *
125654 ATTTATCTCTCTTGAGATAGTTTCACTTGAAATAGAAG
1 ATTTATCTCACTTGAGATTGTTTTTCTT-AAA-ACAAG
*
125692 ATTTATCTAACTTGAGATTGTTTTTCTTAAAACAA
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
125727 ACTTGTTGAA
Statistics
Matches: 343, Mismatches: 72, Indels: 48
0.74 0.16 0.10
Matches are distributed among these distances:
31 7 0.02
32 11 0.03
33 34 0.10
36 92 0.27
37 13 0.04
38 105 0.31
39 81 0.24
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (36 bp):
ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAG
Found at i:125607 original size:74 final size:74
Alignment explanation
Indices: 125219--125726 Score: 520
Period size: 74 Copynumber: 6.9 Consensus size: 74
125209 ACAATTTTTG
* * ** *
125219 TCTCGCTTGAGACAGTCTCA-TTTAATACAGAAAATTTATCTCACTTGAGATTGTTTTTCTTAAA
1 TCTCGCTTGAGATAGTTTCACTCGAA-ACAGAAGATTTATCTCACTTGAGATTGTTTTTCTTAAA
*
125283 ACAAGATTAA
65 ACAAGATTTA
* * * ** *
125293 TCTCGGTTGAGATAG------TCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAA
1 TCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTATCTCACTTGAGATTGTTTTTCT-TAA
*
125352 ACAAAAGATTTTA
64 A-ACAAGA-TTTA
* *
125365 TCTTGCTTGAGATAGTTTCACTCGAAACAGAGGATTTATCTCACTTGAGATTGTTTTTCTTAAAA
1 TCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATTGTTTTTCTTAAAA
* *
125430 CAATATTAA
66 CAAGATTTA
* * * * * * *
125439 TCTCGGTTGAGATAG--T---T-GAAATAGGAGATTTTATCTCGCTTGAGATAGTTTTACTCGAA
1 TCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTATCTCACTTGAGATTGTTTTTCT-TAA
*
125498 ATAGAAGATTTTA
64 A-ACAAGA-TTTA
* * * * *
125511 TCTAGATTTAGATAGTTTCACTCGAAACATAAGATTTAGCTCACTTGAGATTGTTTTTCTTAAAA
1 TCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATTGTTTTTCTTAAAA
*
125576 CAAGATTCA
66 CAAGATTTA
*
125585 TCTCGCTTGAGATAGTTTCACTCAAAACAGAAGATTTATCTCACTTGAGATTGTTTTTCTTAAAA
1 TCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATTGTTTTTCTTAAAA
125650 CAAGATTTA
66 CAAGATTTA
* * * *
125659 TCTCTCTTGAGATAGTTTCACTTGAAATAGAAGATTTATCTAACTTGAGATTGTTTTTCTTAAAA
1 TCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATTGTTTTTCTTAAAA
125724 CAA
66 CAA
125727 ACTTGTTGAA
Statistics
Matches: 354, Mismatches: 60, Indels: 40
0.78 0.13 0.09
Matches are distributed among these distances:
68 15 0.04
69 49 0.14
70 6 0.02
71 9 0.03
72 32 0.09
74 163 0.46
75 9 0.03
76 6 0.02
77 45 0.13
78 20 0.06
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (74 bp):
TCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATTGTTTTTCTTAAAA
CAAGATTTA
Found at i:126862 original size:59 final size:59
Alignment explanation
Indices: 126776--127035 Score: 288
Period size: 59 Copynumber: 4.4 Consensus size: 59
126766 AAAACTACGT
* * * * *
126776 CTCACTTGAGGGGTTAACATTTCCTTTGATCGATTCACAGCACTTCGAATCAACAACGT
1 CTCACTTGAGGGATCAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAACAACGC
* * * * * *
126835 CTTACTTGAGGGATCAACATTTTCTTTGCTCAATTCACAATACTTTGAATCAACAACAC
1 CTCACTTGAGGGATCAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAACAACGC
* * * *
126894 CTCAATTGAGAGATCAACATTTCCTTTGCTCGATTCACAACACTTCAAATCAGCAACGC
1 CTCACTTGAGGGATCAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAACAACGC
* * * * * * * *
126953 CTCATTTGATGGATCAATATTTTCTTTGCTCGATTCACGACATTTCGAATCAGCAATGC
1 CTCACTTGAGGGATCAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAACAACGC
*
127012 CTCACTCGAGGGA-CTAACATTTCC
1 CTCACTTGAGGGATC-AACATTTCC
127036 AATAGATAAT
Statistics
Matches: 165, Mismatches: 35, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
58 1 0.01
59 164 0.99
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32
Consensus pattern (59 bp):
CTCACTTGAGGGATCAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAACAACGC
Found at i:130367 original size:24 final size:24
Alignment explanation
Indices: 130338--130383 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
130328 ATTTACACAA
130338 TGTAAGTGGATCATCTCTCTCTAT
1 TGTAAGTGGATCATCTCTCTCTAT
*
130362 TGTAAGTGGATCCTCTCTCTCT
1 TGTAAGTGGATCATCTCTCTCT
130384 CTCTCCCTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (24 bp):
TGTAAGTGGATCATCTCTCTCTAT
Found at i:130403 original size:24 final size:24
Alignment explanation
Indices: 130376--130421 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
130366 AGTGGATCCT
* *
130376 CTCTCTCTCTCTCCCTGTCCCTCC
1 CTCTCTCTCTCCCCCTCTCCCTCC
130400 CTCTCTCTCTCCCCCTCTCCCT
1 CTCTCTCTCTCCCCCTCTCCCT
130422 ATATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.00, C:0.61, G:0.02, T:0.37
Consensus pattern (24 bp):
CTCTCTCTCTCCCCCTCTCCCTCC
Found at i:130426 original size:2 final size:2
Alignment explanation
Indices: 130421--130456 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
130411 CCCCTCTCCC
130421 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
130457 ATTTTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:130940 original size:23 final size:23
Alignment explanation
Indices: 130907--130973 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 23
130897 AAAATAATAT
130907 AATTAA-ATATTATTTATTTTATAA
1 AATTAATAT-TTATTTATTTTA-AA
*
130931 AATTAATATTTAATTATTTTAAA
1 AATTAATATTTATTTATTTTAAA
130954 AATGTAA-ATTTATTATATTT
1 AAT-TAATATTTATT-TATTT
130974 GTTTAATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
23 11 0.29
24 25 0.66
25 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (23 bp):
AATTAATATTTATTTATTTTAAA
Found at i:132911 original size:2 final size:2
Alignment explanation
Indices: 132857--132892 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
132847 GATTTTGCCA
132857 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
132893 TACTTGTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:140111 original size:2 final size:2
Alignment explanation
Indices: 140104--140143 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
140094 TTACCTCTGA
140104 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
140144 TCAAACAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:147466 original size:26 final size:26
Alignment explanation
Indices: 147426--147476 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
147416 AAGGACACTT
*
147426 TGGTGGGCACAACCTTATTTGTATTA
1 TGGTGGGCACAACCTTATGTGTATTA
*
147452 TGGTGGGCACGACCTTATGTGTATT
1 TGGTGGGCACAACCTTATGTGTATT
147477 GACACTTCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (26 bp):
TGGTGGGCACAACCTTATGTGTATTA
Found at i:150751 original size:33 final size:35
Alignment explanation
Indices: 150713--150785 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
150703 ACCTTACAAC
*
150713 TCCCTAGTTTTT-C-TGGGCTAAACTAGAACCTTT
1 TCCCTAGTTTTTACATGGGATAAACTAGAACCTTT
*
150746 TCCCTAGTTTTTACATGGGATAAGCTAGAACCTTT
1 TCCCTAGTTTTTACATGGGATAAACTAGAACCTTT
*
150781 CCCCT
1 TCCCT
150786 TTACAAAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 12 0.34
34 1 0.03
35 22 0.63
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (35 bp):
TCCCTAGTTTTTACATGGGATAAACTAGAACCTTT
Found at i:151089 original size:20 final size:20
Alignment explanation
Indices: 151064--151103 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
151054 TACGATAGGG
*
151064 GGTATCGGTACCCCTTCATA
1 GGTATCAGTACCCCTTCATA
*
151084 GGTATCAGTACTCCTTCATA
1 GGTATCAGTACCCCTTCATA
151104 AAATTCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.33
Consensus pattern (20 bp):
GGTATCAGTACCCCTTCATA
Found at i:151165 original size:17 final size:18
Alignment explanation
Indices: 151134--151167 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
151124 GTTGTAGCCA
*
151134 GGGGGTATGGATACCCTG
1 GGGGGTATAGATACCCTG
151152 GGGGGTATAG-TACCCT
1 GGGGGTATAGATACCCT
151168 CCGAGCAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.18, G:0.41, T:0.24
Consensus pattern (18 bp):
GGGGGTATAGATACCCTG
Found at i:151241 original size:22 final size:21
Alignment explanation
Indices: 151194--151252 Score: 93
Period size: 21 Copynumber: 2.8 Consensus size: 21
151184 TTGAGCCTTA
151194 AGGGGGTATGGATACCCATGC
1 AGGGGGTATGGATACCCATGC
*
151215 AGGGGGTATGGATACCCCTGC
1 AGGGGGTATGGATACCCATGC
151236 AGGGGGTATCGG-TACCC
1 AGGGGGTAT-GGATACCC
151253 TATAACATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 34 0.94
22 2 0.06
ACGTcount: A:0.20, C:0.22, G:0.39, T:0.19
Consensus pattern (21 bp):
AGGGGGTATGGATACCCATGC
Done.